title: L129_C01

description: single cell


title: L227_D02

status: Public on Nov 24 2014

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: single cell

library_source: transcriptomic

data_processing:
Read quality filtering and barcode extraction: Every read marked as valid by the Illumina control software was processed as follows: a) any 3' bases with a quality score of 'B' were removed; b) the 6 base well-identifying barcode was extracted from the 5' end of the read; c) the following bases should be template switch derived Gs. If the first three were not all Gs or two Gs and one uncalled base, the read was discarded. Else, these plus a maximum of six more consecutive Gs were removed; d) the remaining sequence should be transcript derived. If this ended in a poly(A)-sequence leaving less than 25 bases, the read was discarded; e) if the transcript-derived sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie1 aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. The genome included an artifical chromosome, containing a concatamer of the ERCC control sequences. Any reads with no alignments were re-aligned against another artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incompete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation: The annotation step was performed barcode-by-barcode. Only reads mapping in sense orientation of an exon were considered as potentially transcript derived. Any such read that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more sense mappings to exons, it was assigned at the exon where it was closest to the transcript model 5' end, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads in sense orientation at all its possible mapping positions.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: Usoskin_DataTable.txt is a TAB-delimted text file containing Reads Per Million values for each analyzed feature in each well. Prefix 'r_' indicates repeat types and summarizes total expression from all repeat regions (from RepeatMasker) of that type. Suffix '_locX', X=1,2... indicates alternative loci expressing the same gene.

molecule: total RNA

organism: Mus musculus

source_name: lumbar dorsal root ganglion

growth_protocol: 6-8 week old C57/Bl6 mice

extract_protocol:
Six lumbar DRGs (L4-L6) were dissected and dissociated using papain and collagenase/dispase followed by Percoll gradient centrifugation. The sample was always kept on ice apart from enzyme incubation. In some preparations a cooled microscope stage was used. The final cell pellet was suspended in 300 ml of L15 medium supplemented with B27. Cells were picked on an in house constructed picking setup built around an inverted Nikon microscope. Individual cells were sucked into a glass capillary attached to a CellTram syringe with visual control that individual cells were captured. The capillary tip was positioned in a well of a 96 well plate containing 3 microlitre of lysis buffer into which the cell was released by operating the CellTram syringe. 48 random cells were picked at each time within 40-60 minutes. The lysis buffer contained 20mMTris-HCl at pH8.0, 75 mM KCl, 6 mM MgCl2, 0.02% Tween-20 with 400 nM STRT-V3-T30 (5'-biotin-AAGCAGTGGTATCAACGCAGAGTCGACT(30)VN-3') and 400 nM STRT-V2-n (5'-AAGCAGTGGTATCAACGCAGAGTGCAGTGCTXXXXXXrGrGrG-3', where ‘‘rG’’ denotes a riboguanine and ‘‘XXXXXX’’ was a 6-bp barcode). Each well of the capture plate contained a different template-switching helper oligo with a distinct barcode. Plates were then frozen.
The cell capture plate was thawed, and 5 microlitre reverse transcription mix (4mM DTT, 2mM dNTP, 5U/microlitre SuperscriptII in 100 mM Tris-HCl at pH 8, 375 mM KCl, 0.1% Tween-20, 6 mM MnCl2, 2500 molecules of control mRNA) was added to each well. The synthetic mRNA consisted of 92 different ERCC control RNAs). The plate was incubated (10°C for 10 min, 42°C for 45 min) to complete reverse transcription and template switching. To purify the cDNA and remove unreacted primers, 100 microlitre MyOne carboxylatebeads (Invitrogen) was washed twice in 100 microlitre EBT (10 mM Tris-Cl at pH 8.5, 0.02% Tween-20) and then resuspended in 2 mL 14% PEG-6000 in 0.9 M NaCl, and 20 microlitre of this mixture was added to each well. Beads from all wells were pooled, washed in 70% ethanol twice, dried, and eluted in 37 microlitre EBT in a 1.5-mL polyallomer tube (Beckman). The cDNA was amplified in a single tube in 50 microlitre of 200 microM dNTP, 200 nM STRT-PCR primer (5’-biotin-AAGCAGTGGTATCAACGCAGAGT-3’), 1x Advantage2 DNA Polymerase Mix (Clontech) in 1x Advantage2 PCR buffer (Clontech) with 1 min at 95°C followed by 20 cycles of 15 sec at 95°C, 30 sec at 65°C, 4 min at 68°C,with heated lid.A 5 microlitre aliquot was amplified for another five cycles and visualized on a 1.2% agarose E-gel (Invitrogen) to confirm the range of cDNA lengths. The product was immobilized on MyOne C1 Streptavidin beads. Twenty microliters of beads was washed twice in 50 microlitre 2x BWT (10 mM Tris HCl at pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and added to the remaining 45 microlitre PCR product. After a 10-min incubation at room temperature, the beads were washed three times in 50 microlitre 1x BWT and twice in EBT. Amplified cDNA was fragmented by DNase I in the presence of Mn2+. Beads were resuspended in DNase I buffer supplemented with 10 mM MnCl2 and DNaseI diluted to 0.0003U/microlitre in a total volume of 120 microlitre for exactly 8 min at room temperature. The reaction was stopped by washing the beads five times in 50 microlitre EBT. Beads were resuspended in 25 microlitre EBT, and 25 microlitre NEBNext End Repair reaction mix (New England Biolabs) was added; then the beads were incubated for 30 min at room temperature. The beads were washed twice in EBT, then resuspended in 21 microlitre EBT; 2.5 microlitre NEBNext dA tailing buffer and 1.5 microlitre Klenow exo- (both NEB) were added, and the reaction was incubated for 30 min at 37°C, followed by two washes in 50 microlitre EBT. An adapter containing the Illumina P2 sequence (5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT-3’ and 3’-PHO-GTTCGTCTTCTGCCGTATGCTCGAGAAGGCTAG-PHO-5’) was ligated by resuspending the beads in 25 microlitre EBT and adding 2x ligationmix (2x NEBuffer4, 2 microM adapter,1U/microlitre T4DNAligase,2U/microlitre SalI-HF, and 2mM ATP; all reagents from NEB) and incubating for 30min at 37°C and then washing twice in 25 microlitre EBT. The beads were then used as template in a 100 microlitre PCR reaction (200 microM dNTP, 400 nM each primer of primers 5’-AATGATACGGCGACCACCGAGATCTAAGCAGTGGTATCAACGCAGAGT-3’ and 5’-CAAGCAGAAGACGGCATACGAG-3’, 200 microM dNTP ,0.2U/microlitre Phusion polymerase in PhusionHF buffer ;all from NEB) with 30 sec at 98°C, followed by 12 cycles of [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] followed by 5 min at 72°C. The product was purified by AmPure XP (Beckman Coulter) and resuspended in 20 microlitre EBT. The sample was size-selected on a 2% E-gel with SYBR Safe (Invitrogen), recovering the 200 400 bp range by Qiaquick Gel Extraction (replacing the heating step with 15 min of vigorous agitation). The well indexing barcodes are read as bases 1-6 of the read, or for plates L281 and L282 as bases 5-10 of the read.

tag: cell picking session

value: C

tag: cell picking temperature

value: Cooling

tag: strain

tag: gender

value: male


title: L129_B12

description: single cell

value: A

value: RT


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 3

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
RNA-seq, transcriptome building: Pooled reads were mapped, using Tophat version 2.0.4 (with underlying Bowtie version 0.12.8), against UCSC known transcripts for rn4, supplemented with additional transcripts from Ensembl, and allowing for the identification of novel exon-exon junctions for the reference genome (rn4 supplemented with EST-based sequence at chr1:262,210,923-262,210,894 to partial fill a gap including a part of an exon of Tcf7l2; corresponding fix was introduced also for the UCSC reference transcriptome). Essential Tophat command arguments were: --library-type fr-unstranded --prefilter-multihits --no-coverage-search -G <UCSC+Ensembl known transcripts>.
RNA-seq, transcriptome building: Transcript mappings were further processed using Cufflinks package version 2.0.2 with essential command arguments, for Cufflinks: --frag-bias-correct --multi-read-correct --upper-quartile-norm -g <UCSC+Ensembl known transcripts> --library-type fr-unstranded, and for Cuffcompare: -r <UCSC+Ensembl known transcripts> -R -d 20 -V <.gff output of Cufflinks>.
RNA-seq, transcriptome building: The initial transcriptome was cleaned by removing all transcripts that were identified as fully silent (FPKM=0), strandless (in Cuffcompare class codes u, o, x, and, if also single-exon, i), or likely artifacts (Cuffcompare class codes e, p, r, s and c). The transcripts that did not represent any known rn4 gene were analyzed against mouse (mm10), human (hg19), as well as an updated rat reference transcriptome sequences using discontiguous megablast with stringent cutoffs to provide official gene symbols for a few additional genes.
RNA-seq, timecourse: Reads for time points 3, 6, 9, 12, 15, 18, 48, and 96 hours after Tcf7l2 or scramble siRNA treatment were mapped against the H4IIE-specific transcriptome using Tophat version 2.0.4 (with underlying Bowtie version 0.12.8). Essential Tophat command arguments were: --library-type fr-unstranded --prefilter-multihits --no-novel-juncs --transcriptome-only -G <H4IIE-specific transcriptome>.
RNA-seq, timecourse: Conversion to sorted BAM format using samtools
RNA-seq, timecourse: Differential expression was analyzed using Cuffdiff version 2.0.2., comparing Tcf7l2 against scramble siRNA treatment. Essential Cuffdiff command arguments were: --FDR 0.05 --library-type fr-unstranded --multi-read-correct --upper-quartile-norm --frag-bias-correct <rn4 genome fastas> <H4IIE-specific transcriptome>
ChIP-seq: Alignment to rn4 using Bowtie v0.12.8 with the following essential command line arguments: bowtie -n 1 -m 1 -k 1 --trim5 5 -l 36 --best
ChIP-seq: Conversion to sorted BAM format using samtools
ChIP-seq: Peak calling using MACS2 version 2.0.10.20130306 with the following essential command line arguments: macs2 callpeak –bw 100 –m 5 50 –keep-dup 1 --qvalue=0.01 --bgd
Genome_build: rn4
Supplementary_files_format_and_content: gtf: standard gtf as produced by Cuffcompare
Supplementary_files_format_and_content: differential expression: standard gene_exp.diff files produced by Cuffdiff
Supplementary_files_format_and_content: endocePeak: MACS2-native format that is otherwise like the standard ENCODE-style narrowPeak format except that the 5th column contains transformed p-values (-log10pvalue*10)

organism: Rattus norvegicus

source_name: H4IIE hepatocytes

growth_protocol: Low passage H4IIE cells were purchased from ATCC and used in the lab up to passage 30. The cells were routinely cultured in low glucose (5 mM) DMEM media supplemented with 10% fetal bovine serum in the absence of antibiotics and laboratory stocks tested negative for mycoplasma. After siRNA treatment, cells were immediately plated in 24-well plates in regular culture medium.

extract_protocol:
RNA was extracted standard procedures.
Illumina sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit V2.

treatment_protocol: Silencing of TCF7L2 mRNA and protein levels was achieved using 100 nM Dharmacon SmartPool siRNA (cat #), introduced via Neon electroporation, as described previously (PMID: 21901280). The experiment was performed in 1-3 replicates with separate electroporations being performed on a different passage of cells on a different date.

tag: cell type

value: hepatocytes

tag: treatment

value: siRNA -Tcf7l2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, rep 1


title: L129_C06

description: single cell

value: female


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 1


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 3


title: L129_B10

description: single cell


title: L227_C04

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 2


title: L129_B09

description: single cell


title: L227_C08

description: single cell


title: L227_C02

description: single cell


title: L227_C03

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 6 h, rep 2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 1


title: L129_B07

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 6 h, rep 1


title: L227_C07

description: single cell


title: L227_C05

description: single cell


title: L227_C01

description: single cell


title: L227_C06

description: single cell


title: L227_B12

description: single cell


title: L129_B04

description: single cell


title: L129_B08

description: single cell


title: L227_B09

description: single cell


title: L227_C09

description: single cell


title: L129_B06

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 3 h, rep 1


title: L227_B11

description: single cell


title: L129_B05

description: single cell


title: L227_B10

description: single cell


title: L227_B07

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 96 h, rep 2

value: siRNA - Scrambled


title: L129_B02

description: single cell


title: L129_B11

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 48 h, rep 1


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 3 h, rep 2


title: L129_A11

description: single cell


title: L227_B08

description: single cell


title: L129_B01

description: single cell


title: L227_B05

description: single cell


title: L129_B03

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 48 h, rep 2


title: L129_A10

description: single cell


title: L227_B06

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 18 h, rep 1


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 18 h, rep 2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, rep 2


title: L129_A08

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, rep 1


title: L129_A09

description: single cell


title: L227_B04

description: single cell


title: L227_B01

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 96 h, rep 1


title: L227_B03

description: single cell


title: L227_B02

description: single cell


title: L227_G03

description: single cell


title: L129_H02

description: single cell


title: L129_A07

description: medium


title: L129_A12

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 3


title: L129_A06

description: single cell


title: L129_A05

description: single cell


title: L227_A12

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 1


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 3


title: L227_A11

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 2


title: L227_A09

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 1


title: L129_A03

description: single cell


title: L129_A02

description: single cell


title: L129_A01

description: single cell


title: L227_A07

description: single cell


title: L227_A10

description: single cell


title: L227_A08

description: single cell


title: L128_H12

description: single cell


title: L227_A06

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 6 h, rep 2


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 6 h, rep 1


title: L128_H11

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 3 h, rep 1


title: L227_A04

description: single cell


title: RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 3 h, rep 2


title: L227_A05

description: single cell


title: L227_A03

description: single cell


title: L128_H08

description: single cell


title: L128_H09

description: single cell


title: L129_A04

description: single cell


title: L128_H10

description: single cell


title: L227_A02

description: single cell


title: Replicate C Sort S7

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

state: NY

address: 1 Bungtown Rd

department: Biology

country: USA

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
1: Reads were aligned to sensor construct target sequences using bowtie (allowing zero mismatches)
2: Reads were quantified with unix command uniq -c
3: Reads were normalized to have a sum of 1 for each sample.
4: Samples corresponding to sorts  S1,S3 and S5 were log2 normalize by their corresopnding S0 reads.
5: Corresponding sorts were averaged across replicates
6: For each chip a matrix was constructed where rows correspond to shRNAs/targets and columns to the normalized values of sorts S1, S3 and S5. This is taken as the shRNA efficacy measurment.
Supplementary_files_format_and_content: Initial_Sensor_Summary has three fields for every construct assayed. Field 1: The shRNA guide sequence, Field 2: The shRNA target sequence, Field 3: The calculated shRNA efficacy score

molecule: genomic DNA

organism: synthetic construct

source_name: ERC Cell Line Infected with 1U-Sensor

growth_protocol: DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA Blood Maxi Kit (Qiagen)
Libraries were constructed by PCR of the shRNA guides from the infected cells genomes. PCR primers were tailed with illumina addapter sequences.

treatment_protocol: From Fellmann et al Mol Cell 2011: ERC reporter cells were infected with pSENSOR libraries at singly copy and sorted in iterative cycles, either after treatment with Dox and G418 (500 μg/ml) for 6–7 days (OnDox) or after Dox and G418 withdrawal for 6–7 days (OffDox). The gating was guided by reference cells transduced with small pools of potent (Top5) and weak (Bottom5) control shRNA-Sensor constructs.

tag: host organism

value: Gallus gallus

tag: host cell line

value: ERC

tag: shRNA type

value: shRNA Guide Sequences


title: L227_A01

description: single cell


title: L128_H07

description: single cell


title: Replicate A Sort S7


title: L226_H12

description: empty well


title: Replicate B Sort S7


title: L128_H06

description: single cell


title: L128_H04

description: single cell


title: L226_H11

description: single cell


title: Replicate A Sort S5


title: L226_H10

description: single cell


title: Replicate B Sort S5


title: L128_H03

description: single cell


title: Replicate C Sort S3


title: L226_H09

description: single cell


title: L128_H02

description: single cell


title: L128_H01

description: single cell


title: Replicate B Sort S3


title: L226_H06

description: single cell


title: Replicate A Sort S3


title: L226_H08

description: single cell


title: L226_H07

description: single cell


title: L226_H05

description: single cell


title: Sort 0


title: shERWOOD-ULTRAMIR T6C

description: shERWOOD-ULTRAMIR Time 3C shRNAs

data_processing:
1) For each sample libraries were aligned to the sequences contained on the shRNA library chip using the bowtie algorithm allowing zero mismatches.
2) shRNAs were quantified using unix -c. Each sample was then normalized to have a total count of 1.
3) Each final timepoin was log2 normalized to the initial time point.
4) Each reasultant log ratio was normalized by subtracting a line fit to the log2-fold changes of control shRNAs vs. their GC content.
5) The resultant normalized values were then location normalized against the median of the control shRNA values. The library was also scale normalized so that the standard deviation of the control shRNAs was set to 1.
6) shRNAs were called as depleted or enriched using the limma (bioconductor) package.
Supplementary_files_format_and_content: The file Validation_Screen_Summary.txt can be found on the series record and contains 4 fields:  1) shRNA Library, 2) Gene, 3) shRNA,  4) Normalized Fold Change, 5) FDR on Fold Change

source_name: A385 Cell Line

growth_protocol: DMEM high glucose supplemented with 10% fetal bovine serum, non-essential amino acids and penicillin streptomycin

extract_protocol:
Genomic DNA from each clone was isolated using the QIAamp DNA Blood Maxi Kit
Libraries were constructed using PCR primers targeting the shrNA loop and the PGK promoter located downstream of the shRNA construct. Primers were adapted to contain Illumina adapter sequences. Libraries were sequenced on a Hiseq

treatment_protocol: Cells were infected with retrovirus shRNA libraries. Two days after infection a T0 aliquot was collected. Following this cells were separated into three replicates and each was selected with G418 (Neomycin 1mg/ml) until 95% infection rate was achieved. After 6 passages (~18 doublings) final aliquots were collected.

value: Homo sapiens

value: shRNA Amplicon


title: Sort 1


title: Replicate C Sort S5


title: L226_H03

description: single cell


title: L128_G12

description: single cell


title: L226_H04

description: single cell


title: L128_G09

description: single cell


title: L128_G10

description: single cell


title: L128_G11

description: single cell


title: L128_H05

description: single cell


title: L226_H01

description: single cell


title: L128_G07

description: single cell


title: L128_G08

description: single cell


title: shERWOOD-ULTRAMIR T6B

description: shERWOOD-ULTRAMIR Time 3B shRNAs


title: L226_H02

description: single cell


title: shERWOOD-ULTRAMIR T6A

description: shERWOOD-ULTRAMIR Time 3A shRNAs


title: L226_G12

description: empty well


title: shERWOOD-1U -ULTRAMIR TT6C

description: shERWOOD-1U-ULTRAMIR Time 3C shRNAs


title: L128_G05

description: single cell


title: shERWOOD-ULTRAMIR T0

description: shERWOOD-ULTRAMIR Time 0 shRNAs


title: L128_G04

description: single cell


title: L226_G11

description: single cell


title: shERWOOD-1U-ULTRAMIR T T6B

description: shERWOOD-1U-ULTRAMIR Time 3B shRNAs


title: L226_G10

description: single cell


title: L128_G02

description: single cell


title: shERWOOD-1U-ULTRAMIR T T6A

description: shERWOOD-1U-ULTRAMIR Time 3A shRNAs


title: L226_G09

description: single cell


title: L128_G03

description: single cell


title: L226_G07

description: single cell


title: shERWOOD-1U-ULTRAMIR T0

description: shERWOOD-1U-ULTRAMIR Time 0 shRNAs


title: L226_G08

description: single cell


title: L128_G01

description: single cell


title: TRC T6C

description: TRC Time 3C shRNAs


title: L226_G05

description: single cell


title: TRC T6B

description: TRC Time 3B shRNAs


title: L128_G06

description: single cell


title: TRC T0

description: TRC Time 0 shRNAs


title: L226_G06

description: single cell


title: L128_F11

description: single cell


title: L226_G03

description: single cell


title: shERWOOD T6B

description: shERWOOD Time 3B shRNAs


title: L226_G02

description: single cell


title: TRC T6A

description: TRC Time 3A shRNAs


title: L226_G04

description: single cell


title: L128_F10

description: single cell


title: shERWOOD T6A

description: shERWOOD Time 3A shRNAs


title: shERWOOD T6C

description: shERWOOD Time 3C shRNAs


title: L128_F08

description: single cell


title: L226_G01

description: single cell


title: L128_F09

description: single cell


title: chip 5571 replicate B sort S5

data_processing:
1: Reads were aligned to sensor construct target sequences using bowtie (allowing zero mismatches)
2: Reads were quantified with unix command uniq -c
3: Reads were normalized to have a sum of 1 for each sample.
4: Samples corresponding to sorts  S1,S3 and S5 were log2 normalize by their corresopnding S0 reads.
5: Corresponding sorts were averaged across replicates
6: For each chip a matrix was constructed where rows correspond to shRNAs/targets and columns to the normalized values of sorts S1, S3 and S5. This is taken as the shRNA efficacy measurment.
Supplementary_files_format_and_content: Initial_Sensor_Summary has three fields for every construct assayed. Field 1: Human gene the shRNA is targeting. Field 2: The shRNA guide sequence.  Field 3: The shRNA target sequence. Field 4: The calculated shRNA efficacy score

source_name: ERC Cell Line Infected with Chip 5571


title: chip 5571 replicate B sort S1


title: L128_F07

description: single cell


title: L128_F06

description: single cell


title: shERWOOD T0

description: shERWOOD Time 0 shRNAs


title: chip 5571 replicate B sort S0


title: chip 5571 replicate A sort S5


title: L226_F11

description: single cell


title: chip 5571 replicate A sort S1


title: L226_F10

description: single cell


title: chip 5571 replicate B sort S3


title: L128_F12

description: single cell


title: chip 5541 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 5541


title: L226_F07

description: single cell


title: chip 5541 replicate B sort S3


title: chip 5571 replicate A sort S3


title: L226_F12

description: single cell


title: DSIR T6C

description: DSIR Time 3C shRNAs


title: L128_F05

description: single cell


title: DSIR T6B

description: DSIR Time 3B shRNAs


title: L128_E12

description: single cell


title: shERWOOD-1U T6A

description: shERWOOD-1U Time 3A shRNAs


title: chip 5541 replicate B sort S1


title: L128_E11

description: single cell


title: DSIR T6A

description: DSIR Time 3A shRNAs


title: L128_F04

description: single cell


title: chip 5541 replicate B sort S0


title: shERWOOD-1U T0

description: shERWOOD-1U Time 0 shRNAs


title: L226_F04

description: single cell


title: Knock_Out

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were identified by a 4 nucleotide barcode which was removed
Cutadapt v1.2 was used to remove the 3’ adaptor and discard reads shorter than 15 nucleotides
The trimmed reads were mapped using the Bowtie 2 aligner v 2.1.0 with default settings to the precursor ribosomal RNA (35S rRNA) gene of Saccharomyces cerevisiae s288c (RDN37-1;SGD:S000006486, GeneID: 9164931)
Only reads mapping uniquely and with a minimum of three correct nucleotides at the 5’ or 3’ end were used to compute the number of 3’ read ends (corresponding to the 5’ nt in the sequence insert) and 5’ read ends (corresponding to the 3’ nt in the sequence insert), respectively. In the latter, the counts were shifted one position upstream at the level of the sequence read in order to get the 3’ and 5’ read ends to align to the methylated nucleotide in the reference sequence.
Various scoring systems were used to detect and visualise 2'-O-methylation based on the 5' and 3' read end counts.
Genome_build: n/a, Saccharomyces cerevisiae s288c (RDN37-1;SGD:S000006486, GeneID: 9164931)
Supplementary_files_format_and_content: The processed data files are bed files for visualising the data in the UCSC browser. Each file contains 6 tracks: 5' RNA ends, 3' RNA ends, 5' and 3'. RNA ends combined, score A, score B and Pseudo-U score as described in Birkedal et al. The bed-files may be uploaded to the UCSC browser individually or in combination. The file generic_ribo_info.bed should be included at all times to navigate known RNA modifications.

organism: Saccharomyces cerevisiae

source_name: Yeast

extract_protocol:
RNA was extracted using hot phenol protocol as described in Birkedal et al. Chromatin associated RNA was purified according to: F. Carrillo Oesterreich, S. Preibisch, K. M. Neugebauer, Global analysis of nascent RNA reveals transcriptional
The fragments are ligated to RNA oligos using a tRNA ligase that has been mutated to remove its kinase activity, reverse transcribed and the cDNA used as input for sequencing.

tag: modification

value: carries a plasmid harboring the entire snR67-snR53 region with a single substitution that blocks methylation at LSU-G2619

tag: sample type

value: Whole cell RNA


title: L226_F08

description: single cell


title: L128_F03

description: single cell


title: DSIR T0

description: DSIR Time 0 shRNAs


title: L128_F02

description: single cell


title: L226_F06

description: single cell


title: shERWOOD-1U T6B

description: shERWOOD-1U Time 3B shRNAs


title: L226_F09

description: single cell


title: L128_F01

description: single cell


title: chip 5571 replicate A sort S0


title: shERWOOD-1U T6C

description: shERWOOD-1U Time 3C shRNAs


title: chip 5541 replicate A sort S5


title: L128_E10

description: single cell


title: L226_F03

description: single cell


title: Knock_IN 2

description: Mature ribosomal RNA was gel-purified

value: carries a plasmid encoded artificial snoRNA targeting LSU-U2954

value: Large ribosomal subunit RNA


title: chip 5541 replicate A sort S3


title: L226_F02

description: single cell

value: C

value: Cooling


title: L128_E09

description: single cell

value: A

value: male


title: Knock_IN 1


title: L226_F01

description: single cell


title: wt_SSU

description: Mature ribosomal RNA was gel-purified

value: wild type

value: Small  ribosomal subunit RNA


title: chip 5521 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 5521


title: chip 5521 replicate B sort S3


title: TS_Rs26

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.7, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.12, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk)
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7-14) log2 Expression Value

source_name: Trophoblast Stem Cells

growth_protocol: ES cells, iCdx2 and iCdx2/iRaf ES cells (prior to the start of the reprogramming protocol), were maintained in serum+LIF conditions on a layer of irradiated mouse embryonic fibroblasts (MEFs).  TS cells were maintained in 70% MEF-conditioned media, 30% TS media 25ng/ml bFGF and 1µg/ml Heparin on uncoated tissue culture plastic, as standard.

extract_protocol:
Total RNA was prepared using TRI reagent (Sigma) followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies), according to manufacturers' instructions.
mRNA was isolated from total DNA-free RNA (150-240 ng) using the Dynabeads mRNA purification kit (Life Technologies 61006) and prepared into an indexed, strand-specific library using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106) according to manufacturers‘ instructions.  Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol.

value: Trophoblast Stem Cells

tag: cell line

tag: condition

value: Conventional culture conditions


title: L128_E05

description: single cell

value: RT


title: L128_E07

description: empty well


title: chip 5541 replicate A sort S1

value: Gallus gallus

value: ERC


title: L128_E06

description: single cell


title: L226_E11

description: single cell

value: female


title: L226_E09

description: single cell


title: chip 5541 replicate A sort S0

value: shRNA Guide Sequences


title: L226_E12

description: single cell


title: iCdx2_iRaf_ES_MEF

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells

value: E14 - iCdx2/iRaf

value: 5 days of reprogramming in TS conditions on MEFs, and then replated for a further 3 days on MEFs

tag: treatment protocol

value: During the experimental time course of trans-differentiation, cells were plated on MEFs in TS cell conditions, as specified, with 4HT at a seeding denisty of approximately 1x10E4 cells/25cm2. Media was changed every 2 days.  After 5 days, cells were trypsinised and replated with and without MEFs for a further 3 days culture.  At the end of the trans-differentiation time-course, cells were FACS-purified to remove MEFs.


title: L128_E08

description: single cell


title: L226_E10

description: single cell

value: C


title: L226_F05

description: single cell

value: Cooling


title: wt_LSU

description: Mature ribosomal RNA was gel-purified

value: Large ribosomal subunit RNA


title: chip 5521 replicate A sort S5


title: L226_E07

description: single cell


title: iCdx2_ES_TC_plastic

value: 5 days of reprogramming in TS conditions on MEFs, and then replated for a further 3 days on gelatinised TC plastic (without MEFs)


title: TS_EGFP

value: EGFP


title: L128_E01

description: single cell

value: A

value: male


title: L128_E03

description: single cell


title: chip 5521 replicate B sort S1


title: L128_E04

description: single cell


title: L226_E08

description: single cell


title: iCdx2_iRaf_ES_TC_plastic


title: chip 5521 replicate A sort S3


title: L128_D12

description: single cell


title: L128_E02

description: single cell


title: chip 5521 replicate B sort S0


title: L226_E06

description: single cell


title: chip 5521 replicate A sort S1


title: L226_E05

description: single cell


title: chip 5521 replicate A sort S0


title: iCdx2_ES_MEF


title: ES_J1

value: Conventional culture conditions


title: L128_D10

description: single cell

value: RT


title: ES_E14


title: chip 5511 replicate B sort S3

source_name: ERC Cell Line Infected with Chip 5511

value: Gallus gallus


title: L128_D11

description: single cell


title: L226_E03

description: single cell


title: ES-E14 2i pretr.

data_processing:
Genomic mapping of paired-end reads was performed with Bowtie (v0.12.8) using the following parameters: -m 1 --strata --best -X 700. Reads were mapped to the mouse genome build NCBIM37. Final data analysis was performed using SeqMonk software (www.bioinformatics.babraham.ac.uk).
Genome_build: NCBIM37
genome-wide quantification file: Quantitated MeDIP-Seq files were generated for 1kb non-overlapping genomic tiles using SeqMonk (v0.28.0). The result file carries descriptive column headers and is tab-delimited; the relevant columns are: (1) ID; (2) Chromosome; (3) Start; (4) End; (13-21) Raw read count per 1kb tile

growth_protocol: Prior to the start of the reprogramming protocol, ES and TS cells were cultured in routine conditions on a layer of irradiated mouse embryonicfibroblasts (MEFs). ES cells were maintained in serum+LIF conditions, and TS cells in 70% MEF-conditioned media, 30% TS media, with 25ng/ml bFGF and 1µg/ml Heparin.

extract_protocol:
At the end of the trans-differentiation time-course, cells were FACS-purified to remove MEFs, and DNA extracted with phenol-chloroform according to standard protocols. DNA was used for MeDIP analysis as described previously (Senner et al., Stem Cells 2012).
Genomic DNA was fragmented by sonication (Diagenode Bioruptor), and adaptor ligated with paired-end adaptors 5’-PGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’ (* Phosphorothioate group) and the NEBnext library preparation kit. Subsequently immunoprecipitaions with an anti-5-methylcytosine antibody were carried out in triplicate. IP triplicates –prepared for each cell type – were pooled and MeDIP DNA libraries were column-purified (MinElute, Qiagen) and eluted in 17μl of EB buffer (pre-warmed at 55ºC). DNA unbound fractions were processed in parallel. MeDIP libraries (and unbound DNA fractions, as control) were amplified by PCR for 12 cycles using distinct combinations of primers: PE 1.0 (Fw) AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; PE 2.0 (Rv) CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT; iPCR tag6 (Rv) CAAGCAGAAGACGGCATACGAGATACATTGGCGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC; iPCR tag7 (Rv) CAAGCAGAAGACGGCATACGAGATCAGATCTGGAGA  TCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC; iPCR tag8 (Rv) CAAGCAGAAGACGGCATACGAGATCATCAAGTGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC. Amplified MeDIP libraries (and unbound DNA fractions, as control) were  resolved by 2% agarose gel electrophoresis, and DNA fragments within the 300-500 nt range were cut out and DNA was purified using the Qiagen Gel extraction kit. 5mC immuno-precipitation efficiency was confirmed by analysing ES and TS  cell MeDIP pre- and post-amplification libraries by quantitative PCR for candidate loci (Elf5, Nanog). Library concentration was determined using KAPA Illumina SYBR Universal Lid Q Kit (ANACHEM) and by Bioanalyzer.

treatment_protocol: During the experimental time course of trans-differentiation, cells were plated on MEFs in TS cell conditions as specified with the appropriate inducer (Dox or 4HT) at a seeding density of approximately 1x10E4 cells/25cm2. Media was changed every 2 days. Cells were trypsinized after 6 days of culture and re-plated, again at 1x10E4 cells/25cm2 in TS conditions, for another 6 days.

value: E14 - after 2i pre-treatment

value: 12 days of reprogramming in TS conditions


title: L128_D09

description: single cell


title: L128_D08

description: single cell


title: L226_E02

description: >1 cell

value: female


title: iCdx2/iRaf ES

value: Embryonic Stem Cells


title: L128_D07

description: empty well


title: L226_E01

description: single cell


title: chip 5511 replicate A sort S5

value: ERC

value: shRNA Guide Sequences


title: control_BirA

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

description: control_BirA ChIP DNA from ES cells

data_processing:
Sequences were aligned using the software Bowtie (Langmead et al., 2009) into July 2007 assembly of the mouse genome (mm9, NCBI Build 37). For the identification of DBP bound peaks, software MACS 1.4.2 (Zhang et al., 2008) were used with dynamic local lambda calculation and building shifting model under P-value cutoff at 1e-5.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: WIG file generated from software MACS 1.4.2 (Zhang et al., 2008)

source_name: control_BirA ChIP DNA from ES cells

growth_protocol: Mouse J1 ES cell lines cultured on gelatin coated plates were maintained as described previously (Kim et al., 2008). Briefly, cells were maintained in DMEM (Dulbecco's modified Eagle's medium) supplemented with 15% fetal calf serum, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 1% of nucleoside mix (100× stock, Sigma), 1000 U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and 50 U/ml Penicillin/Streptomycin.

extract_protocol:
The Flag-bio tagged mouse ES cells were fixed in 1% formaldehyde for 7 minutes at room temperature. The formaldehyde was quenched using 2.5M glycine before harvest for extract preparation. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with size of 500-800bp were immunoprecipitated using Streptavidin beads (Dynabeads MyOne Streptavidin T1), and 2% SDS was applied for one of the washing steps.
massive parallel sequencing (bioChIP-Seq)

tag: strain background

value: mouse embryonic stem cells

tag: genotype/variation

value: expressing control BirA

tag: chip beads

value: Dynabeads MyOne Streptavidin T1

tag: chip beads vendor

value: Invitrogen

tag: chip beads cat. #


title: chip 5511 replicate B sort S1


title: L226_D12

description: single cell

tag: cell picking session

value: C

tag: cell picking temperature

value: Cooling

tag: strain


title: chip 5511 replicate A sort S3


title: bioNanog

description: bioNanog ChIP DNA from ES cells

source_name: bioNanog ChIP DNA from ES cells

tag: cell type

value: expressing Flag-bio tagged Nanog


title: L128_D06

description: single cell

value: A

tag: gender

value: male


title: L226_E04

description: single cell


title: L226_D10

description: single cell


title: L226_D11

description: single cell


title: L128_D03

description: single cell

value: RT


title: L226_D09

description: single cell


title: chip 5511 replicate B sort S0

tag: host organism

value: Gallus gallus

tag: host cell line


title: bioDax1_R1

description: bioDax1 ChIP DNA from ES cells, Rep 1

source_name: bioDax1 ChIP DNA from ES cells

value: expressing Flag-bio tagged Dax1


title: L128_D04

description: single cell


title: chip 5511 replicate B sort S5

tag: shRNA type


title: L226_D08

description: single cell


title: bioDax1_R2

description: bioDax1 ChIP DNA from ES cells, Rep 2


title: chip 5511 replicate A sort S1


title: chip 5511 replicate A sort S0


title: bioMax

description: bioMax ChIP DNA from ES cells

source_name: bioMax ChIP DNA from ES cells

value: expressing Flag-bio tagged Max


title: L128_D01

description: single cell


title: chip 5471 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 5471


title: L226_D07

description: single cell

value: female


title: iCdx2 ES

value: Embryonic Stem Cells

value: E14 - iCdx2

value: 12 days of reprogramming in TS conditions


title: L128_C12

description: single cell


title: L226_D06

description: single cell


title: chip 5471 replicate B sort S3

value: ERC

value: shRNA Guide Sequences


title: bioE2F4

description: bioE2F4 ChIP DNA from ES cells

source_name: bioE2F4 ChIP DNA from ES cells

value: mouse embryonic stem cells

value: expressing Flag-bio tagged E2F4

value: Dynabeads MyOne Streptavidin T1


title: L128_D05

description: single cell

source_name: lumbar dorsal root ganglion


title: L128_D02

description: single cell


title: chip 5471 replicate B sort S0


title: L226_D05

description: single cell

value: C

value: Cooling


title: L226_D04

description: single cell


title: L128_C10

description: single cell

value: A


title: bioDmap1

description: bioDmap1 ChIP DNA from ES cells

source_name: bioDmap1 ChIP DNA from ES cells

value: expressing Flag-bio tagged Dmap1

value: Invitrogen


title: chip 5471 replicate B sort S1

value: Gallus gallus


title: L128_C09

description: single cell

value: RT

value: male


title: L226_D03

description: >1 cell

value: female


title: bioMyc_R2

description: bioMyc ChIP DNA from ES cells, Rep 2

source_name: bioMyc ChIP DNA from ES cells

value: expressing Flag-bio tagged Myc


title: L226_D01

description: single cell


title: L226_D02

description: single cell


title: bioTip60

description: bioTip60 ChIP DNA from ES cells

source_name: bioTip60 ChIP DNA from ES cells

value: expressing Flag-bio tagged Tip60


title: chip 5471 replicate A sort S3


title: L128_C08

description: single cell


title: chip 5471 replicate A sort S1


title: chip 5471 replicate A sort S0


title: L226_C12

description: single cell


title: bioMyc_R1

description: bioMyc ChIP DNA from ES cells, Rep 1


title: L226_C11

description: single cell


title: L128_C05

description: single cell


title: L128_C11

description: single cell


title: L226_C10

description: single cell


title: chip 5471 replicate A sort S5


title: L128_C03

description: single cell


title: chip 5461 replicate B sort S1

source_name: ERC Cell Line Infected with Chip 5461


title: L128_C07

description: empty well


title: chip 5461 replicate B sort S0


title: L226_C09

description: single cell


title: L128_C06

description: single cell


title: L128_C01

description: single cell


title: chip 5461 replicate A sort S5


title: L226_C08

description: single cell


title: chip 5461 replicate A sort S3


title: chip 5461 replicate B sort S5


title: L128_B11

description: single cell


title: L128_B10

description: single cell


title: chip 5461 replicate A sort S1


title: chip 5461 replicate A sort S0


title: L128_B12

description: single cell


title: L226_C04

description: single cell


title: L128_C04

description: single cell


title: L226_C03

description: single cell


title: chip 5461 replicate B sort S3


title: L128_B09

description: single cell


title: chip 5431 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 5431


title: chip 5431 replicate B sort S3


title: L128_B08

description: single cell


title: L226_C06

description: single cell


title: L226_C02

description: single cell


title: L128_B07

description: empty well


title: L226_C07

description: single cell


title: L226_C01

description: single cell


title: L128_C02

description: single cell


title: L226_C05

description: single cell


title: L128_B05

description: single cell


title: L226_B12

description: single cell


title: L226_B11

description: single cell


title: L128_B04

description: single cell


title: L128_B03

description: single cell


title: L226_B09

description: single cell


title: L226_B10

description: single cell


title: L128_B01

description: single cell


title: chip 5431 replicate B sort S0


title: chip 5431 replicate B sort S1


title: chip 5431 replicate A sort S0


title: L226_B07

description: single cell


title: chip 5431 replicate A sort S5


title: chip 5421 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 5421


title: chip 5431 replicate A sort S3


title: L226_B06

description: single cell


title: L128_B06

description: single cell


title: L128_A11

description: single cell


title: chip 5431 replicate A sort S1


title: L128_B02

description: single cell


title: chip 5421 replicate B sort S1


title: L226_B05

description: single cell


title: chip 5421 replicate B sort S0


title: chip 5421 replicate B sort S3


title: L128_A10

description: single cell


title: L226_B04

description: single cell


title: chip 5421 replicate A sort S5


title: L128_A09

description: single cell


title: L226_B03

description: single cell


title: L128_A08

description: single cell


title: chip 5421 replicate A sort S1


title: L226_B02

description: single cell


title: L226_B08

description: single cell


title: L128_A07

description: empty well


title: L226_B01

description: single cell


title: L128_A12

description: single cell


title: L226_A12

description: >1 cell


title: chip 4021 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 4021


title: L128_A03

description: single cell


title: L226_A10

description: single cell


title: chip 4021 replicate B sort S3


title: L128_A04

description: single cell


title: L226_A11

description: single cell


title: L128_A06

description: single cell


title: L128_A05

description: single cell


title: L226_A09

description: single cell


title: chip 4021 replicate B sort S0


title: chip 4021 replicate B sort S1


title: L128_A01

description: empty well


title: L128_A02

description: single cell


title: chip 4021 replicate A sort S5


title: chip 4021 replicate A sort S3


title: L226_A07

description: single cell


title: L226_A08

description: single cell


title: L226_A06

description: single cell


title: chip 5421 replicate A sort S3


title: chip 4021 replicate A sort S1


title: L226_A05

description: single cell


title: chip 4021 replicate A sort S0


title: chip 4011 replicate B sort S5

source_name: ERC Cell Line Infected with Chip 4011


title: HC-A13-17

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Reads were aligned to the reference transcriptome generated from the GENCODE reference annotations version 14 using Bowtie version 0.12.9. Expression level abundances for all GENCODE genes were estimated using RSEM version 1.2.3. Differential expression analysis was done for all GENCODE genes using the DESEQ algorithm within the Trinity framework version 2013-02-25.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with FPKM reads

organism: Homo sapiens

source_name: Whole lumbar spinal cord homogenate

extract_protocol:
Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol. RNAseq analysis was performed in Harvard genetic facility. Ribosomal reduction using Qiagen kit gene read rRNA depletion kit - http://www.qiagen.com/Products/Catalog/Assay-Technologies/Next-Generation-Sequencing/GeneRead-rRNA-Depletion-Kit#orderinginformation. Direction mRNA sequencing Integenix protocol - http://www.genome.med.harvard.edu/documents/illumina/IntegenX_Apollo324_mRNA_Seq_Protocol_10012012.pdf
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy donor

tag: tissue

value: whole lumbar spinal cord


title: HC-A12-200


title: HC-A13-18


title: L226_A03

description: single cell


title: chip 5421 replicate A sort S0

value: ERC

value: shRNA Guide Sequences


title: chip 4011 replicate B sort S1


title: chip 4011 replicate B sort S3


title: HC-A13-7


title: HC-A13-14


title: L226_A02

description: single cell


title: HC-A12-243


title: L226_A01

description: single cell


title: HC-A12-5-112


title: chip 4011 replicate B sort S0


title: chip 4011 replicate A sort S5


title: chip 4011 replicate A sort S3


title: HC-A12-231


title: HC-A12-222


title: chip 4011 replicate A sort S1


title: chip 4011 replicate A sort S0


title: HC-A12-241


title: ALS-701-015

value: sALS


title: ALS-701-013 (fALS)

value: fALS


title: chip 4001 replicate B sort S3

source_name: ERC Cell Line Infected with Chip 4001


title: L226_A04

description: single cell

value: C


title: chip 4001 replicate B sort S5


title: chip 4001 replicate B sort S1


title: chip 4001 replicate B sort S0


title: ALS-701-008


title: ALS-701-004


title: ALS-701-001


title: ALS-701-007


title: ALS-701-002


title: ALS-701-006 (fALS)


title: ALS-701-009


title: ALS-701-005


title: chip 4001 replicate A sort S3


title: chip 4001 replicate A sort S1


title: chip 3991 replicate B sort S1

source_name: ERC Cell Line Infected with Chip 3991


title: chip 3991 replicate B sort S0


title: NS D

status: Public on Nov 23 2014

city: Kansas City

first: Malcolm

last: Cook

email: mec@stowers.org, malcolm.cook@gmail.com

state: MO

address: 1000 E 50th Street

department: Big Data AI

institute: Stowers Institute For Medical Research

data_processing:
Bowtie (Langmead et al. 2009) was used to perform alignment of sequence reads, from SR-depleted and control samples, to the Drosophila melanogaster (v5.22) genome, and a database of splice junctions (36 nt on each side of the splice junction) allowing for up to two mismatches and single alignment.
Next, for each annotated alternative splicing event (ASE), the number of reads were tabulated that support the inclusive, exclusive, or both (constitutive) forms. Two Fisher tests are used to compare the tabulated read counts occurring in the SR-depleted and control results for each ASE. One test for significant changes in inclusive counts and another for changes in exclusive counts. To determine the magnitude and direction of splicing change PSI (percent spliced in) values are calculated. This is the relative ratio of reads that provide evidence for the inclusive isoform   [(inclusive/inclusive_length)/[(inclusive/inclusive_length + constitutive/constitutive_length]).
Genome_build: Flybase 5.22
Supplementary_files_format_and_content: For each knockdown, a single ""ocieDiff.tab"" file contrasting, for every splicing event, the frequency of splicing in the knockDown with that in the non-specific (NS) sample.
Supplementary_files_format_and_content: The file is tab delimited with columns describing the splicing event, followed by columns tabulating experimental observations (counts), followed by derivitive calculations (rations and fisher test results)
Supplementary_files_format_and_content: columns describing the splicing event (these are the same in every ocieDiff.tab file and are derived from flybase transcript annotation)
Supplementary_files_format_and_content: '+ ASELabel - unique Alternative splicing event label
Supplementary_files_format_and_content: '+ ASEtype - encodes the type of splicing event (i.e. CD:CompetingDonor, RI : Retained Intron, etc)
Supplementary_files_format_and_content: '+ locusID - name of gene which is spliced
Supplementary_files_format_and_content: '+ strand - coding direction of the gene on the seq_id
Supplementary_files_format_and_content: '+ seq_id - chromosomal identifier
Supplementary_files_format_and_content: '+ begin - position on chromosome at which the splicing event begins (may be either a donor (receptor) site (depending upon the strand)
Supplementary_files_format_and_content: '+ end - position on chromosome at which the splicing event ends
Supplementary_files_format_and_content: '+ inclusive - genomic coordinates of the trascriptionally adjacent nucleotides which are uniq to the inclusive form
Supplementary_files_format_and_content: '+ exclusive - genomic coordinates of the trascriptionally adjacent nucleotides which are uniq to the exclusive form
Supplementary_files_format_and_content: '+ constitutive - genomic coordinates of the trascriptionally adjacent nucleotides which common to both forms, up to the nearest exon
Supplementary_files_format_and_content: columns tabulating experimental observations (counts):
Supplementary_files_format_and_content: '+ ctl.i,ctl.e,ctl.c,ctl.o - in the control (NS) sample, counts of reads which support inclusive,exclusive,constitutive(both),other isoform
Supplementary_files_format_and_content: '+ exp.i,exp.e,exp.o,exp.c - similarly for the knockdown sample
Supplementary_files_format_and_content: colums of rations and fisher test results
Supplementary_files_format_and_content: '+ pval.i & pval.e - fisher test p values contrasting inclusive & exclusive counts to constituitive
Supplementary_files_format_and_content: '+ q.val.i & q.val.e  - p values adjusted for multiple testing
Supplementary_files_format_and_content: '+ PSICtl - 'percent spliced in' (PSI) in the control (NS) experiment
Supplementary_files_format_and_content: '+ PSIExp - 'percent spliced in' (PSI) in the knockdown
Supplementary_files_format_and_content: '+ PSIswitchScore - PSIExp-PSICtl

organism: Drosophila melanogaster

source_name: fly S2 cells

growth_protocol: Schneider media supplemented with 10% FBS

extract_protocol:
RNA-Easy mini-column (following Qiagen protocol)
True-Seq (following Illumina protocol)

treatment_protocol: 1ug of dsRNA targeting the given SR protein or GFP for the non-specific control was added then 48 hours later 1 ug of each dsRNA were added and growth was continued for 48 more hours followed by RNA extraction

tag: exptgroup

value: D

value: NS


title: chip 3991 replicate B sort S3


title: chip 4001 replicate A sort S5


title: chip 3991 replicate A sort S3


title: Rbp1-like S

value: S


title: SF2 S


title: chip 4001 replicate A sort S0


title: SRp54 S


title: SF2-2

data_processing:
The 51bp fastq formatted sequence reads were first reformatted into fasta format (using: fastq_to_fasta -Q33 -n).  Next, read names assigned by Illumina CASAVA pipeline were replaced with sequence numbers (using: fastx_renamer -n COUNT).  Next, they were filtered to remove those lacking the expected sequencing vector, which was clipped from the unfiltered reads (using: fastx_clipper -n -a "TGAGATCGGAAGAGCGGTTCAGC" -M 2 -l 24 -v).
Each set of perfectly identical sequences (including leading barcodes) was then "collapsed", or replaced with a single (unique) representative sequence, whose sequence name was modified to hold a 'cm' tag (collapsed multiplicity), being the count of collapsed sequences (using: fastx_collapser).
Each fasta-formatted sequence was then tagged with its 4bp experimental barcode (eb), being bases 4-7, and its 5bp molecular barcode (mb), being bases 1-3,8-9 (using: custom perl scripts); these 9 bases in total of barcode sequence are not trimmed from the read. By this point, each trimmed and collapsed sequence has been assigned three tags: cm, eb, mb.  These were each encoded using the TAG:TYPE:VALUE convention for user-defined tags borrowed from the samtools format specification, semi-colon delimited, and appended to the read name (sequence number) in the fasta file.  For convenience, the eb tag was duplicated as the value of the RG tag (read-group), making useful IGV's `color by RG` feature.  A typical resulting fasta defline looks like this: ">99999=cm:i:7095;mb:Z:ATGCC;eb:Z:TTGT;RG:Z:TTGT".
This modified fasta was then aligned in a splice-aware fashion to the fly genome, allowing up to two mismatches.  The splice-awareness was implemented by a two stage process: first reads were aligned to the whole genome with bowtie version 1.0.0; reads that failed to align in this way were aligned to an artificial 'splice-junction' database and the coordinates of successful junction alignments were projected back into genomic coordinates (using: custom perl scripts).  Both stages allowed up to two mismatches, and employed bowtie's `-trim5 9` option to cause the leading 9bp (harboring the combined eb and mb) to be skipped during the alignment.  The results of both stages were combined in a single SAM file, which was stream-edited (using: custom perl scripts) so as to transfer the three tags (cm, eb, mb) from where they are embedded in the read name (having been carried forward in the SAM file's QNAME column), and append them as new TAGs on the SAM file, allowing them to be used in downstream analysis.
These SAM formatted alignments, with three custom tags, were then analyzed to identify "co-alignment sets" (alignments to the same chromosome at the same position).  Within each co-alignment set, sequencing errors in the eb and mb barcode segments were identified and corrected using a greedy approach in which less frequent values are replaced with the most frequent value within a hamming radius of 1.  The error-corrected eb and mb value were assigned to new tags RG (read group) and mg (molecular group), respectively.
The error-corrected co-alignment sets were demultiplexed, assigning reads to samples where  on the RG equals the sample barcode.  Within this, co-alignment sets are further collapsed on the mg, there-by eliminating double-counting of PCR duplicates, and thus providing a read-out of the relative count of co-aligned putatively unique (cDNA) molecules, which are finally aggregated based on commonality of the first position of the alignment, being the putative cross-link site, producing xlSites records, each of which is scored with the count of distinct mg from which it was collapsed, and which form the basis of bigwig files.
Genome_build: Flybase 5.25
Supplementary_files_format_and_content: strand specific bigwig files holding locations of candidate cross-link sites at single-bp resolution.  Values represent their observed frequency.

growth_protocol: cells are grown Schneider media supplemented with 10%FBS

extract_protocol:
Immunoprecipitated RNA was eluted with LDS, and isolated using phenol/chloroform followed by ethanol precipitation
Illumina RNA-Seq libraries were constructed by first, reverse-transcribing isolated RNA to cDNA followed by a two-step PCR amplification to produced amplified libraries with ligated adapters for illumina sequencing
Each template sequence should be comprised of at least two bases segment of adapter sequence followed by a nine bp segment of barcode, with the remaining sequence coming from a putative crosslink site and the sequence leading up to it.  The nine bp barcode consists of a 4bp segment of known, sample specific, experimental barcode (eb) followed by a 5bp segment of random "molecular barcode" (mb).  The eb allows for multiplexing experiments within a single lane on the sequencer. The mb provides for identifying PCR duplicates, as described under data processing.

treatment_protocol: No treatment were applied to the cells

tag: chip antibody

value: anti-FLAG M2 magnetic beads


title: Rsf1 S


title: XL6-B52 D


title: NS S


title: chip 3991 replicate B sort S5

value: Gallus gallus


title: SRp54-1


title: SC35-B52 D


title: chip 3991 replicate A sort S0


title: XL6 S


title: chip 3991 replicate A sort S5


title: SC35 S


title: chip 3991 replicate A sort S1


title: Rbp1 S


title: XL6-2


title: SRp54-2


title: SF2-1


title: B52 S


title: XL6-1


title: Healthy control sample 3

status: Public on Nov 22 2014

city: Oxford

first: Hamid

last: Dolatshad

address: John Radcliffe Hospital

department: RDM-NDCLS

institute: University of Oxford

description: Sample name: HC-c

data_processing:
Sequencing: Samples sequenced on Illumina HiSeq 2000.
Base calling: Basecalls were performed using Illumina bclToFastq=1.8.4.
Alignment: RNA-seq reads aligned to the GRCh37 genome assembly using TopHat version 1.4.0 with default parameters for paired-end directional (fr-firststrand) RNA-seq.
Read Counts: Reads aligning to gene features were counted using htseq-count and exon counts generated with dexseq_count (HTSeq version 0.5.3p9).
Gene-level analysis: Differentially expressed genes were evaluated with edgeR.
Exon-level analysis: Differential exon usage was analysed with DEXseq.
Genome_build: GRCh37 (Genome Reference Consortium Human genome build 37)
Supplementary_files_format_and_content: Ensembl gene-level counts in tab-delimited text files (GRCh37 Ensembl release 73).
Supplementary_files_format_and_content: Ensembl exon-level counts in tab-delimited text files (GRCh37 Ensembl release 75).

source_name: CD34+ cells, healthy control

extract_protocol:
Total RNA was extracted using Trizol reagent, DNase treated (Invitrogen) and purified using XP beads (Beckman Coulter).
Purified DNase-treated total RNA (100ng) was processed using NEBNext Ultra directional mRNA Library prep (NEB) as per manufacturer’s protocol for Illumina with two alterations: custom indexes were designed in-house and an additional purification step was performed using XP beads (Beckman Coulter) rather than size selection.

value: bone marrow CD34+ cells

tag: disease status

value: healthy

tag: mds subtype

tag: sf3b1 status


title: SF3B1 wildtype sample 4

description: Sample name: WT-d

source_name: CD34+ cells, MDS, SF3B1 wildtype

value: myelodysplastic syndromes (MDS)

value: RCMD

value: wildtype


title: SF3B1 wildtype sample 2

description: Sample name: WT-b


title: Healthy control sample 2

description: Sample name: HC-b


title: Healthy control sample 1

description: Sample name: HC-a


title: SF3B1 mutated sample 3

description: Sample name: Mut-c

source_name: CD34+ cells, MDS, SF3B1 mutated

value: RCMD-RS

value: mutated


title: Rbp1Like-2


title: SF3B1 mutated sample 6

description: Sample name: Mut-f


title: Rbp1Like-1


title: Rsf1-1


title: SF3B1 wildtype sample 3

description: Sample name: WT-c


title: SC35-1


title: SF3B1 wildtype sample 1

description: Sample name: WT-a


title: Rsf1-2


title: SF3B1 mutated sample 7

description: Sample name: Mut-g


title: Healthy control sample 4

description: Sample name: HC-d


title: SF3B1 mutated sample 8

description: Sample name: Mut-h

value: RARS


title: Healthy control sample 5

description: Sample name: HC-e


title: SF3B1 mutated sample 5

description: Sample name: Mut-e


title: B52-1


title: SF3B1 mutated sample 4

description: Sample name: Mut-d


title: SF3B1 mutated sample 1

description: Sample name: Mut-a


title: SC35-2


title: Rbp1-2


title: gansu-1

status: Public on Nov 21 2014

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

country: China

institute: Chinese Academy of Sciences

data_processing:
The original image data was transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
The dirty raw reads including reads with adaptors, reads in which unknown bases are more than 10% and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) were removed to get the clean reads.
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level was calculated by using RPKM method (Reads Per kb per Million reads) (Mortazavi et al., 2008). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: De novo assembled reference transcriptome generated from the mixture of all six samples
Supplementary_files_format_and_content: Results include the coverage of each gene, RPKM values, toatal number of reads that aligned to gene, and the description of gene for each sample were shown in the tables.

organism: Vitis vinifera

source_name: berry

growth_protocol: The ten-year-old own-rooted vines from the two commercial vineyards in the Changli region of Hebei province (39°22’ to 39°48’N, 118°45’ to 119°20’E, 212 m above sea level) and the Gaotai region of Gansu province (39°18’N, 99°41’E, 1,377 m above sea level) were managed on a modified Vertical-Shoot-Positioned trellis system (12 to 15 buds per vine and 1 to 2 clusters per shoot), arranged in north-south rows with 2.5 m × 1 m vine spacing and drip irrigated. Both of the vineyards were managed according to standard viticulture practices for the cultivar and region. Pest management was carried out according to local standard practices and canopy management practices were all performed manually with no leaf removal.

extract_protocol:
Approximately 50 berries were randomly selected from a 300-berry biological replicate for RNA extraction. Total RNAs for RNA-seq analysis and real-time polymerase chain reaction (PCR) experiments were extracted from frozen deseeded berries using a General Plant Total RNA Extraction Kit (BioTeke, China), and further incubated with DNase I (Promega, USA) according to the manufacturer’s instructions. RNA integrity and quality were assessed by analysis with the Aglient 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: cultivar

value: Cabernet Sauvignon

tag: origin

value: Gaotai region of Gansu province


title: B52-2


title: Rbp1-1


title: SF3B1 mutated sample 2

description: Sample name: Mut-b


title: gansu-2


title: changli-1

value: Changli region of Hebei province


title: changli-3


title: E15.5 Genital tubercle RNAseq

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 2.1.0 with the parameters --end-to-end --sensitive -k 20
Genome_build: mm9
Supplementary_files_format_and_content: Density file (bigWig)

source_name: Total RNA from E15.5 mouse genital tubercle

extract_protocol:
RNA was extracted from a genital tubercle at E15.5 or from a pair of E12.5 forelimb presumptive digits using QIAGEN RNeasy Plus Micro Kit after disruption and homogenization
After ribodepletion, total RNA was prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) by the Genomics Platform of the University of Geneva

tag: Stage

tag: genotype

value: Genital tubercle

value: WT


title: Digits 4C Hoxa13

description: library strategy: 4C

data_processing:
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
4C figures were made using a running mean algorithm with a window size of eleven fragments.
4C-seq was performed as previously described (Noordermeer et al. 2011)
Genome_build: mm9
Supplementary_files_format_and_content: Signal/restriction fragment or smoothed (bedGraph) for each viewpoint

source_name: 4C E12.5 mouse digits

extract_protocol:
Tissue were made single cell by collagenase treatment. Chromatin was crosslinked in the presence of 2% formaldehyde. Cross-linked chromatin was digested with NlaIII, ligated, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq) as described before (Noordermeer et al. 2011, Science).

treatment_protocol: 4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science).

tag: age

value: Forelimb digits

tag: viewpoint


title: E12.5 Digits RNAseq

source_name: Total RNA from E12.5 mouse digits

tag: strain

value: Digits


title: Digits 4C Hoxd13

description: library strategy: 4C


title: unassigned reads_from_biorep2_lane3

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

institute: The Sainsbury Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality-filtered libraries were aligned to the combined genome of Arabidopsis TAIR10 and Hpa Emoy2 v8.3 [7] or Waco9-SNVs-corrected v8.3 using Bowtie version 0.12.8, and reads with up to 10 reportable alignments were selected. Unaligned reads from previous steps were used to align to transcript sequences of Arabidopsis Col-0 (ftp://ftp.Arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated) using Bowtie version 0.12.8. Linking of each sequenced read (Tag) to gene was carried out using the following considerations: reads aligning to each gene limits were assigned to that gene; reads aligning to genes with overlapping gene limits were split equally between them; and reads aligning to more than 10 genes were discarded. Differential expression analysis was performed using the R statistical language version 2.11.1 with the Bioconductor package, edgeR version 1.6.15 with the exact negative binomial test using tagwise dispersions.
Genome_build: Arabidopsis TAIR10 and Hpa Emoy2 v8.3
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown at 22°C and 60% humidity under a 10-h photoperiod and a 14-h dark period in environmentally controlled growth cabinets.

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
[EXPRSS]Typically 3 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library
Each biological replicate set of samples were sequenced as one batch and each batch was sequenced in 4 individual Illumina flowcell lanes. Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. 'The unassigned read_*' samples are for 'nobarcode_biorep[x]_lanne[x].fq'  file containing sequences unassigned to any barcode from respective bioreplicate sequencing lanes.

treatment_protocol: Three week old arabidopsis plants were spray-inoculated to saturation with a spore suspension of 5 x 10^4 conidiospores/ml. Water sprayed and hpa infected plants were harvested at 1, 3 and 5 days post-inoculation (dpi). Tissue collected from intact plants and conidiospores of Emoy2 and Waco9 were considered as 0 dpi time points for H2O, Emoy2 and Waco9 treatment, respectively.

tag: ecotype

value: Columbia (Col-0)

value: Wild type

value: aerial shoots

value: 3 weeks


title: unassigned reads_from_biorep3_lane3

description: Each biological replicate set of samples were sequenced as one batch and each batch was sequenced in 4 individual Illumina flowcell lanes. Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. 'The unassigned read_*' samples are for 'nobarcode_biorep[x]_lanne[x].fq' file containing sequences unassigned to any barcode from respective bioreplicate sequencing lanes.


title: unassigned reads_from_biorep1_lane4


title: unassigned reads_from_biorep1_lane3


title: unassigned reads_from_biorep3_lane1


title: unassigned reads_from_biorep2_lane1


title: unassigned reads_from_biorep3_lane2


title: unassigned reads_from_biorep2_lane2


title: unassigned reads_from_biorep1_lane2


title: unassigned reads_from_biorep3_lane4


title: Waco9_5ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 192

source_name: aerial shoots_Hpa Waco9_5 dpi

tag: inoculated with

value: Hyaloperonospora arabidopsidis (Hpa) Waco9

tag: time point

value: 5 dpi

tag: barcode sequence

value: CAGAGT

tag: barcode position

value: 5' end of the read


title: unassigned reads_from_biorep1_lane1

tag: tissue


title: Input DNA_NB3

first: Rani

last: George

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
For all samples reads were aligned to their indicated build using bowtie with parameters -t -v 2 -m --strata --best.
ChIP-seq peaks were detected using MACS (version 1.4.2) The default p-value threshold of enrichment of 1 x 10−5 was used for all data sets. we ran MACS three times with the options --keep-dup=none, --keep-dup=1, and --keep-dup=all
For each cell type, the three sets of MACS peaks were merged using BEDTools (Quinlan and Hall, 2010). In all cases we used the additional MACS parameter -m 10,500.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: peak positions

source_name: low-MYCN-Neuroblastoma patient cells

growth_protocol: RPMI 1640 + FBS.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: 100 nM THZ1 or DMSO for 3hrs.

tag: cell type

value: Neuroblastoma patient cells

tag: chip antibody


title: Input DNA_NB2

source_name: high-MYCN-Neuroblastoma patient cells


title: H3K27ac ChIP-seq_NB3

value: H3K27ac (Abcam ab4729)


title: Waco9_5ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 190


title: Waco9_5ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 188


title: H3K27ac ChIP-seq_NB2


title: gansu-3

value: Cabernet Sauvignon


title: changli-2


title: Waco9_5ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 189


title: Waco9_5ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 187


title: Waco9_5ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 186


title: Waco9_5ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 185


title: Input DNA_SHSY5Y_THZ1

source_name: low_MYCN-Neuroblastoma cell line

value: Neuroblastoma cell line

tag: cell line

tag: passages


title: Pol_II ChIP-seq_SHSY5Y_THZ1

value: Pol_II (SantaCruz sc-899)


title: Waco9_5ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 184


title: Waco9_5ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 183


title: Waco9_5ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 191


title: Waco9_5ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 182


title: H3K27ac ChIP-seq_SHSY5Y_DMSO


title: Waco9_3ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 179

source_name: aerial shoots_Hpa Waco9_3 dpi

value: 3 dpi

value: GACACT


title: Waco9_5ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 181


title: Input DNA_kelly_THZ1

source_name: high-MYCN-Neuroblastoma cell line

value: kelly


title: Waco9_3ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 180


title: Input DNA_kelly_2_DMSO


title: Pol_II ChIP-seq_kelly_DMSO


title: Waco9_3ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 178


title: Waco9_3ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 177


title: H3K27ac ChIP-seq_kelly_DMSO


title: Waco9_3ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 173


title: Waco9_3ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 175


title: Input DNA_SHSY5Y_DMSO


title: Waco9_3ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 172


title: Waco9_3ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 171


title: Pol_II ChIP-seq_SHSY5Y_DMSO


title: Waco9_3ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 170


title: Pol_II ChIP-seq_kelly_THZ1


title: Waco9_3ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 169


title: Waco9_1ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 167

source_name: aerial shoots_Hpa Waco9_1 dpi

value: 1 dpi

value: CGAGAT


title: Waco9_1ddpi_biorep3_lane2_lib2

description: tag-seq; Sample 164

value: Columbia (Col-0)

value: Wild type

value: TGTGCGAT


title: Waco9_1ddpi_biorep3_lane3_lib2

description: tag-seq; Sample 166

value: aerial shoots

value: 3 weeks

value: Hyaloperonospora arabidopsidis (Hpa) Waco9


title: unassigned reads_from_biorep2_lane4


title: Waco9_1ddpi_biorep2_lane4_lib2

description: tag-seq; Sample 160

value: 5' end of the read


title: Waco9_1ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 159


title: Waco9_1ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 163


title: Waco9_1ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 161


title: Waco9_1ddpi_biorep3_lane1_lib2

description: tag-seq; Sample 162


title: Waco9_1ddpi_biorep2_lane3_lib2

description: tag-seq; Sample 158


title: Waco9_1ddpi_biorep2_lane2_lib2

description: tag-seq; Sample 156


title: Waco9_1ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 157


title: Waco9_1ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 149


title: Waco9_1ddpi_biorep1_lane2_lib2

description: tag-seq; Sample 148


title: Waco9_1ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 151


title: Waco9_1ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 155


title: Waco9_1ddpi_biorep2_lane1_lib2

description: tag-seq; Sample 154


title: Waco9_1ddpi_biorep1_lane1_lib2

description: tag-seq; Sample 146


title: Waco9_1ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 147


title: Waco9_1ddpi_biorep1_lane3_lib2

description: tag-seq; Sample 150


title: Waco9_1ddpi_biorep3_lane4_lib2

description: tag-seq; Sample 168


title: Waco9_1ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 165


title: Waco9_0ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 144

source_name: aerial shoots_Hpa Waco9_0 dpi

value: 0 dpi

value: TTGGAT


title: Waco9_0ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 143


title: Waco9_1ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 145


title: Waco9_0ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 142


title: Waco9_0ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 141


title: Waco9_1ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 153


title: Waco9_0ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 140


title: Waco9_0ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 137


title: Waco9_0ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 139


title: Waco9_0ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 136


title: Waco9_0ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 135


title: Waco9_0ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 134


title: H2O_5ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 129

source_name: aerial shoots_H2O_5 dpi

value: 5 dpi

value: GCAT


title: Waco9_0ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 133


title: H2O_5ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 131


title: H2O_5ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 127


title: H2O_5ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 122


title: H2O_5ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 124


title: H2O_5ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 126


title: H2O_5ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 121


title: H2O_5ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 130


title: H2O_3ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 120

source_name: aerial shoots_H2O_3 dpi

value: CGGT


title: H2O_3ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 119

value: 3 dpi


title: H2O_5ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 125


title: Waco9_0ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 138


title: H2O_3ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 118


title: H2O_3ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 117


title: H2O_5ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 132


title: H2O_3ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 114


title: H2O_3ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 113


title: H2O_3ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 111


title: H2O_3ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 112


title: H2O_3ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 110


title: H3K4me1 ChIP-seq_SHSY5Y_DMSO

value: Neuroblastoma cell line

value: H3K4me1 (Abcam ab8895)


title: H2O_3ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 109


title: H2O_1ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 107

source_name: aerial shoots_H2O_1 dpi

value: 1 dpi

value: TCGT


title: H2O_1ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 108

value: Columbia (Col-0)


title: A684

city: New York

first: Ismael

last: Santa Maria

address: 630W 168TH STREET

department: Pathology & Cell Biology

institute: Columbia University

data_processing:
Samples are demultiplexed by assigning by 5 nt barcodes and adapters and barcodes are removed from fastq files converted to fasta using perl scripts.
Fasta file is collapsed into a non-redundant fasta file in which the read count is contained within the read header and mapped against an in-house ncRNA reference derived from GenBank and an internally curated set of miRNAs.  BWA v0.5.9 used, with parameters aln -n 2 -t 16 -i 0 -d 0 to align reads to the reference.
Multi-mapping reads are first assigned to hits with the lowest number of errors, then the count is split equally between the number of locations mapped.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated file summarizing reads attributed to an internal reference of ncRNAs.  First column is the read, second is the count, last column a comma-separated list of mapped annotation

source_name: brain

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol
small RNA cDNA library according to Hafner et al, Methods, 2012, and Hafner et al., RNA, 2011

treatment_protocol: Fresh-frozen brain tissue was pulverized in liquid nitrogen, lysed in QIAzol and homogenized using QIAshredder columns.

tag: case id

value: Case 13

tag: classification

value: Control


title: A687

value: Case 10


title: A686

value: Case 9

value: TPD


title: A689

value: Case 11


title: H2O_5ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 128

value: Wild type

value: aerial shoots

value: 3 weeks

value: 5' end of the read


title: H2O_1ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 105


title: H2O_3ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 116

value: CGGT


title: A683

value: Case 15


title: H2O_1ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 104


title: A681

value: Case 2

value: AD


title: A682

value: Case 7


title: H3K4me1 ChIP-seq_kelly_DMSO

value: Neuroblastoma cell line

value: kelly

value: H3K4me1 (Abcam ab8895)


title: A679

value: Case 8


title: A685

value: Case 12

value: Control


title: H2O_1ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 101

value: Columbia (Col-0)

value: 1 dpi

value: TCGT


title: H2O_1ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 103

value: Wild type

value: aerial shoots


title: H2O_1ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 102

value: 3 weeks

value: 5' end of the read


title: A677

value: Case 1


title: A676

value: Case 3


title: Input DNA_kelly_1_DMSO


title: H2O_1ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 106


title: H2O_1ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 100


title: A673

value: Case 6

value: AD


title: A675

value: Case 5


title: H2O_1ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 98


title: H2O_0ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 96

source_name: aerial shoots_H2O_0 dpi

value: 0 dpi

value: AGCT


title: H2O_1ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 97


title: H2O_1ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 99


title: A671

value: Case 14


title: Waco9_3ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 176

value: Hyaloperonospora arabidopsidis (Hpa) Waco9

value: 3 dpi

value: GACACT


title: H2O_0ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 95

value: Columbia (Col-0)


title: A678

value: Case 4


title: H2O_0ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 93

value: Wild type


title: H2O_0ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 92

value: aerial shoots


title: H2O_0ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 90

value: 3 weeks


title: H2O_0ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 91

value: 5' end of the read


title: H2O_0ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 89


title: A672

value: Case 16

value: Control


title: H2O_0ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 86


title: Emoy2_5ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 83

source_name: aerial shoots_Hpa Emoy2_5 dpi

value: Hyaloperonospora arabidopsidis (Hpa) Emoy2

value: 5 dpi

value: ATCCT


title: H3K27ac ChIP-seq_NB1

value: Neuroblastoma patient cells

value: H3K27ac (Abcam ab4729)


title: Emoy2_5ddpi_biorep3_lane2_lib2

description: tag-seq; Sample 80

value: AACAGAGT


title: H2O_0ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 94

value: 0 dpi

value: AGCT


title: Emoy2_5ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 81


title: Emoy2_5ddpi_biorep3_lane1_lib2

description: tag-seq; Sample 78


title: Emoy2_5ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 77


title: Emoy2_5ddpi_biorep3_lane3_lib2

description: tag-seq; Sample 82


title: Emoy2_5ddpi_biorep2_lane4_lib2

description: tag-seq; Sample 76


title: Waco9_3ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 174

value: Hyaloperonospora arabidopsidis (Hpa) Waco9

value: 3 dpi

value: GACACT


title: Emoy2_5ddpi_biorep2_lane3_lib2

description: tag-seq; Sample 74

value: Columbia (Col-0)

value: Wild type


title: Emoy2_5ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 75

value: aerial shoots

value: 3 weeks


title: Emoy2_5ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 73

value: 5' end of the read


title: Emoy2_5ddpi_biorep2_lane2_lib2

description: tag-seq; Sample 72


title: Emoy2_5ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 71


title: Emoy2_5ddpi_biorep2_lane1_lib2

description: tag-seq; Sample 70


title: Emoy2_5ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 69


title: H2O_0ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 87


title: Emoy2_5ddpi_biorep3_lane4_lib2

description: tag-seq; Sample 84


title: Emoy2_5ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 67


title: Emoy2_5ddpi_biorep1_lane3_lib2

description: tag-seq; Sample 66


title: H2O_0ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 85


title: Emoy2_5ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 79


title: Emoy2_5ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 65


title: Emoy2_5ddpi_biorep1_lane2_lib2

description: tag-seq; Sample 64


title: Emoy2_5ddpi_biorep1_lane1_lib2

description: tag-seq; Sample 62


title: Emoy2_5ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 63


title: Emoy2_3ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 57

source_name: aerial shoots_Hpa Emoy2_3 dpi

value: ACTGT


title: Emoy2_3ddpi_biorep3_lane3_lib2

description: tag-seq; Sample 58

value: Hyaloperonospora arabidopsidis (Hpa) Emoy2

value: TTGCGCT


title: Emoy2_3ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 59


title: Emoy2_3ddpi_biorep3_lane2_lib2

description: tag-seq; Sample 56


title: Emoy2_3ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 55


title: Emoy2_3ddpi_biorep3_lane1_lib2

description: tag-seq; Sample 54


title: Emoy2_3ddpi_biorep3_lane4_lib2

description: tag-seq; Sample 60


title: Emoy2_3ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 53


title: Emoy2_3ddpi_biorep2_lane3_lib2

description: tag-seq; Sample 50


title: Emoy2_3ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 51


title: Emoy2_3ddpi_biorep2_lane2_lib2

description: tag-seq; Sample 48


title: Emoy2_3ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 49


title: Emoy2_5ddpi_biorep1_lane4_lib2

description: tag-seq; Sample 68

value: 5 dpi


title: Emoy2_3ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 47


title: Emoy2_3ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 45


title: Emoy2_3ddpi_biorep2_lane1_lib2

description: tag-seq; Sample 46


title: Emoy2_3ddpi_biorep1_lane4_lib2

description: tag-seq; Sample 44


title: Emoy2_3ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 43


title: Emoy2_3ddpi_biorep1_lane3_lib2

description: tag-seq; Sample 42


title: Emoy2_3ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 41


title: Emoy2_3ddpi_biorep1_lane2_lib2

description: tag-seq; Sample 40


title: Emoy2_3ddpi_biorep1_lane2_lib1

description: tag-seq; Sample 39


title: Emoy2_3ddpi_biorep2_lane4_lib2

description: tag-seq; Sample 52


title: Emoy2_3ddpi_biorep1_lane1_lib2

description: tag-seq; Sample 38


title: Emoy2_3ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 37


title: Emoy2_1ddpi_biorep3_lane2_lib2

description: tag-seq; Sample 32

source_name: aerial shoots_Hpa Emoy2_1 dpi

value: 1 dpi

value: CATACGT


title: Emoy2_1ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 31

value: GTACT


title: Emoy2_1ddpi_biorep3_lane4_lib2

description: tag-seq; Sample 36


title: Emoy2_1ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 29


title: Emoy2_1ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 35


title: Emoy2_1ddpi_biorep3_lane1_lib2

description: tag-seq; Sample 30


title: Emoy2_1ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 33


title: Emoy2_1ddpi_biorep3_lane3_lib2

description: tag-seq; Sample 34


title: Emoy2_1ddpi_biorep2_lane2_lib2

description: tag-seq; Sample 24


title: Emoy2_1ddpi_biorep2_lane4_lib1

description: tag-seq; Sample 27


title: Emoy2_1ddpi_biorep2_lane2_lib1

description: tag-seq; Sample 23


title: Emoy2_1ddpi_biorep2_lane4_lib2

description: tag-seq; Sample 28


title: Emoy2_1ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 25


title: H2O_0ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 88

value: 0 dpi


title: Emoy2_1ddpi_biorep2_lane3_lib2

description: tag-seq; Sample 26


title: Emoy2_1ddpi_biorep2_lane1_lib1

description: tag-seq; Sample 21


title: Emoy2_1ddpi_biorep1_lane3_lib2

description: tag-seq; Sample 18


title: Emoy2_1ddpi_biorep1_lane4_lib1

description: tag-seq; Sample 19


title: Emoy2_1ddpi_biorep2_lane1_lib2

description: tag-seq; Sample 22


title: Emoy2_1ddpi_biorep1_lane4_lib2

description: tag-seq; Sample 20


title: Emoy2_1ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 17


title: Emoy2_1ddpi_biorep1_lane2_lib2

description: tag-seq; Sample 16


title: Emoy2_1ddpi_biorep1_lane1_lib2

description: tag-seq; Sample 14


title: Input DNA 10-12h

city: Berkeley

first: Wei

last: Zhang

address: University of California at Berkeley

institute: UC Berkeley

data_processing:
Standard FASTQ files were outputed by CASAVA_v1.8.0
All sequencing reads were aligned to the Drosophila melanogaster reference genome (UCSC dm3 release) using Bowtie version 0.12.7 with parameters -k 1 -m 1 -n 2 --best --strata.
We used the model-based analysis of ChIP-Seq (MACS) peak-finding algorithm version 1.4.1 with default parameters to identify the regions of ELAV ChIP-Seq enrichment over input DNA.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using HOMER software; Scores represent reads per 10 million total reads.

source_name: whole embryos

growth_protocol: Drosophila melanogaster yw flies were reared in standard cornmeal food at 25C, embryos were collected on apple juice plates.

extract_protocol:
Whole embryo nuclei extracts were sonicated and ChIP assays were done using a mix of two anti-ELAV antibodies raised against the entire ELAV protein: mouse anti-ELAV-9F8A9 (DSHB) and rat anti-ELAV-7E8A10 (DSHB).
ChIP-seq libraries were constructed with the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina using NEBNext Multiplex Oligos.

tag: hours after fertilization


title: Emoy2_1ddpi_biorep1_lane1_lib1

description: tag-seq; Sample 13

tag: genotype


title: Input DNA 6-8h


title: Emoy2_0ddpi_biorep3_lane4_lib1

description: tag-seq; Sample 12

source_name: aerial shoots_Hpa Emoy2_0 dpi

tag: age

value: GCTCT


title: ELAV 10-12h rep1

value: ELAV

tag: chip antibody vendor

value: Developmental Studies Hybridoma Bank (DSHB)

tag: chip catalog number

value: mouse anti-ELAV-9F8A9

value: rat anti-ELAV-7E8A10


title: ELAV 6-8h rep2


title: ELAV 10-12h rep2


title: Emoy2_0ddpi_biorep3_lane1_lib1

description: tag-seq; Sample 9

tag: ecotype

value: Columbia (Col-0)

value: Wild type


title: Emoy2_0ddpi_biorep3_lane2_lib1

description: tag-seq; Sample 10

value: aerial shoots

value: 3 weeks

tag: inoculated with


title: H2O_5ddpi_biorep1_lane3_lib1

description: tag-seq; Sample 123

tag: time point

value: GCAT

value: 5' end of the read


title: Emoy2_0ddpi_biorep3_lane3_lib1

description: tag-seq; Sample 11

value: Hyaloperonospora arabidopsidis (Hpa) Emoy2

tag: barcode sequence


title: H2O_3ddpi_biorep2_lane3_lib1

description: tag-seq; Sample 115

value: 3 dpi

value: CGGT

tag: barcode position