title: Adult 7-dpi [RNA-seq]

description: Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later

value: 2-4 months


title: KBM7 cell line, clone 14, haploid, sample 124

status: Public on Sep 24 2015

type: SRA

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads are first parsed (using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}) to extract the different parts, i.e. the first 4 random bases (included to make cluster calling on the Illumina Hi-seq 2000 possible), 15bp of adapter sequence, and a stretch of gDNA starting with the GATC site. The gDNA sequences are aligned to the reference genome (hg19, chromosomes 1-22, X, Y, and M) using bowtie2 version 2.1.0, using the --very-sensitive mode and otherwise default parameters. Reads that did not align or aligned more than once were discarded. The remaining reads are assigned to GATC-fragments using a custom R-script. Only reads that precisely flanked a GATC site were associated with GATC-fragments, all other reads were discarded. Because single haploid cells have only one copy of any GATC fragment., multiple reads aligning to the same position must have originated from the same molecule and are therefore counted as one. These reads were then aggregated in genomic segments of 100kb.
Next, the number of mappable unique reads per 100kb segment was divided by the maximum possible number of unique reads, which is determined by the total number of GATC motifs in the segment with uniquely mappable flanking sequences.  To determine these numbers we performed an in silico DnpI digest of the complete genomic reference sequence (chromosomes 1-22, X, Y, and M), defined the complete set of potential DamID-seq reads of 32bp length, and aligned these reads back to the reference genome using the same method and filter criteria as we used for the experimental reads (see above). We then summed the number of unique GATC-flanking reads for each 100kb segment.  Finally, the observed over expected read counts per 100 kb segment (OE) was calculated by taking the ratio of the two counts, and normalizing this ratio for the total number of observed (i.e. unique) reads.
Genome_build: hg19
Supplementary_files_format_and_content: OE values in 100kb windows

molecule: genomic DNA

organism: Homo sapiens

source_name: KBM7 cell line, clone 14, haploid

growth_protocol: KBM7 cells were cultured in IMDM 1X (Gibco), respectively, supplemented with 10% Fetal Bovine Serum (Thermo Scientific HyClone) and 1% penicillin and 1% streptomycin.

extract_protocol:
Based on the FCS and SSC profiles the 2% smallest cells that were double positive for the Fucci markers were single cell sorted in a PCR plate containing lysis buffer and proteinase K (Costar Thermowell). Each well contained 1μl of pick buffer (50mM Tris-HCl pH 8.3, 75mM KCl, 3mM MgCl2, 137mM NaCl) and 2μl of lysis buffer with proteinase K (10mM Tris acetate pH 7.5 (Sigma T1258), 10mM magnesium acetate (Sigma 63052), 50mM potassium acetate (Sigma 95843), 0.67% Tween-20 (Sigma P2287), 0.67% Igepal (Sigma I8896), 0.67mg/ml proteinase K (Roche 03115828001). Proteinase K digestion was performed at 42 °C for 4 hours in a thermoblock with heated lid, followed by heat inactivation for 10 minutes at 80 °C. In the following steps, reagents were added with an Eppendorf Mulipipette plus mounted with a 0.1 ml Combitip. Genomic DNA (gDNA) was digested for 4 hours by the addition of DpnI (1 unit) in 7μl 1* One-Phor-all-buffer plus (10mM Tris acetate, pH7.5, 10mM magnesium acetate, 50mM potassium acetate) at 37 °C, followed by heat inactivation at 80 °C for 20 minutes. Adaptor ligation was performed by the addition of 10μl ligation mix (2* Roche T4 ligation buffer, 0.5 units T4 ligase, 50μM double-stranded DamID adapter {Vogel, 2007, 17545983}) and incubated at 16 °C over night. Heat inactivation at 65 °C for 10 minutes the next day was followed by PCR amplification by the addition of 30 μl PCR mix (5 μl 10* Clontech Advantage cDNA reaction buffer, 4 μl dNTPs (2.5mM each), 1.25 μl primer (50 μM), 1 μl PCR advantage enzyme mix (50*) and 18.75 μl H2O).  The PCR reaction was performed as described {Vogel, 2007, 17545983} with 21 extension steps The PCR primer consists of an additional 4 random nucleotides at the 5' end to meet the Illumina software requirements of generating reads with diverse starting sequences. Of the PCR material 8μL was submitted to standard 1% agarose gel electrophoresis for analytical purpose and the successfully amplified material was purified by column purification (Qiagen PCR purification kit). Next the samples were prepared for Illumina sequencing.
Of 1μg purified PCR product the 3’ or 5’ overhanging ends were blunted in a 50μl reaction following the manufacturers intructions (End-It DNA End-Repair Kit, Epicentre). Next, a 3’ adenine was added by incubation of the DNA at 37°C in a 50 μL reaction mix (1* New Engeland Biolabs restriction buffer 2, 200μM dATP, nuclease-free water) containing klenow 3′ → 5′ exo– (New Engeland Biolabs, 100 units final concentration). After incubating the samples for 45 minutes, the DNA was purified with 1.6X Agencourt AMPure XP beads (Beckman Coulter). To 250 μg of purified DNA Illumina Y-shaped adapters were ligated for two hours at room temperature in a 10μl reaction mix (1* Roche ligation buffer, 0.25 units T4 DNA (Roche 5units/μl, 50μM Y-adapter, nuclease-free water). Next, the T4 ligase reaction was heat inactivated at 65 °C for 10 minutes followed by DNA purification as described for the previous step. For the addition of the Illumina index primers a PCR reaction was performed with 100 ng DNA from the previous step in a 20 μl MyTaq red DNA polymerase (Bioline BIO21110) PCR reaction mixture (10μl 1* MyTaq reaction mixture, 0.25 μM Illumina P5 primer, 0.25 μM Illumina indexing primer (Table S2), nuclease-free H2O). The DNA was amplified for 8 PCR amplification cycles (94 °C 1 minute, 94 °C 30 seconds, 58 °C 30 seconds and 72 °C for 30 seconds) after which 5 μl of each sample was analysed by agarose gel electrophoresis. For Illumina multiplex sequencing typically between 40 and 50 samples were mixed in equimolar ratios based on the agarose gel image.

treatment_protocol: Fifteen hours prior harvesting single cells Dam methylation was induced by treating the cells with 0.5 nM Shield1 (ClonTech) then collected in low serum medium (1%) and sorted on a BD FACSAria I (Becton Dickinson) based on cell size and expression of both Fucci markers {Sakaue-Sawano, 2008, 18267078}.

tag: cell line

tag: ploidy

tag: dam fusion


title: KBM7 cell line, clone 14, haploid, sample 104


title: Neonatal 7-dpi

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

country: USA

institute: Cornell University

description: Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later

library_source: transcriptomic

data_processing:
Reads that had a polyA stretch and 3' adapter were selected
Low quality nucleotides (phred <20) were trimmed from the 3' and 5' ends, and the polyA tail and 3' adapter sequence were trimmed form the 3' end
rRNA was removed using Bowtie2
Remaining reads were uniquely aligned to the genome using Tophat
3' ends of the reads were found using the Genomecov tool from Bedtools, and reads that mapped near a polyadenylation seuqence in a 3'UTR were kept
Genome_build: mm9
Supplementary_files_format_and_content: Text file contains the number of normalized reads that map to different polyadenylation sequences for each sample

molecule: total RNA

organism: Mus musculus

source_name: CD8+ T cells

extract_protocol:
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
PolyA RNA was selected with a biotinylated polyT primer that contained a single RNA base  and magnetic beads. After first strand synthesis, the cDNA was nicked then nick translated. After cleaning up the ends, sequencing adapters were ligated on, the libraries were amplified, and purified from PAGE gels.

treatment_protocol: For the effector CD8+ T cells, they were isolated from adult and neonatal mice, then transferred into a recipient adult mouse which was infected with Listeria. Seven days later, the cells were sorted.

tag: cell state

value: Peak effector (7dpi)

tag: age

value: 6-7 days

tag: cell type

value: CD8+ T cells


title: Adult naïve [RNA-seq]

data_processing:
We trimmed off nucleotides from the ends if they had Phred quality scores <20
Reads that were at least 20 nt long after trimming were aligned to the genome using Tophat
Differential expression of genes between samples was determined using CuffDiff
Genome_build: mm9
Supplementary_files_format_and_content: Text file with the FPKM value and differential expression information for all coding genes that have an FPKM >1 in at least one sample

extract_protocol:
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
25-100 ng of total RNA were used to generate libraries using the RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: For the effector CD8+ T cells, they were isolated from adult and neonatal mice, then transferred into a recipient adult mouse which was infected with Listeria. Five, seven, and fifteen days later, the cells were sorted.

value: Naïve


title: Adult 15-dpi [RNA-seq]

description: Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 15 days later

value: Late effector (15dpi)


title: Adult 7-dpi


title: KBM7 cell line, clone 14, haploid, sample 102


title: Neonatal naïve


title: Adult naïve


title: KBM7 cell line, clone 14, haploid, sample 101


title: KBM7 cell line, clone 14, haploid, sample 100


title: KBM7 cell line, clone 14, haploid, sample 107


title: Neonatal 7-dpi [small RNA_Illumina]

description:
Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later
processed data: Mirdeep_output_Illumina_updated.txt

data_processing:
miRNAs were aligned using Mirdeep2's mapper.pl script to Mirbase's version 21 database of miRNAs using options -d -e -h -i -j -l 18 -m
Known miRNAs were quantified using Mirdeep2's quantifier.pl script using the option -d
Genome_build: mm9
Supplementary_files_format_and_content: Text file contains read counts for each miRNA for each sample

extract_protocol:
Cells were sorted into Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
450 ng of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kit. 30-100 ng of total RNA were used with the NEBNext Small RNA Library kit. Libraries were sequenced on a Hi-Seq 2000, generating 50 bp reads.

treatment_protocol: For the effector CD8+ T cells, they were isolated from adult and neonatal mice, then transferred into a recipient adult mouse which was infected with Listeria. Five and seven days later, the cells were sorted.

tag: animal age


title: KBM7 cell line, clone 14, haploid, sample 098


title: Adult 5-dpi [RNA-seq]

description: Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later

value: Early effector (5dpi)


title: Adult 7-dpi [small RNA_Illumina]

description:
Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later
processed data: Mirdeep_output_Illumina_updated.txt


title: KBM7 cell line, clone 14, haploid, sample 099


title: KBM7 cell line, clone 14, haploid, sample 097


title: Neonatal 5-dpi [small RNA_NEB]

description:
Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later
processed data: Mirdeep_output_NEB.txt


title: Neonatal 5-dpi [small RNA_Illumina]

description:
Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later
processed data: Mirdeep_output_Illumina_updated.txt


title: KBM7 cell line, clone 14, haploid, sample 094


title: KBM7 cell line, clone 14, haploid, sample 096


title: Adult 5-dpi [small RNA_Illumina]

description:
Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later
processed data: Mirdeep_output_Illumina_updated.txt


title: KBM7 cell line, clone 14, haploid, sample 093


title: KBM7 cell line, clone 14, haploid, sample 092


title: KBM7 cell line, clone 14, haploid, sample 091


title: KBM7 cell line, clone 14, haploid, sample 090


title: KBM7 cell line, clone 14, haploid, sample 089


title: KBM7 cell line, clone 14, haploid, sample 095


title: Neonatal 7-dpi [small RNA_NEB]

description:
Naïve CD8+ T cells from a neonatal donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later
processed data: Mirdeep_output_NEB.txt


title: Adult naïve [small RNA_NEB]

description: processed data: Mirdeep_output_NEB.txt


title: KBM7 cell line, clone 14, haploid, sample 088


title: Adult naïve [small RNA_Illumina]

description: processed data: Mirdeep_output_Illumina_updated.txt


title: Adult 7-dpi [small RNA_NEB]

description:
Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 7 days later
processed data: Mirdeep_output_NEB.txt


title: Neonatal naïve [small RNA_NEB]

description: processed data: Mirdeep_output_NEB.txt


title: KBM7 cell line, clone 14, haploid, sample 084


title: KBM7 cell line, clone 14, haploid, sample 085


title: KBM7 cell line, clone 14, haploid, sample 086


title: KBM7 cell line, clone 14, haploid, sample 083


title: Adult 5-dpi [small RNA_NEB]

description:
Naïve CD8+ T cells from an adult donor were transferred into an adult recipient which was infected with Listeria, and the donor cells were isolated 5 days later
processed data: Mirdeep_output_NEB.txt


title: KBM7 cell line, clone 14, haploid, sample 079


title: KBM7 cell line, clone 14, haploid, sample 078


title: KBM7 cell line, clone 14, haploid, sample 081


title: KBM7 cell line, clone 14, haploid, sample 077


title: KBM7 cell line, clone 14, haploid, sample 076


title: KBM7 cell line, clone 14, haploid, sample 072


title: KBM7 cell line, clone 14, haploid, sample 073


title: KBM7 cell line, clone 14, haploid, sample 074


title: KBM7 cell line, clone 14, haploid, sample 071


title: Neonatal naïve [small RNA_Illumina]


title: KBM7 cell line, clone 14, haploid, sample 110


title: KBM7 cell line, clone 14, haploid, sample 087


title: KBM7 cell line, clone 14, haploid, sample 067


title: KBM7 cell line, clone 14, haploid, sample 066


title: KBM7 cell line, clone 14, haploid, sample 068


title: KBM7 cell line, clone 14, haploid, sample 065


title: KBM7 cell line, clone 14, haploid, sample 064


title: KBM7 cell line, clone 14, haploid, sample 062


title: KBM7 cell line, clone 14, haploid, sample 061


title: KBM7 cell line, clone 14, haploid, sample 063


title: KBM7 cell line, clone 14, haploid, sample 059


title: KBM7 cell line, clone 14, haploid, sample 103


title: KBM7 cell line, clone 14, haploid, sample 058


title: KBM7 cell line, clone 14, haploid, sample 075


title: KBM7 cell line, clone 14, haploid, sample 060


title: KBM7 cell line, clone 14, haploid, sample 057


title: KBM7 cell line, clone 14, haploid, sample 080


title: KBM7 cell line, clone 14, haploid, sample 069


title: KBM7 cell line, clone 14, haploid, sample 053


title: KBM7 cell line, clone 14, haploid, sample 056


title: KBM7 cell line, clone 14, haploid, sample 051


title: KBM7 cell line, clone 14, haploid, sample 054


title: KBM7 cell line, clone 14, haploid, sample 070


title: KBM7 cell line, clone 14, haploid, sample 052


title: KBM7 cell line, clone 14, haploid, sample 049


title: KBM7 cell line, clone 14, haploid, sample 045


title: KBM7 cell line, clone 14, haploid, sample 046


title: KBM7 cell line, clone 14, haploid, sample 047


title: KBM7 cell line, clone 14, haploid, sample 044


title: KBM7 cell line, clone 14, haploid, sample 048


title: KBM7 cell line, clone 14, haploid, sample 042


title: KBM7 cell line, clone 14, haploid, sample 043


title: KBM7 cell line, clone 14, haploid, sample 041


title: KBM7 cell line, clone 14, haploid, sample 040


title: KBM7 cell line, clone 14, haploid, sample 039


title: KBM7 cell line, clone 14, haploid, sample 055


title: KBM7 cell line, clone 14, haploid, sample 038


title: KBM7 cell line, clone 14, haploid, sample 037


title: KBM7 cell line, clone 14, haploid, sample 035


title: KBM7 cell line, clone 14, haploid, sample 036


title: KBM7 cell line, clone 14, haploid, sample 082


title: KBM7 cell line, clone 14, haploid, sample 034


title: KBM7 cell line, clone 14, haploid, sample 033


title: KBM7 cell line, clone 14, haploid, sample 050


title: KBM7 cell line, clone 14, haploid, sample 032


title: KBM7 cell line, clone 14, haploid, sample 031


title: KBM7 cell line, clone 14, haploid, sample 027


title: KBM7 cell line, clone 14, haploid, sample 029


title: KBM7 cell line, clone 14, haploid, sample 030


title: KBM7 cell line, clone 14, haploid, sample 025


title: KBM7 cell line, clone 14, haploid, sample 028


title: KBM7 cell line, clone 14, haploid, sample 024


title: KBM7 cell line, clone 14, haploid, sample 026


title: KBM7 cell line, clone 14, haploid, sample 022


title: KBM7 cell line, clone 14, haploid, sample 023


title: KBM7 cell line, clone 14, haploid, sample 020


title: KBM7 cell line, clone 14, haploid, sample 019


title: KBM7 cell line, clone 14, haploid, sample 021


title: KBM7 cell line, clone 14, haploid, sample 018


title: KBM7 cell line, clone 14, haploid, sample 016


title: KBM7 cell line, clone 14, haploid, sample 014


title: KBM7 cell line, clone 14, haploid, sample 017


title: KBM7 cell line, clone 14, haploid, sample 013


title: KBM7 cell line, clone 14, haploid, sample 012


title: KBM7 cell line, clone 14, haploid, sample 015


title: KBM7 cell line, clone 14, haploid, sample 007


title: KBM7 cell line, clone 14, haploid, sample 009


title: KBM7 cell line, clone 14, haploid, sample 011


title: KBM7 cell line, clone 14, haploid, sample 010


title: KBM7 cell line, clone 14, haploid, sample 004


title: KBM7 cell line, clone 14, haploid, sample 006


title: KBM7 cell line, clone 14, haploid, sample 005


title: KBM7 cell line, clone 14, haploid, sample 003


title: KBM7 cell line, clone 14, haploid, sample 002


title: KBM7 cell line, clone 5-8, haploid, sample 024

source_name: KBM7 cell line, clone 5-8, haploid

extract_protocol:
Based on the FCS and SSC profiles the 2% smallest cells that were double positive for the Fucci markers were single cell sorted in a PCR plate containing lysis buffer and proteinase K (Costar Thermowell). Each well contained 1μl of pick buffer (50mM Tris-HCl pH 8.3, 75mM KCl, 3mM MgCl2, 137mM NaCl) and 2μl of lysis buffer with proteinase K (10mM Tris acetate pH 7.5 (Sigma T1258), 10mM magnesium acetate (Sigma 63052), 50mM potassium acetate (Sigma 95843), 0.67% Tween-20 (Sigma P2287), 0.67% Igepal (Sigma I8896), 0.67mg/ml proteinase K (Roche 03115828001). Proteinase K digestion was performed at 42 °C for 4 hours in a thermoblock with heated lid, followed by heat inactivation for 10 minutes at 80 °C. In the following steps, reagents were added with an Eppendorf Mulipipette plus mounted with a 0.1 ml Combitip. Genomic DNA (gDNA) was digested for 4 hours by the addition of DpnI (1 unit) in 7μl 1* One-Phor-all-buffer plus (10mM Tris acetate, pH7.5, 10mM magnesium acetate, 50mM potassium acetate) at 37 °C, followed by heat inactivation at 80 °C for 20 minutes. Adaptor ligation was performed by the addition of 10μl ligation mix (2* Roche T4 ligation buffer, 0.5 units T4 ligase, 50μM double-stranded DamID adapter {Vogel, 2007, 17545983}) and incubated at 16 °C over night. Heat inactivation at 65 °C for 10 minutes the next day was followed by PCR amplification by the addition of 30 μl PCR mix (5 μl 10* Clontech Advantage cDNA reaction buffer, 4 μl dNTPs (2.5mM each), 1.25 μl primer (50 μM), 1 μl PCR advantage enzyme mix (50*) and 18.75 μl H2O).  The PCR reaction was performed with 21 extension steps as described in Vogel et al., 2008, Nature Protocols. The PCR primer consists of an additional 4 random nucleotides at the 5' end to meet the Illumina software requirements of generating reads with diverse starting sequences. Of the PCR material 8μL was submitted to standard 1% agarose gel electrophoresis for analytical purpose and the successfully amplified material was purified by column purification (Qiagen PCR purification kit). Next the samples were prepared for Illumina sequencing.
Of 1μg purified PCR product the 3’ or 5’ overhanging ends were blunted in a 50μl reaction following the manufacturers intructions (End-It DNA End-Repair Kit, Epicentre). Next, a 3’ adenine was added by incubation of the DNA at 37°C in a 50 μL reaction mix (1* New Engeland Biolabs restriction buffer 2, 200μM dATP, nuclease-free water) containing klenow 3′ → 5′ exo– (New Engeland Biolabs, 100 units final concentration). After incubating the samples for 45 minutes, the DNA was purified with 1.6X Agencourt AMPure XP beads (Beckman Coulter). To 250 μg of purified DNA Illumina Y-shaped adapters were ligated for two hours at room temperature in a 10μl reaction mix (1* Roche ligation buffer, 0.25 units T4 DNA (Roche 5units/μl, 50μM Y-adapter, nuclease-free water). Next, the T4 ligase reaction was heat inactivated at 65 °C for 10 minutes followed by DNA purification as described for the previous step. For the addition of the Illumina index primers a PCR reaction was performed with 100 ng DNA from the previous step in a 20 μl MyTaq red DNA polymerase (Bioline BIO21110) PCR reaction mixture (10μl 1* MyTaq reaction mixture, 0.25 μM Illumina P5 primer, 0.25 μM Illumina indexing primer, nuclease-free H2O). The DNA was amplified for 8 PCR amplification cycles (94 °C 1 minute, 94 °C 30 seconds, 58 °C 30 seconds and 72 °C for 30 seconds) after which 5 μl of each sample was analysed by agarose gel electrophoresis. For Illumina multiplex sequencing typically between 40 and 50 samples were mixed in equimolar ratios based on the agarose gel image.

treatment_protocol: Fifteen hours prior harvesting single cells Dam methylation was induced by treating the cells with 0.5 nM Shield1 (ClonTech) then collected in low serum medium (1%) and sorted on a BD FACSAria I (Becton Dickinson) based on cell size and expression of both Fucci markers.

value: DamOnly


title: KBM7 cell line, clone 5-8, haploid, sample 023


title: KBM7 cell line, clone 5-8, haploid, sample 021


title: KBM7 cell line, clone 5-8, haploid, sample 022


title: KBM7 cell line, clone 5-8, haploid, sample 019


title: KBM7 cell line, clone 5-8, haploid, sample 025


title: KBM7 cell line, clone 5-8, haploid, sample 016


title: KBM7 cell line, clone 5-8, haploid, sample 018


title: KBM7 cell line, clone 5-8, haploid, sample 012


title: KBM7 cell line, clone 5-8, haploid, sample 015


title: KBM7 cell line, clone 5-8, haploid, sample 009


title: KBM7 cell line, clone 14, haploid, sample 008


title: KBM7 cell line, clone 5-8, haploid, sample 013


title: KBM7 cell line, clone 5-8, haploid, sample 017


title: KBM7 cell line, clone 5-8, haploid, sample 007


title: KBM7 cell line, clone 5-8, haploid, sample 008


title: KBM7 cell line, clone 5-8, haploid, sample 005


title: KBM7 cell line, clone 14, haploid, sample 001


title: KBM7 cell line, clone 5-8, haploid, sample 010


title: KBM7 cell line, clone 5-8, haploid, sample 014


title: KBM7 cell line, clone 5-8, haploid, sample 011


title: KBM7 cell line, clone 5-8, haploid, sample 020


title: KBM7 cell line, clone 5-8, haploid, sample 006


title: KBM7 cell line, clone 5-8, haploid, sample 004


title: KBM7 cell line, clone 5-8, haploid, sample 026


title: KBM7 cell line, clone 5-8, haploid, sample 002


title: KBM7 cell line, clone 5-8, haploid, sample 001


title: KBM7 cell line, clone 5-8, haploid, sample 003


title: KBM7 cell line, clone 5-5, diploid, sample 035

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
The 51bp reads are first parsed (using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}) to extract the different parts, i.e. the first 4 random bases (included to make cluster calling on the Illumina Hi-seq 2000 possible), 15bp of adapter sequence, and a stretch of gDNA starting with the GATC site. The gDNA sequences are aligned to the reference genome (hg19, chromosomes 1-22, X, Y, and M) using bowtie2 version 2.1.0, using the --very-sensitive mode and otherwise default parameters. Reads that did not align or aligned more than once were discarded. The remaining reads are assigned to GATC-fragments using a custom R-script. Only reads that precisely flanked a GATC site were associated with GATC-fragments, all other reads were discarded. Even though diploid cells have two copies of any GATC fragment, we are under-sequencing to such an extend that we assume that at most one of the two methylated GATC fragment is actually sequenced. However, if both chromosomes are methylated we will detect approximately twice as many GATC fragments in a methylated region as compared to when only a single chromosome in the region is methylated. Thus, also for diploid cells  the multiple reads aligning to the same position are counted as one. These reads were then aggregated in genomic segments of 100kb.
Next, the number of mappable unique reads per 100kb segment was divided by the maximum possible number of unique reads, which is determined by the total number of GATC motifs in the segment with uniquely mappable flanking sequences.  To determine these numbers we performed an in silico DnpI digest of the complete genomic reference sequence (chromosomes 1-22, X, Y, and M), defined the complete set of potential DamID-seq reads of 32bp length, and aligned these reads back to the reference genome using the same method and filter criteria as we used for the experimental reads (see above). We then summed the number of unique GATC-flanking reads for each 100kb segment.  Finally, the observed over expected read counts per 100 kb segment (OE) was calculated by taking the ratio of the two counts, and normalizing this ratio for the total number of observed (i.e. unique) reads.
Genome_build: hg19
Supplementary_files_format_and_content: OE values in 100kb windows

source_name: KBM7 cell line, clone 5-5, diploid


title: KBM7 cell line, clone 5-5, diploid, sample 031


title: KBM7 cell line, clone 5-5, diploid, sample 030


title: KBM7 cell line, clone 5-5, diploid, sample 028


title: KBM7 cell line, clone 5-5, diploid, sample 029


title: KBM7 cell line, clone 5-5, diploid, sample 034


title: KBM7 cell line, clone 5-5, diploid, sample 027


title: KBM7 cell line, clone 5-5, diploid, sample 026


title: KBM7 cell line, clone 5-5, diploid, sample 024


title: KBM7 cell line, clone 5-5, diploid, sample 025


title: KBM7 cell line, clone 5-5, diploid, sample 022


title: KBM7 cell line, clone 5-5, diploid, sample 021


title: KBM7 cell line, clone 5-5, diploid, sample 023


title: KBM7 cell line, clone 5-5, diploid, sample 020


title: KBM7 cell line, clone 5-5, diploid, sample 019


title: KBM7 cell line, clone 5-5, diploid, sample 018


title: KBM7 cell line, clone 5-5, diploid, sample 014


title: KBM7 cell line, clone 5-5, diploid, sample 015


title: KBM7 cell line, clone 5-5, diploid, sample 011


title: KBM7 cell line, clone 5-5, diploid, sample 013


title: KBM7 cell line, clone 5-5, diploid, sample 012


title: KBM7 cell line, clone 5-5, diploid, sample 016


title: KBM7 cell line, clone 5-5, diploid, sample 010


title: KBM7 cell line, clone 5-5, diploid, sample 017


title: KBM7 cell line, clone 5-5, diploid, sample 032


title: KBM7 cell line, clone 5-5, diploid, sample 008


title: KBM7 cell line, clone 5-5, diploid, sample 007


title: KBM7 cell line, clone 5-5, diploid, sample 033


title: KBM7 cell line, clone 5-5, diploid, sample 005


title: KBM7 cell line, clone 5-5, diploid, sample 001


title: KBM7 cell line, clone 5-5, diploid, sample 003


title: KBM7 cell line, clone 5-5, diploid, sample 006


title: KBM7 cell line, clone 5-5, diploid, sample 009


title: KBM7 cell line, clone 5-5, diploid, sample 002


title: KBM7 cell line, clone 5-5, haploid, sample 172

source_name: KBM7 cell line, clone 5-5, haploid


title: KBM7 cell line, clone 5-5, haploid, sample 171


title: KBM7 cell line, clone 5-5, haploid, sample 170


title: KBM7 cell line, clone 5-5, diploid, sample 004


title: KBM7 cell line, clone 5-5, haploid, sample 165


title: KBM7 cell line, clone 5-5, haploid, sample 169


title: KBM7 cell line, clone 5-5, haploid, sample 167


title: KBM7 cell line, clone 5-5, haploid, sample 159


title: KBM7 cell line, clone 5-5, haploid, sample 163


title: KBM7 cell line, clone 5-5, haploid, sample 160


title: KBM7 cell line, clone 5-5, haploid, sample 158


title: KBM7 cell line, clone 5-5, haploid, sample 161


title: KBM7 cell line, clone 5-5, haploid, sample 155


title: KBM7 cell line, clone 5-5, haploid, sample 166


title: KBM7 cell line, clone 5-5, haploid, sample 151


title: KBM7 cell line, clone 5-5, haploid, sample 164


title: KBM7 cell line, clone 5-5, haploid, sample 157


title: KBM7 cell line, clone 5-5, haploid, sample 149


title: KBM7 cell line, clone 5-5, haploid, sample 156


title: KBM7 cell line, clone 5-5, haploid, sample 154


title: KBM7 cell line, clone 5-5, haploid, sample 153


title: KBM7 cell line, clone 5-5, haploid, sample 148


title: KBM7 cell line, clone 5-5, haploid, sample 145


title: KBM7 cell line, clone 5-5, haploid, sample 150


title: KBM7 cell line, clone 5-5, haploid, sample 152


title: KBM7 cell line, clone 5-5, haploid, sample 146


title: KBM7 cell line, clone 5-5, haploid, sample 144


title: KBM7 cell line, clone 5-5, haploid, sample 143


title: KBM7 cell line, clone 5-5, haploid, sample 162


title: KBM7 cell line, clone 5-5, haploid, sample 168


title: KBM7 cell line, clone 5-5, haploid, sample 138


title: KBM7 cell line, clone 5-5, haploid, sample 142


title: KBM7 cell line, clone 5-5, haploid, sample 136


title: KBM7 cell line, clone 5-5, haploid, sample 140


title: KBM7 cell line, clone 5-5, haploid, sample 137


title: KBM7 cell line, clone 5-5, haploid, sample 139


title: KBM7 cell line, clone 5-5, haploid, sample 133


title: KBM7 cell line, clone 5-5, haploid, sample 131


title: KBM7 cell line, clone 5-5, haploid, sample 147


title: KBM7 cell line, clone 5-5, haploid, sample 132


title: KBM7 cell line, clone 5-5, haploid, sample 126


title: KBM7 cell line, clone 5-5, haploid, sample 128


title: KBM7 cell line, clone 5-5, haploid, sample 123


title: KBM7 cell line, clone 5-5, haploid, sample 124


title: KBM7 cell line, clone 5-5, haploid, sample 127


title: KBM7 cell line, clone 5-5, haploid, sample 129


title: KBM7 cell line, clone 5-5, haploid, sample 118


title: KBM7 cell line, clone 5-5, haploid, sample 122


title: KBM7 cell line, clone 5-5, haploid, sample 141


title: KBM7 cell line, clone 5-5, haploid, sample 125


title: KBM7 cell line, clone 5-5, haploid, sample 134


title: KBM7 cell line, clone 5-5, haploid, sample 130


title: KBM7 cell line, clone 5-5, haploid, sample 120


title: KBM7 cell line, clone 5-5, haploid, sample 119


title: KBM7 cell line, clone 5-5, haploid, sample 117


title: KBM7 cell line, clone 5-5, haploid, sample 110


title: KBM7 cell line, clone 5-5, haploid, sample 114


title: KBM7 cell line, clone 5-5, haploid, sample 116


title: KBM7 cell line, clone 5-5, haploid, sample 115


title: KBM7 cell line, clone 5-5, haploid, sample 113


title: KBM7 cell line, clone 5-5, haploid, sample 109


title: KBM7 cell line, clone 5-5, haploid, sample 112


title: KBM7 cell line, clone 5-5, haploid, sample 111


title: KBM7 cell line, clone 5-5, haploid, sample 108


title: KBM7 cell line, clone 5-5, haploid, sample 100


title: KBM7 cell line, clone 5-5, haploid, sample 097


title: KBM7 cell line, clone 5-5, haploid, sample 104


title: KBM7 cell line, clone 5-5, haploid, sample 103


title: KBM7 cell line, clone 5-5, haploid, sample 105


title: KBM7 cell line, clone 5-5, haploid, sample 135


title: KBM7 cell line, clone 5-5, haploid, sample 096


title: KBM7 cell line, clone 5-5, haploid, sample 098


title: KBM7 cell line, clone 5-5, haploid, sample 101


title: KBM7 cell line, clone 5-5, haploid, sample 093


title: KBM7 cell line, clone 5-5, haploid, sample 095


title: KBM7 cell line, clone 5-5, haploid, sample 092


title: KBM7 cell line, clone 5-5, haploid, sample 106


title: KBM7 cell line, clone 5-5, haploid, sample 099


title: KBM7 cell line, clone 5-5, haploid, sample 091


title: KBM7 cell line, clone 5-5, haploid, sample 090


title: KBM7 cell line, clone 5-5, haploid, sample 089


title: KBM7 cell line, clone 5-5, haploid, sample 107


title: KBM7 cell line, clone 5-5, haploid, sample 088


title: KBM7 cell line, clone 5-5, haploid, sample 085


title: KBM7 cell line, clone 5-5, haploid, sample 086


title: KBM7 cell line, clone 5-5, haploid, sample 084


title: KBM7 cell line, clone 5-5, haploid, sample 087


title: KBM7 cell line, clone 5-5, haploid, sample 083


title: KBM7 cell line, clone 5-5, haploid, sample 102


title: KBM7 cell line, clone 5-5, haploid, sample 082


title: KBM7 cell line, clone 5-5, haploid, sample 081


title: KBM7 cell line, clone 5-5, haploid, sample 079


title: KBM7 cell line, clone 5-5, haploid, sample 078


title: KBM7 cell line, clone 5-5, haploid, sample 074


title: KBM7 cell line, clone 5-5, haploid, sample 075


title: KBM7 cell line, clone 5-5, haploid, sample 077


title: KBM7 cell line, clone 5-5, haploid, sample 121


title: KBM7 cell line, clone 5-5, haploid, sample 076


title: KBM7 cell line, clone 5-5, haploid, sample 071


title: KBM7 cell line, clone 5-5, haploid, sample 063


title: KBM7 cell line, clone 5-5, haploid, sample 069


title: KBM7 cell line, clone 5-5, haploid, sample 067


title: KBM7 cell line, clone 5-5, haploid, sample 062


title: KBM7 cell line, clone 5-5, haploid, sample 064


title: L. bicolor MMN 1

city: Lund

first: Anders

last: Tunlid

address: Sölvegatan 37

department: Biology

country: Sweden

institute: Lund University

description: processed_data file = LAB_DE.tab

data_processing:
Genome sequences and annotations files in GFF-format were downloaded from the Joint Genome Insitute, JGI, at http://genome.jgi.doe.gov/. The format of these files are not accepted by the mapping software TopHat2 2.0.8b [1]. A custom made script was run to reformat the files (available on request).
TopHat2 was run with the settings: -T -x 1 -I 5000
The output file in BAM-format was sorted on positions with SAMtools 0.1.19-44428cd [2].
To count the number of reads mapping to genes the software htseq-count 0.5.4p3 [3] was run with the following parameters: -m intersection-nonempty -i gene_id -t CDS
The R package DESeq 1.10.1 [4] was used to normalize the raw read counts of each species and to identify differentially expressed genes, between FH and MMN, with a Benjamini-Hochberg adjusted p-value of < 0.01.
The Proteinortho 4.26 tool [5] was used with default settings to identify one-to-one orthologs in all nine species. The raw read counts of the orthologs were normalized using DESeq 1.14.0.
References:
[1] Kim D, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36.
[2] Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079.
[3] Anders S, Pyl PT, Huber W (2014) HTSeq – a Python framework to work with high-throughput sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btu638
[4] Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106.
[5] Lechner M, et al. (2011) Proteinortho: detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 12(1):124.
Supplementary_files_format_and_content: The tar archive "all_species_DE.tab.tar.gz" contains the  tab-delimited files "*_DE.tab" with the following columns: Joint Genome Institute (JGI) gene model names, JGI protein IDs, normalized read counts for each of the replicates, fold change values between FH versus MMN, p values and p values adjusted for multiple testing with the Benjamini-Hochberg procedure; The tab-delimited file "Orthologs_Expression_Values.tab" contains ortholog IDs and the normalized expression values of the proteins in each ortholog group; The tab-delimited file "Orthologs_Protein_IDs.tab" contains ortholog IDs and the JGI protein IDs of the nine species in each ortholog group.

organism: Laccaria bicolor

source_name: Mycelium_Laccaria bicolor

growth_protocol: Nine fungal species were analyzed including five ECM and four BR fungi. The fungi were grown in Petri dishes on a layer of glass beads immersed in MMN medium. After 9 days of incubation (18 °C and in the dark), the MMN medium was removed with a sterile pipette. The glass beads and the mycelia were washed with 10 ml of sterile MilliQ (MQ) water, and 10 ml of MMN medium without N was added to induce an N-deprived mycelium. After 24 h the mycelium was again washed in MQ water, and finally the organic matter extracts (10 ml) were added. The organic matter extracts were supplemented with glucose to a final concentration similar to that in the MMN medium. The fungi were grown in either the MMN or the organic matter medium using three replicates, respectively. The cultures were incubated for seven days at 18 °C in the dark.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) with the RLC buffer and the on-column DNase treatment according to the manufacturer. Total RNA was eluted in H2O and stored at -20°C until use. For quality assessments all samples were inspected using a RNA 6000 Nano kit on a 2100 Bioanalyzer (Agilent).
TruSeq mRNA-seq sample prep kit (Illumina)

treatment_protocol: The fungi were grown on either a minimum Melin-Norkrans medium (MMN) as a reference or a forest-hot litter extract (FH).

tag: tissue

value: Mycelium

tag: strain

value: (Maire) P.D.Orton

tag: substrate

value: MMN

tag: barcode

value: CAGATC

tag: genome build

value: Laccaria bicolor v2.0 (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 066


title: KBM7 cell line, clone 5-5, haploid, sample 068


title: L. bicolor MMN 2

description: processed_data file = LAB_DE.tab

value: GGCTAC


title: KBM7 cell line, clone 5-5, haploid, sample 059


title: KBM7 cell line, clone 5-5, haploid, sample 070


title: KBM7 cell line, clone 5-5, haploid, sample 061


title: L. bicolor MMN 3

description: processed_data file = LAB_DE.tab

value: GTCCGC


title: L. bicolor FH 3

description: processed_data file = LAB_DE.tab

value: FH

value: ATCACG


title: KBM7 cell line, clone 5-5, haploid, sample 065


title: L. bicolor FH 2

description: processed_data file = LAB_DE.tab

value: ACTGAT


title: KBM7 cell line, clone 5-5, haploid, sample 058


title: KBM7 cell line, clone 5-5, haploid, sample 057


title: KBM7 cell line, clone 5-5, haploid, sample 080


title: L. bicolor FH 1

description: processed_data file = LAB_DE.tab

value: GAGTGG


title: KBM7 cell line, clone 5-5, haploid, sample 055


title: KBM7 cell line, clone 5-5, haploid, sample 072


title: S. lacrymans MMN 3

description: processed_data file = SEL_DE.tab

organism: Serpula lacrymans

source_name: Mycelium_Serpula lacrymans

value: Serpula lacrymans S7.9 v2.0 (http://genome.jgi.doe.gov/SerlaS7_9_2/SerlaS7_9_2.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 056


title: KBM7 cell line, clone 5-5, haploid, sample 073


title: S. lacrymans MMN 2

description: processed_data file = SEL_DE.tab

value: CGTACG


title: KBM7 cell line, clone 5-5, haploid, sample 054


title: KBM7 cell line, clone 5-5, haploid, sample 053


title: S. lacrymans MMN 1

description: processed_data file = SEL_DE.tab

value: CCGTCC


title: KBM7 cell line, clone 5-5, haploid, sample 052


title: C. puteana MMN 3

description: processed_data file = COP_DE.tab

organism: Coniophora puteana

source_name: Mycelium_Coniophora puteana

value: Schum. Ex Fries, RWD-64-598SS-2

value: AGTCAA

value: Coniophora puteana v1.0 (http://genome.jgi.doe.gov/Conpu1/Conpu1.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 060


title: KBM7 cell line, clone 5-5, haploid, sample 049


title: KBM7 cell line, clone 5-5, haploid, sample 050


title: KBM7 cell line, clone 5-5, haploid, sample 094


title: S. lacrymans FH 3

description: processed_data file = SEL_DE.tab

value: Mycelium

value: TAGCTT


title: KBM7 cell line, clone 5-5, haploid, sample 046


title: C. puteana FH 3

description: processed_data file = COP_DE.tab

value: AGTTCC


title: C. puteana MMN 2

description: processed_data file = COP_DE.tab

value: MMN

value: GCCAAT


title: C. puteana FH 2

description: processed_data file = COP_DE.tab


title: KBM7 cell line, clone 5-5, haploid, sample 047


title: C. puteana MMN 1

description: processed_data file = COP_DE.tab

value: ACAGTG


title: C. puteana FH 1

description: processed_data file = COP_DE.tab

value: TGACCA


title: KBM7 cell line, clone 5-5, haploid, sample 048


title: KBM7 cell line, clone 5-5, haploid, sample 044


title: H. pinastri MMN 3

description: processed_data file = HYP_DE.tab

organism: Leucogyrophana pinastri

source_name: Mycelium_Hydnomerulius pinastri

value: GTCCGC

value: Hydnomerulius pinastri v2.0 (http://genome.jgi.doe.gov/Hydpi2/Hydpi2.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 042


title: H. pinastri MMN 1

description: processed_data file = HYP_DE.tab


title: H. pinastri MMN 2

description: processed_data file = HYP_DE.tab

value: CAGATC


title: KBM7 cell line, clone 5-5, haploid, sample 051


title: S. luteus MMN 3

description: processed_data file = SUL_DE.tab

organism: Suillus luteus

source_name: Mycelium_Suillus luteus

value: ATTCCT

value: Suillus luteus UH-Slu-Lm8-n1 v1.0 (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html)


title: S. lacrymans FH 2

description: processed_data file = SEL_DE.tab

value: FH

value: Serpula lacrymans S7.9 v2.0 (http://genome.jgi.doe.gov/SerlaS7_9_2/SerlaS7_9_2.home.html)


title: H. pinastri FH 3

description: processed_data file = HYP_DE.tab


title: S. luteus MMN 1

description: processed_data file = SUL_DE.tab

value: GAGTGG


title: S. luteus MMN 2

description: processed_data file = SUL_DE.tab

value: ACTGAT


title: S. luteus FH 3

description: processed_data file = SUL_DE.tab

value: ATGTCA


title: H. pinastri FH 1

description: processed_data file = HYP_DE.tab

value: Mycelium

value: GTTTCG


title: S. lacrymans FH 1

description: processed_data file = SEL_DE.tab


title: KBM7 cell line, clone 5-5, haploid, sample 045


title: KBM7 cell line, clone 5-5, haploid, sample 040


title: KBM7 cell line, clone 5-5, haploid, sample 037


title: RNAseq of LI_CRwt2

city: Shinjuku-ku

first: Koji

last: Atarashi

state: TOKYO

address: 35 Shinanomachi

department: Dept of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7 and Tophat v1.4.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: Colonic epithelial cells

extract_protocol:
Total RNA was isolated using TRIzol reagent
RNA library preparation was performed using a NEBNext Ultra RNA Library Prep Kit for Illumina

tag: colonization

value: CRwt

value: colonic epithelial cells


title: KBM7 cell line, clone 5-5, haploid, sample 038


title: KBM7 cell line, clone 5-5, haploid, sample 043


title: J. argillacea MMN 3

description: processed_data file = JAA_DE.tab

organism: Jaapia argillacea

source_name: Mycelium_Jaapia argillacea

value: MMN

value: AGTTCC

value: Jaapia argillacea v1.0 (http://genome.jgi.doe.gov/Jaaar1/Jaaar1.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 039


title: S. luteus FH 2

description: processed_data file = SUL_DE.tab

value: CTTGTA


title: RNAseq of LI_CRwt3


title: KBM7 cell line, clone 5-5, haploid, sample 035


title: H. pinastri FH 2

description: processed_data file = HYP_DE.tab

value: TTAGGC

value: Hydnomerulius pinastri v2.0 (http://genome.jgi.doe.gov/Hydpi2/Hydpi2.home.html)


title: J. argillacea MMN 1

description: processed_data file = JAA_DE.tab

value: ACAGTG


title: RNAseq of LI_CReae3

value: CReae


title: RNAseq of LI_CReae2


title: KBM7 cell line, clone 5-5, haploid, sample 034


title: KBM7 cell line, clone 5-5, haploid, sample 041


title: KBM7 cell line, clone 5-5, haploid, sample 033


title: RNAseq of LI_CReae1


title: J. argillacea FH 3

description: processed_data file = JAA_DE.tab

value: FH

value: GCCAAT


title: RNAseq of LI_GF3

value: GF


title: S. luteus FH 1

description: processed_data file = SUL_DE.tab

value: GGCTAC

value: Suillus luteus UH-Slu-Lm8-n1 v1.0 (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html)


title: KBM7 cell line, clone 5-5, haploid, sample 032


title: RNAseq of LI_CRwt1


title: KBM7 cell line, clone 5-5, haploid, sample 031


title: J. argillacea MMN 2

description: processed_data file = JAA_DE.tab

value: Mycelium

value: GATCAG


title: KBM7 cell line, clone 5-5, haploid, sample 029


title: KBM7 cell line, clone 5-5, haploid, sample 030


title: J. argillacea FH 1

description: processed_data file = JAA_DE.tab

value: GTCCGC


title: RNAseq of SI_RSFB3

source_name: Small intestinal epithelial cells

value: IQI

value: RSFB

value: small intestinal epithelial cells


title: RNAseq of LI_GF1

value: colonic epithelial cells


title: RNAseq of SI_RSFB2


title: cell line R5 at P8

city: Boston

first: Mary-Lee

last: Dequeant

email: mdequeant@genetics.med.harvard.edu, fagegalt@cshl.edu, Greg.Hannon@cruk.cam.ac.uk, perrimon@receptor.med.harvard.edu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were mapped to the Drosophila melanogaster genome (BDGP release 5/dm3) and annotated using TopHat (v1.4.1) and a custom Bowtie index (Bowtie v0.12.8) based on Drosophila annotated transcripts from Flybase release dmel-r5.43
We determined read counts using Bedtools
Genome_build: Drosophila melanogaster genome (BDGP release 5/dm3)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

organism: Drosophila melanogaster

source_name: Drosophila cell line R5 at Passage P8

growth_protocol: cells cultured in Schneider's media supplemented with 10% FBS (fetal bovine serum) and antibiotics.

extract_protocol:
RNA isolation using TRIzol reagent.5 micrograms of long RNA species from each sample were depleted from rRNAs using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Epicentre)
RNA libraries were prepared for sequencing starting from 50ng of rRNA-depleted RNAs following the manufacturer's instructions (Script-Seq v2 RNA-Seq; Epicentre)

treatment_protocol: samples were collected from cells cultured in 25 cm2 T flasks

tag: passage


title: RNAseq of SI_MSFB2

value: MSFB


title: RNAseq of SI_RSFB1


title: cell line R5 at P19

source_name: Drosophila cell line R5 at Passage P19


title: cell line R5 at P17

source_name: Drosophila cell line R5 at Passage P17


title: KBM7 cell line, clone 5-5, haploid, sample 026


title: RNAseq of SI_MSFB1


title: KBM7 cell line, clone 5-5, haploid, sample 024


title: cell line R5 at P6

source_name: Drosophila cell line R5 at Passage P6


title: KBM7 cell line, clone 5-5, haploid, sample 025


title: KBM7 cell line, clone 5-5, haploid, sample 027


title: RNAseq of SI_GF2


title: cell line R5 at P7

source_name: Drosophila cell line R5 at Passage P7


title: KBM7 cell line, clone 5-5, haploid, sample 023


title: RNAseq of LI_GF2


title: KBM7 cell line, clone 5-5, haploid, sample 028


title: cell line R5 at P4

source_name: Drosophila cell line R5 at Passage P4


title: KBM7 cell line, clone 5-5, haploid, sample 022


title: cell line R5 at P3

source_name: Drosophila cell line R5 at Passage P3


title: cell line R5 at P16

source_name: Drosophila cell line R5 at Passage P16


title: J. argillacea FH 2

description: processed_data file = JAA_DE.tab

value: CGATGT

value: Jaapia argillacea v1.0 (http://genome.jgi.doe.gov/Jaaar1/Jaaar1.home.html)


title: H. cylindrosporum MMN 3

description: processed_data file = HEC_DE.tab

organism: Hebeloma cylindrosporum

source_name: Mycelium_Hebeloma cylindrosporum

value: Romagnesi TV98IV3

value: MMN

value: Hebeloma cylindrosporum h7 v2.0 (http://genome.jgi.doe.gov/Hebcy2/Hebcy2.home.html)


title: H. cylindrosporum MMN 2

description: processed_data file = HEC_DE.tab

value: GTGGCC


title: KBM7 cell line, clone 5-5, haploid, sample 036

source_name: KBM7 cell line, clone 5-5, haploid


title: cell line R4 at P19

source_name: Drosophila cell line R4 at Passage P19


title: H. cylindrosporum MMN 1

description: processed_data file = HEC_DE.tab

value: CAGATC


title: cell line R5 at P2

source_name: Drosophila cell line R5 at Passage P2


title: KBM7 cell line, clone 5-5, haploid, sample 021


title: KBM7 cell line, clone 5-5, haploid, sample 020


title: KBM7 cell line, clone 5-5, haploid, sample 019


title: H. cylindrosporum FH 2

description: processed_data file = HEC_DE.tab

value: FH

value: GTTTCG


title: cell line R4 at P17

source_name: Drosophila cell line R4 at Passage P17


title: H. cylindrosporum FH 1

description: processed_data file = HEC_DE.tab

value: Mycelium


title: KBM7 cell line, clone 5-5, haploid, sample 018


title: KBM7 cell line, clone 5-5, haploid, sample 017


title: KBM7 cell line, clone 5-5, haploid, sample 016


title: cell line R4 at P12

source_name: Drosophila cell line R4 at Passage P12


title: cell line R4 at P16

source_name: Drosophila cell line R4 at Passage P16


title: RNAseq of SI_GF1

value: GF


title: cell line R4 at P11

source_name: Drosophila cell line R4 at Passage P11


title: H. cylindrosporum FH 3

description: processed_data file = HEC_DE.tab

value: CGTACG


title: cell line R4 at P9

source_name: Drosophila cell line R4 at Passage P9


title: cell line R4 at P7

source_name: Drosophila cell line R4 at Passage P7


title: KBM7 cell line, clone 5-5, haploid, sample 014


title: KBM7 cell line, clone 5-5, haploid, sample 015


title: KBM7 cell line, clone 5-5, haploid, sample 010


title: KBM7 cell line, clone 5-5, haploid, sample 011


title: cell line R4 at P6

source_name: Drosophila cell line R4 at Passage P6


title: KBM7 cell line, clone 5-5, haploid, sample 013


title: cell line R4 at P3

source_name: Drosophila cell line R4 at Passage P3


title: cell line R4 at P5

source_name: Drosophila cell line R4 at Passage P5


title: cell line R4 at P4

source_name: Drosophila cell line R4 at Passage P4


title: cell line R4 at P2

source_name: Drosophila cell line R4 at Passage P2


title: cell line R1 at P19

source_name: Drosophila cell line R1 at Passage P19


title: KBM7 cell line, clone 5-5, haploid, sample 012


title: KBM7 cell line, clone 5-5, haploid, sample 007


title: KBM7 cell line, clone 5-5, haploid, sample 008


title: cell line R1 at P17

source_name: Drosophila cell line R1 at Passage P17


title: cell line R1 at P11

source_name: Drosophila cell line R1 at Passage P11


title: cell line R1 at P16

source_name: Drosophila cell line R1 at Passage P16


title: KBM7 cell line, clone 5-5, haploid, sample 006

source_name: KBM7 cell line, clone 5-5, haploid


title: KBM7 cell line, clone 5-5, haploid, sample 005


title: KBM7 cell line, clone 5-5, haploid, sample 004


title: KBM7 cell line, clone 5-5, haploid, sample 003


title: cell line R1 at P10

source_name: Drosophila cell line R1 at Passage P10


title: cell line R1 at P8

source_name: Drosophila cell line R1 at Passage P8


title: KBM7 cell line, clone 5-5, haploid, sample 002


title: cell line R1 at P7

source_name: Drosophila cell line R1 at Passage P7


title: KBM7 cell line, clone 5-5, haploid, sample 001


title: cell line R1 at P5

source_name: Drosophila cell line R1 at Passage P5


title: cell line R1 at P4

source_name: Drosophila cell line R1 at Passage P4


title: cell line R1 at P3

source_name: Drosophila cell line R1 at Passage P3


title: RNA-seq of GFP control

city: Cambridge

first: Wenwen

last: Fang

state: Massachusetts

address: Room 625, 455 Main Street

institute: Whitehead Institute

data_processing:
To create each dictionary of barcode–variant linkages, paired-end reads were first joined using fastq-join, allowing a maximum difference of 5% (-p 5) in the overlap.  The joined reads were quality filtered using fastq_quality_filter, requiring a minimum quality score of 30 for 90% of the sequences (-q 30 -p 90). 3' adapter was trimmed using cutadapt (default parameters), discarding untrimmed sequences.  A second cutadapt command split the barcode-variant pairs using the constant sequences linking them, generating an info-file from which the barcode-variant pairs could be extracted.
The read for the input barcodes were first adaptor-trimmed using cutadapt, requiring a length between 25 and 35 nt after trimming (-m 25 -M 35).  The trimmed reads were quality-filtered using fastq_quality_filter, requiring a minimum quality score of 30 for all bases in the read (-q 30 -p 100).  The trimmed sequences were barcodes that could be linked to variants using dictionaries generated above.
Read 1 from the cleavage-fragment sequencing was quality-filtered using fastq_quality_filter, requiring a minimum quality score of 30 for 95% of the sequence (-q 30 -p 95). Barcode–cleavage fragment pairs were split using cutadapt and constant sequences linking them to generate an info-file from which the barcode–cleavage fragment pairs could be extracted.
To process small-RNA seq libraries, adaptor sequences were trimmed using cutadapt (default parameters) and quality-filtered by requiring all bases to have a minimum score of 10 (-q 10 -p 100).  Additional random nucleotides that derived from the 5' and 3' adaptors were removed, and the resulting reads were collapsed while recording read counts (fastx_collapser) and mapped to the pri-miRNAs using Geneious 6.1.2 (Kearse et al., 2012).
For RNA-seq libraries, reads were quality-filtered using fastq_quality_filter, requiring a minimum quality score of 30 for 90% of the sequences (-q 30 -p 90), and then mapped to the RefSeq transcriptome (considering for each gene the transcript with the longest open reading frame) using bowtie, requiring unique mapping with ≤1 mismatch (-a -n 1 -m 1 --best --strata ).  Only reads mapping to the correct strand were considered, and only transcripts with more than 20 mapped reads per million total mapped reads were used to calculate expression fold changes.
Genome_build: hg38 RefSeq Genes
Supplementary_files_format_and_content: The "dictionary.txt" files are tab-delimited tables containing the variant sequences (column 2) and their linked barcode sequences (column 3), and the number of times (column 1) this linkage was sequenced in the dictionary sequencing.
Supplementary_files_format_and_content: The "input_barcode_counts.txt" files are tab-delimited tables containg the barcode sequences (column 2) and their read numbers (column 1) in input sequencing.
Supplementary_files_format_and_content: The "barcode_cleavage_fragments.txt" files are tab-delimited tables containing cleavage fragment sequences (coulmn 2) and their linked barcode sequences (column 1).
Supplementary_files_format_and_content: The "variant_counts.txt" files are tab-delimited tables containing variant sequences (column 1) and their counts in the input (column 2) and selection (column 3) sequencing.
Supplementary_files_format_and_content: The "collapsed.fasta" are fasta files containing collapsed read sequences and their read numbers (output of fastx-collapser).
Supplementary_files_format_and_content: The "vs_GFP.txt" files are tab-delimited tables containing the name of each mRNA (column 1), the fold change (column 2) relative to GFP-transfected cells, the GC content (column 3) and length (column 4) of the corresponding 3' UTR, the number of sites in the 3' UTR for the following site types: 8mer (column 5), 7mer-m8 (column 6), 7mer-A1(column 7), 6mer (column 8), and offset 6mer (column 9).
Supplementary_files_format_and_content: *all_scores.xlsx are Excel files that include calculated read counts for each variant, and their cleavage scores.

source_name: human embryonic kidney cells (HEK293T)

growth_protocol: This applies to small RNA and polyA RNA sequencing libraries.  HEK293T cells were cultured under standard conditions in DMEM supllemented to 10% FBS.

extract_protocol:
Total RNA was polyA-selected using Dynabeads Oligo (dT)25 (Life Technologies), and RNA-seq libraries were made using a NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kit (Bioo Scientific) according to manufacturer's instructions.
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.

treatment_protocol: This applies to small RNA and polyA RNA sequencing libraries.  Plasmids co-expressing designated small RNAs and miR-1 were contransfected with GFP plasmids into HEK293T cells using Lipofectamine 2000.

value: CACTCA


title: RNA-seq of A5

value: CAACTA


title: KBM7 cell line, clone 5-5, haploid, sample 009


title: RNA-seq of A4

value: CAAAAG


title: small RNA sequencing of A1.12

description: gel purified small RNA

extract_protocol:
Detailed protocols for small-RNA sequencing are available at http://bartellab.wi.mit.edu/protocols.  Briefly, gel-purified RNA was ligated to pre-adenylated 3' adapter using T4 RNA Ligase 2, truncated KQ in the presence of 10% PEG 8000 (NEB).  The ligated products were gel purified and ligated to 5' adapter using T4 RNA ligase 1 in the presence of 10% PEG 8000 (NEB). The 5' ligation products were gel purified and reverse transcribed by SuperScriptIII (Life Technologies), and amplified by KAPA HiFi PCR kit (10-12 cycles).  The PCR products were purified using the Agencourt AMPure XP system (Beckman Coulter).
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.

value: GATCAG


title: small RNA sequencing of A4, A5, A6

description: gel purified small RNA

value: TGACCA


title: small RNA sequencing of A1.10

description: gel purified small RNA

value: ACTTGA


title: RNA-seq of A6

value: CACCGG


title: cell line R1 at P2

source_name: Drosophila cell line R1 at Passage P2


title: small RNA sequencing of A1.4

description: gel purified small RNA

value: TTAGGC


title: small RNA sequencing of A1.8

description: gel purified small RNA

value: GCCAAT


title: small RNA sequencing of A1

description: gel purified small RNA

value: CGATGT


title: small RNA sequencing of A1, A2, A3

description: gel purified small RNA

extract_protocol:
Detailed protocols for small-RNA sequencing are available at http://bartellab.wi.mit.edu/protocols.  Briefly, gel-purified RNA was ligated to pre-adenylated 3' adapter using T4 RNA Ligase 2, truncated KQ in the presence of 10% PEG 8000 (NEB).  The ligated products were gel purified and ligated to 5' adapter using T4 RNA ligase 1 in the presence of 10% PEG 8000 (NEB). The 5' ligation products were gel purified and reverse transcribed by SuperScriptIII (Life Technologies), and amplified by KAPA HiFi PCR kit (18 cycles).  The PCR products were purified on a formamide-polyacrylamide gel.
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.


title: Neonatal naïve HN2 [human miRNA-seq]

description: Sample name: HN2

data_processing:
miRNAs were aligned using Mirdeep2's mapper.pl script to miRBase's version 21 database of miRNAs using options -d -e -h -i -j -l 18 -m.
Known miRNAs were quantified using Mirdeep2's quantifier.pl script using the option -d.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file contains read counts normalized by reads per million (RPM) for each miRNA for each sample.

source_name: CD8+ T cells, neonatal naïve

extract_protocol:
Cells were placed in Trizol, stored at -80, then RNA was extracted according to the standard Trizol protocol.
1 ug of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kit. Libraries were sequenced on an Illumina HiSeq 2000, generating 50 bp reads.

treatment_protocol: To isolate mononuclear cells from whole blood, samples were mixed with 1-2 times their volume of PBS-EDTA. This diluted blood was layered over Ficoll-paque Plus (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature. Mononuclear cells at the interface between plasma and Ficoll were collected and washed with PBS-EDTA. To isolate CD8+ T cells from this fraction, a Naïve CD8+ T Cell Isolation Kit (human) (Miltenyi) was used according to manufacturer's instructions.

value: cord blood

value: CD8+ T cells

value: naïve

value: neonatal


title: Neonatal naïve HN3 [human miRNA-seq]

description: Sample name: HN3


title: Adult naïve HA2 [human miRNA-seq]

description: Sample name: HA2

source_name: CD8+ T cells, adult naïve

value: whole blood

value: adult


title: Adult naïve HA3 [human miRNA-seq]

description: Sample name: HA3


title: miR-30 selection sequencing time point 1

description:
gel purified RNA fragments after in vitro cleavage by HEK293T lysate
30_variant_counts.txt

organism: synthetic construct

source_name: synthetic

extract_protocol:
The 5' cleavage fragments of each pool were purified on urea-polyacrylamide gels and ligated at their 3' ends to a pre-adenylated adapter using T4 RNA ligase 2, truncated KQ (NEB), in the presence of three oligonucleotides that paired to constant regions of the cleavage fragments to prevent their circularization (0.67 µM of each of the protection oligonucleotides, 10 µM adapter, 10% PEG 8000 (NEB); otherwise, as recommended by the manufacturer). Ligated cleavage fragments were purified on urea-polyacrylamide gels, reverse transcribed, amplified and sequenced, as done for the input barcodes, except sequencing used the 100 × 100 bp paired-end mode.
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.

value: CGGAAT


title: miR-30 selection sequencing time point 2

description:
gel purified RNA fragments after in vitro cleavage by HEK293T lysate
30_barcode_cleavage_fragments.txt
30_variant_counts.txt


title: Neonatal naïve HN1 [human miRNA-seq]

description: Sample name: HN1


title: miR-16 selection sequencing

description:
gel purified RNA fragments after in vitro cleavage by HEK293T lysate
16_variant_counts.txt

value: CACGAT


title: small RNA sequencing of A1.6

description: gel purified small RNA

value: ACAGTG


title: miR-125 selection sequencing

description:
gel purified RNA fragments after in vitro cleavage by HEK293T lysate
125_variant_counts.txt

value: CTCAGA


title: Adult naïve HA1 [human miRNA-seq]

description: Sample name: HA1


title: P. involutus MMN 2

description: processed_data file = PAI_DE.tab

organism: Paxillus involutus

source_name: Mycelium_Paxillus involutus

value: Mycelium

value: MMN

value: Paxillus involutus ATCC 200175 v1.0 (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html)


title: miR-30 input sequencing

description:
RNA from T7 transcription of the degenerate DNA library
30_variant_counts.txt

extract_protocol:
To sample the barcodes of each RNA pool and thereby quantify the amount of each variant in the input, the barcode region of a portion of each RNA pool was sequenced as follows. The region was reverse transcribed using AffinityScript reverse transcriptase (Agilent Technologies) and a primer that paired to the constant region between the barcode and the hairpin.  This primer also added an adapter sequence for Illumina sequencing.  After base hydrolysis of RNA and desalting using Micro Bio-Spin P-30 Gel Columns (BioRad), second-strand synthesis was performed using the KAPA HiFi PCR kit, which added the Illumina adapter sequence to the 5' end.  Products were purified using the Agencourt AMPure XP system (Beckman Coulter), and barcode regions were sequenced on a HiSeq2000 (40 bp single-end mode).
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.

value: CCGTCC


title: miR-125 input sequencing

description:
RNA from T7 transcription of the degenerate DNA library
125_variant_counts.txt

value: CTGATC


title: miR-16 input sequencing

description:
RNA from T7 transcription of the degenerate DNA library
16_variant_counts.txt

value: AGTCAA


title: P. involutus MMN 3

description: processed_data file = PAI_DE.tab

value: ACTTGA


title: P. involutus MMN 1

description: processed_data file = PAI_DE.tab

value: CGATGT


title: miR-30 dictionary sequencing

description: degenerate DNA library made by PCR

extract_protocol:
For each pri-miRNA, subpools of DNA oligonucleotides designed to have an equal mixture of all possible sequences at each of the mutagenized windows but otherwise corresponding to the pri-mRNA hairpin and its flanking sequences were synthesized (IDT) and purified on urea-polyacrylamide gels.  Subpools for each pri-miRNA were mixed and extended at each end with successive primer-extension reactions using KAPA HiFi PCR kit (KAPA Biosystems) and oligonucleotides (IDT) that added the T7 promoter, barcodes and Illumina adapter sequences.  The extended DNA products were purified on formamide-polyacrylamide gels and quantified using Library Quantification Kits (KAPA Biosystems).  A bottleneck was then imposed, drawing 10 million, 16 million, and 16 million molecules from the pri-miR-125, pri-miR-16, and pri-miR-30 pools, and these samples were amplified for 19 cycles using KAPA HiFi PCR kit.  After purification using a QIAquick PCR Purification Kit (Qiagen), a small fraction of each pool was sequenced on a HiSeq2000 (100 × 100 bp paired-end mode) to create the dictionary.
This applies to small RNA and polyA RNA sequencing libraries.  At 48 hour post transfection, total RNA was extracted using TRIzol Reagent following manufacturer's instructions.

value: TAGCTT


title: P. involutus FH 3

description: processed_data file = PAI_DE.tab

value: FH

value: ATCACG


title: miR-16 dictionary sequencing

description: degenerate DNA library made by PCR


title: P. involutus FH 2

description: processed_data file = PAI_DE.tab

value: GTGGCC


title: miR-125 dictionary sequencing

description: degenerate DNA library made by PCR

value: ATTCCT


title: P. involutus FH 1

description: processed_data file = PAI_DE.tab


title: after second flush replicate1

status: Public on Sep 23 2015

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agaricus bisporus var bisporus (H97) v2.0  whole genome using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: Agaricus bisporus var bisporus (H97) v2.0
Supplementary_files_format_and_content: excel file include unique reads number, gene length, coverage, RPKM values and KEGG orthology annotation of genes for each sample.

organism: Agaricus bisporus

source_name: Mycelium colonized compost sample

growth_protocol: A. bisporus commercial heterokaryon strain A15 (Sylvan, USA) was used in this study. Phase I and II mushroom compost, which is based on wheat straw, horse and chicken manure, gypsum and water, were prepared according to commercial practice at CNC (Coӧperatieve Nederlandse Champignonwekersvereniging, Milsbeek, the Netherlands). Phase II compost was inoculated with A. bisporus spawns (Sylvan, USA) and incubated at 25°C for 16 days. Fully colonized compost was covered with casing layer (peat and lime) according to established commercial practice and incubated until first and second flushes of mushrooms were developed and harvested

extract_protocol:
Total RNA was isolated from the collected compost samples using a CsCl gradient centrifugation method (Patyshakuliyeva et al., 2014). RNA integrity and quantity were checked with the RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelium colonized compost samples were collected at the different growth stages of A. bisporus. All samples were immediately frozen and stored at -20°C until being processed.

tag: sampling time

value: after second flush


title: second flush replicate2

value: second flush


title: second flush replicate1


title: after first flush replicate2

value: after first flush


title: after second flush replicate2


title: first flush replicate2

value: first flush


title: pinning stage replicate2

value: pinning stage


title: pinning stage replicate1


title: spawning stage replicate1

value: 16 days


title: spawning stage replicate2


title: ChickRecon_limit-digest-2 nucleosome core particles (MNase +ExoIII)

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

description: Biological replicate 2

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer2) or the mouse genome (mm10) using Bowtie2 with default settings. Bowtie2 was also used to align the reconstituted nucleosome sequences to the plasmid sequence (supplied here).
This paper describes novel nucleosomal particles distinguished by their lengths. DNA fragment length distributions were calculated from the .sam files for all of the data sets and are supplied for the mouse data as text files.
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535. Provided here are bigwig files for the yeast data and text files for the in vitro experiments with pRS-ARG1-B. Occupancy files were not calculated for the mouse nucleosomes, because the coverage is too low (~45m pairs of reads).
This paper describes novel nucleosomal particles distinguished by their lengths. DNA fragment length distributions were calculated from the .sam files for all of the data sets and are supplied for the mouse data as text files.
Genome_build: SacCer2 and mm10 for in vivo data. In vitro reconstitutions: the plasmid sequence (pRS-ARG1-B.fa) is provided here; the S. cerevisiae ARG1 locus (from -1283 to +2936 relative to the start codon) was inserted into pRS414. See paper for more details.
Supplementary_files_format_and_content: Yeast strains (in vivo data): bigwig files showing nucleosome occupancy (all reads included). Reconstituted nucleosomes on plasmid pRS-ARG1B: text files showing nucleosome occupancy at each plasmid coordinate (50-500 bp). Mouse data: length distributions (filenames contain "lengths"): text files with two columns: length (L) in bp, number of molecules of length L.

organism: Synthetic plasmid

source_name: S. cerevisiae plasmid pRS-ARG1-B

growth_protocol: Yeast strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.
MNase-seq and MNase-ExoIII-seq

treatment_protocol:
Yeast nuclei were prepared from unfixed cells and then digested with a range of MNase concentrations at two different ExoIII concentrations. Mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details.
In vitro reconstitutions were performed by mixing recombinant yeast histone octamers or native chicken erythrocyte core histones with purified plasmid pRS-ARG1-B DNA followed by salt dialysis. Reconstituted chromatin was digested to mono-nucleosomes using MNase and ExoIII. See paper for details.
Mouse nuclei were prepared from liver (female E13.5) and mildly digested with MNase only. The nuclei were lysed and soluble long chromatin was depleted of histone H1 using a cation exchange resin. Native chromatin and H1-depleted chromatin were digested with MNase and ExoIII. DNA from three digestion points (increasing MNase with fixed ExoIII) was purified. See paper for details.

tag: strain name

value: in vitro

tag: sample type

value: Native chicken erythrocyte core histones and pRS-ARG1-B

tag: mnase or exoiii

value: MNase limit digest with ExoIII trimming


title: first flush replicate1


title: ChickRecon_less-digested-2 nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2

value: MNase digest with ExoIII trimming


title: ChickRecon_less-digested-1 nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: ChickRecon_limit-digest-1 nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: Donor 3-NaCl

city: Shanghai

first: WUCHANG

last: ZHANG

state: Shanghai

address: 115 Jinzun Road

department: School of stomatology

country: China

institute: Shanghai Jiao Tong University

data_processing:
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to human genome (version: GRCH37) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment [4]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Genome_build: GRCH37
Supplementary_files_format_and_content: Tab-delimited text file including raw counts for each Sample

source_name: Human peripheral bloood

growth_protocol: monocyte differentiation into macrophages were induced by 6-day treatment of 100ng/ml M-CSF.

extract_protocol:
RNA was harvested using Trizol reagent.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: mature macrophages were treated with or without additional 51mM NaCl for 24 hours.

tag: individual

value: Donor 3

tag: factor inducing monocyte differentiation

value: M-CSF

tag: resulting cell type

value: macrophage

tag: protocol

value: Additional 51mM NaCl for 24 hours


title: Donor 3-Control

value: No treatment


title: Gastric organoids

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Gastric organoids

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: young (2-3 months)

value: cultured gastric mouse-derived organoids.


title: Recon_MNase-Exo_less-digested-1

description:
Recombinant yeast histones and pRS-ARG1-B
Biological replicate 1

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie2 with default settings. Bowtie2 was also used to align the reconstituted nucleosome sequences to the plasmid sequence (supplied here).
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535.
The processed data were converted to the bigwig files supplied here (using all sequences).
Genome_build: SacCer2 for in vivo data. In vitro reconstitutions: the plasmid sequence (pRS-ARG1-B.fa) is provided here; the S. cerevisiae ARG1 locus (from -1283 to +2936 relative to the start codon) was inserted into pRS414. See paper for more details.
Supplementary_files_format_and_content: yeast strains (in vivo data): bigwig files showing nucleosome occupancy (all reads included). Reconstituted nucleosomes on plasmid pRS-ARG1B: text files showing nucleosome occupancy at each plasmid coordinate (all lengths).
Supplementary_files_format_and_content: pRS-ARG1-B_688.fa (the plasmid sequence used to align nucleosome reads in the reconstitution experiments).

source_name: nucleosome core particles (MNase +ExoIII)

growth_protocol: Both strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
Nuclei were prepared from unfixed yeast cells and then digested with a range of MNase concentrations at two different ExoIII concentrations. In vitro reconstitutions were performed by mixing recombinant yeast histone octamers with purified plasmid pRS-ARG1-B DNA followed by salt dialysis. In both cases, mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: genotype/variation

tag: plasmid

value: plasmid pRS-ARG1-B


title: Recon_MNase-Exo_limit-digest-2

description:
Recombinant yeast histones and pRS-ARG1-B
Biological replicate 2


title: Recon_MNase-Exo_limit-digest-1


title: Donor 2-NaCl

value: Donor 2


title: Uninjured sample 4

source_name: Uninjured gastric tissue sample

tag: strain

tag: strain status

value: healthy control

tag: tissue

value: Stomach


title: Donor 2-Control


title: Recon_MNase-Exo_less-digested-2


title: Uninjured sample 3


title: Donor 1-NaCl

value: Donor 1


title: after first flush replicate1

value: after first flush


title: Donor 1-Control


title: Uninjured sample 2


title: Uninjured sample 1


title: ulcerated sample 3

source_name: ulcerated gastric tissue sample

value: with ulcers


title: Intact stomach tissue

source_name: Intact stomach tissue

value: Intact stomach tissue


title: ulcerated sample 4


title: Single cell mRNA sequencing data from KMB7 cells

first: Siddharth

middle: Subhas

last: Dey

institute: Hubrecht Institute

data_processing:
After sequencing, the right mate was aligned to the hg19 RefSeq human transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013) using bwa (Li and Durbin, 2010) with default parameters. The left mate contains a barcode identifying the single cell from which the read originated. Barcodes are listed in the README_barcodes.txt supplementary file.
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing transcript counts from each single cell. mRNA count data for all single cells, each column is a single cell and each row is a gene.

source_name: Cell line KBM7,  derived from a patient with chronic myeloid leukemia

extract_protocol:
For single cell mRNA sequencing, single cells were sorted into 96-well plates containing trizol (life technologies).
The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on the Illumina Hiseq 2500 platform using 50 bp paired-end sequencing.

treatment_protocol: Fifteen hours prior harvesting single cells Dam methylation was induced by treating the cells with 0.5 nM Shield1 (ClonTech) and FACS sorted based on cell size and expression of both Fucci markers {Sakaue-Sawano, 2008, 18267078}.

tag: cell line

tag: cell type

value: myeloid leukemia

tag: ploidy


title: ulcerated sample 1


title: ulcerated sample 2


title: rna_hES_shControl-replicate1

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description: rna_hES_shControl_replicate1 and rna_hES_shControl_replicate2 are replicates of each other.

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

source_name: hES cell, treated with sh control

growth_protocol: feeder-free in mTESR1

extract_protocol: RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

tag: treatment

value: lentiviral infection with sh control

value: Standard mRNA-seq


title: rna_ND3_shKBTBD8

source_name: hES cell, treated with sh targeting KBTBD8, ND 3d

growth_protocol: neural conversion with NIM for 3d

value: lentiviral infection with sh KBTBD8


title: rna_ND3_shControl

source_name: hES cell, treated with sh control, ND 3d


title: rna_hES_shTCOF1

source_name: hES cell, treated with sh targeting TCOF1

value: lentiviral infection with sh TCOF1


title: rna_hES_shControl-replicate2


title: rna_hES_shKBTBD8

source_name: hES cell, treated with sh targeting KBTBD8


title: ribo_ND3_shKBTBD8

data_processing:
Library strategy: Ribosome Profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: ribo_hES_shTCOF1


title: rna_ND3_shTCOF1

source_name: hES cell, treated with sh targeting TCOF1, ND 3d


title: ribo_hES_shControl-replicate1

description: ribo_hES_shControl_replicate1 and ribo_hES_shControl_replicate2 are replicates of each other.


title: ribo_hES_shKBTBD8


title: rna_ND1_shControl_replicate2

source_name: hES cell, treated with sh control, ND 1d

growth_protocol: neural conversion with NIM for 1d


title: rna_ND3_shKBTBD8_replicate2


title: rna_hES_shControl_replicate2


title: rna_ND6_shKBTBD8_replicate2

source_name: hES cell, treated with sh targeting KBTBD8, ND 6d

growth_protocol: neural conversion with NIM for 6d


title: rna_ND6_shControl_replicate2

source_name: hES cell, treated with sh control, ND 6d


title: rna_ND1_shKBTBD8_replicate2

source_name: hES cell, treated with sh targeting KBTBD8, ND 1d


title: ribo_ND3_shTCOF1


title: rna_ND6_shKBTBD8_replicate1


title: Trophs_Histone H3

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

description: Chromatin IP using specific antibody

data_processing:
Reference genome was converted to color-space using bowtie-build
ChIP-seq data were mapped using the Bowtie allowing two mismatches.
Bed files generated using Samtools
Genome_build: plasFalc1
Supplementary_files_format_and_content: bed

organism: Plasmodium falciparum

source_name: Trophozoite stage of Plasmodium falciparum

growth_protocol: Plasmodium falciparum strain 3D7 was cultured cultured in RPMI1640 medium supplemented with 25 mM HEPES, 0.5% AlbuMAX I, 1.77 mM sodium bicarbonate, 100 μM hypoxanthine and 12.5 μg ml-1 gentamicin sulfate at 37 °C. RBCs were prepared from fresh whole blood obtained from a healthy donor and stored at 4 °C for at least 1 day. Increased yields were obtained by subculturing every 2 days for 6–8 h before invasion. This was done by equally dividing the contents of each flask into two or more flasks and quickly restoring the hematocrit and medium volume in each of the flasks with fresh erythrocytes and fresh medium to keep the hematocrit between 1 and 1.5% in the required volume of culture medium. The culture was synchronized with 5% sorbitol and the parasites were collected at 18, 30 and 40 hpi for chromatin immunoprecipitation.

extract_protocol:
Lysates were clarified from sonicated nuclei and antibody-DNA complexes were isolated with antibody.
ChIP-seq libraries for all the samples were prepared from around 5 ng of DNA using fragment library construction kit from life technolofies for SoLiD sequencing. Briefly ChIPed DNA samples were end repaired and adapters were ligated using T4 DNA ligase. Ligated DNA were subsequently amplified using adapter specific barcoded primers for 15 cycles. DNA purification at every step was performed using Agencourt XP beads. Library profiles were assessed using Agilent bioanalyzer 2100 high sensitivityDNA kit. Equimolar amount of libraries were pooled and 50 bp reads were sequenced in-house using SoLiD 4.0.

treatment_protocol: No treatment

tag: Stage

value: Trophs

tag: antibody

tag: antibody catalog/vendor

value: Ab1791 (abcam)


title: Trophs_RNA Pol II

description: Chromatin IP using specific antibody

value: Pol II

value: Sc-899 (Santa Cruz)


title: rna_ND1_shKBTBD8_replicate1


title: Rings_RNA Pol II

description: Chromatin IP using specific antibody

source_name: Ring stage Plasmodium falciparum

value: Rings


title: Schizont_Histone H3

description: Chromatin IP using specific antibody

source_name: Schizont stage of Plasmodium falciparum

value: Schizont


title: rna_ND3_shKBTBD8_replicate1


title: ribo_ND3_shControl


title: rna_hES_shKBTBD8_replicate1


title: Rings_Histone H3

description: Chromatin IP using specific antibody


title: ribo_hES_shControl-replicate2


title: rna_ND3_shControl_replicate1


title: Rings_H4ac

description: Chromatin IP using specific antibody


title: rna_ND6_shControl_replicate1


title: rna_hES_shKBTBD8_replicate2


title: Trophs_H4ac

description: Chromatin IP using specific antibody


title: Trophs_H3K79me3

description: Chromatin IP using specific antibody


title: Rings_H3K79me3

description: Chromatin IP using specific antibody


title: rna_ND3_shControl_replicate2


title: rna_ND1_shControl_replicate1


title: Schizont_RNA Pol II

description: Chromatin IP using specific antibody


title: ribo_ND6_shKBTBD8_replicate2


title: Schizont_H3K27me3

description: Chromatin IP using specific antibody


title: rna_hES_shControl_replicate1


title: Schizont_H4ac

description: Chromatin IP using specific antibody


title: ribo_ND3_shKBTBD8_replicate2


title: Trophs_H3K27me3

description: Chromatin IP using specific antibody


title: Rings_H3K27me3

description: Chromatin IP using specific antibody


title: Schizont_H3K79me3

description: Chromatin IP using specific antibody


title: Schizont_H3K27ac

description: Chromatin IP using specific antibody

value: Ab4729  (abcam)


title: Trophs_H3K27ac

description: Chromatin IP using specific antibody


title: Rings_H3K14ac

description: Chromatin IP using specific antibody


title: Schizont_H3K14ac

description: Chromatin IP using specific antibody


title: Rings_H3K27ac

description: Chromatin IP using specific antibody


title: ribo_hES_shKBTBD8_replicate2


title: ribo_ND6_shKBTBD8_replicate1


title: ribo_ND1_shControl_replicate2


title: ribo_ND1_shKBTBD8_replicate2


title: ribo_ND6_shControl_replicate2


title: Schizont_H3K9me3

description: Chromatin IP using specific antibody


title: Rings_H3K9me3

description: Chromatin IP using specific antibody


title: ribo_hES_shKBTBD8_replicate1


title: Schizont_H3K9ac

description: Chromatin IP using specific antibody


title: ribo_ND6_shControl_replicate1


title: ribo_ND1_shKBTBD8_replicate1


title: Trophs_H3K9me3

description: Chromatin IP using specific antibody


title: ribo_ND3_shControl_replicate1


title: ribo_ND1_shControl_replicate1


title: ribo_hES_shControl_replicate2


title: Trophs_H3K14ac

description: Chromatin IP using specific antibody


title: ribo_ND3_shControl_replicate2


title: ribo_hES_shControl_replicate1


title: ribo_ND3_shKBTBD8_replicate1


title: Trophs_H3K9ac

description: Chromatin IP using specific antibody


title: Rings_H3K9ac

description: Chromatin IP using specific antibody


title: Trophs_H3K4me3

description: Chromatin IP using specific antibody


title: virgin_6

city: Egham

first: Fabio

last: Manfredini

state: Surrey

address: Bourne Lab Room 4-17

country: United Kingdom

institute: Royal Holloway University of London

description: Virgin queens were caged along with the CO2-treated queens, but were returned to their respective colonies without narcosis.

data_processing:
Reads were checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality control
Reads were also processed with Trimmomatic to remove adapters and low quality bases: reads less than 36 bases long were filtered out
We also dropped reads that matched ribosomal RNA sequences (rRNA) by means of SortMeRna
Surviving reads were aligned with TopHat for Illumina to the latest version of the honey bee genome (Apis mellifera Assembly 4.5) available on BeeBase (http://hymenopteragenome.org/ beebase/?q=download_sequences) by using the Galaxy web-based platform (https://usegalaxy.org/).
Mapped reads were converted into raw read counts with SAMtools idxstats
Raw read counts were analysed with R using the edgeR package from Bioconductor. Read counts were log2 transformed to correct for the skew to zero and large values. Only genes with at least 10 reads per sample were kept in the analysis (12,992 genes).
Normalization was performed with Trimmed Mean of M-values (TMM), a method that is implemented in the edgeR Bioconductor package
We detected differential levels of gene expression using a modified Fisher’s exact test that takes into account both dispersion and multiple samples. Finally, raw P-values for each gene were corrected for multiple comparisons setting a false discovery rate (FDR) of 5%.
Genome_build: Apis mellifera Assembly 4.5
Supplementary_files_format_and_content: Excel spreadsheet file with two sheets: raw read counts and scaled read counts

organism: Apis mellifera

source_name: brain tissue

growth_protocol: We reared 20 sister queens of standard Australian commercial stock using standard beekeeping techniques from a single source colony. The day before the young queens were due to emerge from their pupal cells we transferred them to an incubator at 35 °C and emerged them in individual glass vials. At one day of age we paint-marked the queens and introduced each of them into their own nucleus colony. The entrance of each hive was covered with a queen excluder – a grid that allows workers to exit and enter, but confines the larger queens within the hive.

extract_protocol:
Head capsules were removed and brains were dissected over dry ice. Brains were placed individually in Trizol and macerated to breakdown tissue. After addition of chloroform, samples were briefly vortexed and then centrifuged at 12000g for 15 min at 4 °C to generate an aqueous phase. After addition of isopropyl alcohol, the aqueous phase was again vortexed and centrifuged (10 min) to produce a pellet. The pellet was then washed with 75% ethanol prior to drying and redissolving in ddH2O. The dissolved RNA was treated with DNAse I buffer (Ambion) to remove gDNA contaminations, prior to centrifugation and collection of the aqueous phase. The RNA content of the sample and the purity of the extracts were assessed using a NanoDrop™ 1000 spectrophotometer (Thermo Scientific Inc., Bremen, Germany).
HiSeq Sequencing Kit Trueseq v3 - library construction performed at the Illumina facility following standard protocols

treatment_protocol: When the queens were 6 days old we randomly assigned the twenty queens to one of three treatments (see above). All queens were harvested when they were 8 days old, at the same time of day (15:00 h), directly into liquid nitrogen and then stored at -80 °C.

value: brain

tag: developmental stage

value: adult

tag: caste

value: queen

value: ligustica

value: control


title: virgin_4


title: 4T1 Vector - sample 9 - RIP

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

data_processing:
Trim adaptor sequences and trailing Ns; in-house perl script
Merge to unique reads; in-house perl script
Build sequence database; formatdb
Map to mm9 reference genome; bwa
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count matrix in text tab-delimited file

source_name: 4T1 RNA immunoprecipitated with M2 FLAG antibody

growth_protocol: 4T1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco®) supplemented with L-Glutamate (Gibco®), 9% fetal bovine serum (FBS) (Gemini BioProducts), and 1% Penicillin and Streptomycin (P/S) (Gemini BioProducts).

extract_protocol:
4T1 cells expressing 8166-M24-658 control vector or FLAG-CNOT7 constructs were grown to ~85% confluence in ten 15cm culture plates. Cells were then rinsed with 15mL ice cold sterile PBS, scraped off, pelleted (~1mL pellet), and snap frozen in liquid nitrogen. Cells were thawed on ice and lysed in 3.5mL lysis buffer (100mM NaCl, 5mM MgCl2, 10mM HEPES (pH 7.3), 0.5% NP40, 200 units RNasin (Promega), Protease inhibitor cocktail (Roche)). The resulting 4mL of cell lysate was spun down twice at 21,000*g for 20 minutes at 4˚C. 40uL of lysate was saved 1% input to confirm immunoprecipitation. 200uL of lysate was saved for 5% RNA-seq input and was purified by TriPure (Roche) RNA extraction. 25uL beads per 1mL lysate of Protein G Dynabeads® were blocked with 1mL 0.5% BSA in PBS at room temperature for 20 minutes then washed twice with 1mL NT2 wash buffer (50mM Tris-HCl (pH 7.4), 150mM NaCl, 1mM MgCl2, 0.05% NP40). 24ug antibody was added to each sample and incubated at 4˚C overnight then beads were added to each sample and rotated for 30 minutes at room temperature. Beads were washed four times in 1mL NT2 buffer. Eighty five percent of beads were subjected to RNA extraction with TriPure. Protein from the remaining 15% of beads was eluted with Laemli buffer to confirm immunoprecipitation.
Library preparation was performed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® with NEBNext® multiplexing oligos using manufacturer’s protocol.  RNA sequencing was conducted on the Illumina® HiSeq 2500.

treatment_protocol: As this was a native RIP protocol, cell were not pretreated prior to the initiation of RIP.

value: mammary gland

value: 4T1 mammary tumor cell line

tag: cells expressing

value: 8166-M24-658 control vector

tag: rip antibody

value: M2 FLAG antibody


title: Schizont_H3K4me2

description: Chromatin IP using specific antibody


title: Trophs_H3K4me2

description: Chromatin IP using specific antibody


title: Rings_H3K4me2

description: Chromatin IP using specific antibody


title: 4T1 Vector - sample 9 - input

source_name: 4T1 cell lysate rRNA-depleted transcriptome


title: 4T1 Vector - sample 8 - RIP


title: CO2_7

description: CO2-treated queens were subjected to 10 min of CO2-narcosis on day 6 and on day 7. The seven caged queens were placed in a zip-lock plastic bag, which was then flushed with compressed CO2 until all queens were completely immobile, and sealed for 10 min. Queens were released in their individual colonies after treatment on both days.

tag: age

value: double narcosis with carbon dioxide


title: virgin_1br


title: Schizont_H3K4me3

description: Chromatin IP using specific antibody


title: 4T1 Vector - sample 7 - RIP


title: CO2_5


title: virgin_2


title: Trophs_H3K4me1

description: Chromatin IP using specific antibody

value: Trophs


title: Rings_H3K4me3

description: Chromatin IP using specific antibody


title: Rings_H3K4me1

description: Chromatin IP using specific antibody


title: Schizont_H3K4me1

description: Chromatin IP using specific antibody


title: mated_1br

description: Mated queens were queens that successfully participated in a mating flight. Early afternoon of the 6th day, we removed the queen excluders, and then monitored the entrances until mating flights with successful mating (as indicated by a mating plug) were observed.

value: naturally mated


title: 4T1 Vector - sample 6 - RIP


title: 4T1 Vector - sample 6 - input


title: CO2_2br


title: 77_MNase-1

description: Biological replicate 1

organism: Saccharomyces cerevisiae

source_name: nucleosome core particles (MNase)

tag: strain name

tag: genotype/variation

value: wild type

tag: genotype

value: MATa can1-100 his3-11,15 leu2-3,112 lys2-delta trp1-1 ura3-1

tag: mnase or exoiii

value: MNase limit digest


title: 4T1 Vector - sample 8 - input

tag: strain

tag: tissue