title: FAIRE_jurkat_re-stim_rottlerin

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description: Jurkat cells pre-treated with rottlerin (15uM, Calbiochem 1h), stimulated for 4h with PMA and Ionomycin and then washed and cultured for 1 day and restimulated with PMA and Ionomycin for 2 h.

data_processing:
Reads were stripped of adapter sequences with CutAdapt -m 10
mapped to the human (Hg19) genome with global alignment in Bowtie2  (only uniquely mapped reads used).
duplicate reads were removed with Picard.
Areas of enrichment in the DMSO FAIRE samples of the compared to the total input sample were determined using MACS2 with the Broad option and using a q value cut-off of <= 0.05 .
bedGraph files from HTSEQ, reads extended 200bp.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files show tag densities for the different cell treatments for FAIRE and Total Input (TI). Bed files are peaks for FAIRE against TI.

source_name: Jurkat cell line, Rottlerin, prestimulation and PMA and Ionomycin

growth_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete  RPMI medium with FCS

extract_protocol:
Cells were fixed in paraformaldehyde (1%) for 10 minutes, treated with glycine (0.125M, 10 min) and then lysed in SDS-buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-Cl at pH 8.0, 1 mM EDTA). Samples were sonicated (Time: 15min; Pulse: ON 5s, OFF 15s; Power: 5, Watt: 90~100) and subjected to phenol-chloroform extraction (equal volume of phenol-chloroform (Sigma  phenol, chloroform, and isoamyl alcohol 25:24:1 saturated with 10 mM Tris at pH 8.0, 1 mM EDTA), before reverse-crosslinking.
50ng of FAIRE DNA, and the corresponding total input (TI), were used to prepare the FAIRE-seq DNA library using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (New England BioLabs Inc, NEB#E6240L) according to the manufacturer’s instructions. FAIRE-DNA size was selected with AMPure XP beads (Beckman Coulter, Inc., Part #: A63881). The selected DNA was repaired with NEBNext End Repair Enzyme Mix and Buffer, followed by treatment with Klenow fragment to generate “A” base overhangs. Subsequent adaptor ligation of the dA-tailed DNA was performed with 1.5μM NEBNext adaptor primers, Quick Ligation Reaction Buffer, and Quick T4 DNA ligase. AMPure beads were used to isolate library fragments ranging between 175 and 225bp in size and the purified DNA was combined with the NEBNext High-Fidelity 2X PCR Master mix, 25μM Universal PCR primer, and 25μM index primer for multiplexing purposes (New England BioLabs Inc, NEBNext® Multiplex Oligos for Illumina®, NEB#E7335L). A total of 15 cycles were used for PCR amplification of the adaptor-ligated DNA. The resultant library was subjected to DNA purification with AMPure beads. The quality of the FAIRE-DNA library was assessed on a Bioanalyzer.

treatment_protocol: The Jurkat T cell line was pre-treated with with rottlerin (15uM, Calbiochem 1h) and was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting. After1 day of resting cells were re-stimulated with PMA and calcium ionophore.

tag: cell line

value: Jurkat

tag: drug

value: rottlerin


title: FAIRE_jurkat_re-stim

status: Public on Mar 22 2017

type: SRA

country: Australia

description: Jurkat cells pre-treated with DMSO, stimulated for 4h with PMA and Ionomycin and then washed and cultured for 1 day and restimulated with PMA and Ionomycin for 2 h.

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Jurkat cell line, DMSO, prestimulation and PMA and Ionomycin

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting. After1 day of resting cells were re-stimulated with PMA and calcium ionophore.

tag: treatment

value: DMSO


title: FAIRE_jurkat_stim

description: Jurkat cells pre-treated with DMSO stimulated for 4h with PMA and Ionomycin

source_name: Jurkat cell line, DMSO, PMA and Ionomycin

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).

value: DMSO, PMA and Ionomycin


title: FAIRE_jurkat_resting

description: Jurkat cells pre-treated with DMSO stimulated for 4h with PMA and Ionomycin and then washed and cultured for 1 day.

source_name: Jurkat cell line, DMSO, prestimulation

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting.

value: DMSO, prestimulation


title: FAIRE_jurkat_resting_rottlerin

description: Jurkat cells pre-treated with rottlerin (15uM, Calbiochem 1h) stimulated for 4h with PMA and Ionomycin and then washed and cultured for 1 day.

source_name: Jurkat cell line, Rottlerin, prestimulation

treatment_protocol: The Jurkat T cell line was pre-treated with with rottlerin (15uM, Calbiochem 1h) and was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting.

value: Rottlerin, prestimulation


title: genomic_jurkat_TI

description: This sample is an equal mixture of total input from Jurkat cells unstimulated and stimulated with PMA and Ionomycin

source_name: Jurkat cell line, total input (TI)

treatment_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete  RPMI medium with DMSO


title: FAIRE_jurkat_stim_rottlerin

description: Jurkat cells pre-treated with rottlerin (15uM, Calbiochem 1h) stimulated for 4h with PMA and Ionomycin

source_name: Jurkat cell line, Rottlerin, PMA and Ionomycin

treatment_protocol: The Jurkat T cell line was pre-treated with with rottlerin (15uM, Calbiochem 1h) and activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).

value: Rottlerin, PMA and Ionomycin


title: FAIRE_jurkat_nonstim_rottlerin

description: Jurkat cells pre-treated with rottlerin (15uM, Calbiochem 1h).

source_name: Jurkat cell line, Rottlerin

treatment_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete  RPMI medium with rottlerin(15uM, Calbiochem 1h).

value: Rottlerin


title: Input_i75

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

country: USA

institute: San Diego Biomedical Research Institute

description: Background control experiment 1

data_processing:
Sequence Analysis - The 50-nt and 75-nt sequence reads identified using Illumina’s Hi-Seq and NextSeq, respectively, were mapped to the genome using the BWA algorithm with default settings.
The ChIP DNA was processed into an Illumina ChIP-Seq library and sequenced to generate >2 million reads, which were aligned to the M.mulatta genome annotation (MacaM/Oct 2014 assembly) and 6.2 million unique aligns (removed duplicates) were obtained
A signal map showing fragment densities along the genome was visualized in the Integrated Genome Browser (IGB) and MACS peak finding was used to identify peaks. Control data was derived from 5.1 million (positive control) and 5.8 million (negative control) alignments. With default settings, 2141 Sirt-1 meaningful peaks genome-wide were identified.
Genome_build: MacaM/Oct 2014 assembly
Supplementary_files_format_and_content: Displays the fragment density for 32-nt bins along the genome and is used in peak finding using MACS.

organism: Macaca mulatta

source_name: Microglia

growth_protocol: Brain immune cells were isolated from all representative areas of the brain (free of meninges), by enzymatic digestion of minced tissue, followed by Percoll (Sigma-Aldrich) gradient.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of microglia chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and Sirt1 antibody (Millipore; lot number 2273971; 4ug per ChIP reaction) and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on on Illumina’s HiSeq2500 or NextSeq 500 (50 or 75 nt reads, respectively, single end). Reads were aligned to the Rhesus monkey genome (rheMac2) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p-value = 1e-7.

tag: pathology

value: Background control

tag: cell type

value: Brain tissue derived microglial cells

tag: chip antibody


title: FAIRE_jurkat_nonstim

description: Jurkat cells pre-treated with DMSO

source_name: Jurkat cell line, DMSO


title: Col-0 rep3

city: Guangzhou

first: Xuncheng

last: Liu

state: Guangdong

address: Xingke Road, Tianhe District

country: China

institute: South China Botanical Garden, Chinese Academy of Sciences

library_source: transcriptomic

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 the Arabidopsis genome TAIR10 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per  Million mapped reads (FPKM) were calculated using Cufflinks cuffdiff.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seeds in FR(Dark) conditions

growth_protocol: Arabidopsis plants were grown under long-day conditions (16 h WL/8 hdark) at 22 oC. Following seed harvesting, seeds were dried in an incubator at 22 oC for about 1 month prior to germination assays.

extract_protocol:
After FR treatment, the seeds were incubated in the dark at 22 oC for 12 h. Total RNA was extracted with TRIZOL Reagent (Invitrogen) according to the manufacture’s protocol.
For whole genomic transcriptome analysis, total RNA was extracted as described as above, and an mRNA-seq library was prepared by using an mRNA Seq Kit (Illumina).

treatment_protocol: After incubated in water for 1 h, seeds of Col and hda15-1 were irradiated under FR (3.82µmol m-2 s-1) for 5 min, and then kept in the dark for 12 h.

tag: ecotype

tag: genotype

value: wild type

value: FR(Dark) conditions

tag: tissue

value: seed


title: hda15-1 rep1


title: hda15-1 rep3


title: BM Derived Macrophages 1

city: Madison

first: Christian

last: Capitini

state: WI

address: 1111 Highland Ave, WIMR 4137

institute: University of Wisconsin

description:
RNAseq MEM-all the genes.xls
Group3-1675

data_processing:
Trimmomatic version 0.32; adapters:2:20:7:1:true, leading:5, trailing:5, slidingwindow:4:10, minlen:21
Log2 transformed FPKM (fragments per kilobase exon-model per million reads mapped) are used for downstream analyses
Expression quantification is done using Cufflinks24 (version 2.2.0).
Log2 transformed FPKM (fragments per kilobase exon-model per million reads mapped) are used for downstream analyses.
Genome_build: hg19

source_name: Human macrophage

growth_protocol: Macrophages (MØs) were isolated from PBMCs on Day +0. MSCs were cultured in alpha MEM media (Corning CellGro, Manassas, VA) supplemented with 10% heat inactivated FBS (Hyclone, Logan, UT), 100X L-Ala-L-Glutamine (Corning GlutaGro), and 100X NEAA (Corning) and frozen at passage 4 or 5.

extract_protocol:
On day +10, CD14+ cells were collected using Stem Pro Accutase cell detachment (Gibco Life Technologies) and re-sorted based on CD14 to eliminate the MSCs in the MEM cultures.
Libraries were prepared to a mean size of 300-500 base pairs and analyzed using the High Sensitivity DNA Kit (Agilent Technologies) with the Bioanalyzer.  Libraries were then diluted 1:10,000 and analyzed using the Kapa Library Quant Kit (Kapa Biosystems, Wilmington, MA) on the LightCycler96 (Roche Diagnostics, Indianapolis, IN).

treatment_protocol: On day +7, MØs were supplemented with fresh media or incubated with human BM-derived MSCs to obtain MEMs, at a ratio of 10: 1 of MØs:MSCs.

value: Macrophage


title: Col-0 rep1


title: Col-0 rep2


title: Rnf20

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Chromatin IP against Rnf20

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using BWA version 0.5.9-r16.
Peaks were called using MACS peak caller with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.

value: mouse embryonic stem cell

value: J1 ES cells containing BirA

value: streptavidin-conjugated beads


title: Pooled_14_input_Rh_i88

description: Background control experment 2


title: 208_Sirt1_Rh_i87

description: Uninfected Young experment 2

value: Uninfected Young

value: anti-Sirt-1 (Millipore; lot number 2273971; 4ug per ChIP reaction)


title: preseq_160min_plus_rep1

city: Cold Spring Harbor

first: Noah

middle: E

last: Dukler

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
nascent RNA
PRO-seq in K562 after 160 minutes of celastrol treatment with D. melanogaster spike in for normalization (plus strand)

data_processing:
All QC filtered reads were removed from each fastq file, then cutadapt (v1.9.1) was run with the following options: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 15
All reads were then trimmed to 34bp in length using fastx_timmer (v0.0.13.2) to avoid biasing read mapping away from gene promoters
The trimmed reads were then aligned to the joint hg19/bdgp6 genome using the STAR aligner (v2.4.0i)
Reads aligning to hg19 and bdgp6 were then separated and bigwigs were created by converting each read to a single count at its 5’ end.
Genome_build: hg19/bdgp6
Supplementary_files_format_and_content: Each count in the bigwig represents th 5' most base in the read which is the position of the last nucleotide incorporated by RNAP

growth_protocol: K562 cells were cultured at 37 °C in RPMI media (Gibco) containing 10% FBS (Gibco), Pen Strep (Gibco) and 2 mM L-Glutamine (Gibco). Biological replicate cell cultures were prepared as follows: after thawing K562 cells and seeding a fresh culture, cells were split into two separate flasks, which would remain separated through six passages and expansions until treatment and collection for preparation of PRO-seq libraries.  Cells from each expanded replicate were seeded onto six 30-mL dishes (one for each time point) at a density of 5x105 cells/mL and then incubated for an additional doubling cycle (~20 hrs).

extract_protocol: Samples were extracted and prepared for sequencing as in Mahat et al (2016, Nat. Protocols)

treatment_protocol: For treatments, fresh celastrol was dissolved in DMSO at a final concentration of 20 mM.  Celastrol-treated samples received celastrol (Sigma) at a final concentration of 3 μM, whereas untreated (0-minute) samples received an equivalent volume of DMSO.  Cells remained in culture dishes in the incubator during the time course. Time-course treatments were carried out in reverse order so that all samples would be collected at the same time (starting with 160-minute time point and ending with the untreated). Samples were then prepared for precision run-on reactions by subjecting cells to permeablizing conditions.  Briefly, cultures were spun down and resuspended in ice cold 1xPBS.  Samples were spun again and washed in 5 mL wash buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 150 mM sucrose; 5 mM MgCl2; 0.5 mM CaCl2; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche); 20 units RNase inhibitor (SUPERase In, Invitrogen)). Cell pellets were then resuspended in permeablization buffer (10 mM Tris-Cl, pH 7.5; 10 mM KCl; 250 mM sucrose; 5 mM MgCl2; 1 EGTA; 0.05% Tween-20; 0.1% NP40; 0.5 mM DTT; 1x Protease inhibitor cocktail (Roche); 20 units RNase inhibitor (SUPERase In, Invitrogen)) and left on ice for 5 minutes.  Cells were checked for penetration by trypan blue to assess permeability (~99% permeable).  Cells were then washed two times in 5 mL wash buffer before being resuspended in 200 μL storage buffer (50mM Tris-Cl, pH 8.3; 40% glycerol; 5 mM MgCl2; 0.1 mM EDTA; 0.5 mM DTT).  A one-to-fifty dilution was prepared using 2 μL of each sample and used to take OD600 measurements.  All samples were then diluted to an equal density (OD600 = 0.181) in a final volume of 110 μL of storage buffer. 5x104 pre-permeabilized S2 cells were then spiked in to each cell count-normalized sample before flash-freezing the permeablized cells and storing them at -80 °C.

value: blood

tag: cancer type

value: chronic myelogenous leukemia

tag: assay

value: PRO-seq


title: DRIP shSMN S9.6 rep2

status: Public on Mar 21 2017

city: Cambridge

first: John

last: Carulli

state: MA

address: 115 Broadway

department: Computational Biology and Genomics

institute: Biogen

data_processing:
Library strategy: DRIP-seq
Reads were mapped using Bowtie2 to the hg38 genome annotation.
Enriched DRIPseq regions were determined using MACS2, comparing S9.6 antibody enrichment to IgG enrichment for each respective set of samples.
Genome_build: mRNA-seq: Gencode M4
Genome_build: DRIP-seq: hg38
Supplementary_files_format_and_content: SMArescue_all_RSEM.genes.results.human_names_split.txt: count matrix
Supplementary_files_format_and_content: SMArescue_d20d30_DvsE_all_DESeqOutput.txt: expression matrix
Supplementary_files_format_and_content: SMArescueIJKvsE.DESeq2ContrastTest.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: hiPSC_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC-MN.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: shCtrlrep1_S96_vs_IgG_summits_win250rep2.bed: peak
Supplementary_files_format_and_content: shSMNrep1_S96_vs_IgG_summits_win250rep2.bed: peak

source_name: SHSY5Y cell line

growth_protocol: SH-SY5Y cells were maintained in Ham's F12:DMEM.

extract_protocol: DRIP was performed as described in Loomis et al. 2014, with the following changes.  Briefly, nucleic acids isolated from ~2x106 cells were digested with a restriction enzyme cocktail (50 units each of BsrGI, XbaI, EcoRI, HindIII, SspI) overnight at 37C in 1x NEB CutSmart buffer.  Digests were purified by phenol/chloroform extraction, and 8.8ug of digested DNA per cell culture condition were treated with 3ul RNase H overnight at 37C.  For each condition, 4.4ug of RNase H-treated or untreated DNA was immunoprecipitated with 10ug S9.6 antibody (Kerafast, Inc., #ENH001), washed 3x with IP buffer, eluted, treated with Proteinase K and phenol/chloroform extracted.  Resulting samples were sonicated using a Bioruptor Pico from Diagenode, with 11 cycles of 15sec ON/ 90sec OFF.  Fragments were prepared for sequencing using the NEBNext Ultra II Library Prep Kit for Illumina with barcodes for sample multiplexing.  Pooled libraries were sequenced on the Illumina NextSeq platform.

treatment_protocol: Chromatin was extracted from lentivirally-infected SH-SY5Y cells induced for 7 days with doxycycline

value: SHSY5Y cell line


title: preseq_0min_plus_rep1

description:
nascent RNA
PRO-seq in K562 with D. melanogaster spike in for normalization (plus strand)


title: DRIP shSMN S9.6 rep1


title: preseq_160min_plus_rep2


title: preseq_20min_plus_rep2

description:
nascent RNA
PRO-seq in K562 after 20 minutes of celastrol treatment with D. melanogaster spike in for normalization (plus strand)


title: preseq_10min_plus_rep2

description:
nascent RNA
PRO-seq in K562 after 10 minutes of celastrol treatment with D. melanogaster spike in for normalization (plus strand)


title: WT

city: Harbin

first: xinxin

last: yu

address: gongbin street

institute: northeast agricultural university

data_processing:
Raw sequencing reads of two samples were performed the following filtration using a stringent process and subsequent mapping to the genome. The adaptor contamination was removed, the reads were screened from the 3’ to 5’ to trim the bases with a quality score of Q<20 using5bp windows and the reads with final length less than 25bp were removed.
High quality reads of every sample were mapped to genome to get the abundance of transcripts using Bowtie/Tophat program. Those transcripts with no reads mapped in all two samples were considered error and removed.
The R package DESeq was performed to get the normalized signal for each gene with the the number of reads mapped to each gene as input.
Genome_build: TAIR10.18
Supplementary_files_format_and_content: genes exression values generated by DESeq for each sample

source_name: WT seedling

extract_protocol:
Samples harvested were immediately frozen in liquid nitrogen and total RNA of each sample was isolated using E.Z.N.A. Plant RNA Kit(OMEGA bio-tek, GA) according to the instructions from the manufacturer.
Illumina Hiseq 2000 library construction was performed according to the manufacturer’s instructions (Illumia, San Diego, CA).

value: control

tag: strain

value: Columbia

value: seedling

tag: age

value: post germination day 10


title: DRIP shCtrl S9.6 rep2


title: preseq_10min_plus_rep1


title: WT+flg22

source_name: WT+flg22  seedling


title: SIV_Sirt1_Rh_i84

description: SIV Young  experment 2

value: SIV positive Young

value: Brain tissue derived microglial cells


title: preseq_60min_plus_rep2

description:
nascent RNA
PRO-seq in K562 after 60 minutes of celastrol treatment with D. melanogaster spike in for normalization (plus strand)


title: preseq_0min_plus_rep2

description:
nascent RNA
PRO-seq in K562 with D. melanogaster spike in for normalization  (plus strand)


title: DRIP shCtrl S9.6 rep1


title: preseq_20min_plus_rep1


title: hda15-1 rep2

value: FR(Dark) conditions

value: seed


title: DRIP shSMN IgG rep1


title: DRIP shCtrl IgG rep1


title: preseq_40min_plus_rep2

description:
nascent RNA
PRO-seq in K562 after 40 minutes of celastrol treatment with D. melanogaster spike in for normalization (plus strand)


title: preseq_40min_plus_rep1


title: preseq_60min_plus_rep1


title: OLD_Sirt1_Rh_i86

description: Uninfected Old experment 2

value: Uninfected Old


title: DRIP shCtrl Input rep2


title: DRIP shSMN Input rep1


title: DRIP shSMN Input rep2


title: siControl, replicate b

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
siControl, replicate b
NCb

data_processing:
RNA-Seq data analyzing was done with rsem(ver. 1.2.3) and Hg19 genome with UCSC known gene set.
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files counts for genes estimated by RSEM

growth_protocol: Human glibolastoma A172 cells were cultured in DMEM with 10% FBS

extract_protocol:
Cells were harvested and total RNA were extracted by miRNeasy kit (QIAGEN).
Preparation of RNA-seq samples was carried out using SENSE mRNA library prep kit V2 (Lexogen), according to manufacture’s protocol.

treatment_protocol: A172 cells are transfected with siControl or siADAR1 on the first day, and next day HA-STAU1plasmid was transfected

value: human glibolastoma cells

tag: transfected with

value: siControl

tag: replicate

value: b


title: siADAR1, replicate a

description:
siADAR1, replicate a
A1a

value: a


title: DRIP shCtrl IgG rep2


title: siADAR1, replicate b

description:
siADAR1, replicate b
A1b


title: siADAR1 and siStaufen1, replicate b

description:
siADAR1 and siStaufen1, replicate b
A1S1b

source_name: A172_siADAR1 and siStaufen1

value: siADAR1 and siStaufen1


title: siADAR1 and siStaufen1, replicate a

description:
siADAR1 and siStaufen1, replicate a
A1S1a


title: DRIP shSMN IgG rep2


title: DRIP shCtrl Input rep1


title: siControl, replicate a

description:
siControl, replicate a
NCa


title: IB_sRNA_rPTG_mPOD_U9

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG

data_processing:
Illumina GA Iix/HiSeq 2000 standard base-calling
RNAworld in-house allingment and annotation pipeline (see PMID: 22836126)
Genome_build: hg19/mmu9/rn4
Supplementary_files_format_and_content: count tables in xlsx format separate for each species; 3 tabs in each file: mature/star miRNA counts, sequence family counts, precursor cluster counts

organism: Rattus norvegicus

source_name: parathyroid

extract_protocol:
TRIzol-based (see PMID: 24489795)
ligation/gel-based small RNA cDNA library (see PMID: 24489795)

value: parathyroid

tag: patient/animal id

tag: parathyroid pathology

tag: barcode


title: IB_sRNA_rPTG_mPOD_C1

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG

value: normal


title: IB_sRNA_rPTG_mPOD_C5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rPTG_mPOD_U6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rat_PT14

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rat_PT13

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rPTG_mPOD_C4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rat_PT12


title: IB_sRNA_rPTG_mPOD_C3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rPTG_mPOD_U8


title: IB_sRNA_rPTG_mPOD_U7


title: IB_sRNA_rat_8wPT1

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rat_PT11


title: IB_sRNA_rPTG_mPOD_U10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rPTG_mPOD_C2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_rat_PT4


title: IB_sRNA_rat_PT3


title: IB_sRNA_rat_PT2


title: IB_sRNA_rat_PT1


title: IB_sRNA_rat_8wPT2

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG


title: MSC 258 CytoD

city: Seattle

first: Pritha

last: Chanana

state: WA

address: 1100 Fairview Ave N, PO Box 19024

department: Shared Resources

institute: Fred Hutchinson Cancer Center

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample
Supplementary_files_format_and_content: file1 - ctrl & cytoD for samples 211, 283; file2 - ctrl & cytoD for sample 258

source_name: mesenchymal stem cells

extract_protocol: RNA for RNA-Seq was isolated using the miRNeasy mini kit (Catalog # 217004, Qiagen).

value: adipose derived mesenchymal stem cells

tag: passages


title: MSC 283 Ctrl


title: MSC 211 Ctrl


title: MSC 283 CytoD


title: act-A-iTr1 rep2

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

data_processing:
For each sequenced file, quality control was assessed, and when required illumina adapters were clipped, and bases with quality less than 10 were trimmed from the 3' end of the reads, allowing reads of a minimum length of 20 bases. The high quality reads were then aligned against the UCSC hg19 human reference genome build, using tophat2 with default settings and keeping only uniquely aligned reads.
Alignments were  processed for differential expression analysis using the metaseqR Bioconductor package. Read counts were calculated on the Ensembl exon set version 69, and effective library sizes were estimated to normalize the counts table (DESeq method). For differential expression statistical testing, DESeq and edgeR Bioconductor packages were combined via the metaseqR package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file includes the normalized counts information for each sample, for each Ensembl exon model (version 69)

source_name: Human peripheral blood

growth_protocol: Peripheral blood mononuclear cells were obtained by Histopaque density-gradient centrifugation. Human naive CD4+ T cells were isolated using magnetic microbeads (CD4+CD25-CD45RO-) or by sorting with a FACS Aria cell sorter.

extract_protocol:
Total RNA was isolated in TRI Reagent according to the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Human naive CD4+ T cells were stimulated with allergen-loaded, mitomycin-treated APCs in the presence of PBS (Tconv) or activin-A (act-A-iTr1) for 3 days.

value: peripheral blood

value: CD4+ T naive cells


title: act-A-iTr1 rep1


title: MSC 211 CytoD


title: Tconv rep2


title: MSC 258 Ctrl


title: mRNA hiPSC-MN shSMN-2 rep1

description:
shSMN_2_R2_hiPSC_MN
mRNA-Seq

data_processing:
RNAseq reads were mapped with the STAR algorithm, aligning to the Gencode version M4 transcript annotation for mouse spinal cord RNA and the hg38 annotation for SH-SY5Y cells and hiPSC-MNs.  We used parameters  --alignIntronMin 20  --alignIntronMax 1000000  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05  --outFilterMultimapNmax 20  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --alignMatesGapMax 1000000  --sjdbOverhang 49.  Aligned reads were assigned to transcripts from the annotations described above using RSEM, and resulting raw read counts were input into DESeq2 for differential gene expression analysis using default parameters.
For general splicing analysis, BAM files produced from STAR mapping were input into rMATS, using the Gencode version M4 transcript annotation for mouse spinal cord RNA and the hg38 annotation for SH-SY5Y and hiPSC-MN RNA samples.  For detection of intron retention, novel human and mouse annotations were generated containing all consecutive spliced and unspliced exon-intron-exon triads from hg38 and Gencode vM4.  To measure retention of U12 introns, a second set of annotations was generated by filtering this novel set of annotations for introns that overlapped exactly with human and mouse U12 introns extracted from U12DB.  These annotations were used to call intron retention in mouse spinal cord, SH-SY5Y, and hiPSC-MN RNAseq datasets using rMATS.  An FDR cutoff of 0.05 was used to define significantly differentially-spliced regions.
Genome_build: mRNA-seq: Gencode M4
Genome_build: DRIP-seq: hg38
Supplementary_files_format_and_content: SMArescue_all_RSEM.genes.results.human_names_split.txt: count matrix
Supplementary_files_format_and_content: SMArescue_d20d30_DvsE_all_DESeqOutput.txt: expression matrix
Supplementary_files_format_and_content: SMArescueIJKvsE.DESeq2ContrastTest.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: SHSY5Y.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: hiPSC_shSMN-1_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC_shSMN-2_vs_shCtrl_FDR0.05.sepnames.txt: expression matrix
Supplementary_files_format_and_content: hiPSC-MN.RSEM.genes.results.human_names.txt: count matrix
Supplementary_files_format_and_content: shCtrlrep1_S96_vs_IgG_summits_win250rep2.bed: peak
Supplementary_files_format_and_content: shSMNrep1_S96_vs_IgG_summits_win250rep2.bed: peak

molecule: polyA RNA

source_name: induced pluripotent cell derived motor neurons

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were derived from lymphoblastoid cell lines (Coriell Cell Repository) with Epi5 Episomal iPSC reprogramming kit (Life Technologies). iPSCs were derived and propagated in mTeSR media (Stem Cell Technologies) on matrigel (life technologies).  The pluripotency of the hiPSCs was confirmed by staining for pluripotency markers and in vitro differentiation into three germ layers. Differentiation of hiPSCs into motor neuron cultures was carried out as previously described  (Maury et al., 2014), with slight modifications. Briefly,  iPSC colonies were dissociated with EDTA and placed in suspension in low adhesion flasks (Corning) to form embryoid bodies in media consisting of DMEM/F12/ Neurobasal medium (Life Technologies), N2 supplement (life technologies), B27 supplement (Life Technologies), ascorbic acid (20 uM), β-mercaptoethanol (0.055 mM). Media was changed every other day and small molecules were added for: neuronal patterning (0.2 uM LDN, 40 uM SB431542, 3uM CHIR 99021); motor neuron induction (1 uM RA, 0.5 uM SAG, 10uM DAPT). On day 14, EBs were dissociated into single cells with papain and plated on matrigel or poly D-Lysin/Laminin coated plates in media containing neurotrophic factors (20 ng/ml BDNF, 10 ng/ml GDNF, 10 ng/ml CNTF).

extract_protocol: 50-500ng DNase-treated total RNA was used to construct libraries using Illumina TruSeq Stranded mRNA HT Sample  Prep Kit (Cat #RS-122-2103) with barcodes for sample multiplexing. The products were purified and enriched with PCR for 13 cycles to create final cDNA library. Libraries were quantified using HT DNA reagent kit (Part Number 760435, Caliper Life Sciences, Hopkinton, MA) using a LabChip GX (Perkin Elmer,Waltham,MA). Multiplexed libraries were equimolarly pooled, diluted to 2nM pool for final analysis on Agilent High sensitivity DNA kit to run on one rapid flowcell per lane and sequenced using 2x50 ntd paired end runs of the Illumina HiSeq 2500 platform.


title: mRNA hiPSC-MN shSMN-1 rep2

description:
shSMN_1_R3_hiPSC_MN
mRNA-Seq

value: induced pluripotent cell derived motor neurons


title: mRNA hiPSC-MN shSMN-1 rep1

description:
shSMN_1_R1_hiPSC_MN
mRNA-Seq


title: Tconv rep1


title: mRNA hiPSC-MN shCtrl rep3

description:
shCtrl_R3_hiPSC_MN
mRNA-Seq


title: mRNA hiPSC-MN shCtrl rep1

description:
shCtrl_R1_hiPSC_MN
mRNA-Seq


title: mRNA SHSY5Y shSMN-1 rep2

description:
shSMN_1_R2_SHSY5Y
mRNA-Seq

treatment_protocol: Total RNA from lentivirally-infected SH-SY5Y cells induced for 7 days with doxycycline, or lentivirally-infected hiPSC-MN cells induced for 5 days with doxycycline was extracted using Trizol  (ThermoFisher, #15596026) and Direct-zol RNA MiniPrep Kit (Zymo Research, #R2050).

value: SHSY5Y cell line


title: mRNA SHSY5Y shSMN-1 rep1

description:
shSMN_1_R1_SHSY5Y
mRNA-Seq


title: mRNA SHSY5Y shSMN-2 rep1

description:
shSMN_2_R1_SHSY5Y
mRNA-Seq


title: mRNA SHSY5Y shSMN-2 rep3

description:
shSMN_2_R3_SHSY5Y
mRNA-Seq


title: mRNA SHSY5Y shSMN-1 rep3

description:
shSMN_1_R3_SHSY5Y
mRNA-Seq


title: mRNA hiPSC-MN shSMN-2 rep2

description:
shSMN_2_R3_hiPSC_MN
mRNA-Seq


title: mRNA SHSY5Y shCtrl rep3

description:
shCtrl_R3_SHSY5Y
mRNA-Seq


title: mRNA SHSY5Y shCtrl rep2

description:
shCtrl_R2_SHSY5Y
mRNA-Seq


title: mRNA SHSY5Y shCtrl rep1

description:
shCtrl_R1_SHSY5Y
mRNA-Seq


title: mRNA hiPSC-MN shCtrl rep2

description:
shCtrl_R2_hiPSC_MN
mRNA-Seq


title: hRWDD3_PTBP2

city: Rotterdam

first: Harmen

middle: Jan George

last: van de Werken

address: Wytemaweg 80

department: Urology

country: Netherlands

institute: Erasmus MC

description: 4C-seq  in RWDD3 - PTBP2 region on hHOR

data_processing:
The sample was sequenced for 36bp or 51 bp on a HiSeq 2000
Mapping and filtering of the sequence reads was done as previously described (Werken et al., 2012,Methods Enzymol. ) with the restriction enzymes HindII and DpnII
Artificial HAC chromosomes were added to the reference genomes before mapping.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located). Scores represent the number of in calculated by a running window approach

source_name: Tig3 cell line

growth_protocol: Both the human (Tig3) and the mouse fibroblasts were grown in DMEM/10% FCS

extract_protocol:
4C templates was prepared as described previously (Splinter et al. 2011 van de Werken 2012 Nat Method). Chromatin was cross-linked with 2% formaldehyde in 10 ml PBS with 10% FCS for 10 min at room temperature, nuclei were isolated in 10ml cold lysis buffer for 10min, and cross-linked DNA was digested with HindIII. Digestion was followed by proximity ligation, removal of cross-links, a secondary restriction digestion with DpnII and a second proximity ligation.
200 ng of the resulting 4C template was used for the subsequent PCR reaction using Expand Long Template Polymerase (Roche). The PCR products were purified using the High Pure PCR Product Purification Kit (Roche) and the QIAquick PCR purification kit (Qiagen).

treatment_protocol: Cells were cross-linked using 2% formaldehyde for 10 minutes at room temperature in 10%FCS/PBS

value: fibroblasts

tag: bait


title: hPTBP2

description: 4C-seq of PTBP2 on hHOR


title: hBCAR3

description: 4C-seq of BCAR3 on hHOR


title: hDPYD

description: 4C-seq of DPYD on hHOR


title: hALG14

description: 4C-seq of ALG14 on hHOR


title: hABCD3

description: 4C-seq of ABCD3 on human HAC Orthology Region (hHOR)


title: IM_sRNA_PT15

description: 3' adapter sequence: TAGGATCGTATGCCGTCTTCTGCTTG

source_name: thyroid-paraffin

value: thyroid


title: IM_sRNA_PT17

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT16

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT19


title: IM_sRNA_PT18


title: mRNA SHSY5Y shSMN-2 rep2

description:
shSMN_2_R2_SHSY5Y
mRNA-Seq


title: IM_sRNA_PT14

description: 3' adapter sequence: TAGAGTCGTATGCCGTCTTCTGCTTG

source_name: parathyroid-paraffin

value: hyperplastic-ESRD


title: IM_sRNA_PT20

description: 3' adapter sequence: TTGGTTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT13

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT12

description: 3' adapter sequence: TAACGTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT11

description: 3' adapter sequence: TTAAGTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT8

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT9

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT1

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG


title: clfswn H3AK27me3 7DAG rep2

city: Sevilla

first: Myriam

last: Calonje

address: Americo Vespucio 49

country: Spain

institute: Institute for Plant Biochemistry and Photosynthesis (CSIC -  University of Sevilla)

description: clfswn H3K27me3 7DAG rep2

data_processing:
Quality control was performed using the software package FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using bowtie with parameters -v 2 --best --strata -m 1 (http://bowtie-bio.sourceforge.net/index.shtml)
Peak calling was performed using MACS2 with default parameters (https://github.com/taoliu/MACS)
Peak annotation was performed using PeakAnalyzer with NDG criterion (http://www.bioinformatics.org/peakanalyzer/wiki/)
Conversion to BED format and manipulation of BED files were carried out using BEDTools (http://bedtools.readthedocs.io/en/latest/)
RPKM and RPM normalizations were performed using the deepTools utility bamCoverage with a bin size of 10 (https://deeptools.readthedocs.io/en/latest/)
Heatmaps were generated using the Bioconductor R package ChIPpeakAnno.
Quantitative comparison between ChIP-seq samples was performed using a variant of MAnorm (http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm) that restricts the set of common peaks serving as a reference to build the rescaling model for normalization to those commons peaks exhibiting a change of ± 20% in raw read count when compared to WT. For the comparison between atbm1a/b/c and the WT we additionally constrained the set of peaks used for normalization to those and whose associated genes did not get differentially expressed.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files including peaks coordinates, raw read counts, rescaled M value, rescaled A value and minus log10 p value.

source_name: Seedlings

growth_protocol: Arabidopsis Col-0 wild type (WT), atbmi1abc, clfswn and lhp1 mutants were grown under long-day conditions at 21 °C on MS agar plates containing 1.5% sucrose and 0.8% agar for seven days.

extract_protocol:
Chromatin was extracted from 7-day old whole seedlings (150 seedlings) as previously described by Reimer & Turck 2010 Methods Mol. Biol. Clifton NJ 631, 139–160 . Anti-H2Aub (Cell signaling technology, 8240S) and anti-H3K27me3 (Diagenode, C15410069) antibodies were used for chromatin immunoprecipitation.
All libraries were prepared by the Ovation® Ultralow Library Systems (NuGEN) following manufacturer’s instruction using 80% of a typical ChIP as starting material. After amplification for 16 PCR cycles, DNA of a size range between (200-500bp) was purified from an agarose gel. Amplification was confirmed by testing an aliquot of the library before and after amplification by quantitative PCR.

value: clf28/swn7 double mutant

value: whole seedling


title: IM_sRNA_PT4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT7

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: IM_sRNA_PT2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: clfswn H3AK27me3 7DAG rep1

description: clfswn H3K27me3 7DAG rep1


title: Col-0 H3K27me3 7DAG rep4

description: WT control of clfswn H3K27me3 7DAG rep2

value: Wild Type


title: input DNA

description:
input DNA
processed data file: none

growth_protocol: Arabidopsis Col-0 wild type (WT), atbmi1abc, clfsw and lhp1 mutants were grown under long-day conditions at 21 °C on MS agar plates containing 1.5% sucrose and 0.8% agar for seven days.


title: Col-0 H3K27me3 7DAG rep3

description: WT control of clfswn H3K27me3 7DAG rep1


title: Col-0 H2AK121ub 7DAG rep6

description:
WT control of lhp1 H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_lhp1_vs_col0_rep2.txt


title: lhp1 H2AK121ub 7DAG rep2

description:
lhp1 H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_lhp1_vs_col0_rep2.txt

value: lhp1 mutant


title: lhp1 H2AK121ub 7DAG rep1

description:
lhp1 H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_lhp1_vs_col0_rep1.txt


title: clfswn H2AK121ub 7DAG rep2

description:
clfswn H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_clfswn_vs_col0_rep2.txt


title: Col-0 H3K27me3 7DAG rep2

description:
WT control of atbmi1abc H3K27me3 7DAG rep2
processed data file: normalized_results_h3k27me3_atbmi1abc_vs_col0_rep2.txt


title: clfswn H2AK121ub 7DAG rep1

description:
clfswn H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_clfswn_vs_col0_rep1.txt


title: Col-0 H2AK121ub 7DAG rep4

description:
WT control of clfswn H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_clfswn_vs_col0_rep2.txt


title: Col-0 H2AK121ub 7DAG rep3

description:
WT control of clfswn H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_clfswn_vs_col0_rep1.txt


title: atbmi1abc H3K27me3 7DAG rep2

description:
atbmi1abc H3K27me3 7DAG rep2
processed data file: normalized_results_h3k27me3_atbmi1abc_vs_col0_rep2.txt

value: atbmi1a/b/c triple mutant


title: IM_sRNA_PT10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG


title: atbmi1abc H3K27me3 7DAG rep1

description:
atbmi1abc H3K27me3 7DAG rep1
processed data file: normalized_results_h3k27me3_atbmi1abc_vs_col0_rep1.txt


title: IM_sRNA_PT5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG


title: Col-0 H2AK121ub 7DAG rep2

description:
WT control of atbmi1abc H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_atbmi1abc_vs_col0_rep2.txt


title: atbmi1abc H2AK121ub 7DAG rep2

description:
atbmi1abc H2AK121ub 7DAG rep2
processed data file: normalized_results_h2aub_atbmi1abc_vs_col0_rep2.txt


title: TypeII KRasEtv wt SAM19521963

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

description:
treatment_name: TypeII KRasEtv wt
sample_id: SAM19521963

data_processing: Reads were aligned to the mm9.IGIS2.3 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from lung

extract_protocol: Type II cells were isolated (EpCAM+;CD24-;CD45-;CD31-;Pdpn-) from the lung of the following mutant mice: (1) KRaswt/d12;RosaCreERT2 n=4 (2) KRaswt/d12; Etv5loxp/loxp;RosaCreERT2 n=4 (3) KRaswt/d12; Etv4KO/KO; Etv5loxp/loxp;RosaCreERT2 n=4 The cells were cultured in 100% matrigel with 100nM 4OHT in BEGM medium right after FACS for four days (medium change every other day), then in BEGM without 4OHT for another one day. The cells were then harvested and RNAs were extracted by RNeasy micro kit.

value: alveolar Type II cells

value: KRasEtv wt


title: Col-0 H2AK121ub 7DAG rep1

description:
WT control of atbmi1abc H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_atbmi1abc_vs_col0_rep1.txt


title: atbmi1abc H2AK121ub 7DAG rep1

description:
atbmi1abc H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_atbmi1abc_vs_col0_rep1.txt


title: TC Skip ASO d30 rep5

data_processing:
RNAseq reads were mapped with the STAR algorithm, aligning to the Gencode version M4 transcript annotation for mouse spinal cord RNA and the hg38 annotation for SH-SY5Y cells and hiPSC-MNs.  We used parameters  --alignIntronMin 20  --alignIntronMax 1000000  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05  --outFilterMultimapNmax 20  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --alignMatesGapMax 1000000  --sjdbOverhang 49.  Aligned reads were assigned to transcripts from the annotations described above using RSEM, and resulting raw read counts were input into DESeq2 for differential gene expression analysis using default parameters.
For general splicing analysis, BAM files produced from STAR mapping were input into rMATS, using the Gencode version M4 transcript annotation for mouse spinal cord RNA and the hg38 annotation for SH-SY5Y and hiPSC-MN RNA samples.  For detection of intron retention, novel human and mouse annotations were generated containing all consecutive spliced and unspliced exon-intron-exon triads from hg38 and Gencode vM4.  To measure retention of U12 introns, a second set of annotations was generated by filtering this novel set of annotations for introns that overlapped exactly with human and mouse U12 introns extracted from U12DB.  These annotations were used to call intron retention in mouse spinal cord, SH-SY5Y, and hiPSC-MN RNAseq datasets using rMATS.  An FDR cutoff of 0.05 was used to define significantly differentially-spliced regions.
genome_build: Gencode M4

source_name: spinal cord

growth_protocol: SMA mice were generated as described in Staropoli et al., 2015.

treatment_protocol: Mice were treated with PBS or Control or SMN ASO at d0 and sacrificed at d20 or d30.

value: spinal cord


title: TC Skip ASO d30 rep6


title: TC Skip ASO d30 rep2


title: TC Skip ASO d30 rep7


title: TypeII KRasEtv wt SAM19521961

description:
treatment_name: TypeII KRasEtv wt
sample_id: SAM19521961


title: TC Skip ASO d30 rep3


title: TypeII KRas;Etv5KO SAM19521959

description:
treatment_name: TypeII KRas;Etv5KO
sample_id: SAM19521959


title: Col-0 H2AK121ub 7DAG rep5

description:
WT control of lhp1 H2AK121ub 7DAG rep1
processed data file: normalized_results_h2aub_lhp1_vs_col0_rep1.txt


title: TC Skip ASO d30 rep4


title: abc_7DAG_1

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (http://cole-trapnell-lab.github.io/cufflinks/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Cufflinks and Cuffdiff
Subsequent data analysis and visualization was performed using the R bioconductor package cummeRbund (http://bioconductor.org/packages/release/bioc/html/cummeRbund.html)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA extraction was performed using Qiagen-RNAesy mini-kit, following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: atbmi1abc triple mutant

value: seedlings


title: TC Skip ASO d20 rep5


title: abc_7DAG_2


title: TypeII KRasEtv wt SAM19521969

description:
treatment_name: TypeII KRasEtv wt
sample_id: SAM19521969


title: Col-0 H3K27me3 7DAG rep1

description:
WT control of atbmi1abc H3K27me3 7DAG rep1
processed data file: normalized_results_h3k27me3_atbmi1abc_vs_col0_rep1.txt


title: TC Skip ASO d20 rep2


title: TC Skip ASO d20 rep3


title: TC Skip ASO d20 rep4


title: TC Skip ASO d20 rep1


title: WT_7DAG_1


title: TypeII KRas;Etv5KO SAM19521966

description:
treatment_name: TypeII KRas;Etv5KO
sample_id: SAM19521966


title: WT_7DAG_2


title: TypeII KRasEtv wt SAM19521967

description:
treatment_name: TypeII KRasEtv wt
sample_id: SAM19521967


title: TC Skip ASO d10 rep5


title: TC Skip ASO d10 rep3


title: StimKDrecovery_72h_2

city: Bangalore

first: Gaiti

last: Hasan

address: GKVK Campus,

country: India

institute: NCBS, TIFR

data_processing:
Illumina Casava software used for basecalling
Good quality sequencing reads after adapter trimming were mapped to Drosophila genome using Tophat v 2.0.11 with parameters -m 1 -F 0 -p 6 -g 1 --microexon-search --no-coverage-search
Mapped reads of both conditions at each individual timepoint were used for differential expression analysis by cuffdiff v2.2.0 using default options
Gene counts for both conditions at each time point were independantly generated using BioConductor packages GenomicRanges and IRanges which were then used to call differentially expressed genes using the Bioconductor package EdgeR
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files with expression levels, fold change and p-values for all genes from cuffdiff and edgeR

organism: Drosophila melanogaster

source_name: Central Nervous Sytem

growth_protocol: Flies were reared on corn meal medium at 25°C and the temperature was raised to 29°C for knockdown

extract_protocol:
Pupal nervous systems were disseced in PBS, immediately transferred to ice and about 10 CNS were pooled together per sample to isolate RNA using Trizol
Libraries were made with 500ng total RNA using Illumina v2 protocol with 1/3rd the kit recommended volumes. Purification and size selection using Ampure beads.

tag: time

value: 72h After Puparium Formation

value: pupal brain

tag: dstim knockdown status

value: 24h knockdown + 36h recovery

value: ElavC155GAL4; dStimRNAi/tubulinGAL80ts


title: StimKDrecovery_72h_1


title: TypeII KRas;Etv5KO SAM19521968

description:
treatment_name: TypeII KRas;Etv5KO
sample_id: SAM19521968

tag: cell type


title: TypeII KRas;Etv5KO SAM19521962

description:
treatment_name: TypeII KRas;Etv5KO
sample_id: SAM19521962


title: TypeII KRas;Etv4KO;Etv5KO SAM19521970

description:
treatment_name: TypeII KRas;Etv4KO;Etv5KO
sample_id: SAM19521970


title: TC Skip ASO d10 rep2


title: TypeII KRas;Etv4KO;Etv5KO SAM19521965

description:
treatment_name: TypeII KRas;Etv4KO;Etv5KO
sample_id: SAM19521965


title: WildType_72h_2

value: wild type

value: Canton S


title: TC Control ASO d30 rep5


title: TC Control ASO d30 rep4


title: WildType_72h_1


title: TC Control ASO d30 rep3


title: TypeII KRas;Etv4KO;Etv5KO SAM19521960

description:
treatment_name: TypeII KRas;Etv4KO;Etv5KO
sample_id: SAM19521960


title: StimKD_36h_2

value: 36h After Puparium Formation

value: 24h knockdown


title: TypeII KRas;Etv4KO;Etv5KO SAM19521964

description:
treatment_name: TypeII KRas;Etv4KO;Etv5KO
sample_id: SAM19521964


title: TC Control ASO d30 rep1


title: TC Skip ASO d30 rep1


title: TC Control ASO d20 rep5


title: TC Control ASO d20 rep4


title: StimKD_36h_1


title: TC Skip ASO d10 rep4


title: TC Control ASO d20 rep3


title: TC Control ASO d20 rep2


title: SpcCre Etv5KO Lung SAM24294953

description:
inventory_sample_name: SpcCre Etv5KO Lung
sample_id: SAM24294953

extract_protocol: Lung tissue was dissectd and type II cells isolate (EpCAM+;tdTomato+;CD45-;CD31-) from the lung of the following mutant mice: (1) SpcCreERT2;RosatdTomato n=5 ; (2) SpcCreERT2;RosatdTomato;Etv5ko/loxp n=5 after 5-day injection of 100mg/kg body weight Tam and waiting for an other 5 days.

value: SpcCre Etv5KO

value: lung


title: TC Control ASO d20 rep1


title: SpcCre AT2 SAM24294937

description:
inventory_sample_name: SpcCre AT2
sample_id: SAM24294937

value: SpcCre


title: TC Skip ASO d10 rep1


title: TC Control ASO d10 rep5


title: SpcCre AT2 SAM24294938

description:
inventory_sample_name: SpcCre AT2
sample_id: SAM24294938


title: TC Control ASO d10 rep4


title: WildType_36h_1


title: VS_sRNA_lowCa_rPTG_10

description: 3' adapter sequence: TCTGATCGTATGCCGTCTTCTGCTTG

value: parathyroid

value: hyperplastic-lowCa


title: SpcCre Etv5KO AT2 SAM24294950

description:
inventory_sample_name: SpcCre Etv5KO AT2
sample_id: SAM24294950

value: alveolar Type II cells


title: TC Control ASO d10 rep3

value: spinal cord


title: TC Control ASO d10 rep2


title: SpcCre Lung SAM24294942

description:
inventory_sample_name: SpcCre Lung
sample_id: SAM24294942


title: TC Control ASO d30 rep2


title: TC Control ASO d10 rep1


title: VS_sRNA_lowCa_rPTG_8

description: 3' adapter sequence: TCTAGTCGTATGCCGTCTTCTGCTTG


title: TC PBS d10 rep5


title: SpcCre Etv5KO Lung SAM24294954

description:
inventory_sample_name: SpcCre Etv5KO Lung
sample_id: SAM24294954


title: TC PBS d10 rep4


title: SpcCre Etv5KO AT2 SAM24294949

description:
inventory_sample_name: SpcCre Etv5KO AT2
sample_id: SAM24294949


title: TC PBS d10 rep2


title: TC PBS d10 rep1


title: WildType_36h_2


title: TC PBS d10 rep3


title: VS_sRNA_lowCa_rPTG_6

description: 3' adapter sequence: TCGATTCGTATGCCGTCTTCTGCTTG


title: VS_sRNA_lowCa_rPTG_7

description: 3' adapter sequence: TCGCGTCGTATGCCGTCTTCTGCTTG


title: VS_sRNA_lowCa_rPTG_5

description: 3' adapter sequence: TCCTATCGTATGCCGTCTTCTGCTTG

value: normal


title: SpcCre Lung SAM24294944

description:
inventory_sample_name: SpcCre Lung
sample_id: SAM24294944


title: mRNA Therapeutic ASO d30 rep2

description:
SMA_K3_SCT
mRNA-Seq

treatment_protocol: Mice were treated with SMN ASO at d0 and treated with Therapeutic ASO at d20, d25, or d30.  Mice were sacrificed at d54.


title: mRNA Therapeutic ASO d30 rep1

description:
SMA_K2_SCT
mRNA-Seq


title: SpcCre Etv5KO Lung SAM24294951

description:
inventory_sample_name: SpcCre Etv5KO Lung
sample_id: SAM24294951


title: mRNA Therapeutic ASO d30 rep3

description:
SMA_K5_SCT
mRNA-Seq


title: mRNA Therapeutic ASO d25 rep5

description:
SMA_J6_SCT
mRNA-Seq


title: mRNA Therapeutic ASO d25 rep3

description:
SMA_J3_SCT
mRNA-Seq


title: VS_sRNA_lowCa_rPTG_9

description: 3' adapter sequence: TCTCCTCGTATGCCGTCTTCTGCTTG


title: SpcCre Etv5KO Lung SAM24294955

description:
inventory_sample_name: SpcCre Etv5KO Lung
sample_id: SAM24294955


title: mRNA Therapeutic ASO d25 rep4

description:
SMA_J5_SCT
mRNA-Seq


title: mRNA Therapeutic ASO d25 rep2

description:
SMA_J2_SCT
mRNA-Seq


title: SpcCre Etv5KO AT2 SAM24294947

description:
inventory_sample_name: SpcCre Etv5KO AT2
sample_id: SAM24294947


title: VS_sRNA_lowCa_rPTG_2

description: 3' adapter sequence: TCATCTCGTATGCCGTCTTCTGCTTG


title: mRNA Therapeutic ASO d20 rep6

description:
SMA_I6_SCT
mRNA-Seq


title: VS_sRNA_lowCa_rPTG_1

description: 3' adapter sequence: TCACTTCGTATGCCGTCTTCTGCTTG


title: mRNA Therapeutic ASO d20 rep4

description:
SMA_I4_SCT
mRNA-Seq


title: SpcCre AT2 SAM24294936

description:
inventory_sample_name: SpcCre AT2
sample_id: SAM24294936


title: mRNA Therapeutic ASO d20 rep2

description:
SMA_I2_SCT
mRNA-Seq


title: SpcCre Etv5KO AT2 SAM24294948

description:
inventory_sample_name: SpcCre Etv5KO AT2
sample_id: SAM24294948


title: WT.plus.UV.R4.IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: WT.plus.UV.longest.bed

data_processing:
Library strategy: MeRIP-seq
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome (hg38) using Tophat v2.0.14 with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene had multiple isoforms. Aligned reads were extended to 150 bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from introns in peak calling. The peak calling method was modified from published work (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. A Fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the FDR < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP samples in the current peak/window (a), median read counts of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and median read counts of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for mRNA-seq (the input samples of m6A-seq), reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: hg38
Supplementary_files_format_and_content: bed, m6A peaks

growth_protocol: WT or METTL3 KO U2OS cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) containing 4,500 mg/L glucose, 10% heat-inactivated fetal bovine serum, 110 mg/L sodium pyruvate, 2 mM L-glutamine and 100 U/ ml penicillin plus 100 µg/ ml streptomycin.

extract_protocol:
Following irradiation, cells were incubated at 37 ºC for 2 minutes, washed once with cold PBS, and then lyzed using TRIzol reagent. Total RNAs were extracted from cells according to the TRIzol manufacturer’s instructions.  Total RNA from U2OS cells was subjected to two rounds of polyA selection.
ChIP-seq libraries were prepared using NEBNext RNA library preparation (E7420) and DNA library preparation (E6000) reagents. The protocol and reagents concentrations are described in the Illumina Multiplex RNA and ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. Libraries were quantified by Qubit (Invitrogen) and sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.

treatment_protocol: Cells were cultured for 24-48 h prior to irradiation with 10 µM BrdU. UVC irradiation was conducted in a Stratalinker 2400 (Stratagene) at a 50 J dose.

tag: cell line

value: U2OS cells

tag: genotype/variation

value: WT


title: mRNA Therapeutic ASO d20 rep1

description:
SMA_I1_SCT
mRNA-Seq

tag: tissue


title: WT.plus.UV.R4.input

description: WT.plus.UV.longest.bed


title: mRNA Control ASO d30 rep5

description:
SMA_E5_SCT
mRNA-Seq


title: mRNA Control ASO d30 rep4

description:
SMA_E4_SCT
mRNA-Seq


title: SpcCre Lung SAM24294945

description:
inventory_sample_name: SpcCre Lung
sample_id: SAM24294945

tag: genotype


title: VS_sRNA_lowCa_rPTG_4

description: 3' adapter sequence: TCCGTTCGTATGCCGTCTTCTGCTTG


title: VS_sRNA_lowCa_rPTG_3

description: 3' adapter sequence: TCCACTCGTATGCCGTCTTCTGCTTG


title: mRNA Therapeutic ASO d25 rep1

description:
SMA_J1_SCT
mRNA-Seq


title: WT.plus.UV.R2.IP

description: WT.plus.UV.longest.bed


title: WT.plus.UV.R3.input

description: WT.plus.UV.longest.bed


title: mRNA Control ASO d30 rep3

description:
SMA_E3_SCT
mRNA-Seq


title: mRNA Control ASO d30 rep2

description:
SMA_E2_SCT
mRNA-Seq


title: mRNA Control ASO d30 rep1

description:
SMA_E1_SCT
mRNA-Seq


title: SpcCre Lung SAM24294943

description:
inventory_sample_name: SpcCre Lung
sample_id: SAM24294943


title: mRNA Skip ASO d30 rep4

description:
SMA_D4_SCT
mRNA-Seq


title: SpcCre Etv5KO AT2 SAM24294946

description:
inventory_sample_name: SpcCre Etv5KO AT2
sample_id: SAM24294946


title: SpcCre Etv5KO Lung SAM24294952

description:
inventory_sample_name: SpcCre Etv5KO Lung
sample_id: SAM24294952


title: SpcCre AT2 SAM24294939

description:
inventory_sample_name: SpcCre AT2
sample_id: SAM24294939


title: mRNA Skip ASO d30 rep5

description:
SMA_D5_SCT
mRNA-Seq


title: mRNA Skip ASO d30 rep3

description:
SMA_D3_SCT
mRNA-Seq


title: mRNA Therapeutic ASO d20 rep3

description:
SMA_I3_SCT
mRNA-Seq


title: WT.plus.UV.R2.input

description: WT.plus.UV.longest.bed


title: mRNA Therapeutic ASO d20 rep5

description:
SMA_I5_SCT
mRNA-Seq


title: mRNA Skip ASO d30 rep2

description:
SMA_D2_SCT
mRNA-Seq


title: mRNA Skip ASO d30 rep1

description:
SMA_D1_SCT
mRNA-Seq


title: SpcCre Lung SAM24294941

description:
inventory_sample_name: SpcCre Lung
sample_id: SAM24294941


title: WT.plus.UV.R1.IP

description: WT.plus.UV.longest.bed


title: mRNA Control ASO d20 rep4

description:
SMA_C4_SCT
mRNA-Seq


title: WT.plus.UV.R1.input

description: WT.plus.UV.longest.bed


title: WT.plus.UV.R3.IP

description: WT.plus.UV.longest.bed


title: mRNA Control ASO d20 rep3

description:
SMA_C3_SCT
mRNA-Seq


title: mRNA Control ASO d20 rep1

description:
SMA_C1_SCT
mRNA-Seq


title: WT.minus.UV.R3.IP

description: WT.minus.UV.longest.bed


title: WT.minus.UV.R3.input

description: WT.minus.UV.longest.bed


title: mRNA Skip ASO d20 rep3

description:
SMA_B3_SCT
mRNA-Seq


title: mRNA PBS d20 rep3

description:
SMA_A3_SCT
mRNA-Seq


title: mRNA PBS d20 rep4

description:
SMA_A4_SCT
mRNA-Seq


title: WT.minus.UV.R1.IP

description: WT.minus.UV.longest.bed


title: WT.minus.UV.R2.IP

description: WT.minus.UV.longest.bed


title: mRNA PBS d20 rep2

description:
SMA_A2_SCT
mRNA-Seq


title: mRNA PBS d20 rep1

description:
SMA_A1_SCT
mRNA-Seq


title: mRNA Skip ASO d20 rep4

description:
SMA_B4_SCT
mRNA-Seq


title: mRwdd3_Ptbp2_lHAC

description: 4C-seq in Rwdd3 – Ptbp2 on mouse HAC orthology Region (mHOR) with cHAC

source_name: Mus musculus + lHAC derived fibroblasts

value: fibroblasts


title: mRNA Skip ASO d20 rep1

description:
SMA_B1_SCT
mRNA-Seq


title: mRNA Skip ASO d20 rep2

description:
SMA_B2_SCT
mRNA-Seq


title: KO.plus.UV.R3.IP

description: KO.plus.UV.longest.bed

value: METTL3 KO


title: mDpyD_lHAC

description: 4C-seq of DpyD on mouse HAC orthology Region (mHOR) with lHAC


title: WT.minus.UV.R2.input

description: WT.minus.UV.longest.bed


title: WT.minus.UV.R1.input

description: WT.minus.UV.longest.bed


title: mDpyD_cHAC

description: 4C-seq of DpyD on mouse HAC orthology Region (mHOR) with cHAC

source_name: Mus musculus + cHAC derived fibroblasts


title: mBcar3_lHAC

description: 4C-seq of Bcar3 on mouse HAC orthology Region (mHOR) with lHAC


title: mBcar3_cHAC

description: 4C-seq of Bcar3 on mouse HAC orthology Region (mHOR) with cHAC


title: mPtbp2_cHAC

description: 4C-seq of Ptbp2 on mouse HAC orthology Region (mHOR) with cHAC


title: mRNA Control ASO d20 rep2

description:
SMA_C2_SCT
mRNA-Seq


title: KO.plus.UV.R3.input

description: KO.plus.UV.longest.bed


title: KO.plus.UV.R1.IP

description: KO.plus.UV.longest.bed


title: mAbcd3_lHAC

description: 4C-seq of Abcd3 on mouse HAC orthology Region (mHOR) with lHAC


title: mAlg14_lHAC

description: 4C-seq of alg14 on mouse HAC orthology Region (mHOR) with lHAC


title: mAlg14_cHAC

description: 4C-seq of alg14 on mouse HAC orthology Region (mHOR) with cHAC


title: KO.plus.UV.R1.input

description: KO.plus.UV.longest.bed


title: mAbcd3_cHAC

description: 4C-seq of Abcd3 on mouse HAC orthology Region (mHOR) with cHAC


title: KO.minus.UV.R3.IP

description: KO.minus.UV.longest.bed


title: hRWDD3_PTBP2_cHAC

description: 4C-seq in RWDD3 - PTBP2 region on cHAC


title: mPtbp2_lHAC

description: 4C-seq of Ptbp2 on mouse HAC orthology Region (mHOR) with lHAC


title: KO.minus.UV.R3.input

description: KO.minus.UV.longest.bed


title: hDPYD_lHAC

description: 4C-seq of DPYD on lHAC


title: hPTBP2_cHAC

description: 4C-seq of PTBP2 on cHAC


title: hPTBP2_lHAC

description: 4C-seq of PTBP2 on lHAC


title: hALG14_lHAC

description: 4C-seq of ALG14 on lHAC


title: KO.minus.UV.R2.input

description: KO.minus.UV.longest.bed


title: hBCAR3_cHAC

description: 4C-seq of BCAR3 on cHAC


title: KO.minus.UV.R1.IP

description: KO.minus.UV.longest.bed


title: hALG14_cHAC

description: 4C-seq of ALG14 on cHAC


title: KO.minus.UV.R1.input

description: KO.minus.UV.longest.bed


title: hABCD3_cHAC

description: 4C-seq of ABCD3 on circular Human Artificial Chromosome (cHAC)


title: IB_sRNA_mouse_PT_DICER_wt_PTG680

description: 3' adapter sequence: TTACATCGTATGCCGTCTTCTGCTTG

source_name: parathyroid-paraffin-LCM


title: hRWDD3_PTBP2_lHAC

description: 4C-seq in RWDD3 - PTBP2 region on lHAC


title: hABCD3_lHAC

description: 4C-seq of ABCD3 on linear Human Artificial Chromosome (lHAC)


title: IB_sRNA_mouse_PT_DICER_wt_PTG679

description: 3' adapter sequence: TGTGTTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_mouse_PT_DICER_wt_PTG672

description: 3' adapter sequence: TAATATCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_mouse_PT_DICER_wt_PTG676

description: 3' adapter sequence: TGATGTCGTATGCCGTCTTCTGCTTG


title: IB_sRNA_mouse_PT_DICER_wt_PTG673

description: 3' adapter sequence: TATCATCGTATGCCGTCTTCTGCTTG


title: MS2-RsaA_TotRNA

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

description: Processed data file: Deseq_TotRNA.xlsx

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2 (for the MS2 samples with duplicates) and Deseq (for the Total RNA with no duplicate)
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: Tables obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values

organism: Staphylococcus aureus

source_name: Total RNA

growth_protocol: For both total RNA extracts and MS2-eluted RNAs, bacteria were grown in Brain Heart Infusion (BHI) medium until late exponential phase of growth (6h). For both MS2-plasmid, erythromycin at 10 ug/ml final concentration was added to the medium.

extract_protocol:
To purify total RNA, bacterial lysis was performed with FastPrep and the RNA purification followed strictly the procedure described for the FastRNA Pro Blue Kit (MP Biomedicals). For MS2-purified RNA, bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus. Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol/chloroform :isoamylalcohol prior to RNAseq analysis.
For both total RNA extracts and MS2-eluted RNAs, DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. The RNAs for total transcriptomics were then treated to deplete abundant rRNAs (Ribozero), and the cDNA libraries were performed using the Random Hexamer approach and sequenced by Fasteris (Switzerland). The standard protocol used is the “TruSeq Stranded mRNA” which is based on the TruSeq Illumina kit and which preserves the information about the orientation of the transcripts and produces reads of 125 nts, which map on the complementary strand. The libraries were sequenced using Illumina Hi-Seq 2500 with High-Output (HO) mode using a V4 chemistry sequencing kit (Illumina).


title: MS2_TotRNA

description: Processed data file: Deseq_TotRNA.xlsx


title: MS2-RsaA_R2

description: Processed data file: Deseq2_MS2RsaA.xlsx

source_name: MS2 affinity purified RNA


title: MS2-Contr_R1


title: MS2-Contr_R2


title: MS2-RsaA_R1


title: P60_31

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

country: United Kingdom

institute: The Roslin Institute

description: Pregnancy, Day 60

data_processing:
sRNAbench, v1
sRNAbench, v1, adapter = TGGAATTCTCGGGTGCCAAGG
sRNA bench mapping, v05/14, bowtie v0.12.9, 1 mismatch allowed, seed length 19, -n, -m 40 (bowtie parameter)
sRNAbench, v1, standard data normalization (RPMM)
Genome_build: bosTau4
Supplementary_files_format_and_content: A single processed data file is provided, "processed_data.xlsx". The file consists of two spreadsheets, "Raw reads" which includes the raw reads obtained after analysis using sRNAbench , and "Normalised reads" which includes the normalized data (reads per million mapped, RPMM).

organism: Bos taurus

extract_protocol:
RNA was extracted from 0.7 mL of plasma using TRIzol LS (Life Technologies, USA), following the manufacturer’s protocol. During the RNA extraction protocol, glycogen (Sigma-Aldrich, USA) was added to each sample to facilitate the precipitation of RNA, and an exogenous miRNA control, syn-cel-miR-39-3p (Qiagen, NL), was spiked into each sample. RNA was re-suspended in 20 μL of RNase-free water and used immediately or frozen at -80 °C.
Small-RNA libraries were prepared using the Illumina TruSeq small-RNA sample preparation kit (Illumina, USA) following the manufacturer’s protocol. Libraries were submitted to 36-base single-end sequencing using the Illumina HiSeq 2000 platform.

tag: subject

value: Day 60

value: Plasma


title: P60_29

description: Pregnancy, Day 60


title: hBCAR3_lHAC

description: 4C-seq of BCAR3 on lHAC


title: P60_28

description: Pregnancy, Day 60


title: hDPYD_cHAC

description: 4C-seq of DPYD on cHAC


title: P60_32

description: Pregnancy, Day 60


title: KO.minus.UV.R2.IP

description: KO.minus.UV.longest.bed


title: Foxo1(f/f) GC#3

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: fpkm

source_name: Foxo1-deficient GC B cells

growth_protocol: C57BL/6 mice were co-transferred with a 1:1 mixture of Foxo1(+/+) ERT2cre B1-8hi CD45.1/1 and Foxo1(f/f) ERT2cre B1-8hi CD45.1/2 B cells, and immunized with NP-CGG precipitated in alum on day 0. On day 7, 8, and 9, mice were orally administered tamoxifen. On day 12, Foxo1(+/+) LZ (CD45.1+CD45.2−B220+NP+GL7+CD38−CD86hiCXCR4lo) and DZ GC B cells (CD45.1+CD45.2–B220+NP+GL7+CD38−CD86loCXCR4hi), and Foxo1f/f GC B cells (CD45.1+CD45.2−B220+NP+GL7+CD38−) were sorted for RNA preparation.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
DNA library was constructed using an NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) from total RNA purified from ~ 1 × 10^4 sorted cells.

tag: strain background

value: spleen

value: Germinal center (GC) B cells


title: Foxo1(+/+) DZ#3

source_name: wild type DZ GC B cells

tag: cell state

value: dark zone (DZ)


title: P60_26

description: Pregnancy, Day 60


title: Foxo1(+/+) LZ#3

source_name: wild type LZ GC B cells

value: light zone (LZ)


title: P60_24

description: Pregnancy, Day 60


title: P60_17

description: Pregnancy, Day 60


title: Foxo1(+/+) DZ#2


title: P60_12

description: Pregnancy, Day 60


title: Foxo1(+/+) LZ#2


title: Foxo1(f/f) GC#1


title: P60_14

description: Pregnancy, Day 60


title: Foxo1(+/+) LZ#1


title: P60_10

description: Pregnancy, Day 60


title: P0_32

description: Pregnancy, Day 0

value: Day 0


title: O 03/12 biological replica 3 (dark)

city: Rosario

first: Alejandra

last: Mussi

state: Santa Fe

address: Suipacha 531

country: Argentina

institute: CEFOBI

description: rRNA was depleted from total RNA with Ribo-Zero Magnetic Kit compatible with A. baumannii

data_processing:
Quality control with FastQC
Normalized transcript abundance estimated with Bowtie2 and eXpress.
Genome_build: Acinetobacter baumannii ATCC 19606 - whole genome shotgun sequencing project - GenBank Accession: JMRY00000000.
Supplementary_files_format_and_content: tab-delimited text files include FPKM (fragments per kilobase of transcript per million fragments mapped) values for each Sample.

organism: Acinetobacter baumannii

growth_protocol: A. baumannii ATCC 19606 cells were grown at 24ºC in LB in stagnant conditions overnight.

extract_protocol:
Total RNA was extracted as follows: Cells were pelleted and immediately mixed with 1 ml lysis buffer (0.1 M sodium acetate, 10 mM EDTA, 1% SDS) in a boiling-water bath. Cell lysates were extracted twice at 60 °C with one volume of phenol, which was adjusted to pH 4.0 with 50 mM sodium acetate, and then once with chloroform at room temperature. The RNA precipitated overnight at -20 °C with 2.5 volumes ethanol was collected by centrifugation, washed with 70% ethanol, and dissolved in DEPC-treated deionized water. Any possible residual gDNA was removed and the RNA was cleaned using Quick-RNA Miniprep according the manufacturer’s recommendation (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were exposed to blue light or incubated in the dark.

tag: strain

value: wild type

tag: exposed to

value: dark


title: O 02/12 biological replica 2 (dark)


title: Foxo1(f/f) GC#2


title: P0_24

description: Pregnancy, Day 0


title: O 25/11 biological replica 1 (dark)


title: P0_26

description: Pregnancy, Day 0


title: L 02/12 biological replica 2 (light)

value: blue light


title: FstEF0409 low level exposure

city: Vermillion

first: Keith

last: Weaver

state: SD

address: 414 E. Clark Street

department: Division of Basic Biomedical Sciences

institute: University of South Dakota Sanford School of Medicine

data_processing:
Illumina RNA-seq library creation and sequencing, using the HiSeq 2500 (paired-end, 125 bp) platform, was performed at the University of Minnesota Genomics Center (UMGC). The fastq CASAVA (version 1.8 Illumina) sequence files were de-multiplexed and deposited in Minnesota Supercomputer Institute (MSI, University of Minnesota).
Sequence analysis on paired end reads was carried out using Galaxy maintained by MSI.  The fastq CASAVA 1.8 files were converted to CASAVA 1.7 and assessed for quality using FastQC Read and Quality Reports.
FASTQ Quality Trimmer by sliding window was used to remove the 3’ends of raw sequencing reads that had a Phred quality score <20.
FASTQ Interlacer and FASTQ de-interlacer were used on the trimmed fastqsanger files to remove any unmatched paired end reads followed by mapping to the OG1RF reference genome (NC_017316.1/CP002621.1) using Bowtie for Illumina.
The Bowtie SAM files were sorted by chromosome and start position using Picard Sortsam.
For each culture condition, Cufflinks was used to assemble the transcripts and determine expression levels (FPKM).   The generated gtf files created for biological replicates, for the two conditions to be compared, were assembled using Cuffmerge.
Cuffdiff was used to determine significant differences in transcriptional expression between culture conditions with the False Discovery Rate at 0.05.
Genome_build: NC_017316.1/CP002621.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, fold change and statistical analysis for Galaxy106, RF5 vs RFE1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, fold change and statistical analysis for Galaxy55, RF5 vs RFE5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, fold change and statistical analysis for Galaxy24, RFE5 vs RFA5

organism: Enterococcus faecalis

source_name: bacterial cellular RNA

growth_protocol: Cultures of the appropriate strain were inoculated from frozen stock and grown overnight in M9YEG supplemented with 25 µg/ml chloramphenicol. In the morning cultures inoculated at 2% into M9YEG supplemented with 10 µg/ml chloramphenicol

extract_protocol:
Cell pellets were resuspended in Bacteria RNA Protect (Qiagen) and incubated at room temperature for 5 minutes. Cells were then pelleted and stored at -80⁰C. Once all samples were collected, pellets were thawed and resuspended in 200µl Tris/EDTA/ mutanolysin/lysozyme solution (10 mM Tris [pH 8.0], 1.0 mM EDTA [pH 8.0], mutanolysin (500U ml-1), lysozyme (30 mg ml-1)) and incubated at 37⁰C for 10 minutes. To the resuspensions, 700 µl of Buffer RLT (Qiagen RNeasy Mini Kit) with 10 µl β-ME was added and vortexed to mix. RNA was then purified using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. Total RNA from biological replicates was treated with TURBO DNase (Ambion / ThermoScientific, Waltham, MA) using the rigorous protocol according to the manufacturer’s instructions. DNase was removed from treated samples using the RNA Clean & Concentrator-25 (Zymo Research). mRNA was enriched by rRNA removal using the MICROBExpress Bacterial mRNA Purification Kit (Ambion/ThermoScientific) according to the manufacturer’s instructions.
University of Minnesota Genomic Center (UMGC) performed QC and library preparation.  mRNA quantified using fluorimetry (RiboGreen assay) and RNA integrity assessed using capillary electrophoresis (e.g., Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN). For a sample to pass QC, mass must be ≥ 1 ug, with a RIN > 8.  Library created using TruSeq RNA V2 kit.  Briefly, cDNA was generated using reverse transcriptase, fragmented and blunt-ended, and ligated to indexed (barcoded) adapters. (Barcode Data: RF_5_pCIE_A, AGTCAA; RF_5_pCIE_B, AGTTCC; RFE_1_A, ACAGTG; RFE_1_B, GCCAAT; RFE_5_A, CAGATC; RFE_5_B, ACTTGA; RFA_5_A, GATCAG; RFA_5_B_TAGCTT). The library was gel size selected to generate inserts of ~200 bp.

treatment_protocol: Cultures inoculated as above were grown for one hour to ensure entrance into log phase and the induced with either 1 ng/ml or 5 ng/ml cCF10 pheromone peptide in DMF. After 1 hour of induction cells were harvested by centrifugation

value: OG1RF (pDAK1010E)

tag: ccf10 pheromone induction

value: 1 ng/ml


title: L 03/12 biological replica 3 (light)


title: FstEF0409 high level exposure

value: 5 ng/ml


title: P0_17

description: Pregnancy, Day 0


title: Foxo1(+/+) DZ#1


title: Empty vector contol

value: OG1RF (pCIE)


title: P60_11

description: Pregnancy, Day 60


title: P0_12

description: Pregnancy, Day 0


title: ID-003339-02_Hfq_noFLAG

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description: anti-FLAG co-IPed RNA

data_processing:
Reads were trimmed for a Phred quality of 20 using the FASTX toolkit version 0.0.13
Adapter trimming using Cutadapt version 1.3
Reads were mapped using the READemption pipeline (Förstner et al., 2014), segemehl, and the lack remapper
Coverage plots (wig files) were produced by READemption

organism: Neisseria meningitidis 8013

source_name: WT, OD 0.5

growth_protocol: N.meningitidis 8013 and its derivatives were either grown on blood agar plates (bioMerieux) or on GC medium base (GCB) plates (Difco) containing Kellogg’s supplements I and II (22.2 mM glucose, 0.68 mM glutamine, 0.45 mM co-carboxylase, 1.23 mM Fe(NO3)3; all from Sigma) and appropriate antibiotics. For liquid cultures, Neisseria grown on plates overnight were harvested and a starter culture was inoculated to a final OD600 nm of 1.0 in 5 ml GC medium base (GCB) liquid supplemented with Kellogg’s I and II (GCBL++). After one hour the starter culture was used to inoculate GCBL++ media to a final OD600 of 0.1. Bacteria were always grown at 37 °C at 220 rpm without added CO2 to the desired OD.

extract_protocol:
For dRNA-seq: N. meningitidis 8013 cells were grown in 50 ml tubes at 37 °C under vigorous shaking in GCBL++ medium and samples were collected by centrifugation at OD600 of 0.5 and 1.5, corresponding to the mid logarithmic and late logarithmic/early stationary growth phase, respectively. Transcription and translation were terminated by the addition of STOP Mix [95% (vol/vol) EtOH and 5% (vol/vol) phenol] and cells were frozen in liquid nitrogen. Samples were stored at −80 °C until RNA preparation. Frozen cell pellets were thawed on ice, and resuspended in a lysis solution consisting of 800 µl of 0.5 mg/ml lysozyme in TE buffer (pH 8.0) and 80 µl 10% SDS. Bacterial cells were lysed by placing the samples for 1–2 minutes at 65°C in a water bath. Total RNA was extracted from the lysates using the hot phenol method (Blomberg 1990). For RIP-seq:For each strain cells equivalent to an OD600 of 50 were collected in parallel and subjected to Hfq coIP and control coIP as described previously (Dugar et al. 2016). Cells were harvested by centrifugation at 6,000g for 20 min at 4 °C. Afterwards, cell pellets were resuspended in 1ml Lysis Buffer (20mM Tris-HCl, pH 8.0, 150mM KCl, 1mM MgCl2, 1mM dithiothreitol (DTT)) and subsequently centrifuged (5 min, 11,000g,4 °C). The pellets were shock-frozen in liquid nitrogen and stored at -80 °C. Frozen pellets were thawed on ice and resuspended in 0.8 ml Lysis Buffer. An equal volume of glass beads was then added to the cell suspension. Cells were then lysed using a Retsch MM40 ball mill (30 s-1, 10min) in pre-cooled blocks (4 °C) and centrifuged for 2min at 15,200g, 4 °C. The supernatant was transferred to a new tube, and an additional 0.4 ml of Lysis Buffer was added to the remaining un-lysed cells with beads. Lysis of the remaining cells was achieved by a second round of lysis at 30 s-1 for 5min. Centrifugation was repeated and this second supernatant was combined with the first one. The combined supernatant was centrifuged again for 30 min at 15,200g, 4 °C for clarification and the resulting supernatant (lysate fraction) was transferred to a new tube. The lysate was incubated with 35 ml anti-FLAG antibody (Monoclonal ANTI-FLAG M2, Sigma, #F1804) for 30 min at 4 °C on a rocker. Next, 75 ml of Protein A-Sepharose (Sigma, #P6649), prewashed with Buffer A, was added and the mixture was rocked for another 30 min at 4 °C. After centrifugation at 15,200g for 1min, the supernatant was removed. Pelleted beads were washed five times with 1 ml Lysis Buffer. Finally, 500 ml Lysis Buffer was added to the beads and RNA and proteins were separated by phenol-chloroform-isoamyl alcohol (ROTH 985.1) extraction and precipitated as described previously (Chao et al. 2012).
For dRNA-seq: cDNA libraries of dRNAseq samples for were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al. 2006), but omitting the RNA size-fractionation step prior to cDNA synthesis. In brief, total RNA samples were used for the preparation of two libraries each, either covering all transcripts or being specifically enriched for primary transcripts by treatment with terminator exonuclease (TEX, Epicentre). Next, equal amounts of RNA samples were poly(A)-tailed with poly(A) polymerase. The 5'-triphosphate structures were removed with tobacco acid pyrophosphatase (TAP). Afterwards, a 5’-RNA adapter was ligated and the first-strand cDNA was synthesized with an oligo(dT)-adapter primer and MMLV reverse transcriptase. A PCR-based amplification step with a high-fidelity DNA polymerase was then used to increase the cDNA concentration to 20-30 ng/µl. A library-specific barcode for multiplexing was included in the 3'-sequencing adapter. For RIP-seq: RIP-seq samples were constructed according to instructions of the NEBnext Multiplex Small RNA library set for Illumina ECL but omitting the TEX treatment.

tag: sample type


title: P0_11

description: Pregnancy, Day 0


title: ID-001740-NH_41_Neisseria8013_-TEX

description: total RNA


title: L 25/11 biological replica 1 (light)


title: P0_31

description: Pregnancy, Day 0


title: ID-001738-NH_40_Neisseria8013_-TEX

description: total RNA


title: ID-003337-01_Hfq_noFLAG

description: anti-FLAG co-IPed RNA


title: P0_28

description: Pregnancy, Day 0


title: FstpAD1 high level exposure

description: RFA

value: OG1RF (pDAK1010A)


title: P0_10

description: Pregnancy, Day 0


title: ID-001739-NH_40_Neisseria8013_+TEX

description: TEX treated total RNA

value: terminator exonuclease


title: K562 ChIP H3K9me2 exp. 2

status: Public on Mar 20 2017

city: Cambridge

first: Anna

last: Salzberg

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0.
Domains were called using the RSEG software version 0.4.8 RC with the provided deadzone file “deadzones-k41-hg19.bed” and the following parameters: -s 10000 -i 20 -duplicates.  The chrX and chrY mapped sequences of the male samples were duplicated prior to calling RSEG.
To comply with Penn State's IRB, sequence reads had individual SNPs eliminated based on hg19.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain domains output by RSEG

source_name: K562  strain

growth_protocol: Normal polymorphonuclear granulocytes (predominantly neutrophils) were isolated from discarded fresh white blood cells (buffy coats) from unidentified healthy donors using standard OptiPrep density centrifugation, resuspended in PBS buffer and fixed with 1% formaldehyde. Cryopreserved CD34+ bone marrow hematopoietic progenitors were obtained from Allcells, Emeryville, Ca. Cryopreserved AML cellswere  isolated from bone-marrow samples by Ficoll-Pacque density gradient centrifugation. The cryopreserved samples  were thawed, resuspended in PBS, and fixed with 1% formaldehyde immediately after thawing. The human samples were collected and analyzed under Penn State Hershey IRB protocols  2000-186,  HY03-136EP-A, and STUDY00002518.   Cultured cells K562 (ATCC CCL-243) were  grown in suspension as recommended by ATCC, washed  with PBS and fixed with 1% formaldehyde.

extract_protocol:
cells were fixed with 1% formaldehyde for 10 min. After fixation, nuclei were isolated, the nuclear DNA was digested by micrococcal nuclease to 150-200 bp DNA fragments,  the DNA fragments with attached proteins were resuspended in SDS-containing lysis buffer, and immunoprecipitated by antibodies against various histone modifications.
For Illumina Hi-Seq 2500 sequencing we used New England BioLabs NEBNext ChIP-Seq library preparation reagent set for Illumina and and constructed library as described in the E6240 instruction manual.  For  SOLiD  sequencing we used Applied Biosystems SOLiD 4 System and constructed library as described in the SOLiD 4 System Library Preparation Guide.

treatment_protocol: Some K562 samples (K562-UNC0638) were grown for 5 days with 0.5 micromole UNC0638, a specific  inhibitor of histone methyltransferase G9a, before isolation.

tag: sample id

tag: gender

value: female


title: ID-001741-NH_41_Neisseria8013_+TEX

description: TEX treated total RNA


title: K562 ChIP input  exp. 2

tag: chip antibody

value: H3K9me2 (ab1220 Abcam)


title: AML 14 ChIP H3K9me2 exp. 1

source_name: AML blast cells from blood

value: AML 14

value: male


title: AML 16 ChIP H3K9me2 exp. 1

value: AML 16


title: AML 8 ChIP H3K9me2 exp. 1

value: AML 8


title: AML 11 ChIP H3K9me2 exp. 1

value: AML 11


title: AML 15 ChIP H3K9me2 exp. 1

value: AML 15


title: AML 10 ChIP H3K9me2 exp. 1

value: AML 10


title: ID-003340-02_Hfq_FLAG

description: anti-FLAG co-IPed RNA

source_name: Hfq FLAG tag, OD 0.5

value: anti-FLAG co-IPed


title: AML 7 ChIP H3K9me2 exp. 1

value: AML 7


title: AML 13 ChIP H3K9me2 exp. 1

value: AML 13


title: Granulocyte 3 ChIP input

source_name: Granulocyte from blood

value: Granulocyte 3


title: Granulocyte 3 ChIP H3K9me2 exp. 1


title: BCR/ABL+DFC+BCI 2

city: Cincinnati

first: Mohammad

last: Azam

state: OH

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

data_processing:
RNA-Seq analysis is based on the TopHat/Cufflinks pipeline.  First, sequences were aligned to the reference genome with TopHat, which efficiently aligns reads spanning known or novel splice junctions.  Each sample is then independently processed with Cufflinks2 in order to generate an initial transcriptome.  We then used the Cuffmerge tool to merge the private transcriptomes into a single reference, and at the same time annotate known genes and extend partial transcripts.  This common transcriptome was then  used in a second pass with Cufflinks, which  quantified each transcript and gene (known or novel) in each sample.  The reference annotation used is based on the UCSC knownGenes table and includes the long non-coding RNAs.
Genome_build: mm10
Supplementary_files_format_and_content: abundance

source_name: Kit+ Bone marrow cells

growth_protocol: Kit+ cells from the bonemarrow of WT and ROSACreERT2c-Fosfl/fl /Dusp1-/- mice were isolated using the CD117 MicroBead Kit (Miltenyi biotec) according to their instructions. These cells were incubated overnight in IMDM media supplemented with 10% FBS and cytokine cocktail of FLT3, IL-6, IL-3, and mSCF.

extract_protocol:
Total RNA was isolated using miRNA easy Mini Kit according to the manufacturers protocol. (Qiagen)
TruSeq Stranded mRNA library preparation method.  The protocol was followed as per the manufacturer.

treatment_protocol: After 12 hours of stimulation cells were transduced with BCR/ABL-IRES-YFP virus using retronectin (Takara). One to two million positive cells (isolated by FACS) from each group was treated for four hours with imatinib alone, DFC+BCI, and imatinib+DFC+BCI (3 mM of Imatinib, 0.2 mM of DFC and 0.5 mM of BCI alone or in combinations in duplicates).

value: Kit+ Bone marrow cells


title: BCR/ABL+DFC+BCI 1


title: c-Fos-/-Dusp1-/- BCR/ABL+Im


title: BCR/ABL+IM+DFC+BCI 1


title: BCR/ABL+IM 1


title: BCR/ABL 2


title: c-Fos-/-Dusp1-/- BCR/ABL


title: ID-003338-01_Hfq_FLAG

description: anti-FLAG co-IPed RNA


title: BCR/ABL 1


title: Vector control


title: P0_29

description: Pregnancy, Day 0

tag: time

value: Day 0

value: Plasma


title: AML 9 ChIP H3K9me2 exp. 1

value: AML 9


title: Mad2 wt; p53 wt; Lck-Cre- Thymus 0 Cell control

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

institute: University Medical Center Groningen

data_processing:
Basecalling was done with bcl2fastq v1.8.2
Reads were mapped with bowtie2 v2.1.0
PCR duplicates were marked with BAMUtil v.1.0.3
Sortind and indexing of BAM files was done with Samtools v0.1.18
BAM files were analysed using BAIT v1.0 (Hills et al., 2013 - Genome Medicine 5(9):82)
Chromosome copy numbers were determined per cell library using the BAIT read outs, manually curated based on read counts per megabase, and plotted in Excel
Genome_build: mm10
Supplementary_files_format_and_content: Excel files contain the individual cell IDs and chromosome copy number counts as determined through manual curating of BAIT read outs

source_name: thymus

growth_protocol: Mad 2f/f; p53 f/f mice were crossed with Lck-Cre+ mice to generate Mad2 f/f; p53 f/f; Lck-Cre+ mice.

extract_protocol:
Tumours were harvested from mice displaying T-ALL (enlarged thymus and peripheral lymph nodes) and were then homogenized using scalpels and cell strainers. Upon sorting, cells were incubated in a PI/Hoechst staining butter with NP-40 to dissociate the cytoplasm. Single cell nuclei were then sorted into a 96-well plate and stored at -80°C in freezing medium until library preperation.
Genomic DNA was digested using Mnase to 150 bp fragments. Subsequent end-repair, A-tailing and adapter ligation were peformed, followed by a nested indexed PCR.
Whole genome seq

treatment_protocol: Experimental mice were monitored for 3-4 months and sacrificed upon signs of dyspnea

value: Mad2 wt; p53 wt; Lck-Cre-

value: thymus

value: T-cell


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 46


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 43


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 45


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 39


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 44


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 38


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 42


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 41


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 36


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 40