title: WTREP1_ZT0

description: mRNA-seq

value: WT

value: Regular Chow

value: Liver


title: GAF RNAi CLAMP IP Replicate 1

status: Public on Feb 01 2018

type: SRA

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
ChIP-Seq reads aligned to fb5_22 release of Drosophila melanogaster genome using bowtie (rel 0.12.9) options -t -p 12 -m 1 -I 50 -X 500 --solexa-quals --best --chunkmbs 256
Peaks were called using MACS2 callpeak (version 2.1.1) and p-value threshold of 0.05. For MSL3 IP, the --broad flag was used.
Genome_build: fb5_22/dm3
Supplementary_files_format_and_content: bedgraph files were generated using MACS2 bdgcmp (version 2.1.1)  with the -m FE flag. Scores represent local fold enrichment.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
Cells were cross linked in 1% formaldehyde and quenched with glycine prior to incubation in lysis buffer, and sonicated six times with 5 min cycles of 30s on/off o a Bioruptor sonicator. Samples were immunoprecipitated with either GAF, CLAMP, or MSL3 antibodies, and DNA clean-up was performed including RNase and Proteinase-K digestion steps.
Libraries were prepared using the NEBNext Ultra II DNA library prep kit

treatment_protocol: S2 cells were treated with 4.5 ug/mL dsRNA

tag: RNAi treatment

value: GAF

tag: chip antibody

value: rabbit anti-CLAMP


title: HSC_PBS inj-5FU-rep4

city: Dresden

first: Triantafyllos

last: Chavakis

address: Fiedlerstraße 42

department: Klinische Pathobiochemie

country: Germany

institute: Medizinische Fakultät der TU Dresden

library_source: transcriptomic

data_processing:
basecalling: bcl2fastq 1.8.4
alignment of read data against mm10 with gsnap version v2014-12-17,v2016-06-30,v2016-09-23; splice sites were supported by using Ensembl version 81 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-81.ss.mm10.iit -n 1 -A sam)
counting was done with featureCounts version 1.5.0,1.5.1 (-a EnsemblGene-81.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 81 gtf file
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files from featureCounts (featureCounts.mm10.e81.first.csv.gz, featureCounts.mm10.e81.second.csv.gz, featureCounts.mm10.e81.third.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the Conditions and their replicates

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
RNA was harvested from sorted cells using RNeasy Plus Micro Kit from Qiagen (Cat#74034)
Samples were prepped with the SMARTer Ultra HV v2 protocol (TaKaRa Bio)

tag: cell type

value: long-term hematopoietic stem cells

tag: age

value: 10 weeks

tag: strain


title: GFP RNAi MSL3 IP Replicate 1

value: GFP

value: goat anti-MSL3


title: GFP RNAi GAF IP Replicate 1

value: rabbit anti-GAF


title: HSC_PBS inj-5FU-rep3


title: GFP RNAi CLAMP IP Replicate 1


title: GFP RNAi Input Replicate 1


title: HSC_PBS inj-5FU-rep2


title: MPP_β-glucan inj-day28-rep2

value: multipotent progenitors


title: MDA-MB-231_HM.LNm5_5

city: Melbourne

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

country: Australia

institute: Monash University

description:
Batch 2
Illumina index 17
HM_old_2

data_processing:
In order to assign reads to H.Sapiens: Reads are first stripped of poly(A) sequence and adaptors using Tail Tools (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools). Reads are then aligned to the human genome using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Reads assigned to the genome are then processed using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools):  Reads are aligned using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.  Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.  Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene, but not extending into another gene on the same strand, are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: H. sapiens from release 82 of Ensembl
Supplementary_files_format_and_content: Names in the files are Ensembl gene ids. The ..._count.csv files give read counts for each gene in each sample. ..._tail.csv files give average poly(A) tail length for each gene in each sample. ..._tail_count.csv give the number of reads having a poly(A) tail. (The average poly(A) tail length is a less accurate estimate of tail length where there are fewer reads with a poly(A) tail.)

organism: Homo sapiens

source_name: mouse xenograft primary breast tumour

growth_protocol: Viable tumor cells resuspended in PBS were mixed with 10-30% Cultrex and inoculated (1x106 cells) into the right-side inguinal mammary gland of NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immuno-deficient mice and then surgically resected at a size of 200-400mm3.

extract_protocol:
Resected primary tumors were disaggregated by digestion with collagenase I and bovine pancreatic DNase I at 37oC and filtered through a series of sieves prior to sorting for viable tumor cells by flow cytometry. Hydroxystilbamidine was used to exclude non-viable cells. Total RNA was prepared from sorted cells using the Trizol and the Direct-zol RNA mini kit with on-column DNase I digestion.
Library construction was by the PAT-seq approach. Breifly this involves a modified the ePAT approach to tagging adenylated RNA to generate libraries suitable for deep sequencing. Adenylated RNA is sequence specifically extended by dNTPs using Klenow polymerase and an annealed DNA anchor oligonucleotide. This takes advantage of the native function of DNA polymerase to extend an RNA primer from a DNA template in second strand synthesis. Importantly, any unwanted priming to internal poly(A)-tracts in RNA is avoided by a requirement for 3’ extension in subsequent fragment selection and reverse transcription. No ribosome depletion is necessary. Here, the anchor sequence was compatible with the Illumina index primers and included a 5’ biotin moiety to facilitate handling. In a second step, the 3’ tagged RNA was subject to limited fragmentation by RNase T1. This cleaves RNA after G-residues and ensures that cleavage is only possible within the body of the RNA, not the poly(A)-tract or the DNA sequence of the extended tag. The fragmented RNA was 5’ phosphorylated to allow RNA Ligase 2 mediated ligation of an Illumina compatible splinted-linker to the RNA fragments. Reverse transcription was primed from the anchor sequence. Note: All manipulations after limited fragmentation were performed in association with streptavidin magnetic beads. The cDNA PAT-seq libraries was eluted from beads, size-selected by Urea PAGE and amplified with primers that introduce the features for directional Illumina sequencing and indexing. Note: all reads run in 5’ to 3’ direction from unique sequence into a variable length of poly(A) homopolymers. This means that color balance is preserved and that any low fidelity within the homopolymers is limited to the end of the read.
Cluster Generation batch 1: 6pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012.
Sequencing chemistry batch 1: 1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012
Cluster Generation batch 2: 9pM of libraries per lane using Illumina c-bot. Illumina Protocol 15035788 RevD, Apr 2014.
Sequencing chemistry batch 2: 150bp SR sequencing using Illumina HiSeq Rapid Mode and HiSeqV2 chemistry. Illumina Protocol 15035788 Rev D, Apr 2014

tag: tissue

value: mouse xenograft primary breast tumour


title: GFP RNAi Input Replicate 2


title: MPP_β-glucan inj-day28-rep3


title: MPP_β-glucan inj-day28-rep4


title: MDA-MB-231_HM.LNm5_2

description:
Batch 1
Illumina index 10
HM_LNM5TOM_M3


title: MDA-MB-231_HM.LNm5_1

description:
Batch 1
Illumina index 9
HM_LNM5TOM_M1


title: MDA-MB-231_HM.LNm5_3

description:
Batch 1
Illumina index 11
HM_LNM5TOM_M4


title: MPP_β-glucan inj-day28-rep1


title: MPP_PBS inj-day28-rep4


title: MPP_PBS inj-day28-rep3


title: MDA-MB-231_LM2_6

description:
Batch 2
Illumina index 23
LM2_old_3


title: MDA-MB-231_HM.LNm5_6

description:
Batch 2
Illumina index 19
HM_old_3


title: MPP_PBS inj-day28-rep2


title: HSC_β-glucan inj-5FU-rep4


title: MDA-MB-231_LM2_4

description:
Batch 2
Illumina index 20
LM2_old_1


title: HSC_β-glucan inj-5FU-rep1


title: MDA-MB-231_LM2_3

description:
Batch 1
Illumina index 8
LM2TOM_M4


title: MDA-MB-231_LM2_1

description:
Batch 1
Illumina index 6
LM2TOM_M2


title: MDA-MB-231_LM2_2

description:
Batch 1
Illumina index 7
LM2TOM_M3


title: HSC_β-glucan inj-day28-rep4


title: MDA-MB-231_LM2_5

description:
Batch 2
Illumina index 22
LM2_old_2


title: MPP_PBS inj-day28-rep1


title: HSC_PBS inj-5FU-rep1


title: HSC_β-glucan inj-day28-rep3


title: MDA-MB-231_LNA_5

description:
Batch 2
Illumina index 22
LNA_old_2


title: HSC_β-glucan inj-day28-rep2


title: MDA-MB-231_LNA_4

description:
Batch 2
Illumina index 20
LNA_old_1


title: MDA-MB-231_LNA_3

description:
Batch 1
Illumina index 5
LNA_M4


title: HSC_β-glucan inj-day28-rep1


title: HSC_PBS inj-day28-rep4


title: HSC_PBS inj-day28-rep3


title: MDA-MB-231_LNA_1

description:
Batch 1
Illumina index 3
LNA_M1


title: HSC_PBS inj-day28-rep1


title: HSC_β-glucan inj-day7-rep3


title: MDA-MB-231_LNA_2

description:
Batch 1
Illumina index 4
LNA_M3


title: MDA-MB-231_ATCC_1

description:
Batch 1
Illumina index 1
NIC_M3


title: HSC_PBS inj-day7-rep2


title: MDA-MB-231_LNA_6

description:
Batch 2
Illumina index 23
LNA_old_3


title: HSC_PBS inj-day7-rep4


title: HSC_β-glucan inj-day7-rep1


title: HSC_PBS inj-day28-rep2


title: HSC_β-glucan inj-day7-rep2


title: HSC_PBS inj-day7-rep1


title: CcTJ-1

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

country: China

institute: Huazhong Agricultural University

data_processing:
Raw sequence reads were filtered for quality using the FASTX-Toolkit (Blankenberg et al. 2010) with default parameters by removing low-quality reads, and adaptor sequences. All clean reads were mapped to the citrus reference genome (Wu et al. 2014) using HISAT software (Kim et al. 2015) with default settings. Next, transcripts were assembled individually for each by StringTie (Pertea et al. 2015). Assembled transcripts were combined using Cuffmerge and then compared to annotation using Cuffcompare (Trapnell et al. 2012). Differential expression analysis was performs using the DESeq2 package (Love et al. 2014). A padj < 0.05 and 4-fold difference were used as a cutoff to identify differential expression genes (DEGs).
Genome_build: GCF_000493195.1
Supplementary_files_format_and_content:FPKM represent the expression of genes.

organism: Citrus x clementina

source_name: Citrus

growth_protocol: The materials from Clementine mandarin and Kumquat were collected in the experiment fields of the National Citrus Breeding Center at Huazhong Agricultural University (30°28′ N, 114°21′ E, 30).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies), and then treated with RNase-free DNase I (Life Technologies), according to the manufacturer's instructions.
Total RNA was sent to Beijing Genomics Institute (Shenzhen, China) where the libraries were produced and sequenced using Illumina's Genome Analyzer (Solexa).

treatment_protocol: No treatment

value: Fruit

tag: development stage

value: The five developmental stages of Clementine mandarin fruit were collected at 15, 30, 45, 100 and 180 days after flowering (DAF)


title: pQ input DNA

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
B6.HttQ111/+ mice obtained from JAX (Strain 003456).
The bedGraph file for the input sample is a merge of data for both the WT and pQ samples. File is available on GSM2345425.

data_processing:
We used Bowtie2 (v2.2.5) to align paired-end 25bp reads to release mm9 of the M.musculus genomic sequence obtained from UCSC
We extracted properly paired reads (Supplementary file .bed)
Peak-calling on each sample was performed with MACS v2.1, scaling each library to the size of the input DNA sequence library to improve comparability between samples
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Mouse striatum

growth_protocol: Cohorts of heterozygote and wild-type littermate mice were generated by crossing B6.HttQ111/+ and B6.Htt+/+ mice. Male mice were sacrificed at 122 ± 2 days of age (or 16 weeks) via a sodium phenobarbital based euthanasia solution (Fatal Plus, Henry Schein).

extract_protocol:
Striatal tissue was homogenized in glass dounce and fixed with formaldehyde for 10 min at room temperature.  Chromatin was fragmented using MNase digestion followed by sonication. SMAD3- or RNA Pol2-DNA complexes were isolated using antibody.
Modified ChIP-seq (see PMID 22025700)

treatment_protocol: Both hemispheres of each animal’s brain was microdissected on ice into striatum, cortex, and remaining brain regions. These tissues were snap frozen and stored in -80°C.

value: striatum

value: 4 months

tag: htt genotype

tag: gender

value: male


title: CcTJ-2

department: College of Horticulture and Forestry Science


title: RNAPol2_pQ_02_ChIPSeq

description: B6.HttQ111/+ mice obtained from JAX (Strain 003456).

value: Anti-RNA polymerase II CTD repeat YSPTSPS antibody [8WG16] (Abcam #ab817 [ChIP grade])


title: WT input DNA

value: WT


title: MDA-MB-231_ATCC_2

description:
Batch 1
Illumina index 2
NIC_M4


title: RNAPol2_WT_02_ChIPSeq


title: RNAPol2_WT_01_ChIPSeq


title: SMAD3_pQ_02_ChIPSeq

value: Anti-SMAD3 antibody (Abcam #ab28379 [ChIP grade])


title: MDA-MB-231_HM.LNm5_4

description:
Batch 2
Illumina index 16
HM_old_1


title: SMAD3_WT_01_ChIPSeq


title: RNAPol2_pQ_01_ChIPSeq


title: CcTJ-3


title: HSC_PBS inj-day7-rep3


title: ∆nusG UvsW_replicate2

city: Hyderabad

first: J

last: Gowrishankar

state: Telangana

address: Survey Nos. 728-730,Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: rRNA-depleted total RNA

data_processing:
bcl2fastq2 v2.15.0 (Demultiplexing), Fastqc 0.11.5 (read quality), Cutadapt-1.9.1 (adaptor trimming)
Reads were aligned using MG15655 as reference genome (NC000913.2) using Bowtie2 tool.
Aligned reads were designated to top and bottom strands using Samtools
Strand specific base read counts were determined for each of 4091 ORFs for the 15 samples
Genome_build: NC000913.2 MG1655
Supplementary_files_format_and_content: The text file contains sense and antisense raw base read counts for each of the 4091 ORFs for all the 15 samples, and the explanation key is included in the file.

organism: Escherichia coli K-12

source_name: Bacterial cells

growth_protocol: Viable clones of the UvsW-expressing strains GJ13531 (Δrho) and GJ13507 (ΔnusG) were obtained as white colonies from their respective shelter plasmid-carrying derivatives GJ13531/pHYD2411 and GJ13507 /pHYD2412 on glucose-minimal A plates supplemented with Xgal and IPTG at 200 μM (for Δrho) or 3 μM (for ΔnusG), as previously described

extract_protocol:
At the appropriate optical density, culture growth was instantaneously arrested by addition of an equal volume of chilled 100% ethanol, and the cells were stored at –80°C until they were processed for RNA extraction. The cells were lysed and total RNA was prepared by the hot phenol method essentially as described, after chromosomal DNA has been digested with RNase-free DNase.
Strand-specific RNA-Seq data were generated, following rRNA depletion with a Ribo-Zero kit, with the aid of the di-tagged cDNA strategy (ScriptSeq) on an Illumina NextSeq platform

treatment_protocol: Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations

tag: substrain

tag: genotype

value: {delta}nusG


title: SMAD3_pQ_01_ChIPSeq


title: SMAD3_WT_02_ChIPSeq


title: ∆nusG UvsW_replicate1

description: rRNA-depleted total RNA


title: ∆nusG UvsW_replicate3

description: rRNA-depleted total RNA


title: ∆rho UvsW_replicate3

description: rRNA-depleted total RNA

value: {delta}rho


title: ∆rho UvsW_replicate1

description: rRNA-depleted total RNA


title: WT glucose_replicate2

description: rRNA-depleted total RNA

value: wild type


title: ∆rho UvsW_replicate2

description: rRNA-depleted total RNA


title: WT UvsW_replicate1

description: rRNA-depleted total RNA


title: WT_glycerol_replicate2

description: rRNA-depleted total RNA


title: WT_glycerol_replicate3

description: rRNA-depleted total RNA


title: WT_glycerol_replicate1

description: rRNA-depleted total RNA


title: WT UvsW_replicate3

description: rRNA-depleted total RNA


title: WT glucose_replicate3

description: rRNA-depleted total RNA


title: WT glucose_replicate1

description: rRNA-depleted total RNA


title: WT UvsW_replicate2

description: rRNA-depleted total RNA


title: imb_koenig_2014_03_08_JKRS10_30000

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Basic quality checks were applied to all sequenced reads using FastQC  (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, iCLIP reads were filtered based on sequencing quality (Phred score) in the barcode region. Only reads with at most one position with a Phred score < 20 in the experimental barcode (positions 4 to 7) and without any position with a Phred score < 17 in the random barcode (positions 1 to 3 and 8 to 9) were kept for further analysis. The reads were then de-multiplexed based on the experimental barcode at positions 4 to 7 using Flexbar (version 2.4) without allowing mismatches (Dodt et al., 2012).  The following analysis steps were applied to all individual samples: Remaining adapter sequences were trimmed from the read ends using Flexbar (version 2.4) allowing one mismatch in 10 nt, requiring a minimal overlap of 1 nt between read and adapter as well as removing all reads with a remaining length of less than 24 nt (including the 9-nt barcode). After adapter trimming, quality checks were repeated on individual samples using FastQC. Afterwards, the first 9-nt of each read containing the barcode were trimmed off and added to the header of the read in the fastq file, such that the information is kept for downstream analysis.  Filtered and trimmed reads were mapped to the human genome (hg19/GRCh37) and its annotation (GENCODE release 19) (Harrow et al., 2012) using STAR (version 2.4.0h) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapped, unspliced reads were kept for further analysis. Un-spliced reads were defined as reads mapping without N-stretches longer than 5 in the CIGAR string. The nucleotide position upstream of each aligned read was considered as the ‘crosslink nucleotide’, with each read counted as individual ‘crosslink event’.   After mapping and filtering, duplicate reads were marked in selected samples using the dedup function from bamUtil (version 1.0.7) (https://github.com/statgen/bamUtil), which defines duplicates as reads whose 5' ends map to the same position in the genome. We then removed all marked duplicates with an identical random barcode representing technical duplicates, while all real biological duplicates with different random barcodes were kept.  Samtools (Li et al., 2009) was used to sort and index the resulting bam files. Based on the bam files, bedgraph files were created, considering only the position upstream of the 5' mapping position of the read. bedgraph files were then transformed to bigWig format using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010). BigWig files were normalized by the normalization factor ('N' in the equation in Figure 3A, more details can be found in the Supplement I) derived from our model.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: 795_binding_sites.bed: Bed file contains binding sites defined in the data.

organism: synthetic gene

source_name: 15µM U2AF65 replicate 4

extract_protocol:
The in vitro iCLIP protocol was developed by modifying the early steps of the standard iCLIP protocol (Huppertz et al., 2014; Sutandy et al., 2016). Briefly, beads were prepared by twice washing 40 µl of protein-G Dynabeads per sample with dilution buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate; corresponding to the lysis buffer in the in vivo iCLIP protocol). After the second wash, 40 µl of dilution buffer was added to resuspend the beads and then followed by mixing with 3 µg of anti-U2AF65 antibody. The beads were rotated at room temperature for 30-60 min. One-time high-salt buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) and twice dilution buffer washes were applied to wash the beads before proceeding with immunoprecipitation.  The in vitro transcripts were preheated for 5 min at 70°C to reduce large-scale RNA secondary structures. Titrated concentrations (30 nM, 50 nM, 150 nM, 250 nM, 450 nM, 750 nM, 1.5 µM, 3 µM, 5 µM, 15 µM) of U2AF65RRM12 and 2.2 nM in vitro transcript mix (eleven transcripts) were used for the Kd measurements. For the initial hnRNPC1 titration experiment, 1 µM U2AF65RRM12 was mixed with 6.75 nM in vitro transcript mix (nine transcripts; excluding MALAT1 and MIRLET7A2) and different concentrations of recombinant hnRNPC1 (200 nM, 500 nM, and 1 µM) in binding buffer. For the co-factor experiments, 500 nM U2AF65RRM12 was mixed with 6.75 nM in vitro transcript mix (nine transcripts) and different concentrations of eleven recombinant RBPs in binding buffer. In addition, 500 nM BSA was added to 500 nM U2AF65RRM12 and 6.75 nM in vitro transcript mix as a control for in vitro iCLIP co-factor assays.    All in vitro mixtures were incubated for 10 min at 37°C. After the incubation, the mixtures were placed on top of a parafilm-coated plate and UV-irradiated with 5 mJ/cm2 250 nm UV wavelength (Stratalinker 2400). The irradiated in vitro mixtures were pooled back to the tubes, and dilution buffer was added to fill the samples to a volume of 1 ml. To normalize the final in vitro iCLIP libraries, 10 µl of crosslinked mixture containing 250 nM U2AF65RRM12 and 6 nM NUP133 in vitro transcript was spiked in to each sample. Partial RNase digestion was performed by adding 10 µl of 1:1500 diluted RNase I (Ambion) to each sample. In addition, 2 µl of TURBO DNase was added to each sample to avoid DNA contamination. The sample mixtures were incubated for 3 min at 37°C, added to the prepared beads, and incubated for 2 h at 4°C. Beads were washed twice with high-salt buffer and twice with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20).   Henceforth, we followed the steps of the standard iCLIP protocol. Briefly, 3' end RNA dephosphorylation was performed by resuspending the beads in 20 µl of mixture containing 4 µl of 5x PNK buffer (350 mM Tris-HCl pH 6.5, 50 mM MgCl2, 5 mM DTT), 0.5 µl of PNK (NEB), 0.5 µl RNasin Ribonuclease Inhibitor (Promega), and 15 µl water, followed by incubation for 20 min at 37°C. The beads were washed once with wash buffer, once with high-salt buffer and twice with wash buffer.  For the linker ligation, pre-adenylated L3 linker (5’-App-AGATCGGAAGAGCGGTTCAG-dideoxycytidine-3') was ligated by resuspending the beads in the ligation mixture containing 5 µl 4x ligation buffer (200 mM Tris-HCl pH 7.8, 40 mM MgCl2, 4 mM DTT), 1 µl T4 RNA ligase (NEB), 0.5 µl RNasin, 1.5 µl pre-adenylated L3 linker (20 µM), 4 µl PEG400, and 8 µl water. The samples were incubated at 16°C overnight. The next day, the samples were washed twice with high-salt buffer and twice with wash buffer.   Interacting RNAs were radioactively labeled by resuspending the beads in hot PNK mix (0.2 µl PNK [NEB], 0.4 µl 10x PNK buffer [NEB], 0.4 µl 32P-γ-ATP, and 3 µl water). The beads were incubated at 1,100 rpm for 5 min at 37°C. Supernatants were removed and the beads were boiled in 20 µl 1x NuPAGE loading buffer (Invitrogen) for 5 min at 70°C. Boiled beads were placed on a magnetic rack. The supernatants were then loaded into the 4-12% NuPAGE Bis-Tris gel (Invitrogen) and run in 1x MOPS buffer for 50 min at 180 V. Protein-RNA complexes from the gel were transferred to a nitrocellulose membrane for 1 h at 30 V.  To extract the interacting RNAs, the membrane was cut into pieces and digested with 10 µl proteinase K (Roche) in 200 µl PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA) for 20 min at 37°C. Another 200 µl PK buffer containing 7 M urea were added for further 20 min incubation at 37°C. The RNA-containing mixtures were transferred to Phase Lock Gel Heavy tubes and mixed with 400 µl phenol/chloroform by shaking with 1,100 rpm for 5 min at 30°C. RNAs were extracted by centrifugation for 5 min at 16,000 xg to separate the phases followed by transferring the top aqueous phase containing RNAs to new tubes. The samples were then mixed with 0.75 µl glycoblue (Ambion), 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and incubated overnight at -20°C. To precipitate the RNAs, the samples were centrifuged with 21,000 xg for 20 min at 4°C, washed with 80% ethanol, and resuspended in 5 µl water.
cDNA synthesis was performed by adding 1 µl dNTP mix and 1 µl RT primers containing different barcode sequences to each sample, and incubating them for 5 min at 70°C. The reaction was started by adding RT mixture (4 µl 5x RT buffer [Invitrogen], 1 µl 0.1 M DTT, 0.5 µl RNasin, 0.5 µl Superscript III [Invitrogen], 7 µl water) to the samples and incubating them for 5 min at 25°C, 20 min at 42°C, 40 min at 50°C, 5 min at 80°C, and hold at 4°C. To hydrolyze hot RNA templates, 1.65 µl 1 M NaOH was added, followed by 20 min incubation at 98°C. After the incubation, 20 µl 1 M Hepes-NaOH was added to neutralize the samples’ pH. The cDNA libraries were mixed with 0.75 µl glycoblue, 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and incubated overnight at -20°C. The next day, the cDNA libraries were precipitated by spinning the samples with 21,000 xg for 20 min at 4°C, washing with 80% ethanol, and resuspension in 6 µl water.   cDNA libraries were mixed with 6 µl 2x TBE-urea loading buffer (Invitrogen), heated for 5 min at 80°C, and then loaded and run in a 6% TBE-urea gel for 40 min at 180 V. DNA low molecular weight size marker (NEB) was used as the ladder. The libraries were size-selected by cutting out the gel within the range of 80-100 nt based on the ladder. Each piece of the gel was then crushed into smaller pieces and mixed with 400 µl diffusion buffer (0.5 M ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% SDS). The mixtures were incubated for 30 min at 50°C, and moved to a Costar SpinX column (Corning) prepared with two 1 cm glass pre-filters (Whatman). To extract the cDNA libraries, the mixtures were spun at 16,000 xg for 5 min, and the eluates were added together with 400 µl phenol/chloroform into a Phase Lock Gel Heavy tube. The samples were incubated for 5 min at 30°C, and spun at 16,000 xg for 5 min to separate the phases. The aqueous top layers containing the libraries were moved to new tubes, mixed with 1 µl glycoblue, 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and then stored at -20°C overnight.  For circularization, libraries were centrifuged with 21,000 xg for 20 min at 4°C, washed with 80% ethanol, and resuspended in 8 µl of ligation mixture (0.8 µl 10x CircLigase buffer II [Epicentre], 0.4 µl 50 mM MnCl2, 0.3 µl CircLigase II [Epicentre], and 6.5 µl water). The libraries were transferred into PCR tubes and incubated for 1 h at 60°C. To re-linearize the libraries, 30 µl oligo annealing mix containing 3 µl FastDigest buffer (Thermo Fischer), 1 µl 10 µM cut_oligo (5’-GTTCAGGATCCACGACGACGACGCTCTTCaaaa-3'), and 26 µl water were added. The annealing program was performed by running the samples in succ

tag: technique

value: in vitro iCLIP

tag: iped-protein

tag: barcode

value: CACA


title: imb_koenig_2014_03_11_JKRS14_30000nM

source_name: 15µM U2AF65 replicate 1

value: CGCC


title: imb_koenig_2014_03_09_JKRS11_30000nM

source_name: 15µM U2AF65 replicate 2


title: imb_koenig_2014_03_08_JKRS10_50000

source_name: 25µM U2AF65 replicate 4

value: AGAA


title: imb_koenig_2014_03_12_JKRS15_30000nM

source_name: 15µM U2AF65 replicate 3

value: CGAG


title: imb_koenig_2014_03_08_JKRS10_10000

source_name: 5µM U2AF65 replicate 4

value: ATAC


title: imb_koenig_2014_03_09_JKRS11_10000nM

source_name: 5µM U2AF65 replicate 2

value: GAAA


title: imb_koenig_2014_03_08_JKRS10_6000

source_name: 3µM U2AF65 replicate 4


title: imb_koenig_2014_03_11_JKRS14_10000nM

source_name: 5µM U2AF65 replicate 1


title: imb_koenig_2014_03_12_JKRS15_06000nM

source_name: 3µM U2AF65 replicate 3


title: imb_koenig_2014_03_09_JKRS11_06000nM

source_name: 3µM U2AF65 replicate 2


title: imb_koenig_2014_03_11_JKRS14_06000nM

source_name: 3µM U2AF65 replicate 1


title: imb_koenig_2014_03_08_JKRS10_900

source_name: 750nM U2AF65 replicate 4


title: imb_koenig_2014_03_12_JKRS15_01500nM

source_name: 750nM U2AF65 replicate 3

value: TATT


title: imb_koenig_2014_03_12_JKRS15_03000nM

source_name: 1.5µM U2AF65 replicate 3


title: imb_koenig_2014_03_09_JKRS11_03000nM

source_name: 1.5µM U2AF65 replicate 2


title: imb_koenig_2014_03_11_JKRS14_01500nM

source_name: 750nM U2AF65 replicate 1

value: TTAA


title: imb_koenig_2014_03_08_JKRS10_500

source_name: 250nM U2AF65 replicate 4

value: ATCG


title: imb_koenig_2014_03_11_JKRS14_00900nM

source_name: 450nM U2AF65 replicate 1


title: imb_koenig_2014_03_09_JKRS11_00500nM

source_name: 250nM U2AF65 replicate 2


title: imb_koenig_2014_03_11_JKRS14_00500nM

source_name: 250nM U2AF65 replicate 1


title: imb_koenig_2014_03_09_JKRS11_01500nM

source_name: 750nM U2AF65 replicate 2

value: GCGT


title: imb_koenig_2014_03_08_JKRS10_300

source_name: 150nM U2AF65 replicate 4


title: imb_koenig_2014_03_09_JKRS11_00300nM

source_name: 150nM U2AF65 replicate 2


title: imb_koenig_2014_03_12_JKRS15_00300nM

source_name: 150nM U2AF65 replicate 3


title: imb_koenig_2014_03_08_JKRS10_1500

source_name: 450nM U2AF65 replicate 4

value: TACG


title: imb_koenig_2014_03_12_JKRS15_00900nM

source_name: 450nM U2AF65 replicate 3


title: imb_koenig_2014_03_11_JKRS14_00300nM

source_name: 150nM U2AF65 replicate 1


title: imb_koenig_2014_03_12_JKRS15_10000nM

source_name: 5µM U2AF65 replicate 3


title: imb_koenig_2016_01_05_JKRS24_1uM_U2AF65

data_processing:
Basic quality checks were applied to all sequenced reads using FastQC  (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, iCLIP reads were filtered based on sequencing quality (Phred score) in the barcode region. Only reads with at most one position with a Phred score < 20 in the experimental barcode (positions 4 to 7) and without any position with a Phred score < 17 in the random barcode (positions 1 to 3 and 8 to 9) were kept for further analysis. The reads were then de-multiplexed based on the experimental barcode at positions 4 to 7 using Flexbar (version 2.4) without allowing mismatches (Dodt et al., 2012).  The following analysis steps were applied to all individual samples: Remaining adapter sequences were trimmed from the read ends using Flexbar (version 2.4) allowing one mismatch in 10 nt, requiring a minimal overlap of 1 nt between read and adapter as well as removing all reads with a remaining length of less than 24 nt (including the 9-nt barcode). After adapter trimming, quality checks were repeated on individual samples using FastQC. Afterwards, the first 9-nt of each read containing the barcode were trimmed off and added to the header of the read in the fastq file, such that the information is kept for downstream analysis.  Filtered and trimmed reads were mapped to the human genome (hg19/GRCh37) and its annotation (GENCODE release 19) (Harrow et al., 2012) using STAR (version 2.4.0h) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapped, unspliced reads were kept for further analysis. Un-spliced reads were defined as reads mapping without N-stretches longer than 5 in the CIGAR string. The nucleotide position upstream of each aligned read was considered as the ‘crosslink nucleotide’, with each read counted as individual ‘crosslink event’.  After mapping and filtering, duplicate reads were marked in selected samples using the dedup function from bamUtil (version 1.0.7) (https://github.com/statgen/bamUtil), which defines duplicates as reads whose 5' ends map to the same position in the genome. We then removed all marked duplicates with an identical random barcode representing technical duplicates, while all real biological duplicates with different random barcodes were kept.  Samtools (Li et al., 2009) was used to sort and index the resulting bam files. Processed data files are derived as follows: In order to facilitate direct comparisons, reads from each in vitro iCLIP co-factor replicate were downsampled to 100,000 reads, followed by removal of PCR duplicates by means of random barcodes. Bedgraph files were created, considering only the position upstream of the 5' mapping position of the read. Spike-in normalization was done to account for differences in sequencing depth. iCLIP counts were represented as 'signal-over-background' (SOB). Background was defined as the 75% quantile of signal on all nucleotides within introns (minus binding sites +/- 2 nt) per in vitro transcript. The processed full length sample (imb_koenig_2016_01_02_JKRS21_U2AF65FL.se5N.plus.bw) was processed as follows: Based on the bam files, bedgraph files were created, considering only the position upstream of the 5' mapping position of the read. bedgraph files were then transformed to bigWig format using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010).
Genome_build: hg19/GRCh37

source_name: 1µM U2AF65 replicate 2


title: imb_koenig_2014_03_11_JKRS14_03000nM

source_name: 1.5µM U2AF65 replicate 1


title: imb_koenig_2016_01_02_JKRS21_U2AF65RRM12

source_name: 1µM U2AF65 replicate 1


title: imb_koenig_2016_01_05_JKRS24_500nM_U2AF65

source_name: 500nM U2AF65 replicate 4


title: imb_koenig_2016_01_02_JKRS21_U2AF65FL

source_name: 500nM U2AF65 full length


title: imb_koenig_2016_01_06_JKRS28_U2AF65

source_name: 500nM U2AF65 replicate 5


title: imb_koenig_2016_01_04_JKRS22_U2AF65RRM12_2

source_name: 500nM U2AF65 replicate 3


title: imb_koenig_2016_01_04_JKRS22_U2AF65RRM12_1

source_name: 500nM U2AF65 replicate 2


title: imb_koenig_2016_01_06_JKRS28_BSA_1

source_name: 500nM U2AF65 500nM BSA replicate 1


title: imb_koenig_2016_01_01_JKRS20_U2AF65RRM12

source_name: 500nM U2AF65 replicate 1


title: imb_koenig_2016_01_06_JKRS28_BSA_2

source_name: 500nM U2AF65 500nM BSA replicate 2


title: imb_koenig_2016_01_06_JKRS28_MBNL1

source_name: 500nM U2AF65 500nM MBNL1 replicate 2


title: imb_koenig_2016_01_01_JKRS20_MBNL1

source_name: 500nM U2AF65 500nM MBNL1 replicate 1


title: imb_koenig_2014_03_12_JKRS15_00500nM

source_name: 250nM U2AF65 replicate 3


title: imb_koenig_2016_01_05_JKRS24_RBM41vsU2AF65

source_name: 500nM U2AF65 288nM RBM41 replicate 2


title: imb_koenig_2016_01_01_JKRS20_KHDRBS1

source_name: 500nM U2AF65 213nM KHDRBS1 replicate 1


title: imb_koenig_2016_01_04_JKRS22_RBM41

source_name: 500nM U2AF65 288nM RBM41 replicate 1


title: imb_koenig_2016_01_01_JKRS20_SNRPA1

source_name: 500nM U2AF65 500nM SNRPA replicate 1


title: imb_koenig_2016_01_06_JKRS28_ELAVL1

source_name: 500nM U2AF65 114nM ELAVL1 replicate 2


title: imb_koenig_2016_01_01_JKRS20_RBM24

source_name: 500nM U2AF65 500nM RBM24 replicate 1

value: GGTC


title: imb_koenig_2016_01_05_JKRS24_FUBP1vsU2AF65

source_name: 500nM U2AF65 500nM FUBP1 replicate 2


title: imb_koenig_2016_01_04_JKRS22_BRUNOL6

source_name: 500nM U2AF65 280nM BRUNOL6 replicate 1


title: imb_koenig_2016_01_04_JKRS22_SNRPA

source_name: 500nM U2AF65 500nM SNRPA replicate 2


title: imb_koenig_2016_01_04_JKRS22_ELAVL1

source_name: 500nM U2AF65 114nM ELAVL1 replicate 1


title: imb_koenig_2016_01_04_JKRS22_FUBP1

source_name: 500nM U2AF65 500nM FUBP1 replicate 1


title: imb_koenig_2016_01_04_JKRS22_PCBP1

source_name: 500nM U2AF65 500nM PCBP1 replicate 1


title: imb_koenig_2016_01_06_JKRS28_PTBP1_2

source_name: 500nM U2AF65 200nM PTBP1 replicate 2


title: imb_koenig_2016_01_05_JKRS24_PCBP1vsU2AF65

source_name: 500nM U2AF65 500nM PCBP1 replicate 2


title: imb_koenig_2016_01_06_JKRS28_HNRNPC_2

source_name: 500nM U2AF65 200nM hnRNPC1 replicate 2


title: imb_koenig_2016_01_06_JKRS28_HNRNPC_1

source_name: 500nM U2AF65 200nM hnRNPC1 replicate 1


title: imb_koenig_2016_01_06_JKRS28_PTBP1_1

source_name: 500nM U2AF65 200nM PTBP1 replicate 1


title: imb_koenig_2016_01_05_JKRS24_500nM_hnRNPCvsU2AF65

source_name: 1µM U2AF65 500nM hnRNPC1 replicate 2


title: imb_koenig_2016_01_05_JKRS24_1000nM_hnRNPCvsU2AF65

source_name: 1µM U2AF65 1µM hnRNPC1 replicate 2


title: JG9-3

organism: Citrus japonica

source_name: Citrus

value: Fruit

value: The five developmental stages of Clementine mandarin fruit were collected at 15, 30, 45, 80 and 120  days after flowering (DAF)

tag: cultivar

value: Kumquat


title: imb_koenig_2016_01_02_JKRS21_HCvsU2_500nM

source_name: 1µM U2AF65 500nM hnRNPC1 replicate 1


title: imb_koenig_2016_01_06_JKRS28_KHDRBS1

source_name: 500nM U2AF65 213nM KHDRBS1 replicate 2


title: JG9-2


title: imb_koenig_2016_01_02_JKRS21_HCvsU2_200nM

source_name: 1µM U2AF65 200nM hnRNPC1 replicate 1


title: JG9-1


title: WT LPS 1hr-p65_ChIPSeq-rep.2

status: Public on Jan 31 2018

city: Seoul

first: Dongha

last: Kim

address: 599 Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
ChIP-seq reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie (Langmead et al. 2009). Only unique reads were used for peak calling and annotation by HOMER (Heinz et al. 2010)
BedGraph files were generated and viewed on the University of California at Santa Cruz Genome Browser
Genome_build: mm9

source_name: bone marrow-derived macrophages (BMDM)

growth_protocol: BMDMs were cultured in RPMI-1640+10% FBS(Gibco)+Antibiotics at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For ChIP experiments, cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with LSD1 and p65 antibodies.
ChIP-seq libraries were prepared for sequencing using the KAPA library preparation kit, according to the manufacturer's instructions

treatment_protocol: BMDMs were serum starved for 24 hours and treated with LPS (1 mg/ml) for 1 hour.

tag: antibody

tag: genotype/variation

value: wild type

tag: treatment

value: LPS 1hr

value: bone marrow-derived macrophages (BMDM)

tag: passages


title: WT 0hr-p65_ChIPSeq-rep.2

value: control

tag: cell type


title: WT LPS 1hr-p65_ChIPSeq-rep.1


title: imb_koenig_2016_01_05_JKRS24_200nM_hnRNPCvsU2AF65

source_name: 1µM U2AF65 200nM hnRNPC1 replicate 2

value: in vitro iCLIP

value: AGAA


title: imb_koenig_2016_01_06_JKRS28_RBM24

source_name: 500nM U2AF65 500nM RBM24 replicate 2

value: CGCC


title: WT 0hr-LSD1_ChIPSeq-rep.1


title: WT LPS 1hr-LSD1_ChIPSeq-rep.1


title: WT 0hr-LSD1_ChIPSeq-rep.2


title: WT LPS 1hr-LSD1_ChIPSeq-rep.2


title: WT 0hr-Input_ChIPSeq-rep.2

value: input


title: WT LPS 1hr-Input_ChIPSeq-rep.2


title: WT LPS 1hr-Input_ChIPSeq-rep.1


title: imb_koenig_2016_01_02_JKRS21_HCvsU2_1000nM

source_name: 1µM U2AF65 1µM hnRNPC1 replicate 1


title: WT_rep3

city: Ann Arbor

first: Aaron

middle: David

last: denDekker

state: MI

address: 1301 Catherine Street

department: Pathology

institute: University of Michigan

description:
barcode=GGCTAC
1792

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie Tophat with parameters --read-realign-edit-dist 0 -o 1717_60915 -i 50.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads
Reads were counted by htseq-count and normalized. Differentially expressed genes with log fold change ≥ ±1 and adjusted P value <0.05 were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: Text files contain normalized counts for each sample and differential expression data for MOF∆ vs. WT.
Supplementary_files_format_and_content: differential expression: resSigFDR5_logFC1.csv
Supplementary_files_format_and_content: normalized read counts: norm_counts.txt

source_name: whole liver

extract_protocol:
Liver was flash frozen on dry ice. RNA was extracted using Trizol followed by phenol/chloroform/ethanol extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.  Samples were barcoded and multiplexed onto a single lane.

value: liver

value: Mx1-Cre(-), MOF flox


title: MOFKO_rep1

description:
barcode=TTAGGC
1718

value: Mx1-Cre(+), MOF flox


title: Lsd1SA/SA KI(knock-in) 2hr-rep.2

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D).
read counts were obtained for each sample for RNA-seq data.
The reads were normalized (based on Generalized Linear Models ) using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Lsd1SA/SA KI(knock-in) 2hr_BMDMs

extract_protocol:
RNA were harvested using Trizol and RNA were extracted using Qiagen Rneasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BMDMs were serum starved for 24 hours and treated with LPS (1 mg/ml) for 2 hours.

tag: strain background

value: Lsd1SA/SA KI (knock-in)

tag: treated with

value: LPS for 2hrs


title: MOFKO_rep3

description:
barcode=ATTCCT
1791

tag: strain

tag: tissue


title: WT_rep2

description:
barcode=ACTGAT
1754


title: MOFKO_rep2

description:
barcode=GATCAG
1753


title: Lsd1SA/SA KI(knock-in) 0hr-rep.2

source_name: Lsd1SA/SA KI(knock-in) 0hr_BMDMs

value: none (untreated control)


title: Lsd1SA/SA KI(knock-in) 0hr-rep.1


title: WT_rep1

description:
barcode=CCGTCC
1717


title: Lsd1SA/SA KI(knock-in) 2hr-rep.1


title: WT 0hr-rep.2

source_name: WT 0hr_BMDMs


title: mobHSC

city: San Francisco

first: Yuet Wai

last: Kan

state: CA

address: 513 Parnassus Avenue, HSW901E

department: Medicine

institute: University of California, San Francisco

data_processing:
HiSeq Software Suite of HCS3.3.76, RTA2.7.6 and bcl2fastq2-v2.16 used for basecalling and quality scoring.
Sequenced reads cantaminated by adaptor sequence and of for low-quality were filtered, then mapped to hg19 gene reference refMrna using bowtie v2.1.0 with parameters -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Fragments Per Kilobase of gene per Million mapped reads(FPKM) were calculated using RSEM v1.2.12 with parameters --paired-end -p 8.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue source

value: Peripheral blood

value: without MLL-AF4


title: CD34_w

source_name: In vitro culture

value: In vitro culture

value: with MLL-AF4


title: CD34_w/o


title: WT 0hr-rep.1

value: wild type


title: MNC


title: WT-LPS 2hr-rep.1

source_name: WT-LPS 2hr_BMDMs

value: bone marrow-derived macrophages (BMDM)


title: WT 0hr-p65_ChIPSeq-rep.1

value: control


title: MN_w/o


title: WT 0hr-Input_ChIPSeq-rep.1


title: MN_wk12

source_name: Bone marrow

tag: host strain

value: NSG

value: Bone marrow

tag: post-transplant

value: 12 weeks


title: MN_wk16

value: 16 weeks


title: HSC_w


title: CD34_wk12


title: CD34_wk16


title: CD34_wk9

value: 9 weeks


title: WT-LPS 2hr-rep.2


title: PT2

city: Clermont Ferrand

first: Christiane

last: Forestier

address: 28 Place Henri Dunant

department: Université de Pharmacie

country: France

institute: Laboratoire Microorganismes Génome et Enironnement

description: Ribosomal RNA were removed with the RiboZero kit

data_processing:
Reads were mapped against the genome of the reference strain S. aureus  NCTC 8325 with the Bowtie2 v2.2.6 software. Only reads without mismatch were counted. Differentially expressed genes between biofilm treated with fosfomycin and its control (not treated) were determined by RSEM v1.2.23 software. Transcripts were considered at differentially expressed using the following criteria :  adjusted p-value< 0.01 and |fold-change| > 2.
Transcrits were identified using a BLASTn searches against the reference strain S. aureus  NCTC 8325.
genome build: NC_007795.1

organism: Staphylococcus aureus

source_name: Biofilm PT2

extract_protocol:
Libraries were produced by the ScriptSeq Complete Kit (Bacteria - Illumina)
RNA-seq : Libraries were sequenced with the Hiseq2500 system (Illumina) with a paired-end protocol and read lengths of 100bp

value: sessile cells

tag: condition

value: 4h-old-biofilm formed without fosfomycin - Replica 2


title: CT3

source_name: Biofilm CT3

value: 24h-old-biofilm not treated with fosfomycin  for 24h- Replica 3


title: PF1

source_name: Biofilm PF1

value: 4h-old-biofilm formed with 0.25µg/mL of fosfomycin - Replica 1


title: PF3

source_name: Biofilm PF3

value: 4h-old-biofilm formed with 0.25µg/mL of fosfomycin - Replica 3


title: CT1

source_name: Biofilm CT1

value: 24h-old-biofilm not treated with fosfomycin  for 24h - Replica 1


title: CF2

source_name: Biofilm CF2

value: 24h-old-biofilm treated with 16 µg/mL of fosfomycin for 24h - Replica 2


title: CF3

source_name: Biofilm CF3

value: 24h-old-biofilm treated with 16 µg/mL of fosfomycin for 24h - Replica 3


title: CF1

source_name: Biofilm CF1

value: 24h-old-biofilm treated with 16 µg/mL of fosfomycin for 24h - Replica 1


title: PT1

source_name: Biofilm PT1

value: 4h-old-biofilm formed without fosfomycin - Replica 1


title: Epc_S2_GFPChIP2

city: baltimore

first: Xin

last: Chen

state: MD

address: 3400 N Charles St

department: Biology

institute: The Joihns Hopkins University

data_processing:
FASTQ raw data files were filtered with quality control software Fastqc (www.bioinformatics.babraham.ac.uk/projects/fastqc/). BOWTIE program (version 0.12.7113) was utilized to align reads to Drosophila genome (dm3), with the running parameters (bowtie -p 8 -t -a --phred33 -quals -n 2 -e 70 -l 48 -m 1 --best --strata). Pair-end reads were treated as separate single reads. At each chromosome position, only one read was retained to get a non-redundant read count data. SAM formatted alignment files will be uploaded onto NIH GEO database upon paper acceptance. Enrichment of reads across the genome was analyzed by MACS2 for peak calling. The peak calling was performed with paired experiment and control genome input under default parameter settings. UCSC genome browser customized visualization tools were also applied in the analysis. SAMtools software suite was utilized to convert between related read formats.
Genome_build: Drosophila genome (dm3),

source_name: Drosohpila s2 cells

growth_protocol: To perform S2 cell ChIP, transfection with 1ug Actin-Gal4 and 1ug UAS-E(Pc) cDNA-GFP plasmids were done following manufacturer’s protocol of Effectene® Transfection Reagent (#301425, Qiagen). S2 cells were split the day before the transfection experiment. On the day of transfection, 4X10^6 cells per 25 cm2 flask were seeded in 4ml growth medium containing serum and antibiotics. After transfection, S2 cells were incubated at room temperature for 40-48h to obtain maximal level of gene expression.

extract_protocol:
S2 cell fixation and following ChIP were performed with ChIP-IT high sensitivity kit (#53040, Active motif) following the manufacturer’s instruction. Sonication of S2 cells were done with Bioruptor sonicator (UCD-200, diagenode) using following setting 0.5min on, 1min off for total 15min. Fragment size were around 500-600bp. ChIP grade GFP antibody (Abcam, ab290) were used to pulled down sheared chromatin.
Libraries were generated using reagents provided in the Illumina TruSeq ChIP Sample Preparation Kit (IP-202-1012).

value: S2 cells

tag: transfection

value: Actin-Gal4 and UAS-E(Pc) cDNA-GFP plasmids

tag: chip-antibody

value: GFP (Abcam, ab290)


title: Epc_S2_input2


title: MN_w

value: In vitro culture

value: with MLL-AF4


title: Epc_S2_GFPChIP1


title: NChIP_Input_(20170405_JT_HsSc_1bS0IN)

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: NChIP_Total MNase digested DNA

data_processing:
Library strategy:  CUT-and-RUN
Genome_build: UCSC hg19
Paired reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters -q 30 (quality) and -L 25 (minimum merged pair length). SeqPrep also removed adaptors and low-quality reads. The supplementary fasta file contains the SeqPrep merged pairs.

source_name: Total MNase digested DNA

extract_protocol:
NChIP_Salt.rtf
PMID 25827087

tag: cell line

value: CENP-A-FLAG expressing HT1080-1b cells

value: FLAG magnetic beads (Sigma-Aldrich; #M8823)


title: NChIP_500mM_IP_(20170405_JT_HsSc_1b_M2500IP)

description: Micrococcal nuclease digested 500 mM salt fraction

source_name: Chromatin immunoprecipitated DNA


title: NChIP_300mM_IP_(20170405_JT_HsSc_1b_M2S300IP)

description: Micrococcal nuclease digested 300 mM salt fraction


title: cde-1 rep2

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
For differential expression analysis, genes were only included in the analysis if they had at least 1 count per million in all of the control samples or all of the experiment samples.
After applying this filter, differentially expressed genes were then called using EdgeR (Robinson, et al. 2010).
For the correlation matrix, Pairwise Pearson correlation values were calculated between all samples.
genome build: C.elegans WS220 / Ce10.
Supplementary_files_format_and_content: Raw Counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological triplicates.

extract_protocol:
Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines.
mRNA libraries were prepared using the NEBNext Ultra directional RNA library kit (NEB) with poly(A) selection and deep sequencing was produced with an Illumina HiSeq machine (single read 50).

treatment_protocol: Orsay virus infection as described above.

tag: agent

value: Orsay virus


title: cde-1 rep3


title: WT rep2

value: WT


title: WT rep3


title: PF2

source_name: Biofilm PF2

value: sessile cells

value: 4h-old-biofilm formed with 0.25µg/mL of fosfomycin - Replica 2


title: CT2

source_name: Biofilm CT2

value: 24h-old-biofilm not treated with fosfomycin  for 24h- Replica 2


title: PT3

source_name: Biofilm PT3

value: 4h-old-biofilm formed without fosfomycin - Replica 3


title: CUTnSalt_K27_pe_(20170405_SH_HsSc_K27_pe_0321)

description: CUT&RUN human H3K27me3 pellet 10 min

source_name: Chromatin immunocleavage and release

value: human K562 cells

tag: antibody

value: anti-K27me3 Cell Signalling #9733


title: NChIP_No_salt_IP_(20170405_JT_HsSc_1b_M2S0IP)

description: Micrococcal nuclease digested 0 mM salt fraction


title: WT rep1

tag: genotype/variation


title: CUTnSalt_K27_hi_(20170405_SH_HsSc_K27_hi_0321)

description: CUT&RUN human H3K27me3 high-salt 10 min


title: cde-1 rep1


title: MDA-MB-231_control_ASO_R2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
Remove adapter reads (Cutadapt v1.6). Trim low quality base calls from both ends,  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v25). Genes with very low expression (<5  counts) were removed from the analysis.
Differential gene expression was calculated by using the DESeq2 version 1.8.1 package in R 3.2.0.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the normalized counts from the HTSeq-count quantification and DESeq2 analysis.

source_name: mammary gland/breast epithelial cell

growth_protocol: MDA-MB-231 cells were grown in DMEM: F12 (Hyclone-SH30271), 10% FBS (Atlanta Biologicals), Pen/Strep (Life Technologies) and Glutamine (Life Technologies).

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit

treatment_protocol: Cells were seeded at 2.5x105 cells per well in a 6-well plate. Cells were transfected with 25 nM negative control A ASO or ASO targeting MANCR using DharmaFECT 4 (Dharmacon). 48 hours post-transfection, cells were washed twice with phosphate buffered saline (PBS) and stored at -80C in TRIzol.

value: breast

value: metastatic site derived

tag: neoplasia type

value: adenocarcinoma

tag: atcc id

value: ATCC HTB-26


title: CUTnSalt_K27_lo_(20170405_SH_HsSc_K27_lo_0321)

description: CUT&RUN human H3K27me3 low-salt 10 min


title: MDA-MB-231_MANCR_ASO_R1

tag: cell type


title: MDA-MB-231_MANCR_ASO_R2


title: MDA-MB-231_MANCR_ASO_R3


title: MDA-MB-231_control_ASO_R1


title: Epc_S2_input1

value: S2 cells

value: Actin-Gal4 and UAS-E(Pc) cDNA-GFP plasmids


title: MDA-MB-231_control_ASO_R3


title: CUTnSalt_IgG_pe_(20170405_SH_HsSc_IgG_pe_0321)

description: CUT&RUN human IgG pellet 10 min

value: guinea pig anti-rabbit Antibodies Online ABIN101961


title: CUTnSalt_IgG_lo_(20170405_SH_HsSc_IgG_lo__0321)

description: CUT&RUN human IgG low-salt 10 min


title: NChIP_150mM_IP_(20170405_JT_HsSc_1b_M2S150IP)

description: Micrococcal nuclease digested 150 mM salt fraction

value: CENP-A-FLAG expressing HT1080-1b cells


title: CUTnSalt_IgG_hi_(20170405_SH_HsSc_IgG_hi__0321)

description: CUT&RUN human IgG high-salt 10 min


title: CUTnSalt_CeC_lo_(20170405_SH_HsSc_CeC_lo_0321)

description: CUT&RUN human CENP-C low-salt 10 min

value: anti-CENP-C Abcam ab33034


title: CUTnSalt_CeC_pe_(20170405_SH_HsSc_CeC_pe_0321)

description: CUT&RUN human CENP-C pellet 10 min


title: CUTnSalt_CeB_hi_(20170405_SH_HsSc_CeB_hi_0321)

description: CUT&RUN human CENP-B high-salt_1 10 min

value: anti-CENP-B Abcam ab25734


title: CUTnSalt_CeB_lo_(20170405_SH_HsSc_CeB_lo_0321)

description: CUT&RUN human CENP-B low-salt_1 10 min


title: CUTnSalt_CeB_pe_(20170405_SH_HsSc_CeB_pe_0321)

description: CUT&RUN human CENP-B pellet_1 10 min


title: CUTnSalt_CeB_pe_N30_(20170510_SH_HsSc_CeBpN30m0501)

description: CUT&RUN human CENP-B pellet_2 30 min

data_processing:
Library strategy:  CUT-and-RUN
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19.  2. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to UCSC sacCer3.  3. We extracted properly paired reads from both alignments (Supplementary files .bed.gz .SC.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to S.cervisiae) to create a normalized yeast track file (Supplementary file .bedgraph.gz).


title: CUTnSalt_CeB_hi_N30_(20170510_SH_HsSc_CeBhN30m0501)

description: CUT&RUN human CENP-B high-salt_2 30 min


title: CUTnSalt_CeC_hi_(20170405_SH_HsSc_CeC_hi_0321)

description: CUT&RUN human CENP-C high-salt 10 min


title: CUTnSalt_CeB_pe_N10_(20170510_SH_HsSc_CeBpN10m0501)

description: CUT&RUN human CENP-B pellet_2 10 min


title: CUTnSalt_CeB_lo_N30_(20170516_SH_HsSc_CeBlN30m0501)

description: CUT&RUN human CENP-B low-salt_2 30 min


title: CUTnSalt_CeB_hi_N10_(20170510_SH_HsSc_CeBhN10m0501)

description: CUT&RUN human CENP-B high-salt_2 10 min


title: Single P7 FB mouse dopaminergic neuron (TH_020_H12)

city: Baltimore

first: Loyal

middle: A

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description: scRNA-Seq

data_processing:
Paired-end reads were aligned to the mouse reference genome (mm10) supplemented with the Th-EGFP+ transgene contig, using HISAT2 with default parameters except: -p 8.
Aligned reads from individual samples were quantified against a reference transcriptome (GENCODE vM8) supplemented with the addition of the eGFP transcript.
Quantification was performed using cuffquant with default parameters and the following additional arguments: --no-update-check –p 8.
Normalized expression estimates across all samples were obtained using cuffnorm with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing a matrix of normalized FPKM expression estimates for each gene/cell

molecule: polyA RNA

source_name: Single P7 FB mouse Th-eGFP+ sorted dopaminergic neuron

growth_protocol: The Th:EGFP BAC transgenic mice (Tg(Th-EGFP)DJ76Gsat/Mmnc) used in this study were generated by the GENSAT Project and were purchased through the Mutant Mouse Resource & Research Centers (MMRRC) Repository. Mice were maintained on a Swiss Webster (SW) background with female SW mice obtained from Charles River Laboratories. The Tg(Th-EGFP)DJ76Gsat/Mmnc line was primarily maintained through matings between Th:EGFP positive, hemizygous male mice and wild-type SW females (dams). Timed matings for cell isolation were similarly established between hemizygous male mice and wild-type SW females. The observation of a vaginal plug was defined as embryonic day 0.5 (E0.5). All work involving mice (husbandry, colony maintenance and euthanasia) were reviewed and pre-approved by the institutional care and use committee.

extract_protocol:
Resected brain tissues were dissociated using papain (Papain Dissociation System, Worthington Biochemical Corporation; Cat#: LK003150) following the trehalose-enhanced protocol reported by Saxena, et. al, 201217 with the following modifications: The dissociation was carried out at 37oC in a sterile tissue culture cabinet. During dissociation, all tissues at all timepoints were triturated every 10 minutes using a sterile Pasteur pipette. For E15.5 tissues, this was continued for no more than 40 minutes. For P7, this was continued for up to 1.5 hours or until the tissue appeared to be completely dissociated. Additionally, for P7 tissues, after dissociation but before cell sorting, the cell pellets were passed through a discontinuous density gradient in order to remove cell debris that could impede cell sorting. This gradient was adapted from the Worthington Papain Dissociation System kit. Briefly, after completion of dissociation according to the Saxena protocol, the final cell pellet was resuspended in DNase dilute albumin-inhibitor solution, layered on top of 5 mL of albumin-inhibitor solution, and centrifuged at 70g for 6 minutes. The supernatant was then removed.  For each timepoint-region condition, pellets were resuspended in 200 μL of media without serum comprised of DMEM/F12 without phenol red, 5% trehalose (w/v), 25 μM AP-V, 100 μM kynurenic acid, and 10 μL of 40 U/μl RNase inhibitor (RNasin® Plus RNase Inhibitor, Promega) at room temperature. The resuspended cells were then passed through a 40 uM filter and introduced into a FACS machine (Beckman Coulter MoFlo Cell Sorter or Becton Dickinson FACSJazz). Viable cells were identified via propidium iodide staining, and individual neurons were sorted based on their fluorescence (EGFP+ intensity, See Figure S4B) directly into lysis buffer in individual wells of 96-well plates for single-cell sequencing (2 μL Smart-Seq2 lysis buffer + RNAase inhibitor, 1 μL oligo-dT primer, and 1 μL dNTPs) according to Picelli et al., 201418. Blank wells were used as negative controls for each plate collected. Upon completion of a sort, the plates were briefly spun in a tabletop microcentrifuge and snap-frozen on dry ice. Single cell lysates were subsequently kept at -80°C until cDNA conversion.
Library preparation and amplification of single-cell samples were performed using a modified version of the Smart-Seq2 protocol18. Briefly, 96-well plates of single cell lysates were thawed to 4°C, heated to 72°C for 3 minutes, then immediately placed on ice. Template switching first-strand cDNA synthesis was performed as described above using a 5’-biotinylated TSO oligo. cDNAs were amplified using 20 cycles of KAPA HiFi PCR and 5’-biotinylated ISPCR primer. Amplified cDNA was cleaned with a 1:1 ratio of Ampure XP beads and approximately 200 pg was used for a one-quarter standard sized Nextera XT tagmentation reaction. Tagmented fragments were amplified for 14 cycles and dual indexes were added to each well to uniquely label each library. Concentrations were assessed with Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and samples were diluted to ~2 nM and pooled. Pooled libraries were sequenced on the Illumina HiSeq 2500 platform to a target mean depth of ~8.0 x 105 50bp paired-end fragments per cell at the Hopkins Genetics Research Core Facility.

treatment_protocol: At 15.5 days after the timed mating, pregnant dams were euthanized and the entire litter of embryonic day 15.5 (E15.5) embryos were dissected out of the mother and immediately placed in chilled Eagle’s Minimum Essential Media (EMEM). Individual embryos were then decapitated and heads were placed in fresh EMEM on ice. Embryonic brains were then removed and placed in Hank’s Balanced Salt Solution (HBSS) without Mg2+ and Ca2+ and manipulated while on ice. The brains were immediately observed under a fluorescent stereomicroscope and EGFP+ brains were selected. EGFP+ regions of interest in the forebrain (hypothalamus) and the midbrain were then dissected and placed in HBSS on ice. This process was repeated for each EGFP+ brain. Brain regions from four EGFP+ mouse pups were pooled together for dissociation.  For P7 brains, pregnant females were sorted into their own cages and checked daily for newly born pups. The morning the pups were born was considered day P0. Once the mice were aged to P7, all the mice from the litter were euthanized and the brains were then quickly dissected and placed in HBSS without Mg2+ and Ca2+ on ice. As before, the brains were then observed under a fluorescent microscope, EGFP+ status for P7 mice was determined, and EGFP+ brains were retained.  For each EGFP+ brain, the entire olfactory bulb was first resected and placed in HBSS on ice. Immediately thereafter, the EGFP+ forebrain and midbrain regions for each brain were resected and also placed in distinct containers of HBSS on ice. Brain regions from five EGFP+ P7 mice were pooled together for dissociation.

tag: well

value: B

value: TCGACGTC

value: TCTCTCCG

value: TCGACGTC,TCTCTCCG

tag: project

value: TH

tag: age

tag: region

value: FB

value: Th-eGFP+ sorted dopaminergic neuron

value: FALSE


title: CUTnSalt_CeB_pe_D30_(20170510_SH_HsSc_CeBpD30m0501)

description: CUT&RUN human CENP-B pellet_2 30 min

value: human K562 cells


title: CUTnSalt_CeB_lo_N10_(20170510_SH_HsSc_CeBlN10m0501)

description: CUT&RUN human CENP-B low-salt_2 10 min


title: CUTnSalt_CeB_lo_D30_(20170510_SH_HsSc_CeBlD30m0501)

description: CUT&RUN human CENP-B low-salt_2 30 min


title: CUTnSalt_CeAm_pe_(20170405_SH_HsSc_CeAm_pe_0306)

description: CUT&RUN human CENP-A pellet_1 10 min

value: anti-CENP-A Abcam ab13939


title: CUTnSalt_CeB_lo_D10_(20170516_SH_HsSc_CeBlD10m0501)

description: CUT&RUN human CENP-B low-salt_3 10 min


title: CUTnSalt_CeB_hi_D10_(20170510_SH_HsSc_CeBhD10m0501)

description: CUT&RUN human CENP-B high-salt_3 10 min


title: CUTnSalt_CeAm_lo_(20170405_SH_HsSc_CeAm_lo_0306)

description: CUT&RUN human CENP-A low-salt_1 10 min


title: Single P7 FB mouse dopaminergic neuron (TH_020_H11)

description: scRNA-Seq

value: TGCAGCTA

value: TGCAGCTA,TCTCTCCG

value: TRUE


title: CUTnSalt_CeAm_hi_(20170405_SH_HsSc_CeAm_hi_0306)

description: CUT&RUN human CENP-A high-salt_1 10 min


title: Single P7 FB mouse dopaminergic neuron (TH_020_H09)

description: scRNA-Seq

value: CCTAAGAC

value: CCTAAGAC,TCTCTCCG


title: Single P7 FB mouse dopaminergic neuron (TH_020_H07)

description: scRNA-Seq

value: TAGCGCTC

value: TAGCGCTC,TCTCTCCG


title: Single P7 FB mouse dopaminergic neuron (TH_020_H10)

description: scRNA-Seq

value: B

value: CGATCAGT

value: CGATCAGT,TCTCTCCG


title: Single P7 FB mouse dopaminergic neuron (TH_020_H08)

description: scRNA-Seq

value: ACTGAGCG

value: TCTCTCCG

value: ACTGAGCG,TCTCTCCG


title: Single P7 FB mouse dopaminergic neuron (TH_020_H06)

description: scRNA-Seq

value: ATGCGCAG

value: ATGCGCAG,TCTCTCCG

value: TH

value: FB

value: Th-eGFP+ sorted dopaminergic neuron


title: OuJ_inf3

city: Montreal

first: Samantha

last: Gruenheid

state: Quebec

address: 3649 Promenade Sir-William-Osler, Room 365

department: Microbiology and Immunology

country: Canada

institute: McGill University

data_processing:
RNA quality was assessed by a Bioanalyzer
Trimming was done with the Trimmomatic software
filtered reads were aligned to the mm10 mouse genome assembly with the combination of the TopHat/Bowtie software
Genome_build: mm10
Supplementary_files_format_and_content: text files include raw counts for each sample

source_name: Distal colonic tissues

extract_protocol:
Distal colons were harvested and snap frozen in liquid nitrogen for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C. rodentium strain DBS100 was grown overnight in 3 ml of LB medium shaking at 37oC. Five-week-old female mice (three per group) were infected by oral gavage with 0.1 ml of LB medium containing 2.7 x 108 colony-forming units of bacteria

tag: strain

value: Infected

value: 5 weeks

tag: post-infection period

value: 9 days

tag: genotype

value: WT


title: CUTnSalt_CeB_hi_D30_(20170510_SH_HsSc_CeBhD30m0501)

description: CUT&RUN human CENP-B high-salt_2 30 min

value: human K562 cells

value: anti-CENP-B Abcam ab25734


title: CUTnSalt_CeA_lo_(20170405_SH_HsSc_CeA_lo_0321)

description: CUT&RUN human CENP-A low-salt_2 10 min

value: anti-CENP-A Abcam ab13939


title: OuJ_inf2

tag: condition


title: OuJ_inf1


title: OuJ_ui2

value: Uninfected


title: O.B6_inf4

value: introgressed segment of chromosome 15 from C57BL/6 mice


title: CUTnSalt_CeA_pe_(20170405_SH_HsSc_CeA_pe_0321)

description: CUT&RUN human CENP-A pellet_2 10 min


title: CUTnSalt_CeA_hi_(20170405_SH_HsSc_CeA_hi_0321)

description: CUT&RUN human CENP-A high-salt_2 10 min


title: Single P7 FB mouse dopaminergic neuron (TH_020_H05)

description: scRNA-Seq

value: B

value: TACGCTGC

value: TACGCTGC,TCTCTCCG

value: TRUE


title: OuJ_ui4


title: Single P7 FB mouse dopaminergic neuron (TH_020_H04)

description: scRNA-Seq

value: CGGAGCCT

value: TCTCTCCG

value: CGGAGCCT,TCTCTCCG


title: Single P7 FB mouse dopaminergic neuron (TH_020_H03)

description: scRNA-Seq

value: GCGTAGTA

value: GCGTAGTA,TCTCTCCG

value: TH

value: FB

value: Th-eGFP+ sorted dopaminergic neuron


title: CUTnSalt_CeB_pe_D10_(20170510_SH_HsSc_CeBpD10m0501)

description: CUT&RUN human CENP-B pellet_3 10 min

value: human K562 cells


title: O.B6_inf2

value: Infected

value: 5 weeks

value: 9 days


title: Single P7 FB mouse dopaminergic neuron (TH_020_H02)

description: scRNA-Seq

value: GGAGCTAC

value: GGAGCTAC,TCTCTCCG


title: O.B6_inf1

value: introgressed segment of chromosome 15 from C57BL/6 mice


title: shLAD1_EGF_40min_2

city: Rehovot

first: Yehoshua

last: Enuka

address: Herzl 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
sixty base-pair long, single-end, RNA-Seq reads were aligned to the human genome with STAR (Dobin et al., 2013).
Reads per gene were counted using the summarizeOverlaps function from the GenomicAlignments package in R with the Refseq transcriptome as reference. Reads per gene were normalized across samples using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized (according to library size) reads for all Refseq genes

growth_protocol: HCC70 cells were cultured in RPMI Medium supplemented with 10% fetal bovine serum

extract_protocol:
RNA was extracted using the 5-prime kit and poly-A selected on magnetic beads using the TruSeq RNA Library Preparation Kit v2
Library were constructed using the TruSeq RNA Library Preparation Kit v2

treatment_protocol: Cells were starved overnight in medium without serum and then stimulated with 50ng/ml EGF 0,40,240 minutes before sequencing

value: stably expressing LAD1 targeting shRNA

tag: treated with

value: 50ng/ml EGF for 40min


title: O.B6_ui3

value: Uninfected


title: Single P7 FB mouse dopaminergic neuron (TH_020_H01)

description: scRNA-Seq

value: B

value: ACTCGCTA

value: TCTCTCCG

value: ACTCGCTA,TCTCTCCG

value: FALSE


title: O.B6_ui1


title: shLAD1_EGF_240min_2

value: 50ng/ml EGF for 240min


title: Single P7 FB mouse dopaminergic neuron (TH_020_G12)

description: scRNA-Seq

value: A

value: ATCTCAGG

value: CGTCTAAT

value: ATCTCAGG,CGTCTAAT

value: TH

value: FB

value: Th-eGFP+ sorted dopaminergic neuron


title: shLAD1_EGF_240min_1


title: Single P7 FB mouse dopaminergic neuron (TH_020_G11)

description: scRNA-Seq

value: GCTCATGA

value: GCTCATGA,CGTCTAAT

value: TRUE


title: OuJ_ui1

value: Uninfected

value: 5 weeks

value: WT


title: BB2309

city: New York

first: Yu

state: NY

address: 1237 York Ave.

institute: Memorial Sloan Kettering Cance

data_processing:
The sequenced reads from fastq files were mapped to mm9 using STAR and and downstream processing was done using cuffquant
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

source_name: BRAF V600E Bap1 KO

extract_protocol:
RNA was harvested using Ribozol and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Skin tumor

value: BRAF V600E Bap1 KO


title: BB2306


title: shLAD1_starve_2

tag: cell line

value: stably expressing LAD1 targeting shRNA

value: none (untreated)


title: BG2299

source_name: GNA11 Q209L Bap1 KO

value: GNA11 Q209L Bap1 KO


title: Single P7 FB mouse dopaminergic neuron (TH_020_G10)

description: scRNA-Seq

value: A

value: GTAGAGGA

value: GTAGAGGA,CGTCTAAT


title: TGB 609


title: BG2218_T3


title: BG2218_T1


title: shScramble_EGF_240min_1

value: stably expressing scramble shRNA control

value: 50ng/ml EGF for 240min


title: Single P7 FB mouse dopaminergic neuron (TH_020_G09)

description: scRNA-Seq

value: AAGAGGCA

value: CGTCTAAT

value: AAGAGGCA,CGTCTAAT

value: TH

value: FB

value: Th-eGFP+ sorted dopaminergic neuron

value: FALSE


title: Single P7 FB mouse dopaminergic neuron (TH_020_G08)

description: scRNA-Seq

value: CGAGGCTG

value: CGAGGCTG,CGTCTAAT

value: TRUE


title: O.B6_ui4

value: Uninfected

value: 5 weeks

value: introgressed segment of chromosome 15 from C57BL/6 mice


title: shScramble_EGF_240min_2


title: BG2407

source_name: GNA11 Q209L

value: Skin tumor

value: GNA11 Q209L


title: Single P7 FB mouse dopaminergic neuron (TH_020_G07)

description: scRNA-Seq

value: A

value: CTCTCTAC

value: CTCTCTAC,CGTCTAAT


title: BB2145

value: BRAF V600E Bap1 KO


title: MO91

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000> and masked genes with length <200
Supplementary_files_format_and_content: matrix of fpkm values per sample

source_name: osteosarcoma

extract_protocol:
total RNA was extracted using Thermo Fisher TotalRNA kit
TruSeq RNA v2
average insert size of 200 selected

value: Sleeping Beauty-p53 Dominant Negative

value: osteosarcoma

tag: tumor type

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_G06)

description: scRNA-Seq

value: TAGGCATG

value: CGTCTAAT

value: TAGGCATG,CGTCTAAT

value: TH

value: FB

value: Th-eGFP+ sorted dopaminergic neuron


title: shScramble_EGF_40min_2

value: stably expressing scramble shRNA control

value: 50ng/ml EGF for 40min


title: shScramble_EGF_40min_1

value: EGF


title: MO89


title: MO88


title: Single P7 FB mouse dopaminergic neuron (TH_020_G05)

description: scRNA-Seq

value: GGACTCCT

value: GGACTCCT,CGTCTAAT

value: TRUE


title: shScramble_starve_2

value: none (untreated)


title: MO87-1


title: Single P7 FB mouse dopaminergic neuron (TH_020_G04)

description: scRNA-Seq

value: A

value: TCCTGAGC

value: TCCTGAGC,CGTCTAAT

value: FALSE


title: MO82MC

value: Sleeping Beauty-p53 Dominant Negative

value: osteosarcoma

value: metastatic cell line


title: shScramble_starve_1


title: MO82

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_G03)

description: scRNA-Seq

value: AGGCAGAA

value: CGTCTAAT

value: AGGCAGAA,CGTCTAAT

value: TH

value: FB


title: MO82C

value: primary cell line


title: Single P7 FB mouse dopaminergic neuron (TH_020_G02)

description: scRNA-Seq

value: CGTACTAG

value: CGTACTAG,CGTCTAAT

value: Th-eGFP+ sorted dopaminergic neuron


title: MO60C


title: MO67


title: BG2378

value: Skin tumor

value: GNA11 Q209L


title: MO68


title: MO60-1


title: Single P7 FB mouse dopaminergic neuron (TH_020_G01)

description: scRNA-Seq

value: A

value: TAAGGCGA

value: TAAGGCGA,CGTCTAAT

value: TRUE


title: MO63

value: p53 Dominant Negative

value: osteosarcoma


title: MO87-5

value: Sleeping Beauty-p53 Dominant Negative

value: primary


title: MO519


title: MO57


title: Single P7 FB mouse dopaminergic neuron (TH_020_F12)

description: scRNA-Seq

value: C

value: ATCTCAGG

value: AAGGCTAT

value: ATCTCAGG,AAGGCTAT


title: Single P7 FB mouse dopaminergic neuron (TH_020_F11)

description: scRNA-Seq

value: GCTCATGA

value: GCTCATGA,AAGGCTAT

value: TH

value: FB


title: MO507


title: Single P7 FB mouse dopaminergic neuron (TH_020_F10)

description: scRNA-Seq

value: GTAGAGGA

value: GTAGAGGA,AAGGCTAT

value: Th-eGFP+ sorted dopaminergic neuron


title: Single P7 FB mouse dopaminergic neuron (TH_020_F09)

description: scRNA-Seq

value: AAGAGGCA

value: AAGAGGCA,AAGGCTAT


title: MO504-1


title: MO69


title: MO45

value: p53 Dominant Negative


title: MO457

value: osteosarcoma


title: MO60-2

value: Sleeping Beauty-p53 Dominant Negative


title: W0016_SMB304

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: lymphocyte

growth_protocol: Sample 5-10: Lymphocytes were sorted from peripheral blood mononuclear cells of healthy donor. Sample1-4,11-18: Regenerated T cells were stimulated by PHA-P in the presence of rhIL-7 and rhIL-15 using allogeneic PBMC as antigen presenting cells (APCs) in 14-day intervals.

extract_protocol:
cDNA was synthesized using SMARTer Ultra Low Input RNA for Illumina Sequencing-HV kit (Clontech), after which the Illumina library was prepared using a Low Input Library Prep kit (Clontech). The libraries were sequenced using a HiSeq 2500 in 101 cycle Single-Read mode.
The sequencing libraries were constructed using KAPA stranded mRNA-seq Kit (KAPA Biosystems) from 20 ng or higher amount of total RNA and were sequenced in 100 cycle Single-Read mode of HiSeq2500.

value: lymphocyte

value: re-T CD4_posi


title: MO464

value: primary


title: MO445


title: MO44

value: Sleeping Beauty


title: W0016_SMB303

description: Bulk RNA-Seq data

value: re-T CD4_neg


title: Single P7 FB mouse dopaminergic neuron (TH_020_F05)

description: scRNA-Seq

value: C

value: GGACTCCT

value: AAGGCTAT

value: GGACTCCT,AAGGCTAT

value: TRUE


title: Single P7 FB mouse dopaminergic neuron (TH_020_F08)

description: scRNA-Seq

value: CGAGGCTG

value: CGAGGCTG,AAGGCTAT

value: TH

value: FB


title: Single P7 FB mouse dopaminergic neuron (TH_020_F07)

description: scRNA-Seq

value: CTCTCTAC

value: CTCTCTAC,AAGGCTAT

value: Th-eGFP+ sorted dopaminergic neuron


title: shLAD1_starve_1

value: stably expressing LAD1 targeting shRNA

value: none (untreated)


title: W0016_SMB302

description: Bulk RNA-Seq data

value: lymphocyte

value: re-T mock_posi


title: MO429

value: p53 Dominant Negative

value: osteosarcoma

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_F06)

description: scRNA-Seq

value: C

value: TAGGCATG

value: AAGGCTAT

value: TAGGCATG,AAGGCTAT


title: MO441


title: BB2310

value: Skin tumor

value: BRAF V600E Bap1 KO


title: Single P7 FB mouse dopaminergic neuron (TH_020_F04)

description: scRNA-Seq

value: TCCTGAGC

value: TCCTGAGC,AAGGCTAT

value: TH

value: FB

value: TRUE


title: MO411C

value: primary cell line


title: Single P7 FB mouse dopaminergic neuron (TH_020_F03)

description: scRNA-Seq

value: AGGCAGAA

value: AGGCAGAA,AAGGCTAT

value: Th-eGFP+ sorted dopaminergic neuron


title: W0016_SMB301

description: Bulk RNA-Seq data

value: lymphocyte

value: re-T mock_neg


title: MO411

value: p53 Dominant Negative

value: osteosarcoma

value: primary


title: MO425


title: MO504-2

value: Sleeping Beauty-p53 Dominant Negative


title: MO410


title: W0016_SMB296

description: Bulk RNA-Seq data

value: re-T CD4_posi


title: MO404-2


title: W0016_SMB295

description: Bulk RNA-Seq data

value: re-T CD4_neg


title: MO404-1


title: Single P7 FB mouse dopaminergic neuron (TH_020_F02)

description: scRNA-Seq

value: C

value: CGTACTAG

value: AAGGCTAT

value: CGTACTAG,AAGGCTAT


title: MO430


title: MO399C


title: Single P7 FB mouse dopaminergic neuron (TH_020_F01)

description: scRNA-Seq

value: TAAGGCGA

value: TAAGGCGA,AAGGCTAT

value: TH

value: FB

value: TRUE


title: W0016_SMB294

description: Bulk RNA-Seq data

value: lymphocyte

value: re-T mock_posi


title: W0016_SMB293

description: Bulk RNA-Seq data

value: re-T mock_neg


title: Single P7 FB mouse dopaminergic neuron (TH_020_E11)

description: scRNA-Seq

value: B

value: TGCAGCTA

value: AAGGAGTA

value: TGCAGCTA,AAGGAGTA

value: Th-eGFP+ sorted dopaminergic neuron


title: MO385

value: Sleeping Beauty-p53 Dominant Negative

value: osteosarcoma

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_E12)

description: scRNA-Seq

value: TCGACGTC

value: TCGACGTC,AAGGAGTA


title: MO399-1


title: MO379


title: W0033_SMB-399

description: Bulk RNA-Seq data

value: NK


title: Single P7 FB mouse dopaminergic neuron (TH_020_E09)

description: scRNA-Seq

value: CCTAAGAC

value: CCTAAGAC,AAGGAGTA

value: TH


title: W0036_SMB-426

description: Bulk RNA-Seq data

value: lymphocyte

value: gdT


title: MO376


title: Single P7 FB mouse dopaminergic neuron (TH_020_E08)

description: scRNA-Seq

value: ACTGAGCG

value: ACTGAGCG,AAGGAGTA

value: FB

value: TRUE


title: MO374-1


title: MO374-2


title: Single P7 FB mouse dopaminergic neuron (TH_020_E10)

description: scRNA-Seq

value: B

value: CGATCAGT

value: AAGGAGTA

value: CGATCAGT,AAGGAGTA


title: W0033_SMB-397

description: Bulk RNA-Seq data

value: abT


title: W0033_SMB-396

description: Bulk RNA-Seq data

value: ILC


title: MO370

value: Sleeping Beauty-p53 Dominant Negative

value: osteosarcoma

value: primary


title: MO380


title: Single P7 FB mouse dopaminergic neuron (TH_020_E07)

description: scRNA-Seq

value: TAGCGCTC

value: TAGCGCTC,AAGGAGTA

value: Th-eGFP+ sorted dopaminergic neuron


title: MO374-3


title: MO392


title: W0033_SMB-395

description: Bulk RNA-Seq data

value: lymphocyte


title: MO360-2


title: MO399-2


title: Single P7 FB mouse dopaminergic neuron (TH_020_E06)

description: scRNA-Seq

value: ATGCGCAG

value: ATGCGCAG,AAGGAGTA

value: TH


title: MO363


title: MO359-2


title: MO359-1


title: W0033_SMB-394

description: Bulk RNA-Seq data


title: MO347


title: MO336

value: p53 Dominant Negative


title: W0033_SMB-393

description: Bulk RNA-Seq data

value: re-T c-kit-CD161+


title: shLAD1_EGF_40min_1

value: stably expressing LAD1 targeting shRNA

value: 50ng/ml EGF for 40min


title: Single P7 FB mouse dopaminergic neuron (TH_020_E04)

description: scRNA-Seq

value: B

value: CGGAGCCT

value: AAGGAGTA

value: CGGAGCCT,AAGGAGTA

value: FB

value: TRUE


title: MO360-1

value: Sleeping Beauty-p53 Dominant Negative

value: osteosarcoma

value: primary


title: W0033_SMB-392

description: Bulk RNA-Seq data

value: lymphocyte

value: re-T c-kit-CD161-


title: MO326


title: Single P7 FB mouse dopaminergic neuron (TH_020_E03)

description: scRNA-Seq

value: GCGTAGTA

value: GCGTAGTA,AAGGAGTA

value: Th-eGFP+ sorted dopaminergic neuron


title: MO320

value: p53 Dominant Negative


title: W0033_SMB-391

description: Bulk RNA-Seq data

value: re-T c-kit+CD161+


title: MO315MC

value: metastatic cell line


title: W0033_SMB-390

description: Bulk RNA-Seq data

value: re-T c-kit+CD161-


title: MO315C

value: primary cell line


title: MO315


title: MO314

value: Sleeping Beauty


title: Single P7 FB mouse dopaminergic neuron (TH_020_E02)

description: scRNA-Seq

value: B

value: GGAGCTAC

value: AAGGAGTA

value: GGAGCTAC,AAGGAGTA

value: TH


title: Single P7 FB mouse dopaminergic neuron (TH_020_E01)

description: scRNA-Seq

value: ACTCGCTA

value: ACTCGCTA,AAGGAGTA

value: FB

value: TRUE


title: MO313

value: osteosarcoma

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_D12)

description: scRNA-Seq

value: A

value: ATCTCAGG

value: ACTGCATA

value: ATCTCAGG,ACTGCATA

value: Th-eGFP+ sorted dopaminergic neuron


title: Single P7 FB mouse dopaminergic neuron (TH_020_E05)

description: scRNA-Seq

value: TACGCTGC

value: TACGCTGC,AAGGAGTA


title: MO311MC

value: Sleeping Beauty-p53 Dominant Negative

value: metastatic cell line


title: WT-MK-D6

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: H1 samples collected from day 6 after megakaryocytic differentiation

growth_protocol: WT and MEIS deleted H1 were induced for stepwise megakaryocytic differentiation. H1 cells were first induced for hematopoietic differentiation using the mAGM-S3 co-culture system. After 12 days of differentiation, cobblestone-like cells were mechanically detached and centrifuged at 1,200 rpm for 4 minutes. Cells (at the density of 1×105/mL) were replated onto mitotically inactivated mAGM-S3 stromal cells in the hematopoietic differentiation media plus Y-27632 (10 μM, Calbiochem), TPO (50 ng/mL), SCF (20 ng/mL), IL-3 (20 ng/mL), IL-6 (10 ng/mL), IL-9 (20 ng/mL) and IL-11 (20 ng/mL) for another 6 days.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild Type


title: MO343


title: Single P7 FB mouse dopaminergic neuron (TH_020_D11)

description: scRNA-Seq

value: GCTCATGA

value: GCTCATGA,ACTGCATA

value: TH

value: FALSE


title: MUT-MK-D6

source_name: MEIS1-/- H1 samples collected from day 6 after megakaryocytic differentiation


title: Single P7 FB mouse dopaminergic neuron (TH_020_D10)

description: scRNA-Seq

value: GTAGAGGA

value: GTAGAGGA,ACTGCATA

value: FB

value: TRUE


title: MO311-1C

value: osteosarcoma

value: primary cell line


title: MO304-1

value: Sleeping Beauty

value: primary


title: MO302


title: MO310

value: p53 Dominant Negative


title: Single P7 FB mouse dopaminergic neuron (TH_020_D07)

description: scRNA-Seq

value: A

value: CTCTCTAC

value: ACTGCATA

value: CTCTCTAC,ACTGCATA

value: Th-eGFP+ sorted dopaminergic neuron


title: MO298

value: Sleeping Beauty-p53 Dominant Negative


title: MO274


title: MO281


title: MO311


title: Single P7 FB mouse dopaminergic neuron (TH_020_D09)

description: scRNA-Seq

value: AAGAGGCA

value: AAGAGGCA,ACTGCATA

value: TH


title: MO304-2


title: brush-2

city: shanghai

first: wei

last: zuo

state: shanghai

address: chifeng road #50

department: medicine

institute: tongji university

data_processing:
The original image data is transferred into sequence data via base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then We use BWA to map clean reads to genome reference and use Bowtie to gene reference
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for each Sample

source_name: lung epithelum

growth_protocol: Clone samples were grew in the medium favour stem cell expansion.

extract_protocol:
standard Total RNA extraction using Qiagen RNeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

value: lung


title: Single P7 FB mouse dopaminergic neuron (TH_020_D06)

description: scRNA-Seq

value: TAGGCATG

value: TAGGCATG,ACTGCATA

value: FB

value: TRUE


title: Single P7 FB mouse dopaminergic neuron (TH_020_D08)

description: scRNA-Seq

value: CGAGGCTG

value: CGAGGCTG,ACTGCATA


title: clone-1


title: clone-2


title: MO243

value: osteosarcoma

value: primary


title: Single P7 FB mouse dopaminergic neuron (TH_020_D02)

description: scRNA-Seq

value: A

value: CGTACTAG

value: ACTGCATA

value: CGTACTAG,ACTGCATA


title: MO272

value: Sleeping Beauty-p53 Dominant Negative


title: MO237


title: brush-1


title: MO290

value: p53 Dominant Negative


title: MO282


title: MO270


title: MO230


title: Single P7 FB mouse dopaminergic neuron (TH_020_D05)

description: scRNA-Seq

value: GGACTCCT

value: GGACTCCT,ACTGCATA

value: TH

value: Th-eGFP+ sorted dopaminergic neuron

value: FALSE


title: MO248


title: MO229


title: Single P7 FB mouse dopaminergic neuron (TH_020_D03)

description: scRNA-Seq

value: AGGCAGAA

value: AGGCAGAA,ACTGCATA

value: FB


title: BG2264

value: Skin tumor

value: GNA11 Q209L Bap1 KO


title: MO224

value: osteosarcoma

value: primary


title: MO228-1


title: Single P7 FB mouse dopaminergic neuron (TH_020_C12)

description: scRNA-Seq

value: C

value: ATCTCAGG

value: CCTAGAGT

value: ATCTCAGG,CCTAGAGT

value: TRUE


title: MO203

value: Sleeping Beauty-p53 Dominant Negative


title: MO236

value: Sleeping Beauty


title: MO220-2

value: p53 Dominant Negative


title: MO220-1


title: MO218


title: MO219


title: Single P7 FB mouse dopaminergic neuron (TH_020_C11)

description: scRNA-Seq

value: GCTCATGA

value: GCTCATGA,CCTAGAGT

value: TH

value: Th-eGFP+ sorted dopaminergic neuron


title: MO167


title: MO209


title: MO155


title: MO142


title: MO202


title: MO228-2


title: MO103-2


title: MO171


title: MO113


title: MO113C

value: primary cell line


title: MO112


title: MO163


title: Single P7 FB mouse dopaminergic neuron (TH_020_D01)

description: scRNA-Seq

value: A

value: TAAGGCGA

value: ACTGCATA

value: TAAGGCGA,ACTGCATA

value: FB


title: MO165C

value: osteosarcoma


title: WT_Saline_5

city: Aurora

first: Kenneth

last: Eyring

state: CO

address: 12700 East 19th Avernue, 8611

department: Department of Medicine

institute: University of Colorado School of Medicine

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38474

data_processing:
aligned with bwa-meth
extraced counts with bwa-meth (via samtools mpileup)
Genome_build: mm10
Supplementary_files_format_and_content: text files were generated; counts.txt represents total read counts at site; methylated.txt represents total counts called as methylated

source_name: whole lung

extract_protocol:
Lungs were perfused with phosphate buffered saline then removed and flash frozen in liquid nitrogen.  DNA was extraced using Qiagen's Dneasy Columns.  Agilent's SureSelect Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing kit was used with 4 ug of DNA for the construction of sequencing libraries.
Methyl-seq libraries were preapared for sequencing using SureSelect Human Methyl-Seq Protocol Version B using SureSelect Methyl-Seq Reagent Kit and Mouse Methyl-Seq Capture Library.

value: whole lung

value: wild-type

tag: treatment

value: saline


title: WT_Saline_4

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38401


title: WT_Saline_6

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38484


title: WT_Saline_2

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38387


title: MTHFR_KO_Saline_5

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38493

value: MTHFR-/-


title: MTHFR_KO_Saline_3

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38490


title: MTHFR_KO_Saline_2

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38481


title: WT_Saline_3

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38395


title: MTHFR_KO_Saline_4

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38492


title: WT_HDM_9

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38483

value: house dust mite


title: MO103-1

value: Sleeping Beauty-p53 Dominant Negative

value: primary


title: WT_Saline_1

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38378


title: MTHFR_KO_Saline_1

description:
MTHFR_KO_Saline_vs_WT_Saline_counts.txt
MTHFR_KO_Saline_vs_WT_Saline_methylated.txt
38480


title: WT_HDM_6

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38472


title: WT_HDM_1

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38376


title: WT_HDM_4

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38411


title: WT_HDM_3

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38400


title: WT_HDM_5

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38418


title: WT_HDM_2

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38399


title: MTHFR_KO_HDM_9

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38489


title: WT_HDM_7

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38473


title: MTHFR_KO_HDM_6

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38486


title: MTHFR_KO_HDM_5

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38485


title: MTHFR_KO_HDM_4

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38479


title: MTHFR_KO_HDM_3

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38478


title: MTHFR_KO_HDM_2

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38477


title: MTHFR_KO_HDM_7

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38487


title: MTHFR_KO_HDM_1

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38476


title: WT_HDM_8

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38482


title: Single P7 FB mouse dopaminergic neuron (TH_020_C09)

description: scRNA-Seq

value: C

value: AAGAGGCA

value: CCTAGAGT

value: AAGAGGCA,CCTAGAGT

value: TRUE


title: Single P7 FB mouse dopaminergic neuron (TH_020_C10)

description: scRNA-Seq

value: GTAGAGGA

value: GTAGAGGA,CCTAGAGT

value: TH

value: Th-eGFP+ sorted dopaminergic neuron


title: Single P7 FB mouse dopaminergic neuron (TH_020_C08)

description: scRNA-Seq

value: CGAGGCTG

value: CGAGGCTG,CCTAGAGT

value: FB


title: MTHFR_KO_HDM_8

description:
MTHFR_KO_HDM_vs_WT_HDM_counts.txt
MTHFR_KO_HDM_vs_WT_HDM_methylated.txt
38488

value: whole lung


title: Single P7 FB mouse dopaminergic neuron (TH_020_C06)

description: scRNA-Seq

value: TAGGCATG

value: TAGGCATG,CCTAGAGT


title: Single P7 FB mouse dopaminergic neuron (TH_020_C05)

description: scRNA-Seq

value: GGACTCCT

value: GGACTCCT,CCTAGAGT


title: Single P7 FB mouse dopaminergic neuron (TH_020_B10)

description: scRNA-Seq

value: B

value: CGATCAGT

value: TATCCTCT

value: CGATCAGT,TATCCTCT


title: Single P7 FB mouse dopaminergic neuron (TH_020_B11)

description: scRNA-Seq

value: TGCAGCTA

value: TGCAGCTA,TATCCTCT

value: TRUE


title: Single P7 FB mouse dopaminergic neuron (TH_020_B12)

description: scRNA-Seq

value: TCGACGTC

value: TCGACGTC,TATCCTCT

value: TH


title: Single P7 FB mouse dopaminergic neuron (TH_020_B09)

description: scRNA-Seq

value: CCTAAGAC

value: CCTAAGAC,TATCCTCT

value: Th-eGFP+ sorted dopaminergic neuron


title: Single P7 FB mouse dopaminergic neuron (TH_020_B05)

description: scRNA-Seq

value: TACGCTGC

value: TACGCTGC,TATCCTCT

value: FB


title: Single P7 FB mouse dopaminergic neuron (TH_020_B06)

description: scRNA-Seq

value: ATGCGCAG

value: ATGCGCAG,TATCCTCT


title: Single P7 FB mouse dopaminergic neuron (TH_020_C02)

description: scRNA-Seq

value: C

value: CGTACTAG

value: CCTAGAGT

value: CGTACTAG,CCTAGAGT

value: FALSE


title: Single P7 FB mouse dopaminergic neuron (TH_020_B04)

description: scRNA-Seq

value: B

value: CGGAGCCT

value: TATCCTCT

value: CGGAGCCT,TATCCTCT

value: TRUE


title: Single P7 FB mouse dopaminergic neuron (TH_020_B07)

description: scRNA-Seq

value: TAGCGCTC

value: TAGCGCTC,TATCCTCT

value: TH


title: Single P7 FB mouse dopaminergic neuron (TH_020_B03)

description: scRNA-Seq

value: GCGTAGTA

value: GCGTAGTA,TATCCTCT

value: Th-eGFP+ sorted dopaminergic neuron


title: Single P7 FB mouse dopaminergic neuron (TH_020_A11)

description: scRNA-Seq

value: A

value: GCTCATGA

value: CTCTCTAT

value: GCTCATGA,CTCTCTAT

value: FB