title: EPL1HA6 rep1 tp pt15 H4K8ac


title: CTR-3-Untreated

status: Public on Oct 26 2020

type: SRA

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

library_source: transcriptomic

data_processing:
Reads obtained from Illumina sequencing were assessed for quality using FASTQC version 0.11.7 (Andrews, 2018). Salmon version 0.11.3 (Patro et al., 2017) was used for quasi-mapping-based quantification of transcript abundances from the paired end reads over a reference set of human transcript sequences obtained from Gencode version 29 (Frankish et al., 2018). Transcript-level counts generated by Salmon were summarized to gene-level counts using tximport R/Bioconductor package version 1.2.3 (Soneson et al., 2015).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.txt.gz - gzipped tab delimited text file containing a matrix of read counts over genes summarized using tximport R/Bioconductor package
Supplementary_files_format_and_content: tpm.txt.gz - gzipped tab delimited text file containing a matrix of normalized read counts over genes in transcript per million summarized using tximport R/Bioconductor package
Supplementary_files_format_and_content: effective_length.txt.gz - gzipped tab delimited text file containing a matrix of effective gene lengths estimated by tximport R/Bioconductor package

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: RPMI1640 + 10% FBS + 1x Sodium Pyruvate + 1x Pan/Strep

extract_protocol:
Total RNA was extracted from bulk cells in two steps, RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) and the aqueous phase was processed using Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). Purified RNA samples were quality checked using Agilent RNA 6000 Pico assay (Agilent Technologies, Paolo Alto, CA). Reverse transcription and amplification were performed according to established method (Picelli et al., 2014).
cDNA was synthesized from 2ng of purified total RNA using modified oligo(dT) primers along with 1ul of a 1: 50,000 dilution of ERCC RNA Spike in control (Ambion® Thermo Fisher Scientific). To generate sufficient quantities of cDNA for downstream library preparation steps, 13 cycles of PCR amplification was performed. The quantity and integrity of cDNA was assessed using DNA High Sensitivity Reagent Kit, Perkin Elmer LabChip GX (PerkinElmer, Waltham, MA, USA). Subsequently, pooled cDNA libraries were prepared (250 pg of cDNA per sample) using Nextera XT Kit (Illumina, San Diego, CA, USA) with dual indices for de-multiplexing. The libraries were qPCR quantified (Kapa Biosystems, Wilmington, MA) to ascertain the loading concentration. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.

treatment_protocol: Untreated or treated with 500 ng/ml LPS

tag: cell line

tag: knockout

value: Control (Targeted with non-specific gRNAs)

tag: treatment

value: Untreated

tag: time point

tag: sample batch

value: C


title: RBG32855_Plate19_D10_noB_Meis1_sg1

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv

data_processing:
For RNA-Seq: sequencing reads alignment with STAR (default settings). Aligned as single-end data.
For RNA-seq: Counting of reads to exons or introns, summarised per gene - featureCounts. Ensembl v93 genome annotation. Only read1 used for counting.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with either total number of reads mapping to exonic or intronic regions, summed per gene.

molecule: total RNA

organism: Mus musculus

source_name: Hoxb8-FL cell line

growth_protocol: Hoxb8-FL cells were grown in: DMEM with 10% FCS, 5% Flt3L-conditioned medium, 50 uM 2-Mercaptoethanol, 1% Penicillin + Streptomycin, 1% Glutamine solution, either with or without 1 uM β-Estradiol

extract_protocol:
375 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

treatment_protocol:
treatment1:  Cells were transduced with constructs carrying sgRNAs expression cassettes (Perturb-Seq GBC library backbone) targeting indicated genes. Cells were harvested 48h after transduction.
treatment2:  30h after transduction cells were washed with media and cultured for another 18h either with or without beta-estradiol.

tag: tissue

value: bone marrow

tag: cell type

value: early hematopoietic progenitor cells

tag: genotype

value: Cas9 expressing, Hoxb8 expressing

value: Treated with Meis1_sg1

value: cultured without beta-estradiol

tag: time

value: day 2


title: CTR-2-LPS

value: LPS

value: B


title: tp0 rep2 H4K12ac

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

description:
Associated MNase input deposited at GSM2443149
BM131_CCGTCC_L002

library_source: genomic

data_processing:
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 500 bp and larger than 90 bp were selected for using AWK
Coverage per million fragments was calculated and converted to wig file format
Genome_build: saccer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: tp0 H4K12ac

growth_protocol: Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes

extract_protocol:
MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using NucleoMag solid phase reversible immobilization paramagnetic beads. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) NucleoMag solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent Tape Station to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

treatment_protocol: 1% formaldehyde crosslinking

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

tag: chip antibody


title: RBG32854_Plate19_C10_noB_Meis1_sg1


title: ChIPseq_input_J1_H3K27acRep1

city: Hong Kong

first: Qinghong

last: Jiang

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

source_name: Embryonic stem cell

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 80% confluency.

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with Mnase.
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cell

tag: strain

value: WT


title: ChIPseq_input_G9aDKO_H3K27ac_Rep2


title: CTR-2-Untreated


title: pt15 rep2 Input

source_name: pt15 Input

growth_protocol: Yeast strains were arrested in G1 with alpha factor, treated with 400 μg/mL 1,10-phenanthroline monohydrate for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes


title: EPL1HA6 rep2 tp0 H4K8ac

source_name: EPL1HA6 tp0 H4K8ac

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 EPL1-6HA

value: H4K8ac (Abcam ab45166, clone EP1002Y)


title: RBG32853_Plate19_B10_noB_Meis1_sg1


title: RBG32858_Plate19_G10_noB_Meis1_sg1


title: CTR-1-LPS


title: ChIPseq_input_G9aCM_H3K27ac_Rep2


title: CTR-1-Untreated


title: ChIPseq_input_G9aCM_H3K27acRep1_H3K4me3


title: mC_brain_octopus_subesophageal

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
CASAVA v1.8.2
Adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.8 before methylation quantification with CGmaptools
Genome_build: Monodelphis domestica we used ENSEMBL Monodelphis_domestica.BROADO5.dna.toplevel.fa
Genome_build: Ornithorhynchus anatinus we used ENSEMBL Ornithorhynchus_anatinus.OANA5.dna.toplevel.fa
Genome_build: Gallus gallus we used ENSEMBL Gallus_gallus.Galgal4.dna.toplevel.fa
Genome_build: Callorhinchus milii we used calMil1 (GCA_000165045.2)
Genome_build: Lethenteron camtschaticum we used LetJap1.0 (GCA_000466285.1)
Genome_build: Apis mellifera we used ENSEMBL Apis_mellifera.GCA_000002195.1.31.dna.genome.fa
Genome_build: Octopus bimaculoides we used ENSEMBL Octopus_bimaculoides.PRJNA270931.dna.toplevel.fa
Genome_build: Branchiostoma lanceolatum we used ENSEMBL Branchiostoma_lanceolatum.BraLan2.dna.toplevel.fa
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).

organism: Octopus bimaculoides

source_name: Subesophageal brain

extract_protocol:
DNeasy Blood & Tissue kit (Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

tag: source

value: Ragsdale laboratory, Chicago


title: ChIPseq_input_DnmtTKO_H3K27ac_Rep2


title: pt15 rep1 H4K12ac

source_name: pt15 H4K12ac


title: RBG32850_Plate19_G9_emptyV

value: Treated with controlNT

value: control (full media)


title: RBG32851_Plate19_H9_emptyV


title: CTR-3-LPS

value: Control (Targeted with non-specific gRNAs)

value: C


title: mC_brain_octopus_supraesophageal

source_name: Supraesophageal brain


title: tp0 rep1 H4K12ac

description:
Associated MNase input deposited at GSM2443145
BM117_TGACCA_L002

growth_protocol: Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes.


title: RBG32849_Plate19_F9_emptyV

value: bone marrow

value: early hematopoietic progenitor cells


title: tsa15 rep1 H4K12ac

description:
Associated MNase input deposited at GSM2443146
BM119_GCCAAT_L002

source_name: tsa15 H4K12ac

growth_protocol: Yeast strains were arrested in G1 with alpha factor, treated with 25 μM TSA for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes


title: ChIPseq_input_G9aDKO_H3K27acRep1_H3K4me3


title: ChIPseq_input_DnmtTKO_H3K27acRep1


title: N0814: BALBc WT (25 weeks old) Thymus NKT17, 499.000 cells (DNase treatment)

city: Hanover

first: Günter

last: Bernhardt

address: Carl Neuberg Strasse 1

department: Institue of Immunology

country: Germany

institute: Hannover Medical School

description:
an additional DNase treatment of the total RNA sample (used for N0813) was applied for N0814.
N0802-N0814_Galaxy_DESeq normalized counts from all 25 weeks vs all 6 weeks samples_adjusted p-values.xlsx

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
The FASTQ files were adapter and quality trimmed using Trim Galore! (version 0.4.1) with default settings as described in the User Guide except for the setting of the quality cutoff (-q/--quality) which was set to a Phred score of 15. Trim Galore! used Cutadapt (version 1.9.1) as subroutine. Quality control of FASTQ files was performed by FastQC (version 0.11.4) before and after trimming.
After trimming, FASTQ files were mapped against a reference genome with the splice-aware aligner STAR (version 2.5.0c) to generate BAM files. The BAM files were built in a 2-pass Mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate). All other setting have been left as default as described in the manual. The genome index files were created by STAR with default settings using Mus musculus sequence and annotation data (UCSC, built mm10) available on illumina’s iGenome site (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Generated BAM files were imported to our local Galaxy instance (release 17.05). Read counting was performed by featureCounts (Galaxy Tool Version 1.4.6.p5) with default settings except for “Strand specificity of the protocol” which was set to “Stranded (reverse)” and “Minimum mapping quality per read” which was set to 10. Mus musculus annotation data (UCSC, build Mm10) were used.
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.39) with default settings except for “Output normalized counts table” with was set to “Yes”.
Genome_build: UCSC, built mm10
Supplementary_files_format_and_content: DESeq2 was used to generate normalized read counts for all thirteen samples. Additional DESeq2 analyses were applied to retrieve adjusted p-values for the most relevant pairwise comparisons (see orange cells and descriptions within respective header cells).

source_name: Thymus

extract_protocol:
Isolation of total RNA using Rneasy Plus Mini Kit (QIAGEN) from live cells immediately following sorting.
1-5ng of total RNA were used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (#634413; Takara/Clontech) according to conditions recommended in user manual #063017. Generated libraries were barcoded with dual indexing approach and were finally amplified with 11 cycles of pcr. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific). Equal molar amounts of thirteen libraries in total were pooled for a common sequencing run. Accordingly, each analyzed library constitutes 7.7% of overall flowcell capacity. The combined library pool was denatured with NaOH and was finally diluted to 1.5pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for 75bp single reads (#FC-404-2005; Illumina).

value: BALB/c

value: thymus

tag: age

value: 25 weeks old


title: ChIPseq_input_DnmtDKO_H3K27acRep1

value: Dnmt 3a/3b-/-


title: C4_WT_T0 (input)

city: la jolla

first: Brian

last: Reilly

state: CA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

country: USA

institute: UC San Diego

description: HMCP-Seq (5hmC pull-down sequencing), input

data_processing:
Library strategy: 5hmC-seq
Sequencing reads from HMCP were aligned to a combined genome of hg19 and the T4 phage genome (GenBank: AF158101.6) using a 2-step mapping procedure where raw reads were first mapped with BWA mem v0.7.15 (options: -M -t 8); and then any unaligned reads were trimmed for low quality base calls and adapter content with Trim-galore v0.4.3 (options: –paired –length 35 –stringency 3 –three_prime_clip_R1 1 –three_prime_clip_R2 1) before realignment using BWA-mem with more stringent mapping parameters (options: -M -t 8 -B 6).
Reads aligning to ENCODE Blacklisted regions or random chromosomes, as well as any reads which mapped to both the T4 and hg19 genomes were removed.
Normalization was performed based on a scaling factor for each sample which was calculated as in Orlando et al. with the modification that T4 phage genomic reads were calculated instead of Drosophila genomic reads.
processed data files "sample.50bp_binned.counts-ExoScaled.bw" are bigwig format files which have been both input-scaled as well as scaled to exogenous genome (T4 phage) spike-in which was equal across all samples.
Genome_build: hg19/GRCh37, AF158101.6
Supplementary_files_format_and_content: bigwig

source_name: TF1 erythroleukemia cell line

growth_protocol: The human GM-CSF cytokine dependent erythroleukemia cell line TF-1 (ATCC CRL-2003) was maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Omega Scientific) and 1% penicillin/streptomycin/L-glutamine.  Cells were maintained at a density between 5x10e4 and 5x10e5 viable cells/mL and passaged every 2-3 days.

extract_protocol: We employed the HMCP with reference exogenous genome (ChIP-Rx) method of Orlando et al. for quantitative normalization of HMCP signal according to an exogenous spike-in genome (Orlando et al. 2014). As exogenous control we used the DNA isolated from phage T4gt, which carries mutations in both -agt and -bgt glycosyltransferases and thus the vast majority of cytosines are only hydroxymethylated without glycosylation (Weigele and Raleigh 2016). HMCP was carried out using the 5-hydroxymethylcytosine pull-down assay (Cambridge Epigenetix) according to manufacturer instructions with slight modifications. Exogenous phage T4gt DNA was spiked into the TF1 cell DNA at a 1:50,000 ratio before shearing with a Covaris E220 to an average length of 150 bp. Sheared DNA samples were end-repaired and adapter ligated with barcoded Illumina TruSeq adapters. Libraries were denatured and a new copy strand was synthesized.  DNA fragments containing 5hmC were pulled down using a two-step process where 5hmC were first glycosylated with T4BGT (Thermofisher) using UDP-6-azide-glucose, followed by labeling with PEG (polyethylene glycol)-biotin via copper-free CLICK chemistry. The biotin-containing DNA was then pulled down and purified using streptavidin magnetic beads. Finally, purified libraries were PCR amplified with Kapa real-time library amplification kit and sequenced using single end 50bp protocol on the Illumina NovaSeq.

treatment_protocol: These samples were taken immediately prior to treatment (no treatment).

value: TF1 erythroleukemia cell line

tag: clone id

tag: tet2 genotype

value: pre-treatment

tag: time after first treatment

tag: sample type

value: input

tag: sample experimental batch


title: N0813: BALBc WT (25 weeks old) Thymus NKT17, 499.000 cells

description: N0802-N0814_Galaxy_DESeq normalized counts from all 25 weeks vs all 6 weeks samples_adjusted p-values.xlsx


title: N0812: BALBc WT (25 weeks old) Thymus NKT2, 74.600 cells


title: RBG32847_Plate19_D9_emptyV

tag: cell line

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: ChIPseq_input_DnmtDKO_H3K27ac_Rep2

value: Embryonic stem cell


title: RBG32852_Plate19_A10_noB_Meis1_sg1

value: Treated with Meis1_sg1

value: cultured without beta-estradiol


title: pt15 rep1 H3K23ac

source_name: pt15 H3K23ac

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

value: H3K23ac (Active Motif, 39131, Lot:104)


title: ChIPseq_input_TT2_CTCF

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with sonication.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.

value: WT


title: N0811: BALBc WT (25 weeks old) Thymus NKT1, 500.000 cells


title: A7_WT_T0 (input)

tag: treatment


title: A12_KO_T0 (input)


title: ChIPseq_input_J1_CTCF


title: RBG32888_Plate20_E2_noB

value: bone marrow

value: Treated with controlNT


title: N0810: BALBc WT (25 weeks old) Thymus NKT17, 500.000 cells

value: BALB/c


title: ChIPseq_input_G9aKO_CTCF


title: F4_KO_T0 (input)


title: RBG32844_Plate19_A9_emptyV

value: early hematopoietic progenitor cells

value: control (full media)


title: RBG32848_Plate19_E9_emptyV


title: N0809: BALBc WT (25 weeks old) Thymus NKT2, 73.800 cells

value: thymus

value: 25 weeks old


title: ChIPseq_input_G9aDKO_CTCF


title: pt15 rep1 Input


title: RBG32843_Plate19_H8_Meis1_sg4

value: Treated with Meis1_sg4


title: A7_WT_T0 (5hmC_HMCP)

description: HMCP-Seq (5hmC pull-down sequencing)

value: TF1 erythroleukemia cell line

value: pre-treatment

value: pulldown


title: N0807: BALBc WT (6 weeks old) Thymus NKT17, 157.000 cells

value: 6 weeks old


title: N0808: BALBc WT (25 weeks old) Thymus NKT1, 468.000 cells


title: ChIPseq_input_DnmtTKO_CTCF

value: Embryonic stem cell


title: ChIPseq_input_G9aCM_CTCF


title: N0806: BALBc WT (6 weeks old) Thymus NKT2, 315.000 cells


title: F4_KO_T0 (5hmC_HMCP)

description: HMCP-Seq (5hmC pull-down sequencing)


title: RBG32841_Plate19_F8_Meis1_sg4

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: RBG32842_Plate19_G8_Meis1_sg4


title: N0805: BALBc WT (6 weeks old) Thymus NKT1, 105.000 cells


title: RBG32846_Plate19_C9_emptyV


title: RBG32840_Plate19_E8_Meis1_sg4


title: A12_KO_T264_DMSO_BATCH2 (5mC_BSPP)

data_processing:
Sequencing reads were trimmed for low quality bases and adapter content using TrimGalore v0.4.0 and cutadapt v.1.18 before alignment to a 3-letter (bisulfite converted) version of the hg19 reference genome as previously described (Guo et al. Nature Genetics. 2017). For alignment, trimmed reads were encoded such that all cytosines converted to thymines and for the reverse complement strand, all guanines to adenines, so that the reads could align to the three-letter genome. Reads were then mapped separately to both the Watson and Crick strands of the bisulfite-converted hg19 genome using BWA mem v.0.7.12 (options: ‘-B2 -c1000’). Alignment with mapping quality scores below 5 were discarded and for reads which mapped to more than one position, and only the highest quality mapping was kept for each read. Overlapping paired-end reads were clipped with BamUtil clipOverlap function. Encoded read sequences were replaced by the original read sequences in the final BAM alignment files which were then used for extracting methylation levels for CpGs.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: MethylScore' file contains the methylation calls for each CpG covered by >10 unique sequencing reads. This file is a tab-separated text file with 7 columns and is described in the Bioconductor methylKit package vignette (https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html)

extract_protocol:
Bisulfite treated
bisulfite badlock probe
BSPP libraries were constructed as previously described, and sequenced using a standard 150bp paired-end sequencing protocol on the Illumina NovaSeq (Diep et al. Nature Methods. 2012).

treatment_protocol: TF1 cells were treated with either 200nM 5-azacytidine (in DMSO vehicle) or dimethylsulfoxide (DMSO) at equivalent concentrations for 3 consecutive days. DNA and RNA were extracted pre-treatment, and 72hrs and 264hrs after 1st treatment.

value: DMSO daily x 3 days


title: ChIPseq_input_DnmtDKO_CTCF

value: Dnmt 3a/3b-/-


title: RBG32845_Plate19_B9_emptyV

value: bone marrow


title: ChIPseq_H3K9me2_TT2

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with Mnase. The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: H3K9me2 (abcam:ab1220)

value: WT


title: N0804: BALBc WT (6 weeks old) Thymus NKT17, 217.000 cells

value: BALB/c


title: C4_WT_T0 (5hmC_HMCP)

description: HMCP-Seq (5hmC pull-down sequencing)


title: RBG32839_Plate19_D8_Meis1_sg4

value: early hematopoietic progenitor cells

value: control (full media)


title: F4_KO_T264_DMSO_BATCH2 (5mC_BSPP)


title: ChIPseq_H3K9me2_J1


title: RBG32838_Plate19_C8_Meis1_sg4


title: N0803: BALBc WT (6 weeks old) Thymus NKT2, 327.000 cells

value: thymus


title: ChIPseq_H3K9me2_G9aKO


title: N0802: BALBc WT (6 weeks old) Thymus NKT1, 103.000 cells


title: RBG32837_Plate19_B8_Meis1_sg4

value: Treated with Meis1_sg4


title: A12_KO_T72_DMSO_BATCH2 (5mC_BSPP)

value: TF1 erythroleukemia cell line


title: A12_KO_T0 (5hmC_HMCP)

description: HMCP-Seq (5hmC pull-down sequencing)

value: pre-treatment


title: ChIPseq_H3K9me2_G9aDKO


title: F4_KO_T72_DMSO_BATCH2 (5mC_BSPP)


title: RBG32836_Plate19_A8_Meis1_sg4


title: A12_KO_T0_DMSO_BATCH2 (5mC_BSPP)


title: ChIPseq_H3K9me2_G9aCM


title: F4_KO_T0_DMSO_BATCH2 (5mC_BSPP)


title: RBG32834_Plate19_G7_Meis1_sg3

value: Treated with Meis1_sg3


title: RBG32835_Plate19_H7_Meis1_sg3


title: ChIPseq_H3K9me2_DnmtTKO


title: oschz1_input_rep1

city: Shanghai

first: Liufan

last: Yin

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

data_processing:
Cleaned paired reads and single reads were mapped to the reference genome by Bowtie2. Samtools was used to remove reads with low mapping quality (Q< 20) and potential PCR duplicates. Reads were normalized as reads per kilobase per million mapped reads (RPKM) in windows of 10 bp using the bamCoverage tool in deepTools. SICER was used to call peak (parameter:W=200, G=200, FDR=0.05).
Genome_build: MSU7
Supplementary_files_format_and_content: bigwig files were generated using DeepTools with binsize of 10. bed files contained the enrichment regions generated by SICER software. It has the format: chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold.

organism: Oryza sativa

source_name: 30-day-old seddlings grown up under long-day condition (14 h light at 30°C and 10 h dark at 28°C)

growth_protocol: The husked rice seeds were surface-sterilized by treatment with 0.1% HgCl2 for 20 min and washed with sterilized water. After sterilization, seeds were then cultured on half-strength MS medium in artificial growth chambers under LD conditions (14 h 30 °C : 10 h 28°C, light : dark) for 10 days. Then, seedlings were transferred to MS medium and cultured under LD conditions for 20 days.

extract_protocol:
ChIP was performed as previously described (Johnson et al., 2002).
ChIP-seq libraries were prepared using the method previously described (Barski, Cuddapah et al. 2007).

value: seedling

tag: development stage


title: ChIPseq_H3K9me2_DnmtDKO

value: Embryonic stem cell


title: C4_WT_T264_DMSO_BATCH1 (5mC_BSPP)

value: Wild-type


title: RBG32833_Plate19_F7_Meis1_sg3

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: A7_WT_T264_DMSO_BATCH1 (5mC_BSPP)

value: DMSO daily x 3 days


title: RBG32832_Plate19_E7_Meis1_sg3

value: bone marrow


title: oschz1_input_rep2


title: RBG32831_Plate19_D7_Meis1_sg3


title: oschz1_H3_rep1

value: anti-H3 (ab1791, Abcam)


title: A12_KO_T264_DMSO_BATCH1 (5mC_BSPP)


title: oschz1_H3_rep2


title: F4_KO_T264_DMSO_BATCH1 (5mC_BSPP)


title: oschz1_H2AZ_rep2

value: anti-H2A.Z (Abmart)


title: mC_brain_chicken

organism: Gallus gallus

source_name: brain

value: Collected in Seville, Spain


title: RBG32830_Plate19_C7_Meis1_sg3

value: early hematopoietic progenitor cells


title: ChIPseq_H3K4me3_G9aCM

value: H3K4me3 (Active Motif:39915)


title: ChIPseq_H3K4me3_G9aDKO


title: oschz1_H2AZ_rep1


title: ChIPseq_H3K4me3_TT2

value: WT


title: RBG32829_Plate19_B7_Meis1_sg3

value: control (full media)


title: ChIPseq_H3K27ac_TT2_Rep2

value: H3K27ac (Active Motif:39133)


title: NIP_input_rep2


title: A7_WT_T264_Aza_BATCH1 (5mC_BSPP)

value: TF1 erythroleukemia cell line

value: 200nM 5-Aza daily x 3 days


title: C4_WT_T264_Aza_BATCH1 (5mC_BSPP)


title: NIP_input_rep1

value: seedling


title: ChIPseq_H3K27ac_J1_Rep2

value: Embryonic stem cell


title: RBG32827_Plate19_H6_Meis1_sg1

value: Treated with Meis1_sg1


title: ChIPseq_H3K27ac_J1_Rep1


title: NIP_H3_rep2


title: RBG32826_Plate19_G6_Meis1_sg1

value: Cas9 expressing, Hoxb8 expressing


title: F4_KO_T264_Aza_BATCH1 (5mC_BSPP)


title: RBG32825_Plate19_F6_Meis1_sg1

value: day 2


title: NIP_H3_rep1


title: ChIPseq_H3K27ac_G9aDKO_Rep2


title: ChIPseq_H3K27ac_G9aDKO_Rep1


title: NIP_H2AZ_rep2


title: C4_WT_T72_DMSO_BATCH1 (5mC_BSPP)

value: Wild-type

value: DMSO daily x 3 days


title: RBG32824_Plate19_E6_Meis1_sg1

value: bone marrow


title: A12_KO_T72_DMSO_BATCH1 (5mC_BSPP)


title: RBG32828_Plate19_A7_Meis1_sg3

value: Treated with Meis1_sg3


title: RBG32823_Plate19_D6_Meis1_sg1


title: F4_KO_T72_DMSO_BATCH1 (5mC_BSPP)


title: ChIPseq_H3K27ac_G9aCM_Rep2


title: ChIPseq_H3K27ac_G9aCM_Rep1


title: A12_KO_T264_Aza_BATCH1 (5mC_BSPP)


title: C4_WT_T72_Aza_BATCH1 (5mC_BSPP)


title: RBG32822_Plate19_C6_Meis1_sg1


title: RBG32821_Plate19_B6_Meis1_sg1


title: ChIPseq_H3K27ac_TT2_Rep1


title: ChIPseq_H3K27ac_DnmtTKO_Rep2


title: A7_WT_T72_Aza_BATCH1 (5mC_BSPP)


title: ChIPseq_H3K27ac_DnmtDKO_Rep2

value: Dnmt 3a/3b-/-


title: ChIPseq_H3K27ac_DnmtTKO_Rep1


title: RBG32820_Plate19_A6_Meis1_sg1

value: early hematopoietic progenitor cells


title: A12_KO_T72_Aza_BATCH1 (5mC_BSPP)


title: NIP_H2AZ_rep1

value: anti-H2A.Z (Abmart)


title: A7_WT_T72_DMSO_BATCH1 (5mC_BSPP)


title: RBG32819_Plate19_H5_R26

value: Treated with controlR26


title: F4_KO_T72_Aza_BATCH1 (5mC_BSPP)


title: ChIPseq_H3K27ac_DnmtDKO_Rep1


title: C4_WT_T0_pre-treatment_BATCH1 (5mC_BSPP)

value: pre-treatment


title: A7_WT_T0_pre-treatment_BATCH1 (5mC_BSPP)


title: RBG32817_Plate19_F5_R26

value: control (full media)


title: RBG32816_Plate19_E5_R26


title: RBG32818_Plate19_G5_R26


title: ChIPseq_CTCF_TT2

extract_protocol:
Crosslinked cells were lysed and chromatin were sonicated. Histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Anti-CTCF (Active Motif:61311)

value: WT


title: RBG32815_Plate19_D5_R26


title: F4_KO_T0_pre-treatment_BATCH1 (5mC_BSPP)

value: TF1 erythroleukemia cell line


title: ChIPseq_CTCF_J1

value: Embryonic stem cell


title: A12_KO_T0_pre-treatment_BATCH1 (5mC_BSPP)


title: ChIPseq_CTCF_G9aDKO


title: ChIPseq_CTCF_G9aCM


title: RBG32814_Plate19_C5_R26


title: A12_KO_T264_DMSO_BATCH2 (RNA-seq)

description:
Sample 26
featureCounts.all.txt
column name: B28_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

data_processing:
Fastq files were trimmed to remove polyA signals and adapter content using cutadapt and quality checked using FastQC.
Reads were aligned to the hg19 genome using STAR v2.6.1d and GENCODE v19. Reads mapping to repetitive elements were removed.
Transcript counts were summarized using featureCounts v1.6.2 and differential gene expression was calculated using the R package ‘DESeq2’.
featureCounts.all.txt' is a tab delimited file containing raw expression counts for each sample for each gene. It is the result of running featureCounts v1.6.2 on the bam files with the options  "-p -T 8 -t exon -a gencode.v19.annotation.gff3 -o featureCounts.all.txt bam1 bam2 ...." - it produces a matrix of the read counts for each sample for each gene in GENCODE v19.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: featureCounts.all.txt

extract_protocol:
Total RNA was isolated from cell lines using the Machery-Nagel Nucleospin RNA kit according to manufacturer instructions.
RNA sequencing libraries were constructed using the Illumina TruSeq stranded mRNA kit and sequenced on an Illumina NovaSeq by NovoGene Inc.

value: vehicle (DMSO) treated daily x 3 days

tag: sequencing qc pass/fail

value: PASS

tag: experimental batch


title: RBG32813_Plate19_B5_R26

tag: tissue

tag: cell type

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: F4_KO_T264_DMSO_BATCH2 (RNA-seq)

description:
Sample 25
featureCounts.all.txt
column name: B27_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: RBG32812_Plate19_A5_R26

tag: genotype

tag: time


title: treatment of roots with 1µM rac-GR24 at 6h, biological rep 3

type: RNA

city: Freising

first: Caroline

last: Gutjahr

address: Emil Ramann Str. 4

department: TUM School of Life Sciences Weihenstephan

institute: Technical University of Munich

description: Gene expression data from KAR or rac-GR24 treated Lotus japonicus roots

hyb_protocol: Probe labeling, chip hybridization and scanning were performed according to the manufacturer’s instructions for IVT Express Labeling Kit (Affymetrix).

data_processing: The Microarray raw data was normalized with the Robust Multiarray Averaging method (RMA)  using the Bioconductor  package “Methods for Affymetrix Oligonucleotide Arrays” (affy version 1.48.0). Control and rhizobial probesets were removed before statistical analysis.

label: biotin

organism: Lotus japonicus

source_name: roots

growth_protocol: 17 days on 0.5x Hoagland solution containing agar plates (1%), in 16h/8H light dark cycles and 24°C. Roots were covered with black paper.

extract_protocol: Spectrum Plant Total RNA Kit (Sigma)

treatment_protocol: Plants were placed with root into 0.5x Hoagland solution, containing solvent or 1µM KAR1 or 1µM rac-GR24 for 1h, 2h or 6h

tag: ecotype

value: Gifu

tag: growth protocol

value: 17 days old roots grown on 0.5x Hoagland solution in Petri dishes

value: SL

value: roots


title: ChIPseq_CTCF_DnmtTKO

tag: chip antibody

tag: strain


title: treatment of roots with 1µM rac-GR24 at 6h, biological rep 1

scan_protocol: Probe labeling, chip hybridization and scanning were performed according to the manufacturer’s instructions for IVT Express Labeling Kit (Affymetrix).


title: treatment of roots with 1µM rac-GR24 at 1h, biological rep 3

label_protocol: Probe labeling, chip hybridization and scanning were performed according to the manufacturer’s instructions for IVT Express Labeling Kit (Affymetrix).


title: treatment of roots with 1µM rac-GR24 at 2h, biological rep 2


title: treatment of roots with 1µM rac-GR24 at 1h, biological rep 2


title: treatment of roots with 1µM rac-GR24 at 6h, biological rep 2


title: treatment of roots with 1µM rac-GR24 at 2h, biological rep 3


title: ChIPseq_CTCF_G9aKO


title: treatment of roots with 1µM KAR1 at 6h, biological rep 3

value: KAR


title: treatment of roots with 1µM rac-GR24 at 1h, biological rep 1


title: treatment of roots with 1µM rac-GR24 at 2h, biological rep 1


title: RBG32811_Plate19_H3_noB

value: bone marrow

value: early hematopoietic progenitor cells

value: Treated with controlNT

value: cultured without beta-estradiol


title: A12_KO_T72_DMSO_BATCH2 (RNA-seq)

description:
Sample 24
featureCounts.all.txt
column name: B26_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

tag: clone id

tag: tet2 genotype


title: ChIPseq_CTCF_DnmtDKO

value: Anti-CTCF (Active Motif:61311)

value: Dnmt 3a/3b-/-


title: ATACseq_TT2_Va_Rep3

data_processing:
Reads with Phred score ≤20 were removed and adaptors were trimmed under paired-end mode default setting in trim_galore v0.4.3.
Reads were aligned to GRCm38/mm10 assembly by Bowtie2 v2.3.3.1 (Langmead and Salzberg, 2012) with parameters -N 1 -L 25 -X 2000 --no-discordant --no-mixed.
Reads with more than one best alignment were removed. Duplicates were removed by Picard MarkDuplicates v2.9.0.
Duplicates were removed by Picard MarkDuplicates v2.9.0.
The alignments were then adjusted using MACS2 v2.1.0 (Zhang et al., 2008) with parameters --shift -75 --extsize 150 to make the start site of each read represent the center of the transposase binding (Buenrostro et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent the RPM signal of piled up center adjusted alignments
BigWig files for replicates merged samples were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent the RPM signal of piled up center adjusted alignments from replicates merged samples.

extract_protocol:
Fresh cells were lysed in cold lysis buffer (10mM Tris-Cl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630, 1X PIC).
ATAC-seq libraries were prepared using Tn5 tagmentation (Vazyme) coupled with Illumina compatible indices according to manufacturer protocol.

value: WT


title: F4_KO_T72_DMSO_BATCH2 (RNA-seq)

description:
Sample 23
featureCounts.all.txt
column name: B25_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: TF1 erythroleukemia cell line

tag: time after first treatment


title: A12_KO_T0_DMSO_BATCH2 (RNA-seq)

description:
Sample 22
featureCounts.all.txt
column name: B22_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: vehicle (DMSO) treated daily x 3 days

value: pre-treatment


title: ATACseq_TT2_Va_Rep2

value: Embryonic stem cell


title: RBG32810_Plate19_G3_noB

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: F4_KO_T0_DMSO_BATCH2 (RNA-seq)

description:
Sample 21
featureCounts.all.txt
column name: B21_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: PASS


title: ATACseq_TT2_Va_Rep1


title: RBG32808_Plate19_E3_noB


title: treatment of roots with 1µM KAR1 at 6h, biological rep 2

value: Gifu

value: 17 days old roots grown on 0.5x Hoagland solution in Petri dishes


title: treatment of roots with 1µM KAR1 at 6h, biological rep 1

value: KAR

value: roots


title: RBG32807_Plate19_D3_noB

value: bone marrow

value: early hematopoietic progenitor cells


title: C4_WT_T264_DMSO_BATCH1 (RNA-seq)

description:
Sample 20
featureCounts.all.txt
column name: B20_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_J1_Va_Rep3


title: A7_WT_T264_DMSO_BATCH1 (RNA-seq)

description:
Sample 19
featureCounts.all.txt
column name: B19_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: treatment of roots with 1µM KAR1 at 2h, biological rep 3


title: ATACseq_J1_Va_Rep2


title: treatment of roots with 1µM KAR1 at 2h, biological rep 1


title: A12_KO_T264_DMSO_BATCH1 (RNA-seq)

description:
Sample 18
featureCounts.all.txt
column name: B18_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: RBG32809_Plate19_F3_noB

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv

value: Treated with controlNT

value: cultured without beta-estradiol


title: RBG32805_Plate19_B3_noB


title: RBG32806_Plate19_C3_noB


title: ATACseq_G9aDKO_Va_Rep3


title: RBG32804_Plate19_A3_noB


title: ATACseq_J1_Va_Rep1


title: F4_KO_T264_DMSO_BATCH1 (RNA-seq)

description:
Sample 17
featureCounts.all.txt
column name: B17_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: C4_WT_T264_Aza_BATCH1 (RNA-seq)

description:
Sample 16
featureCounts.all.txt
column name: B16_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: 200 nM 5-Aza daily x 3 days


title: RBG32803_Plate19_H2_noB


title: RBG32802_Plate19_G2_noB


title: A7_WT_T264_Aza_BATCH1 (RNA-seq)

description:
Sample 15
featureCounts.all.txt
column name: B15_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_G9aDKO_Va_Rep4


title: ATACseq_G9aDKO_Va_Rep2


title: A12_KO_T264_Aza_BATCH1 (RNA-seq)

description:
Sample 14
featureCounts.all.txt
column name: B14_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_G9aDKO_Va_Rep1


title: F4_KO_T264_Aza_BATCH1 (RNA-seq)

description:
Sample 13
featureCounts.all.txt
column name: B13_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: treatment of roots with 1µM KAR1 at 1h, biological rep 3

value: WT


title: RBG32800_Plate19_E2_noB


title: treatment of roots with 1µM KAR1 at 2h, biological rep 2


title: treatment of roots with 1µM KAR1 at 1h, biological rep 1


title: treatment of roots with 1µM KAR1 at 1h, biological rep 2


title: control treatment of roots at 6h, biological rep 3

value: Control


title: ATACseq_G9aCM_Va_Rep3


title: control treatment of roots at 6h, biological rep 1


title: control treatment of roots at 2h, biological rep 3


title: C4_WT_T72_DMSO_BATCH1 (RNA-seq)

description:
Sample 12
featureCounts.all.txt
column name: B12_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: TF1 erythroleukemia cell line

value: vehicle (DMSO) treated daily x 3 days


title: ATACseq_G9aCM_Va_Rep2

value: Embryonic stem cell


title: control treatment of roots at 2h, biological rep 2


title: RBG32798_Plate19_C2_noB

value: Cas9 expressing, Hoxb8 expressing


title: ATACseq_G9aCM_Va_Rep1


title: RBG32801_Plate19_F2_noB

value: day 2


title: A7_WT_T72_DMSO_BATCH1 (RNA-seq)

description:
Sample 11
featureCounts.all.txt
column name: B11_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: PASS


title: A12_KO_T72_DMSO_BATCH1 (RNA-seq)

description:
Sample 10
featureCounts.all.txt
column name: B10_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_DnmtTKO_Va_Rep3


title: control treatment of roots at 6h, biological rep 2

description: Gene expression data from KAR or rac-GR24 treated Lotus japonicus roots

value: Gifu


title: F4_KO_T72_DMSO_BATCH1 (RNA-seq)

description:
Sample 9
featureCounts.all.txt
column name: B9_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: FAIL


title: C4_WT_T72_Aza_BATCH1 (RNA-seq)

description:
Sample 8
featureCounts.all.txt
column name: B8_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_DnmtTKO_Va_Rep2


title: RBG32796_Plate19_A2_noB


title: RBG32795_Plate19_H1_emptyV

value: control (full media)


title: ATACseq_DnmtTKO_Va_Rep1


title: ATACseq_DnmtDKO_Va_Rep3

value: Dnmt 3a/3b-/-


title: control treatment of roots at 2h, biological rep 1

value: 17 days old roots grown on 0.5x Hoagland solution in Petri dishes

value: roots


title: A12_KO_T72_Aza_BATCH1 (RNA-seq)

description:
Sample 6
featureCounts.all.txt
column name: B6_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: RBG32794_Plate19_G1_emptyV

value: bone marrow

value: early hematopoietic progenitor cells

value: Treated with controlNT


title: A7_WT_T72_Aza_BATCH1 (RNA-seq)

description:
Sample 7
featureCounts.all.txt
column name: B7_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: 200 nM 5-Aza daily x 3 days


title: RBG32797_Plate19_B2_noB

value: cultured without beta-estradiol


title: RBG32799_Plate19_D2_noB


title: ATACseq_DnmtDKO_Va_Rep2


title: Fish, EVs,  4 Day 1

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

institute: Memorial University of Newfoundland

description:
Sample 7
small RNA

data_processing:
RNA-seq reads were mapped using bowtie2 (version 2.2.5)  using mirbase build 21 version of index files.
parameters used are as follows with Bowtie2: --end-to-end --norc --very-sensitive
FeatureCounts (version 1.4.6-p4) to extract the raw counts
We calculated normalized TMM values using edgeR  ( version 3.18.1)
Genome_build: ICSASG V2
Supplementary_files_format_and_content: Csv file with samples raw  counts from all 8 samples.

organism: Salmo salar

source_name: EVs from Atlantic salmon primary head kidney cells

growth_protocol: White blood cells from the head kidney of Atlantic salmon were isolated using a Percoll gradient. The cells that adhered to the culture plate were cultured for up to 5 days. On day 1 and day 5, the culture media (L-15) was replaced with vesicle free culture media (L-15). Twenty-four hours later, the media (now containing vesicles released from the cells) was harvested. The media was centrifuged at 1800g for 5 min, followed by 17000g for 15 min before storage at -80C.

extract_protocol:
Extracellular vesicles were isolated from the culture media using VN96 (New England Peptide) following the manufacturer's protocol. Total RNA was extracted using the mirVana kit (Invitrogen) following the manufacturer's protocol.
RNA quality was assessed on Fragment analyzer using HS RNA assay and HS small RNA assay (Agilent Technologies). Small RNA library was prepared using Clean Tag Small RNA library prep kit following manufacturer recommended conditons (TriLink Biotech). Ion Torrent specific RT primer and barcodes were used during the library construction. Barcoded cDNA libraries were subjected to double size selection using Ampure XP beads (Beckman Coulter) to enrich for miRNA transcripts.  Quality of the library was analyzed using D1000 assay on Tapestation 2200 (Agilent Technologies). Libraries were equally pooled at a loading concentration of 7pM and amplified onto Ion Sphere™ Particles (Ion Pi HiQ OT2 kit, Life Technologies). ISP enriched library was sequenced using Ion Proton (ThermoFisher).

treatment_protocol: No treatment; media harvested after 1 day or 5 days of culture

value: Normal

value: Day 1


title: control treatment of roots at 1h, biological rep 2

value: WT

value: Control


title: control treatment of roots at 1h, biological rep 3


title: control treatment of roots at 1h, biological rep 1


title: Fish, EVs,  4 Day 5

description:
Sample 8
small RNA

value: Atlantic salmon primary head kidney cells

value: Day 5


title: Fish, EVs,  3 Day 5

description:
Sample 6
small RNA


title: RBG32793_Plate19_F1_emptyV

value: Cas9 expressing, Hoxb8 expressing

value: day 2


title: RBG32791_Plate19_D1_emptyV

value: control (full media)


title: F4_KO_T72_Aza_BATCH1 (RNA-seq)

description:
Sample 5
featureCounts.all.txt
column name: B5_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: TF1 erythroleukemia cell line

value: PASS


title: ATACseq_DnmtDKO_Va_Rep1

value: Embryonic stem cell

value: Dnmt 3a/3b-/-


title: Fish, EVs,  3 Day 1

description:
Sample 5
small RNA


title: ATACseq_TT2_G9ai_250nM_D4

data_processing:
Reads with Phred score ≤20 were removed and adaptors were trimmed under paired-end mode default setting in trim_galore v0.4.3.
Reads were aligned to GRCm38/mm10 assembly by Bowtie2 v2.3.3.1 (Langmead and Salzberg, 2012) with parameters -N 1 -L 25 -X 2000 --no-discordant --no-mixed.
Reads with more than one best alignment were removed. Duplicates were removed by Picard MarkDuplicates v2.9.0.
Duplicates were removed by Picard MarkDuplicates v2.9.0.
The alignments were then adjusted using MACS2 v2.1.0 (Zhang et al., 2008) with parameters --shift -75 --extsize 150 to make the start site of each read represent the center of the transposase binding (Buenrostro et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent the RPM signal of piled up center adjusted alignments

treatment_protocol: Cells are treated with 250uM UNC0638 (G9a inhibitor, Selleck Chemicals) or DMSO as control and collect on day 2, 4 and 14.


title: RBG32792_Plate19_E1_emptyV

value: bone marrow

value: early hematopoietic progenitor cells


title: C4_WT_T0_pre-treatment_BATCH1 (RNA-seq)

description:
Sample 4
featureCounts.all.txt
column name: B4_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam

value: pre-treatment


title: A7_WT_T0_pre-treatment_BATCH1 (RNA-seq)

description:
Sample 3
featureCounts.all.txt
column name: B3_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: Fish, EVs,  2 Day 1

description:
Sample 3
small RNA


title: RBG32790_Plate19_C1_emptyV

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv

value: Treated with controlNT


title: Fish, EVs,  2 Day 5

description:
Sample 4
small RNA

value: Normal


title: ATACseq_TT2_G9ai_Control


title: A12_KO_T0_pre-treatment_BATCH1 (RNA-seq)

description:
Sample 2
featureCounts.all.txt
column name: B2_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: ATACseq_TT2_G9ai_250nM_D2


title: RBG32789_Plate19_B1_emptyV


title: Fish, EVs,  1 Day 1

description:
Sample 1
small RNA

value: Day 1


title: ATACseq_TT2_G9ai_250nM_D14

value: WT


title: RBG32788_Plate19_A1_emptyV


title: F4_KO_T0_pre-treatment_BATCH1 (RNA-seq)

description:
Sample 1
featureCounts.all.txt
column name: B1_1.fq.polyATrim.adapterTrim.rmRep.sorted.rg.bam


title: Fish, EVs,  1 Day 5

description:
Sample 2
small RNA


title: SBI-756 Rep 2

status: Public on Oct 25 2020

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

description:
RNA isolated from polysome fractions containing 4 or more ribosomes
features_counts.txt

data_processing:
Sequenced reads were trimmed using trimmomatic v0.33
Reads were aligned using tophat v2.0.9/bowtie v1.0.0.0 to UCSC hg19 genome using UCSC hg19 transcriptome annotations
Aligned reads were quantified using htseq version 0.6.1p1
Differential analysis was performed using voom normalization / Limma linear modeling
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file includes counts for each sample

source_name: OCI-LY1 cells

growth_protocol: OCI-LY1 cells were grown per standard protocols

extract_protocol:
Cells were treated with 0.1mg/mL cycloheximide for minutes at 37℃, washed with PBS containing cycloheximide and lysed. Lysates were applied to a sucrose gradient and polysome analysis was performed. RNA was isolated from polysome fractions using standard RNA isolation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with SBI-756 for 4 hours.

value: B-cell non-Hodgkin lymphoma cell line

value: treated with SBI-756 for 4 hours

tag: molecule

value: translated RNA


title: SBI-756 total Rep 2

description:
Total RNA
features_counts.txt

value: Total RNA


title: SBI-756 total Rep 1

description:
Total RNA
features_counts.txt


title: Vehicle total Rep 2

description:
Total RNA
features_counts.txt

value: untreated


title: Vehicle total Rep 1

description:
total RNA
features_counts.txt


title: SBI-756 Rep 1


title: Vehicle Rep 2


title: Vehicle Rep 1


title: PC-3-docetaxel resistant-rep1

city: Barcelona

first: Begoña

last: Mellado

address: Villarroel 170

department: Oncology

country: Spain

institute: Hospital Clínic of Barcelona

description: PC-3-docetaxel resistant-rep1

hyb_protocol: Following fragmentation, 5.2 µg of ss-cDNA were hybridized for 16h at 45ºC on GeneChip Human Gene 2.0 ST Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneCHip Scanner 3000 System

data_processing: Raw expression data from microarrays were normalized using the robust multiarray algorithm with a custom probe set definition that mapped probes to Entrez Gene IDs (hugene20st_Hs_ENTREZG). After this step, a filtering was done to obtain the 5% genes with the lowest coefficient of variation. Finally, to identify differentially expressed genes between the different microarray study groups, we employed LIMMA to estimate moderated t-statistics and to select statistically differentially expressed genes.

source_name: PC-3 cell line resistant to docetaxel

label_protocol: Biotinylated ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit.

growth_protocol: DU-145, DU-145DR and DU-145CZR cell lines were cultured in RPMI 1640 medium (Gibco, Life Technologies), and PC-3, PC-3DR and PC3-CZR in F-12K nutrient mixture medium (Gibco), both supplemented with 10% fetal bovine serum.

extract_protocol: Trizol lysis was performed according to the manufacturer's instructions. Total RNA was purified (from aqueous phase of Trizol lysis) using RNeasy Micro kit (Qiagen).

treatment_protocol: The human prostate carcinoma cell lines DU-145 and PC-3 (obtained from American Type Culture Collection) were converted to docetaxel-resistant cells and to cabazitaxel-resistant cells by exposing them to an initial dose of 1.4 nM of docetaxel and 0.6 nM of cabazitaxel, respectively, and culturing surviving cells with stepwise increasing doses  in an intermittent regimen during 1 year approximately. Docetaxel and cabazitaxel (MedChem) were dissolved in DMSO (10 mM).

tag: disease

value: metastatic prostate cancer

tag: cell line

value: PC-3 cell line resistant to docetaxel


title: PC-3-docetaxel resistant-rep2

description: PC-3-docetaxel resistant-rep2


title: DU-145-docetaxel resistant-rep1

description: DU-145-docetaxel resistant-rep1

source_name: DU-145 cell line resistant to docetaxel

value: DU-145 cell line resistant to docetaxel


title: PC-3-rep1

source_name: PC-3 cell line original

value: PC-3 cell line original


title: PC-3-cabazitaxel resistant-rep2

description: PC-3-cabazitaxel resistant-rep2

source_name: PC-3 cell line resistant to cabazitaxel

value: PC-3 cell line resistant to cabazitaxel


title: PC-3-cabazitaxel resistant-rep3

description: PC-3-cabazitaxel resistant-rep3


title: DU-145-docetaxel resistant-rep2

description: DU-145-docetaxel resistant-rep2


title: PC-3-rep3


title: DU-145-rep1

source_name: DU-145 cell line original

value: DU-145 cell line original


title: single_cell_RNA-seq_reinduction_cell_90

city: Oxford

first: Wojciech

last: Siwek

state: Oxfordshire

address: Department of Biochemistry, South Parks Road

institute: Oxford University

data_processing:
Mapping was performed with bwa-mem software version 0.7.17.1 in Simple Illumina mode.
Gene counts were estimated with htseq count software version 0.9.1. Parameters: union mode, feature type exon, ID Attribute gene_id.
Genome_build: hg38
Supplementary_files_format_and_content: Gene readcounts were corrected with the following procedure: corrected gene readcounts = gene readcounts / (total mapped reads / 1000000). Table with mapped reads per cell is added as a supplementary file.

source_name: HeLa cells

growth_protocol: Cell lines were grown at 37°C, 5% CO2 in DMEM containing glucose, glutamine and pyruvate (Gibco, 41966-029) supplemented with 10% newborn calf serum (Gibco, 16010-159) and 1% Penicillin-Streptomycin (Gibco, 15140-122).

extract_protocol: The material was used for the single cell Smart-Seq2, Nextera XT library preparation and sequenced on the HiSeq4000 System (Illumina) with 75bp read length in paired end mode.

treatment_protocol: Cells were cultured and split into two parallel cultures. One was mock treated with medium and the other with IFNγ (Merck) for 24h. Cells were then washed three times with PBS and trypsinized (Gibco) to remove residual INFγ and cleave the extracellular domains of plasma membrane proteins, including the INFγ receptor, to stop residual signaling. Fresh medium was added and cells were allowed to proliferate for 48h. Next IFNγ was added or not to the primed and naïve cells. After 24h cells were washed, trypsinized and processed for single cell sorting (one 96 well plate per condition) with an additional viability staining using SYTOX AADvanced (Thermo Fisher Scientific). Viable single cells were collected to Lysis Buffer (0.8% Triton X-100, 2U/µl RiboLock (Thermo Fisher Scientific)).

value: HeLa

tag: treatment

value: cell reinduced with interferon gamma for 24h


title: single_cell_RNA-seq_reinduction_cell_91


title: single_cell_RNA-seq_reinduction_cell_88


title: single_cell_RNA-seq_reinduction_cell_89


title: PC-3-docetaxel resistant-rep3

description: PC-3-docetaxel resistant-rep3


title: DU-145-docetaxel resistant-rep3

description: DU-145-docetaxel resistant-rep3


title: DU-145-cabazitaxel resistant-rep3

description: DU-145-cabazitaxel resistant-rep3

source_name: DU-145 cell line resistant to cabazitaxel


title: DU-145-rep3


title: PC-3-cabazitaxel resistant-rep1

description: PC-3-cabazitaxel resistant-rep1


title: DU-145-cabazitaxel resistant-rep1

description: DU-145-cabazitaxel resistant-rep1

value: DU-145 cell line resistant to cabazitaxel


title: PC-3-rep2


title: single_cell_RNA-seq_reinduction_cell_87


title: single_cell_RNA-seq_reinduction_cell_86


title: single_cell_RNA-seq_reinduction_cell_85


title: single_cell_RNA-seq_reinduction_cell_83


title: single_cell_RNA-seq_reinduction_cell_82


title: single_cell_RNA-seq_reinduction_cell_84


title: single_cell_RNA-seq_reinduction_cell_81


title: DU-145-rep2


title: single_cell_RNA-seq_reinduction_cell_80


title: single_cell_RNA-seq_reinduction_cell_79


title: single_cell_RNA-seq_reinduction_cell_77


title: single_cell_RNA-seq_reinduction_cell_75


title: DU-145-cabazitaxel resistant-rep2

description: DU-145-cabazitaxel resistant-rep2


title: single_cell_RNA-seq_reinduction_cell_76


title: single_cell_RNA-seq_reinduction_cell_74


title: single_cell_RNA-seq_reinduction_cell_73


title: single_cell_RNA-seq_reinduction_cell_70


title: single_cell_RNA-seq_reinduction_cell_68


title: single_cell_RNA-seq_reinduction_cell_64


title: single_cell_RNA-seq_reinduction_cell_66


title: single_cell_RNA-seq_reinduction_cell_72


title: single_cell_RNA-seq_reinduction_cell_63


title: single_cell_RNA-seq_reinduction_cell_61


title: single_cell_RNA-seq_reinduction_cell_62


title: single_cell_RNA-seq_reinduction_cell_59


title: single_cell_RNA-seq_reinduction_cell_58


title: single_cell_RNA-seq_reinduction_cell_60


title: single_cell_RNA-seq_reinduction_cell_54


title: single_cell_RNA-seq_reinduction_cell_57


title: single_cell_RNA-seq_reinduction_cell_56


title: single_cell_RNA-seq_reinduction_cell_53


title: single_cell_RNA-seq_reinduction_cell_52


title: single_cell_RNA-seq_reinduction_cell_78


title: single_cell_RNA-seq_reinduction_cell_49


title: single_cell_RNA-seq_reinduction_cell_50


title: single_cell_RNA-seq_reinduction_cell_46


title: single_cell_RNA-seq_reinduction_cell_47


title: single_cell_RNA-seq_reinduction_cell_48


title: single_cell_RNA-seq_reinduction_cell_71


title: single_cell_RNA-seq_reinduction_cell_69


title: single_cell_RNA-seq_reinduction_cell_65


title: single_cell_RNA-seq_reinduction_cell_67


title: single_cell_RNA-seq_reinduction_cell_45


title: single_cell_RNA-seq_reinduction_cell_44


title: single_cell_RNA-seq_reinduction_cell_41


title: single_cell_RNA-seq_reinduction_cell_40


title: single_cell_RNA-seq_reinduction_cell_39


title: single_cell_RNA-seq_reinduction_cell_36


title: single_cell_RNA-seq_reinduction_cell_37


title: single_cell_RNA-seq_reinduction_cell_51


title: single_cell_RNA-seq_reinduction_cell_34


title: single_cell_RNA-seq_reinduction_cell_33


title: single_cell_RNA-seq_reinduction_cell_31


title: single_cell_RNA-seq_reinduction_cell_32


title: single_cell_RNA-seq_reinduction_cell_42


title: single_cell_RNA-seq_reinduction_cell_38


title: single_cell_RNA-seq_reinduction_cell_30


title: single_cell_RNA-seq_reinduction_cell_55


title: single_cell_RNA-seq_reinduction_cell_27


title: single_cell_RNA-seq_reinduction_cell_35


title: single_cell_RNA-seq_reinduction_cell_25


title: single_cell_RNA-seq_reinduction_cell_23


title: single_cell_RNA-seq_reinduction_cell_24


title: single_cell_RNA-seq_reinduction_cell_22


title: single_cell_RNA-seq_reinduction_cell_21


title: single_cell_RNA-seq_reinduction_cell_19


title: single_cell_RNA-seq_reinduction_cell_20


title: single_cell_RNA-seq_reinduction_cell_18


title: single_cell_RNA-seq_reinduction_cell_43


title: single_cell_RNA-seq_reinduction_cell_16


title: single_cell_RNA-seq_reinduction_cell_17


title: single_cell_RNA-seq_reinduction_cell_15


title: single_cell_RNA-seq_reinduction_cell_14


title: single_cell_RNA-seq_reinduction_cell_11


title: single_cell_RNA-seq_reinduction_cell_10


title: single_cell_RNA-seq_reinduction_cell_29


title: single_cell_RNA-seq_reinduction_cell_12


title: single_cell_RNA-seq_reinduction_cell_28


title: single_cell_RNA-seq_reinduction_cell_9


title: single_cell_RNA-seq_reinduction_cell_8


title: single_cell_RNA-seq_reinduction_cell_6


title: single_cell_RNA-seq_reinduction_cell_5


title: single_cell_RNA-seq_reinduction_cell_1


title: single_cell_RNA-seq_reinduction_cell_2


title: single_cell_RNA-seq_priming_cell_89

value: cell induced with interferon gamma for 24h


title: single_cell_RNA-seq_reinduction_cell_4


title: single_cell_RNA-seq_reinduction_cell_7


title: single_cell_RNA-seq_priming_cell_88


title: single_cell_RNA-seq_priming_cell_87


title: single_cell_RNA-seq_reinduction_cell_26


title: single_cell_RNA-seq_priming_cell_84


title: single_cell_RNA-seq_priming_cell_85


title: single_cell_RNA-seq_priming_cell_80


title: single_cell_RNA-seq_priming_cell_79


title: single_cell_RNA-seq_priming_cell_81


title: single_cell_RNA-seq_priming_cell_82


title: single_cell_RNA-seq_priming_cell_83


title: single_cell_RNA-seq_reinduction_cell_13


title: single_cell_RNA-seq_priming_cell_78


title: single_cell_RNA-seq_priming_cell_77


title: single_cell_RNA-seq_priming_cell_76


title: single_cell_RNA-seq_priming_cell_75


title: single_cell_RNA-seq_priming_cell_74


title: single_cell_RNA-seq_priming_cell_72


title: single_cell_RNA-seq_priming_cell_73


title: single_cell_RNA-seq_reinduction_cell_3


title: single_cell_RNA-seq_priming_cell_66


title: single_cell_RNA-seq_priming_cell_67


title: single_cell_RNA-seq_priming_cell_71


title: single_cell_RNA-seq_priming_cell_65


title: single_cell_RNA-seq_priming_cell_68


title: single_cell_RNA-seq_priming_cell_70


title: single_cell_RNA-seq_priming_cell_63


title: single_cell_RNA-seq_priming_cell_69


title: single_cell_RNA-seq_priming_cell_61


title: single_cell_RNA-seq_priming_cell_86


title: single_cell_RNA-seq_priming_cell_60


title: single_cell_RNA-seq_priming_cell_58


title: single_cell_RNA-seq_priming_cell_57


title: single_cell_RNA-seq_priming_cell_59


title: single_cell_RNA-seq_priming_cell_56


title: single_cell_RNA-seq_priming_cell_55


title: single_cell_RNA-seq_priming_cell_54


title: single_cell_RNA-seq_priming_cell_53


title: single_cell_RNA-seq_priming_cell_52


title: single_cell_RNA-seq_priming_cell_50


title: single_cell_RNA-seq_priming_cell_51


title: single_cell_RNA-seq_priming_cell_48


title: single_cell_RNA-seq_priming_cell_49


title: single_cell_RNA-seq_priming_cell_47


title: single_cell_RNA-seq_priming_cell_46


title: single_cell_RNA-seq_priming_cell_43


title: single_cell_RNA-seq_priming_cell_64


title: single_cell_RNA-seq_priming_cell_45


title: single_cell_RNA-seq_priming_cell_62


title: single_cell_RNA-seq_priming_cell_38


title: single_cell_RNA-seq_priming_cell_44


title: single_cell_RNA-seq_priming_cell_42


title: single_cell_RNA-seq_priming_cell_35


title: single_cell_RNA-seq_priming_cell_39


title: single_cell_RNA-seq_priming_cell_32


title: single_cell_RNA-seq_priming_cell_37


title: single_cell_RNA-seq_priming_cell_30


title: single_cell_RNA-seq_priming_cell_31


title: single_cell_RNA-seq_priming_cell_40


title: single_cell_RNA-seq_priming_cell_29


title: single_cell_RNA-seq_priming_cell_33


title: single_cell_RNA-seq_priming_cell_41


title: single_cell_RNA-seq_priming_cell_25


title: single_cell_RNA-seq_priming_cell_26


title: single_cell_RNA-seq_priming_cell_24


title: single_cell_RNA-seq_priming_cell_28


title: single_cell_RNA-seq_priming_cell_23


title: single_cell_RNA-seq_priming_cell_22


title: single_cell_RNA-seq_priming_cell_20


title: single_cell_RNA-seq_priming_cell_21


title: single_cell_RNA-seq_priming_cell_36


title: single_cell_RNA-seq_priming_cell_19


title: single_cell_RNA-seq_priming_cell_27


title: single_cell_RNA-seq_priming_cell_17


title: single_cell_RNA-seq_priming_cell_18


title: single_cell_RNA-seq_priming_cell_15


title: single_cell_RNA-seq_priming_cell_16


title: single_cell_RNA-seq_priming_cell_14


title: single_cell_RNA-seq_priming_cell_13


title: single_cell_RNA-seq_priming_cell_12


title: single_cell_RNA-seq_priming_cell_10


title: single_cell_RNA-seq_priming_cell_8


title: single_cell_RNA-seq_priming_cell_9


title: single_cell_RNA-seq_priming_cell_34


title: single_cell_RNA-seq_priming_cell_7


title: single_cell_RNA-seq_priming_cell_4


title: single_cell_RNA-seq_priming_cell_3


title: single_cell_RNA-seq_priming_cell_2


title: single_cell_RNA-seq_priming_cell_11


title: single_cell_RNA-seq_priming_cell_5


title: single_cell_RNA-seq_priming_cell_1


title: single_cell_RNA-seq_naive_cell_90

value: naive cell


title: single_cell_RNA-seq_naive_cell_87


title: single_cell_RNA-seq_naive_cell_89


title: single_cell_RNA-seq_naive_cell_88


title: single_cell_RNA-seq_naive_cell_86


title: single_cell_RNA-seq_naive_cell_85


title: single_cell_RNA-seq_naive_cell_82


title: single_cell_RNA-seq_naive_cell_81


title: single_cell_RNA-seq_naive_cell_80


title: single_cell_RNA-seq_naive_cell_79


title: single_cell_RNA-seq_naive_cell_76


title: single_cell_RNA-seq_naive_cell_73


title: single_cell_RNA-seq_priming_cell_6


title: single_cell_RNA-seq_naive_cell_75


title: single_cell_RNA-seq_naive_cell_74


title: single_cell_RNA-seq_naive_cell_69


title: single_cell_RNA-seq_naive_cell_72


title: single_cell_RNA-seq_naive_cell_70


title: single_cell_RNA-seq_naive_cell_83


title: single_cell_RNA-seq_naive_cell_65


title: single_cell_RNA-seq_naive_cell_63


title: single_cell_RNA-seq_naive_cell_68


title: single_cell_RNA-seq_naive_cell_67


title: single_cell_RNA-seq_naive_cell_64


title: single_cell_RNA-seq_naive_cell_78


title: single_cell_RNA-seq_naive_cell_62


title: single_cell_RNA-seq_naive_cell_59


title: single_cell_RNA-seq_naive_cell_60


title: single_cell_RNA-seq_naive_cell_57


title: single_cell_RNA-seq_naive_cell_66


title: single_cell_RNA-seq_naive_cell_84


title: single_cell_RNA-seq_naive_cell_61


title: single_cell_RNA-seq_naive_cell_56


title: single_cell_RNA-seq_naive_cell_58


title: single_cell_RNA-seq_naive_cell_54


title: single_cell_RNA-seq_naive_cell_55


title: single_cell_RNA-seq_naive_cell_52


title: single_cell_RNA-seq_naive_cell_77


title: single_cell_RNA-seq_naive_cell_51


title: single_cell_RNA-seq_naive_cell_45


title: single_cell_RNA-seq_naive_cell_49


title: single_cell_RNA-seq_naive_cell_48


title: single_cell_RNA-seq_naive_cell_44


title: single_cell_RNA-seq_naive_cell_50


title: single_cell_RNA-seq_naive_cell_46


title: single_cell_RNA-seq_naive_cell_42


title: single_cell_RNA-seq_naive_cell_41


title: single_cell_RNA-seq_naive_cell_43


title: single_cell_RNA-seq_naive_cell_39


title: single_cell_RNA-seq_naive_cell_38


title: single_cell_RNA-seq_naive_cell_37


title: single_cell_RNA-seq_naive_cell_53


title: single_cell_RNA-seq_naive_cell_34


title: single_cell_RNA-seq_naive_cell_33


title: single_cell_RNA-seq_naive_cell_32


title: single_cell_RNA-seq_naive_cell_36


title: single_cell_RNA-seq_naive_cell_35


title: single_cell_RNA-seq_naive_cell_31


title: single_cell_RNA-seq_naive_cell_28


title: single_cell_RNA-seq_naive_cell_30


title: single_cell_RNA-seq_naive_cell_47


title: single_cell_RNA-seq_naive_cell_27


title: single_cell_RNA-seq_naive_cell_29


title: single_cell_RNA-seq_naive_cell_26


title: single_cell_RNA-seq_naive_cell_23


title: single_cell_RNA-seq_naive_cell_24


title: single_cell_RNA-seq_naive_cell_40


title: single_cell_RNA-seq_naive_cell_25


title: single_cell_RNA-seq_naive_cell_19


title: single_cell_RNA-seq_naive_cell_22


title: single_cell_RNA-seq_naive_cell_21


title: single_cell_RNA-seq_naive_cell_20


title: single_cell_RNA-seq_naive_cell_17


title: single_cell_RNA-seq_naive_cell_18


title: single_cell_RNA-seq_naive_cell_13


title: single_cell_RNA-seq_naive_cell_12


title: single_cell_RNA-seq_naive_cell_16


title: single_cell_RNA-seq_naive_cell_15


title: single_cell_RNA-seq_naive_cell_11


title: single_cell_RNA-seq_naive_cell_7


title: single_cell_RNA-seq_naive_cell_6


title: single_cell_RNA-seq_naive_cell_5


title: single_cell_RNA-seq_naive_cell_10


title: single_cell_RNA-seq_naive_cell_9


title: single_cell_RNA-seq_naive_cell_4


title: single_cell_RNA-seq_naive_cell_3


title: SF-539 cells, shControl

city: Dalian

first: Huizhe

last: Xu

address: lvshun south road no.9

institute: Dalian Medical University

data_processing:
clean reads were retained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw fastq data using in-house perl scripts
RNASeq reads were aligned to the hg38 genome assembly using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to generate gene-level count matrix as input for edgeR’s statistical model
Differential expression analysis between shFKBP9 and shControl cells was performed using the edgeR package
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include FPKM expression value and gene annotation

source_name: SF-539 cells

growth_protocol: Cells were routinely generated by re-plating with DMEM supplied with 10% FBS.

extract_protocol:
RNA was isolated from SF-539-shFKBP9 or SF539-shControl cells using TRIzol Reagent.
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.

treatment_protocol: SF-539 cells were infected with pGIPZ-CTRL and FKBP9-shRNA lentiviruses, and stable clones were selected using puromycin.

value: epithelial glioma cells

tag: passages

value: brain

value: shControl


title: single_cell_RNA-seq_naive_cell_2


title: SF-539 cells, shFKBP9


title: single_cell_RNA-seq_naive_cell_14


title: single_cell_RNA-seq_naive_cell_1


title: single_cell_RNA-seq_naive_cell_8


title: E12_3

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

data_processing:
Illumina sequencing
FastQ raw reads alligned to mm10  using bowtie based TopHat
Cufflinks and cuffdiff-based quantification and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression file

source_name: Pancreas

extract_protocol:
Thermo Fisher mirVana™ miRNA Isolation Kit  was used to isolate RNA. RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Inc.) and all of the RINs (RNA integrity numbers) were 10.
Library preparation was achieved using Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol.

value: Pancreas

tag: age

value: 50 weeks

value: KrasG12D; Pdx-1cre; Muc5ac-/- mouse


title: E12_1

tag: tissue


title: SC Treated 3

first: Viviana

last: Cremasco

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

data_processing:
Sequence intensity files were generated using the Illumina Real Time Analysis
Intensity files were demultiplexed and then aligned to the transcriptome using the 10x Genomics Cellranger software package
bam files were generated and sorted using 10x Genomics Cellranger software
Count matrices were generated using 10x Genomics Cellranger software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix csv files for each sample containing raw expression counts of every gene for each cell; commas used in place of decimals and semicolon used as separator

source_name: Dissociated & enriched syngeneic tumor

growth_protocol: Tumors were implanted s.c. or in fat pad, as noted in characteristics(implantation)

extract_protocol:
All tumors were digested using the same combination of mechanical and enzymatic processing, and enriched for CD90 and/or CD31 positive cells
Libraries were prepared according to 10x Genomics Chromium Single Cell platform

treatment_protocol: Mice were treated with relevant compounds for 2 weeks, starting 2 days after tumor inoculation

tag: model

tag: implantation

value: subcutaneous


title: SC Treated 2


title: FP Treated 1

value: fat pad


title: E12_2

tag: genotype


title: SC Untreated 3


title: FP Untreated 4


title: FP Untreated 3


title: FP Treated 4


title: SC Treated 4


title: SC Untreated 2


title: SC Untreated 5


title: SC Untreated 4


title: SC Treated 1


title: FP Treated 3


title: FP Untreated 1


title: FP Treated 2


title: SC Untreated 1


title: E11_4

value: KrasG12D; Pdx-1cre mouse


title: FP Untreated 2


title: E11_3


title: E11_1


title: E11_2


title: single_cell_RNA-seq_naive_cell_71


title: E10_3

value: 20 weeks


title: E12_4


title: E10_1


title: E10_2


title: E9_3


title: E9_2


title: E9_4


title: E9_1


title: E10_4


title: HFWL7BBXY_1_IDT_DUI_NXT_76

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Smart-seq2 and SMARTer sequencing data were aligned with TopHat2 version 2.1.1 (Kim et al., 2013)
GRCm38 (mm10) mouse genome reference was used for alignment and gene annotation from UCSC.
Read counts for genes were calculated using velocyto version 0.17 (La Manno et al., 2018) and the cell-gene count matrix obtained was used for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CSV file containing the raw read counts matrix of all the samples from the experiment calculated using the tool velocyto.

source_name: Thymocytes

extract_protocol:
For replicate 1, full-length single-cell RNA-seq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. Thymocytes were sorted into 96-well plates containing the lysis buffer (0.2% Triton-100, 1U/µl RNase inhibitor)Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems) and IS PCR primer (IDT), with 25 cycles of amplification. For replicate 2, full-length single-cell RNA-seq libraries were prepared using the SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing (Takara Bio). All reactions were downscaled to one quarter of the original protocol and performed following thermal cycling manufacturer’s conditions. Thymocytes were sorted into 96-well plates containing 2.5 µl of the Reaction buffer (1x Lysis Buffer, RNase Inhibitor 1U/µl). Reverse transcription was performed using 2.5 µl of the RT MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio). cDNA was amplified using 8 µl of the PCR MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio) with 25 cycles of amplification.
Replicate 1 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq2000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes. Replicate 2 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with double indexed Nextera PCR primers (IDT). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE100) reads with library indexes corresponding to cell barcodes.

tag: replicate

value: MHCII KO

tag: cell type

value: Thymocytes

tag: cell population

tag: protocol

value: SMARTer


title: mpimg_L16011-1_129-FL-E9-5-scRNAseq

city: Berlin

first: Lila

last: Allou

address: 63-73 Ihnestrasse

department: FG Development and Disease

institute: Max Planck Institute For Molecular Genetics

description:
barcode_metadata.txt
genes.txt
umi_count_matrix.mtx

data_processing:
The Cell Ranger pipeline version 3 (10x Genomics lnc.) was used for each scRNA-seq sample to de-multiplex the raw base call files, generate the fastq files, and perform the alignment against a custom mouse reference genome mm10, including Maenli coordinates (ENSMUSG00000099336.2), to create the UMI count matrix.
Only cells with a detected number of UMI counts among 500 and 40,000, a detected number of genes among 200 and 5,000, and less than 10% of mitochondrial UMI counts were considered for further analysis.
We used scrublet (https://doi.org/10.1016/j.cels.2018.11.005) to identify potential duplets in our dataset. We filtered out cells with a scrublet score higher than 0.2.
Each sample dataset was normalized independently using the SCT method (10.1186/s13059-019-1874-1) implemented in Seurat3 (10.1038/nbt.4096) R package and then integrated the datasets using the Seurat3 IntegrateData function and considering the top 6000 most variable genes.
The first 20 Principal Components of this joint dataset were calculated and used for UMAP projection and cell clustering. To delimitate the major forelimb bud cell types, we used the Louvain algorithm implemented in the Seurat3 function FindClusters with resolution equal 0.02. We identified marker genes for each of the main cell types using the ROC method of the Seurat3 FindAllMarkers function. We only considered genes expressed in at least 10% of each cell-cluster and a log2 fold-change average higher than 0.25.
Genome_build: Mm10
Supplementary_files_format_and_content: barcode_metadata.txt, genes.txt, umi_count_matrix.mtx

source_name: Forelimb

extract_protocol:
The cell concentration was determined using an automated cell counter (Bio-Rad) and cells were subjected to single-cell RNA-sequencing (10x Genomic, ChromiumTM Single Cell 3’ v2; one reaction per time point and per strain has been used) aiming for a target cell recovery of up to 10,000 sequenced cells per sequencing library (time point and strain). Single-cell libraries were generated according to the manufacturer’s instructions with the following conditions: 8 PCR cycles were ran during cDNA amplification and 12 PCR cycles were ran during library generation/sample indexing to increase library complexity. Libraries were sequenced with a minimum of 230 million paired end reads.
scRNA-seq 10X Genomics

treatment_protocol: Limbs from E9.5 and E10.5 mouse embryos were dissected in PBS. A single-cell suspension was obtained by incubating the tissue for 10 min at 37 °C in 200 µL Gibco trypsin-EDTA 0.05% (Thermo Fisher Scientific) and 20 µL 5% BSA (Sigma-Aldrich). Digestion was then blocked by adding 400 µL of BSA 5%. Cells were then resuspended by pipetting and filtered using a 0.40 µm cell strainer (Falcon). Cells were washed once with 0.04% BSA with a centrifugation step performed for 5 min at 1200 r.p.m then resuspended in 0.04% BSA.

value: Forelimb

value: Wild Type

tag: embryonic stage

tag: strain


title: HFWL7BBXY_3_IDT_DUI_NXT_44


title: HFWL7BBXY_3_IDT_DUI_NXT_58


title: HFWL7BBXY_2_IDT_DUI_NXT_258


title: HFWL7BBXY_3_IDT_DUI_NXT_380


title: HFWL7BBXY_1_IDT_DUI_NXT_122


title: HFWL7BBXY_3_IDT_DUI_NXT_370


title: HFWL7BBXY_3_IDT_DUI_NXT_340


title: HFWL7BBXY_1_IDT_DUI_NXT_134


title: HFWL7BBXY_1_IDT_DUI_NXT_152


title: HFWL7BBXY_2_IDT_DUI_NXT_10


title: HFWL7BBXY_1_IDT_DUI_NXT_190


title: HFWL7BBXY_1_IDT_DUI_NXT_254


title: HFWL7BBXY_3_IDT_DUI_NXT_294


title: HFWL7BBXY_2_IDT_DUI_NXT_38


title: HFWL7BBXY_1_IDT_DUI_NXT_38


title: HFWL7BBXY_3_IDT_DUI_NXT_86


title: HFWL7BBXY_3_IDT_DUI_NXT_158


title: HFWL7BBXY_3_IDT_DUI_NXT_164


title: HFWL7BBXY_2_IDT_DUI_NXT_284


title: mpimg_L13771-1_WTBL6-FL-E10-5-scRNAseq


title: HFWL7BBXY_3_IDT_DUI_NXT_54


title: HFWL7BBXY_1_IDT_DUI_NXT_274


title: HFWL7BBXY_2_IDT_DUI_NXT_208


title: HFWL7BBXY_1_IDT_DUI_NXT_48

value: TCRhiDP


title: HFWL7BBXY_3_IDT_DUI_NXT_154


title: HFWL7BBXY_3_IDT_DUI_NXT_82


title: HFWL7BBXY_3_IDT_DUI_NXT_330


title: HFWL7BBXY_2_IDT_DUI_NXT_34


title: HFWL7BBXY_3_IDT_DUI_NXT_90


title: HFWL7BBXY_1_IDT_DUI_NXT_342


title: HFWL7BBXY_1_IDT_DUI_NXT_20


title: HFWL7BBXY_1_IDT_DUI_NXT_90


title: HFWL7BBXY_3_IDT_DUI_NXT_270


title: HFWL7BBXY_3_IDT_DUI_NXT_242


title: HFWL7BBXY_2_IDT_DUI_NXT_214


title: HFWL7BBXY_2_IDT_DUI_NXT_342


title: HFWL7BBXY_3_IDT_DUI_NXT_224


title: HFWL7BBXY_2_IDT_DUI_NXT_274


title: HFWL7BBXY_1_IDT_DUI_NXT_58


title: HFWL7BBXY_2_IDT_DUI_NXT_144


title: HFWL7BBXY_3_IDT_DUI_NXT_336


title: HFWL7BBXY_2_IDT_DUI_NXT_176


title: HFWL7BBXY_3_IDT_DUI_NXT_42


title: HFWL7BBXY_3_IDT_DUI_NXT_50


title: HFWL7BBXY_1_IDT_DUI_NXT_278


title: HFWL7BBXY_1_IDT_DUI_NXT_62


title: HFWL7BBXY_2_IDT_DUI_NXT_148


title: HFWL7BBXY_3_IDT_DUI_NXT_14


title: HFWL7BBXY_1_IDT_DUI_NXT_234


title: HFWL7BBXY_1_IDT_DUI_NXT_68


title: HFWL7BBXY_3_IDT_DUI_NXT_144


title: HFWL7BBXY_2_IDT_DUI_NXT_26


title: HFWL7BBXY_2_IDT_DUI_NXT_122


title: HFWL7BBXY_3_IDT_DUI_NXT_152


title: HFWL7BBXY_3_IDT_DUI_NXT_228


title: HFWL7BBXY_3_IDT_DUI_NXT_258


title: HFWL7BBXY_1_IDT_DUI_NXT_382


title: HFWL7BBXY_3_IDT_DUI_NXT_202


title: HFWL7BBXY_1_IDT_DUI_NXT_104


title: HFWL7BBXY_2_IDT_DUI_NXT_212


title: HFWL7BBXY_1_IDT_DUI_NXT_310


title: HFWL7BBXY_3_IDT_DUI_NXT_366


title: HFWL7BBXY_2_IDT_DUI_NXT_370


title: HFWL7BBXY_2_IDT_DUI_NXT_250


title: HFWL7BBXY_3_IDT_DUI_NXT_134


title: HFWL7BBXY_1_IDT_DUI_NXT_120


title: HFWL7BBXY_2_IDT_DUI_NXT_182


title: HFWL7BBXY_1_IDT_DUI_NXT_362


title: HFWL7BBXY_1_IDT_DUI_NXT_354


title: HFWL7BBXY_2_IDT_DUI_NXT_360


title: HFWL7BBXY_3_IDT_DUI_NXT_194


title: HFWL7BBXY_1_IDT_DUI_NXT_344


title: HFWL7BBXY_1_IDT_DUI_NXT_86


title: HFWL7BBXY_3_IDT_DUI_NXT_236


title: HFWL7BBXY_1_IDT_DUI_NXT_140


title: HFWL7BBXY_1_IDT_DUI_NXT_94


title: HFWL7BBXY_3_IDT_DUI_NXT_230


title: HFWL7BBXY_1_IDT_DUI_NXT_178


title: HFWL7BBXY_2_IDT_DUI_NXT_204


title: HFWL7BBXY_2_IDT_DUI_NXT_302


title: HFWL7BBXY_3_IDT_DUI_NXT_250


title: HFWL7BBXY_1_IDT_DUI_NXT_256


title: HFWL7BBXY_2_IDT_DUI_NXT_168


title: HFWL7BBXY_2_IDT_DUI_NXT_92


title: HFWL7BBXY_2_IDT_DUI_NXT_326


title: HFWL7BBXY_2_IDT_DUI_NXT_352


title: HFWL7BBXY_2_IDT_DUI_NXT_216


title: HFWL7BBXY_3_IDT_DUI_NXT_130


title: HFWL7BBXY_2_IDT_DUI_NXT_112


title: HFWL7BBXY_3_IDT_DUI_NXT_172


title: HFWL7BBXY_3_IDT_DUI_NXT_94


title: HFWL7BBXY_1_IDT_DUI_NXT_154


title: HFWL7BBXY_2_IDT_DUI_NXT_268


title: HFWL7BBXY_2_IDT_DUI_NXT_70


title: HFWL7BBXY_2_IDT_DUI_NXT_54


title: HFWL7BBXY_3_IDT_DUI_NXT_92


title: HFWL7BBXY_2_IDT_DUI_NXT_232


title: HFWL7BBXY_3_IDT_DUI_NXT_254


title: HFWL7BBXY_3_IDT_DUI_NXT_266


title: HFWL7BBXY_1_IDT_DUI_NXT_6


title: HFWL7BBXY_3_IDT_DUI_NXT_20


title: HFWL7BBXY_3_IDT_DUI_NXT_246


title: HFWL7BBXY_3_IDT_DUI_NXT_290


title: HFWL7BBXY_1_IDT_DUI_NXT_208


title: HFWL7BBXY_2_IDT_DUI_NXT_180


title: HFWL7BBXY_3_IDT_DUI_NXT_138


title: HFWL7BBXY_1_IDT_DUI_NXT_232


title: HFWL7BBXY_2_IDT_DUI_NXT_334


title: HFWL7BBXY_2_IDT_DUI_NXT_200


title: HFWL7BBXY_2_IDT_DUI_NXT_86


title: HFWL7BBXY_3_IDT_DUI_NXT_324


title: HFWL7BBXY_3_IDT_DUI_NXT_110


title: HFWL7BBXY_1_IDT_DUI_NXT_166


title: HFWL7BBXY_3_IDT_DUI_NXT_350


title: HFWL7BBXY_2_IDT_DUI_NXT_32


title: HFWL7BBXY_2_IDT_DUI_NXT_100


title: HFWL7BBXY_2_IDT_DUI_NXT_56


title: HFWL7BBXY_3_IDT_DUI_NXT_166


title: HFWL7BBXY_3_IDT_DUI_NXT_188


title: HFWL7BBXY_1_IDT_DUI_NXT_42


title: HFWL7BBXY_3_IDT_DUI_NXT_314


title: HFWL7BBXY_3_IDT_DUI_NXT_346


title: HFWL7BBXY_2_IDT_DUI_NXT_280


title: HFWL7BBXY_2_IDT_DUI_NXT_6


title: HFWL7BBXY_2_IDT_DUI_NXT_270


title: HFWL7BBXY_1_IDT_DUI_NXT_132


title: HFWL7BBXY_2_IDT_DUI_NXT_116


title: HFWL7BBXY_1_IDT_DUI_NXT_32


title: HFWL7BBXY_3_IDT_DUI_NXT_334


title: HFWL7BBXY_2_IDT_DUI_NXT_248


title: HFWL7BBXY_3_IDT_DUI_NXT_262


title: HFWL7BBXY_1_IDT_DUI_NXT_206


title: HFWL7BBXY_2_IDT_DUI_NXT_44


title: HFWL7BBXY_1_IDT_DUI_NXT_30


title: HFWL7BBXY_2_IDT_DUI_NXT_346


title: HFWL7BBXY_1_IDT_DUI_NXT_210


title: HFWL7BBXY_3_IDT_DUI_NXT_238


title: HFWL7BBXY_3_IDT_DUI_NXT_30


title: HFWL7BBXY_3_IDT_DUI_NXT_354


title: HFWL7BBXY_3_IDT_DUI_NXT_312


title: HFWL7BBXY_1_IDT_DUI_NXT_14


title: HFWL7BBXY_2_IDT_DUI_NXT_172


title: HFWL7BBXY_2_IDT_DUI_NXT_252


title: HFWL7BBXY_2_IDT_DUI_NXT_322


title: HFWL7BBXY_2_IDT_DUI_NXT_68


title: HFWL7BBXY_3_IDT_DUI_NXT_272


title: HFWL7BBXY_2_IDT_DUI_NXT_310


title: HFWL7BBXY_3_IDT_DUI_NXT_104


title: HFWL7BBXY_3_IDT_DUI_NXT_66


title: HFWL7BBXY_3_IDT_DUI_NXT_200


title: HFWL7BBXY_2_IDT_DUI_NXT_166


title: HFWL7BBXY_2_IDT_DUI_NXT_94


title: HFWL7BBXY_1_IDT_DUI_NXT_318


title: HFWL7BBXY_2_IDT_DUI_NXT_132


title: HFWL7BBXY_1_IDT_DUI_NXT_184


title: HFWL7BBXY_1_IDT_DUI_NXT_160


title: HFWL7BBXY_2_IDT_DUI_NXT_282


title: HFWL7BBXY_2_IDT_DUI_NXT_300


title: HFWL7BBXY_1_IDT_DUI_NXT_130


title: HFWL7BBXY_2_IDT_DUI_NXT_178


title: HFWL7BBXY_1_IDT_DUI_NXT_56


title: HFWL7BBXY_1_IDT_DUI_NXT_162


title: HFWL7BBXY_1_IDT_DUI_NXT_314


title: HFWL7BBXY_1_IDT_DUI_NXT_338


title: HFWL7BBXY_2_IDT_DUI_NXT_272


title: HFWL7BBXY_2_IDT_DUI_NXT_382


title: HFWL7BBXY_2_IDT_DUI_NXT_230


title: HFWL7BBXY_2_IDT_DUI_NXT_186


title: HFWL7BBXY_1_IDT_DUI_NXT_112


title: HFWL7BBXY_2_IDT_DUI_NXT_4


title: HFWL7BBXY_2_IDT_DUI_NXT_82


title: HFWL7BBXY_3_IDT_DUI_NXT_216


title: HFWL7BBXY_3_IDT_DUI_NXT_306


title: HFWL7BBXY_1_IDT_DUI_NXT_358


title: HFWL7BBXY_3_IDT_DUI_NXT_322


title: HFWL7BBXY_2_IDT_DUI_NXT_152


title: HFWL7BBXY_1_IDT_DUI_NXT_36


title: HFWL7BBXY_1_IDT_DUI_NXT_242


title: HFWL7BBXY_3_IDT_DUI_NXT_12


title: HFWL7BBXY_1_IDT_DUI_NXT_176


title: HFWL7BBXY_2_IDT_DUI_NXT_130


title: HFWL7BBXY_1_IDT_DUI_NXT_182


title: HFWL7BBXY_2_IDT_DUI_NXT_28


title: HFWL7BBXY_2_IDT_DUI_NXT_98


title: HFWL7BBXY_1_IDT_DUI_NXT_150


title: HFWL7BBXY_3_IDT_DUI_NXT_132


title: HFWL7BBXY_2_IDT_DUI_NXT_88


title: HFWL7BBXY_3_IDT_DUI_NXT_68


title: HFWL7BBXY_3_IDT_DUI_NXT_160


title: HFWL7BBXY_1_IDT_DUI_NXT_198


title: HFWL7BBXY_1_IDT_DUI_NXT_200


title: HFWL7BBXY_3_IDT_DUI_NXT_204


title: HFWL7BBXY_1_IDT_DUI_NXT_226


title: HFWL7BBXY_1_IDT_DUI_NXT_364


title: HFWL7BBXY_2_IDT_DUI_NXT_354


title: HFWL7BBXY_2_IDT_DUI_NXT_22


title: HFWL7BBXY_2_IDT_DUI_NXT_356


title: HFWL7BBXY_2_IDT_DUI_NXT_206


title: HFWL7BBXY_3_IDT_DUI_NXT_116


title: HFWL7BBXY_1_IDT_DUI_NXT_46


title: HFWL7BBXY_1_IDT_DUI_NXT_116


title: HFWL7BBXY_3_IDT_DUI_NXT_146


title: HFWL7BBXY_1_IDT_DUI_NXT_78


title: HFWL7BBXY_1_IDT_DUI_NXT_124


title: HFWL7BBXY_2_IDT_DUI_NXT_242


title: HFWL7BBXY_2_IDT_DUI_NXT_124


title: HFWL7BBXY_1_IDT_DUI_NXT_302


title: HFWL7BBXY_1_IDT_DUI_NXT_28


title: HFWL7BBXY_1_IDT_DUI_NXT_270


title: HFWL7BBXY_1_IDT_DUI_NXT_186


title: HFWL7BBXY_2_IDT_DUI_NXT_276


title: HFWL7BBXY_3_IDT_DUI_NXT_108


title: HFWL7BBXY_2_IDT_DUI_NXT_74


title: HFWL7BBXY_2_IDT_DUI_NXT_236


title: HFWL7BBXY_1_IDT_DUI_NXT_26


title: HFWL7BBXY_2_IDT_DUI_NXT_164


title: HFWL7BBXY_1_IDT_DUI_NXT_356


title: HFWL7BBXY_1_IDT_DUI_NXT_352


title: HFWL7BBXY_1_IDT_DUI_NXT_108


title: HFWL7BBXY_3_IDT_DUI_NXT_220


title: HFWL7BBXY_1_IDT_DUI_NXT_324


title: HFWL7BBXY_3_IDT_DUI_NXT_338


title: HFWL7BBXY_3_IDT_DUI_NXT_176


title: HFWL7BBXY_1_IDT_DUI_NXT_24


title: HFWL7BBXY_3_IDT_DUI_NXT_170


title: HFWL7BBXY_2_IDT_DUI_NXT_260


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