title: GIST-T1_DMSO_H3K27Ac

description: ChIP-seq or input control from human cell line

source_name: KIT-dependent GIST cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon).

value: H3K27ac, Abcam ab4729

tag: treatment

value: DMSO for 24 hours.


title: MPP7_Tet2KO_MO180

status: Public on Jan 22 2019

type: SRA

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

description: DNA, fragmented and adaptor ligated by Tn5 transposase

library_source: genomic

data_processing:
Trimming of the adapters with Trimmomatic v0.33 with ILLUMINACLIP:NexteraPE-PE.fa:1:10:4:1:true TRAILING:3 MINLEN:20 parameters.
Aligned to mm10 genome using Bowtie2 v2.2.9 with -X 2000 -t –very-sensetive parameters.
Removed reads with MAPQ quality < 10 using samtools and awk scripts.
Removed mitochondrial reads using samtools and awk scripts.
Read start sites are adjusted +4/-5 using samtools and awk scripts.
Using PicardTools v2.9.0 sorted by coordinate and removed duplicated reads.
Removed indels with CIGAR “ID” using samtools and awk scripts.
Bam files are transfromed to bigwig files using Biconductor package GenomicAlignments coverage() function.
Genome_build: mm10
Supplementary_files_format_and_content: Binary bigwig files containing trimmed, mapped and de-duplicated reads (mm10)

molecule: genomic DNA

organism: Mus musculus

source_name: Hematopoietic cells sorted from bone marrow

growth_protocol: Embryonic stem cells were grown in gelation-coated plates in Dulbecco's Modified Eagle Medium (DMEM, Invitrogen Cat. No. 41966) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM Glutamax (GIBCO), 0.1 mM 2-Mercaptoethanol (GIBCO), 1x non-essential amino acids (GIBCO), 1x Pen-Strep (GIBCO), 3μM GSK-3 inhihibtor (CHIR99021), 1 μM MEK1 inhibitor (PD0325901) and leukemia inhibitory factor (LIF, lab made). Acute myeloid leukemia cells were cultured in suspension in non-tissue culture treated plasticware in StemPro-34 SFM media (ThermoFisher Scientific, Cat: 10639011) supplemented with 2mM GlutaMAX (GIBCO), 1X pen/strep (GIBCO), 0.1mM 2-mercaptoethanol (SIGMA), as well as the cytokines SCF (50ng/ml), IL-3 (10ng/ml), and IL-6 (10ng/ml) (PEPROTECH).

extract_protocol:
ATAC-seq libraries were generated as described previously (Buenrostro et al. 2013; Lara-Astiaso et al. 2014). Briefly, 10,000 freshly isolated cells (MPP, GMP, AML, and ES) were sorted by FACS into ice-cold FACS buffer (PBS + 2%FBS). The cells were pelleted using a swinging bucket centrifuge (500 x g, 10min, 4oC) with settings for low acceleration/deceleration and washed once in ice-cold PBS. The cell pellets were resuspended in 50μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) by gentle pipetting and immediately centrifuged one additional time (500 x g, 10min, 4oC). The supernatant was discarded and the pellet containing released nuclei were resuspended gently in 25μl 1xTD buffer containing 1.25μl Tn5 transposase (Nextera sample preparation kit, Illumina). The transposition reaction was allowed to proceed for 45min at 37oC whereafter DNA fragments were isolated using MinElute PCR purification columns (Qiagen) according to manufacturer’s instruction.
To generate multiplex libraries, the transposed DNA was initially amplified for 5x PCR cycles using 2.5μl each of dual-index primers (Nextera index kit, Illumina) and 2.5μl PCR primer cocktail (PPC, Illumina) in a 25μl reaction volume of 1x KAPA HiFi hot-start ready-mix (Kapa BioSystems). The hot-start polymerase was activated prior to adding to the reaction mix by performing a brief pre-incubation step of 3min at 95oC. The amplified fragments were size-selected with AMPure XP beads (0.5X) to remove fragments larger than 600bp and an aliquot was quantified to determine the optimal PCR cycle number to obtain 1/3 of maximum fluorescence intensity (Library quantification kit, Kapa Biosystems). Finally, PCR amplification was performed using the optimal number of cycles determined for each library (max. 18 cycles in total), size-selected with AMPure XP beads (0.5X) and eluted in resuspension buffer (Illumina). The size distribution of the libraries was evaluated on Bioanalyzer (Agilent) and sequenced on NextSeq 550 (Illumina) using 150bp or 75bp paired-end sequencing.

tag: cell type

value: Multipotent Progenitors (MPPs), Lin-cKit+Sca1+CD48+CD150-

tag: genotype

tag: transgene

value: No transgene


title: RNAseq_T2_SunTag_VP64_EVD_9_rep3

city: Los Angeles

first: Ashot

last: Papikian

state: CA

address: 4045 Terasaki Life Sciences Building

country: USA

institute: University of California, Los Angeles

library_source: transcriptomic

data_processing:
For BS-seq samples, reads were uniquely aligned to the TAIR10 genome using BS-Seeker2 along with Bowtie.
For BS-seq samples, a filter was implemented to remove reads with three or more consecutively methylated cytosines in the CHH context, as previously described in Cokus et al., 2008 (Nature).
For BS-seq samples, after alignment, methylation was called using BS-Seeker2.
For RNA-seq samples, sequencing reads were first aligned to the TAIR10 gene annotation dataset using TopHat (2 mismatches allowed). If reads did not map to genes, they were aligned to the TAIR10 genome. Read counts were obtained by implementing HTSeq and subsequent differential expression analyses were done using DESeq (Bioconductor) and custom R scripts.
For ChIP-seq samples, analysis was done by uniquely aligning reads to the TAIR10 genome using Bowtie allowing two mismatches (-v 2). Subsequently, peaks were called using MACS2 with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq samples, processed data files are in the wig format.
Supplementary_files_format_and_content: For RNA-seq samples, processed data files are provided as text files.
Supplementary_files_format_and_content: For ChIP-seq samples, processed data files are in the bigWig format.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
For RNA-seq experiments, total RNA was first extracted using the Direct-zol RNA MiniPrep kit (Zymo).
For RNA-seq experiments, 1μg of total RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA-seq kit (Illumina). Libraries for SunTag VP64 targeting EVD were treated with Ribo-zero using the Ribo-Zero Plant Kit (Illumina).

tag: ecotype

value: Col

tag: tissue

value: leaf


title: RNAseq_T2_SunTag_VP64_EVD_10_rep2


title: RNAseq_T2_SunTag_VP64_EVD_10_rep1


title: RNAseq_T2_SunTag_VP64_EVD_10_rep4


title: MPP4_WT_MO16


title: RNAseq_T2_SunTag_VP64_EVD_3_rep3


title: RNAseq_T2_SunTag_VP64_EVD_10_rep3


title: MPP6_Tet2KO_MO178


title: RNAseq_T2_SunTag_VP64_EVD_9_rep1


title: AML_Tet2KO2

source_name: Leukemic cells sorted from in vitro culture

value: Acute Myeloid Leukemia (AML) progenitor cells, CD11b-Gr1-CD16/32intCD34+

value: Npm1+/cA; Fl3+/ITD; Tet2-/-


title: MPP5_Tet2KO_MO170


title: RNAseq_T2_SunTag_VP64_EVD_9_rep2


title: RNAseq_T2_SunTag_VP64_EVD_3_rep1


title: MPP1_WT_MO172


title: RNAseq_T2_SunTag_VP64_EVD_3_rep2


title: MPP3_WT_MO14


title: MPP2_WT_MO184


title: RNAseq_T2_SunTag_VP64_nog_2_for_EVD_rep2


title: RNAseq_T2_SunTag_VP64_nog_2_for_EVD_rep1


title: Ctrl Pol II_1

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

description: Sample_imb_roignant_2016_25_JA_Wt_Pol_II_1

data_processing:
The data was sequenced on a Illumina HiSeq 2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) .   Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks

organism: Drosophila melanogaster

source_name: ChIP Seq of total Pol II in Ctrl Knockdown condition (earlier passage)

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.

tag: cell line

value: S2R+ Cells

value: Embryonic

tag: genotype/variation

value: control knockdown

tag: chip antibody

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11


title: Ctrl Pol II_2

description: Sample_imb_roignant_2016_25_JA_Wt_Pol_II_2


title: Input_ Ctrl KD

source_name: Input sample for Ctrl knockdown (earlier passage)

value: Input Sample


title: RNAseq_Col0_rep3_forT2_SunTag_VP64_EVD

value: wildtype


title: Mago Pol II_2

description: Sample_imb_roignant_2016_25_JA_Mago_Pol_II_2

source_name: ChIP Seq of total Pol II in Mago Knockdown condition (earlier passage)

value: Mago Knockdown


title: Input_Mago KD

description: Sample_imb_roignant_2016_25_JA_Mago_Input

source_name: Input sample for Mago knockdown (earlier passage)


title: Mago Pol II_1

description: Sample_imb_roignant_2016_25_JA_Mago_Pol_II_1


title: RNAseq_Col0_rep1_forT2_SunTag_VP64_EVD


title: tri_2h_r3

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 --library-type fr-firststrand
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

molecule: polyA RNA

source_name: 12 day old seedlings

growth_protocol: Seedlings were grown in1x MS medium supplemented with 0.5 % sucrose and 0.1 % claforan for 12 days in a light chamber at long day conditions (16 h light / 8 h dark).

extract_protocol:
Total RNA was extracted from 100 mg of untreated or flg22-treated seedlings using the TRI Reagent Solution from Applied Biosystems (AM9738) following the manufacturer´s instructions. The RNA was treated with DNAse I (Roche) and purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany).
RNA-seq libraries were prepared by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq Stranded RNA sample preparation v2 guide (Illumina).

treatment_protocol: The seedlings were treated with flg22 by replacing the growth medium with medium containing 1 µM flg22 for 2 h.

value: Col-0 wrky18 wrky40 wrky33 triple mutant

tag: time-point

value: 12 day old seedlings


title: tri_0h_r3

value: untreated


title: tri_2h_r1


title: tri_0h_r2


title: tri_2h_r2


title: tri_0h_r1


title: wt_2h_r1

value: Col-0 WT


title: wt_0h_r3


title: RNAseq_T2_SunTag_VP64_nog_2_for_EVD_rep3


title: wt_0h_r1


title: wt_2h_r3


title: wt_2h_aWrky_2

description: Sample 14

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Trimming and filtering of LinDA adapters and low quality sequences was performed using 1) cutadapt  v1.2.1 with options –e 0.2, -n 2 and –m 36 and 2) PRINSEQ lite v0.20.2 with options –trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie version 2.0.5 with option -S and subsequently filtered by mapping quality (MAPQ >= 10) to remove non-uniquely aligned read using samtools  version 0.1.18
Peak calling was performed for each replicate using the program QuEST v2.4 in transcription factor mode (option “2”) with permissive parameter settings (option “3”) and suppling the corresponding input or mock-treated sample as negative controls in peak calling
Annotation of peak locations with respect to annotated gene features in TAIR10 was performed using the annotatePeaks.pl function from the Homer suite
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files with peak coordinates, enrichment scores, and annnotation information

extract_protocol:
For the ChIP experiments, 2 g of seedlings were processed as described earlier (Birkenbihl et al., 2012) following the modified protocol of Grendel et al. (2005). For IP an anti-all-WRKY immune serum (Turck et al., 2004) was used. The precipitated DNA was purified with the Qia quick PCR purification kit (Qiagen, Germany) before library construction.
To prepare the ChIP-seq libraries, the DNA was first amplified by two rounds of linear DNA amplification (LinDA) (Shankaranarayanan et al., 2011) and then libraries were constructed with the DNA Smart ChIP-seq kit (Clontech Laboratories, Cat. No. 634865).
The ChIP-seq libraries were sequenced with an Illumina HiSeq2500, resulting in 10-20 million 100 bp single-end reads per sample.


title: tri_0h_aWrky_2

description: Sample 15


title: wt_0h_input_2

description:
Sample 9
Negative control for peak calling only (for Sample 13)


title: wt_2h_input_2

description:
Sample 10
Negative control for peak calling only (for Sample 14)


title: tri_0h_input_2

description:
Sample 11
Negative control for peak calling only (for Sample 15)


title: tri_2h_aWrky_2

description: Sample 16


title: tri_0h_aWrky_1

description: Sample 7


title: wt_0h_r2


title: tri_2h_aWrky_1

description: Sample 8


title: tri_2h_input_2

description:
Sample 12
Negative control for peak calling only (for Sample 16)


title: wt_0h_aWrky_1

description: Sample 5


title: RNAseq_Col0_rep2_forT2_SunTag_VP64_EVD


title: wt_0h_aWrky_2

description: Sample 13


title: tri_0h_input_1

description:
Sample 3
Negative control for peak calling only (for Sample 7)


title: wt_0h_input_1

description:
Sample 1
Negative control for peak calling only (for Sample 5)


title: wt_2h_r2


title: PAS-CLASH: control-2

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

country: China

institute: sysu

description: QuantSeq Rev 3' mRNA sequencing library prep kit (Lexogen, Cat. 016.24)

data_processing:
Library strategy: PAS-CLASH
Bioinformatics pipeline Hyb was used to detect and extract the chimeric reads for further analysis.  Travis, A.J., Moody, J., Helwak, A., Tollervey, D. and Kudla, G. (2014) Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods, 65, 263-273.
Following filtering steps to remove reads that were not mapped to known poly(A) sites, chimeras were categorized into intra- and inter-molecular interactions. For selecting significant intra-molecular interactions, we used a cutoff value (Average RPM>50, fold change>2, P value<0.05, AMT+ versus AMT-). For selecting significant inter-molecular interactions, we quantified read counts for each individual inter-molecular chimera and used a cutoff value (Average RPM>4, fold change>2, P value<0.05, AMT+ versus AMT-) to select enriched chimeric reads.
Genome_build: hg19
Supplementary_files_format_and_content: csv file contains genes combined with polya site.

organism: Homo sapiens

source_name: HeLa Cell

growth_protocol: HeLa cells were cultured in DMEM with 10% FBS.

extract_protocol:
Crude nuclei were prepared  using a nuclear/cytoplasm fractionation kit (BioVision).Total Nuclear cross-linked RNAs were prepared using Trizol reagent, and were further fragmented to 60-200 nt sizes using RNA fragmentation buffer (Thermofisher).RNA-RNA ligation was carried out on oligo d(T) beads using T4 RNA ligase (NEB). Forcross-link reversal, RNA was resuspended in TS buffer and was irradiated for 20 min at 254 nm.
PAS-CLASH libraries were prepared using the photoreversed RNAs and QuantSeq Rev 3' mRNA sequencing library prep kit (Lexogen,Cat. 016.24), and sequenced with Hiseq.

treatment_protocol: 2x107 cells was resuspended in 2 mL cold TS buffer (0.15 M NaCl/0.01M Tris-HCl, pH 7.2)and AMT (Sigma) was added to a final concentration of 20mg/mL. Cells were incubated for 10 min on ice, transferred to an open 60 mm petridish placed on ice, and irradiated at 365 nm UV for 30 min at a distance of 10 cm from UV light source.

value: HeLa

tag: passages

value: 5 to 7

tag: gender

value: female


title: PAS-CLASH: AMT-1


title: PAS-seq: U1_AMO-2

data_processing:
Library strategy: PAS-seq
read1 of PAS-seq raw reads were reversed complemented and mapped to human genome. Bowtie2 -p 28 -N 1 -k 1
Reads filtering and clustering, poly(A) site identification were performed essentially as previously reported.  Shepard, P.J., Choi, E.A., Lu, J., Flanagan, L.A., Hertel, K.J. and Shi, Y. (2011) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA, 17, 761-772.
For PAS annotation, we divided the mapped genome into five groups and mapped the PASs using the following hierarchy: 3’ UTR, exonic (excluding the 3’ UTR), intronic, noncoding, intergenic, others. The last distal PAS at 3’ UTR was assigned to canonical PAS. A cutoff value (Average RPM>20, Fold change>2, P<0.05) was applied to select PASs showing significant change upon U1 AMO treatment.
Genome_build: hg19
Supplementary_files_format_and_content: csv,clustal pos which represent polya site.

source_name: Hela

extract_protocol:
Total RNAs were extracted with Trizol Reagent.
QuantSeq Rev 3' mRNA sequencing library prep kit (Cat. 016-24) were used to construct the PAS-seq library.

treatment_protocol: Cells were transfected with U1 AMO or control AMO for 12 hours


title: PAS-CLASH: control-1


title: PAS-seq: control_AMO-2


title: Input_MagoKD_K4Me3

description: ChIP Seq of Input_MagoKD

data_processing:
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19. The libraries contain a Yeast spike in.
Mapping was done using bowtie2 (v. 2.2.8) against BDGP6 fo the Drosophila genome
Bigwig tracks were produced using bedTools (v.2.25) and bedGraphToBigwig
Genome_build: BDGP6
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks

extract_protocol:
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA II library preparation kit, following manufacturer's protocol

treatment_protocol: S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.

value: Input control


title: PAS-seq: U1_AMO-1


title: PAS-seq: control_AMO-1


title: wt_2h_aWrky_1

description: Sample 6


title: Input_ControlKD_K4Me3

description: ChIP Seq of Input_controlKD


title: Mago_Dam_2

description:
Dam alone in Mago KD condition Rep-2
Mago_cdk9_avg_sub_smooth_sorted_UCSC.bw

data_processing:
Library strategy: DamID-seq
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6.
Mapped reads were processed through a script wrtten in perl damidseq_pipeline availbale on github(https://owenjm.github.io/damidseq_pipeline/)
The produced BedGraph files were averaged and smoothed using BEDOPS (v. 2.4.30)
The average bedGraph was coverted to bigwig files using SeqPlot
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks and readcounts per gene

source_name: S2R+ cells

extract_protocol:
The DNA was isolated using QIAamp DNA Micro Kit (Qiagen, cat. no. 56304) and after DpnI digestion using PCR Purification Kit (Qiagen, cat. no. 28104)
Purified and processed genomic DNA of two biological duplicates was subjected to library preparation using the NebNext DNA Ultra II library kit (New England Biolabs) following manufacturer's protocol

treatment_protocol: pUAST- LT3- ORF1 vector (kind gift from A. Brand) were used to clone Cdk9 as a C-terminal Dam-fusion protein. The Dam-Cdk9 itself was downstream of mcherry (as a primary ORF) separated by stop codon. This ensured low level expression of the Dam-Cdk9 fusion protein. S2R+ cells were plated in 10 cm dish and subjected to control and Mago knockdowns using dsRNA, as decribed earlier. On the sixth day of knockdown pUAST-LT3-Dam-Cdk9 was contransfected with pActin-Gal4 vector to induce Dam-Cdk9 expression, using effectene transfection reagent according to manufacturer’s protocol. The Dam alone control was similarly transfected in control and Mago depleted S2R+ cells. DNA was isolated from cells after 16 hours of transfection and subsequent treatments were performed as described (Marshall et al., 2016)

tag: developmental stage

tag: induced expression

value: Dam-only


title: Mago_Cdk9_Dam_2

description:
Cdk9-Dam alone in Mago KD condition Rep-2
Mago_cdk9_avg_sub_smooth_sorted_UCSC.bw


title: tri_2h_input_1

description:
Sample 4
Negative control for peak calling only (for Sample 8)


title: wt_2h_input_1

description:
Sample 2
Negative control for peak calling only (for Sample 6)


title: B_Input_controlKD

description: ChIP Seq of Input_controlKD


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_minus_rep2

value: Col

value: leaf


title: Mago_Cdk9_Dam_1

description:
Cdk9-Dam alone in Mago KD condition Rep-1
Mago_cdk9_avg_sub_smooth_sorted_UCSC.bw

value: S2R+ Cells

value: Embryonic


title: Ctrl_Dam_2

description:
Dam alone in Ctrl KD condition Rep-2
Ctrl_cdk9_avg_sub_smooth_sorted_UCSC.bw

value: Ctrl knockdown


title: Ctrl_Dam_1

description:
Dam alone in Ctrl KD condition Rep-1
Ctrl_cdk9_avg_sub_smooth_sorted_UCSC.bw


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_minus_rep1


title: Ctrl_Cdk9_Dam_2

description:
Cdk9-Dam alone in Ctrl KD condition Rep-2
Ctrl_cdk9_avg_sub_smooth_sorted_UCSC.bw


title: Ctrl_Cdk9_Dam_1

description:
Cdk9-Dam alone in Ctrl KD condition Rep-1
Ctrl_cdk9_avg_sub_smooth_sorted_UCSC.bw


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_plus_rep5


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_plus_rep3


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_plus_rep4


title: PAS-CLASH: AMT-2


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_plus_rep2


title: RNAseq_fwa_rep3_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2

value: fwa


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_plus_rep1


title: RNAseq_Col0_rep2_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2

value: wildtype


title: RNAseq_fwa_rep1_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2


title: RNAseq_Col0_rep1_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2


title: RNAseq_Col0_rep3_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2


title: Mago_Dam_1

description:
Dam alone in Mago KD condition Rep-1
Mago_cdk9_avg_sub_smooth_sorted_UCSC.bw

value: Mago Knockdown


title: B_Input_MagoKD

description: ChIP Seq of Input_MagoKD


title: B_Input_RnpS1KD

description: ChIP Seq of Input_RnpS1KD


title: RNAseq_fwa_rep2_forT2_22aa_SunTag_NtDRMcd_g4_10_g18_2


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_3_rep4


title: RNAseq_T2_22aa_SunTag_NtDRMcd_g4_10_g18_2_minus_rep3


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_3_rep3


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_3_rep2


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_3_rep1


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_2_rep4


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_2_rep3


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_2_rep2


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_1_rep3


title: SCNT_CROC+K+M_2

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
Paired-end sequencing reads were mapped to mm9 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cryopreserved oocytes SCNT 2-cell embryo injected with Kdm4a mRNA and treated with melatonin

growth_protocol: The fresh and vitrified/warmed oocytes were enucleated in M2 medium containing 5μg/ml cytochalasin B. For nuclear transfer, cumulus cells were injected into enucleated oocytes in M2 medium using a piezo-driven micromanipulator (Primetech LTD, Tsuchiura-shi, Japan). After nuclear transfer, the reconstructed embryos were activated for 6 h by 10mM SrCl2, 2 mM EGTA, and 5 μg/ml cytochalasin B in M16 (Millipore) medium and then cultured in KSOM in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA-Seq experiments with total RNA samples (50~100 embryos) extracted from 2-3 biological replicates were performed. Total RNA was extracted from SCNT_FOC+K, SCNT-CROC+K and SCNT_CROC+K+M embryos using RNeasy Plus Mini Kit (74134, Qiagen) and its amount and quality of the total RNA were evaluated using Bioanalyzer (Agilent). RNA samples with >7.0 RNA Integrity Number (RIN) value were used for RNA-Seq library preparation using combined SMARTer Ultra Low Input RNA cDNA preparation kit (TAKARA) with ScriptSeq v2 kit (Illumina) according to manufacturer’s instruction.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse Kdm4a-injected 2-cell and blastocyst SCNT embryos were treated with vehicle or 10μM melatonin.

tag: strain

value: preimplantation embryo

tag: age

value: Wild type


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_2_rep1


title: SCNT_CROC+K_2

source_name: Cryopreserved oocytes SCNT 2-cell embryo injected with Kdm4a mRNA


title: SCNT_CROC+K+M_1


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_1_rep2


title: 10xfemale head 10uM 5'aza-dC for 48 h 48h Sample 53

city: St. Andrews

first: David

last: Shuker

address: Greenside Place

department: School of Biology

institute: University of St Andrews

data_processing:
Reads were trimmed for quality and adapter sequence contamination using Cutadapt version 1.12 with a quality threshold of 30.
Reads were aligned to the reference genome (Nasonia vitripennis version 2.1) using Bismark (v0.16) with the parameter "bowtie2".
PCR duplicates were removed using samtools.
Data for each CpG was extracted using the Bioconductor package "methylKit" (v0.99.3) with R (v3.3.1). Methylation status was calculated using the function "processBismarkAln"
Genome_build: Nasonia vitripennis version 2.1 (Nvit_2.1)
Supplementary_files_format_and_content: .csv containing the proportion of methylated reads (after processing) for each CpG for all samples.

organism: Nasonia vitripennis

source_name: 10xfemale head

growth_protocol: The females used in this experiment were from the wild-type AsymC strain, originally isolated in 1986 by curing the wild-type strain LabII of Wolbachia. Wasps have been maintained on Calliphora vomitoria or C. vicina hosts at 25 °C, 16L:8D light conditions ever since and the genome of the strain was recently sequenced (Werren et al. 2010).

extract_protocol:
Briefly, tissue was homogenised using a micropestle in 350 µl CTAB (Hexadecyltrimethylammonium Bromide) buffer with subsequent overnight proteinase K digestion (400 µg) at 56 °C. Samples were cooled to room temperature prior to RNase A digestion for 1 hour at 37 °C. A chloroform:isoamyl-alcohol wash (300 µl) was performed twice before ethanol/sodium acetate precipitation of the DNA. DNA purity was analysed using the Nanodrop spectrophotometer with all samples having a 260/280 ratio of ≥1.8. DNA integrity was confirmed using agarose gel electrophoresis.
Bisulphite conversion, library preparation and sequencing were carried out by Edinburgh Genomics. Briefly, bisulphite conversion was carried out using the EZ DNA Methylation Kit (Zymo Research, Irvine USA), designed to reduce template degradation during the harsh bisulphite treatment whilst ensuring complete conversion of the DNA. Library preparation was carried out using the TruSeq DNA methylation Kit which takes the single-stranded DNA that results from bisulphite treatment and converts it into an illumina sequencing library. Sequencing of bisulphite-treated DNA was carried out on the Illumina HiSeq 2500 in high output mode with 125bp paired-end reads. Library preparation failed for three of the samples due to low levels of input DNA, leaving only two biological replicates for three out of 18 treatment combinations and a total of 51 Bisulphite-sequenced samples

treatment_protocol: Females were allocated to one of three 5-aza-dC exposure regimes and were harvested post-feeding at three time points. Exposure regimes were a) 20% sucrose for 24h, b) 20% sucrose supplemented with 10 µM 5-aza-dC for 24h and c) 20% sucrose supplemented with 10 µM 5-aza-dC for 48h. For each of the three regimes, females were harvested at 0, 24 or 48h post-exposure.

tag: feeding regime

value: 10uM 5'aza-dC for 48 h

tag: harvest timepoint

value: Heads


title: 10xfemale head 10uM 5'aza-dC for 48 h 48h Sample 54


title: RNAseq_fwa_rep3_forT2_22aa_SunTag_VP64_g4_g17


title: 10xfemale head 10uM 5'aza-dC for 48 h 48h Sample 52


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 48h Sample 50

source_name: 10xfemale thorax/abdomen

value: Bodies


title: SCNT_FOC+K_2

source_name: SCNT 2-cell embryos injected with Kdm4a mRNA


title: SCNT_FOC+K_1


title: RNAseq_T2_22aa_SunTag_VP64_g4_g17_1_rep1


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 48h Sample 51


title: RNAseq_fwa_rep2_forT2_22aa_SunTag_VP64_g4_g17


title: 10xfemale head 10uM 5'aza-dC for 48 h 24h Sample 48


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 24h Sample 49


title: SCNT_CROC+K_3


title: 10xfemale head 10uM 5'aza-dC for 48 h 24h Sample 47


title: Ad-GFP Iso3 rep3

city: Neuherberg

first: Carmelo

last: Quarta

address: Ingolstaedter Landstraße 1

institute: Helmholtz Center Munich

data_processing:
Basecalls performed using Illumina HiSeq Controll Software: RTA
GEM mapper (v 1.7.1) with modified parameter settings (mismatches = 0.04, min-decoded-strata = 2) was used for split-read alignment against the mouse genome assembly mm9 (NCBI37) and UCSC knownGene annotation
Number of reads mapping to annotated genes quantified using HTseq-count (v0.6.0).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Primary neurons

extract_protocol:
RNA sequencing was performed in primary neurons isolated from Tbx3loxP/loxP mice and treated with Ad-Cre or Ad-GFP viruses. Sequencing was performed in three independent neuronal isolations. One μg of total RNA per sample was used for library preparation
Library construction was performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina) in an automated manner, using the Bravo Automated Liquid Handling Platform (Agilent). cDNA libraries were multiplexed and sequenced as 100 bp paired-end runs on an Illumina HiSeq2500 platform.

value: hypothalamus

value: Embryonic Day 14

tag: isolation

value: Isolation 3


title: 10xfemale head 10uM 5'aza-dC for 48 h 24h Sample 46


title: Ad-GFP Iso3 rep2

tag: genotype


title: HepG2_miR-493-5p (2nd)

type: RNA

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

description: Gene expression after miR-493-5p overexpression versus control

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The raw data were processed using Agilent’s Feature Extraction Software version 10.7.3.1 to analyze the array and calculate the intensities of the measured spots.

source_name: HepG2, miR-493-5p mimic, 72 hours

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol. Cyanine-3 (Cy3)

growth_protocol: Human Hep3B and HepG2 cells were purchased from the American Type Culture Collection and maintained in DMEM (Gibco) supplemented with penicillin (50 IU/mL; Gibco), streptomycin (50 µg/mL; Gibco), and 10 % fetal bovine serum (FBS; Thermo Scientific).

extract_protocol: mRNA and miRNA were purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Total RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and the integrity of the RNA was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For characterization of miR-493-5p targets, total RNAs were collected from Hep3B and HepG2 cells 72 hours after cell transfection using miR-493-5p and negative control miRNA mimics (100 nM).

tag: cell type

value: hepatocellular carcinoma

tag: transfection


title: Hep3B_miR-493-5p (2nd)

source_name: Hep3B, miR-493-5p mimic, 72 hours


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 24h Sample 44

tag: tissue


title: Hep3B_control (2nd)

source_name: Hep3B, negative control miRNA mimic, 72 hours

tag: cell line

value: negative control miRNA


title: RNAseq_T2_22aa_SunTag_VP64_nog_1_rep4

source_name: leaf

tag: ecotype

value: Col

value: leaf


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 24h Sample 45


title: Ad-GFP Iso3 rep1


title: HepG2_control (2nd)

source_name: HepG2, negative control miRNA mimic, 72 hours


title: SCNT_CROC+K_1


title: RNAseq_T2_22aa_SunTag_VP64_nog_1_rep3


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 0h Sample 43


title: 10xfemale head 10uM 5'aza-dC for 48 h 0h Sample 42


title: Ad-Cre Iso3 rep3


title: Ad-Cre Iso3 rep2


title: RNAseq_T2_22aa_SunTag_VP64_nog_1_rep1


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 0h Sample 39


title: Ad-Cre Iso3 rep1

value: Isolation 2


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 48h Sample 37


title: 10xfemale head 10uM 5'aza-dC for 48 h 0h Sample 41


title: RNAseq_T2_22aa_SunTag_VP64_nog_1_rep2


title: RNAseq_Col0_rep3_forT2_22aa_SunTag_VP64_g4_g17


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 48 h 0h Sample 38


title: Ad-GFP Iso2 rep6


title: 10xfemale head 10uM 5'aza-dC for 24 h 48h Sample 35

value: 10uM 5'aza-dC for 24 h


title: RNAseq_fwa_rep1_forT2_22aa_SunTag_VP64_g4_g17

value: fwa


title: RNAseq_Col0_rep2_forT2_22aa_SunTag_VP64_g4_g17

value: wildtype


title: Ad-GFP Iso2 rep5


title: Ad-GFP Iso2 rep4


title: 10xfemale head 10uM 5'aza-dC for 24 h 48h Sample 34


title: RNAseq_T2_SunTag_VP64_g4_3_rep4

source_name: leaf tissue


title: RNAseq_Col0_rep1_forT2_22aa_SunTag_VP64_g4_g17


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 48h Sample 32


title: RNAseq_T2_SunTag_VP64_g4_3_rep3


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 48h Sample 33


title: Ad-GFP Iso2 rep3


title: Experimental Group in vivo (EG in vivo)_male_BiolRep3-TechRep2_pool

city: Ankara

first: Bengi

last: CINAR KUL

address: İrfan Bastug Caddesi

department: Genetics

country: Turkey

institute: Ankara University

description:
Replicate 2
K2M-8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with PureLink RNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with MultiskanGo (Thermo) spectrophotometer.

value: male

value: C57BL/6 X BALBc

value: day18 of gestation


title: Experimental Group in vivo (EG in vivo)_male_BiolRep3-TechRep3_pool

description:
Replicate 3
K2M-9


title: Ad-GFP Iso2 rep2


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 24h Sample 31


title: Ad-GFP Iso2 rep1


title: 10xfemale head 10uM 5'aza-dC for 24 h 24h Sample 29


title: Ad-Cre Iso2 rep5


title: RNAseq_T2_SunTag_VP64_g4_3_rep2


title: 10xfemale head 10uM 5'aza-dC for 24 h 24h Sample 28


title: Experimental Group in vivo (EG in vivo)_male_BiolRep2-TechRep2_pool

description:
Replicate 2
K2M-5


title: Experimental Group in vivo (EG in vivo)_male_BiolRep2-TechRep3_pool

description:
Replicate 3
K2M-6


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 24h Sample 27


title: RNAseq_T2_SunTag_VP64_g4_3_rep1


title: Experimental Group in vivo (EG in vivo)_male_BiolRep3-TechRep1_pool

description:
Replicate 1
K2M-7


title: RNAseq_T2_SunTag_VP64_g4_2_rep3


title: Experimental Group in vivo (EG in vivo)_male_BiolRep1-TechRep3_pool

description:
Replicate 3
K2M-3


title: RNAseq_T2_SunTag_VP64_g4_2_rep2


title: Experimental Group in vivo (EG in vivo)_male_BiolRep1-TechRep2_pool

description:
Replicate 2
K2M-2


title: Experimental Group in vivo (EG in vivo)_male_BiolRep2-TechRep1_pool

description:
Replicate 1
K2M-4


title: Ad-Cre Iso2 rep3


title: Experimental Group in vivo (EG in vivo) _male_BiolRep1-TechRep1_pool

description:
Replicate 1
K2M-1


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 24h Sample 26


title: RNAseq_T2_SunTag_VP64_g4_1_rep4


title: Ad-Cre Iso2 rep2


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 0h Sample 25


title: RNAseq_T2_SunTag_VP64_g4_2_rep1


title: Ad-Cre Iso2 rep1


title: RNAseq_T2_SunTag_VP64_g4_1_rep3


title: 10xfemale head 10uM 5'aza-dC for 24 h 0h Sample 23


title: 10xfemale head 10uM 5'aza-dC for 24 h 0h Sample 22


title: Ad-GFP Iso1 rep1

value: Isolation 1


title: RNAseq_T2_SunTag_VP64_g4_1_rep2


title: RNAseq_T2_SunTag_VP64_g4_1_rep1


title: Ad-Cre Iso1 rep2


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 0h Sample 21


title: Ad-Cre Iso2 rep4


title: RNAseq_fwa_rep3_forT2_SunTag_VP64_g4


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 0h Sample 20


title: RNAseq_fwa_rep2_forT2_SunTag_VP64_g4


title: 10xfemale head 20% Sucrose for 24h 48h Sample 18

value: 20% Sucrose for 24h

value: Heads


title: 10xfemale thorax/abdomen 10uM 5'aza-dC for 24 h 48h Sample 19

value: Bodies


title: 10xfemale head 20% Sucrose for 24h 48h Sample 17


title: RNAseq_fwa_rep1_forT2_SunTag_VP64_g4


title: Ad-Cre Iso1 rep1

value: hypothalamus

value: Embryonic Day 14


title: RNAseq_T2_SunTag_VP64_nog_2_for_g4_rep4


title: 10xfemale head 10uM 5'aza-dC for 24 h 0h Sample 24


title: RNAseq_T2_SunTag_VP64_nog_2_for_g4_rep3


title: 10xfemale head 20% Sucrose for 24h 48h Sample 16


title: RNAseq_T2_SunTag_VP64_nog_2_for_g4_rep2


title: Ad-GFP Iso1 rep2


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 48h Sample 15


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 48h Sample 14


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 24h Sample 13


title: RNAseq_Col0_rep2_forT2_SunTag_VP64_g4


title: S169A_HFHC_K27ac_rep3

city: London

first: Ines

last: Pineda-Torra

address: 5 University Street

institute: University College London

data_processing:
RAW files (fastq files) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie with parameters "-m 1". Only sequences mapping to exactly one location were kept.
SAM files where then imported to Homer to construct tag directories and Homer was used for peak calling, annotation and to extract raw tag counts.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bedGraph files were generated using HOMER. Peak heights were normalized to the total number of uniquely mapped reads and displayed as the number of tags per 10 million tags.

source_name: Liver

extract_protocol:
Fresh mouse livers were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 9 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: Mice were fed a High Fat-High Cholesterol diet (17,2% Cocoa Butter, 2,8% Soybean Oil, 1,25% Cholesterol, 0,5% Sodium Cholate; AIN-76A/Clinton Diet #4, Test Diet Limited, UK) for 6 weeks ad libitum.

tag: background strain

value: Liver

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

value: 16-week old

tag: Sex

value: female

tag: diet

value: HFD


title: 10xfemale head 20% Sucrose for 24h 24h Sample 11


title: S169A_HFHC_K27ac_rep2


title: WGBS_T2_22aa_SunTag_VP64_g4_g17_3_minus

extract_protocol:
For BS-seq experiments, genomic DNA was isolated using the DNeasy Plant Mini Kit (Qiagen).
For BS-seq experiments, 100ng of DNA was then used for subsequent shearing using a Covaris Ultrasonicator. Libraries were then prepared using either the Ovation Ultralow Methyl-Seq kit (NuGen) in conjuction with the EpiTect Bisulfite Kit (Qiagen), or the KAPA Hyper Prep Kit (KAPA Biosystems) in conjuction with either the EZ DNA Methylation-Lightning Kit (Zymo) or the EpiTect Bisulfite Kit (Qiagen).

value: Col

value: leaf


title: S169A_HFHC_K27ac_rep1


title: 10xfemale head 20% Sucrose for 24h 24h Sample 10


title: WGBS_T2_22aa_SunTag_VP64_g4_g17_3_plus


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 24h Sample 9


title: WGBS_T1_22aa_SunTag_VP64_g4_g17_3


title: WT_HFHC_K27ac_rep3

value: WT


title: RNAseq_T2_SunTag_VP64_nog_2_for_g4_rep1


title: WT_HFHC_K27ac_rep2


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 24h Sample 8


title: WGBS_T1_22aa_SunTag_VP64_g4_g17_2


title: WGBS_T1_22aa_SunTag_VP64_g4_g17_1


title: WGBS_Col0_forT1T2_22aa_SunTag_VP64_g4_g17

value: wildtype


title: 10xfemale head 20% Sucrose for 24h 0h Sample 6


title: RNAseq_Col0_rep3_forT2_SunTag_VP64_g4


title: WT_HFHC_K27ac_rep1


title: 10xfemale head 20% Sucrose for 24h 0h Sample 5


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 0h Sample 7


title: 10xfemale head 20% Sucrose for 24h 24h Sample 12


title: RNAseq_Col0_rep1_forT2_SunTag_VP64_g4


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_g4_g10_g18_3


title: 10xfemale head 20% Sucrose for 24h 0h Sample 4


title: 12_Control

city: Shanghai

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: control

hyb_protocol: Standard Agilent procedures

scan_protocol: Standard Agilent procedures

data_processing: Signal intensities were extracted from scanned images using Agilent Feature Extraction Software 10.5.1.1 (protocol: GE1_105_Dec08 and Grid: 021169_D_F_20100217)

source_name: Seedlings_10 days_0 mg/L kanamycin

label_protocol: Total RNA was reversely transcribed into double-strand cDNA. 2 µg cDNA was used for probe labeling according to the instructions of Agilent Arabidopsis GeneArray.

growth_protocol: The seeds were planted in a plastic pot with a mixture soil of vermiculite, peat moss, and perlite (18:6:1 v/v) and growing at 23 °C and 60% humidity condition.

extract_protocol: The seedlings in 2 cm length were harvested for RNA extraction.

treatment_protocol: kanamycin treatments were conducted at 21 days and sustained ten days.

value: seedlings

tag: treatment

value: none (control)


title: 14_Treatment with 1400 mg/L kanamycin

description: treatment

source_name: Seedlings_10 days_1400 mg/L kanamycin

value: 1400 mg/L kanamycin for 10days


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_g4_g10_g18_2


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 0h Sample 3

value: 20% Sucrose for 24h


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_g4_g10_g18_1


title: 10xfemale thorax/abdomen 20% Sucrose for 24h 0h Sample 2


title: WGBS_fwa_forT1_22aa_SunTag_NtDRMcd_noNLS_g4_g10_g18

value: fwa


title: 10xfemale thorax/abdomen 20% Sucrose for 24h characteristics: Harvest timepoint Sample 1

value: Bodies


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_SUP_3

source_name: inflorescence

value: Ler

value: inflorescence


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_SUP_2


title: WGBS_T1_22aa_SunTag_NtDRMcd_SUP_4


title: WGBS_T1_22aa_SunTag_NtDRMcd_noNLS_SUP_1


title: WGBS_T1_22aa_SunTag_NtDRMcd_SUP_3


title: 186 stage 2

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

description: gene expression of RE

hyb_protocol: Fragmented and labelled samples were hybridized to GeneChip Human Gene 2.1 ST Arrays.

scan_protocol: GeneChips were scanned using Affymetrix GeneTitanTM MC Instrument

data_processing: Affymetrix expression consoleTM software (v1.4.1.46), normalized by RMA-sketch algorithm

source_name: cortical grey matter

label_protocol: Biotinylated cRNA samples were prepared using the Affymetrix GeneChip WT Pico Reagent Kit from 2 ng total RNA.

extract_protocol: total RNA was extracted using Roche High Pure FFPE RNA Micro Kit

value: cortical grey matter

tag: disease stage

value: stage 2

tag: diagnosis

value: Rasmussen Encephalitis


title: 188 stage 1

description: gene expression of RE

value: stage 1


title: 192 stage 2

description: gene expression of RE


title: 181 control

description: gene expression of epileptic control

value: control

value: epilepsy


title: The mRNA and lncRNA profiles of MDMs EV from donor 3

first: fei

last: chen

address: yanjiangxi road

institute: sun yat-sen university

description: This sample was from extracellular vesicles of MDMs from donor 3.

hyb_protocol: After purification with the RNeasy Mini Kit, hybridization was performed using a Gene Expression Hybridization Kit in a Hybridization Oven (Agilent Technology, Santa Clara, CA, USA).

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent Microarray Scanner (Agilent Technology, Santa Clara, CA, USA). Array images were analyzed and raw data were extracted using the Agilent Feature Extraction software.

data_processing:
GeneSpring software was employed to finish the basic analysis of the raw data.
Differentially expressed lncRNAs between the two groups were then identified through fold change, and adjusted p-value (q-value) was calculated using multiple tests. Statistically significant differential expression of lncRNA was displayed through volcano plot filtering with a threshold of fold change ≥ 2 and q < 0.05.

source_name: extracellular vesicles-packaged RNA

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Macrophages were isolated from peripheral blood of healthy donors and cultured in growth medium (DMEM with 10% FBS).

extract_protocol: Extracellular vesicle-packaged RNA extraction was performed with SeraMir Exosome RNA Purification for Media & Urine (RA806TC-1, System Biosciences, USA).

treatment_protocol: For the polarization of tumor associated macrophages, MDMs were treated with 30%CM from MDA-MB-231 for 6 days.

tag: source

value: extracellular vesicles

tag: donor


title: 179 stage 0

description: gene expression of RE

value: stage 0


title: 184 stage 1

description: gene expression of RE


title: WGBS_T1_22aa_SunTag_NtDRMcd_SUP_2

data_processing:
For BS-seq samples, reads were uniquely aligned to the TAIR10 genome using BS-Seeker2 along with Bowtie.
For BS-seq samples, a filter was implemented to remove reads with three or more consecutively methylated cytosines in the CHH context, as previously described in Cokus et al., 2008 (Nature).
For BS-seq samples, after alignment, methylation was called using BS-Seeker2.
For RNA-seq samples, sequencing reads were first aligned to the TAIR10 gene annotation dataset using TopHat (2 mismatches allowed). If reads did not map to genes, they were aligned to the TAIR10 genome. Read counts were obtained by implementing HTSeq and subsequent differential expression analyses were done using DESeq (Bioconductor) and custom R scripts.
For ChIP-seq samples, analysis was done by uniquely aligning reads to the TAIR10 genome using Bowtie allowing two mismatches (-v 2). Subsequently, peaks were called using MACS2 with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq samples, processed data files are in the wig format.
Supplementary_files_format_and_content: For RNA-seq samples, processed data files are provided as text files.
Supplementary_files_format_and_content: For ChIP-seq samples, processed data files are in the bigWig format.


title: The mRNA and lncRNA profiles of MDMs EV from donor 2

description: This sample was from extracellular vesicles of MDMs from donor 2.


title: The mRNA and lncRNA profiles of MDMs EV from donor 1

description: This sample was from extracellular vesicles of MDMs from donor 1.


title: 178 stage 1

description: gene expression of RE


title: 193 stage 1

description: gene expression of RE


title: The mRNA and lncRNA profiles of TAMs EV from donor 1

description: This sample was from extracellular vesicles of TAMs from donor 1.


title: WGBS_T1_22aa_SunTag_NtDRMcd_SUP_1


title: 182 control

description: gene expression of epileptic control


title: 177 stage 2

description: gene expression of RE


title: 180 stage 2

description: gene expression of RE


title: WGBS_Ler_forT1_22aa_SunTag_NtDRMcd_and_noNLS_SUP_metaplots_rep2

value: wildtype


title: 176 stage 2

description: gene expression of RE


title: The mRNA and lncRNA profiles of TAMs EV from donor 3

description: This sample was from extracellular vesicles of TAMs from donor 3.


title: The mRNA and lncRNA profiles of TAMs from donor 3

description: This sample was from donor 3 and polarized to TAMs.

source_name: tumor associated macrophages

extract_protocol: Total RNA of macrophages was extracted and purified by the RNeasy Mini Kit (Qiagen, GmBH, Hilden, Germany) according to the manufacturer’s recommendation. Purified total RNA was quantified using the NanoDrop ND-1000 spectrophotometer (Nano-Drop Technologies Wilmington, DE) and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

value: tumor associated macrophages


title: The mRNA and lncRNA profiles of TAMs from donor 2

description: This sample was from donor 2 and polarized to TAMs.


title: The mRNA and lncRNA profiles of MDMs from donor 2

description: This sample was from donor 2 and untreated.

source_name: monocytes-derived macrophages

value: monocytes-derived macrophages


title: 174 stage 0

description: gene expression of RE


title: The mRNA and lncRNA profiles of TAMs EV from donor 2

description: This sample was from extracellular vesicles of TAMs from donor 2.


title: WGBS_T2_SunTag_VP64_EVD_10

value: Col

value: leaf


title: The mRNA and lncRNA profiles of MDMs from donor 3

description: This sample was from donor 3 and untreated.


title: WGBS_Ler_forT1_22aa_SunTag_NtDRMcd_and_noNLS_SUP_T1_22aa_SunTag_NtDRMcd_and_noNLS_SUP_metaplots_rep1


title: WGBS_T2_SunTag_VP64_EVD_3


title: The mRNA and lncRNA profiles of MDMs from donor 1

description: This sample was from donor 1 and untreated.


title: WGBS_T2_SunTag_VP64_EVD_9


title: 173 stage 0

description: gene expression of RE


title: WGBS_T1_22aa_SunTag_NtDRMcd_nog_2


title: The mRNA and lncRNA profiles of breast cancer cells cocultured with TAM_3

description: This sample was from breast cancer cells cocultured with TAM_3.

source_name: breast cancer cells

growth_protocol: Breast cancer cells (MDA-MB-231) were cultured in growth medium (DMEM with 10% FBS).

treatment_protocol: Breast cancer cells were cocultured with TAMs for 3hr in transwell system.

value: breast cancer cells

value: cocultured with TAM


title: nicotine-exposed_EB scRNA-seq [N]

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
Cellranger
Seurat
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger count output

source_name: hES spontaneously differentiated cells

growth_protocol: Control_EBs/spheroids were generated from AggreWell™800 plates at day 0 and then transferred into an ultra-Low attachment 6 well plate with differentiating medium cultured for 21 days.

extract_protocol:
Within each GEM reaction vesicle, a single cell is lysed, the Gel Bead is dissolved to free the identically barcoded RT oligonucleotides into solution, and reverse transcription of polyadenylated mRNA occurs.
Single cells were collected from two independent EB differentiation experiments from day 21 EBs (control and nicotine-exposed) and dissociated using ACCUTASE™ (STEMCELL Technologies). They were prepared for the single-cell library separately. In brief, cells were washed with 1X DPBS (GIBCO) three times, strainer-filtered, and re-suspended in 0.04% BSA. Viable single cells were loaded to GemCode Instrument (10X Genomics, Pleasanton, CA) to generate single-cell barcoded droplets (GEMs) using the 10X Single Cell 3’ v2 chemistry and 10X Chromium system as per the manufacturer’s protocol.
R2: biological, R1: technical (16bp 10x barcode+10bp UMI), I1: index

treatment_protocol: Nicotine_EBs/spheroids were treated with 10 μM nicotine in differentiating medium and cultured for 21 days.

tag: cell origin

value: H7 hESC line

value: hESC-derived embryoid bodies (EBs)/spheroids

value: 10 μM nicotine

tag: time point

value: day 21


title: Control_EB scRNA-seq [D]

value: Vehicle


title: WGBS_T1_22aa_SunTag_NtDRMcd_nog_1

tag: genotype


title: The mRNA and lncRNA profiles of TAMs from donor 1

description: This sample was from donor 1 and polarized to TAMs.

tag: cell type


title: NP_sel2R2

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

data_processing:
Sequencing of the libraries was performed by the Genomics Service Unit (LMU, Andreas Brachmann).
Sequencing reads were imported into CLC Genomics Workbench v10.0 and analysed using mostly standard parameters.
Trimming of the 5' PL promoter sequence and the 3' RybB backbone sequence was performed using the trim reads command with the following settings: 1. PL promoter Sequence = GGATAACAAGATACTGAGCAC, Strand = Plus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4; 2. RybB backbone Sequence = CACAAAATGGGGACATCAAAGAAA, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4; 3. Filter on length: Discard reads below 9 nt, Discard reads above 9 nt
Resulting sequence lists with all 9 nt variants were exported as tab delimited text.
Exported text files were used as input for the python script "Frequency Analyzer" to count the abundance of any of the 262.144 possible variants, generating file "sRNA_libraries_variant_counts". (Python script available on Github: https://github.com/Loxos/srna-tool-kit-python)
File "sRNA_libraries_variant_counts" was used as input for the python script "Result Filter" to filter for variants that were detected in sel 0, sel 3 R1 and sel 3 R2, generating file "sRNA_libraries_variant_counts_sel3". (Python script available on Github: https://github.com/Loxos/srna-tool-kit-python)
Supplementary_files_format_and_content: count table for all possible 262.144 sRNA variants, csv format
Supplementary_files_format_and_content: count table for all sRNA variants that were detected in sel 0, sel 3 R1 and sel 3 R2, csv format

organism: Vibrio cholerae C6706

source_name: whole bacterial cells

growth_protocol: Vibrio cholerae C6706 ΔrpoE strains carrying the respective sRNA library were grown to exponential phase (OD600=0.2) in 10ml LB media containing 20µg/ml chloramphenicol and 1mM IPTG. At this point 3.5% ethanol was added for 6 hours. Cells were plated on LB agar containing 20µg/ml chloramphenicol and grown overnight.

extract_protocol:
Plasmid DNA was isolated using the PureYield™ Plasmid Midiprep System (Promega) and digested with XbaI and XhoI. The sRNA fragments were isolated by agarose gel extraction and used as input for library generation.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) according to the manufacturers instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: The cells were treated with 3.5% ethanol in exponential phase phase (OD600=0.2). After 6 hours of treatment, cells were plated on LB agar and grown overnight. At least 1 million clones were harvested by washing colonies off the plates with sterile PBS. Cell suspensions from one replicate were pooled and centrifuged. Cell pellets were stored at -20°C until further processing.

tag: strain

value: <delta>vchM <delta>rpoE + psRNA library (sel 2 R2)

tag: induction

value: 1mM IPTG

value: 3.5% ethanol

tag: molecule subtype

value: plasmid DNA


title: NP_sel3R2

value: <delta>vchM <delta>rpoE + psRNA library (sel 3 R2)


title: NP_sel3R1

value: <delta>vchM <delta>rpoE + psRNA library (sel 3 R1)


title: X3hao [small RNA-seq]

description: processed data file: miRNA_expression.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using Bowtie.
The number of reads aligned to each miRNA was normalized by TMM (trimmed mean of M values) method, and then converted to TPM for standardization of miRNA expression.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: miRNA_expression.txt: Tab-delimited text file includes TPM values for each Sample.

source_name: Extracellular vesicles from tumor associated macrophages

growth_protocol: Peripheral blood monocytes (PBMs) from healthy donors were isolated by Ficoll density gradient centrifugation as previously described. Monocytes derived macrophages (MDMs) were grown in DMEM (GIBCO) supplemented with 10% fetal bovine serum, 50 U/ml penicillin (GIBCO) and 50 μg/ml streptomycin (GIBCO). To induce tumor associated macrophages (TAMs), MDMs were treated with 30% CM from MDA-MB-231 cells for 6 days.

extract_protocol:
Total RNA was isolated from TAMs or TAM EVs using RNeasy mini kit (Qiagen, Germany) or SeraMir Exosome RNA Purification for Media & Urine (RA806TC-1, System Biosciences, USA).
According to the experimental instructions, the purified total RNA was ligated with a 3'-end linker, a 5'-end linker, reverse transcription, amplification, cDNA library size selection, purification, etc., to complete sequencing sample library construction.

treatment_protocol: Monocytes derived macrophages (MDMs) were as control macrophages, polarized-tumor associated macrophages (TAMs) were stimulated by 30% CM from MDA-MB-231 cells for 6 days.

value: extracellular vesicles from tumor associated macrophages


title: The mRNA and lncRNA profiles of breast cancer cells cocultured with TAM_2

description: This sample was from breast cancer cells cocultured with TAM_2.

tag: cell line


title: 169 control

description: gene expression of epileptic control

tag: tissue

value: cortical grey matter

value: control

value: epilepsy


title: 168 control

description: gene expression of epileptic control


title: 166 stage 0

description: gene expression of RE

value: stage 0

value: Rasmussen Encephalitis


title: 163 stage 1

description: gene expression of RE

value: stage 1


title: 161 control

description: gene expression of RE


title: 164 stage 2

description: gene expression of RE

value: stage 2


title: WGBS_fwa_forT1_22aa_SunTag_NtDRMcd_g4_g10_g18

tag: ecotype

value: Col

value: leaf

value: fwa


title: NP_sel2R1

value: <delta>vchM <delta>rpoE + psRNA library (sel 2 R1)


title: X1 [small RNA-seq]

source_name: Tumor associated macrophages

value: tumor associated macrophages


title: WGBS_fwa_forT2_22aa_SunTag_NtDRMcd_g4_g10_g18_2_T2_22aa_SunTag_NtDRMcd_g4_g10_g18_metaplots_rep2


title: NP_sel1R2

value: <delta>vchM <delta>rpoE + psRNA library (sel 1 R2)

value: 1mM IPTG

value: 3.5% ethanol


title: NP_sel1R1

value: <delta>vchM <delta>rpoE + psRNA library (sel 1 R1)

value: plasmid DNA


title: The mRNA and lncRNA profiles of untreated breast cancer cells_3

description: This sample was from untreated breast cancer cells_3.

value: breast cancer cells

value: untreated


title: 155 control

description: gene expression of epileptic control

value: cortical grey matter

value: control

value: epilepsy


title: 158 stage 1

description: gene expression of RE

value: stage 1

value: Rasmussen Encephalitis


title: WGBS_fwa_forT2_5aa_SunTag_NtDRMcd_g4_T1_22aa_SunTag_NtDRMcd_g4_nog_T2T3T4_22aa_SunTag_NtDRMcd_g4_g10_g18_metaplots_rep1

value: Col


title: The mRNA and lncRNA profiles of untreated breast cancer cells_2

description: This sample was from untreated breast cancer cells_2.


title: X3hao [RNA-seq]

description: processed data file: gene_expression.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
Total RNA was isolated from TAMs or TAM EVs using RNeasy mini kit (Qiagen, Germany) or SeraMir Exosome RNA Purification for Media & Urine (RA806TC-1, System Biosciences, USA).
According to the experimental instructions, the purified total RNA was subjected to rRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, terminal repair, 3' end plus A, ligation linker, enrichment and other steps to complete the library construction of the samples.

value: extracellular vesicles from tumor associated macrophages


title: X1 [RNA-seq]


title: The mRNA and lncRNA profiles of breast cancer cells cocultured with TAM_1

description: This sample was from breast cancer cells cocultured with TAM_1.

value: cocultured with TAM


title: NP_sel0

value: <delta>vchM <delta>rpoE + psRNA library (sel 0)


title: The mRNA and lncRNA profiles of untreated breast cancer cells_1

description: This sample was from untreated breast cancer cells_1.


title: NDV2_ACTTGA: VrrA rep2

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group)
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 in either condition and a FDR adjusted p-value < 1E-8 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

growth_protocol: Vibrio cholerae C6706 ΔvrrA ΔmicV strains carrying pBAD-ctr, pBAD-vrrA or pBAD-micV plasmids were grown to early stationary phase (OD600=1.5) in 50ml LB media containing 50µg/ml kanamycin. At this point 0.2% L-arabinose was added to induce micV/vrrA expression and cells were harvested 10minutes after induction.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNAse digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: The cells were treated with 0.2% L-arabinose in early stationary phase (OD600=1.5). After 10minutes of treatment 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

value: <delta>micV <delta>vrrA + pBAD-vrrA

tag: growth phase

value: early stationary phase

value: 0.2% L-arabinose


title: WGBS_T2_22aa_SunTag_NtDRMcd_g4_g10_g18_2_minus

value: leaf


title: WGBS_T2_22aa_SunTag_NtDRMcd_g4_g10_g18_2_plus


title: WGBS_T1_22aa_SunTag_NtDRMcd_g4_g10_g18_2


title: NDV3_GATCAG: VrrA rep3


title: 154 control

description: gene expression of epileptic control


title: NDM2_ACAGTG: MicV rep2

value: <delta>micV <delta>vrrA + pBAD-micV


title: WGBS_T4_22aa_SunTag_NtDRMcd_g4_g10_g18_1_minus


title: WGBS_T3_22aa_SunTag_NtDRMcd_g4_g10_g18_1_minus


title: NDM3_GCCAAT: MicV rep3


title: 159 stage 0

description: gene expression of RE

value: stage 0


title: WGBS_T3_22aa_SunTag_NtDRMcd_g4_g10_g18_1_plus


title: NDM1_TGACCA: MicV rep1


title: 424439A02_20131212332420

city: Matsue

first: Ikuhisa

last: Nishida

state: Shimane

address: 1060 Nishikawatsu

department: Life Sciences

institute: Shimane University

description: This sample is of pka1 disruptant Schizosaccharomyces pombe YMP37. It is the second of two pka1 disruptant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: NimbleGen Hybridization Mix was prepared according to the NimbleGen Hybridization Kit protocol. The hybridization mix was incubated on an array (Schizosaccharomyces pombe (4-Plex Array) v2 (A6187-00-02, NimbleGen)) in an Agilent Microarray Hybridization Oven for 16–20 hours at 42°C, and then the microarray was washed with wash buffer in a slide container at 42°C.

scan_protocol: The hybridized array was scanned on a Microarray Scanner (Agilent G2565BA).

data_processing: Fluorescence intensities were extracted using Nimblegen DEVA software.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe YMP37 (Δpka1)

label_protocol: Double-strand cDNA was prepared using the Invitrogen SuperScript Double-strand cDNA Synthesis Kit. Purified cDNA was labeled using the NimbleGen One-color Labeling Kit, and the labeled products were precipitated with isopropanol and dried. The dried pellets were dissolved in NimbleGen Sample Tracking Control.

growth_protocol:
Pre-cultures of PR110 (wild type), YMP41 (Δcgs1), YMP37 (Δpka1), or OG1 (Δppt1) cells were inoculated into 50 mL main cultures (starting concentration, 6×10^5 cells/mL) and incubated with rotation at 30°C. Aliquots of cells were taken after 8 hours (logarithmic growth phase).
The yeasts were cultivated in YES liquid compelete medium.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with a Thermo Scientific™ NanoDrop 1000 are full-spectrum, UV-Vis spectrophotometer at Thermo Fisher Scientific, Inc. (Waltham, MA, USA.).

value: Single disruptant Δpka1:h+, leu1-32, ura4-D18, pka1::ura4


title: NDV1_CAGATC: VrrA rep1


title: NDC3_TTAGGC: control rep3

value: <delta>micV <delta>vrrA + pBAD-ctr


title: WGBS_T2_22aa_SunTag_NtDRMcd_g4_g10_g18_1_minus


title: 424439A04_20131212332420

description: This sample is of ppt1 disruptant Schizosaccharomyces pombe OG1. It is the second of two ppt1 disruptant biological replicates used in this experiment, each from separate cultures.

source_name: Schizosaccharomyces pombe OG1 (Δppt1)

value: Single disruptant Δppt1:h+, leu1-32, ura4-D18, ppt1::kanMX6


title: 424439A03_20131212332420

description: This sample is of cgs1 disruptant Schizosaccharomyces pombe YMP41. It is the second of two cgs1 disruptant biological replicates used in this experiment, each from separate cultures.

source_name: Schizosaccharomyces pombe YMP41 (Δcgs1)

value: Single disruptant Δcgs1:h+, leu1-32, ura4-D18, cgs1::ura4


title: WGBS_T2_22aa_SunTag_NtDRMcd_g4_g10_g18_1_plus

source_name: leaf tissue


title: 424439A01_20131212332420

description: This sample is of wild type Schizosaccharomyces pombe PR110. It is the second of two wild type biological replicates used in this experiment, each from separate cultures.

source_name: Schizosaccharomyces pombe PR110 (Wild type)

value: Wild type:h+, leu1-32, ura4-D18


title: 424439A04_20131210332476

description: This sample is of ppt1 disruptant Schizosaccharomyces pombe OG1. It is the first of two ppt1 disruptant biological replicates used in this experiment, each from separate cultures.


title: WGBS_T1_22aa_SunTag_NtDRMcd_g4_g10_g18_1


title: HAR_AGO2_IP_miRNA

status: Public on Jan 21 2019

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

description: miRNA

data_processing:
The adapter sequences were removed from the 3’ end of the sequenced reads using the FASTX program (version 0.0.14)(-l 1 -c)
The miRNA expression level was determined by the number of reads that mapped to the mature miRNA sequences annotated in miRbase (version 21), allowing -2 or +2 nt to be templated by the corresponding genomic sequence at the 3’ end
Genome_build: hg38.p7
Supplementary_files_format_and_content: txt

source_name: embryonic kidney cells

growth_protocol: Lenti-X 293T cells were maintained in Dulbecco’s Modified Eagle’s Medium with 10% fetal bovine serum. To produce the lentiviruses, Lenti-X 293T cells were transfected with a virus vector encoding the expression cassette as well as the VSVG and ΔR8.91 plasmids. Viruses were harvested 48 hours post-transfection. RBP-expressing Lenti-X 293T stable cell lines were generated by transduction with lentiviruses in the presence of 8 μg/ml of polybrene overnight, followed by selection with 1 μg/ml puromycin for one week. To induce RBP expression, 1 ng/ml dox was added to the cell culture medium, and the cells were harvested 48 hours after induction.

extract_protocol:
RNAs were extracted using TRIzol LS reagent, according to the manufacturer’s instructions.
Briefly, UV-crosslinked cells were lysed under mild condition, and RBP-bound RNAs were partially digested with RNase I. The tagged RBP was enriched from the cell lysate by FLAG IP, and a 3’-biotinylated DNA adapter was ligated to the 3’ end of the captured RNA fragments. The ligated RNPs were released into solution by PreScission Protease cleavage and then covalently coupled to the SpyCatcher beads. The covalently linked RNP were extensively washed under denaturing conditions to remove any residual proteins and RNAs bound nonspecifically. The RNA fragments linked to biotinylated 3’ adaptors were released from RBP by proteinase K digestion and captured by Streptavidin beads. After reverse transcription (RT), the cDNAs were ligated to a second DNA adapter containing a unique molecular identifier (UMI-adapter), and the resultant cDNA library was PCR amplified and subjected to deep sequencing.
SpyCLIP sequence

treatment_protocol: To induce acute translation suppression, Lenti-X 293T cells were treated with 2μg/ml harrington for 1 hour at 37C before harvesting.

value: Lenti-X 293T

value: harringtonine


title: PTBP1_spyCLIP

description: PTBP1 binding RNA

data_processing:
The unique molecular identifier (UMI, 10 nt random sequence) added to the 5’ end of each read during library construction was removed and used as the read name in the following analysis.
The adapter sequence at the 3’ end of the sequenced reads was removed with the FASTX program (version 0.0.14) (-l 1 -c). Insert cDNAs that were either too short (less than 30 nt) or too long (more than 65 nt) were discarded
The remaining reads were mapped to the human genome (version hg38) using the STAR program with --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMultimapNmax 1 (version 2.5.2b)
Reads that mapped to the same genomic position and had identical UMIs were categorized as PCR duplicates and then collapsed into a single read
Because the 5’ end of the insert cDNA was the RBP crosslinking site, peaks were called based on the 5’ start position of usable reads using the iCount program with 3 nt clustering
The number of usable reads in each cluster was normalized to RPM (reads per million genome mapped reads) and considered the abundance
To remove noise signals, SpyCLIP clusters were normalized against input clusters. The abundance of each cluster in SpyCLIP and input sample was calculated. SpyCLIP clusters exhibiting at least an 15-fold enrichment over their corresponding input counterparts were regarded as RBP-specific clusters
Genome_build: hg38.p7
Supplementary_files_format_and_content: bed

extract_protocol:
RNAs were extracted using TRIzol LS reagent, according to the manufacturer’s instructions.
Briefly, UV-crosslinked cells were lysed under mild condition, and RBP-bound RNAs were partially digested with RNase I. The tagged RBP was enriched from the cell lysate by FLAG IP, and a 3’-biotinylated DNA adapter was ligated to the 3’ end of the captured RNA fragments. The ligated RNPs were released into solution by PreScission Protease cleavage and then covalently coupled to the SpyCatcher beads. The covalently linked RNP were extensively washed under denaturing conditions to remove any residual proteins and RNAs bound nonspecifically. The RNA fragments linked to biotinylated 3’ adaptors were released from RBP by proteinase K digestion and captured by Streptavidin beads. After reverse transcription (RT), the cDNAs were ligated to a second DNA adapter containing a unique molecular identifier (UMI-adapter), and the resultant cDNA library was PCR amplified and subjected to deep sequencing.


title: 424439A03_20131210332476

description: This sample is of cgs1 disruptant Schizosaccharomyces pombe YMP41. It is the first of two cgs1 disruptant biological replicates used in this experiment, each from separate cultures.


title: RBFOX2_spyCLIP_low_input

description:
RBFOX2 binding RNA
using less cells as input


title: PTBP1_spyCLIP_input

description: PTBP1 spyCLIP input RNA


title: SLBP_spyCLIP_low_input

description:
SLBP binding RNA
lower doxycycline

data_processing:
The unique molecular identifier (UMI, 10 nt random sequence) added to the 5’ end of each read during library construction was removed and used as the read name in the following analysis.
The adapter sequence at the 3’ end of the sequenced reads was removed with the FASTX program (version 0.0.14) (-l 1 -c). Insert cDNAs that were either too short (less than 30 nt) or too long (more than 65 nt) were discarded
The remaining reads were mapped to the human genome (version hg38) using the STAR program with --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMultimapNmax 1 (version 2.5.2b)
Reads that mapped to the same genomic position and had identical UMIs were categorized as PCR duplicates and then collapsed into a single read
Because the 5’ end of the insert cDNA was the RBP crosslinking site, peaks were called based on the 5’ start position of usable reads using the iCount program with 3 nt clustering
The number of usable reads in each cluster was normalized to RPM (reads per million genome mapped reads) and considered the abundance
To remove noise signals, SpyCLIP clusters were normalized against input clusters. The abundance of each cluster in SpyCLIP and input sample was calculated. SpyCLIP clusters exhibiting at least an 15-fold enrichment over their corresponding input counterparts were regarded as RBP-specific clusters
Genome_build: hg38.p7
Supplementary_files_format_and_content: bed
The adapter sequences were removed from the 3’ end of the sequenced reads using the FASTX program (version 0.0.14)(-l 1 -c)
The miRNA expression level was determined by the number of reads that mapped to the mature miRNA sequences annotated in miRbase (version 21), allowing -2 or +2 nt to be templated by the corresponding genomic sequence at the 3’ end


title: 424439A02_20131210332476

description: This sample is of pka1 disruptant Schizosaccharomyces pombe YMP37. It is the first of two pka1 disruptant biological replicates used in this experiment, each from separate cultures.


title: 424439A01_20131210332476

description: This sample is of wild type Schizosaccharomyces pombe PR110. It is the first of two wild type biological replicates used in this experiment, each from separate cultures.


title: AGO2_HAR_SpyCLIP_input

description: input RNA

data_processing:
The unique molecular identifier (UMI, 10 nt random sequence) added to the 5' end of each read during library construction was removed and used as the read name in the following analysis.
The adapter sequence at the 3' end of the sequenced reads was removed with the FASTX program (version 0.0.14) (-l 1 -c). Insert cDNAs that were either too short (less than 30 nt) or too long (more than 65 nt) were discarded
The remaining reads were mapped to the human genome (version hg38) using the STAR program with --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMultimapNmax 1 (version 2.5.2b)
Reads that mapped to the same genomic position and had identical UMIs were categorized as PCR duplicates and then collapsed into a single read
Because the 5' end of the insert cDNA was the RBP crosslinking site, peaks were called based on the 5' start position of usable reads using the iCount program with 3 nt clustering
The number of usable reads in each cluster was normalized to RPM (reads per million genome mapped reads) and considered the abundance
To remove noise signals, SpyCLIP clusters were normalized against input clusters. The abundance of each cluster in SpyCLIP and input sample was calculated. SpyCLIP clusters exhibiting at least an 15-fold enrichment over their corresponding input counterparts were regarded as RBP-specific clusters
Genome_build: hg38.p7
Supplementary_files_format_and_content: bed


title: AGO2_DMSO_SpyCLIP

description: AGO2 binding RNA

value: DMSO


title: SLBP_SpyCLIP

description: SLBP binding RNA


title: SpyCLIP_input

description: input RNA


title: AGO2_HAR_SpyCLIP

description: AGO2 binding RNA


title: AGO2_DMSO_SpyCLIP_input

description: input RNA


title: RBFOX2_SpyCLIP

description: RBFOX2 binding RNA


title: NDC1_ATCACG: control rep1


title: NDC2_CGATGT: control rep2


title: DMSO_AGO2_IP_miRNA

description: miRNA


title: JM8N4.rep2.L [Repli-Seq KLF4]

city: Tallahassee

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description:
Control replicate 2
processed data file: klf4_RT_chr4_IQRnorm_mm10_12-27-18.txt

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools (RPM).
Log2 ratio of early to late coverage is calculated in 5kb windows.
Log2 ratio data were quantile normalized.
Genome_build: mm10
Supplementary_files_format_and_content: klf4_RT_chr4_IQRnorm_mm10_12-27-18.txt: Tab-delimited text file

growth_protocol: Cells were maintained as described in Xie et al., 2017.

extract_protocol:
Genome-wide RT profiles were constructed as previously described. Briefly, cells were pulse labeled with BrdU for 2 hours and separated into early and late S-phase fractions by Propidium iodide staining and flow cytometry. BrdU-substituted DNA from 40k early and late S-phase cells was immunoprecipitated by anti-BrdU antibody (Becton Dickinson 347580).
Sequencing libraries were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: mESC

tag: s phase fraction

value: Late S fraction


title: KLF4_E [Repli-Seq KLF4]

description:
Klf4 enhancer deletion
processed data file: klf4_RT_chr4_IQRnorm_mm10_12-27-18.txt

value: Early S fraction


title: YY1dTAGR2_E [Repli-Seq YY1]

description:
2 days post dTAG treatment replicate2
processed data file: YY1_depletion_400k_Loess-Quantile-mm10_12-27-18.txt

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools (RPM).
Log2 ratio of early to late coverage is calculated in 5kb windows.
Log2 ratio data were quantile normalized.
Genome_build: mm10
Supplementary_files_format_and_content: YY1_depletion_400k_Loess-Quantile-mm10_12-27-18.txt: Tab-delimited text file

growth_protocol: Cells were maintained as dedcribed in Weintraub et al., 2017.

treatment_protocol: Cells were treated as described in Weintraub et al., 2017.


title: JM8N4.rep2.E [Repli-Seq KLF4]


title: Klf4.del.rep2.E [Repli-Seq KLF4]

description:
Klf4 enhancer deletion replicate 2
processed data file: klf4_RT_chr4_IQRnorm_mm10_12-27-18.txt


title: YY1dTAGR2_L [Repli-Seq YY1]


title: JM8N4_L [Repli-Seq KLF4]

description:
Control
processed data file: klf4_RT_chr4_IQRnorm_mm10_12-27-18.txt


title: JM8N4_E [Repli-Seq KLF4]


title: YY1contR2_L [Repli-Seq YY1]

description:
Control replicate2
processed data file: YY1_depletion_400k_Loess-Quantile-mm10_12-27-18.txt


title: YY1dTAGL [Repli-Seq YY1]

description:
2 days post dTAG treatment
processed data file: YY1_depletion_400k_Loess-Quantile-mm10_12-27-18.txt


title: YY1contR2_E [Repli-Seq YY1]


title: YY1CtlE [Repli-Seq YY1]

description:
Control
processed data file: YY1_depletion_400k_Loess-Quantile-mm10_12-27-18.txt


title: YY1CtlL [Repli-Seq YY1]


title: Klf4.del.rep2.L [Repli-Seq KLF4]


title: Sample 2_py2tlt_bmp2_meki_d7_rep2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

institute: University of Basel

description: BSSE_QGF_38098_C817EANXX_2_3_py2tlt5_GAGTGGA_S22_L002

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

growth_protocol: Cells were seeded at density of 20,000 cells/cm2 and incubated overnight at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated from cells of 2 independent experiments using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.
200 ng of RNA was utilized for library preparation with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). Poly-A+ RNA was sequenced by HiSeq SBS kit v4 (Illumina) on an Illumina HiSeq 2500 using protocols defined by the manufacturer.

treatment_protocol: To induce differentiation of 3T3-L1, the growth medium was replaced with medium containing 5μg/ml insulin, 1μM Dexamethasone (dissolved in ethanol), 2μM Rosiglitazone (dissolved in DMSO) for 48 hours, then in medium containing 5μg/ml insulin for 48h, then in medium containing 1μM Rosiglitazone. To induce differentiation in cancer cells, cells were seeded and incubated overnight, incubated with 200ng/ml human recombinant BMP2 (Sigma) for 3 days with 200ng/ml BMP2 and 2μM Rosiglitazone (Rosi) for 4 days, and with medium containing 2μM Rosiglitazone for another 3 days. The addition of other growth factors or inhibitors is indicated in the figures, usually from day 0 to day 7 such as human recombinant TGF1 at 2ng/ml, the MEK inhibitor PD98059 at 40μM and the TGFR1 inhibitor SB431542 at 10μM. Control cells were treated with medium containing DMSO.

value: Py2T long term cells

tag: treatment

tag: time

value: 7 days


title: Sample 3_py2tlt_meki_d7_rep1

description: BSSE_QGF_38086_C817EANXX_2_1_py2tlt4_TAGCTTA_S10_L002

value: meki


title: Sample 1_py2tlt_bmp2_meki_d7_rep1

description: BSSE_QGF_38087_C817EANXX_2_1_py2tlt5_GGCTACA_S11_L002


title: Sample 7_dln_rosi_d7_rep1

description: BSSE_QGF_38084_C817EANXX_2_1_dln2_ACTTGAA_S8_L002

value: mesenchymal breast cancer cells (MT{delta}ECad)

value: rosi


title: Sample 5_py2tlt_control_d7_rep1

description: BSSE_QGF_38085_C817EANXX_2_1_py2tlt3_GATCAGA_S9_L002

value: control


title: Sample 9_dln.control.rep1

description: BSSE_QGF_38083_C817EANXX_2_1_dln1_CAGATCA_S7_L002


title: Sample 6_py2tlt_control_d7_rep2

description: BSSE_QGF_38096_C817EANXX_2_3_py2tlt3_GTTTCGG_S20_L002


title: Sample 8_dln_rosi_d7_rep2

description: BSSE_QGF_38095_C817EANXX_2_3_dln2_GTGGCCT_S19_L002


title: KLF4_L [Repli-Seq KLF4]


title: Sample 4_py2tlt_meki_d7_rep2

description: BSSE_QGF_38097_C817EANXX_2_3_py2tlt4_CGTACGT_S21_L002


title: WT4Dbf.E [Repli-seq epha4]

description: processed data file: epha4_RT_chr1_Quqntile_400kb_mm10_12-4-17.txt

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools.
Log2 ratio of early to late coverage is calculated in 5kb windows.
Log2 ratio data were quantile normalized.
Genome_build: mm10
Supplementary_files_format_and_content: epha4_RT_chr1_Quqntile_400kb_mm10_12-4-17.txt: Tab-delimited text file

growth_protocol: Mouse ESCs were maintained as described in Lupiáñez et al. Cell 2015.

treatment_protocol: CRISPR-mediated deletion or inversions.


title: WT4Dbf.L [Repli-seq epha4]


title: YY1dTAGE [Repli-Seq YY1]


title: InvF.E [Repli-seq epha4]


title: InvF.L [Repli-seq epha4]


title: DelBs.L [Repli-seq epha4]


title: G4.WT.E [Repli-seq epha4]


title: G4.WT.L [Repli-seq epha4]


title: Dbf.L [Repli-seq epha4]


title: Sample 10_dln.control.rep2

description: BSSE_QGF_38094_C817EANXX_2_3_dln1_GTGAAAC_S18_L002


title: DelB.L [Repli-seq epha4]


title: DelB.E [Repli-seq epha4]


title: noauxin.rep2.E [Repli-Seq CTCF Auxin]

description:
No auxin treatment control, replicate 2
processed data file: CTCFdegron_QuantileNorm-mm10_1-17-16.txt
processed data file: CTCFdegron2Days_EtoL_0.01_diff1.txt
processed data file: CTCFdegron2Days_LtoE_0.01_diff1.txt

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools (RPM).
Log2 ratio of early to late coverage is calculated in 5kb windows.
Log2 ratio data were quantile normalized.
Genome_build: mm10
Supplementary_files_format_and_content: CTCFdegron_QuantileNorm-mm10_1-17-16.txt: Tab-delimited text file includes Repli-seq profiles.
Supplementary_files_format_and_content: CTCFdegron2Days_EtoL_0.01_diff1.txt: Tab-delimited text file includes Repli-seq fingerprints changing from early to late after removing CTCF.
Supplementary_files_format_and_content: CTCFdegron2Days_LtoE_0.01_diff1.txt: Tab-delimited text file includes Repli-seq fingerprints changing from late to early after removing CTCF.

growth_protocol: Cells were maintained as described in Nora et al. 2016 Cell. E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550μM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x10^5 cells / cm2 by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

treatment_protocol: For induction of the auxin-inducible degron, indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500μM from a 1000X stock diluted in sterile water. Stocks were kept at 4°C up to 4 weeks or -20°C for long term storage.


title: noauxin.rep2.L [Repli-Seq CTCF Auxin]


title: auxin2days.rep1.L [Repli-Seq CTCF Auxin]

description:
2days post Auxin induced CTCF depletion, replicate 1
processed data file: CTCFdegron_QuantileNorm-mm10_1-17-16.txt
processed data file: CTCFdegron2Days_EtoL_0.01_diff1.txt
processed data file: CTCFdegron2Days_LtoE_0.01_diff1.txt

value: Auxin


title: auxin2days.rep2.L [Repli-Seq CTCF Auxin]

description:
2days post Auxin induced CTCF depletion, replicate 2
processed data file: CTCFdegron_QuantileNorm-mm10_1-17-16.txt
processed data file: CTCFdegron2Days_EtoL_0.01_diff1.txt
processed data file: CTCFdegron2Days_LtoE_0.01_diff1.txt


title: auxin2days.rep1.E [Repli-Seq CTCF Auxin]


title: c.del.B11 [Bru-seq]

description:
Nascent RNA
processed data file: RPKM-9-7-18.txt

data_processing:
Library strategy: Bru-seq
Reads are mapped to mm10 using bowtie2.
Allele-specific analysis was performed using harp (http://github.com/dvera/harp).
RPM-normalized read densities were calculated with bedtools2 (Quinlan and Hall, 2010) genomecov, using a scaling factor of 1000000/(number of parsed reads in library).
Genome_build: mm10
Supplementary_files_format_and_content: *bed: bed files
Supplementary_files_format_and_content: RPKM-9-7-18.txt: Tab-delimited text file

growth_protocol: Mouse ESCs were maintained on 1% gelatin coated dishes. 46C was grown in GMEM supplemented with 10% FBS and LIF; hybrid cells (Cas/129 and V6.5) in DMEM supplemented with 2i plus LIF.

extract_protocol:
Trizol
Nascent RNA was pulled down using anti-BrdU antibodies conjugated magnetic beads. Strand specific cDNA libraries were constructed using 300ng Bru-labeled RNA and sequenced on Illumina HiSeq 2500 with 100bp single end.

treatment_protocol: Cells was pulse labeled with 2 mM bromouridine (Bru) for 30 minutes.

tag: hybrid cells


title: F121-9R1 [Bru-seq]


title: F121-9R2 [Bru-seq]


title: bc.del.B3 [Bru-seq]


title: abc.del.E2 [Bru-seq]


title: abc.del.A6 [Bru-seq]


title: ab.del.D10 [Bru-seq]


title: 350k del [4C-seq]

description:
350kb boundary deletion
processed data file: 4C_inbred_5kb_smoothed_w30.txt

data_processing:
Library strategy: 4C-seq
Reads are mapped to mm9 or mm10 using bowtie2.
Each profile was then normalized to RPM.
Binned to 10kb windows.
Smoothed using rolling mean smoothing.
Genome_build: M. musculus (hybrid cas/129): mm10; M. musculus: mm9
Supplementary_files_format_and_content: abc-4C-SNPsParse1_5kwin-Smoothed.RPM_mm10_2-16-18.txt
Supplementary_files_format_and_content: 4C_inbred_5kb smoothed_w30.mm9.txt

source_name: 350k del

extract_protocol: 4C-seq was performed as previously described with minor modifications. 10 million cells were fixed in 1% formaldehyde, and chromatin was digested using HindIII before proximity ligation, followed by DpnII after reverse crosslinking. 4C libraries were prepared using inverse-PCR primers that contain Illumina adapters and anneal to the pBACe3.6 bacterial sequences (forward primer: 5’-ATAAACTACCGCATTAAAGC; reverse primer: 5’-GGAGCCACTATCGACTACGC). Libraries were sequenced with 3-7 million mappable reads using 50bp single-end sequencing with Illumina HiSeq 2500.

tag: bait sequence

value: Forward AGCGTGAGGTACATGAAAGC  Reverse CCTGAAGAGCTGGTACCAAA


title: 45k del [4C-seq]

description:
45kb boundary deletion
processed data file: 4C_inbred_5kb_smoothed_w30.txt

source_name: 45k del


title: 680kinv.B10 [Bru-seq]


title: DelBs.E [Repli-seq epha4]


title: Dbf.E [Repli-seq epha4]


title: WGBS_T2_SunTag_VP64_nog_2

city: Los Angeles

first: Ashot

last: Papikian

address: 4045 Terasaki Life Sciences Building

institute: University of California, Los Angeles

data_processing:
For BS-seq samples, reads were uniquely aligned to the TAIR10 genome using BS-Seeker2 along with Bowtie.
For BS-seq samples, a filter was implemented to remove reads with three or more consecutively methylated cytosines in the CHH context, as previously described in Cokus et al., 2008 (Nature).
For BS-seq samples, after alignment, methylation was called using BS-Seeker2.
For RNA-seq samples, sequencing reads were first aligned to the TAIR10 gene annotation dataset using TopHat (2 mismatches allowed). If reads did not map to genes, they were aligned to the TAIR10 genome. Read counts were obtained by implementing HTSeq and subsequent differential expression analyses were done using DESeq (Bioconductor) and custom R scripts.
For ChIP-seq samples, analysis was done by uniquely aligning reads to the TAIR10 genome using Bowtie allowing two mismatches (-v 2). Subsequently, peaks were called using MACS2 with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq samples, processed data files are in the wig format.
Supplementary_files_format_and_content: For RNA-seq samples, processed data files are provided as text files.
Supplementary_files_format_and_content: For ChIP-seq samples, processed data files are in the bigWig format.

extract_protocol:
For BS-seq experiments, genomic DNA was isolated using the DNeasy Plant Mini Kit (Qiagen).
For BS-seq experiments, 100ng of DNA was then used for subsequent shearing using a Covaris Ultrasonicator. Libraries were then prepared using either the Ovation Ultralow Methyl-Seq kit (NuGen) in conjuction with the EpiTect Bisulfite Kit (Qiagen), or the KAPA Hyper Prep Kit (KAPA Biosystems) in conjuction with either the EZ DNA Methylation-Lightning Kit (Zymo) or the EpiTect Bisulfite Kit (Qiagen).

value: Col

value: leaf


title: noauxin.rep1.E [Repli-Seq CTCF Auxin]

description:
No auxin treatment control, replicate 1
processed data file: CTCFdegron_QuantileNorm-mm10_1-17-16.txt
processed data file: CTCFdegron2Days_EtoL_0.01_diff1.txt
processed data file: CTCFdegron2Days_LtoE_0.01_diff1.txt


title: noauxin.rep1.L [Repli-Seq CTCF Auxin]


title: abc.del.A6 [4C-seq]

description:
del:chr16:48308399-48311882;48396806-48437301;48581359-48620367
processed data file: abc-4C-SNPsParse1_5kwin-Smoothed.RPM_mm10_2-16-18.txt

value: Forward TTTGGGATTTTGGAGTGAAGC   Reverse CTGCTGGACTTGTCAACTGAA


title: WT [4C-seq]

description:
46C WT
processed data file: 4C_inbred_5kb_smoothed_w30.txt

source_name: WT


title: abc.del.E2 [4C-seq]


title: 46C.L (repli-seq)

data_processing:
Reads are mapped to mm10 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Log2 ratio of early to late coverage is calculated in 5kb windows
Log 2 ratio data were IQR normalized to 4.59
Genome_build: mm10
Supplementary_files_format_and_content: All .txt datasets are normalized to RPM for both early and late fractions before taking log2 ratios, and then Loess smoothed

extract_protocol:
Genome-wide RT profiles were constructed as previously described. Briefly, cells were pulse labeled with BrdU for 2 hours and separated into early and late S-phase fractions by Propidium iodide staining and flow cytometry. BrdU-substituted DNA from 40k early and late S-phase cells was immunoprecipitated by anti-BrdU antibody (Becton Dickinson 347580)
Sequencing libraries were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: CRISPR-mediated deletion or inversions

tag: protocol


title: ac.del.E4.rep2.E (repli-seq)


title: auxin2days.rep2.E [Repli-Seq CTCF Auxin]


title: ac.del.E4.rep1.L (repli-seq)


title: 435k.inv.C5.L (repli-seq)


title: ac.del.E4.rep1.E (repli-seq)


title: 435k.inv.C5.E (repli-seq)