title: H3K9me3_ChIPSeq [H18511]


title: SNAI1 replicate 1

status: Public on Apr 25 2018

type: SRA

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

country: USA

institute: The Children's Hospital of Philadelphia

description:
HME_SNAI1_R33
processed data file:
rMATS_unfiltered_output_SNAI1_vs_EGFP.xlsx

library_source: transcriptomic

data_processing:
Nextera adapters were trimmed using Trimmomatic (v0.33)
Trimmed reads were aligned to the reference human genome (hg19 with Gencode V19 annotations) using STAR (v2.5.2b)
Differential alternative splicing was quantified using rMATS (v3.2.5) with the following parameters: -t paired -len 100 -analysis U -libType fr-unstranded -novelSS 0
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are contained in an excel spreadsheet and consist of  "ReadsOnTargetandJunctionCounts" output from rMATS analysis of alternative splicing compared between cells expressing each ORF ("Sample 1": HCRED, QKI, RBFOX1, SNAI1) or EGFP ("Sample 2"). Within each file, data are divided into individual sheets containing an event type (A3SS, A5SS, MXE, RI, SE).

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from cells usingthe RNeasy Mini Kit (Qiagen)
Libraries were constructed using the Nextera unstranded mRNA protocol according to the manufacturer's instructions (Illumina)

tag: cell type

value: Immortalized mammary epithelial cells (HME)

tag: genotype/variation

value: overexpressing candidate ORF SNAI1


title: SNAI1 replicate 2

description:
HME_SNAI1_R34
processed data file:
rMATS_unfiltered_output_SNAI1_vs_EGFP.xlsx


title: HUVEC_at_passage16

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

data_processing:
Alignment with STAR
Processing, normalization and filtering with CellRanger
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices
Genome_build: hg19
Supplementary_files_format_and_content: count data for each detected transcript

source_name: HUVEC

extract_protocol:
Drop-seq with the 10X Genomics chromium system
Single-cell RNA-seq library according to the 10X Genomics protocol version v1

tag: passage


title: HUVEC_at_passage4


title: 3T3_Control_DMSO_rep2

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Control_DMSO_replicate2
Processed file sample name: X3T3_control_DMSO_rep_1

data_processing:
Fastq files were aligned to mouse genome build mm9 using HiSat with default parameters.
Transcripts were assembled and FPKM values were generated using cuff quant and cuffnorm from the cufflinks pipeline (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: dTAG_all_fpkm_exprs_norm.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

molecule: polyA RNA

organism: Mus musculus

growth_protocol: NIH/3T3 cells (ATCC, DMEM supplemented with 10% bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin) cells were cultured at 37 ºC and 5% CO2. Cells that were transduced with lentivirus were additionally cultured with 2 mg/mL puromycin.

extract_protocol:
NIH/3T3 cells were treated in triplicate with DMSO, 1 µM dTAG-13 for four and eight hours, 10 nM of Trametinib for four and eight hours, lysed, homogenized using Qiashredder columns (Qiagen), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cell count normalized RNA samples were mixed with the ERCC RNA Spike-In Mix #1 (Life Technologies) prior to library preparation.
Libraries for Illumina sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) and equimolar multiplexed libraries were sequenced on an Illumina NextSeq 500 (single end 75 bp reads) .

treatment_protocol: Cells were treated with DMSO, 1 μM dTAG-13, or 10 nM Trametinib for the times indicated.

tag: cell line

tag: associated experiment

value: KRAS-related experiment

tag: stable transduction

value: Untransduced control

tag: culture condition

value: DMEM + 10% Bovine Serum + 1% Pen/Strep

tag: treatment

value: DMSO

tag: time

value: 8 hours


title: H3K9me3_ChIPSeq [H28815]

city: Chicago

first: Michelle

middle: C

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
Processed data file: H3K9me3_counts_hg19.txt
Processed data file: H3K9me3_counts_panTro3.txt

library_source: genomic

data_processing:
Paired-end ChIP-seq reads from each species were mapped to their respective genome (hg19 or panTro3) using BWA (version 0.7.12) (Li and Durbin 2009) and a mapping quality filter of MAQ >10. PCR duplicates were removed by samtools (version 0.1.19)(Li et al. 2009). Properly-paired reads only were selected for further analysis.
ChIP and Input reads from each individual were used to call peaks using MACS2 (Zhang et al. 2008) with the broadpeak option at various qvalue cut-offs. A lenient threshold of qvalue=0.1 was used in subsequent analysis to maximize the number of regions in each species. Peaks called in each species were concatenated to generate a final peak set across both species.
Peak coordinates in each species were then converted to the alternative genome using liftOver (Speir et al. 2016) and the best reciprocal chain (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/reciprocalBest/) between hg19 and panTro3. Peak regions that could be reciprocally and uniquely mapped between the two genomes were kept to generate a list of orthologous peaks.
The number of reads falling into these orthologous peak regions was determined using HTSeq (Anders et al. 2015).
Genome_build: hg19 (GRCh37), panTro3 (Pan_troglodytes-2.1.3)
Supplementary_files_format_and_content: *txt: H3K9me3 ChIP-seq read counts for all orthologous regions in all samples with region coordinates on both the human genome (hg19) and the chimpanzee genome (panTro3).

molecule: genomic DNA

source_name: induced pluripotent stem cells, H3K9me3 ChIP

growth_protocol: Human and chimpanzee feeder-independent induced pluripotent stem cell lines were maintained at 70% confluence on Matrigel hESC-qualified Matrix (354277, Corning, Bedford, MA, USA) at a 1:00 dilution. Cells were cultured in Essential 8 Medium (A1517001, ThermoFisher Scientific, Waltham, MA, USA) at 37°C with 5% (vol/vol) CO2 with daily media changes. Cells were passaged by enzyme-free dissociation (0.5 mM EDTA, 300 mM NaCl in PBS), and seeded with ROCK inhibitor Y-27632 (ab120129, Abcam, Cambridge, MA, USA).

extract_protocol:
ChIP-seq experiments were largely performed according to a published protocol (Schmidt et al. 2009). Briefly, 30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature followed by quenching with 2.5 M glycine. Following cell lysis and sonication (Covaris S2: 4 min, duty cycle 10%, 5 intensity, 200 cycles per burst in 4x 6 x 16 mm tubes per individual), lysates were incubated with 5 μg H3K9me3 antibody (8898, Abcam) overnight.
Libraries were prepared using the Illumina TruSeq ChIP Sample Preparation kit. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

value: induced pluripotent stem cells

tag: Sex

value: Male

tag: population

value: Caucasian

tag: chip antibody


title: RBFOX1 replicate 2

description:
HME_RBFOX1_R25
processed data file:
rMATS_unfiltered_output_RBFOX1_vs_EGFP.xlsx

value: overexpressing candidate ORF RBFOX1


title: RBFOX1 replicate 3

description:
HME_RBFOX1_R42
processed data file:
rMATS_unfiltered_output_RBFOX1_vs_EGFP.xlsx


title: H3K9me3_ChIPSeq [H18489]

value: Female

value: Yoruba


title: QKI replicate 1

description:
HME_QKI_R28
processed data file:
rMATS_unfiltered_output_QKI_vs_EGFP.xlsx

value: overexpressing candidate ORF QKI


title: H3K9me3_ChIPSeq [H28126]


title: RBFOX1 replicate 1

description:
HME_RBFOX1_R24
processed data file:
rMATS_unfiltered_output_RBFOX1_vs_EGFP.xlsx


title: H3K9me3_ChIPSeq [H20682]


title: H3K9me3_ChIPSeq [H20961]


title: HcRed replicate 3

description:
HME_HCRED_R4
processed data file:
rMATS_unfiltered_output_HCRED_vs_EGFP.xlsx

value: overexpressing negative control protein HcRed


title: QKI replicate 2

description:
HME_QKI_R29
processed data file:
rMATS_unfiltered_output_QKI_vs_EGFP.xlsx


title: H3K9me3_ChIPSeq [H21792]


title: input_for_Lamin B TSA-Seq Condition 2 (TSA+Sucrose)

city: Urbana

first: Andrew

middle: S

last: Belmont

address: 601 S Goodwin Ave, CLSL B509

institute: University of Illinois at Urbana-Champaign

description:
Sample 19
processed data file: LaminB_TSA-Seq_Score_Condition2.bw

data_processing:
Library strategy: TSA-Seq
The raw .bcl files were converted into demultiplexed compressed fastq files using the bcl2fastq v1.8.2 and later v2.17.1.14 conversion software (Illumina).
Raw sequencing reads were first mapped to the human genome (UCSC hg19) using Bowtie 2 version 2.0.2 with default parameters. Chromosome Y was excluded in the reference genome to reduce mapping bias since the K562 cell line was derived from a female.
PCR duplicates reads were removed using samtools version 0.1.19 with default parameters.
We normalized and processed the TSA-Seq data using a sliding window approach as follows. The normalized SON-TSA score was calculated as the log 2 ratio of  (TSA-Seq pulldown reads in a 20 kb window divided by total mapped reads for this pulldown sample) / (input reads in the same 20 kb window divided by total mapped reads for this input). This approach can be interpreted as the fold change between the pulldown sample and the input corrected by the total number of mapped reads in each sample. The window slides on the genome with a step size of 100 bp.
We partitioned the genome into non-overlapping 20 kb bins, averaging the TSA-Seq score over the 100 bp intervals within this bin for the new TSA-Seq 20 kb score.  The values for these 20 kb bins were then smoothed by convolution using a Hanning window of length 21 (21 x 20 kb or 420 kb).  This new smoothed TSA-Seq score with 20 kb sampling was used for SON TSA-Seq decile calculations and comparisons with other genome features
Genome_build: hg19
Supplementary_files_format_and_content: normalized TSA signals were in bigWig format, and the 10 deciles are in BED format. Other data files from analyzing public datasets are in bigWig or bigBed formats.

source_name: bone marrow

growth_protocol: K562 Cells were grown according to the ENCODE protocol, in RPMI with 10% FBS (Sigma-Aldrich) and Antibiotic-antimycotic (GIBCO) at density of 0.4 x 10^6-0.75 x 10^6 /ml

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-15 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

treatment_protocol: TSA labeling was done in independent cell batches.  For each batch, cells were divided equally and stained according to four labeling protocols: “Condition 1”, “Condition 2”, “Condition 3”, and “No 1o control”.  Identical staining conditions were used except that 50% sucrose was included in the TSA staining buffer for the “Condition 2” protocol, 0.75mM DTT in addition to 50% sucrose was added in the TSA staining buffer for the “Condition 3” protocol, and the anti-SON primary antibody was omitted for the “No 1o control” protocol.  Cells were fixed by adding 10 ml of 8% paraformaldehyde (Sigma-Aldrich) freshly prepared in CMF-PBS (calcium, magnesium-free phosphate buffered saline) to 40 ml of cells in culture media, incubating for 20 min at room temperature (RT), and quenching aldehydes by addition of 5.6 ml of 1.25 M glycine (Fisher Scientific) and incubation for 5 min at RT.  All incubation steps used a rotating platform to mix the cell suspension.  Cells were then pelleted by centrifugation and resuspended in CMF-PBS buffer with 0.5% Triton-X100 (Sigma-Aldrich) for 30 min at RT.  All centrifugations were for 5 min at 100-200g.  Cells were centrifuged at RT and resuspended in 1.5% H2O2 (Fisher Scientific) in CMF-PBS for 1h at RT to quench endogenous peroxidases, followed by 3 washes at RT in PBST (0.1%Triton-X100/CMF-PBS) by repeated centrifugation and cell pellet resuspension.  Cells were resuspended in IgG Blocking Buffer (5% Normal Goat Serum (Sigma-Aldrich) in PBST) at a concentration of 10^7 cells/ml for 1 hr, followed by centrifugation and resuspension in primary antibody solution (Rabbit-anti-SON primary antibodies (Ab1, Atlas antibodies cat # HPA023535) diluted 1:1000 or 1:2000 in IgG Blocking buffer, or rabbit polyclonal-anti-SON primary antibodies (Ab2) diluted 1:2000 in IgG Blocking buffer, or mouse-anti-phosphorylated SC35 primary antibodies (Sigma-Aldrich cat # S4045) diluted 1:500 in IgG Blocking buffer, or mouse monoclonal anti-lamin A/C primary antibody (Clone 5G4) diluted 1:1000 in IgG Blocking buffer, or mouse monoclonal anti-lamin B primary antibodies (Clone 2D8) diluted 1:1000 in IgG Blocking buffer) at 10^7 cells/ml, or mouse monoclonal anti-RNA polymerase II primary antibodies (clone 4H8) (Millipore cat # 05-623) at 0.5 x 107 cells/ml and incubated 20-24 hrs at 4°C (See METHODS for more information about anti-lamin antibodies). For the no primary control, cells were incubated in IgG Blocking buffer only.  Cells were then washed 3x with PBST, resuspended in IgG Blocking buffer with secondary antibodies at 10^7 cells/ml, and incubated 20-24 hrs at 4°C.  Secondary antibodies (Jackson, ImmunoResearch) used were HRP conjugated, goat-anti-rabbit secondary antibody diluted 1:1000 or HRP conjugated goat-anti-mouse secondary antibody diluted 1:200 or 1:1000. Cells then were washed 3x in PBST and resuspended in reaction buffer A (CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Condition 2, or CMF-PBS with 50% sucrose and 1.5mM DTT for Condition 3) at 2 x 10^7 cells/ml.  Equal volumes of buffer B (8mM tyramide-biotin stock solution diluted 1:5000 with 0.003% H2O2 in CMF-PBS for Condition 1, or CMF-PBS with 50% sucrose for Conditions 2 and 3) were then added.  Cells were incubated for 10 min and then washed 3x in PBST at RT.  Validation of TSA labeling is done by biotin immunostaining.

tag: disease

value: chronic myelogenous leukemia (CML)

tag: tsa-seq target

value: Lamin B

tag: primary antibody

value: none (input control)


title: HcRed replicate 1

description:
HME_HCRED_R1
processed data file:
rMATS_unfiltered_output_HCRED_vs_EGFP.xlsx

value: Immortalized mammary epithelial cells (HME)


title: H3K9me3_ChIPSeq [H21194]


title: EGFP replicate 2

value: overexpressing negative control protein EGFP


title: input_for_Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose)

description:
Sample 17
processed data file: LaminAC_TSA-Seq_Score_Condition2.bw

value: Lamin A/C


title: input_for_SON TSA-Seq Condition 3 (TSA+Sucrose+DTT)

description:
Sample 13
processed data file: SON_TSA-Seq_Score_Condition3.bw
processed data file: Speckle_distance_Condition3.bw

value: SON


title: input_for_SON TSA-Seq Condition 2 (TSA+Sucrose) Replicate

description:
Sample 11
processed data file: SON_TSA-Seq_Score_Condition2.Replicate.bw


title: acx4_bisulfite sequencing_rep2

city: Beijing

first: Yusheng

last: Zhao

address: Yuanmingyuan Road #2, Haidian District

country: China

institute: China agricultural university

description:
processed data files:
CHG_acx4.bedGraph
CHH_acx4.bedGraph
CpG_acx4.bedGraph

data_processing:
For Bisulfite-seq analysis, the raw sequence data were demultiplexed and converted to fastq files using bcl2fastq2 Conversion Software (version v2.16.0) under default parameters. Mapping, deduplication, and methylation extraction were performed using bismark software (V0.7.4),of which mapping using bowtie2 (2.0.5) to TAIR10.
genome build: TAIR10
processed data files format and content: bedgraph files with CHG, CHH and CpG methylation levels.

organism: Arabidopsis thaliana

source_name: young seedlings

growth_protocol: Seeds were grown on MS medium plates supplemented with 20 g/L sucrose and 0.8% agar at 22°C under long-day (23 h) illumination

extract_protocol:
Genomic DNAs were extracted from seedlings using the DNeasy Plant Mini Kit (QIAGEN)
For Bisulfite-seq, 5-μg of genomic DNAs was sonicated then end-repaired with the End Repair Enzyme Mix (New England BioLabs, Ipswich, MA).The blunt-ended DNA were treated with Klenow fragment (New England BioLabs, Ipswich, MA) and  dATP to 3’-dA-tailed and ligated to methylated adapters.The ligated DNA fragments were treated using the EpiTect bisulfite Kit (Qiagen, Valencia, CA). The bisulfite-treated DNAs were amplified by PCR with Illumina primers for 15 cycles and fragments of 250-350 bp were excised from an agarose gel and purified.  Paired end sequencing of each library was performed to around 100 cycles on the Illumina HiSeq 2000 or HiSeq 4000 according to manufacturer's protocols.

tag: developmental stage

value: 7-day-old whole seedlings

tag: ecotype

tag: genotype

value: acx4 mutant


title: acx4_RNA_rep1

description:
processed data file:
genes and TEs up and down regulated in acx4.xls

data_processing:
For RNA-seq process, paired-end reads were selected and aligned to the Arabidopsis reference genome (version: TAIR10), using TopHat (v2.1.1) and Cuffdiff (v2.1.1).
genome build: TAIR10
processed data files format and content: Excel file with log2 fold-changes and P-values for genes and Tes identified as either up- or down-regulated.

extract_protocol:
total RNAs extracted from seedlings using the RNeasy Plant Mini Kit (QIAGEN)
For RNA-seq library, a 3-μg mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s protocol. RNA-seq was conducted using the Illumina Hiseq 2500 platform for both C24 and acx4 plants.


title: BM1077-HSC-Frozen-160105-28

status: Public on Apr 26 2018

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions.
Genome_build: hg19
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

source_name: Bone Marrow CD34+

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. All cells described here were FACS sorted prior to performing the assay.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: tissue

value: CD34+ Bone Marrow

tag: cell type

value: HSC


title: WT_RNA_rep1

value: wild type


title: WT_RNA_rep2


title: EGFP replicate 1

tag: genotype/variation


title: input_for_SON TSA-Seq Condition 1 (TSA only) Replicate

description:
Sample 9
processed data file: SON_TSA-Seq_Score_Condition1_Replicate.bw

tag: cell line


title: p153trmwt_cuffdiff_out_gene_exp.diff

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Base-calling were performed by Illumina Real-Time Analysis software v1.13 or v1.17.
Reads were aligned by bowtie version 0.12.7 against the Arabidopsis TAIR10 genome assembly with parameters " -m 1 --best --strata -S --chunkmbs 200".
Peaks called with MACS2 version 2.0.10 with paramteers " --call-summits --nomodel --shiftsize 150 --keep-dup auto".
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by MACS2.
Supplementary_files_format_and_content: CuffDiff results

source_name: whole seedlings

growth_protocol: Recommending gene tagging of BARRs (ARR1.2, ARR10, ARR12, ARR14)  were carried out as described previously (Zhou et al., The Plant Journal 2011; PMID 21294796).  Seedling were germinated and grown on LS lates for 72 hours under long day light conditions unless indicated.

extract_protocol:
After nuclei isolation, chromatin was sonicated to 100-400 bp fragments. Ypet tagged BARRs in the transgenic lines were immunoprecipitated by a rabbit polyclonal GFP antibody (Thermo Fisher Scientific, (Cat A11111), USA). Either rabbit IgG or input genomic DNA as control,  respectively.
Libraries were prepared according to Illumina's instructions accompanying TruSeq DNA sample prep kit and sequenced by Illumina HiSeq 2500 according to the manufacturer's instructions.

treatment_protocol: 10 uM 6BA treatment for 4 hours or DMSO treatment as mock, p6BA=72hours 10uM 6BA treatment on LS plates.

tag: accession

tag: age

value: 3 days

tag: light condition

value: long day

value: pmpmp=q1, barrtiple(trm)=q2, WT=q3


title: acx4_bisulfite sequencing_rep1


title: input_control

description: input

tag: tag-line

value: Ypet tag

tag: treatment

value: 10uM 6BA, 4hours


title: IgG_control

description:
IgG
IP


title: p127RNA-seq_cuffdiff_out_2_gene_exp.diff

value: Dex:CKX3 in ARR1.2Ypet

value: DMSO, 4hours=q1, 10uM Dex 4hours=q2, 10uM 6BA 4hours=q3


title: acx4_RNA_rep2


title: HcRed replicate 2

description:
HME_HCRED_R3
processed data file:
rMATS_unfiltered_output_HCRED_vs_EGFP.xlsx

value: overexpressing negative control protein HcRed


title: EGFP replicate 3

value: Immortalized mammary epithelial cells (HME)


title: ARR12Ypet_6BA

description:
ChIP antibody: GFP antibody (Thermo Fisher Scientific, A11111)
IP


title: DDK_e

value: 10uM Dex, 4hours


title: ARR10_ypet16_1_mock

value: DMSO, 4hours


title: ARR12Ypet_mock


title: ARR10_ypet16_1_6BA


title: ARR1.2ypet_LD_6BA


title: ARR1.2Ypet_LD_mock


title: LIN-41_IP2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data (51bp read length) were mapped to the c.elegans genome (ce10) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS220). The command used to create the count table was qCount(proj,exons,orientation="opposite",selectReadPosition="end"), which counts all the reads on the opposite strand of the gene (produced by this sample preparation protocol). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 38.1M reads which represents the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts. To account for non-linear scaling between the samples we quantile normalized the data using the function normalize.quantiles from the R package preprocessCore. IP enrichments were then calculated by subtracting the input samples from the respective IP samples.
Genome_build: ce10
Supplementary_files_format_and_content: ce_geneExpression_lin41RipSeq_rawCounts.txt
Supplementary_files_format_and_content: ce_geneExpression_lin41RipSeq_normalized.txt

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Pico pure RNA isolation  kit (Invitrogen)
FLAG-GFP tagged LIN-41 was immunoprecipitated using FLAG dynabeads (Sigma) from lysates of young adult C.elegans. After washing steps, bound fraction (IP) was eluted from beads and associated RNAs were isolated by using the Pico pure RNA isloation kit (Invitrogen)
mRNA sequencing Illumina (stranded)

tag: Stage

value: young adult

tag: strain

value: Lab strain# 1587

value: lin-41(rrr3) (I); rrrSi367 [Plin-41::FLAG-GFP-TEV-LIN-41::lin-41 full-length 3'UTR; unc-119(+)]  (II)

tag: antibody


title: LIN-41_IP1


title: Input2


title: Input1


title: input for "RNA Pol II TSA-Seq Condition 1 (TSA only) Replicate"

extract_protocol:
Cell lysis and protease digestion were done at 55°C with constant mixing in 10mM Tris, 10mM EDTA, 0.5% SDS and 500µg/ml proteinase K (NEB) for 8-12 hrs (10^7 cells/ml).  NaCl was added for a final 0.2 M concentration and the lysate incubated 20-24 hrs at 65°C with constant mixing to reverse formaldehyde crosslinking.  DNA was extracted 2x using an equal volume of phenol (Fisher)/chloroform/isoamyl alcohol (25:24:1) and 1x with an equal volume of chloroform/isoamyl alcohol (24:1).  Tubes were kept at 55°C for 1h with the cap off to evaporate phenol residues, and then treated with 25 µg/ml RNaseA (Qiagen) at 37o C for 1hr and extracted again.  DNA was then precipitated with 1/10 volume of 3M Na Acetate, pH 5.2, and 2 volumes of 100% EtOH at -20 oC for 20 min – 2 hrs.
For each of the TSA-Seq experiment staining conditions, input and Streptavidin pull-down DNA were used to make sequencing libraries, using the Kapa Hyper Prep Kit (Kapa Biosystems).  DNA was blunt-ended, 3’-end A-tailed, and ligated to indexed adaptors with 6nt barcodes. PCR amplification selectively enriched for those fragments with adapters on both ends. Amplification was carried out for 8-16 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA).  An Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) was used to determine library fragment sizes.  Library fragment concentrations were measured by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

tag: disease

value: chronic myelogenous leukemia (CML)

tag: tsa-seq target

value: RNA Pol II


title: Dhh.Naive.DRG.IP.2

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description: Sample 76

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm9 (sample 1-45) or mm10 (sample46-77) using STAR2.4.0
Count read using HT-seq0.6.1 using mm9/mm10 RefSeq as reference
Normalization (TMM) and differential expression analysis using EdgeR.
Genome_build: mm9/mm10
Supplementary_files_format_and_content: Raw and TMM normalized counts Dhh.IP2 was removed as an outlier)

extract_protocol:
DRG tissue lysates were subjected to HA IP protocol along with protein G magnetic beads. RNA was eluted with Qiagene RNAeasy micro kit
TruSeq HT

value: ICR

value: Ribotag(Homo) X Dhh cre(Het)

value: DRG

value: sensory neurons

tag: protocol

value: IP naïve

tag: ip antibody

value: Dhh + HA (Roche, catalog number 11 867 423)

tag: fraction

value: IP fraction


title: RNA Pol II TSA-Seq Condition 1 (TSA only) Replicate


title: Dhh.Naive.DRG.IP.3

description: Sample 77

tag: genotype

tag: tissue


title: No primary Control for RNA Pol II TSA-Seq Replicate

description: NoPrimaryCtrl_for_pol2_TSA-Seq_Replicate.bw


title: input for "RNA Pol II TSA-Seq Condition 1 (TSA only)"


title: Dhh.Naive.DRG.IP.1

description: Sample 75

tag: cell type


title: Dhh.4hr.DRG.IP.2

description: Sample 73

value: IP injury 4h


title: Dhh.4hr.DRG.IP.3

description: Sample 74


title: Dhh.4hr.DRG.IP.1

description: Sample 72


title: Dhh.24hr.DRG.IP.3

description: Sample 71

value: IP injury 24h


title: ARR14ypet_p6BA

value: Ypet tag

value: 3 days

value: long day

value: 10uM 6BA, 72hours


title: pSC35 TSA-Seq Condition 1 (TSA only) Replicate

description: pSC35 TSA-Seq Condition1 Replicate.bw

tag: cell line


title: input for "No primary Control for pSC35 TSA-Seq Replicate"

description: NoPrimaryCtrl_for_pSC35_TSA-Seq_Replicate.bw


title: input for "pSC35 TSA-Seq Condition 1 (TSA only) Replicate"

description: pSC35 TSA-Seq_Condition1 Replicate.bw


title: ARR1.2ypet_S89S99_LD_p6BA_3D

tag: accession


title: ARR1.2ypet_etiolated_mock

tag: age

value: etiolated

value: DMSO, 4hours


title: input for "Lamin B TSA-Seq Condition 2 (TSA+Sucrose) Replicate"

value: chronic myelogenous leukemia (CML)

value: Lamin B1/B2


title: Dhh.12hr.DRG.IP.3

description: Sample 69

value: ICR

value: IP injury 12h


title: No primary Control for pSC35 TSA-Seq Replicate


title: Lamin B TSA-Seq Condition 2 (TSA+Sucrose) Replicate


title: Dhh.24hr.DRG.IP.1

description: Sample 70

value: Ribotag(Homo) X Dhh cre(Het)

value: DRG


title: Dhh.12hr.DRG.IP.2

description: Sample 68

value: sensory neurons


title: input for "No primary Control for Lamin B TSA-Seq Replicate"

description: NoPrimaryCtrl_for_LaminB_TSA-Seq_Replicate.bw


title: Dhh.12hr.DRG.IP.1

description: Sample 67

value: Dhh + HA (Roche, catalog number 11 867 423)


title: Islt.Naive.DRG.IP.3

description: Sample 66

value: Ribotag(Homo) X Isl1 cre(Het)

value: IP naïve

value: Islt + HA (Roche, catalog number 11 867 423)

value: IP fraction


title: input for "Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose) Replicate"

value: Lamin A/C


title: Islt.Naive.DRG.IP.2

description: Sample 65


title: input for "No primary Control for RNA Pol II TSA-Seq Replicate"


title: Lamin A/C TSA-Seq Condition 2 (TSA+Sucrose) Replicate


title: RNA Pol II TSA-Seq Condition 1 (TSA only)

value: RNA Pol II


title: Islt.Naive.DRG.IP.1

description: Sample 64


title: Islt.24hr.DRG.IP.1

description: Sample 61

value: IP injury 24h


title: Islt.24hr.DRG.IP.3

description: Sample 63


title: No primary Control for Lamin A/C TSA-Seq Replicate

description: NoPrimaryCtrl_for_LaminAC_TSA-Seq_Replicate.bw


title: Islt.24hr.DRG.IP.2

description: Sample 62


title: Islt.12hr.DRG.IP.3

description: Sample 60


title: input for "No primary Control for Lamin A/C TSA-Seq Replicate"


title: Islt.12hr.DRG.IP.1

description: Sample 58


title: Islt.12hr.DRG.IP.2

description: Sample 59


title: Islt.4hr.DRG.IP.3

description: Sample 57

value: IP injury 4h


title: Islt.4hr.DRG.IP.1

description: Sample 55


title: Islt.Naive.DRG.input.1

description: Sample 52

value: Naïve input

value: Total tissue lysate


title: Islt.24hr.DRG.input.3

description: Sample 51

value: input injury 24h


title: Islt.4hr.DRG.IP.2

description: Sample 56

value: ICR


title: Islt.Naive.DRG.input.3

description: Sample 54


title: Islt.12hr.DRG.input.3

description: Sample 49

value: input injury 12h


title: Islt.Naive.DRG.input.2

description: Sample 53


title: Islt.4hr.DRG.input.3

description: Sample 47

value: input injury 4h


title: Islt.4hr.DRG.input.2

description: Sample 46

value: DRG


title: Runx.sup.2

description: Sample 44

value: Ribotag(Homo) X Runx3 cre(Het)

value: Proprioceptive neurons

value: Naïve sup

value: Runx + HA (Roche, catalog number 11 867 423)

value: Supernatant


title: Runx.IP.3

description: Sample 42

value: Naïve IP

value: IP fraction


title: Runx.sup.1

description: Sample 43


title: Runx.sup.3

description: Sample 45


title: Islt.24hr.DRG.input.2

description: Sample 50

value: Ribotag(Homo) X Isl1 cre(Het)

value: sensory neurons

value: Islt + HA (Roche, catalog number 11 867 423)


title: Runx.input.3

description: Sample 39

value: Naïve input


title: Runx.IP.2

description: Sample 41


title: Runx.input.2

description: Sample 38

value: Total tissue lysate


title: Runx.input.1

description: Sample 37


title: PGK.sup.3

description: Sample 36

value: Ribotag(Homo) X PGK cre(Het)

value: All tissue cells

value: PGK + HA (Roche, catalog number 11 867 423)


title: PGK.sup.2

description: Sample 35


title: PGK.IP.3

description: Sample 33


title: PGK.sup.1

description: Sample 34


title: PGK.IP.2

description: Sample 32


title: PGK.input.3

description: Sample 30


title: PGK.input.2

description: Sample 29


title: PGK.input.1

description: Sample 28


title: Islt.12hr.DRG.input.2

description: Sample 48

value: ICR

value: input injury 12h


title: Islt.sup.2

description: Sample 26

value: DRG


title: Islt.IP.2

description: Sample 23


title: Islt.sup.1

description: Sample 25


title: Islt.IP.3

description: Sample 24


title: Islt.IP.1

description: Sample 22


title: Islt.sup.3

description: Sample 27


title: Dhh.sup.3

description: Sample 18

value: Ribotag(Homo) X Dhh cre(Het)

value: Glia

value: Dhh + HA (Roche, catalog number 11 867 423)


title: Islt.input.2

description: Sample 20


title: Runx.IP.1

description: Sample 40

value: Ribotag(Homo) X Runx3 cre(Het)

value: Proprioceptive neurons

value: Runx + HA (Roche, catalog number 11 867 423)


title: Dhh.sup.2

description: Sample 17

value: Naïve sup

value: Supernatant


title: Dhh.sup.1

description: Sample 16


title: Dhh.IP.2

description: Sample 14

value: Naïve IP

value: IP fraction


title: Dhh.input.3

description: Sample 12

value: Naïve input

value: Total tissue lysate


title: Dhh.input.1

description: Sample 10


title: Adv.sup.2

description: Sample 8

value: Ribotag(Het) X Adv cre(Het)

value: sensory neurons

value: Adv + HA (Roche, catalog number 11 867 423)


title: PGK.IP.1

description: Sample 31

value: Ribotag(Homo) X PGK cre(Het)

value: All tissue cells

value: PGK + HA (Roche, catalog number 11 867 423)


title: Dhh.IP.3

description: Sample 15

value: ICR

value: Ribotag(Homo) X Dhh cre(Het)

value: DRG

value: Glia


title: Adv.sup.1

description: Sample 7


title: Adv.IP.3

description: Sample 6


title: Adv.IP.2

description: Sample 5


title: Adv.sup.3

description: Sample 9


title: Adv.IP.1

description: Sample 4


title: Adv.input.2

description: Sample 2


title: input for "pSC35 TSA-Seq Condition 1 (TSA only)"

value: chronic myelogenous leukemia (CML)


title: Islt.input.3

description: Sample 21

value: Ribotag(Homo) X Isl1 cre(Het)

value: Islt + HA (Roche, catalog number 11 867 423)


title: Islt.input.1

description: Sample 19


title: input for "SON TSA-Seq (Ab2) Condition 2 (TSA+Sucrose)"

value: SON


title: pSC35 TSA-Seq Condition 1 (TSA only)


title: Adv.input.1

description: Sample 1


title: Adv.input.3

description: Sample 3


title: Dhh.IP.1

description: Sample 13

value: Naïve IP

value: Dhh + HA (Roche, catalog number 11 867 423)

value: IP fraction


title: SON TSA-Seq (Ab2) Condition 2 (TSA+Sucrose)


title: Dhh.input.2

description: Sample 11

value: Naïve input

value: Total tissue lysate


title: XH7_GX-1A

city: Qingdao

first: Yu

last: Shen

state: Shandong

address: binhai road 72

department: Microbiology and Biotechnology Institute

institute: Shandong University

description:
pho13::XI, gre3::PPP, XK, 3δ::XI,adaptive evolution in xylose
XH7_GX-VS-XH7_X.GeneDiffExp.xls
XH7_GX-VS-XH7_X.GeneDiffExpFilter.xls

data_processing:
Raw reads was produced by Illumina HiSeqTM 2000.
Raw reads was subjected to quality control (QC).
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
If alignment result passes QC, we will proceed with downstream analysis including gene and isoform expression,deep analysis based on gene expression(PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure,refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection, gene fusion. Deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor were performed.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows to make clean data:
1) Remove reads with adapters;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Genome_build: R64
Supplementary_files_format_and_content: FPKMs

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: The fermentation media were Yeast Nitrogen Base (YNB) medium (1.7 g/L yeast nitrogen base (Sangon, China), 5 g/L ammonium sulfate (Sangon, China) ) supplemented with 20 g/L xylose or the mixture of 20 g/L glucose and 20 g/L xylose as carbon source. The fermentation was performed at 30 °C, pH 5.5, 0.06 vvm air sparging, and a stirring speed of 200 rpm. The pH was maintained by automatically pumping 5 mol/L NaOH and 5 mol/L H3PO4, respectively.

extract_protocol:
The cells in each samples were collected by centrifuging at 5000 rpm, 4°C, for 5 minutes. Then the pellets were rapidly freezed in liquid nitrogen and stored at −80°C. UNIQ-10 Trizol RNA Purification Kit (Sangon Biotech, China) was used to extract total RNA.
The total RNA was extracted and fragmented, the DNA was digested with DNase I, enriching the eukaryotic mRNA with the magnetic beads with Oligo (dT) (if it is a prokaryote, then remove the rRNA from the reagent into the next). Add interrupting agent in Thermomixer to break the mRNA into short fragments. The cDNA is synthesized using the short fragments mRNA as template, then the two-stranded cDNA was synthesized by make two chain synthesis reaction system, the Short fragments are purified and resolved by the kit, the 3 'end of cDNA is connected with the base "A" and is connected with the connector, then suitable fragments were selected and the PCR amplification is performed. The constructed library is analyzed with the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System,then sequenced using Illumina HiSeqTM 2000.

treatment_protocol: The samples taken at 14h in glucose-xylose co-fermentation were samples of GX stage. The samples taken at 12h in fermentation using xylose as sole carbon source were samples of X stage.

tag: engineered strain

value: Saccharomyces cerevisiae XH7,derived from CEN.PK 113-5D

tag: genotype/variation

value: pho13::XI, gre3::PPP, XK, 3{delta}::XI,adaptive evolution in xylose

value: GX stage


title: XH7_GX-2A


title: HUVEC_D2_HMGB2-KD_HiC

data_processing:
Raw reads were mapped to the reference genome iteratively using BWA, duplicates were removed using PicardTools.
Custom R scripts were used to bin the genome into non-overlapping bins (typically 10-kbp ones), assign reads to bins, remove read pairs not representing valid interactions, and to normalize read counts to library size.
Genome_build: hg19
Supplementary_files_format_and_content: Compressed (zip) text files (two for each chromosome) representing normalized read counts and their corresponding bin names.

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs from single, apparently healthy, donors (passage 2; Lonza Inc.) were continuously passaged to replicative exhaustion in complete Endopan-2 supplemented with 2% FBS under 5% CO₂. Cells were constantly seeded at ~10,000 cells/cm2, except late passages that were seeded at ~20,000 cells/cm2. Single-donor IMR90s (I90-10 and -79, passage 5; Coriell Biorepository) were continuously passaged to replicative exhaustion in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 20% FBS under 5% CO₂. Mesenchymal stromal cells (MSCs) were isolated at the Aachen Medical School, and cultured to senescence.

extract_protocol:
Hi-C was performed as previously described (Belton et al., 2012)  under conditions where nuclei remained largely intact. In brief, 25-35 million crosslinked cells (1%, 10min, RT) were lysed (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.4% NP40, 1x protease inhibitor cocktail) twice for 20 min on ice, washed with 1x NEBuffer 2 twice, and distributed into 4-5 tubes. Following SDS treatment (0.1%) for 10 min at 65°C and quenching with Triton-X for 15 min at 37°C, chromatin was digested with 600 units of HindIII overnight at 37°C under constant agitation. Next day, digestion was extended for another hour with an additional 600 units of HindIII for 1-2 hours. DNA overhangs were filled-in using a biotin-dCTP containing mix (1.5µl dATP, 1.5 µl dGTP, 1.5 µl dTTP, 37.7 µl biotin-dCTP, each 10 mM stock; Invitrogen) in the presence of 1.5 µl 50 U/µl Klenow (NEB) for 45min at 37°C, and all enzymes are inactivated by adding 86 µl 10% SDS to all tubes and incubating for 30min at 65°C. Next, each individual mixture was transferred into a 15 ml tube, incubated for 10-20min on ice to quench SDS, and a mixture containing 745 µl of 10% Triton-X, 745 µl 10x ligation buffer (500 mM Tris-HCl pH 7.5, 100 mM MgCl2, 100 mM DTT), 80 µl of a 10 mg/ml BSA stock, 80 µl of 100 mM ATP and 5.96 ml milliQ water is added to each tube, and blunt-end ligation initiated by adding 15 µl of 5 U/µl T4 DNA ligase (Invitrogen) and incubated for 6 hours at 16°C. Crosslinks were then reversed and proteins degraded by adding 35 µl of 15mg/ml proteinase K and incubated overnight at 65°C. Next day, an additional 35 µl of proteinase K was added for 2 hours at 65°C, mixtures were cooled to room temperature, transferred to 50 ml conical tubes, and DNA was extracted twice with phenol:chloroform (ph 8.0) and ethanol precipitated. The resulting pellets were dissolved in 450 µl 1x TE, transferred to 1.7ml tubes, DNA was re-extracted twice, precipitated, pellets were washed once in 70% ethanol, air-dried, and resuspended in 25 µl 1x TE. Subsequently, three tubes, each with ~5 µg of the Hi-C template, were incubated for 2 h at 12°C in the presence of 1 µl 10 mg/ml BSA, 10 µl 10x NEBuffer 2, 1 µl 10 mM dATP, 1 µl 10 mM dGTP (for NcoI samples dCTP was used instead) and 5 units of T4 DNA polymerase (NEB) in a total volume of 100 µl to remove biotin-16-dCTP at non-ligated DNA ends. Reactions were stopped by adding 2 µl of 0.5 M EDTA pH 8.0, and the DNA was subsequently purified by phenol:chloroform extraction followed by ethanol precipitation. DNA pellets were resuspended and pooled in a total of 100µl of milliQ water, and residual salts were removed via Amicon 30K columns using three washing steps (1x 200 µl and 2x 100 µl milliQ water). Finally, DNA was sheared to a size of 300-600 bp on a Bioruptor Plus (Diagenode; 2x 10 cycles of 30 sec on and 30 sec off, at the highest power setting). For IMR90 cells, the procedure was slightly modified to follow the in situ Hi-C protocol (Rao et al. 2014). Approx. 20 million cells were lysed twice in 900 µl lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.4% NP-40, 1x protease inhibitor cocktail) for 15 min on ice, nuclei were pelleted and washed once in 1x NEBuffer 2, distributed into 4 tubes, resuspended in 200 µl 0.5% SDS/NEBuffer 2, and incubated for 10 min at 62°C. After repelleting, SDS-treated nuclei were resuspended in 150µl 1% Triton-X/NEBuffer 2, and digested overnight using 400 units of HindIII at 37°C with constant agitation. Next day, another 400 units of HindIII were added for another 1-2 h at 37°C. Following heat inactivation for 20 min at 62°C, nuclei were pelleted by centrifugation and resuspend in 256 µl NEBuffer 2. DNA ends were then biotinylated by adding 50 µl of a biotin-dCTP-Klenow mix (37.5µl of 0.4 mM biotin-dCTP, 1.5µl of 10 mM dTTP, dATP, and dGTP, and 1.5µl of 50 U/μl Klenow) to each tube and incubating for 1 h at 37°C. Subsequently, 900 µl of ligation mix (603 µl H2O, 240 µl 5x Invitrogen ligation buffer, 30 µl of 10% Triton-X, 12 µl of 10 mg/ml BSA, and 15 µl ligase) was added to each sample, mixed, and incubated for 6 h at 16°C; tubes were inverted frequently. Nuclei were next pelleted and a volume of 900 µl was removed. Following reversal of crosslinking and proteinase K addition, DNA is phenol:chloroform extracted and ethanol precipitated; all subsequent steps were performed as described above.
Hi-C DNA was used as template for adding sequencing linkers via only 10 PCR cycles. Then, Hi-C libraries were sequenced to generate at least 400 million paired-end reads (50-75 bp in length) per each donor/condition in a HiSeq4000 platform (Illumina).

treatment_protocol: Cell proliferation was monitored by MTT assays at different passages. In brief, ~5,000 cells are seeded in 96-well format plates in quadruplicates. On the next day, the medium is replaced with 100 µl fresh medium plus 10 µl of a 12 µM MTT stock solution (Invitrogen), and cells are incubated at 37°C for 4 h. Subsequently, all but 25 μl of the medium is removed from the wells, and formazan dissolved in 50 μl DMSO, mixed thoroughly and incubated at 37°C for 10 min. Samples are then mixed again and absorbance read at 530 nm. Measurements are taken at 24, 48 and 72 h post-seeding, background subtracted, and normalized to the 24 h time point. Senescence-associated β-galactosidase assay (Cell Signaling) was performed according to the manufacturer’s instructions to evaluate the fraction of senescent cells at different passages. Finally, DNA methylation at six selected CpG islands (Franzen et al. 2017) was measured by isolating genomic DNA at the different cell states and performing targeted pyrosequencing (Cygenia GmbH).Knockdown was performed using Accell siRNAs(Dharmacon) targeting HMGB2 or a control (NTC) on HUVEC according to the manufacturer’s instruction. RNA was isolated from cells 72h post transfection.

value: human umbilical vein endothelial cells

tag: donor

value: single donor

tag: treatment

value: treated with siRNA targeting HMGB2 (HMGB2-KD)

value: WT


title: XH7_X-2A

tag: strain

tag: Stage

value: X stage


title: HUVEC_D2_NTC_HiC

value: treated with non-targeting control siRNA (NTC)


title: BSGX001_GX-1A

description:
Ru-XI, XK, gre3::PPP, cox4Δ, adaptive evolution in xylose
BSGX001_GX-VS-BSGX001_X.GeneDiffExp.xls
BSGX001_GX-VS-BSGX001_X.GeneDiffExpFilter.xls

value: Saccharomyces cerevisiae BSGX001,derived from CEN.PK 113-5D

value: Ru-XI, XK, gre3::PPP, cox4{delta}, adaptive evolution in xylose


title: XH7_X-1A


title: MSC_D_HiC (senescent)

source_name: mesenchymal stromal cells

value: mesenchymal stromal cells

value: senescent (replicative)


title: BSGX001_X-2A


title: HUVEC_D3_HiC (senescent)


title: HUVEC_D2_HiC (senescent)


title: vector_mnase_rep1

city: Vancouver

first: Nicholas

last: Irwin

state: British Columbia

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: University of British Columbia

description: Processed files size selected to be less than 200 bp.

data_processing:
Sequence reads were aligned using BWA v.0.7.13 with default settings.
Reads with mapping quality scores less than 10 were filtered using Samtools v0.7.13
Bed files were generated using Samtools v0.7.13
Sequence fragment sizes were filtered to narrow the fragment size distribution.
Bed files were converted to wig files using the BaseAlignCounts function in Java Genomics Toolkit (downloaded from http://palpant.us/javagenomics-toolkit/)
Wig files were normalized to the average genomic coverage which was determined using the wigmath.summary tool in Java Genomics Toolkit. Rpb3 ChIPs were also normalized to spike-in controls.
Genome_build: Saccer3 (released February 3, 2011; downloaded from http://www.yeastgenome.org)
Supplementary_files_format_and_content: size selected, normalized wig files

source_name: whole cell

growth_protocol: In all cases, cells were grown overnight in synthetic dropout media lacking uracil with 2% dextrose to saturation. Cell were then diluted and grown in the same media but containing 2% galactose to induce DVNP-3HA-NLS expression.

extract_protocol:
Mnase digestions were performed as previously described (Lawrence et al. 2017. Genetics)
Libraries were constructed as per Brind'Amour et al. (2015, Nat. Commun.) using 2 ng of DNA per library.

treatment_protocol: Cells either expressed or did not express DVNP-3HA-NLS.

tag: chip antibody

tag: fragmentation method

value: Mnase digestion


title: vector_mnase_rep2


title: MSC_D_HiC (proliferating)

value: proliferating


title: DVNP_mnase_rep2


title: DVNP_mnase_rep1


title: HUVEC_D1_HiC (senescent)


title: DVNP_input_rep3

description: Processed files size selected between 45 and 750 bp.

extract_protocol:
ChIP was performed as previously described (Maltby et al. 2012. PNAS).
Libraries were constructed as per Brind'Amour et al. (2015, Nat. Commun.) using 2 ng of DNA per library.

value: Sonication


title: DVNP_input_rep2


title: IMR90_I79_HiC (proliferating)

source_name: fetal lung fibroblast cells

value: fetal lung fibroblast cells


title: DVNP_input_rep1


title: IMR90_I10_HiC (proliferating)


title: BSGX001_GX-2A


title: HUVEC_D2_HiC (proliferating)


title: IMR90_I10_HiC (senescent)


title: DVNP_ChIP_rep3

value: anti-HA (Roche, high affinity clone 3F10 monoclonal)


title: BSGX001_X-1A


title: IMR90_I79_HiC (senescent)


title: HUVEC_D1_HiC (proliferating)


title: 10X_HSC_H3K4me3

city: Houston

first: Hyun Jung

last: Park

state: TX

address: One Baylor Plaza

department: Dan L. Duncan Cancer Center

institute: Baylor College of Medicine

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.1.0 with 1 mismatch in seed allowed. Peak calling was performed on uniquely aligned reads  with Macs2 version 2.0, command=macs2 callpeak -B -f BAMPE --keep-dup 2 -q 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: The peak files include chromosome, start, end, -log(q-value). The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.

source_name: 10 times transplanted Dnmt3a KO HSCs

extract_protocol: Illumina ChIP-Seq

value: Dnmt3a knockout

value: Hematopoietic stem cells


title: DVNP_ChIP_rep2


title: HUVEC_D2_HMGB2-KD_RNA-Seq

description:
polyA+ RNA
strand-specific RNA-seq

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human reference genome and read counts assigned per exon using the QuickNGS pipeline (Waggle et al 2015)
Read counts were normalized using RUVseq (Risso et al 2014) and used to calculated differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts, differential gene expression

extract_protocol:
Total/Factory RNA was isolated using Tripure reagent according to the manufacturer’s instructions (Roche). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina) following ribodepletion (Ribozero Gold Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human umbilical vein endothelial cells


title: DVNP_ChIP_rep1


title: 10X_HSC_H3K27me3


title: RNA-seq:FB-Fosl1_cloneC2 (low expression)

city: Austin

first: Jonghwan

last: Kim

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

data_processing:
Sequences were aligned using the software STAR into the mouse genome (mm9, NCBI Build 37). The expression levels were determined using rpkmforgenes.pyASTQ files were aligned to the mouse genome (mm9, NCBI Build 37) using STAR version 2.4.2 (Dobin et al. 2012). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al. 2009).
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: Gene expression values in BirA-expressing ES cells- expressing BirA only or BirA and biotin-tagged Fosl1 (clone B11 and C12).

source_name: embryonic stem cells

growth_protocol: Mouse J1 ES cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 18% fetal bovine serum (FBS), 50U/ml penicillin/streptomycin (Gibco), 2mM L-glutamine (Gibco), 100μM MEM nonessential amino acids (Gibco), nucleosides (Millipore), 100μM β-mercaptoethanol (Sigma) and 1000U/ml recombinant leukemia inhibitory factor (LIF, Millipore). ES cells were cultured on 0.1% gelatin-coated plates. Mouse TS cells were maintained at a ratio of 3:7 of TS medium to MEF-conditioned TS medium with 25ng/mL Fgf4 and 1μg/mL heparin. The TS medium consisted of RPMI 1640 (Gibco) supplemented with 20% FBS, 100μM β-mercaptoethanol, 2mM L-glutamine, 1mM sodium pyruvate, 50U/mL penicillin, and 50mg/mL streptomycin. The MEF-conditioned medium was TS medium conditioned by MEF cells. Mitomycin-treated MEF cells were cultured in TS medium for 3 days and the medium was collected every 3 days three times. HEK293T cells were maintained in DMEM supplemented with 10% FBS, 2mM L-glutamine, and 50U/mL penicillin/streptomycin. All cells were incubated in 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy® Plus Mini Kit (Qiagen).
1μg of RNA was used to prepare libraries for RNA-sequencing using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs).

value: ES cells expressing FB-Fosl1 (clone C2)


title: HUVEC_D1_HMGB2-KD_RNA-Seq

description:
polyA+ RNA
strand-specific RNA-seq

value: single donor

value: treated with siRNA targeting HMGB2 (HMGB2-KD)


title: RNA-seq:BirA_control

value: ES cells expressing BirA


title: RNA-seq:FB-Fosl1_cloneB11 (high expression)

value: ES cells expressing FB-Fosl1 (clone B11)


title: Fosl1-FB_cloneC2 (low expression)

data_processing:
Sequences were aligned using the software Bowtie2 into the mouse genome (mm9, NCBI Build 37). For the identification of Fosl1 bound regions, software MACS 1.4.2 were used with dynamic local lambda calculation and building shifting model under P-value cutoff at 1e-5.
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: Bed files showing the binding sites of Fosl1 in clone b11 and c2

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 7 min at room temperature and the reaction was quenched for 5 minutes by adding glycine to final concentration of 125mM. Fixed cells were rinsed with PBS and collected in a tube after which the cells were rinsed with PBS twice. Cells were centrifuged and the pellets were used immediately for experiments or stored at -80°C. Cells were re-suspended in ChIP buffer (1% TritonX-100, 2mM EDTA, 20mM TrisCl, pH 8.1, 150mM NaCl, 0.1% SDS and protease inhibitor). Cells were then sonicated for 30 min (30 sec on / 1 min off) and centrifuged at maximum speed for 10 min. The supernatant was transferred to new tubes and pre-cleared with Protein A beads for 4 hours, rotating in 4°C. The samples were then centrifuged and the supernatant was incubated in 10μg streptavidin beads overnight (Roche). The beads were washed for 8 minutes, twice with 2% SDS, once with high salt buffer (0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES (pH 7.5), and 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP40, 0.5% Deoxycholate, 1mM EDTA, and10mM TrisCl pH 8.1) and twice with TE buffer. Samples were eluted by incubating the beads in 150μl of SDS Elution buffer (1% SDS, 10mM EDTA and 50mM TrisCl pH 8.1) overnight in 65°C water bath, then for 30 min in 65°C water bath with 50ul of SDS Elution buffer. 200μl of TE buffer was added to the eluted samples and were treated with 1μg RNase A for 30 minutes in 37°C and 1μg Protease K for at least 2 hours in 37°C.
ChIP-seq library prep kits (New England BioLabs) were used to generate ChIP-seq libraries. ChIP-seq libraries were sequenced using an Illumina HiSeq 2500 at the Genomic Sequencing and Analysis Facility (GSAF) of The University of Texas at Austin.

value: Streptavidin-conjugated beads


title: 9X_HSC_RNA

data_processing:
RNA-sequencing reads were mapped to mm9 using TopHat 2.0.10 pipleline.
Genome_build: mm9
Supplementary_files_format_and_content: TXT files include gene name, chromosome, start, end, FPKM of Gene.

source_name: 9 times transplanted Dnmt3a KO HSCs

growth_protocol: 9 times transplanted mouse HSCs

extract_protocol:
RNA extraction by Qiagen Rneasy micro kit
Followed the manufacturer protocol of Illumia TruSeq stranded mRNA Library Preparation kit

treatment_protocol: LSK CD48- CD150+ HSCs are isolated from 9 times transplanted mouse

value: Hematopoietic stem cell


title: HUVEC_D2_NTC_RNA-Seq

description:
polyA+ RNA
strand-specific RNA-seq

value: treated with non-targeting control siRNA (NTC)

value: WT


title: HUVEC_D3_HiC (proliferating)


title: WT_HSC_RNA

source_name: HSC cell lines of 24months WT mouse


title: BirA_control


title: HUVEC_D1_NTC_RNA-Seq

description:
polyA+ RNA
strand-specific RNA-seq


title: MSC_D_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq

value: mesenchymal stromal cells

value: senescent (replicative)


title: MSC_C_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq


title: Input DNA [C4955]

description:
Processed data file: H3K9me3_counts_hg19.txt
Processed data file: H3K9me3_counts_panTro3.txt

organism: Pan troglodytes

source_name: induced pluripotent stem cells, input

extract_protocol:
ChIP-seq experiments were largely performed according to a published protocol (Schmidt et al. 2009). Briefly, 30 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature followed by quenching with 2.5 M glycine. Following cell lysis and sonication (Covaris S2: 4 min, duty cycle 10%, 5 intensity, 200 cycles per burst in 4x 6 x 16 mm tubes per individual), lysates were incubated with 5 μg H3K9me3 antibody (8898, Abcam) overnight.
Libraries were prepared using the Illumina TruSeq ChIP Sample Preparation kit. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

value: induced pluripotent stem cells

tag: Sex

value: Male

tag: population

value: Chimpanzee


title: Input DNA [C40280]

value: Female


title: MSC_B_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq


title: AkCk_29

city: Cincinnati

first: Keri

middle: Anne

last: Drake

state: Ohio

address: 3333 Burnet Avenue

department: Nephrology

institute: Cincinnati Children's Hospital Medical Center

description: run1008_lane12_index21-none=AkCk_E18.5_29

data_processing:
Strand NGS 2.6 software was used for gene alignment, quantification, normalization (RPKM), and differential gene expression analysis
Bam files were generated using mouse build mm10. Data was filtered on read quality metrics standard in Strand NGS 2.6 software, including removal of reads aligning to more than one position in the genome, average base quality < 20, failure of vendor quality control, as well as expression level, requiring at least 5 NRPKM in 3 of 12 samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt; complete gene list of normalized signal values in each sample

source_name: kidney

extract_protocol:
E18.5 whole kidneys were removed from embryos. RNA was isolated using RNeasy Miniprep kit (Qiagen; Cat#74134); 100-300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed background

tag: developmental stage

value: kidney


title: Input DNA [C40210]

data_processing:
Paired-end ChIP-seq reads from each species were mapped to their respective genome (hg19 or panTro3) using BWA (version 0.7.12) (Li and Durbin 2009) and a mapping quality filter of MAQ >10. PCR duplicates were removed by samtools (version 0.1.19)(Li et al. 2009). Properly-paired reads only were selected for further analysis.
ChIP and Input reads from each individual were used to call peaks using MACS2 (Zhang et al. 2008) with the broadpeak option at various qvalue cut-offs. A lenient threshold of qvalue=0.1 was used in subsequent analysis to maximize the number of regions in each species. Peaks called in each species were concatenated to generate a final peak set across both species.
Peak coordinates in each species were then converted to the alternative genome using liftOver (Speir et al. 2016) and the best reciprocal chain (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/reciprocalBest/) between hg19 and panTro3. Peak regions that could be reciprocally and uniquely mapped between the two genomes were kept to generate a list of orthologous peaks.
The number of reads falling into these orthologous peak regions was determined using HTSeq (Anders et al. 2015).
Genome_build: hg19 (GRCh37), panTro3 (Pan_troglodytes-2.1.3)
Supplementary_files_format_and_content: *txt: H3K9me3 ChIP-seq read counts for all orthologous regions in all samples with region coordinates on both the human genome (hg19) and the chimpanzee genome (panTro3).


title: IMR90_I79_fact_RNA-Seq (senescent)

description:
nascent (factory) RNA
strand-specific RNA-seq

value: fetal lung fibroblast cells

tag: genotype


title: MSC_A_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq

value: single donor


title: Input DNA [C3651]


title: Input DNA [C3649]


title: AkCk_24

description: run1008_lane12_index12-none=AkCk_E18.5_24

tag: tissue


title: AkCk_27

description: run1008_lane12_index20-none=AkCk_E18.5_27


title: AhCk_115


title: AhCk_110


title: IMR90_I10_fact_RNA-Seq (senescent)

tag: cell type


title: Fosl1-FB_cloneB11 (high expression)

tag: cell line


title: Input DNA [C3647]


title: AkCh_33

description: run1008_lane12_index11-none=AkCh_E18.5_33


title: H3K9me3_ChIPSeq [C8861]

source_name: induced pluripotent stem cells, H3K9me3 ChIP


title: AhCk_38


title: IMR90_I10_polyA_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq


title: AkCh_31

description: run1008_lane12_index10-none=AkCh_E18.5_31


title: H3K9me3_ChIPSeq [C4955]


title: IMR90_I79_polyA_RNA-Seq (senescent)

description:
polyA+ RNA
strand-specific RNA-seq


title: HUVEC_D3_RNA-Seq (senescent)

description:
total RNA (ribominus)
strand-specific RNA-seq

value: human umbilical vein endothelial cells


title: Input DNA [C8861]


title: H3K9me3_ChIPSeq [C40280]


title: Wt_55

value: Wild type


title: AkCh_20

description: run1008_lane12_index9-none=AkCh_E18.5_20


title: H3K9me3_ChIPSeq [C40210]


title: HUVEC_D1_RNA-Seq (senescent)


title: Wt_37


title: H3K9me3_ChIPSeq [C3651]


title: Wt_30


title: H3K9me3_ChIPSeq [C3649]


title: MSC_D_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq

value: proliferating


title: H3K9me3_ChIPSeq [C3647]


title: MSC_A_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq


title: MSC_C_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq


title: vector_rpb3_input_rep2

description: Processed files size selected between 75 and 250 bp.

value: Sonication


title: IMR90_I79_fact_RNA-Seq (proliferating)


title: IMR90_I79_polyA_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq


title: DVNP_rpb3_input_rep2


title: IMR90_I10_polyA_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq


title: DVNP_rpb3_input_rep1


title: vector_rpb3_ChIP_rep2

value: anti-Rpb3 (Abcam, ab81859, monoclonal clone 1y26(ly27))


title: HUVEC_D2_RNA-Seq (senescent)


title: vector_rpb3_ChIP_rep1


title: HUVEC_D1_RNA-Seq (proliferating)


title: Zt10_Ta_D_02

city: Kiel

first: Janine

last: Haueisen

address: Am Botanischen Garten 1-9

department: Botanical Institute

institute: Christian-Albrechts University of Kiel

data_processing:
Removal of residual TruSeq adapter sequences, Trimmomatic version 0.33
Trimming of 12 nucleotides at 5' end of all reads, Trimmomatic version 0.33
Filtering of reads based on quality scores: At least 80 % of bases must have a quality score ≥ 20 or read was dropped. FASTX-toolkit version 0.0.14
Masking of low quality bases: Nucleotides with quality score < 20 were masked with ‘N’. FASTX-toolkit version 0.0.14
Mapping of reads to genomes of Z. tritici isolates, TopHat2 version 2.0.9
Manipulation of RNA-seq read alignments: SAMtools version 0.1.19
Counting of mapped sequencing reads per gene: HTSeq version 0.6.1p1
Genome_build: reference assembly Zt05 (Zt05 = MgDk09_U34) available through NCBI BioProject PRJNA312067
Genome_build: reference assembly Zt09 / IPO323Δchr 19 is available at: http://genome.jgi.doe.gov/Mycgr3/Mycgr3.home.html
Genome_build: reference assembly Zt10 (Zt10 = STIR01_A26b) is available at GenBank GCA_000223645.2
Supplementary_files_format_and_content: comma separated text file including raw counts of sequencing reads for all Z. tritici genes shared between the three isolates

organism:
Triticum aestivum
Zymoseptoria tritici

source_name: Z. tritici infection of Triticum aestivum Obelisk leaves

growth_protocol: To produce fungal inoculum, cells of Zymoseptoria tritici isolates were inoculated from glycerol stocks onto YMS agar and grown at 18 °C. Single cells were grown in liquid YMS (200 rpm, 18 °C) and harvested at 3500 rpm for 10 min.

extract_protocol:
total RNA from Z. tritici-infected wheat material was isolated using the TRIzol™ reagent according to the manufacturer’s instructions
NEBNext UltraTM Directional RNA Library Prep Kit
strand-specific RNA-seq libraries including polyA enrichment

treatment_protocol: 14-day-old seedlings of Triticum aestivum Obelisk were brush-inoculated with fungal inoculum adjusted to 1 x 10^8 cells/ml in 0.1 %Tween 20

tag: t. aestivum cultivar

value: Obelisk

value: 14-day-old seedlings

tag: z. tritici isolate

value: Zt10 / STIR01_A26b

tag: days post infection (dpi)

tag: infection stage

value: D


title: HUVEC_D3_RNA-Seq (proliferating)

tag: donor

value: WT


title: Zt10_Ta_C_02

tag: age

value: C


title: Zt10_Ta_D_01


title: DVNP_rpb3_ChIP_rep2

tag: strain


title: Zt10_Ta_C_01


title: Zt10_Ta_B_02

value: B


title: Zt10_Ta_A_02

value: A


title: Zt10_Ta_B_01


title: MSC_B_RNA-Seq (proliferating)

description:
polyA+ RNA
strand-specific RNA-seq

value: mesenchymal stromal cells

tag: treatment


title: IMR90_I10_fact_RNA-Seq (proliferating)


title: Zt09_Ta_D_01

value: Zt09 / IPO323<delta>chr 18


title: Zt10_Ta_A_01


title: Zt09_Ta_C_01


title: Zt09_Ta_C_02


title: Y5_3_3

city: Tianjin

first: man

last: wang

address: yaguan road

institute: Tianjin University

description: transformation of heterologous genes

data_processing:
Quality control
Reads mapping to the reference genome Yarrowia lipolytica CLIB122 (assembly ASM252v1)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq R package (1.18.0).
Supplementary_files_format_and_content: processed data (read counts) contained RPKM for each gene in different samples

organism: Yarrowia lipolytica

source_name: yeast cell

growth_protocol: 96 h cultivation in flask, 250 rpm, 28 ℃

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agelent, USA)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample.

treatment_protocol: Yarrowia lipolytica cells were pelleted and quickly frozen by liquid nitrogen.

tag: source


title: vector_rpb3_input_rep1

tag: chip antibody

tag: fragmentation method


title: Zt09_Ta_D_02


title: Zt09_Ta_A_01


title: HUVEC_D2_RNA-Seq (proliferating)


title: Y5_3_1

description: transformation of heterologous genes


title: Zt09_Ta_B_01


title: Zt09_Ta_A_02


title: Y5_3_2

description: transformation of heterologous genes


title: Zt05_Ta_D_02


title: Y5_2_3

description: transformation of heterologous genes


title: Y5_2_2

description: transformation of heterologous genes


title: Zt05_Ta_C_02


title: Zt05_Ta_D_01


title: Zt05_Ta_B_02


title: kat2-3_bisulfite sequencing

description:
processed data file:
KAT2-3.bedGraph

data_processing:
For Bisulfite-seq analysis, the raw sequence data were demultiplexed and converted to fastq files using bcl2fastq2 Conversion Software (version v2.16.0) under default parameters. Mapping, deduplication, and methylation extraction were performed using bismark software (V0.7.4),of which mapping using bowtie2 (2.0.5) to TAIR10.
genome build: TAIR10
processed data files format and content:bedgraph file with single-base resolution of cytosine methylation

source_name: young seedlings

extract_protocol:
Genomic DNAs were extracted from seedlings using the DNeasy Plant Mini Kit (QIAGEN)
For Bisulfite-seq, 5-μg of genomic DNAs was sonicated then end-repaired with the End Repair Enzyme Mix (New England BioLabs, Ipswich, MA).The blunt-ended DNA were treated with Klenow fragment (New England BioLabs, Ipswich, MA) and  dATP to 3’-dA-tailed and ligated to methylated adapters.The ligated DNA fragments were treated using the EpiTect bisulfite Kit (Qiagen, Valencia, CA). The bisulfite-treated DNAs were amplified by PCR with Illumina primers for 15 cycles and fragments of 250-350 bp were excised from an agarose gel and purified.  Paired end sequencing of each library was performed to around 100 cycles on the Illumina HiSeq 2000 or HiSeq 4000 according to manufacturer's protocols.

value: 14-day-old whole seedlings

tag: ecotype

value: kat2-3 mutant


title: Zt05_Ta_C_01


title: mfp2-2_bisulfite sequencing

description:
processed data file:
MFP2-2.bedGraph

tag: developmental stage

value: mfp2-2 mutant


title: DVNP_rpb3_ChIP_rep1


title: Zt05_Ta_B_01


title: acx4-1_bisulfite sequencing

description:
processed data file:
ACX4-1.bedGraph

tag: genotype

value: acx4-1 mutant


title: ctrl_2

description: transformation of heterologous genes

value: ctrl


title: ctrl_3

description: transformation of heterologous genes


title: Y5_2_1

description: transformation of heterologous genes


title: Col-0_bisulfite sequencing

description:
processed data file:
Col-0.bedGraph


title: ros1-4_bisulfite sequencing

description:
processed data file:
ros1-4.bedGraph

value: ros1-4 mutant


title: Zt05_Ta_A_02


title: Zt05_Ta_A_01


title: ctrl_1

description: transformation of heterologous genes


title: Zt09_Ta_B_02


title: shEZH2 rep3

status: Public on Apr 24 2018

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat v2.0.13 with default parameters
Differences in expression were determined using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: fibroblast

growth_protocol: HDFs were cultured in DMEM medium supplemented with 10% fetal bovine serum,100U/mL penicillin and 100μg/mL streptomycin at 37℃ in 5% CO2

extract_protocol:
A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer instruction, and were sequenced on an Illumina HiSeq X-10).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA were extracted using Trizol reagent and used for mRNA capture.

value: fibroblast

value: lenti-virus mediated EZH2 shRNA

tag: passages


title: H3.1K27M rep3

tag: cell type

value: lenti-virus mediated H3.1K27M overexpression


title: shEZH2 rep2


title: shEZH2 rep1


title: shNC rep2

value: lenti-virus mediated negative control shRNA


title: shNC rep3


title: H3.1K27M rep2


title: H3.1K27M rep1


title: H3.1K27A rep3

value: lenti-virus mediated H3.1K27A overexpression


title: H3.1K27A rep2


title: shNC rep1


title: H3.1K27A rep1


title: H3.1WT rep2

value: lenti-virus mediated H3.1WT overexpression


title: H3.1WT rep3


title: SOX9_Si

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description: Non-differentiated

data_processing:
The samples from ILLUMINA  system were aligned using Tophat
All alignments were made using hg19 as reference genome assembly
The reads are quantified using featureCounts (subRead)
Normalization of reads performed as Reads Per Kilobase Million  (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as table ('GeneID' followed by normalized counts, RPKM from samples,"Csi","SOX9_Si")

source_name: non-differentiated KELLY cells

growth_protocol: SH-SY5Y cells were routinely cultured in DMEM media supplemented with 10% FBS. For differentiation cells were treated with 10 mM RA for 7 days in DMEM/F12 media (1:1) supplemented with 10% FBS. Sphere formation was carried out in sphere forming media.

extract_protocol:
Cells were collected 48 hours post-transfection and RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat #  RS-122-2201)

treatment_protocol: stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

tag: cell line

value: KELLY cells

tag: shRNA/sirna

value: siRNA ID:SASI_Hs02_00302379 (Sigma Aldrich)

tag: culture status

value: non-differentiated


title: K562_R3

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

description: HI-C 2.0___K562_R3

data_processing:
HI-C 2.0 was  performed as described in the supplementary protocol
Iterative mapping and error filtering of the chromatin interaction data were performed as previously described in The Hitchhiker's Guide to Hi-C Analysis: Practical guidelines, Lajoie et. al., Methods 2015
Genome_build: hg19
Supplementary_files_format_and_content: Format:interacting pairs in tab separated format as described in Lajoie et. al., Methods, 2015
Supplementary_files_format_and_content: Content: Aligned HiC data, where each interacting pair is reported in one line

source_name: K562 cells

growth_protocol: RPMI Medium  (Gibco)15% FBS (Gibco) 1% Antibiotic-Antimycotic (Gibco)  1% L-Glutamine (Gibco)

extract_protocol:
Hi-C 2.0 : We performed an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. One adaptation to the base protocol is the removal of a SDS solubilization step after digestion to better preserve nuclear structure. This prevents random ligation between released chromatin fragments by ligation in situ, i.e. in intact nuclei as previously described by (Rao SS,  et al .A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 2014, 1665–1680). A second adaptation in recently developed protocols increases the resolution of Hi-C through the use of restriction enzymes that digest more frequently, such as DpnII, or also described by Rao  et al .Thirdly, experimental steps can be included to reduce the number of uninformative sequences such as unligated (“dangling”) ends as described (Lieberman-Aiden, E. et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289–293 (2009). Briefly, Cells were lysed and chromatin was digested with DpnII, then digested ends were filled in with biotinylated dATP and ligated in situ.  After reversing the formaldehyde crosslinks by incubation at 65 C with Proteinase K overnight, unligated biotinylated ends were removed by incubation with T4 DNA polymerase.
The ligation products were fragmented by Covaris sonication and then size selected by Ampure fractionation.  The DNA ends were prepared for Illumina sequencing adapter ligation by repairing the DNA ends and adding an ‘A’ to each end.  The biotinylated junctions were then pulled down using MyOne streptavidin beads. Illumina paired end adapters were ligated onto the DNA ends and then the fragments were PCR amplified.   Samples were sequenced on an Illumina HiSeq 4000 using either a PE50 or PE100 bp read (reads were truncated to 50bp during mapping).

treatment_protocol: No treatment

value: lymphoblast

tag: Sex

value: Female


title: K562_R1

description: HI-C 2.0___K562_R1


title: Csi

description: Non-differentiated

value: scrambled non-mammalian target control


title: e12.5HET_2

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

description: mRNA fraction selected from total RNA before conversion to cDNA

data_processing:
Quality of raw sequencing files was checked using FastQC version 0.11.2 and trimming of adaptor sequences and the first 12 bases from the 5’ end of all reads was performed using Trim Galore! Version 0.4.1
Reads were aligned to mouse genome mm10 using TopHat version 2.1.0 with parameters  -bowtie1 -r 150, -mate-std-dev=50, -p 8
Reads were counted using FeatureCounts version 1.5.0 with parameters -p -T 8 -F GTF
Read counts from technical replicates (i.e. from both lanes) were summed using the Deseq2 version 1.10.1 CollapseReplicates function.  Deseq2 version 1.10.1 was used for differential expression testing, using the DESeq command.
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Text file containing read counts for all samples assigned to features (genes)

source_name: Cortex

extract_protocol:
Total RNA was extracted from brain tissue samples using Trizol Reagent. RNA was purified using the Direct-Zol RNA Miniprep Kit (Zymo Research, CA, USA; Catalogue No. R2050) according to the manufacturer's recommendations.
Library Prep was performed by the Oxford Genomics Centre (Oxford, United Kingdom). mRNA was selected from total RNA and converted to cDNA. dUTP was incorporated during second strand cDNA synthesis. CDNA was end-repaired, A-tailed and adaptor ligated. Uridine digestion was performed before amplification of samples. Prepared libraries were size selected and multiplexed and paired-end sequencing was performed across 2 lanes of a flow cell on the Illumina HiSeq 4000 platform.

tag: tissue

value: Cortex

tag: strain background

value: Embryonic day 12.5


title: cl8_rep1_GCCAAT_S3_R1_001

city: Stanford

first: Aaron

middle: F

last: Straight

address: 279 Campus Drive, B409A

institute: Stanford University

description:
RNA-bridge-DNA chimera
cl8.ChARdnaRna.ribominus.sense.concat_masterfile_v4.sorted.repeatmasked.20bpmin.custom.txt.gz
cl8.ChARdnaRna.ribominus.antisense.concat_masterfile_v4.sorted.repeatmasked.20bpmin.custom.txt.gz

data_processing:
Custom processing: see https://gitlab.com/charseq/flypipe
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text file with bed-formated DNA and RNA contacts and RNA-specific info parsed from Flybase transcriptome

molecule: other

organism: Drosophila melanogaster

growth_protocol: grown in T-75 flasks at 27ºC in Shields & Sang M3 media supplemented with 5 µg/mL insulin, 2% FBS, 2% fly extract and 100 µg/mL Pen-Strep

extract_protocol: Custom protocol, see Extended Methods: https://doi.org/10.1101/118786

treatment_protocol: Approximately 100-400 million cells were harvested for each library by centrifugation at 2000 x g for 2-4 minutes, resuspended in fresh media plus 1% formaldehyde and fixed for 10 minutes at room temperature. Fixation was quenched by adding 0.2 M glycine and mixing for 5 minutes at room temperature. Cells were centrifuged at 2000 x g for 2-4 minutes, resuspended in 1 mL of PBS, and centrifuged again at 2000 x g for 2 minutes. The supernatant was aspirated and discarded, and the cell pellet was flash frozen in liquid nitrogen and stored at -80C until needed.

value: CME-W1-cl8+ wing-disc cell line


title: e12.5HET_1

tag: age


title: e12.5HET_3


title: cl8_rep3_CAGATC_S12_R1_001


title: cl8_rep2_CAGATC_S1_R1_001


title: e12.5CTRL_3


title: K562_R2

description: HI-C 2.0___K562_R2


title: cl8_rep4A_GCCAAT_S11_R1_001


title: Input_RIS_H3K4me1_Rep2

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

description: ChIP-Seq

data_processing:
Reads were mapped to the human reference (hg19) with BWA (version 0.7.12)
Peak calling was performed with MACS2 (version 2.1.0) 84.
Coverage files were generated using MACS2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: .narrowPeak = peaks
Supplementary_files_format_and_content: .bedgraph = coverage data

extract_protocol:
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells are treated for 6 days with 4OHT.

tag: vector 1

value: Yes

tag: passage


title: Input_RIS_H3K4me1_Rep3

description: ChIP-Seq


title: cl8_rep4B_GCCAAT_S3_R1_001


title: OE Rif1-MNase 2'30''

city: Geneva

first: Lukas

last: Hafner

state: Geneva

address: 30 quai Ernest-Ansermet

department: Molecular Biology

institute: University of Geneva

description: ChEC-seq

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "--end-to-end --sensitive -k 20"
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
reads were extended by read length (50bp)
for ChEC-seq: ChrM was ommited from reference genome
Genome_build: Saccer3
Supplementary_files_format_and_content: .bw

source_name: whole organism

growth_protocol: 50 ml of cells were grown in YPAD to OD600=0.7

extract_protocol:
DNA was extracted with MasterPure Yeast DNA purification Kit (Epicentre), dissolved in 50ul and treated with RNAse RNAse A 200ug/ml for 20min at 37°C. ChEC DNA was subjected to Ampure XP beads (Agencourt) size selection (amount of beads: 2.5:1 v/v). The un-bound fraction (supernatant) containing the small fragments was recovered
Library preparation was carried out using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina protocol kit (Biolabs)

treatment_protocol: Cells were washed three times with 1 ml of Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1X complete EDTA-free mini protease inhibitors, Roche, 1 mM PMSF). Cells were permealized in 1ml of Buffer A with 0.1% digitonin at 30°C for 5 min, then MNase activated adding 5mM CaCl2. At each time point, 200μl aliquot was taken and reaction stopped by adding 250 mM EGTA.

tag: strain

value: FY1679 ura3-52, leu2-1, his3-200, Gal2, CMVp (tetR'-SSN6)::LEU2, trp1::tTA,, KanMX4::tetO2-RIF1-MNase-3xFLAG::HPHMX4R

tag: phase

value: unsynchronized

tag: time point

tag: treatment

value: Chromatin endogenous cleavage


title: Input_Growing_H3K4me1_Rep3

description: ChIP-Seq

value: No

tag: chip antibody


title: OE Rif1-MNase 1'30''

description: ChEC-seq

tag: genotype


title: Input_RIS_H3K4me1_Rep1

description: ChIP-Seq


title: OE Rif1-MNase 5'

description: ChEC-seq


title: Input_RIS_H3K4me1_Rep4

description: ChIP-Seq


title: OE Rif1-MNase 1

description: ChEC-seq


title: OE Rif1-MNase 10''

description: ChEC-seq


title: e12.5CTRL_2


title: e12.5CTRL_1


title: OE Rif1-MNase 30''

description: ChEC-seq


title: Input_Growing_H3K4me1_Rep4

description: ChIP-Seq


title: H3.1WT rep1

value: fibroblast

tag: passages


title: Input_Growing_H3K4me1_Rep2

description: ChIP-Seq


title: Input_Growing_H3K4me1_Rep1

description: ChIP-Seq


title: Input_RIS_H3K27Ac_Rep4

description: ChIP-Seq


title: Input_RIS_H3K27Ac_Rep3

description: ChIP-Seq


title: Input_RIS_H3K27Ac_Rep2

description: ChIP-Seq


title: Input_Growing_H3K27Ac_Rep2

description: ChIP-Seq


title: Input_RIS_H3K27Ac_Rep1

description: ChIP-Seq


title: Input_Growing_H3K27Ac_Rep3

description: ChIP-Seq


title: WT pol2 ChIP 75'

description: genotype: W303-1, RAD5+, bar1∆, POL2-13MYC::KANMX4R, 3XFlag-POL1

growth_protocol: Growth conditions as in Mattarocci et al. 2014 (PMID: 24685139 DOI: 10.1016/j.celrep.2014.03.010)

extract_protocol:
Cells were homogenized by bead beating and treated with proteinase K, followed by Phenol-Chloroform extraction.
Library preparation was carried out at the genomics platform of the University of Geneva using the Illumina DNA-seq nano kit

treatment_protocol: Synchronisation as in Mattarocci et al. 2014 (PMID: 24685139 DOI: 10.1016/j.celrep.2014.03.010)

value: W303-1, RAD5+, bar1delta, POL2-13MYC::KANMX4R, 3XFlag-POL1

value: release from G1 block

value: 9E10 from culture supernatant; Custom mouse monoclonal anti-myc

value: alpha factor


title: rif1 delta pol2 ChIP 75'

description: genotype: W303-1, RAD5+, bar1∆, POL2-13MYC::KANMX4R, 3XFlag-POL1, rif1::NatMX4

value: W303-1, RAD5+, bar1delta, POL2-13MYC::KANMX4R, 3XFlag-POL1, rif1::NatMX4


title: rif1 delta pol2 ChIP 90'


title: rif1 delta pol2 ChIP 105'

value: W303-1, RAD5+, bar1<delta>, POL2-13MYC::KANMX4R, 3XFlag-POL1, rif1::NatMX4


title: rif1 delta pol2 ChIP 30'


title: WT pol2 ChIP 60'


title: Input_Growing_H3K27Ac_Rep1

description: ChIP-Seq


title: ChIP_RIS_H3K4me1_Rep2

description: ChIP-Seq

value: H3K4me1 (Clone CMA302; in house; Kimura et al., 2008; also available from MBL life sciences, CAT MABI0302)


title: rif1 delta pol2 ChIP 45'


title: Input_Growing_H3K27Ac_Rep4

description: ChIP-Seq


title: rif1 delta pol2 ChIP 60'


title: ChIP_RIS_H3K4me1_Rep3

description: ChIP-Seq


title: WT pol2 ChIP 45'


title: ChIP_RIS_H3K4me1_Rep4

description: ChIP-Seq


title: rif1_rbm G2 phase

description: genotype: W303-1, RAD5+, bar1∆, POL2-13MYC::KANMX4R, 3XFlag-POL1, rif1-rbm(I1762R-I1764R)

data_processing:
Library strategy: sort-seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "--end-to-end --sensitive -k 20"
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
reads were extended by read length (50bp)
for ChEC-seq: ChrM was ommited from reference genome
Genome_build: Saccer3
Supplementary_files_format_and_content: .bw

growth_protocol: 100 ml of cells were grown OD600 0.5-0.7

treatment_protocol: Cells were fixed with 70% Ethanol, then treated with RNAse A 200ug/ml in 50mM Tris-HCl pH 7.5 and stained with SYTOX green 50mM in 2 ml of 50mM Sodium-Citrate pH7 for at least 24h at 4°C. G2 and S phase cells were sorted by  a Beckman Coulter MoFlo Astrios.

value: W303-1, RAD5+, bar1delta, POL2-13MYC::KANMX4R, 3XFlag-POL1, rif1-rbm(I1762R-I1764R)

value: S phase


title: WT pol2 ChIP 30'


title: rif1_rvxf/silk G2 phase

description: genotype: W303-1, RAD5+, bar1∆, POL2-13MYC::KANMX4R, rif1-RVxF/SILK (V116R-F118R-I147R-L148R-R149A)

value: W303-1, RAD5+, bar1delta, POL2-13MYC::KANMX4R, rif1-RVxF/SILK (V116R-F118R-I147R-L148R-R149A)


title: ChIP_Growing_H3K4me1_Rep4

description: ChIP-Seq


title: ChIP_RIS_H3K4me1_Rep1

description: ChIP-Seq


title: rif1 delta G2 phase


title: ChIP_Growing_H3K4me1_Rep3

description: ChIP-Seq


title: WT pol2 ChIP 105'


title: WT G2 phase


title: WT pol2 ChIP 90'


title: rif1_rbm S phase


title: ChIP_Growing_H3K4me1_Rep1

description: ChIP-Seq


title: Free Mnase 20'

description: ChEC-seq

value: W303 RAD5+, MAT::loxP, ADE2::loxP, LEU2::pGAL-HO, LYS2::loxP, MNT2::TG80-HO-CA80-ADE2-LYS2, pREB1-MNase-3xFLAG-URA3


title: ChIP_RIS_H3K27Ac_Rep2

description: ChIP-Seq

value: Yes

value: H3K27Ac (Clone CMA309; in house; Kimura et al., 2008; also available from MBL life sciences, CAT MABI0309)


title: ChIP_RIS_H3K27Ac_Rep3

description: ChIP-Seq


title: rif1_rvxf/silk S phase


title: rif1 delta S phase


title: ChIP_Growing_H3K27Ac_Rep4

description: ChIP-Seq


title: WT S phase


title: ChIP_RIS_H3K27Ac_Rep1

description: ChIP-Seq


title: Rif1_RBM-MNase 1'30''

description: ChEC-seq

value: W303 RAD5+, MAT::loxP, ADE2::loxP, LEU2::pGAL-HO, LYS2::loxP, MNT2::TG80-HO-CA80-ADE2-LYS2, RIF1-rbm-MNase-3xFLAG-KANMX4

value: unsynchronized


title: ChIP_Growing_H3K27Ac_Rep1

description: ChIP-Seq

value: No


title: Free Mnase 5'

description: ChEC-seq

value: Chromatin endogenous cleavage


title: ChIP_Growing_H3K27Ac_Rep3

description: ChIP-Seq


title: GGD54 WT

city: Strasbourg

first: Patrice

last: Dunoyer

state: Alsace

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

description:
Immunoprecipited RNA
IR71_seeds_RPM.txt
IR2039_seeds_RPM.txt
miR822_seeds_RPM.txt
TAS1a_seeds_RPM.txt
TAS1b_seeds_RPM.txt
TAS1c_seeds_RPM.txt
TAS2_seeds_RPM.txt
TAS3a_seeds_RPM.txt
TAS3b_seeds_RPM.txt
TAS4_seeds_RPM.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped using Hisat2 (v.2.0.5) (55), with the default parameters, to   the TAIR10 assembly,
Genome coverage of the loci of interest were made with genomeCoverageBed from bedtools suite (v.2.25.0)
Coordinates of miR (miRBase, v23), EndoIR-siRNAs (Montavon et. al., A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing, Nucleic Acids Res. 2017), tasiRNA producing loci given by tasiRNAdb (last update September 1 2013)
normalisation : Data were normalized with the total output number of reads obtained for each corresponding library (coverage normalized per library size)
Genome_build: Col-0 TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised coverage of loci of interest

source_name: Seedlings

growth_protocol: Plant seeds were stratified for 2–4 days at 4°C before growth in soil under standard conditions at 22◦ C with a 16 h light/ 8 h dark cycle

extract_protocol:
Immunoprecipitated RNA from Col-0, pDCL4-DCL4-6:FHA/dcl4-2 and pDCL4-DCL4-8:FHA/dcl4-2 seedlings or flowers was extracted with Tri-Reagent (Sigma) and used for library preparation.
The libraries were constructed using the TruSeq SBS kit V3 from Illumina following manufacturer's  instructions and the libraries were sequenced as single-end 50 nt reads using an Illumina HiSeq 2500  (Fasteris, Switzerland)

tag: ecotype

value: Columbia

value: Seedlings

value: wild type


title: Rif1_RBM-MNase 2'30''

description: ChEC-seq


title: ChIP_Growing_H3K27Ac_Rep2

description: ChIP-Seq


title: GGD52 DCL4-8:FHA

description:
Immunoprecipited RNA
IR71_flower_RPM.txt
IR2039_flower_RPM.txt
miR822_flowers_RPM.txt
TAS1a_flowers_RPM.txt
TAS1b_flowers_RPM.txt
TAS1c_flowers_RPM.txt
TAS2_flowers_RPM.txt
TAS3a_flowers_RPM.txt
TAS3b_flowers_RPM.txt
TAS4_flowers_RPM.txt

source_name: Flowers

value: Flowers


title: Rif1_RBM-MNase 30''

description: ChEC-seq


title: d41_RNASeq

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description:
cortical_d41_1
cell culture duplicate

data_processing:
Library strategy: RNQ-Seq
Illumina CASAVA v1.8 standard
Reads were trimmed for adaptor sequence, then mapped to UCSC g1000 using bowtie2, duplicate fragments were then removed using Picard.
RPKM value of each gene was counted using home-developed R script
Genome_build: g1000
Supplementary_files_format_and_content: the RPKM counts of each gene at different stages were stored in an Excel spreadsheet (RNASeq.xlsx). Column values are self-explanatory in row 1

source_name: Cortical neurons differentiated from iPSC

growth_protocol: For iPSC culture and cortical neuron differentiation, we have adopted the protocol (Shi et al., Nature Protocols, 2012) to our iPSCs growing In feeder-free medium (mTeSR). In brief, we plate 5 wells of iPSCs (on a 6-well plate) onto one well of Geltrax-coated 12-well plate in 800ul of mTeSR media, allowing cells to attach overnight and reaching 100% confluence 1 day after plating. For neural induction, we switched the cell culture media to neural induction media (NIM) containing 1uM of Dorsomorphin. After 10 days of neural induction when a homogeneous neuroepithelial layer is formed, we passaged the cells onto laminin-coated 35-mm dish and switched the cell culture media to Neural Maintenance Medium (NMM). Upon appearance of neural rosettes, we added 20ng/ml of FGF2 for 2-4 days to promote the expansion of neural stem cells (NSCs). At about day 20 after neural induction, we passaged the cells for the first NSC expansion (1: 3). After another round of NSC expansion at day 25, we passaged the NSC culture at ~day 30 using Accutase at a ratio of 1:4 onto laminin-coated 35-mm dish (for collecting cells later) and laminin-coated coverslips (for immunofluorescence staining). We continued the neural differentiation for the plated cells in NMM until the specified days to collect the cells.

extract_protocol:
For RNA-seq, we harvested 500,000 cells (iPSCs, induced NSCs at 33 and 41 post neural induction) by centrifugation at 500g x 5 min at 4°C. Total RNA was extracted using ThermoFisher mirVana RNA-extraction kit, reverse-transcribed, and sequenced on a HiSeq 2500 with 5 pooled samples in a single line
The library was generated and sequenced at University of Minnesota Genomic Center.

value: female

tag: cell type

value: Cortical neurons at day 41 of neuronal differentiation

tag: passage number


title: GGD51 DCL4-6:FHA


title: d33_2_RNASeq

description:
cortical_d33_2
day 33 culture; but was  considered as duplicate of day 30 because of high correlation with day 27 sample

source_name: Cortical neuron stem cells differentiated from iPSC

value: Cortical NSC/neurons at day 33 of neuronal  differentiation


title: GGD53 WT


title: Rif1_RBM-MNase 10''

description: ChEC-seq


title: ChIP_Growing_H3K4me1_Rep2

description: ChIP-Seq

value: H3K4me1 (Clone CMA302; in house; Kimura et al., 2008; also available from MBL life sciences, CAT MABI0302)


title: d33_1_RNASeq

description:
cortical d33_1
day 27 culture; but was  considered as duplicate of day 30 because of high correlation with day 33 sample

value: Cortical NSC/neurons at day 33 of neuronal differentiation


title: ChIP_RIS_H3K27Ac_Rep4

description: ChIP-Seq


title: GGD50 DCL4-8:FHA


title: Rif1_RBM-MNase 5'

description: ChEC-seq


title: Rif1-MNase 5'

description: ChEC-seq

value: W303 RAD5+, MAT::loxP, ADE2::loxP, LEU2::pGAL-HO, LYS2::loxP, MNT2::TG80-HO-CA80-ADE2-LYS2, RIF1-MNase-3xFLAG-KANMX4


title: ips_2_RNASeq

description:
iPS2
iPSC cell culture duplicate

source_name: iPSC derived from fibroblast cells of GM01835 from Coriell Cell Repositories

value: iPSC


title: ips_1_RNASeq

description:
iPS1
iPSC cell culture duplicate


title: Rif1-MNase 1'30''

description: ChEC-seq


title: Rif1-MNase 1

description: ChEC-seq


title: Rif1-MNase 2'30''

description: ChEC-seq


title: Rif1-MNase 30''

description: ChEC-seq


title: Rif1_RBM-MNase 1'

description: ChEC-seq