title: MEFs transduced with wildtype YAP fused to GFP (wtYAP-GFP), replicate 2

source_name: wtYAP02 MEF

value: YAP (wtYAP-GFP)


title: A549_TGFB_nutin_p53cs_r2

status: Public on May 16 2019

type: SRA

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

country: USA

institute: University of Pittsburgh, School of Medicine

description:
A549_p53_chipseq
chipseq_tgfb.bed

library_source: genomic

data_processing:
ChIP-Seq: Alignment done with Bowtie version 1.1.1, with -m 1; Tag directories and UCSC bedGraph files generated with HOMER version 4-6, reads were quantified within peaks and normalized across samples
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis pipeline38 using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against hg19 genome and hg19 RefSeq.gtf transcript annotations were used.
Genome_build: hg19
Supplementary_files_format_and_content: chipseq_tgfb.bed
Supplementary_files_format_and_content: rnaseq_tgfb.tsv

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were passaged as at least twice post-thaw and used at a passage number of 6-14.  ~70% confluent plates were treated and harvested

extract_protocol:
ChIPseq lysates were clarified from sonicated nuclei and IPed with DO-1 anti-p53  antibody ( DO-1, Santa Cruz Biotechnology, SC-126X, Lot:G0115).   RNA samples were extracted with Trizol, purified on Zymo columns, and 500ng polyA selected.
DNA and mRNA libraries were prepared with standard illumina compatible protocols (NEBnext Kit)

treatment_protocol: Cells were treated with nutlin (5uM, 2hrs), and in some cases treated with TGFB for 5 days at 2.5ng/ml prior to nutlin treatment

tag: cell line

tag: antibody

tag: agent


title: A549_TGFB_nutin_p53cs_r1

description:
A549_p53_chipseq
chipseq_tgfb.bed


title: sham1w1722 input

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequencing reads were alligned to mm10 and hg38 using STAR tools
Low quality reads were filtered out and onlys readz >30 qc were rpcessed further
MeRIP peaks were identified using MeTPeak package
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Gene count files are provided as processed files, with read numbers detected and summed per gene for given sample.

molecule: total RNA

organism: Mus musculus

source_name: heart tissue

extract_protocol:
RNA was extracted with Trizol reagent, treated with DNAse and cleaned up with Zymoresearch RNA clean-up and concentrator kit.
Libraries were constructed according to Illumina's protocol for TrueSeq stranded RNA library prep kit

tag: experimental condition

value: sham treated (sham) mouse (ID 1722) after 1 week (1w)

tag: merip antibody

tag: sample type

value: RNAseq


title: WT2 TT-Seq  RNAPII mNET-Seq rep2

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description:
RNAPII 3'end associated RNA
mNET-Seq

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Reads were adapter trimmed using TrimGalore v0.4.4 with the following settings: “--paired --quality 20 -e 0.05 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a2 GATCGTCGGACTGTAGAACTCTGAAC --length 10”.
Paired reads were aligned against the GRCh38 genome using HISAT2 v2.04 in a strand-specific manner.
SAMtools was used to remove multi-mapping, duplicate and improperly paired reads.
The last base incorporated by the polymerase was isolated as the most 5' end of the second mate read and given the strand information of the first using the python script “get_SNR_bam.py” (https://github.com/tomasgomes/mNET_snr).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting single-bp BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 100 μg/ml hygromycin, 15 μg/ml blasticidin.  Additionally, 100 ng/mL doxycycline was used to induce SCAF4 or SCAF8 rescue constructs where applicable.

extract_protocol:
Cellular extracts were fractionated to generate nuclear and chromatin fractions as previously described (Nojima et al. 2016 Nature Protocols). Isolated chromatin was digested with MNase (40 U/mL, NEB, M0247) on a Thermomixer (1,400 rpm) at 37oC for 90 sec. MNase was inactivated by EGTA (25 mM) addition immediately after the reaction and soluble digested chromatin was collected by 13,000 rpm centrifuge for 5 min and diluted in NET-2 buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl and 0.05% (v/v) NP-40) and added to Pol II antibody-conjugated beads (MABI0601, MBL International). Immunoprecipitation was performed at 4oC for one hour. The beads were washed with 1 mL of NET-2 buffer 6 times and once with 500 mL of 1xPNKT (1xPNK buffer and 0.05 % Triton X-100) buffer in the cold room. The washed beads were incubated in 100 mL of PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/mL T4 PNK 3'phosphatase minus (NEB) on Thermomixer (1,400 rpm) at 37oC for 6 min. After the reaction beads were washed with 1 mL of NET-2 buffer and RNA was extracted with TRIzol (Thermo Fisher Scientific, 15596026). RNA was resolved on 8 % denaturing acrylamide 7 M urea gels for size purification. 35-100 nt fragments were eluted from the gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) and RNA was precipitated in 75 % Ethanol.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB)

treatment_protocol:
plus 100ng/mL doxycycline
None

tag: crispr status

value: WT

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8


title: sham1w1721 input

value: sham treated (sham) mouse (ID 1721) after 1 week (1w)


title: WT2 TT-Seq  RNAPII mNET-Seq rep1

description:
RNAPII 3'end associated RNA
mNET-Seq


title: A549_NT_nutin_p53cs_r1

description:
A549_p53_chipseq
chipseq_tgfb.bed

value: nutlin


title: SCAF8KO1  RNAPII mNET-Seq rep1

description:
RNAPII 3'end associated RNA
mNET-Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox

treatment_protocol:
wash out of GFP-rescue protein
None

value: SCAF8 single KO


title: sham1w1722 IP

value: Antibody against N6-methyladenosine (Synaptic Systems, cat. no. 202 003)


title: SCAF8KO1  RNAPII mNET-Seq rep2

description:
RNAPII 3'end associated RNA
mNET-Seq


title: MEFs transduced with control empty-vector (EV) encoding GFP, replicate 2

city: New Haven

first: Amaleah

middle: Ann

last: Hartman

state: CT

address: 10 Amistad St.

department: Cell Biology

institute: Yale University

data_processing:
For data analysis, RNA-seq reads were aligned to the mouse genome mm10 using Tophat followed by differential gene expression analysis with Cufflinks in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs
Supplementary_files_format_and_content: DifferentiallyExpressedGenes

source_name: EV02 MEF

growth_protocol: MEFs were cultured in standard MEF medium with 1 ug/mL Dox.

extract_protocol:
RNA was extracted with Trizol
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101)

treatment_protocol: Overexpression was achived by lentiviral mediated viral delivery

tag: transduction vector

value: EV (GFP)


title: MEFs transduced with control empty-vector (EV) encoding mCherry, replicate 1

source_name: EV03 MEF

value: EV (mCherry)


title: SCAF4KO3  RNAPII mNET-Seq rep1

description:
RNAPII 3'end associated RNA
mNET-Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox

value: SCAF4 single KO


title: sham1w1719 input

value: sham treated (sham) mouse (ID 1719) after 1 week (1w)


title: WT2 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

data_processing:
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 86 transcript annotations.
Reads were aligned against GRCh38 and Ensembl release 86 transcript annotations using STAR v2.5.2a via the transcript quantification software RSEM v1.2.31.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufacture’s instruction including the on-column DNase treatment. 2μg total RNA was used for oligo(dT) purification.
TruSeq HT kit (Illumina)


title: MEFs transduced with control empty-vector (EV) encoding GFP, replicate 1

source_name: EV01 MEF


title: Seedling in darkness 37ºC 24 hours replicate 1

type: RNA

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

hyb_protocol: Hybridization and slide washing were carried out with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively

scan_protocol: Scanned on Agilent Technologies Scanner G2505B at a resolution of 5 microns per pixel,using the double scanning as Agilent’s recommended settings. Images were quantified using Agilent Feature Extraction Software (version 9.5.1)

data_processing: Interarray analyses were performed with the GeneSpring 12.1 software. To ensure a high-quality data set, control features were removed, and only features for which the ‘IsWellAboveBG’ parameter was 1 in at least three out of four biological replicates were selected

organism: Arabidopsis thaliana

source_name: Seedling in darkness 37ºC 24 hours

label_protocol: 0.5 µg of total RNA 0.5 were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit. Agilent’s Spike-In Kit was used to assess the labeling and hybridization efficiencies

growth_protocol: Seeds were sterilized by treatment with 70% ethanol for 20 min, commercial bleach (2.5% sodium hypochlorite) containing 0.05%  Triton X-100 for 10 min, and finally, four washes with sterile distilled water  . Seeds were sown placed onto Whatmann paper (Whatmann ) placed into Murashige and Skoog (MS) medium plates (Duchefa). Plates were kept in the dark at 4°C for 96 hours for stratification, and incubated during 8 hours in light in at 22°C to promote germination.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations.  Total RNA integrity was tested with the 2100 Bioanalyzer (Agilent).

treatment_protocol: Plates were transferred to darkness at 22ºC for 72 hours. At this moment plates were either kept at 22 ºC or transferred to 37º C. Seedlings were harvested at 0 and 24 hours with four biological replicates.

tag: tissue

value: Whole seedling

tag: genotype

tag: temperature

tag: time

value: 24 hours


title: sham1w1720 input

value: sham treated (sham) mouse (ID 1720) after 1 week (1w)


title: Non-pluripotent YAPmCherry+ colonies from YAP transduced MEF cultures, replicate 3

data_processing:
For data analysis, RNA-seq reads were aligned to the mouse genome mm10 using Tophat followed by differential gene expression analysis with Cufflinks in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Non-pluripotent coloneis from YAP-expressing culture

growth_protocol: Reprogramming cells were cultured in standard mouse ES cell medium with 1 ug/mL Dox. ES cells or iPS cells were cultured in standard ES cell medium on feeder layer. Non-pluripotent colonies emerging from YAP-transduced culture were kept in standard ES cell medium on feeder layer, with 1 ug/mL Dox.

tag: genotype/variation

value: YAPmCherry+


title: MEFs transduced with control empty-vector (EV) encoding mCherry, replicate 2

source_name: EV04 MEF


title: SCAF8 chr CLIP rep3

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.cRIP.r3.clusters.bed

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Reads were adapter trimmed using the CutAdapt wrapper TrimGalore with the following settings:   “--quality 20 –e 0.1 –a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC –length 10”.
Trimmed reads were aligned against the Homo sapiens GRCh38 genome build using Bowtie2 v2.2.9 with the following settings: “-S –n 2 –m 100 –k 1 –1 10 –chunkmbs –best --strata”
Resulting genome alignments had duplicated reads removed using Picard.
Reads both soluble and chromatin enriched fractions were combined prior to binding cluster calling.
Genome_build: GRCh38
Supplementary_files_format_and_content: Binding clusters were called using PARalyzer v1.5 with the following settings: "PARBANDWIDTH=3 CONVERSION=T>C MINIMUM_READ_COUNT_PER_GROUP=10.MINIMUM_READ_COUNT_PER_CLUSTER=3 MINIMUM_READ_COUNT_FOR_KDE=5 MINIMUM_CLUSTER_SIZE=2 MINIMUM_CONVERSI  ON_LOCATIONS_FOR_CLUSTER=2 MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=2 MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=2 MINIMUM_READ_LENGTH=13 MAXIMUM_NUMBER_OF_NON_CONVER  SION_MISMATCHES=5  EXTEND_BY_READ".  Binding clusters are reported in BED format.

source_name: HEK293 Flp-in T-Rex FLAG-SCAF8, plus 4SU and 365nm UV crosslinking

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine.

extract_protocol:
Cellular extracts were fractionated into soluble and chromatin fractions and used for FLAG immunoprecipitations using limited RNaseI (Thermo Fisher Scientific, AM2294) and TURBO DNase (Thermo Fisher Scientific, AM2238) to solubilize chromatin associated RNA-protein complexes. Both soluble and chromatin enriched extracts were additionally treated with 30U/mL RNaseI (Thermo Fisher Scientific, AM2294) for 3 min at 37 oC prior to FLAG-immunoprecipitation using ANTI-FLAG® M2 Affinity Gel (Sigma-Aldrich, A2220). SCAF4 and SCAF8 protein-RNA complexes were FLAG peptide eluted and treated with 4 mg/mL ProtinaseK (Sigma-Aldrich, 3115887001) with the addition of 2% SDS to the FLAG elution buffer for 30 min at 50 oC. Fragmented RNA was extracted using the miRNeasy kit (Qiagen, 217004) from ProtinaseK treated SCAF4 and SCAF8 protein-RNA complexes and 1% input samples taken prior to FLAG immunoprecipitations (including on-column DNase treatment). RNA was analysed on bioanalyzer to determine the size range end-repaired using T4 PNK (NEB, EK0031) prior to library preparation.
NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB)

treatment_protocol:
100ng/mL doxycycline and 100 uM 4-thiouridine overnight, 2hrs 500 uM 4-thiourdine pulse and 365nm UV crosslinking (2000J/m2)
Addtion of 100 uM 4-thiouridine to cell media overnight, followed by an additonal 500 uM 4-thiourdine pulse for 2hrs prior to RNA-protein crosslinking by 365nm UV crosslinking at 2000J/m2. 100 ng/mL doxycycline were added to SCAF4 or SCAF8 cells to allow for overnight induction of proteins.

value: HEK293 Flp-in T-Rex FLAG-SCAF8

tag: fraction

value: chromatin

tag: replicate

value: replicate 3


title: Non-pluripotent YAPmCherry+ colonies from YAP transduced MEF cultures, replicate 1


title: MEFs transduced with wildtype YAP fused to GFP (wtYAP-GFP), replicate 1

source_name: wtYAP01 MEF

value: YAP (wtYAP-GFP)


title: iPSCs (which have lost YAP-overexpression) from YAP-overexpression transduced MEF cultures, replicate 3

source_name: Induced pluripotent stem cell colonies from YAP-expressing culture


title: iPSCs (which have lost YAP-overexpression) from YAP-overexpression transduced MEF cultures, replicate 2


title: iPSCs (which have lost YAP-overexpression) from YAP-overexpression transduced MEF cultures, replicate 1


title: SCAF4 sol CLIP rep3

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.cRIP.r3.clusters.bed

source_name: HEK293 Flp-in T-Rex FLAG-SCAF4, plus 4SU and 365nm UV crosslinking

value: WT

value: HEK293 Flp-in T-Rex FLAG-SCAF4

value: soluble


title: Control chr CLIP rep3

description:
protein crosslinked RNA
PAR-CLIP
293.cRIP.r3.clusters.bed

source_name: HEK293 Flp-in T-Rex , plus 4SU and 365nm UV crosslinking

treatment_protocol:
100 uM 4-thiouridine overnight, 2hrs 500 uM 4-thiourdine pulse and 365nm UV crosslinking (2000J/m2)
Addtion of 100 uM 4-thiouridine to cell media overnight, followed by an additonal 500 uM 4-thiourdine pulse for 2hrs prior to RNA-protein crosslinking by 365nm UV crosslinking at 2000J/m2. 100 ng/mL doxycycline were added to SCAF4 or SCAF8 cells to allow for overnight induction of proteins.

value: HEK293 Flp-in T-Rex


title: iPSCs from empty vector control transduced MEF cultures, replicate 2

source_name: Control induced pluripotent stem cell colonies


title: iPSCs from empty vector control transduced MEF cultures, replicate 1


title: iPSCs from empty vector control transduced MEF cultures, replicate 3


title: SCAF8 sol CLIP rep3


title: Control sol CLIP rep3


title: Proprioceptor_1

city: Boston

first: David

last: Ginty

state: MA

address: 210 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

data_processing:
bcbio-nextgen (0.9.1a-b73c090) (STAR-htSeq(0.6.1)-DESeq2(1.14.1) pipeline) were used for mapping&aligning, counting reads and generation of rlog transformed count values for differential expression analysis.
Cufflink-Cuffdiff pipeline was also used for generation of expression reported in rpkm (reads per million mapped reads per kilobase) values.
quality was checked with fastqc(0.11.3)
Genome_build: mm10
Supplementary_files_format_and_content: annotated raw count in csv file, rlog transformed data (DESeq2), rpkm data in csv file, project summary in csv file

source_name: dorsal root ganglia

extract_protocol:
DRGs were dissected and dissociated acutely then kept on ice for FACS. Sorted cells were collected in RNA-later. See Zheng et al. 2019 Neuron for details.
RNA libraries were prepared with Nugen RNAseq for amplification, then with illumina TruSeq library prep kit.

tag: neuron subtype

value: Proprioceptors

tag: age

value: Adult (P23 beyond)

tag: tamoxifen reatment for mice


title: SCAF8 chr CLIP input rep3

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.input.r3.clusters.bed

tag: cell line


title: Proprioceptor_2


title: Non-pluripotent YAPmCherry+ colonies from YAP transduced MEF cultures, replicate 2


title: SCAF4 chr CLIP input rep3

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.input.r3.clusters.bed


title: Proprioceptor_3


title: SCAF4 chr CLIP rep3


title: SCAF4KO1 mRNA-Seq rep2

description:
poly(A)+ mRNA
mRNA-Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 minus Dox

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4


title: Aβ Field-LTMR_2

description: Aβ Field-LTMR_2

value: Abeta Field-LTMRs

value: TrkCCreER;Retf(GFP)

value: Tamoxifen 2mg/day P13-14(P14-15)


title: Control chr CLIP input rep3

description:
protein crosslinked RNA
PAR-CLIP
293.input.r3.clusters.bed


title: Aβ Field-LTMR_1

description: Aβ Field-LTMR_1


title: Aβ Field-LTMR_3

description: Aβ Field-LTMR_3


title: Aβ SA1-LTMR_3

description: Aβ SA1-LTMR_3

value: Abeta SA1-LTMRs

value: Tamoxifen 3mg/day E12.5 (before 1pm)


title: Aβ SA1-LTMR_1

description: Aβ SA1-LTMR_1


title: Aβ RA-LTMR_3

description: Aβ RA-LTMR_3

value: Abeta RA-LTMRs


title: Aβ SA1-LTMR_2

description: Aβ SA1-LTMR_2


title: Scla_TSS_N1

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
Scla_N1_1
processed data file: Scla_TSS.gff

data_processing:
library strategy: dRNA-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome.
The reads were aligned to the S. clavuligerus genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
Genome_build: CP027858, CP027859
Supplementary_files_format_and_content: Scla_RNA_ETLS_readcount.txt, and Scla_Ribo_ETLS_readcount.txt : tab-delimited txt files that raw mapped read count within each gene and normalized expression of each gene in each sample.
Supplementary_files_format_and_content: Scla_TSS.gff : tab-lelimited gff file that is finally determined and categorized TSS list. TSS position, strand, TSS name were represented

organism: Streptomyces clavuligerus

source_name: Pooled (E,T,L,S)_mycelium cells

growth_protocol: Streptomyces clavuligerus ATCC 27064 cells were inoculated from its 20% glycerol stock of spores to 50 ml of R5- liquid complex medium with 8 g of glass beads (3 ± 0.3 mm diameter) in 250 ml of a baffled flask, and grown at 30 °C, 250 rpm

extract_protocol:
Lysate for all samples were prepared by resuspended at polysome buffer and grinding in liquid nitrogen
RNA-seq libraries were constructed with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Ribosome profiling libraries were additionally treated with 20 μM thiostrepton. dRNA-seq libraries were treated with RNA 5'-polyphosphatase (TAP) or none (N).

tag: growth phase

value: Pooled (E,T,L,S)

tag: cell sample

tag: treatment

tag: cell type

value: Mycelium cells from liquid culture


title: SCAF8 sol CLIP input rep3

tag: crispr status

value: HEK293 Flp-in T-Rex FLAG-SCAF8

value: replicate 3


title: Scla_TSS_N2

description:
Scla_N2_1
processed data file: Scla_TSS.gff


title: SCAF4 sol CLIP input rep3

value: WT


title: Aβ RA-LTMR_5

description: Aβ RA-LTMR_5


title: Aβ RA-LTMR_4

description: Aβ RA-LTMR_4


title: Control sol CLIP input rep3


title: Aδ-LTMR_3

value: Adelta-LTMRs

value: Tamoxifen 2mg/day E12-13


title: Aδ-LTMR_2


title: Scla_TSS_TAP2

description:
Scla_TAP2_1
processed data file: Scla_TSS.gff

value: tobacco acid pyrophosphatase, TAP


title: C-LTMR_3

value: C-LTMRs


title: Aδ-LTMR_1

value: Adult (P23 beyond)


title: Control chr CLIP rep2

description:
protein crosslinked RNA
PAR-CLIP
293.cRIP.r2.clusters.bed

value: HEK293 Flp-in T-Rex

value: chromatin

value: replicate 2


title: C-LTMR_2

value: Tamoxifen 2mg/day P13-14(P14-15)


title: C-LTMR_1


title: Scla_TSS_TAP1

description:
Scla_TAP1_1
processed data file: Scla_TSS.gff


title: Aβ RA-LTMR_2

description: Aβ RA-LTMR_2


title: Scla_Ribo_S1

description:
Scla_Ribo_S1_1
processed data file: Scla_Ribo_ETLS_readcount.txt

data_processing:
library strategy: Ribosome profiling
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome.
The reads were aligned to the S. clavuligerus genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
Genome_build: CP027858, CP027859
Supplementary_files_format_and_content: Scla_RNA_ETLS_readcount.txt, and Scla_Ribo_ETLS_readcount.txt : tab-delimited txt files that raw mapped read count within each gene and normalized expression of each gene in each sample.
Supplementary_files_format_and_content: Scla_TSS.gff : tab-lelimited gff file that is finally determined and categorized TSS list. TSS position, strand, TSS name were represented

source_name: Stationary phase (S)_mycelium cells

value: Stationary phase (S)

value: thiostrepton


title: SCAF4 chr CLIP rep2

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.cRIP.r2.clusters.bed

value: HEK293 Flp-in T-Rex FLAG-SCAF4


title: Scla_Ribo_S2

description:
Scla_Ribo_S2_1
processed data file: Scla_Ribo_ETLS_readcount.txt


title: SCAF8 sol CLIP rep2

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.cRIP.r2.clusters.bed

value: soluble


title: Aβ RA-LTMR_1

description: Aβ RA-LTMR_1

value: Abeta RA-LTMRs


title: Peptidergic Nociceptor_2

description: Peptidergic Nociceptor_2

value: Peptidergic nociceptors

value: CGRP-GFP


title: Peptidergic Nociceptor_3

description: Peptidergic Nociceptor_3


title: SCAF4 sol CLIP rep2

value: WT


title: Peptidergic Nociceptor_1

description: Peptidergic Nociceptor_1


title: Nonpeptidergic Nociceptor_3

description: Nonpeptidergic Nociceptor_3

value: MrgD+ nonpeptidergic nocicpeptors

value: MrgD-EGFP


title: Nonpeptidergic Nociceptor_1

description: Nonpeptidergic Nociceptor_1


title: Scla_Ribo_L2

description:
Scla_Ribo_L2_1
processed data file: Scla_Ribo_ETLS_readcount.txt

source_name: Late-exponential phase (L)_mycelium cells

value: Late-exponential phase (L)

value: Mycelium cells from liquid culture


title: SCAF8 chr CLIP rep2

value: HEK293 Flp-in T-Rex FLAG-SCAF8


title: Oxy_Mnase-seq_naked_nomethylDNA

city: New York

first: Leslie

last: Beh

state: NY

department: Biochemistry & Molecular Biophysics

institute: Columbia University

description:
Biological replicate A
L533_BC27x_r12_twotelo_len100to150_readcenters_perbpcov_intn_nsmoo_sigma15.txt

data_processing:
All Illumina sequencing data were quality trimmed (minimum quality score = 20) and length-filtered (minimum read length = 40 nt) using Galaxy. MNase-seq and m6dA IP-seq reads were mapped to the Oxytricha trifallax JRB310 (August 2013 build) macronuclear reference genome using Bowtie 2 with default settings, while poly(A)+ RNA-seq and TSS-seq reads were mapped using TopHat2 with August 2013 Oxytricha gene models and default settings.
Read pairs of length 122-172bp were used for MNase-seq analysis, while read pairs of length 100-150bp were used for naked gDNA-seq analysis. Reads from all biological replicates from each dataset were merged before downstream processing. The per-basepair coverage of Oxytricha MNase-seq read pair centers (termed “nucleosome occupancy”) and full m6dA IP-seq reads were respectively computed across the genome.  Subsequently, the per-basepair coverage values were normalized by the average coverage within each chromosome to account for differences in DNA copy number (and hence, read depth) between Oxytricha chromosomes. The per-bp coverage values were then smoothed using a Gaussian filter of standard deviation = 15 (cite ref). For RNA-seq data, the number of reads per kilobase of chromosome per million mapped reads (RPKM) was calculated for each chromosome without normalization by DNA copy number since there is no known correlation between Oxytricha DNA and transcript levels. Oxytricha TSS-seq data were processed using CAGEr; with clusterCTSS parameters (threshold = 1.6, thresholdIsTpm = TRUE, nrPassThreshold = 1, method = "paraclu", removeSingletons = TRUE, keepSingletonsAbove = 5). Only TSSs with tags per million counts > 0.1 were used for downstream analysis. All processed data files (.txt) format were generated using these normalization procedures.
Oxytricha trifallax JRB310 macronuclear genome (August 2013 build)
the reference Contignnn sequences are part of the Oxytricha trifallax macronuclear genome, can be accessed at OxyDB: http://oxy.ciliate.org/index.php/home/welcome
SMRT-seq data were processed with SMRTPipe v1.87.139483 in the SMRT Analysis 2.3.0 environment using, in order, the P_Fetch, P_Filter (with minLength = 50, minSubreadLength = 50, readScore = 0.75, and artifact = -1000), P_FilterReports, P_Mapping (with gff2Bed = True, pulsemetrics = DeletionQV, IPD, InsertionQV, PulseWidth, QualityValue, MergeQV, SubstitutionQV, DeletionTag, and loadPulseOpts = byread), P_MappingReports, P_GenomicConsensus (with algorithm = quiver, outputConsensus = True, and enableMapQVFilter = True), P_ConsensusReports, and P_ModificationDetection (with identifyModifcations = True, enableMapQVFilter = False, and mapQvThreshold = 10) modules. All other parameters were set to the default. Tetrahymena SMRT-seq reads were mapped to the June 2014 reference genome build.
Genomic coordinates of all Tetrahymena epigenetic modifications are listed in "Tth_PacBio_modifications_all_021716.gff". Only "m6A" calls were used for downstream analysis.
Genome_build: Tetrahymena thermophila SB210 macronuclear genome (June 2014 build).

organism: Oxytricha trifallax

source_name: PCR-Amplified genomic DNA

extract_protocol:
Naked DNA MNase digest protocol: Native (methylated) or PCR-amplified (no methyl) gDNA was digested with MNase to approximately mononucleosome-sized fragments. Note that naked DNA was used: no histones were present. Mononucleosome-sized DNA fragments were gel-purified using a QIAquick gel extraction kit (QIAGEN) for subsequent paired-end sequencing on an Illumina HiSeq 2500 according to manufacturer’s instructions.
Naked gDNA-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

value: in vitro

tag: presence of n6-methyladenine on dna template

value: No

tag: strain

tag: source of histones used for chromatin assembly

tag: growth protocol

value: Vegetative Oxytricha trifallax strain JRB310 was cultured at a density of 1.5 × 107 cells/L to 2.5 × 107 cells/L in Pringsheim media (0.11 mM Na2HPO4, 0.08 mM MgSO4, 0.85 mM Ca(NO3)2, 0.35 mM KCl, pH 7.0) and fed daily with Chlamydomonas reinhardtii. Cells were filtered through cheesecloth to remove debris and collected on a 10 μm Nitex mesh for subsequent experiments. To obtain native genomic DNA (containing methylation), macronuclei were purified from vegetative Oxytricha trifallax strain JRB310 using and a Nucleospin Tissue kit (Macherey-Nagel). gDNA was processed further by sucrose gradient ultracentrifugation in preparation for chromatin assembly, but not for m6dA IP-seq and MNase digest of naked DNA. Ultracentrifugation protocol:gDNA was loaded on a 15%-40% linear sucrose gradient and centrifuged in a SW40Ti rotor (Beckman Coulter) at 160,070 x g for 22.5hr at 20oC. Sucrose solutions were in 1 M NaCl, 20 mM Tris pH 7.5, 5 mM EDTA. Individual fractions from the sucrose gradient were analyzed on 0.9% agarose-TAE gels. Fractions containing high molecular weight DNA that migrated at the mobility limit were discarded as such DNA species were found to interfere with downstream chromatin assembly. All other fractions were pooled, ethanol precipitated, and adjusted to 0.5mg/mL DNA. To obtain genomic DNA lacking methylation for in vitro reconstitution, 98 chromosomes were individually PCR-amplified and purified using a MinElute PCR purification kit (QIAGEN), then mixed in equimolar ratios to obtain “mini-genome” DNA. The sample was concentrated by ethanol precipitation and adjusted to a final concentration of ~1.6 mg/ml. Xenopus histones were recombinantly expressed and purified, while Oxytricha histones were acid-extracted from purified nuclei. Xenopus or Oxytricha histones were combined in equimolar amounts in 6 M guanidine hydrochloride, 20 mM Tris pH 7.5 and the final concentration was adjusted to 1 mg/mL. The solution was dialyzed against 2 M NaCl, 10 mM Tris, 1 mM EDTA, and the octamers were purified from the tetramers and dimer species using size-exclusion chromatography on a Superdex 200 10/300 column (GE Healthcare Life Sciences). The purity of the fractions was analyzed by SDS-PAGE and pure fractions were combined, concentrated and stored in 50% glycerol at -20°C.


title: Oxy_Mnase-seq_naked_methylDNA

description:
Biological replicate A
L533_BC27_r12_twotelo_len100to150_readcenters_perbpcov_intn_nsmoo_sigma15.txt

source_name: Native genomic DNA

value: Yes


title: Nonpeptidergic Nociceptor_2

description: Nonpeptidergic Nociceptor_2

tag: genotype

value: Adult (P23 beyond)


title: Scla_Ribo_T2

description:
Scla_Ribo_T2_1
processed data file: Scla_Ribo_ETLS_readcount.txt

source_name: Transition phase (T)_mycelium cells

value: Transition phase (T)

value: thiostrepton


title: SCAF8 chr CLIP input rep2

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.input.r2.clusters.bed

value: chromatin

value: replicate 2


title: Scla_Ribo_E2

description:
Scla_Ribo_M2_1
processed data file: Scla_Ribo_ETLS_readcount.txt

source_name: Early-exponential phase (E)_mycelium cells

value: Early-exponential phase (E)


title: SCAF8 sol CLIP input rep2

value: soluble


title: Oxy_MNase-seq_invivo_replB

description:
Biological replicate B
L533_BC21_BC22_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt

source_name: Purified nuclei

extract_protocol:
Oxytricha in vivo MNase-seq protocol: 3 x 105 vegetative Oxytricha cells were fixed in 1% (w/v) formaldehyde for 10 min at room temperature with gentle shaking, and then quenched with 125 mM glycine. Macronuclei were subsequently isolated by sucrose gradient centrifugation from fixed cells as previously described25. Purified nuclei were pelleted by centrifugation at 4000 x g, washed in 50 ml TMS buffer (10 mM Tris pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.25 M sucrose), resuspended in a final volume of 300 μl, and equilibriated at 37oC for 5 min. Chromatin was then digested with MNase (New England BioLabs) at a final concentration of 15.7 Kunitz Units / μl at 37oC for 1 min 15 sec, 3 min, 5 min, 7 min 30sec, 10 min 30 sec, and 15 min respectively. Reactions were stopped by adding 1/2 volume of PK buffer (300 mM NaCl, 30 mM Tris pH 8, 75 mM EDTA pH 8, 1.5% (w/v) SDS, 0.5 mg/ml Proteinase K). Each sample was incubated at 65oC overnight to reverse crosslinks and deproteinate samples. Subsequently, nucleosomal DNA was purified through phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.  Each sample was loaded on a 2% agarose-TAE gel to check the extent of MNase digestion. The sample exhibiting ~80% mononucleosomal species was selected for MNase-seq analysis. Mononucleosome-sized DNA was gel-purified using a QIAquick gel extraction kit (QIAGEN) for subsequent paired-end sequencing on an Illumina HiSeq 2500 according to manufacturer’s instructions.
MNase-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

value: Vegetative

value: Oxytricha trifallax


title: Oxy_TSSseq_replB

description:
Biological replicate B
Oxy_TSSclus2_veg310_0hr_threshold1.6_width.txt

source_name: Whole cells

extract_protocol:
Oxytricha 5'-capped RNAseq protocol: The 5’ ends of capped RNAs were enriched from vegetative Oxytricha total RNA and used for Illumina library construction, following the RNA Annotation and Mapping of Promoters for Analysis of Gene Expression (RAMPAGE) protocol.
TSS-seq (Single-read sequencing); RNA Annotation and Mapping of Promoters for Analysis of Gene Expression (RAMPAGE) protocol (Batut, Dobin, Plessy et al., Genome Res 2013)


title: Oxy_TSSseq_replC

description:
Biological replicate C
Oxy_TSSclus2_veg310_0hr_threshold1.6_width.txt


title: Scla_Ribo_L1

description:
Scla_Ribo_L1_1
processed data file: Scla_Ribo_ETLS_readcount.txt


title: Scla_Ribo_T1

description:
Scla_Ribo_T1_1
processed data file: Scla_Ribo_ETLS_readcount.txt


title: Control sol CLIP input rep2

description:
protein crosslinked RNA
PAR-CLIP
293.input.r2.clusters.bed

value: WT

value: HEK293 Flp-in T-Rex


title: Scla_RNA_S1

description:
S_cla_ST1_1
processed data file: Scla_RNA_ETLS_readcount.txt

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the Ribo-seq libraries before being aligned to the genome.
The reads were aligned to the S. clavuligerus genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion cost 3, length fraction 0.9, and similarity fraction 0.9.
Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
The 5' end position of dRNA-seq reads from TAP treated library were considered to be potential TSSs. Briefly, the potential TSSs apart less than 100 bp from the ones located neighboring positions were clustered together. Then, the potential TSSs located adjacent positions in each cluster were sub-clustered together based on the standard deviation of their genomic positions (< 10). Only the potential TSS clusters with more than three read counts were considered and the potential TSSs with maximum read counts within each sub-cluster were selected as TSSs. Then the read counts of selected TSS positions from TAP treated and TAP untreated libraries were compared and positions with more read counts in TAP untreated library were discarded. Then, the selected TSSs were manually inspected using the corresponding RNA-seq profile
Genome_build: CP027858, CP027859
Supplementary_files_format_and_content: Scla_RNA_ETLS_readcount.txt, and Scla_Ribo_ETLS_readcount.txt : tab-delimited txt files that raw mapped read count within each gene and normalized expression of each gene in each sample.
Supplementary_files_format_and_content: Scla_TSS.gff : tab-lelimited gff file that is finally determined and categorized TSS list. TSS position, strand, TSS name were represented

value: Stationary phase (S)

value: Mycelium cells from liquid culture


title: SCAF4 chr CLIP input rep2

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.input.r2.clusters.bed

value: HEK293 Flp-in T-Rex FLAG-SCAF4


title: Oxy_MNase-seq_invivo_replA

description:
Biological replicate A
L533_BC21_BC22_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: Oxy_polyA_RNAseq_replA

description:
Biological replicate A
L265_BC43_BC45_BC47_all_minlen45_310mapped_chrrpkm_plmireads.txt and L265_mRNAseq_BC43_45_47_FPKM.txt

extract_protocol:
Oxytricha polyA+ RNAseq protocol: Vegetative Oxytricha cells were lysed in TRIzol reagent (Thermo Fisher Scientific) for total RNA isolation according to manufacturer’s instructions. Poly(A)+ RNA was then purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). The Oxytricha poly(A)+ RNA was prepared for RNA-seq using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina).
polyA+ RNAseq (Single-read sequencing); ScriptSeq v2 RNA-Seq library preparation protocol


title: Oxy_TSSseq_replA

description:
Biological replicate A
Oxy_TSSclus2_veg310_0hr_threshold1.6_width.txt


title: Oxy_6mA_input_replC

description:
Biological replicate C
EH_input_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt

extract_protocol:
Oxytricha DNA N6-methyladenine IP-seq protocol: Native Oxytricha genomic DNA was sheared into 150 bp fragments using a Covaris LE220 ultra-sonicator (Covaris). Samples were gel-purified on a 2% agarose-TAE gel, blunted with Klenow polymerase (New England Biolabs, MA), and purified using MinElute spin columns (QIAGEN). The fragmented DNA was dA-tailed using Klenow Fragment (3' -> 5' exo-) (New England BioLabs) and ligated to Illumina adaptors following manufacturer's instructions. Subsequently, 2.2μg of adaptor-ligated DNA containing m6dA was immunoprecipitated using an anti-N6-methyladenosine antibody (m6A; Synaptic Systems) conjugated to Dynabeads (Life Technologies). The immunoprecipitated and input libraries were respectively treated with proteinase K, phenol:chloroform extracted, and ethanol precipitated. Finally, they were PCR-amplified using Phusion Hot Start polymerase (New England BioLabs) and used for Illumina sequencing.
m6dA IP-seq (Single-read sequencing); standard TruSeq Illumina library construction protocol


title: Scla_Ribo_E1

description:
Scla_Ribo_M1_1
processed data file: Scla_Ribo_ETLS_readcount.txt


title: Oxy_polyA_RNAseq_replB

description:
Biological replicate B
L265_BC43_BC45_BC47_all_minlen45_310mapped_chrrpkm_plmireads.txt and L265_mRNAseq_BC43_45_47_FPKM.txt


title: Scla_RNA_S2

description:
S_cla_ST2_1
processed data file: Scla_RNA_ETLS_readcount.txt


title: Oxy_polyA_RNAseq_replC

description:
Biological replicate C
L265_BC43_BC45_BC47_all_minlen45_310mapped_chrrpkm_plmireads.txt and L265_mRNAseq_BC43_45_47_FPKM.txt


title: SCAF8 chr CLIP rep1

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.cRIP.r1.clusters.bed

source_name: HEK293 Flp-in T-Rex FLAG-SCAF8, plus 4SU and 365nm UV crosslinking

value: HEK293 Flp-in T-Rex FLAG-SCAF8

value: replicate 1


title: Scla_RNA_L2

description:
S_cla_LE2_1
processed data file: Scla_RNA_ETLS_readcount.txt

value: Late-exponential phase (L)


title: Control sol CLIP rep2

description:
protein crosslinked RNA
PAR-CLIP
293.cRIP.r2.clusters.bed


title: Oxy_6mA_input_replB

description:
Biological replicate B
EH_input_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt

value: Yes

value: Vegetative Oxytricha trifallax strain JRB310 was cultured at a density of 1.5 × 107 cells/L to 2.5 × 107 cells/L in Pringsheim media (0.11 mM Na2HPO4, 0.08 mM MgSO4, 0.85 mM Ca(NO3)2, 0.35 mM KCl, pH 7.0) and fed daily with Chlamydomonas reinhardtii. Cells were filtered through cheesecloth to remove debris and collected on a 10 μm Nitex mesh for subsequent experiments. To obtain native genomic DNA (containing methylation), macronuclei were purified from vegetative Oxytricha trifallax strain JRB310 using and a Nucleospin Tissue kit (Macherey-Nagel). gDNA was processed further by sucrose gradient ultracentrifugation in preparation for chromatin assembly, but not for m6dA IP-seq and MNase digest of naked DNA. Ultracentrifugation protocol:gDNA was loaded on a 15%-40% linear sucrose gradient and centrifuged in a SW40Ti rotor (Beckman Coulter) at 160,070 x g for 22.5hr at 20oC. Sucrose solutions were in 1 M NaCl, 20 mM Tris pH 7.5, 5 mM EDTA. Individual fractions from the sucrose gradient were analyzed on 0.9% agarose-TAE gels. Fractions containing high molecular weight DNA that migrated at the mobility limit were discarded as such DNA species were found to interfere with downstream chromatin assembly. All other fractions were pooled, ethanol precipitated, and adjusted to 0.5mg/mL DNA. To obtain genomic DNA lacking methylation for in vitro reconstitution, 98 chromosomes were individually PCR-amplified and purified using a MinElute PCR purification kit (QIAGEN), then mixed in equimolar ratios to obtain “mini-genome” DNA. The sample was concentrated by ethanol precipitation and adjusted to a final concentration of ~1.6 mg/ml. Xenopus histones were recombinantly expressed and purified, while Oxytricha histones were acid-extracted from purified nuclei. Xenopus or Oxytricha histones were combined in equimolar amounts in 6 M guanidine hydrochloride, 20 mM Tris pH 7.5 and the final concentration was adjusted to 1 mg/mL. The solution was dialyzed against 2 M NaCl, 10 mM Tris, 1 mM EDTA, and the octamers were purified from the tetramers and dimer species using size-exclusion chromatography on a Superdex 200 10/300 column (GE Healthcare Life Sciences). The purity of the fractions was analyzed by SDS-PAGE and pure fractions were combined, concentrated and stored in 50% glycerol at -20°C.


title: Control chr CLIP input rep2


title: Oxy_6mA-IP-seq_replC

description:
Biological replicate C
EH_IP_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt


title: Oxy_6mA_input_replA

description:
Biological replicate A
EH_input_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt


title: Control chr CLIP rep1

description:
protein crosslinked RNA
PAR-CLIP
293.cRIP.r1.clusters.bed


title: SCAF4 chr CLIP rep1

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.cRIP.r1.clusters.bed


title: Oxy_6mA-IP-seq_replB

description:
Biological replicate B
EH_IP_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt


title: MNase-seq_invitro_nomethylDNA_XenOctamers_replB

description:
Biological replicate B
L533_BC15_BC18_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt

source_name: in vitro reconstituted chromatin

extract_protocol:
Oxytricha in vitro MNase-seq protocol: Chromatin was reconstituted in vitro through salt gradient dialysis. Assembled chromatin was adjusted to 50 mM Tris pH 7.9, 5 mM CaCl2 and digested with MNase (New England BioLabs) to mainly mononucleosomal DNA. Mononucleosome-sized DNA was gel-purified and used for paired-end sequencing on an Illumina HiSeq 2500, according to manufacturer’s instructions.
MNase-seq (Paired-end sequencing); standard TruSeq Illumina library construction protocol

value: in vitro

value: No

value: Xenopus laevis


title: Oxy_6mA-IP-seq_replA

description:
Biological replicate A
EH_IP_BC8_BC9_BC10_StarveABC_ext_s_readoccu_perbpcov_intn_nsmoo_sigma15.txt


title: Scla_RNA_T2

description:
S_cla_TR2_1
processed data file: Scla_RNA_ETLS_readcount.txt

value: Transition phase (T)


title: SCAF4 sol CLIP rep1

value: soluble


title: Scla_RNA_E2

description:
S_cla_EE2_1
processed data file: Scla_RNA_ETLS_readcount.txt

value: Early-exponential phase (E)


title: MNase-seq_invitro_methylDNA_XenOctamers_replB

description:
Biological replicate B
L533_BC15_BC18x_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: Scla_RNA_L1

description:
S_cla_LE1_1
processed data file: Scla_RNA_ETLS_readcount.txt


title: Control sol CLIP rep1


title: MNase-seq_invitro_methylDNA_XenOctamers_replA

description:
Biological replicate A
L533_BC15_BC18x_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: MNase-seq_invitro_methylDNA_OxyOctamers_replB

description:
Biological replicate B
L533_BC5_BC7x_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt

value: Oxytricha trifallax


title: SCAF4 sol CLIP input rep2

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.input.r2.clusters.bed

value: WT

value: replicate 2


title: Scla_RNA_T1

description:
S_cla_TR1_1
processed data file: Scla_RNA_ETLS_readcount.txt


title: MNase-seq_invitro_nomethylDNA_XenOctamers_replA

description:
Biological replicate A
L533_BC15_BC18_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: SCAF8 chr CLIP input rep1

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.input.r1.clusters.bed

value: chromatin


title: SCAF8 sol CLIP rep1

description:
protein crosslinked RNA
PAR-CLIP
SCAF8.cRIP.r1.clusters.bed


title: MNase-seq_invitro_nomethylDNA_OxyOctamers_replA

description:
Biological replicate A
L533_BC5_BC7_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: Scla_RNA_E1

description:
S_cla_EE1_1
processed data file: Scla_RNA_ETLS_readcount.txt

value: Mycelium cells from liquid culture


title: Tet_m6A_SMRTseq_replA

description:
Biological replicate A
Tth_PacBio_modifications_all_021716.gff

organism: Tetrahymena thermophila

extract_protocol:
Tetrahymena SMRT-seq protocol: Macronuclei were isolated from vegetative Tetrahymena cells through differential centrifugation. Genomic DNA was then purified through phenol:chloroform extraction and ethanol precipitation. Subsequently, the DNA was sheared and ligated to SMRTbell adapters for sequencing on 21 SMRTcells using P5-C3 and P6-C4 chemistry, according to manufacturer's instructions.
SMRT-seq; Standard Pacific Biosicences SMRT-seq library construction protocol

value: Vegetative

value: Vegetative Tetrahymena thermophila strain SB210 was cultured in 1xSPP media as previously described at a density of ~35x104 cells/mL and collected by centrifuged at 1000 x g for 5 min for subsequent experiments.


title: 2425_P1

city: Guelph

first: Sanjay

last: Mallikarjunappa

state: ON

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

data_processing:
FASTQC was used to assess the quality of sequence reads. Low quality reads and adapters were trimmed using Trimmomatic software
Trimmed reads were mapped to Bovine Reference Genome Assembly BTA_UMD3.1 (ftp://ftp.ensembl.org/pub/release-91/fasta/bos_taurus/dna/) using STAR RNA-seq aligner and to generate read counts
Differential expression analysis carried out using DESEq2 software
Genome_build: Bovine Reference Genome Assembly BTA_UMD3.1
Supplementary_files_format_and_content: excel files with  read counts of each sample

organism: Bos taurus

source_name: parotid salivary gland - dorsal section

extract_protocol:
RNA was extracted using Trizol and using RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions
TruSeq (Illumina TruSeq RNA Library v2 construction)

treatment_protocol: Tissue collected from two groups of cattle - A) Challenged group - group challenged with bacteria MAP; B) Control no MAP-Challenged group

tag: tissue

value: parotid salivary gland

tag: sample collection time during experimental trial

value: 33 months' post-experimental challenge


title: MNase-seq_invitro_nomethylDNA_OxyOctamers_replB

description:
Biological replicate B
L533_BC5_BC7_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt


title: 2425_P2

source_name: parotid salivary gland - ventral section


title: MDA-MB-468_DEDD-KD_S5

city: South Bend

first: Siyuan

last: Zhang

state: IN

address: 1234 N Notre Dame Ave

institute: University of Notre Dame

description: Sample 5

data_processing: generation of normalized counts

growth_protocol: MDA-MB-468 cell lines were cultured in DMEM/Ham’s F-12 (1:1) supplemented with 10% FBS and 1% Pen-Strep.

extract_protocol: mRNA extraction using Trizol reagent

treatment_protocol: MDA-MB-468 cells were transfected with Lentiviral particles containing either PLKO.1 or anti-DEDD shRNAs. Stable knockdown  were selected by culturing cells with puromycin (1-5μg/mL) for at least 48 hours. The uninfected cells were also treated with puromycin as a control. Infected cells have MOI around 0.3-0.6.

tag: cancer type

value: triple-negative breast cancer

tag: breast cancer subtype

value: ER-, PR-, HER2 normal

tag: lentiviral transfection vector

value: DEDD knockdown

tag: sequencer

value: Illumina miSeq


title: SCAF8 sol CLIP input rep1

tag: cell line

value: HEK293 Flp-in T-Rex FLAG-SCAF8

tag: fraction

tag: replicate

value: replicate 1


title: 2409_P1


title: MDA-MB-468_PLKO.1_S3

description: Sample 3


title: MNase-seq_invitro_methylDNA_OxyOctamers_replA

description:
Biological replicate A
L533_BC5_BC7x_r12_twotelo_len122to172_readcenters_perbpcov_intn_nsmoo_sigma15.txt

value: in vitro

value: Yes

value: Vegetative Oxytricha trifallax strain JRB310 was cultured at a density of 1.5 × 107 cells/L to 2.5 × 107 cells/L in Pringsheim media (0.11 mM Na2HPO4, 0.08 mM MgSO4, 0.85 mM Ca(NO3)2, 0.35 mM KCl, pH 7.0) and fed daily with Chlamydomonas reinhardtii. Cells were filtered through cheesecloth to remove debris and collected on a 10 μm Nitex mesh for subsequent experiments. To obtain native genomic DNA (containing methylation), macronuclei were purified from vegetative Oxytricha trifallax strain JRB310 using and a Nucleospin Tissue kit (Macherey-Nagel). gDNA was processed further by sucrose gradient ultracentrifugation in preparation for chromatin assembly, but not for m6dA IP-seq and MNase digest of naked DNA. Ultracentrifugation protocol:gDNA was loaded on a 15%-40% linear sucrose gradient and centrifuged in a SW40Ti rotor (Beckman Coulter) at 160,070 x g for 22.5hr at 20oC. Sucrose solutions were in 1 M NaCl, 20 mM Tris pH 7.5, 5 mM EDTA. Individual fractions from the sucrose gradient were analyzed on 0.9% agarose-TAE gels. Fractions containing high molecular weight DNA that migrated at the mobility limit were discarded as such DNA species were found to interfere with downstream chromatin assembly. All other fractions were pooled, ethanol precipitated, and adjusted to 0.5mg/mL DNA. To obtain genomic DNA lacking methylation for in vitro reconstitution, 98 chromosomes were individually PCR-amplified and purified using a MinElute PCR purification kit (QIAGEN), then mixed in equimolar ratios to obtain “mini-genome” DNA. The sample was concentrated by ethanol precipitation and adjusted to a final concentration of ~1.6 mg/ml. Xenopus histones were recombinantly expressed and purified, while Oxytricha histones were acid-extracted from purified nuclei. Xenopus or Oxytricha histones were combined in equimolar amounts in 6 M guanidine hydrochloride, 20 mM Tris pH 7.5 and the final concentration was adjusted to 1 mg/mL. The solution was dialyzed against 2 M NaCl, 10 mM Tris, 1 mM EDTA, and the octamers were purified from the tetramers and dimer species using size-exclusion chromatography on a Superdex 200 10/300 column (GE Healthcare Life Sciences). The purity of the fractions was analyzed by SDS-PAGE and pure fractions were combined, concentrated and stored in 50% glycerol at -20°C.


title: SCAF4KO3_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Reads were trimmed using Cutadapt v1.9.1 to remove 5bp 5’ anchored barcodes
Reads were aligned against the Homo sapiens GRCh38 genome build using Bowtie2 v2.2.9
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

molecule: polyA RNA

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufactures’ instruction including the on-column DNase treatment. 25 μg of RNA were heat-fragmented for 12 minutes in 1x Fragmentation Buffer (Ambion) at 70°C to generate RNA fragments of ~100 nucleotides. Next, the 3’end poly(A) RNA fragments were selected using the Oligotex mRNA Kit (Qiagen, 70022) and RNA was end-repair with T4 polynucleotide kinase for 45 minutes at 37°C following manufacturer’s instructions
RNA 3’ends were blocked for ligation by incubation with 1mM Cordycepin 5′-triphosphate (Sigma, C9137) and 10U of polyA polymerase (PAP, NEB, M0276), in 1x PAP buffer for 30 minutes at 37°C. Finally, a P7 RNA adapter (5’-CAAGCAGAAGACGGCAUACGAGAU-3’) was ligated to the 5’end using 2U of T4 RNA ligase I and 2.5uM of RNA adapter, for 4h at room temperature. Between each step, RNA was purified using Agencourt RNAClean XP magnetic beads (Beckman Coulter, A63987) following the manufacturer’s instructions. At this point, RNA fragments were converted to cDNA employing the Superscript III RT kit (Thermo Fisher Scientific, 18080051) and an anchored oligo(d)T stem loop primer containing a barcoded Illumina adaptor. Next, cDNA was purified twice with Agentcourt AMPure XP magnetic beads (Beckman Coulter, A63881) using a ratio 1.5:1 beads:sample. To generate the final 3’Seq library, the cDNA with the correct adaptor sequences was enriched/amplified using Phusion DNA polymerase (Thermo Fisher Scientific, F530L) and primers P7 and Illumina_Truseq, for 12 cycles following manufacture’s recommendations. Finally, the 3’Seq library was size selected with AMPure XP magnetic beads by two rounds of purification with a ratio 1:1 beads:sample.

value: SCAF4 single KO

tag: treatment

value: plus 100ng/mL doxycycline


title: Control chr CLIP input rep1

description:
protein crosslinked RNA
PAR-CLIP
293.input.r1.clusters.bed

source_name: HEK293 Flp-in T-Rex , plus 4SU and 365nm UV crosslinking

value: WT

value: HEK293 Flp-in T-Rex

value: chromatin


title: SCAF4SCAF8dKO4_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8 minus Dox

value: SCAF4 and SCAF8 double KO

value: wash out of GFP-rescue protein


title: NBT24

city: Beijing

first: Fan

last: Xiaolong

address: No.19,Waida Jie,Xinjie Kou, Haiding District

country: China

institute: Beijing Normal University

hyb_protocol: cRNA was fragmented and hybridized to Affymetrix human Clariom D® arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All arrays were scanned using Affymetrix® GeneChip Command Console (AGCC) installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method

label: biotin

source_name: traumatic brain injury

label_protocol: cDNA was synthesized using one-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA, USA), and cRNA was generated using a GeneChip WT Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted from about 30mg frozen  tissue using AllPrep DNA/RNA Mini Kit (QIAGEN,Cat No./ID: 80204)

tag: histology

value: TBI

tag: grade

tag: gender

tag: age

tag: idh mutation

tag: 1p19q co-deletion

tag: em/pm subtype

value: EMlowPMlow


title: MDA-MB-468_DEDD-KD_S6

description: Sample 6

value: triple-negative breast cancer

value: ER-, PR-, HER2 normal


title: 661


title: 654


title: NBT16


title: NBT8_1


title: 2405_P2

tag: tissue

value: parotid salivary gland

value: 33 months' post-experimental challenge


title: 2425_M2

source_name: mandibular salivary gland - ventral section

value: mandibular salivary gland

tag: sample collection time during experimental trial


title: NBT23


title: SCAF4 chr CLIP input rep1

description:
protein crosslinked RNA
PAR-CLIP
SCAF4.input.r1.clusters.bed

source_name: HEK293 Flp-in T-Rex FLAG-SCAF4, plus 4SU and 365nm UV crosslinking

tag: crispr status

value: HEK293 Flp-in T-Rex FLAG-SCAF4

value: replicate 1


title: SCAF4 sol CLIP input rep1

value: soluble


title: SCAF4SCAF8dKO3_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 minus Dox


title: MDA-MB-468_DEDD-KD_S4

description: Sample 4

tag: cancer type

tag: breast cancer subtype

value: DEDD knockdown

value: Illumina miSeq


title: 2409_P2


title: Control sol CLIP input rep1

source_name: HEK293 Flp-in T-Rex, plus 4SU and 365nm UV crosslinking

value: WT


title: NBT5


title: MDA-MB-468_PLKO.1_S2

description: Sample 2

tag: lentiviral transfection vector

tag: sequencer


title: 2409_M2


title: 2425_M1

source_name: mandibular salivary gland - dorsal section


title: 2405_M2

description: It was not involved in our analysis and data results interpretation as they did not meet our initial analysis criteria [no processed data]


title: WT2_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

tag: cell line

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8

value: plus 100ng/mL doxycycline


title: 1540

source_name: glioma

value: GBM

value: Female

value: non co-deletion

value: EM


title: MDA-MB-468_PLKO.1_S1

description: Sample 1

value: triple-negative breast cancer


title: SCAF8KO1_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox

value: SCAF8 single KO

value: wash out of GFP-rescue protein


title: 2409_M1

value: 33 months' post-experimental challenge


title: 1537

value: Male


title: NBT8_2

value: TBI

value: EMlowPMlow


title: 2405_M1

value: mandibular salivary gland


title: SCAF4KO2_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 plus Dox

value: SCAF4 single KO


title: NBT6


title: 2398_P2

value: parotid salivary gland


title: 2405_P1


title: SCAF8KO3_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 plus Dox


title: SCAF4SCAF8dKO2_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4 minus Dox

value: SCAF4 and SCAF8 double KO


title: 2398_P1

source_name: parotid salivary gland - dorsal section


title: SCAF8KO2_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 plus Dox


title: 2398_M2


title: 2398_M1


title: 1521

value: WT


title: WT1_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 plus Dox

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4

value: plus 100ng/mL doxycycline


title: SCAF4SCAF8dKO1_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4 minus Dox


title: 1534

value: GBM-O

value: Female

value: MT

value: PM


title: 1518

value: AO

value: non co-deletion


title: 2395_P1

value: 33 months' post-experimental challenge


title: 2395_M2


title: SCAF4KO3_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF4 plus Dox


title: 1503

value: GBM

value: Male

value: EM


title: 2395_P2

source_name: parotid salivary gland - ventral section


title: SCAF4KO1_3Seq_rep2

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4 minus Dox

value: wash out of GFP-rescue protein


title: 1514


title: SCAF4SCAF8dKO4_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO4/GFP-SCAF8 minus Dox


title: 2395_M1

value: mandibular salivary gland


title: SCAF4KO2_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: SCAF4 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8


title: 2420_P2

value: parotid salivary gland


title: 1501

value: WT

value: EMlowPMlow


title: 1497

value: AOA


title: 1494


title: 2420_P1


title: 1508


title: SCAF4SCAF8dKO3_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO3/GFP-SCAF8 minus Dox

value: SCAF4 and SCAF8 double KO


title: 1491

value: MT


title: 2420_M1


title: 2420_M2

source_name: mandibular salivary gland - ventral section


title: 1486


title: 1378

value: co-deletion

value: PM


title: hFB_HG_187days

type: genomic

first: Gabriel

last: Sturm

address: 40 Haven Avenue

department: Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: DNA methylation data was processed in R (Version 3.5.0). Quality control preprocessing was applied by checking for correct sex prediction, probe quality, sample intensities, and excluding SNPs and non-CpG probes. All samples passed our quality control and no samples were excluded. Data was then normalized using Functional Normalization. Using the R package SVA, both RCP and ComBat adjustments were applied for probe-type and plate bias, respectively.

label: Cy5 and Cy3

source_name: primary human fibroblast, high glucose, 187 days grown

label_protocol: Standard Illumina Protocol

growth_protocol: Primary human dermal fibroblasts were obtained with informed consent from the upper arm of a healthy 29-year-old male donor (IRB #AAAB0483). Cryopreserved cells were seeded cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher #10569044) containing, 1 mM pyruvate, 4 mM GlutaMAXTM, supplemented with 10% fetal bovine serum (FBS; not heat inactivated), 1% non-essential amino acids (NEAA), and either normal (5.5mM) or high (25mM) glucose. After initial plating cells were frozen using cryo-media (10% DMSO in DMEM) in liquid nitrogen and later thawed for experimentation. Cells were maintained in standard 5% CO2 and atmospheric O2 at 37°C in T75 flasks. Cells were passaged approximately every five days, which corresponded to ~90% confluency, with 500,000 cells replated each passage. As cell growth slowed the number of days between passages was also continually extended to maintain 90% confluency at the point passage. At each passage, cells were counted using the Countess II Automated Cell Counter (Thermo Fisher Scientific cat#AMQAX1000), and the counts used to compute population doublings.

extract_protocol: Genomic DNA was extracted and purified using Qiagen DNeasy Kit (Qiagen cat#69506) according to manufacter's protocol. At least 150 ng of DNA was submitted in 50 µl of ddH2O

treatment_protocol: At passage 4, cells were split into two flasks and chronically treated either with normal 5.5 mM glucose  or high 25 mM glucose.

value: male

value: high

value: primary human fibroblast


title: WT2_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 plus Dox

value: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8

value: plus 100ng/mL doxycycline


title: SCAF8KO3_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: SCAF8 single KO

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO2/GFP-SCAF4


title: 2194_P2

value: 33 months' post-experimental challenge


title: SCAF4SCAF8dKO2_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: wash out of GFP-rescue protein


title: 1357

source_name: glioma

value: Female

value: non co-deletion


title: SCAF8KO2_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: HEK293 Flp-in T-Rex SCAF4SCAF8 dKO1/GFP-SCAF4


title: 1339

value: O

value: Male


title: 1371

value: GBM

value: WT

value: EM


title: 2194_P1

value: parotid salivary gland


title: 2194_M2

value: mandibular salivary gland


title: SCAF8KO1_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

source_name: HEK293 Flp-in T-Rex SCAF8 KO/GFP-SCAF8 minus Dox


title: 2194_M1

source_name: mandibular salivary gland - dorsal section


title: hFB_HG_92days

source_name: primary human fibroblast, high glucose, 92 days grown

value: male

value: high

value: primary human fibroblast


title: SCAF4SCAF8dKO1_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: SCAF4 and SCAF8 double KO


title: hFB_HG_72days

source_name: primary human fibroblast, high glucose, 72 days grown


title: WT1_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: HEK293 Flp-in T-Rex SCAF4 KO/GFP-SCAF4

value: plus 100ng/mL doxycycline


title: hFB_HG_86days

source_name: primary human fibroblast, high glucose, 86 days grown


title: 1333

value: PM


title: 1318

value: OA

value: MT


title: 1321

value: non co-deletion


title: SCAF4KO1_3Seq_rep1

description:
3'ends of poly(A)+ mRNAs
3'Seq

value: SCAF4 single KO

value: wash out of GFP-rescue protein


title: 2402_P2

value: 33 months' post-experimental challenge


title: hFB_HG_144days

source_name: primary human fibroblast, high glucose, 144 days grown


title: 1312

value: GBM

value: Male

value: WT


title: 1317

value: O

value: co-deletion


title: ChIPseq_pGI_ZT8_rep1

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: GI ChIPseq at ZT8 replicate 3

data_processing:
For ChIP-seq data analysis, raw sequencing reads from the sequencer were demultiplexed and quality controlled with FastQC (v0.11.3). Reads with high quality were then aligned to the Arabidopsis reference genome (TAIR10) with Bowtie (v1.0.0) (Langmead et al., 2009), allowing only uniquely mapping reads with fewer than two mismatches, and duplicated reads were combined into one read.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

source_name: GI ChIPseq at ZT8 replicate 3

growth_protocol: Wildtype, mutant, and transgenic lines used in this study were Arabidopsis thaliana ecotype Columbia 0 (Col- 0). gi-2 (Fowler et al., 1999), GIox (David et al., 2006), PIF5-HA (Lorrain et al., 2008), PIF4-Flash (Pedmale et al., 2016), pif3-1 (SALK_030753) (Kim et al., 2003), pif4-101 (Garlic_114_G06) (Lorrain et al., 2008), pif5-1 (SALK_087012) (Fujimori et al., 2004), pifQ (Leivar et al., 2008), and CCA1::LUC (Salome and McClung, 2005) have been previously described. pif3-1 and pifQ lines were obtained from the Arabidopsis Biological Research Center (ABRC) collection. The gi-2 mutation is a deletion (Δ670-677) that introduces a premature stop codon and is considered a null mutation predicted to encode a nonfunctional 114 aa polypeptide rather than the 1173 aa GI protein (Fowler et al., 1999).  Seeds were chlorine gas sterilized and plated on 0.5x Linsmaier and Skoog medium (LS, Caisson Laboratories) with 0.8% agar (Sigma). After stratification in the dark at 4 °C

extract_protocol:
Approximately 4 g of fresh weight whole seedlings were harvested at the indicated ZTs and cross-linked with 1%
ChIP-seq libraries were prepared with the NuGEN Ovation® Ultralow System as per manufacturer’s instructions.

value: whole seedlings

tag: genotype

value: GI expression from endogenous promoter (pGI;gi-2)

tag: ecotype

value: Columbia 0


title: hFB_HG_113days

source_name: primary human fibroblast, high glucose, 113 days grown

value: male

value: high

value: primary human fibroblast


title: hFB_HG_68days

source_name: primary human fibroblast, high glucose, 68 days grown


title: 2402_M1

value: mandibular salivary gland


title: hFB_HG_56days

source_name: primary human fibroblast, high glucose, 56 days grown


title: hFB_HG_60days

source_name: primary human fibroblast, high glucose, 60 days grown


title: 2402_P1

source_name: parotid salivary gland - dorsal section

value: parotid salivary gland


title: ChIPseq_col_16_rep2

description: Col-0 ChIP seq at ZT16 replicate 2 - control


title: ChIPseq_col_IP_ZT8_rep2

description: Col-0 ChIP seq at ZT8 replicate 2 - control


title: ChIPseq_col_16_rep1

description: Col-0 ChIP seq at ZT16 replicate 1 - control


title: hFB_HG_45days

source_name: primary human fibroblast, high glucose, 45 days grown


title: hFB_HG_107days

source_name: primary human fibroblast, high glucose, 107 days grown


title: 2176_P2

source_name: parotid salivary gland - ventral section


title: hFB_NG_187days

source_name: primary human fibroblast, normal glucose, 187 days grown

value: normal


title: 2176_P1


title: hFB_HG_152days

source_name: primary human fibroblast, high glucose, 152 days grown


title: 2402_M2

source_name: mandibular salivary gland - ventral section


title: ChIPseq_P3_gi_16_rep2

description: PIF3 ChIPseq in gi-2 at ZT16 replicate 2 - quantitative


title: hFB_HG_49days

source_name: primary human fibroblast, high glucose, 49 days grown


title: 2176_M1

source_name: mandibular salivary gland - dorsal section


title: 1309

source_name: glioma

tag: histology

value: MT

value: PM


title: hFB_HG_35days

source_name: primary human fibroblast, high glucose, 35 days grown


title: 2155_P2

value: 33 months' post-experimental challenge


title: 1289

value: OA

tag: grade

value: Female


title: 1291

tag: gender

value: Male


title: 1297

value: AOA

tag: age

value: WT

value: non co-deletion

value: EM


title: ChIPseq_P3_col_16_rep2

description: PIF3 ChIPseq in Col-0 at ZT16 replicate 2 - quantitative

value: whole seedlings

value: Columbia 0


title: hFB_NG_144days

source_name: primary human fibroblast, normal glucose, 144 days grown

value: male


title: 2155_M2


title: hFB_NG_92days

source_name: primary human fibroblast, normal glucose, 92 days grown

value: primary human fibroblast


title: hFB_NG_113days

source_name: primary human fibroblast, normal glucose, 113 days grown


title: ChIPseq_P3_col_16_rep1

description: PIF3 ChIPseq in Col-0 at ZT16 replicate 1 - quantitative


title: hFB_NG_132days

source_name: primary human fibroblast, normal glucose, 132 days grown


title: 1269

value: O

tag: idh mutation

value: co-deletion


title: 1286

tag: 1p19q co-deletion


title: 1239

tag: em/pm subtype


title: 2155_M1

tag: tissue

value: mandibular salivary gland


title: ChIPseq_GIox_ZT8_rep2

description: GI ChIPseq at ZT8 replicate 2

source_name: GI ChIPseq at ZT8 replicate 2

value: GI overexpression (GIox;gi-2)


title: Exd+Hth_input (transient)

status: Public on May 15 2019

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

data_processing:
ChIP-seq reads were aligned to the dm6 genome assembly (excluding Scaffolds) using bowtie version 1.2.2 with the -m1 option.
Peaks were called using macs2 version 2.1.1.20160309 using single tags and q-value thresholds of q1e-2 and q1e-10.
Genome_build: dm6
Supplementary_files_format_and_content: Bed files contain the union peak regions across both replicates at macs2 thresholds q1e-2 and q1e-10, locations of plasmid sequence matches to the genome were excluded. Bedgraph files are 20 bp bins of reads from both replicates, scaled to reads-per-million of reads overlapping peak regions.

organism: Drosophila melanogaster

source_name: Transiently transfected Kc167 cells

growth_protocol: Drosophila Kc167 cells were cultured in Schneider’s medium supplemented with 5% fetal calf serum and antibiotics at 25°C.

extract_protocol:
Cells were harvested and fixed using 1% formaldehyde in PBS for 10 min at 23°C in an Eppendorf Thermomixer at 700 rpm, then sorted using a MoFlo FACS machine (Beckman Coulter) to standardise levels of Hox-GFP proteins across experiments, and finally sonicated to provide chromatin fragments of approximately 500 bp in length. Fragmented chromatin was immunoprecipitated using an anti-GFP antibody (SIGMA, G1544) and DNA was purified using a standard phenol-chloroform extraction.
Sequencing libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara Bio Inc.) in accordance with the sample preparation guide.

treatment_protocol: Cells harvested in log phase were used to seed 10 cm dishes at a density of 2.5 × 10^7 cells per dish and let to adhere. Transfection was performed using FuGENE 6 Transfection Reagent (Promega E2691) according to the manufacturer’s instructions. Dishes were then incubated at 25°C for ~14 hours. After this period, gene expression was induced for 4 hours using CuSO4 at final concentration of 1mM.

value: Kc167 cells

tag: plasmid

tag: chip antibody


title: Exd+Hth_232 (transient)

description:
Exd_Hth.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz

value: Anti-GFP (Sigma, G1544)


title: Exd+Hth_233 (transient)


title: hFB_NG_107days

source_name: primary human fibroblast, normal glucose, 107 days grown

value: normal


title: Hth_209 (transient)

description:
Hth.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz

value: pMT-Hth-eGFP


title: Antp+Hth_75 (transient)

description:
Antp_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: Antp+Hth_76 (transient)


title: 1235

value: Female

value: MT

value: PM


title: Scr+Hth_119 (transient)

description:
Scr_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: 1233

value: OA

value: Male

value: non co-deletion


title: Scr_input (transient)

value: pMT-eGFP-Scr


title: Scr_116 (transient)

description:
Scr.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz


title: Scr_115 (transient)


title: Antp_input (transient)

value: pMT-eGFP-Antp


title: Antp_68 (transient)

description:
Antp.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz


title: hFB_NG_86days

source_name: primary human fibroblast, normal glucose, 86 days grown

value: male

value: primary human fibroblast


title: Dfd+Hth_118 (transient)

description:
Dfd_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: Scr+Hth_input (transient)


title: Scr+Hth_120 (transient)


title: Hth_210 (transient)


title: Antp_67 (transient)


title: Dfd+Hth_117 (transient)


title: Pb+Hth_input (transient)


title: hFB_NG_35days_rep6

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 6


title: Dfd_114 (transient)

description:
Dfd.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz

value: pMT-eGFP-Dfd


title: Dfd_input (transient)


title: Hth_input (transient)


title: Dfd_113 (transient)


title: Pb+Hth_204 (transient)

description:
Pb_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: Lab+Hth_input (transient)


title: Lab+Hth_228 (transient)

description:
Lab_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: hFB_NG_68days

source_name: primary human fibroblast, normal glucose, 68 days grown


title: Pb+Hth_203 (transient)


title: Lab_225 (transient)

description:
Lab.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz

value: pMT-Lab-eGFP


title: Pb_201 (transient)

description:
Pb.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz

value: pMT-eGFP-pb


title: 2155_P1

source_name: parotid salivary gland - dorsal section

value: parotid salivary gland

tag: sample collection time during experimental trial

value: 33 months' post-experimental challenge


title: Pb_input (transient)

value: Kc167 cells


title: Antp+Hth_input (transient)


title: Lab_226 (transient)

value: Anti-GFP (Sigma, G1544)


title: ChIPseq_P3_gi_16_rep1

description: PIF3 ChIPseq in gi-2 at ZT16 replicate 1 - quantitative

value: whole seedlings

value: Columbia 0


title: Hth_stable_input

source_name: Stably transfected Kc167 cells

growth_protocol: Drosophila Kc167 cells, cultured in Schneider’s medium supplemented with 5% fetal calf serum and antibiotics at 25°C, were transfected using FuGENE 6 Transfection Reagent (Promega E2691; according to the manufacturer’s instructions) with pMT-puro-Hox constructs and let undergo selection on the same medium supplemented with 5mg/ml Puromycin to generate stable lines.

extract_protocol:
Induced cells were harvested and fixed using 1% formaldehyde in PBS for 10 min at 23°C in an Eppendorf Thermomixer at 700 rpm, then sorted using a MoFlo FACS machine (Beckman Coulter) to standardise levels of Hox-GFP protein expression across experiments, and finally sonicated to provide chromatin fragments of approximately 500 bp in length. Fragmented chromatin was immunoprecipitated using an anti-GFP antibody (SIGMA G1544) and DNA was purified using a standard phenol-chloroform extraction.
Sequencing libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara Bio Inc.) in accordance with the sample preparation guide.

treatment_protocol: Once stable lines were fully established, we adjusted CuSO4 concentrations and induction times for each line to optimise GFP-Hox expression level prior to FACS sorting.

tag: cell type

value: Kc167 cells with pMT-puro-Hth-eGFP

tag: copper concentration

value: 1 mM CuSO4

tag: induced

value: 18 hour induction


title: Hth_stable_216

description:
Hth_stable.bedgraph.gz
Hox_macs_q1e-2.bed
Hox_macs_q1e-10.bed
Hox_Hth_macs_q1e-2.bed
Hox_Hth_macs_q1e-10.bed
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed


title: Gcm_stable_220

description:
Gcm_stable.bedgraph.gz
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-eGFP-gcm

value: 2.5 mM CuSO4

value: 24 hour induction


title: Hth_stable_215


title: hFB_NG_35days_rep3

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 3

value: male

value: normal


title: Gcm_stable_219


title: AbdB+Hth_stable_241

description:
AbdB_Hth_stable.bedgraph.gz
Hox_Hth_macs_q1e-2.bed
Hox_Hth_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-AbdB


title: Gcm_stable_input


title: AbdB_stable_239

description:
AbdB_stable.bedgraph.gz
Hox_macs_q1e-2.bed
Hox_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-eGFP-AbdB

value: 0.5 mM CuSO4


title: AbdB_stable_240


title: AbdB_stable_input


title: Ubx+Hth+Gcm_stable_input

value: Kc167 cells with pMT-puro-Hth-2A-gcm-2A-eGFP-Ubx


title: hFB_NG_35days_rep5

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 5

value: primary human fibroblast


title: Ubx+Hth+Gcm_stable_238

description:
Ubx_Hth_Gcm_stable.bedgraph.gz
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed


title: AbdB+Hth_stable_242


title: Ubx+Hth+Gcm_stable_237


title: AbdB+Hth_stable_input


title: Ubx+Gcm_stable_236

description:
Ubx_Gcm_stable.bedgraph.gz
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-gcm-2A-eGFP-Ubx


title: hFB_NG_49days

source_name: primary human fibroblast, normal glucose, 49 days grown


title: hFB_NG_72days

source_name: primary human fibroblast, normal glucose, 72 days grown


title: Ubx+Hth_stable_input

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-Ubx


title: hFB_NG_35days_rep2

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 2


title: Ubx+Hth_stable_214

description:
Ubx_Hth_stable.bedgraph.gz
Hox_Hth_macs_q1e-2.bed
Hox_Hth_macs_q1e-10.bed

value: Anti-GFP (Sigma, G1544)


title: Dfd+Hth_input (transient)

tag: cell line

value: Kc167 cells


title: Lab_input (transient)

value: pMT-Lab-eGFP


title: Ubx+Gcm_stable_input


title: Ubx+Hth_stable_213

value: 1 mM CuSO4


title: Ubx+Gcm_stable_235


title: Ubx_stable_217

description:
Ubx_stable.bedgraph.gz
Hox_macs_q1e-2.bed
Hox_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-eGFP-Ubx

value: 18 hour induction


title: Dfd+Hth+Gcm_stable_input

value: Kc167 cells with pMT-puro-Hth-2A-gcm-2A-eGFP-Dfd

value: 3.7 mM CuSO4

value: 22 hour induction


title: Dfd+Hth+Gcm_stable_246

description:
Dfd_Hth_Gcm_stable.bedgraph.gz
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed


title: Dfd+Hth+Gcm_stable_245


title: Ubx_stable_input


title: Dfd+Gcm_stable_249

description:
Dfd_Gcm_stable.bedgraph.gz
Hox_Gcm_macs_q1e-2.bed
Hox_Gcm_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-gcm-2A-eGFP-Dfd

value: 3.2 mM CuSO4

value: 24 hour induction


title: Dfd+Gcm_stable_input


title: Dfd_stable_248

description:
Dfd_stable.bedgraph.gz
Hox_macs_q1e-2.bed
Hox_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-eGFP-Dfd

value: 2 mM CuSO4


title: Dfd+Hth_stable_243

description:
Dfd_Hth_stable.bedgraph.gz
Hox_Hth_macs_q1e-2.bed
Hox_Hth_macs_q1e-10.bed

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-Dfd

value: 2.66 mM CuSO4


title: Dfd+Hth_stable_244


title: Dfd_stable_247


title: Dfd+Gcm_stable_250


title: Ubx_stable_218


title: Dfd+Hth_stable_input


title: ATAC_Ubx_stable_n_65

data_processing:
ATAC-seq reads were aligned to the dm6 genome assembly (excluding Scaffolds) using bowtie version 1.2.2 with the -m1 option. All reads aligning to the + strand  were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp to represent the center of the transposon binding.
The ATAC_Kc.bed contains the open chromatin regions identified with macs2 version 2.1.1.20160309 using single tags with options --shift -50 --extsize 100 -q 1e-2.
For the bedgraph files the reads were extended by 100bp centered on the Tn5 cut-site. The reads were then scaled to rpm for reads within the ATAC_Kc.bed (basal) open regions.
Genome_build: dm6
Supplementary_files_format_and_content: bed files contain the union peak regions present in at least two of the three replicates detected using macs2 --shift -50 --extsize 100 -q 1e-2. Bedgraph files: the reads were extended by 100bp centered on the Tn5 cut-site. The reads were then scaled to rpm for reads within the ATAC_Kc.bed (basal) open regions.

extract_protocol:
Induced cells were sorted using a MoFlo FACS machine (Beckman Coulter) to standardize levels of Hox-GFP protein expression across experiments.
ATAC libraries were prepared for sequencing using standard protocols

value: not induced


title: hFB_NG_45days

source_name: primary human fibroblast, normal glucose, 45 days grown

value: male

value: normal

value: primary human fibroblast


title: hFB_NG_35days_rep1

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 1


title: hFB_NG_35days_rep4

source_name: primary human fibroblast, normal glucose, 35 days grown, technical replicate 4


title: ATAC_Hth_stable_n_61

value: Kc167 cells with pMT-puro-Hth-eGFP


title: ATAC_Hth_stable_n_60


title: ATAC_Ubx+Hth_stable_n_57

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-Ubx


title: ATAC_Hth_stable_i_58

value: 1 mM CuSO4

value: 18 hour induction


title: ATAC_Ubx+Hth_stable_n_56


title: ATAC_Ubx+Hth_stable_i_55


title: Lab+Hth_229 (transient)

value: Kc167 cells

value: Anti-GFP (Sigma, G1544)


title: ATAC_Dfd+Gcm_stable_n_121

value: Kc167 cells with pMT-puro-gcm-2A-eGFP-Dfd


title: ATAC_Dfd+Gcm_stable_n_120


title: ATAC_Ubx_stable_n_64

value: Kc167 cells with pMT-puro-eGFP-Ubx


title: ATAC_Dfd+Gcm_stable_i_119

value: 3.2 mM CuSO4

value: 24 hour induction


title: ATAC_Dfd_stable_i_115

value: Kc167 cells with pMT-puro-eGFP-Dfd

value: 2 mM CuSO4


title: ATAC_Dfd_stable_n_116


title: Pb_202 (transient)

value: pMT-eGFP-pb


title: ATAC_Dfd_stable_i_114


title: ATAC_Ubx_stable_i_63


title: ATAC_Dfd+Gcm_stable_i_118


title: ATAC_Dfd+Hth_stable_n_109

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-Dfd

value: not induced


title: ATAC_Dfd+Hth_stable_i_106

value: 2.66 mM CuSO4

value: 22 hour induction


title: ATAC_Ubx+Hth+Gcm_stable_n_97

value: Kc167 cells with pMT-puro-Hth-2A-gcm-2A-eGFP-Ubx


title: ATAC_Ubx+Hth+Gcm_stable_n_96


title: ATAC_Ubx+Hth+Gcm_stable_i_94

value: 2.5 mM CuSO4


title: ATAC_Ubx+Gcm_stable_n_92

value: Kc167 cells with pMT-puro-gcm-2A-eGFP-Ubx


title: ATAC_Dfd+Hth_stable_n_108


title: ATAC_Ubx+Hth+Gcm_stable_i_95


title: ATAC_Hth_stable_i_59

value: Kc167 cells with pMT-puro-Hth-eGFP

value: 1 mM CuSO4

value: 18 hour induction


title: ATAC_Ubx+Gcm_stable_n_93


title: ATAC_Ubx+Hth_stable_i_54

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-Ubx


title: ATAC_Ubx+Gcm_stable_i_91


title: ATAC_Ubx+Gcm_stable_i_90


title: ATAC_Gcm_stable_n_89

value: Kc167 cells with pMT-puro-eGFP-gcm


title: ATAC_Gcm_stable_n_88


title: ATAC_Gcm_stable_i_87


title: ATAC_Dfd_stable_n_117


title: ATAC_Gcm_stable_i_86


title: ATAC_AbdB+Hth_stable_n_105

value: Kc167 cells with pMT-puro-Hth-2A-eGFP-AbdB


title: ATAC_AbdB+Hth_stable_i_103

value: 24 hour induction


title: ATAC_AbdB+Hth_stable_n_104


title: ATAC_Dfd+Hth_stable_i_107


title: ATAC_AbdB+Hth_stable_i_102


title: Dfd_stable_input

value: Kc167 cells with pMT-puro-eGFP-Dfd


title: ATAC_AbdB_stable_n_101

value: Kc167 cells with pMT-puro-eGFP-AbdB


title: ATAC_AbdB_stable_i_99

value: 0.5 mM CuSO4


title: ATAC_AbdB_stable_i_98


title: ATAC_AbdB_stable_n_100


title: ATAC_Dfd_Hth_Gcm_stable_n_113

value: Kc167 cells with pMT-puro-Hth-2A-gcm-2A-eGFP-Dfd


title: ATAC_Dfd+Hth+Gcm_stable_n_112

value: not induced


title: ATAC_Dfd+Hth+Gcm_stable_i_111

value: 3.7 mM CuSO4


title: ATAC_Kc_10

description:
ATAC_Kc.bedgraph.gz
ATAC_Kc.bed.gz

source_name: Kc167 cells

value: Kc167 cells

value: basal


title: ATAC_Kc_11

description:
ATAC_Kc.bedgraph.gz
ATAC_Kc.bed.gz


title: ATAC_Dfd+Hth+Gcm_stable_i_110

value: 22 hour induction


title: cer2

city: Wenzhou

first: Chaohao

last: Huang

address: Nanbaixiang Town, Ouhai District, Wenzhou City, Zhejiang Province, China 325000, China,

department: Department of Surgery

institute: First affiliated hospital of Wenzhou Medical University

data_processing:
RTA2 software used for basecalling.
Trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
Clean reads were mapped to mouse mm10 reference genome with STAR
The alignment bam files were used as htseq-sount（command of python package HTSeq）
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt files include reads counts for each Sample

source_name: acute pancreatitis_pancreas

extract_protocol:
Pancreas were removed, stored in RNAlater buffer, and RNA was harvested using Pure Link™ RNA Mini Kit（Cat no. 12183018A, invitrogen, Thermo Fisher Scientific）. Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat)(Illumina, MRZG12324)  and NEBNext Ultra Directional RNA Libra（NEB, E7420L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.

tag: strain

tag: genotype

value: wild type

value: post natal week 8

tag: treated with

value: cerulein

value: pancreas


title: cer1


title: cp1

value: polyI:C plus cerulein


title: ctrl1

value: saline


title: ctrl2


title: PATZRU blood 1

first: Gonzalo

last: Lopez

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

hyb_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

data_processing: IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array versions HumanHap550 v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1

label: Cy3, Cy5

source_name: neuroblastoma

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: usi

value: PATZRU

value: blood

value: male

tag: cog risk

value: high

tag: inss stage

tag: mycn status

value: non-amp

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: PAUHYY blood 1

scan_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PAUHYY

tag: tissue

tag: gender

value: diploid (=1.0)


title: PAUFUS blood 1

label_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PAUFUS

value: female


title: PAUFKX blood 1

value: PAUFKX


title: PAUFPG blood 1

value: PAUFPG

value: amp


title: PAUCGP blood 1

value: PAUCGP


title: PAUCKF blood 1

value: PAUCKF


title: PAUCFI blood 1

value: PAUCFI


title: PAUHFW blood 1

value: PAUHFW


title: PATUVB blood 1

value: PATUVB


title: PATUWG blood 1

value: PATUWG

value: blood


title: PAUBDC blood 1

value: PAUBDC

value: high


title: PATUWE blood 1

value: PATUWE

value: male


title: PATUNZ blood 1

value: PATUNZ

value: diploid (=1.0)


title: PAUKLK blood 1

value: PAUKLK


title: PAUAZA blood 1

value: PAUAZA

value: female

value: non-amp

value: hyperdiploid (>1.0)


title: PAUBEC blood 1

value: PAUBEC


title: cp2

value: wild type

tag: age

value: post natal week 8

value: polyI:C plus cerulein

value: pancreas


title: PAUEZU blood 1

value: PAUEZU

value: blood


title: PATNCI blood 1

value: PATNCI

value: high


title: ATAC_Kc_7

description:
ATAC_Kc.bedgraph.gz
ATAC_Kc.bed.gz

value: Kc167 cells

value: basal


title: PATMXC blood 1

value: PATMXC


title: PATNEA blood 1

value: PATNEA

value: diploid (=1.0)


title: PATNGD blood 1

value: PATNGD

value: male


title: PATMPC blood 1

value: PATMPC

value: non-amp


title: PAUGRP blood 1

value: PAUGRP

value: amp


title: PAUAKT blood 1

value: PAUAKT

value: hyperdiploid (>1.0)


title: PAUATG blood 1

value: PAUATG

value: female


title: PAUSPJ blood 1

value: PAUSPJ

value: blood


title: PAUELT blood 1

value: PAUELT

value: high


title: PATMFL blood 1

value: PATMFL


title: PATVSU blood 1

value: PATVSU


title: PAUTLP blood 1

value: PAUTLP


title: PATVNW blood 1

value: PATVNW

value: diploid (=1.0)


title: PATVJX blood 1

value: PATVJX


title: PATWDW blood 1

value: PATWDW

value: male

value: non-amp


title: PAUDDS blood 1

value: PAUDDS


title: PATUEH blood 1

value: PATUEH


title: PAUKAP blood 1

value: PAUKAP

value: amp

value: hyperdiploid (>1.0)


title: PAUAIN blood 1

value: PAUAIN

value: blood


title: PATVHB blood 1

value: PATVHB

value: high


title: PATVZB blood 1

value: PATVZB


title: PATVDI blood 1

value: PATVDI

value: female


title: PAUAHC blood 1

value: PAUAHC

value: diploid (=1.0)


title: PATVWA blood 1

value: PATVWA


title: PAUDFR blood 1

value: PAUDFR


title: PATVTL blood 1

value: PATVTL

value: male


title: PATVDP blood 1

value: PATVDP


title: PAUDIK blood 1

value: PAUDIK

value: non-amp


title: PATVGK blood 1

value: PATVGK

value: amp


title: PAULMT blood 1

value: PAULMT

value: blood

value: hyperdiploid (>1.0)


title: PATMRZ blood 1

value: PATMRZ

value: high


title: PAUBGW blood 1

value: PAUBGW


title: PAUBFU blood 1

value: PAUBFU


title: PAUJLH blood 1

value: PAUJLH


title: PATMSR blood 1

value: PATMSR


title: PAULNF blood 1

value: PAULNF

value: female

value: diploid (=1.0)


title: PAUBWP blood 1

value: PAUBWP

value: male


title: PAUDMU blood 1

value: PAUDMU

value: non-amp


title: PATXYA blood 1

value: PATXYA

value: amp


title: PATTPW blood 1

value: PATTPW

value: blood


title: PATTNA blood 1

value: PATTNA


title: PATTPC blood 1

value: PATTPC

value: high


title: PAURPZ blood 1

value: PAURPZ


title: PAUBVN blood 1

value: PAUBVN


title: PAURPL blood 1

value: PAURPL

value: hyperdiploid (>1.0)


title: PAUFFP blood 1

value: PAUFFP

value: female


title: PAUBSW blood 1

value: PAUBSW

value: diploid (=1.0)


title: PATRXC blood 1

value: PATRXC


title: PATKSX blood 1

value: PATKSX

value: non-amp


title: PATRMB blood 1

value: PATRMB

value: male

value: amp


title: PATRGW blood 1

value: PATRGW

value: blood


title: PATLKI blood 1

value: PATLKI

value: high


title: PATRJG blood 1

value: PATRJG


title: PAUBHV blood 1

value: PAUBHV


title: PATLLI blood 1

value: PATLLI


title: PATRHD blood 1

value: PATRHD

value: hyperdiploid (>1.0)


title: PATTPL blood 1

value: PATTPL


title: PATSPZ blood 1

value: PATSPZ


title: PATSRD blood 1

value: PATSRD


title: PAUCRL blood 1

value: PAUCRL

value: female

value: diploid (=1.0)


title: PATNRI blood 1

value: PATNRI

value: non-amp


title: PATSKE blood 1

value: PATSKE

value: male


title: PATSDR blood 1

value: PATSDR

value: blood

value: amp


title: ATAC_Ubx_stable_i_62

value: Kc167 cells with pMT-puro-eGFP-Ubx

value: 1 mM CuSO4

value: 18 hour induction


title: PATTDY blood 1

value: PATTDY

value: high

value: hyperdiploid (>1.0)


title: PATPXJ blood 1

value: PATPXJ


title: PATPFG blood 1

value: PATPFG


title: PAUSJB blood 1

value: PAUSJB

value: female


title: PAUSFW blood 1

value: PAUSFW


title: PATSVA blood 1

value: PATSVA


title: PATPYK blood 1

value: PATPYK


title: PATNPW blood 1

value: PATNPW

value: male


title: PAURZH blood 1

value: PAURZH

value: blood

value: non-amp


title: PATSXC blood 1

value: PATSXC

value: amp

value: diploid (=1.0)


title: PATXUG blood 1

value: PATXUG

value: high


title: PAUPDY blood 1

value: PAUPDY


title: PATPPK blood 1

value: PATPPK


title: PATYPH blood 1

value: PATYPH


title: PATYWX blood 1

value: PATYWX

value: hyperdiploid (>1.0)


title: PATPET blood 1

value: PATPET

value: female


title: PAUNWR blood 1

value: PAUNWR


title: PAURGD blood 1

value: PAURGD


title: PATKUK blood 1

value: PATKUK


title: PAUPRN blood 1

value: PAUPRN

value: blood


title: PATYWM blood 1

value: PATYWM


title: PATKIR blood 1

value: PATKIR

value: male

value: non-amp


title: PATPPU blood 1

value: PATPPU

value: high

value: diploid (=1.0)


title: PATKPD blood 1

value: PATKPD

value: amp


title: PATKPR blood 1

value: PATKPR

value: hyperdiploid (>1.0)


title: PATKHS blood 1

value: PATKHS

value: female


title: PATJZF blood 1

value: PATJZF


title: PATLCM blood 1

value: PATLCM


title: PATZBH blood 1

value: PATZBH


title: PATJIN blood 1

value: PATJIN

value: blood


title: PATXKG blood 1

value: PATXKG


title: PATXHC blood 1

value: PATXHC

value: male


title: PATXHW blood 1

value: PATXHW

value: non-amp


title: PAUPGV blood 1

value: PAUPGV

value: high


title: PAUNTY blood 1

value: PAUNTY

value: amp


title: PATXHT blood 1

value: PATXHT

value: diploid (=1.0)


title: PATXXI blood 1

value: PATXXI

value: hyperdiploid (>1.0)


title: PATTHA blood 1

value: PATTHA


title: PATTMM blood 1

value: PATTMM


title: PATXXF blood 1

value: PATXXF


title: PATYBZ blood 1

value: PATYBZ

value: blood

value: female


title: PATYMS blood 1

value: PATYMS

value: male


title: PAUMMZ blood 1

value: PAUMMZ


title: PATYDC blood 1

value: PATYDC

value: non-amp


title: PATXWS blood 1

value: PATXWS

value: high


title: PATJHU blood 1

value: PATJHU

value: amp


title: PATWTW blood 1

value: PATWTW

value: diploid (=1.0)


title: PATYMK blood 1

value: PATYMK

value: hyperdiploid (>1.0)


title: PATYEJ blood 1

value: PATYEJ


title: PARASL blood 1

value: PARASL


title: PATKSX tumor 1

value: PATKSX

value: neuroblastoma


title: PATYCM blood 1

value: PATYCM

value: blood

value: female


title: PATNGD tumor 1

value: PATNGD

value: male


title: PATPPU tumor 1

value: PATPPU

value: non-amp


title: PATXDV blood 1

value: PATXDV

value: high


title: PATMFL tumor 1

value: PATMFL

value: amp


title: PATMPC tumor 1

value: PATMPC

value: diploid (=1.0)


title: PATNEA tumor 1

value: PATNEA