title: K14Cre/+ Il12rb2fl/fl naive rep1

value: K14Cre/+ Il12rb2fl/fl

value: untreated


title: SAMPLE 1_genomic DNA from fetal tissues

status: Public on Aug 03 2021

type: genomic

city: Shanghai

first: Ye

last: Liu

state: Shanghai

address: No. 1961, Huashan Road

department: School of Medicine

country: China

institute: The International Peace Maternity and Child Health Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K  Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2; the 'signal intensities.txt' contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: fetal tissues

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fetal tissues samples using Qiagen DNeasy Kit according to standard instructions

tag: sample group

value: ETP

tag: gender

value: female

tag: tissue

value: embryo


title: Il12rb2fl/fl Aldara rep2

type: SRA

city: Zürich

first: Pascale

last: Zwicky

address: Wintherturerstrasse 190

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
The raw reads were aligned to mouse genome build GRCm38 using the STAR aligner, with FeatureCounts (part of Subread package) used to calculate read counts per gene based on GENCODE gene annotation version M16
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: skin

extract_protocol:
Total RNA of IF keratinocytes was isolated using the Qiagen RNeasy Micro kit according to the manufacturers’ protocol.
Library preparation was performed according to illumina`s “smartseqII” protocol (Picelli et al., 2014). The Novaseq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocols. Sequencing was single end 100bp.

tag: strain

value: skin

tag: cell type

value: interfollicular keratinocytes

tag: genotype

tag: treatment

value: Aldara (topical) - day 1


title: BAZ1B WT Rep3 - D6

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCh39/hg38 + Gencode 31
Supplementary_files_format_and_content: raw gene counts

growth_protocol: Cells were grown in expansion media and the cells were allowed to mature in differentiation media. Cells were taken at D0 and D6 of differentiation.

extract_protocol: The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

tag: cell line

tag: differentiation day

value: BAZ1B WT


title: WT rep3

city: London

first: Yi-Fang

last: Wang

address: Du Cane Road

country: United Kingdom

institute: MRC LMS

description:
Expression profile of WT E14 ES cells
Gene_featurecounts.txt

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat2 (2.0.11) with parameters -r 100 --library-type fr-firststrand -N 2 --b2-very-sensitive --b2-L 25 -p 8
Gene annotations were obtained from Ensembl Mouse genome (NCBIM37). Gene-based read count and ERCC count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes Gene counts for each Sample

molecule: polyA RNA

source_name: WT E14 ES cells

growth_protocol: Cells were grown in 15% FBS

extract_protocol:
Cells were collected and counted. RNA was extracted from 2 million cells using Trizol (ThermoFisher), 2 ul of a 1:10 dilution of ERCC Spike-in Mix (ThermoFisher) were added to each sample.
500 ng of RNA were used to prepare a polyA RNA library using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Embryonic stem cells

value: wild type


title: BAZ1B WT Rep1 - D0


title: CK-3

city: haikou

first: zhang

last: chuanling

address: renmin Road NO.58

institute: Hainan University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Hisat2 mapping to reference genome
count counting
Genome_build: Tair10
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Six days in MS medium

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: silver nanoparticles and silver ions

tag: ecotype

value: Columbia

value: six days

tag: agent

value: CK

tag: adenovirus

value: leaves


title: Ag+-1

value: Ag+


title: Rep1_TFIIS2-2_IP

status: Public on Aug 02 2021

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology

library_source: genomic

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Genome_build: HGAP3_Tb427v9.2
Supplementary_files_format_and_content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

organism: Trypanosoma brucei brucei

source_name: cultured cells

growth_protocol: Cell lines were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). Cell lines with tagged proteins were grown in the presence of 5 µg/ml blasticidin.

extract_protocol:
Briefly, 4 x 10^8 parasites were harvested and fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 s on, 30 s off) using the high setting on a Bioruptor sonicator (Diagenode). Input samples were taken before incubating the rest of the cell lysates overnight with 10 µg rabbit anti-GFP antibody (Thermo Fisher Scientific) and Protein G Dynabeads. The beads were washed and the DNA eluted from them was treated with RNAse and Proteinase K. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were constructed using 0.5-20 ng of immunoprecipitated or input DNA. Following blunt-ending and poly(A)-tailing, NEXTflex (Bioo Scientific) adapters containing barcodes were ligated to each DNA fragment. Fragments were size selected using AMPure beads (Beckman Coulter). The amount of DNA in the resulting libraries was quantified by Qubit fluorometer using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution was assessed by 2100 Bioanalyzer Instrument (Agilent Technologies) using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Ideally, the libraries had a peak at 300 bp (~ 150 bp fragment DNA + ~ 150 bp adapter sequence). Libraries were sequenced on Illumina MiniSeq, HiSeq or NextSeq. In all cases, 75 bp paired-end sequencing was performed.

tag: antibody

value: anti-GFP

value: Lister 427

tag: developmental stage

value: bloodstream slender form

tag: chromatin factor


title: Rep1_PHD5_IP


title: Rep1_PHD4_input


title: BAZ1B KO Rep2 - D0

value: BAZ1B KO


title: Rep1_ZCW1_input


title: Rep1_ZCW1_IP


title: Rep1_PHD2_input


title: Rep1_PHD1_IP


title: Rep1_untagged_IP

value: untagged


title: Rep1_PHD1_input


title: Rep1_EAF6_IP


title: Rep1_JMJ2_IP


title: Rep1_JMJ2_input


title: BAZ1B KO Rep3 - D0


title: Rep1_HDAC3_IP


title: Rep1_ELP3b_input


title: Il12rb2fl/fl naive  rep1

value: untreated


title: Rep1_CRD1_IP


title: Rep1_BDF4_input


title: Rep1_BDF5_input


title: Il12rb2fl/fl naive  rep3

value: skin


title: Rep1_BDF4_IP


title: Rep1_CRD1_input


title: Rep1_BDF2_input


title: Rep1_HDAC3_input


title: Rep1_AGO1_IP


title: Rep1_PHD5_input


title: Rep1_AGO1_input


title: WT rep1


title: CK-1


title: Rep1_EAF6_input


title: Rep1_untagged_input


title: LM_PATU8902_sgSMAD4_2_rep3

city: BOSTON

first: William

middle: C

last: Hahn

state: Massachusetts

address: 450 Brookline Avenue, Dana 1538

institute: DANA-FARBER CANCER INSTITUTE

description:
gGFP_3_vs_gSMAD4_5.csv
gGFP_4_vs_gSMAD4_5.csv

data_processing:
Image analysis and base calling were done using the standard Illumina pipeline, and then demultiplexed into FASTQ files. Reads were aligned with Tophat 2.0.2(Ghosh and Chan, 2016) using the human hg19 transcriptome and genome annotation from the UCSC genome browser. Transcripts were assembled and tested for abundance and differential expression using HTseq(Anders et al., 2015) and DEseq2(Love et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: read counts and differential expression

extract_protocol:
RNA-seq was performed on in vitro and in vivo cell and tumor samples. Specifically, we performed RNA-seq on the following in vitro samples from parental and derivative cell lines: (1) PANC1 and PATU8902 cells with SMAD4 gene-deletion via CRISPR-Cas9 using 2 SMAD4-targeting sgRNA or a control sgRNA, and (2) HPAC and PANC0327 cells with restored SMAD4 expression or expression of Luciferase as negative control. Each parental or derivative cell line was treated either with vehicle (1mg/mL BSA, 4mM HCl) or 10ng/mL TGFß for 24 hours. For in vivo conditions, we performed RNA-seq on the following tumors: (1) matched subcutaneous xenograft tumors from isogenic Lac-Z or SMAD4-expressing HPAC cells harvested at ~300mm3, (2) matched xenograft tumors formed from PATU8902 cells expressing a doxycycline-inducible shSMAD4 shRNA, or its corresponding seed control shRNA (shSMAD4 c7-9), and (3) micro-dissected metastatic tumor from isogenic PATU8902 cells with SMAD4-WT or SMAD4-null genetic status. To obtain matched xenograft tumors formed from PATU8902 cells with dox-inducible shSMAD4, we generated 4 PATU8902 derivative lines, expressing dox-inducible shSMAD4_1, shSMAD4_2, or their corresponding seed control hairpins. Xenograft tumors were first formed in the absence of shRNA knockdown, and when tumors reached ~100mm3, shRNA was induced for 6 days with doxycycline diet (625ppm for 0.6-2 mg/kg in diet) prior to tumor harvest. Snap frozen xenograft tumors were transitioned in RNAlater-Ice (Life Technologies) at -20°C overnight prior to RNA extraction using RNeasy Plus Mini kit (Qiagen). Metastatic tumors from isogenic PATU8902 cell pairs with SMAD4-WT or SMAD4-null genetic status were micro-dissected from mouse lungs embedded in OCT compound (Tissue Tek), and total RNA was extracted using RNeasy Micro kit (Qiagen).
Libraries were prepared by tagmentation (Nextera XT DNA Sample Preparation Kit, Illumina) using index primers (Nextera XT Index kit, Illumina) to facilitate multiplexing

tag: smad4 status

value: KO

tag: tgfb

tag: in vitro/in vivo

value: in vivo

tag: source location

value: Lung Metastasis


title: Rep1_TFIIS2-2_input


title: Rep1_PHD4_IP


title: Rep1_ELP3b_IP


title: LM_PATU8902_sgSMAD4_2_rep1


title: LM_PATU8902_sgGFP_4_rep3

value: WT


title: LM_PATU8902_sgSMAD4_1_rep1


title: LM_PATU8902_sgGFP_3_rep3


title: LM_PATU8902_sgGFP_4_rep1

description:
gCTRL_vs_gSMAD4_5.csv
gGFP_3_vs_gGFP_4.csv


title: LM_PATU8902_sgGFP_3_rep2


title: Input_shPAX9_1

city: Chicago

first: Lu

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq ATAC-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9 and STAR version 2.5.2.  Only uniquely mapping reads with at most two mismatches were retained.
ATAC-seq reads were aligned to UCSC hg19 using BWA version 0.7.12. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: cells were maintained with DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. For ATAC-seq, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience). 50K to 100K nuclei were then centrifuge (pre-chilled) at 500 g for 10 min. Supernatant was then removed and the nuclei were resuspended in 50 uL of tagmentated DNA by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer shaking at 1,000 rpm, and then cleaned up by the MiniElute reaction clean up kit (Qiagen).
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE.
ATAC-seq: Tagmentated DNA was amplified with barcode primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 50M PE reads (25M in each direction) per sample.

treatment_protocol: Cells were treated with either DMSO or HDAC1/2 inhibitor MERCK60 or EZH2 inhibitior GSK126 for 24 to 96 hours.

value: small cell lung cancer

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: cells transduced with PAX9 shRNA #1

value: PAX9 depletion


title: LM_PATU8902_sgGFP_3_rep1

description:
gCTRL_vs_gSMAD4_2.csv
gGFP_3_vs_gGFP_4.csv


title: Rep1_HAT2_input

tag: strain


title: subQ_PATU8902_shSMAD4_956_rep1

value: KD

value: subcutaneous tumor


title: subQ_PATU8902_shSMAD4_956-_C7-9_rep1


title: Rep1_BDF3_IP

value: anti-GFP


title: subQ_PATU8902_shSMAD4_458_rep3


title: Rep1_BDF2_IP

value: Lister 427


title: subQ_PATU8902_shSMAD4_458_rep2


title: Rep1_PHD2_IP

value: bloodstream slender form


title: Rep1_ELP3a_IP


title: Rep1_BDF5_IP


title: subQ_PATU8902_shSMAD4_458_C7-9_rep2


title: subQ_PATU8902_shSMAD4_458_C7-9_rep3


title: Rep1_HAT2_IP


title: SubQ_HPAC_FUW-SMAD4_rep2

source_name: HPAC

value: HPAC

value: OVX


title: LM_PATU8902_sgSMAD4_2_rep2


title: LM_PATU8902_sgSMAD4_1_rep3


title: Rep1_BDF3_input


title: subQ_PATU8902_shSMAD4_956_rep2


title: LM_PATU8902_sgGFP_4_rep2


title: subQ_PATU8902_shSMAD4_956_rep3


title: Rep1_ELP3a_input


title: subQ_PATU8902_shSMAD4_956_C7-9_rep3


title: subQ_PATU8902_shSMAD4_458_rep1


title: SubQ_HPAC_FUW-LacZ_rep1


title: SubQ_HPAC_FUW-SMAD4_rep1


title: SubQ_HPAC_FUW-SMAD4_rep3


title: subQ_PATU8902_shSMAD4_956_C7-9_rep2


title: LM_PATU8902_sgSMAD4_1_rep2


title: PATU8902_gSMAD4_B_vehicle_rep_1

description: PATU8902_gSMAD4_B_vehicle_VS_PATU8902_gSMAD4_E_vehicle.txt

value: in vitro


title: PATU8902_gSMAD4_B_TGFb_rep_2

value: added


title: SubQ_HPAC_FUW-LacZ_rep2


title: SubQ_HPAC_FUW-LacZ_rep3


title: PATU8902_gSMAD4_E_TGFb_rep_2

description: PATU8902_gSMAD4_E_TGFb_VS_PATU8902_gSMAD4_E_vehicle.txt

value: KO


title: PATU8902_gSMAD4_E_vehicle_rep_2


title: subQ_PATU8902_shSMAD4_458_C7-9_rep1

value: in vivo


title: PATU8902_gEmptyT_vehicle_rep_1

description: PATU8902_gSMAD4_B_vehicle_VS_PATU8902_gEmptyT_vehicle.txt


title: PATU8902_gEmptyT_TGFb_rep_2

description:
PATU8902_gSMAD4_B_TGFb_VS_PATU8902_gEmptyT_TGFb.txt
PATU8902_gEmptyT_TGFb_VS_PATU8902_gEmptyT_vehicle.txt


title: PATU8902_gEmptyT_TGFb_rep_1


title: PATU8902_gEmptyT_vehicle_rep_2


title: PATU8902_gSMAD4_B_TGFb_rep_1

description: PATU8902_gSMAD4_B_TGFb_VS_PATU8902_gSMAD4_B_vehicle.txt


title: PATU8902_gSMAD4_E_vehicle_rep_1

description: PATU8902_gSMAD4_E_vehicle_VS_PATU8902_gEmptyT_vehicle.txt


title: PANC1_gSMAD4_E_vehicle_rep1

description: PANC1_gSMAD4_E_vehicle_VS_PANC1_gEmptyT_vehicle.txt


title: PANC1_gSMAD4_E_vehicle_rep2

description: PANC1_gSMAD4_E_vehicle_VS_PANC1_gSMAD4_B_vehicle.txt


title: PANC1_gSMAD4_E_TGFb_rep1

description: PANC1_gSMAD4_E_TGFb_VS_PANC1_gEmptyT_TGFb.txt


title: PANC1_gSMAD4_B_vehicle_rep2

description:
PANC1_gSMAD4_B_vehicle_VS_PANC1_gEmptyT_vehicle.txt
PANC1_gSMAD4_B_TGFb_VS_PANC1_gSMAD4_B_vehicle.txt


title: PANC1_gSMAD4_B_TGFb_rep1

description:
PANC1_gSMAD4_B_TGFb_VS_PANC1_gSMAD4_E_TGFb.txt
PANC1_gSMAD4_B_TGFb_VS_PANC1_gEmptyT_TGFb.txt


title: PATU8902_gSMAD4_E_TGFb_rep_1

description: PATU8902_gSMAD4_E_TGFb_VS_PATU8902_gSMAD4_B_TGFb.txt


title: PATU8902_gSMAD4_B_vehicle_rep_2

description: PATU8902_gSMAD4_E_TGFb_VS_PATU8902_gEmptyT_TGFb.txt


title: PANC1_gEmptyT_vehicle_rep1

description: PANC1_gEmptyT_TGFb_VS_PANC1_gEmptyT_vehicle.txt


title: PANC1_gSMAD4_B_TGFb_rep2


title: PANC1_gSMAD4_B_vehicle_rep1


title: PANC1_gEmptyT_TGFb_rep2


title: PANC0327_SMAD4_TGFb_rep_2

description:
PANC0327_SMAD4_TGFb_VS_PANC0327_LUC_vehicle.txt
PANC0327_SMAD4_TGFb_VS_PANC0327_LUC_TGFb.txt


title: PANC0327_SMAD4_vehicle_rep_2

description:
PANC0327_SMAD4_vehicle_VS_PANC0327_LUC_vehicle.txt
PANC0327_SMAD4_TGFb_VS_PANC0327_SMAD4_vehicle.txt


title: PANC1_gEmptyT_TGFb_rep1


title: PANC0327_LUC_vehicle_rep_1

description: PANC0327_LUC_TGFb_VS_PANC0327_LUC_vehicle.txt


title: PANC0327_SMAD4_vehicle_rep_1


title: PANC0327_LUC_TGFb_rep_1

description:
PANC0327_SMAD4_TGFb_VS_PANC0327_LUC_TGFb.txt
PANC0327_LUC_TGFb_VS_PANC0327_LUC_vehicle.txt


title: HPAC_FUW-SMAD4_vehicle_rep2


title: PANC1_gSMAD4_E_TGFb_rep2

description: PANC1_gSMAD4_E_TGFb_VS_PANC1_gSMAD4_E_vehicle.txt


title: PANC0327_LUC_vehicle_rep_2


title: HPAC_FUW-LacZ_TGFb_rep2

description:
LacZ_TGFb_vs_SMAD4_TGFb.csv
LacZ_vehicle_vs_LacZ_TGFb.csv


title: HPAC_FUW-LacZ_vehicle_rep2

description:
LacZ_vehicle_vs_LacZ_TGFb.csv
LacZ_vehicle_vs_SMAD4_vehicle.csv


title: HPAC_FUW-LacZ_vehicle_rep1


title: HPAC_FUW-LacZ_TGFb_rep1


title: PANC1_gEmptyT_vehicle_rep2


title: HPAC_FUW-SMAD4_vehicle_rep1


title: HPAC_FUW-SMAD4_TGFb_rep1


title: 17-G3-LCMV-M-MDSC

city: Cambridge

first: Gozde

last: Kar

address: Cambridge

institute: AstraZeneca

description: fixed M-MDSC isolated fromLCMV infected mice

data_processing:
Reads were mapped to Mus musculus genome genome using Star version 2.6 for each sample.
Uniquely mapped reads were counted using htseq-count version 0.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from 0.5-1 million macrophages using the Direct-zol RNA Microprep (Zymo Research, Irvine, CA). RNA quantity was determined using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and the quality was validated using the TapeStation RNA ScreenTape (Agilent, Santa Clara, CA).
500 ng of DNAse I treated, total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen, Vienna, Austria). Library quantity was determined using qPCR (KAPA Biosystem, Wilmington, MA). Overall library size was determined using the Agilent TapeStation and the DNA High Sensitivity D5000 ScreenTape (Agilent, Santa Clara, CA). Equimolar amounts of each sample library were pooled, denatured and High-Output

treatment_protocol: See "disease state" in the sample section

tag: tissue

value: spleen

tag: cell type

value: M-MDSC

tag: disease state

value: 14 days after LCMV being infected


title: 15-G3-LLC-M-MDSC

description: fixed M-MDSC isolated from LLC TM mice

source_name: fixed M-MDSC isolated from LLC TM mice

value: 21 days after LLC tumor being implanted


title: 5-G1-LCMV-M-MDSC

source_name: fixed M-MDSC isolated fromLCMV infected mice


title: 11-G2-LCMV-M-MDSC


title: 3-G1-LLC-M-MDSC

description: fixed M-MDSC isolated from LLC TM mice


title: 13-G3-naïve-M-MDSC

description: fixed M-MDSC isolated from naïve mice

source_name: fixed M-MDSC isolated from naïve mice

value: naïve


title: HPAC_FUW-SMAD4_TGFb_rep2

tag: cell line


title: PANC0327_SMAD4_TGFb_rep_1


title: 9-G2-LLC-M-MDSC

description: fixed M-MDSC isolated from LLC TM mice


title: B2G02_2moNoH13_cumulus

city: Kobe

first: Tomoya

middle: S

last: KITAJIMA

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description:
count_GENCODEvM15_oocyte_cumulus_rep2.txt.gz
rpkm_GENCODEvM15_oocyte_cumulus_rep2.txt.gz

data_processing:
fastq files were aligned to mouse reference genome GRCm38 using the Hisat2 v2.0.5
BAM files resulting from the alignments were summarized to genes using the featureCounts v1.5.1 with the parameters '-M -O --fraction'
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

source_name: an oocyte surrownding cumulus cells pool of a fully grown follicle

extract_protocol:
single oocyte or their surrownding cumulus cells pool were lysed using cell lysis buffer [10 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher Scientific), and RNase-free water (TAKARA)] in 0.2 mL single tube.
RamDA-seq sequencing libraries were constructed by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0). However, to adapt to the manually picked single oocyte and their cumulus cells, the reaction volume from the cell lysis to the genomic DNA digestion step was modified. For details, refer to the protocol in "Aging-associated effects on transcriptome landscape and chromosome cohesion in single oocytes are influenced by life stage and calorie restriction".

tag: age

value: 2 months with AL diet without hyperovulation

tag: mouse

tag: oocyte-cumulus complex


title: B2H02_2moNoH13_cumulus


title: B2E02_2moNoH13_cumulus


title: B2F02_2moNoH13_cumulus


title: SHSY5Y - Flag2 magnetic beads rep1

city: Ulm

first: Karin

middle: M

last: Danzer

state: Baden-Wurttemberg

address: University of Ulm Campus, Building N24, R3306 Albert-Einstein-Allee 11

department: Department of Neurology

country: Germany

institute: University of Ulm / DZNE, Ulm

data_processing:
Basecalls performed using CASAVA version 1.4.
For each sample, after quality control as mentioned above, reads were separately aligned to the latest human genome (NCBI; GRCh38) using Bowtie with the parameter “-m 1” to retain uniquely mapped reads only. The R packages ChIPQC v1.20.0 and PhantomPeakQualTools v1.2.2 were used to confirm the quality of the aligned bam files based on the ChIP-seq guidelines by ENCODE consortium (NSC >= 1.05; RSC >= 0.8, Qtag={-2,-1,0,1,2}). QC-confirmed bam files were subject to differential peak calling using MACS v1.4.220 with the following parameters: -t Sample.sam -c Control.sam --format SAM -g hs -B -S --call-subpeaks. Peak annotation and visualization were done using the R packages ChIPseeker v1.20.0 and clusterProfiler v3.12.0, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bedgraph files generated from peak files built from reads mapping uniquely to the genome contain coordinates of the genomic location of each peak called

source_name: SHSY5Y neuroblastoma cell line

growth_protocol: Human SHSY-5Y neuroblastoma cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % heat-inactivated fetal bovine serum (FBS) and 1 % penicillin/streptomycin (Gibco-Invitrogen, Carlsbad, CA).

extract_protocol:
After cross-linking and fractionation steps, PARIS DNA binding sites were enriched by immunoprecipitation of the DNA-PARIS complexes using magnetic beads and flag antibodies. The same protocol was used for the control sample. Protein-bound DNA was extracted for the preparation of sequencing libraries.
CHIP-seq high sensitivity kit (ab185908, Abcam) was further used for ChIP-Seq library preparation according to manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq 2000 sequencer.

treatment_protocol: For transient transfection, cells were transfected with indicated amounts of either flag-PARIS or flag using Fugene HD (Promega, Madison, WI) according to manufacturer’s instructions. After 48 hours incubation, SHSY-5Y cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and 125 mM glycine were then added to inactivate the formaldehyde.

value: bone marrow-derived metastatic cancer tissue

value: Flag antibody

tag: genotype

value: flag

tag: treatment

value: transfected with flag


title: SHSY5Y - PARIS-Flag2 magnetic beads rep1

value: PARIS-flag

value: transfected with flag-PARIS


title: PANC0327_LUC_TGFb_rep_2

value: WT


title: B2B02_2moNoH12_cumulus


title: B2D02_2moNoH12_cumulus


title: B2H01_2moNoH11_cumulus


title: 7-G2-naïve-M-MDSC

description: fixed M-MDSC isolated from naïve mice


title: B2G01_2moNoH11_cumulus


title: B2A02_2moNoH12_cumulus


title: B1H06_2moNoH9_cumulus


title: B2A01_2moNoH10_cumulus


title: B2E01_2moNoH11_cumulus


title: B2D01_2moNoH10_cumulus


title: B1F06_2moNoH9_cumulus


title: B2C01_2moNoH10_cumulus


title: B1D06_2moNoH8_cumulus


title: B2B01_2moNoH10_cumulus


title: B2C02_2moNoH12_cumulus


title: B2F01_2moNoH11_cumulus


title: B1C06_2moNoH8_cumulus


title: B1H05_2moNoH7_cumulus


title: B1G05_2moNoH7_cumulus


title: B1E05_2moNoH7_cumulus


title: B1B06_2moNoH8_cumulus


title: B1E06_2moNoH9_cumulus


title: B1A06_2moNoH8_cumulus


title: B1C05_2moNoH6_cumulus


title: B1G06_2moNoH9_cumulus


title: B1F05_2moNoH7_cumulus


title: B1B05_2moNoH6_cumulus


title: B1D05_2moNoH6_cumulus


title: B1A05_2moNoH6_cumulus


title: B2G12_14mo41_cumulus

value: 14 months with AL diet


title: B2B12_14mo40_cumulus


title: B2E12_14mo41_cumulus


title: B2H12_14mo41_cumulus


title: B1D12_14mo37_cumulus


title: B2D12_14mo40_cumulus


title: B1C12_14mo37_cumulus


title: B1E12_14mo38_cumulus


title: B2A12_14mo40_cumulus


title: B1A12_14mo37_cumulus


title: B2F12_14mo41_cumulus


title: B2G05_9mo24_cumulus

value: 9 months with AL diet


title: B2F05_9mo24_cumulus


title: B1H09_9mo22_cumulus


title: B2E05_9mo24_cumulus


title: B1G12_14mo39_cumulus


title: B1F12_14mo38_cumulus


title: B1D09_9mo21_cumulus


title: B1E09_9mo22_cumulus


title: B1C09_9mo21_cumulus


title: B1A09_9mo21_cumulus


title: B2B05_9mo23_cumulus


title: B1G09_9mo22_cumulus


title: B1H12_14mo39_cumulus


title: B2G07_4mo29_cumulus

value: 4 months with AL diet


title: B2F07_4mo29_cumulus


title: B1B12_14mo37_cumulus


title: B2D05_9mo23_cumulus


title: B2E07_4mo29_cumulus


title: B2D07_4mo28_cumulus


title: B1F09_9mo22_cumulus


title: B2B07_4mo28_cumulus


title: B2A07_4mo28_cumulus


title: B2G06_4mo27_cumulus


title: B2H05_9mo24_cumulus


title: B2H06_4mo27_cumulus


title: B2C06_4mo26_cumulus


title: B2E06_4mo27_cumulus


title: B2D06_4mo26_cumulus


title: B2A06_4mo26_cumulus


title: B2A05_9mo23_cumulus


title: B1H10_4mo25_cumulus


title: B2C07_4mo28_cumulus


title: B2C05_9mo23_cumulus


title: B1B09_9mo21_cumulus


title: B2F06_4mo27_cumulus


title: B2H07_4mo29_cumulus


title: B2B06_4mo26_cumulus


title: B1H04_4mo5_cumulus


title: B1G04_4mo5_cumulus


title: B1F04_4mo5_cumulus


title: B1E04_4mo5_cumulus


title: B1F10_4mo25_cumulus


title: B1D04_4mo5_cumulus


title: B1A04_4mo5_cumulus


title: B1B04_4mo5_cumulus


title: B1G03_4mo4_cumulus


title: B1B10_4mo25_cumulus


title: B1F03_4mo4_cumulus


title: B1B03_4mo3_cumulus


title: B1C03_4mo3_cumulus


title: B1C04_4mo5_cumulus


title: B1D03_4mo3_cumulus


title: B2G11_2mo36_cumulus

value: 2 months with AL diet


title: B1H03_4mo4_cumulus


title: B1G10_4mo25_cumulus


title: B1E03_4mo4_cumulus


title: B1C10_4mo25_cumulus


title: B2D11_2mo35_cumulus


title: B2H11_2mo36_cumulus


title: B1H11_2mo34_cumulus


title: B2A11_2mo35_cumulus


title: B2E11_2mo36_cumulus


title: B1E11_2mo34_cumulus


title: B1E10_4mo25_cumulus


title: B2F11_2mo36_cumulus


title: B1D10_4mo25_cumulus


title: B2B11_2mo35_cumulus


title: B1G11_2mo34_cumulus


title: B1G01_2mo2_cumulus


title: B1F01_2mo2_cumulus


title: B2C11_2mo35_cumulus


title: B1E01_2mo2_cumulus


title: B1C11_2mo34_cumulus


title: B2G02_2moNoH13_oocyte

source_name: a single oocyte of a fully grown follicle


title: B1A03_4mo3_cumulus


title: B1F11_2mo34_cumulus


title: B1A01_2mo1_cumulus


title: B2C12_14mo40_cumulus


title: B1H01_2mo2_cumulus


title: B1B11_2mo34_cumulus


title: B1A11_2mo34_cumulus


title: B1D11_2mo34_cumulus


title: B1D01_2mo1_cumulus


title: B1C01_2mo1_cumulus


title: B2A02_2moNoH12_oocyte


title: B2C02_2moNoH12_oocyte


title: B2H01_2moNoH11_oocyte


title: B2H02_2moNoH13_oocyte


title: B1B01_2mo1_cumulus


title: B1A10_4mo25_cumulus


title: B2E02_2moNoH13_oocyte


title: B2D02_2moNoH12_oocyte


title: B1G06_2moNoH9_oocyte


title: B2E01_2moNoH11_oocyte


title: B2A01_2moNoH10_oocyte


title: B2F02_2moNoH13_oocyte


title: B1A06_2moNoH8_oocyte


title: B1C06_2moNoH8_oocyte


title: B1F06_2moNoH9_oocyte


title: B1H05_2moNoH7_oocyte


title: B2G01_2moNoH11_oocyte


title: B2B02_2moNoH12_oocyte


title: B1E06_2moNoH9_oocyte


title: B2F01_2moNoH11_oocyte


title: B2C01_2moNoH10_oocyte


title: B1E05_2moNoH7_oocyte


title: B2D01_2moNoH10_oocyte


title: B1A05_2moNoH6_oocyte


title: B1G05_2moNoH7_oocyte


title: B1F05_2moNoH7_oocyte


title: B2H12_14mo41_oocyte


title: B2G12_14mo41_oocyte


title: B1B05_2moNoH6_oocyte


title: B1H06_2moNoH9_oocyte


title: B2E12_14mo41_oocyte


title: B2D12_14mo40_oocyte


title: B1B06_2moNoH8_oocyte


title: B1D06_2moNoH8_oocyte


title: B2B01_2moNoH10_oocyte


title: B2C12_14mo40_oocyte


title: B2F12_14mo41_oocyte


title: B1F12_14mo38_oocyte


title: B1G12_14mo39_oocyte


title: B1E12_14mo38_oocyte


title: B1B12_14mo37_oocyte


title: B2A12_14mo40_oocyte


title: B1C05_2moNoH6_oocyte


title: B2D05_9mo23_oocyte


title: B1D05_2moNoH6_oocyte


title: B1D09_9mo21_oocyte


title: B1D12_14mo37_oocyte


title: B2G07_4mo29_oocyte


title: B2H07_4mo29_oocyte


title: B2E07_4mo29_oocyte


title: B1H12_14mo39_oocyte


title: B2F07_4mo29_oocyte


title: B2G05_9mo24_oocyte


title: B2F05_9mo24_oocyte


title: B2E05_9mo24_oocyte


title: B1F09_9mo22_oocyte


title: B1C09_9mo21_oocyte


title: B1A12_14mo37_oocyte


title: B1C12_14mo37_oocyte


title: B1B09_9mo21_oocyte


title: B1H09_9mo22_oocyte


title: B2C05_9mo23_oocyte


title: B1G09_9mo22_oocyte


title: B1A09_9mo21_oocyte


title: B2G06_4mo27_oocyte


title: B2F06_4mo27_oocyte


title: B2B05_9mo23_oocyte


title: B2B12_14mo40_oocyte


title: B2H05_9mo24_oocyte


title: B2A06_4mo26_oocyte


title: B2C06_4mo26_oocyte


title: B2A05_9mo23_oocyte


title: B2C07_4mo28_oocyte


title: B1F10_4mo25_oocyte


title: B2A07_4mo28_oocyte


title: B1D10_4mo25_oocyte


title: B1B10_4mo25_oocyte


title: B1H04_4mo5_oocyte


title: B1C10_4mo25_oocyte


title: B1F04_4mo5_oocyte


title: B1E04_4mo5_oocyte


title: B1D04_4mo5_oocyte


title: B1C04_4mo5_oocyte


title: B2D06_4mo26_oocyte


title: B1E10_4mo25_oocyte


title: B2H06_4mo27_oocyte


title: B1A04_4mo5_oocyte


title: B2E06_4mo27_oocyte


title: B1H10_4mo25_oocyte


title: B1G03_4mo4_oocyte


title: B1A10_4mo25_oocyte


title: B2B07_4mo28_oocyte


title: B1B03_4mo3_oocyte


title: B1A03_4mo3_oocyte


title: B1G04_4mo5_oocyte


title: B2D07_4mo28_oocyte


title: B2G11_2mo36_oocyte


title: B2E11_2mo36_oocyte


title: B1E09_9mo22_oocyte


title: B2B06_4mo26_oocyte


title: B2H11_2mo36_oocyte


title: B1G10_4mo25_oocyte


title: B1B04_4mo5_oocyte


title: B1D11_2mo34_oocyte


title: B1C11_2mo34_oocyte


title: B1B11_2mo34_oocyte


title: B1E11_2mo34_oocyte


title: B1D03_4mo3_oocyte


title: B1H03_4mo4_oocyte


title: B1B01_2mo1_oocyte


title: B1H11_2mo34_oocyte


title: B1C03_4mo3_oocyte


title: B2A11_2mo35_oocyte


title: B1F03_4mo4_oocyte


title: B2D11_2mo35_oocyte


title: B1G11_2mo34_oocyte


title: B2F11_2mo36_oocyte


title: B1G01_2mo2_oocyte


title: B2C11_2mo35_oocyte


title: B1A11_2mo34_oocyte


title: cDMD.A5 cardiac snRNA-seq

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

description: single-nucleus RNAseq

data_processing:
The Cell Ranger Single-Cell Software Suit was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
Doublets were identified using Scrublet and removed from downstream analysis
For quantity filtering, we removed cells that had more than 2500 or fewer than 200 detected genes. We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. To account for variation in the number of genes and UMI detected in each cell, we normalized the scaled expression matrix using the ScaleData function and set the vars.to.regress to nUMI and nGenes.  IntegrateData function implemented in Seurat V3 was used to correct batch effects between samples and to merge samples into one Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

source_name: cadiac nuclei

extract_protocol:
For WT and DMD samples, we pooled two hearts of the same group for nucleus isolation. Additionally, we collected ventricular tissue from two cDMD mouse hearts that each was processed separately for nucleus isolation and sequencing. Cardiac nuclei isolation was performed as previously described
Total cardiac nuclei were used to generate single nucleus RNA-seq libraries using Single Cell 3’ Reagent Kits v3 (10xGenomics) according to the manufacturer’s protocol

treatment_protocol: 18- to 22-month-old WT, DMD, and cDMD mice were used for snRNA-seq. After euthanasia, hearts were extracted and dissected in ice-cold PBS.  A transverse cut along the midline of base-apex axis was made for each heart and ventricular heart tissue below the cut was collected.

value: purified nuclei from heart

value: AAV-corrected DMD


title: cDMD.A2 cardiac snRNA-seq

description: single-nucleus RNAseq


title: B1E01_2mo2_oocyte


title: CR3_CR007_cumulus

description:
count_GENCODEvM15_oocyte_cumulus.txt.gz
rpkm_GENCODEvM15_oocyte_cumulus.txt.gz

data_processing:
fastq files were aligned to mouse reference genome GRCm38 using the Hisat2 v2.0.5
BAM files resulting from the alignments were summarized to genes using the featureCounts v1.5.1 with the parameters '-M -O --fraction'
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values or rpkms for each sample

source_name: an oocyte surrounding cumulus cells pool of a fully grown follicle

extract_protocol:
single oocyte or their surrounding cumulus cells pool were lysed using cell lysis buffer [10 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher Scientific), and RNase-free water (TAKARA)] in 0.2 mL single tube.
RamDA-seq sequencing libraries were constructed by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0). However, to adapt to the manually picked single oocyte and their cumulus cells, the reaction volume from the cell lysis to the genomic DNA digestion step was modified. For details, refer to the protocol in "Aging-associated effects on transcriptome landscape and chromosome cohesion in single oocytes are influenced by life stage and calorie restriction".

tag: age/diet

value: CR (9 months with calorie restriction)

value: cumulus


title: B2B11_2mo35_oocyte


title: B1H01_2mo2_oocyte


title: CR3_CR015_cumulus


title: CR3_CR014_cumulus


title: B1C01_2mo1_oocyte


title: B1D01_2mo1_oocyte


title: CR3_CR008_cumulus


title: CR3_CR013_cumulus


title: CR3_CR010_cumulus


title: B1F11_2mo34_oocyte


title: CR2_CR024_cumulus


title: WT cardiac snRNA-seq

description: single-nucleus RNAseq

value: Wildtype


title: CR3_CR016_cumulus


title: CR3_CR012_cumulus


title: CR3_CR009_cumulus


title: CR3_CR005_cumulus


title: CR3_CR011_cumulus


title: CR2_CR023_cumulus


title: DMD cardiac snRNA-seq

description: single-nucleus RNAseq

value: DMD


title: CR3_CR004_cumulus


title: CR1_CR003_cumulus


title: CR2_CR019_cumulus


title: CR1_CR001_cumulus


title: CR2_CR018_cumulus


title: CR2_CR021_cumulus


title: CR2_CR020_cumulus


title: Old3_GV048_cumulus

value: Old (14 months with AL diet)


title: CR1_CR002_cumulus


title: CR2_CR022_cumulus


title: CR2_CR025_cumulus


title: Old3_GV047_cumulus


title: Old3_GV045_cumulus


title: Old3_GV046_cumulus


title: Old3_GV044_cumulus


title: Old1_2_GV038_cumulus


title: Old1_2_GV040_cumulus


title: Old1_2_GV037_cumulus


title: CR2_CR017_cumulus


title: Old1_2_GV035_cumulus


title: Old1_2_GV042_cumulus


title: Old1_2_GV034_cumulus


title: Middle4_GV040_cumulus

value: Middle (9 months with AL diet)


title: Old1_2_GV041_cumulus


title: Middle4_GV038_cumulus


title: Middle4_GV037_cumulus


title: Old1_2_GV043_cumulus


title: Middle4_GV039_cumulus


title: Middle3_GV048_cumulus


title: Middle2_GV046_cumulus


title: Old1_2_GV033_cumulus


title: Middle3_GV047_cumulus


title: Middle2_GV045_cumulus


title: Middle2_GV043_cumulus


title: Middle2_GV044_cumulus


title: Old1_2_GV039_cumulus


title: Middle2_GV041_cumulus


title: Middle1_GV036_cumulus


title: Middle2_GV042_cumulus


title: Middle1_GV035_cumulus


title: Middle1_GV033_cumulus


title: B1F01_2mo2_oocyte


title: Old1_2_GV036_cumulus


title: Middle1_GV034_cumulus


title: Young2_GV040_cumulus

value: Young (2 months with AL diet)


title: CR3_CR006_cumulus


title: Young2_GV047_cumulus


title: Young2_GV046_cumulus


title: Young2_GV041_cumulus


title: Young2_GV043_cumulus


title: Young2_GV045_cumulus


title: Young2_GV038_cumulus


title: Young1_GV035_cumulus


title: Young2_GV039_cumulus


title: Young2_GV042_cumulus


title: CR3_CR016_oocyte

value: oocyte


title: CR3_CR008_oocyte


title: Young1_GV034_cumulus


title: CR3_CR015_oocyte


title: Young2_GV048_cumulus


title: CR3_CR007_oocyte


title: CR3_CR014_oocyte


title: Young2_GV044_cumulus


title: CR3_CR011_oocyte


title: CR3_CR013_oocyte


title: CR3_CR006_oocyte


title: CR3_CR004_oocyte


title: CR3_CR010_oocyte


title: CR3_CR012_oocyte


title: CR2_CR022_oocyte


title: Young2_GV037_cumulus


title: CR2_CR020_oocyte


title: CR3_CR005_oocyte


title: CR2_CR021_oocyte


title: CR2_CR019_oocyte


title: Young1_GV036_cumulus


title: CR3_CR009_oocyte


title: CR1_CR001_oocyte


title: CR2_CR024_oocyte


title: CR2_CR023_oocyte


title: Old3_GV047_oocyte


title: Old3_GV045_oocyte


title: CR1_CR003_oocyte


title: Old1_2_GV039_oocyte


title: CR2_CR025_oocyte


title: Old1_2_GV036_oocyte


title: CR2_CR026_oocyte


title: CR2_CR027_oocyte


title: Old3_GV044_oocyte


title: CR2_CR017_oocyte


title: Old1_2_GV042_oocyte


title: CR1_CR002_oocyte


title: Old1_2_GV038_oocyte


title: Old1_2_GV040_oocyte


title: CR2_CR018_oocyte


title: Old3_GV048_oocyte


title: Old3_GV046_oocyte


title: Middle4_GV038_oocyte


title: Old1_2_GV037_oocyte


title: B1A01_2mo1_oocyte


title: Old1_2_GV034_oocyte


title: Old1_2_GV035_oocyte


title: Middle4_GV040_oocyte


title: Old1_2_GV041_oocyte


title: Old1_2_GV033_oocyte


title: Middle4_GV037_oocyte


title: Klf15_dCas9VPR_P14_input

city: Goettingen

first: Laura

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

institute: University Medical Center, Goettingen

data_processing:
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated using MACS2. Narrowpeaks and Broadpeaks were called on dCas9VPR bound regions. RPKM normalized bigwigs were generated using bamCoverage in Galaxy deepTools platform with default settings.

source_name: cardiac ventricles

growth_protocol: P14 murine cardiac ventricles; mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
For each IP, ventricles from P14 hearts were washed in PBS, minced finely and fixed in 2% Formaldehyde for 25 min. The nuclei from tissue extracts were sonicated for 50 cycles to obtain the fragmented chromatin. Chromatin extracts containing DNA fragments with an average size of 300 bp were immunoprecipitated using 2 µg / IP of anti-Cas9 antibody (Diagenode, #C15200203-100).
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions

treatment_protocol: AAV TRISPR Klf15, AAV TRISPR Mef2d or saline, respectively

value: dCas9VPR (TG)

tag: chip-seq antibody

value: anti-Cas9 antibody (Diagenode, #C15200203-100) - 2 ug / IP

tag: biological replicates

value: AAV TRISPR Klf15


title: Middle4_GV039_oocyte


title: saline_dCas9VPR_P14_input

value: saline


title: Middle3_GV047_oocyte


title: Middle2_GV046_oocyte


title: Middle2_GV045_oocyte


title: saline_dCas9VPR_P14


title: Mef2d_dCas9VPR_P14

value: AAV TRISPR Mef2d


title: Klf15_dCas9VPR_P14


title: Mef2d_dCas9VPR_P14_input


title: Middle2_GV043_oocyte


title: Myh6-dCas9VPR + saline 3

description: C3 DCAS9 only count

data_processing:
cDNA libraries were amplified and sequenced by using the cBot and HiSeq4000 from Illumina (SR; 1x50 bp; 51 cycles with single indexing; 6 GB ca. 30- 35 million reads per sample).
Sequence reads were aligned to the mouse reference assembly (UCSC version mm9) using Bowtie 2.0
For each gene, the number of mapped reads was counted using htseqcount and DESeq2 was used to analyze the differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Excel file contains the output from DESeq2: normalized counts of the raw data.

source_name: Cardiac ventricles

growth_protocol: mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
RNA was isolated from mice cardiac tissue using TRIZOL/Chloroform and isopropanol precipitation. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 weeks

value: TG (Myh6-dCas9VPR)

tag: agent


title: Middle1_GV034_oocyte


title: Myh6-dCas9VPR + saline 2

description: C2 DCCAS9 ONLY COUNT


title: Middle2_GV044_oocyte


title: Middle2_GV042_oocyte


title: Old1_2_GV043_oocyte


title: Middle2_GV041_oocyte


title: Myh6-dCas9VPR + AAV9 TRISPR Mef2d 3

description: D3 both count


title: Middle1_GV033_oocyte


title: wild-type + AAV9 TRISPR Mef2d 2

description: B2 TRISPR only count

value: WT


title: Middle3_GV048_oocyte


title: Myh6-dCas9VPR + AAV9 TRISPR Mef2d 1

description: D1 both count


title: Young2_GV045_oocyte


title: Young2_GV048_oocyte


title: Young2_GV047_oocyte


title: wild-type + saline 3

description: A3 saline count


title: Myh6-dCas9VPR + saline 1

description: C1 DCAS9 only count


title: Middle1_GV036_oocyte


title: Young2_GV046_oocyte


title: Young2_GV039_oocyte


title: wild-type + AAV9 TRISPR Mef2d 3

description: B3 TRISPR only count


title: Young2_GV042_oocyte


title: Myh6-dCas9VPR + AAV9 TRISPR Mef2d 2

description: D2 both count


title: Young1_GV036_oocyte


title: P6_3.

extract_protocol:
RNA was isolated from mice cardiac tissue using NucleoSpin RNA kit from Macherey-Nagel (Cat no: 740955.10). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: postnatal day 6


title: wild-type + AAV9 TRISPR Mef2d 1

description: B1 TRISPR only


title: Young2_GV040_oocyte


title: P6_2.


title: GATA4_P6

data_processing:
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and files were generated using MACS2. Narrowpeaks and Broadpeaks were called on TCF7L2, GATA4 and H3K27ac bound regions respectively. RPKM normalized bigwigs were generated using bamCoverage in Galaxy deepTools platform with default settings.

growth_protocol: P6 murine cardiac ventricles; mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
For each IP, ventricles from 10 P6 hearts were pooled, washed in PBS, minced finely and fixed in 1.3% Formaldehyde for 20 min. The nuclei from tissue extracts were sonicated for 45 cycles to obtain the fragmented chromatin. Chromatin extracts containing DNA fragments with an average size of 300 bp were immunoprecipitated using 2µg/IP of different antibodies.
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions

value: Wild-type (WT)

value: anti-GATA4 (sc-25310 X, Santacruz)- 2µg/IP (each IP=10 hearts pooled)


title: wild-type + saline 1

description: A1 saline count


title: wild-type + saline 2

description: A2 saline count


title: H3K27ac_P6

value: anti-H3K27ac (C15410196, Diagenode)- 2µg/IP (each IP=10 hearts pooled)


title: TCF7L2_P6

value: anti-TCF7L2 (17-10109, Millipore)- 2µg/IP (each IP=10 hearts pooled)


title: Young2_GV041_oocyte


title: ZSF-1OB Gr2 Enalapril 2012 Kidney

city: South San Francisco

first: Yang

state: California

address: 213 E Grand Ave

institute: Merck

description: FPKM.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was generated for following process
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: rat kidney

growth_protocol: All rats are ZSF-1OB given drug in feed, implanted with telemetry device. Start dosing @22 week old and last for 6 months

extract_protocol:
Kidney tissues were extracted from experimental animals and immediately snap-frozen in liquid nitrogen and stored at −80°C until used. Stat-60 solution was used to homogenize the samples. The homogenate was then transferred to an RNase-free centrifuge tube, after which RNase-free water were added. Samples were incubated, centrifuged, and the supernatant collected. The aqueous phase into a total RNA extraction procedure that is bead based MagMax MirVana (A27828, Thermo Fisher Scientific, Waltham, MA)  that was automated on a KingFisher instrument(Thermo Fisher Scientific, Waltham, MA). The RNA quantity and quality was assessed using a Fragment Analyzer. Equal molar concentration of about 0.75nM as the running concentration for all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats are in 4 groups, treated with vehicle, Enalapril, Compound1, Enalapril+Compound1, respectively

value: kidney

value: Enalapril


title: P6_1.


title: Young1_GV034_oocyte

value: Young (2 months with AL diet)


title: ZSF-1OB Gr3 Compound1 3011 Kidney

description: FPKM.txt


title: Young2_GV043_oocyte

value: oocyte


title: ZSF-1OB Gr3 Compound1 3103 Kidney

description: FPKM.txt


title: Young1_GV033_oocyte


title: ZSF-1OB Gr4 Enalapril + Compound1 4005 Kidney

description: FPKM.txt

value: Enalapril + Compound1


title: Input_P6


title: Young2_GV037_oocyte


title: Young1_GV035_oocyte


title: Young2_GV044_oocyte


title: Young2_GV038_oocyte


title: Rep1_BDF1_IP

tag: antibody

value: anti-GFP

value: Lister 427

tag: developmental stage

value: bloodstream slender form

tag: chromatin factor


title: Rep1_DOT1B_input

tag: strain


title: ZSF-1OB Gr4 Enalapril + Compound1 4011 Kidney

description: FPKM.txt

tag: tissue


title: ZSF-1OB Gr2 Enalapril 2011 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4012 Kidney

description: FPKM.txt


title: Rep1_BDF7_input


title: Rep1_BDF7_IP


title: ZSF-1OB Gr2 Enalapril 2005 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4008 Kidney

description: FPKM.txt


title: Rep1_CLD1_input


title: Rep1_BDF6_IP


title: ZSF-1OB Gr4 Enalapril + Compound1 4006 Kidney

description: FPKM.txt


title: Rep1_BDF1_input


title: ZSF-1OB Gr4 Enalapril + Compound1 4009 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4003 Kidney

description: FPKM.txt


title: Rep2_RPB1_IP

description: DNA crosslinked to protein

extract_protocol:
Briefly, 4 x 10^8 parasites were harvested and fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 s on, 30 s off) using the high setting on a Bioruptor sonicator (Diagenode). Input samples were taken before incubating the rest of the cell lysates overnight with 10 µg rabbit anti-GFP antibody (Thermo Fisher Scientific) and Protein G Dynabeads. The beads were washed and the DNA eluted from them was treated with RNAse and Proteinase K. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were constructed using 0.5-20 ng of immunoprecipitated or input DNA. Following blunt-ending and poly(A)-tailing, NEXTflex (Bioo Scientific) adapters containing barcodes were ligated to each DNA fragment. Fragments were size selected using AMPure beads (Beckman Coulter). The amount of DNA in the resulting libraries was quantified by Qubit fluorometer using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution was assessed by 2100 Bioanalyzer Instrument (Agilent Technologies) using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Ideally, the libraries had a peak at 300 bp (~ 150 bp fragment DNA + ~ 150 bp adapter sequence). Libraries were sequenced on Illumina MiniSeq, HiSeq 4000 or NextSeq 550. In all cases, 75 bp paired-end sequencing was performed.


title: Rep2_RPC1_input

description: DNA crosslinked to protein


title: Rep1_RPC1_IP

description: DNA crosslinked to protein


title: ZSF-1OB Gr3 Compound1 3012 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4001 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4010 Kidney

description: FPKM.txt


title: ZSF-1OB Gr3 Compound1 3010 Kidney

description: FPKM.txt


title: Rep2_RPC1_IP

description: DNA crosslinked to protein


title: ZSF-1OB Gr4 Enalapril + Compound1 4002 Kidney

description: FPKM.txt


title: ZSF-1OB Gr4 Enalapril + Compound1 4007 Kidney

description: FPKM.txt


title: Rep1_RPB1_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr3 Compound1 3008 Kidney

description: FPKM.txt


title: Rep1_BDF6_input


title: Rep2_RPB1_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr4 Enalapril + Compound1 4004 Kidney

description: FPKM.txt


title: Rep1_RPC1_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr3 Compound1 3007 Kidney

description: FPKM.txt


title: ZSF-1OB Gr3 Compound1 3006 Kidney

description: FPKM.txt


title: Rep1_CLD1_IP


title: Rep2_TRF_IP

description: DNA crosslinked to protein


title: ZSF-1OB Gr3 Compound1 3009 Kidney

description: FPKM.txt


title: ZSF-1OB Gr3 Compound1 3104 Kidney

description: FPKM.txt


title: Rep1_RPB1_IP

description: DNA crosslinked to protein


title: Rep2_TRF_input

description: DNA crosslinked to protein


title: Rep2_TBP_IP

description: DNA crosslinked to protein


title: Rep1_TRF_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr3 Compound1 3001 Kidney

description: FPKM.txt


title: ZSF-1OB Gr3 Compound1 3102 Kidney

description: FPKM.txt


title: Rep1_TRF_IP

description: DNA crosslinked to protein


title: ZSF-1OB Gr2 Enalapril 2007 Kidney

description: FPKM.txt


title: Rep2_ELP3b_input

description: DNA crosslinked to protein


title: Rep1_TBP_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr2 Enalapril 2009 Kidney

description: FPKM.txt


title: ZSF-1OB Gr2 Enalapril 2103 Kidney

description: FPKM.txt


title: Rep2_NUP110_input

tag: chip antibody

tag: molecule subtype

value: DNA crosslinked to protein


title: ZSF-1OB Gr2 Enalapril 2010 Kidney

description: FPKM.txt


title: ZSF-1OB Gr1 Vehicle ctrl 1012 Kidney

description: FPKM.txt

value: Vehicle ctrl


title: ZSF-1OB Gr2 Enalapril 2001 Kidney

description: FPKM.txt


title: Rep1_TBP_IP

description: DNA crosslinked to protein


title: ZSF-1OB Gr2 Enalapril 2008 Kidney

description: FPKM.txt


title: Rep1_NUP110_input


title: ZSF-1OB Gr1 Vehicle ctrl 1011 Kidney

description: FPKM.txt


title: Rep1_NUP110_IP


title: Rep2_DOT1A_IP


title: Rep2_NUP110_IP


title: ZSF-1OB Gr1 Vehicle ctrl 1009 Kidney

description: FPKM.txt


title: ZSF-1OB Gr3 Compound1 3105 Kidney

description: FPKM.txt


title: Rep2_DOT1A_input


title: Rep2_ELP3b_IP

description: DNA crosslinked to protein


title: Rep1_DOT1A_input


title: ZSF-1OB Gr1 Vehicle ctrl 1007 Kidney

description: FPKM.txt


title: Rep1_DOT1A_IP


title: Rep3_DMT_IP


title: ZSF-1OB Gr1 Vehicle ctrl 1006 Kidney

description: FPKM.txt


title: ZSF-1OB Gr1 Vehicle ctrl 1010 Kidney

description: FPKM.txt


title: ZSF-1OB Gr1 Vehicle ctrl 1004 Kidney

description: FPKM.txt


title: Rep2_TBP_input

description: DNA crosslinked to protein


title: ZSF-1OB Gr1 Vehicle ctrl 1008 Kidney

description: FPKM.txt


title: Rep3_DMT_input


title: TRAP-PARIS mutant (C571A) rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
The TRAP-seq dataset composed of a total of 10 fastq files representing 4 different treatment groups was processed using the “alternate” differential expression workflow, a modified version of the “new” Tuxedo pipeline at http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq. Briefly, after quality control (FASTQC v0.11.6) read alignment was performed using HISAT2 v2.1.0, default parameters with “min-intronlen 74” and “max-intronlen 75000”. After multi-mapped reads were identified exclusively specific for rRNA genes, StringTie v2.0’s by-default multi-mapping correction was enabled during transcript abundance estimations and generation of read coverage tables not to compromise the dataset by discarding multi-mapped reads, keeping the sample size (i.e. per-replicate-read-number) above the accepted threshold. StringTie output was directly analyzed for transcript-level differential expression (DE) using the R package Ballgown v2.16.0 while the same output was preprocessed using the author-supplied script “prepDE.py” at the website above for format conversion. These preprocessed files were fed into the R package DESeq2 v1.24.0 for gene-level DE analysis, which ultimately generated the input for the rest of the downstream analysis presented here. The R package NOISeq(sim) v2.28.0 was used for DE analysis of pairwise comparisons with single replicate.
Genome_build: BDGP assembly release 6.28 (Ensembl release 99)
Supplementary_files_format_and_content: Unmapped_hits.bam files: the only use of the unmapped_<...>.bam files provided here is to confirm insertion of the human PARIS gene in the engineered fly genome after a successful TRAP experiment, thereby, reproducing the information presented as Fig. 1d in the manuscript. TopHat v2.0.13 was the choice of aligner with "-G" and "-N 0" arguments to identify unmapped reads in the input fastq files. Bam-to-fastq data conversion before mapping the unmapped reads to the PARIS (ZNF746) DNA sequence (GRCh38) can be made using Hydra v0.5.3, which requires for each input bam file read name sorting by 'samtools sort' with the "-n" argument. If necessary, the repair.sh tool in the BBMap suite can be used to repair the read pairs before alignment. GeneCountMatrix_<...>.txt files: text files containing raw read count information.

organism: Drosophila melanogaster

source_name: dopaminergic neurons

growth_protocol: Human PARIS and C571A constructs cloned and expressed in pUAST plasmid (DGRC) were microinjected into w1118 embryos (The BestGene, Inc). Transgenic dTH-Gal4 lines were obtained from the Bloomington Drosophila Stock Center (BDSC). All experimental maintenance and crosses between transgenic lines were made at 25 °C. Drosophila melanogaster fly stocks were handled using standard protocols, maintained in a 12 h light/dark cycle and fed Drosophila standard diet consisting of cornmeal, agar, yeast, sucrose, and dextrose.

extract_protocol:
The libraries were prepared from three independent biological samples from 500 (control and hPARIS mutant lines) - 1,500 (hPARIS wt line) of a mixture of male and female heads, whereas a sequencing library using the total mRNA from whole head was prepared for one biological sample to provide quality-assurance of DA neuron-specific translatome.
Libraries for RNA sequencing were prepared with the TruSeq RNA Sample preparation v2 kit (Illumina) and sequenced on an Illumina HiSeq 2000 sequencer.

treatment_protocol: For trap experiments, both male and female flies were used. In each experiment, the dTH-Gal4 heterozygous flies were used as control. For the TRAP analysis of fly DA neurons, translated mRNAs in DA neurons were purified from dTH-GAL4/UAS-GFP::RpL10A with and without hPARIS wt or mutant (C571A)

value: brain

value: post natal day 30

value: dTH+TRAP(hPARIS C571A)


title: Rep3_CRD1_input


title: Rep3_BDF6_IP


title: ZSF-1OB Gr1 Vehicle ctrl 1002 Kidney

description: FPKM.txt


title: ZSF-1OB Gr1 Vehicle ctrl 1003 Kidney

description: FPKM.txt


title: ZSF-1OB Gr1 Vehicle ctrl 1001 Kidney

description: FPKM.txt


title: Rep2_ZCW1_input


title: Rep2_untagged_IP

value: untagged


title: Rep2_ZCW1_IP


title: TRAP-PARIS mutant (C571A) rep1


title: Rep3_BDF6_input


title: TRAP-PARIS wild type rep2

value: dTH+TRAP(hPARIS wild type)


title: Rep3_CRD1_IP


title: TRAP-PARIS mutant (C571A) rep2


title: TRAP-PARIS wild type rep3


title: TRAP-PARIS wild type rep1


title: Rep2_DMT_input

value: TbDMT


title: TRAP control rep1


title: Rep2_Sir2rp3_input


title: TRAP control rep3


title: Rep2_DMT_IP


title: HiSeq_Method2 schizont parasites enriched

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

data_processing:
The raw reads from fastq files  were  trimmed of 5’ adapters from ends with Cutadapt 1.18 for libraries with 5' adapter added by method1. Adapter sequence in the 3′ end of reads was trimmed and low quality reads removed using fastp with default settings
Filtered reads were mapped to the combined reference genome (Pf3D7_SIRvome_combined_correct.fasta) with HISAT2, guided by annotations in the Pf3D7_SIRvome_combined.gtf file.
Normalized depth values for each library at all positions and the associated enrichment scores were calculated from mapped sense-strand reads (read 1 only) of method1 and method2.  P-values of enrichment at each nucleotide were calculated using the ToNER program with the combine p-value option.
Genome_build: Plasmodium falciparum 3D7 v3.2 (Böhme et al. 2019) / SIRVomeERCCome (Lexogen) combined reference genome (Pf3D7_SIRvome_combined_correct.fasta)
Supplementary_files_format_and_content: Tab-delimited text files of position, normalized depth and enrichment score for each library.

organism: Plasmodium falciparum

source_name: In vitro cultured malaria parasite

growth_protocol:
Plasmodium falciparum strain K1 was cultured in vitro in human O+ erythrocytes and medium containing pooled human serum and buffered RPMI as described previously (Shaw et al 2007). Cultured parasites were synchronized to ring stage by Percoll gradient enrichment of mature stages followed by sorbitol treatment. Parasites were harvested immediately (ring stage), 12 h (trophozoite stage) and 24 h (schizont stage) after sorbitol treatment. Parasites were liberated from the host cell by treatment with 0.1% (w/v) saponin.
[enrichment protocol]  The GST-PfeIF4E protein, which has been demonstrated to possess 5′ cap binding activity (Shaw et al. 2007), was used for enrichment of full-length cDNA. GST-PfeIF4E protein was expressed as recombinant protein in Escherichia coli and purified by SP-sepharose cation exchange chromatography as described previously (Shaw et al. 2007). Purified protein was buffer-exchanged and stored in a solution of 15% glycerol/RNase-free phosphate-buffered saline (PBS, Ambion). 5′ cap binding activity was determined by m7GTP pulldown assay as described previously (Shaw et al. 2007), except that gamma-aminophenyl-m7GTP (C10-spacer)-agarose (Jena Bioscience) was used as the affinity support. For each full-length cDNA enrichment, approximately 100 μg of SP-sepharose purified GST-PfeIF4E protein was immobilized on 50 μL of glutathione magnetic beads (Thermo Scientific) in PBS. The glutathione magnetic beads were washed four times with 0.5 mL of PBS to remove unbound protein, and then resuspended in 100 μL of PBS. The remainder of the purified mRNA/cDNA was incubated with bead-bound GST-PfeIF4E protein for 20 min at 25°C with agitation (750 rpm Thermomixer). The beads were then washed thrice with 0.5 mL PBS and the mRNA/cDNA eluted in 100 μL of 1% sodium dodecyl sulfate/0.2 M sodium chloride. The eluted mRNA/cDNA was purified with an equal volume of Agencourt® AMPure® XP beads (Beckman Coulter) and recovered from beads in 20 μL of nuclease-free water. RNA was removed from enriched and unenriched cDNA samples by alkaline hydrolysis (15 min treatment at 65°C with 0.2 N NaOH). Alkaline-treated cDNA was neutralized with an equal volume of 1 M HEPES pH 7.4 solution. First-strand cDNA was purified with an equal volume of Agencourt® AMPure® XP beads (Beckman Coulter) and recovered from beads in 20 μL of nuclease-free water.

extract_protocol:
Parasite total RNA was obtained using Trizol reagent according to the manufacturer’s instructions (Invitrogen). Purified total RNA was stored in 75% ethanol at -80°C prior to use. On the day of library preparation, total RNA was dried and then resuspended in nuclease-free water. Total RNA concentration was estimated by Nanodrop ND1000 measurement assuming A260 = 1.0 is equivalent to 40 μg/mL RNA. Up to 100 μg of total RNA was used for mRNA enrichment using a Dynabeads oligo dT25 mRNA kit (Thermo), which enriches for mRNA with oligo dT magnetic beads. The oligo dT-enriched mRNA was then further enriched for 5′ capped mRNA by treatment with 1 unit of XRN-1 nuclease (New England Biolabs) for 30 min at 37°C. XRN-1 enriched mRNA was purified by acidic phenol:chloroform extraction and ethanol precipitation. The mRNA was redissolved in 20 μL of nuclease-free water and genomic DNA was removed using a Turbo DNA-free kit (Ambion).
[5' adapter ligation method: method1] A ribo-G tail of was added to the purified single-stranded cDNA primed with RTNGS1 using terminal transferase (TdT, New England Biolabs). The tail length is limited to three or four Gs (Schmidt and Mueller, 1996). The TdT tailing reactions contained 2 mM GTP, 0.25 mM CoCl2, 1 unit of TdT enzyme in 1x TdT enzyme buffer and first-strand cDNA. TdT reactions were performed in 20 μL reaction volumes for 20 min at 37°C. Ribo-tailed cDNA was purified with an equal volume of Agencourt® AMPure® XP beads (Beckman Coulter) and recovered from beads in 20 μL of nuclease-free water. Double-stranded DNA adapter was made by combining 4 nmol each of NGS1 and NGS1COMP oligonucleotides in a volume of 100 μL with 10 mM NaCl and 10 mM Tris pH 8.0. The NGS1 oligonucleotide is 5′-phosphorylated to act as a donor in ligation and blocked with a three-carbon spacer at the 3′ end to prevent concatamerization of adapters. Annealing was accomplished by heating the mixture for 3 min at 80°C followed by slow cooling to 25°C (-0.1°C/min). Double-stranded DNA adapter was ligated to first-strand cDNA using T4 RNA ligase 2 (RNL2, New England Biolabs). The ligation reactions contained 40 pmol of DNA adapter, 7.5% (w/v) PEG6000, 1x RNL2 enzyme buffer, 2.5 units of RNL2 enzyme and first strand cDNA in a volume of 20 μL. The ligation reactions were performed for 99 cycles of 37°C for 30 s, 22°C for 30 s. After the completion of the RNL2 adapter ligation reactions, cDNA was diluted to 100 μL with nuclease-free water and purified with an equal volume of Agencourt® AMPure® XP beads (Beckman Coulter). Purified cDNA was recovered in 50 μL of nuclease-free water.
[5' adapter ligation method: method2 ] Purified first strand cDNA primed with RTCIRC in which RNA had been removed by alkaline treatment was circularized with 100 U of CircLigaseII enzyme, 2.5 mM MnCl2, 1 M betaine, and 1x CircLigaseII buffer in a reaction volume of 20 μL as recommended by the manufacturer (Epicentre Biotechnologies). The reaction was incubated at 60°C for 1 h and the reaction terminated by heating to 80°C for 10 min. The reaction was diluted to 100 μL with nuclease-free water and cDNA purified using half the volume of Agencourt® AMPure XP beads (Beckman Coulter). Purified cDNA was recovered in 50 μL of nuclease-free water.
Synthesis of cDNA:  In vitro synthesized spike-in RNA SIRV-Set 3 (Iso Mix E0/ERCC, Lexogen) was 5′ capped with Vaccinia capping system (New England Biolabs) following the manufacturer’s instructions. A 100–200 ng sample of parasite mRNA (estimated by Nanodrop measurement) was mixed with 1.5 ng of SIRV-Set 3 RNA. 5′ capped SIRV-Set 3 RNA was added to samples of ring and trophozoite stage parasite mRNA. The mRNA/SIRV-Set 3 RNA mixture was fragmented by heating at 94°C for 3 min in 1x first-strand cDNA synthesis buffer supplied with SuperscriptIV reverse transcriptase enzyme (Invitrogen). Fragmented mRNA was chilled on ice for 5 min prior to reverse-transcription with 50 pmol of 5′ tagged random primer (RTNGS1 (Table S1) for adapter ligation method 1, RTCIRC (Table S1) for adapter ligation method2; see below) with SuperscriptIV as described by the manufacturer in a final volume of 20 μL. After addition of SuperscriptIV enzyme, reactions were heated to 25°C for 5 min, followed by heating to 37°C for 30 min, 50°C for 30 min, and then 70°C for 15 min. First-strand cDNA was diluted to 100 μL with 10 mM Tris 1 mM EDTA and digested with 1 μL of RNaseA/T1 mix (Thermo Scientific) for 10 min at 37°C to remove incompletely reverse-transcribed RNA. The mRNA/cDNA hybrid was purified using an equal volume of Agencourt® AMPure® XP beads (Beckman Coulter) and recovered from beads in 100 μL nuclease-free water. A 20 μL sample of purified mRNA/cDNA was kept for processing as the unenriched control sample. Adapter-ligated cDNA was used as a template for PCR amplification to make sequencing library. PCRs contained 2.5 pmol each of PE1 and ScriptSeq primers (Table S1), 200 µM dNTPs, 0.625 U PrimeSTAR® GXL DNA polymerase (Takara) and 1x buffer supplied with enzyme in a reaction volume of 25 μL. The PCR program used was 98°C for 30 s, followed by 18-25 cycles of 98°C for 10 s, 68°C for 60 s and a final extension of 68°C for 5 min. PCR products were separated in 1.5% agarose gel. DNA fragments 400-600 bp in size were excised from the gel and purified using a MinElute gel extraction kit (Qiagen), with the modification that agarose was solubilized in QG buffer at room temperature. DNA was quantified using a  Qubit™ dsDNA HS Assay kit (Invitrogen).  Libraries were pooled in equimolar ratios according to the ScriptSeq index primer recommendations (Illumina). Pooled libraries were submitted to Novogene AIT (Singapore) for standard sequencing on a HiSeq2000 instrument (Illumina).

value: schizont

tag: full-length cdna enrichment

value: enriched

tag: 5' adapter ligation method


title: Rep2_Sir2rp3_IP


title: Rep2_Sir2rp2_input


title: TRAP control rep2

tag: age


title: Rep2_Sir2rp1_IP


title: Rep2_untagged_input


title: whole brain rep1

value: wild type


title: Rep2_Sir2rp2_IP


title: HiSeq_Method2 schizont parasites unenriched

value: unenriched


title: HiSeq_Method2 trophozoite parasites enriched

value: trophozoite


title: HiSeq_Method2 trophozoite parasites unenriched


title: Rep2_Sir2rp1_input


title: Rep2_SET27_IP


title: Rep2_SET26_IP


title: Rep2_SET27_input


title: HiSeq_Method1 schizont parasites enriched


title: Rep2_SET29_input


title: HiSeq_Method2 ring parasites unenriched

value: ring


title: Rep2_SET26_input


title: HiSeq_Method1 ring parasites enriched


title: HiSeq_Method1 trophozoite parasites unenriched


title: Rep2_SET29_IP

value: anti-GFP


title: HiSeq_Method2 ring parasites enriched


title: HiSeq_Method1 schizont parasites unenriched


title: Rep2_SET25_input

value: Lister 427


title: Rep2_SET23_IP

value: bloodstream slender form


title: HiSeq_Method1 ring parasites unenriched


title: Rep2_SET28_input


title: Rep2_SET24_IP


title: CRC-26

city: Iruma-gun

first: Toshiaki

last: Miyazaki

state: Saitama

address: 38 Morohongo, Moroyama-machi

department: Social Medicine

institute: Saitama Medical University

data_processing:
Basecalls performed using Illumina BaseSpace v1.1.0
Sequenced reads were mapped to hg19 whole genome using TopHat
Cufflinks were used to procude aligned reads, variant calls and FPKM abundance estimates of reference genes and transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: GSE167395_Gene_and_FPKM_6_samples_addition.xlsx

source_name: primary colon cancer

extract_protocol:
Human CRC spheroid cells (1x10^5), cultured in Spheroid buffer, were collected by centrifugation at 500 xg for 1min at 4C. Cells were then washed twice with PBS(-) and total RNAs were purified with RNAeasy kit (Qiagen) according to the manufacturers instruction. Indexed cDNA libraries were generated from each 500 ng of the purified RNA with TruSeq stranded mRNA kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: primary colon cancer


title: CRC-24


title: CRC-23M

source_name: Liver metastasis colon cancer

value: Liver metastasis colon cancer


title: Rep2_SET24_input

source_name: cultured cells

extract_protocol:
Briefly, 4 x 10^8 parasites were harvested and fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 s on, 30 s off) using the high setting on a Bioruptor sonicator (Diagenode). Input samples were taken before incubating the rest of the cell lysates overnight with 10 µg rabbit anti-GFP antibody (Thermo Fisher Scientific) and Protein G Dynabeads. The beads were washed and the DNA eluted from them was treated with RNAse and Proteinase K. DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were constructed using 0.5-20 ng of immunoprecipitated or input DNA. Following blunt-ending and poly(A)-tailing, NEXTflex (Bioo Scientific) adapters containing barcodes were ligated to each DNA fragment. Fragments were size selected using AMPure beads (Beckman Coulter). The amount of DNA in the resulting libraries was quantified by Qubit fluorometer using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution was assessed by 2100 Bioanalyzer Instrument (Agilent Technologies) using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Ideally, the libraries had a peak at 300 bp (~ 150 bp fragment DNA + ~ 150 bp adapter sequence). Libraries were sequenced on Illumina MiniSeq, HiSeq or NextSeq. In all cases, 75 bp paired-end sequencing was performed.


title: Rep2_SET22_IP


title: CRC-38M


title: CRC-49


title: CRC-35M


title: Rep2_SET23_input


title: Rep2_SET25_IP


title: Rep2_SET22_input


title: Rep2_SET28_IP


title: Rep2_SET21_IP


title: Rep2_SET21_input


title: Rep2_SET20_input


title: Rep2_SET19_IP


title: Rep2_SET18_input


title: Rep2_SET20_IP


title: Rep2_SET15_IP


title: Rep2_SET18_IP


title: Rep2_SET16_IP


title: Rep2_SET16_input


title: Rep2_SET17_input


title: Rep2_SET19_input


title: Rep2_SET14_input


title: Rep2_SET14_IP


title: Rep2_SET17_IP


title: Rep2_SET7_IP


title: Rep2_SET9_input


title: Rep2_SET11_input


title: Rep2_SET8_IP


title: Rep2_SET13_input


title: Rep2_SET13_IP


title: Rep2_SET11_IP


title: Rep2_SET9_IP


title: Rep2_SET7_input


title: Rep2_SET8_input


title: s05_hda3_biorep1

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

description:
Nascent RNA
NET-Seq of strain with hda3 gene deletion (replicate 1)

data_processing:
Library strategy: NET-Seq
Illumina Casava v1.7 software was used for basecalling.
1) Trim 4bp UMI barcodes from 5' ends of both R1 and R2 reads (UMI-Tools extract v0.5.3);
2) Align R2 reads to TAIR10 (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT);
3) Sort BAM files (Samtools v1.3.1);
4) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci from Araport11 (BEDTools v2.17.0);
5) Remove reads with MAPQ < 10 (Samtools v1.3.1);
6) Remove PCR duplicates (UMI-Tools dedup);
7) Convert BAM to stranded bedGraph files (BEDtools genomecov);
8) Normalize bedGraph files to 1M tags (awk).
Genome_build: SacCer3
Supplementary_files_format_and_content: BigWig files show strand-specific sequencing coverage of first bases in NET-seq reads (no signal smoothing, transformation or normalization were applied).

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast strain were grown in standard YPD liquid medium to mid-log phase, then rapidly harvested by filtration, flash frozen in liquid nitrogen and grinded.

extract_protocol:
Cell grindate (1 gram) was dissolved in cold Lysis buffer. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen).
NGS libraries were constructed from nascent RNA using NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific) following the protocol described in Kindgren et al., 2020 (PMID 31863587).

tag: genotype

tag: protocol

value: NET-Seq


title: Rep2_SET6_IP


title: Rep2_SET15_input


title: s04_hda1_biorep2

description:
Nascent RNA
NET-Seq of strain with hda1 gene deletion (replicate 2)


title: Rep2_SET5_IP


title: s03_hda1_biorep1

description:
Nascent RNA
NET-Seq of strain with hda1 gene deletion (replicate 1)


title: s06_hda3_biorep2

description:
Nascent RNA
NET-Seq of strain with hda3 gene deletion (replicate 2)


title: s02_WT_biorep2

description:
Nascent RNA
NET-Seq of wild type strain (replicate 2)

value: Wild type


title: Rep2_SET5_input


title: Rep2_SET4_input


title: s01_WT_biorep1

description:
Nascent RNA
NET-Seq of wild type strain (replicate 1)


title: Rep2_SET3_IP


title: Rep2_SET4_IP


title: Rep2_SET3_input


title: Rep2_TFIIS2-2_IP


title: Sample 56

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
FastQC Preprocessing: nohup ./ fastqc <Fastq.gz location> <Fastq.gz location> <As many fasrq.gz files as you want> --outdir=/<output directory location> &
adaptor trimming using rimmomatic version 0.36: ohup java -jar <location of trimmomatic.jar> SE -phred33 <location of fastq.gz file> <output name/location>
aligned to tomato and pepper genome using bowtie2:   nohup bowtie2 -x <Index Name> -U <Fastq file> -S <Alignment Name.sam> --no-unal &
convert from *.sam to *.bam files using samtools: samtools view -Sb <alignment.sam> > <alignment.bam>
sort using samtools: nohup samtools sort <file.bam> -o <sorted file.bam> &
index using samtools: nohup samtools index <sorted file.bam> <sorted file.bai> &
analyze alignments using Bedtools Multicov:   bedtools multicov -D -bams <sorted bam file.bam> -bed <GFF filed.gff> > <Text file.txt> &
Supplementary_files_format_and_content: Sorted, indexed alignments (*.bai). Alignments to tomato genome are named without prefix to the file name. Alignments against pepper genome have "Pepper_" prior to the file name.

organism:
Capsicum annuum
Solanum lycopersicum

source_name: Solanum lycopersicum cv. M82 and Capsicum annuum variety Big Dipper

extract_protocol:
Trizol total RNA extraction
mRNA was extracted following the NEBNext Poly(A) mRNA Magnetic Isolation Module protocol and libraries were prepared using the NEBNext mRNA Library Prep set for Illumina (New England Biolabs)

value: Stem graft junction

tag: timepoint

value: 2 weeks after grafting

tag: library

value: Tomato:pepper graft junction


title: Sample 58


title: Sample 55


title: Sample 53

value: Pepper:tomato graft junction


title: Sample 54


title: Sample 57


title: Rep2_TFIIS2-2_input

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Genome_build: HGAP3_Tb427v9.2
Supplementary_files_format_and_content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome


title: Rep2_PHD5_IP


title: Rep2_SET6_input


title: Sample 47

value: 5 days after grafting


title: Rep2_PHD5_input


title: Sample 52


title: Sample 46


title: Sample 48


title: ATAC-seq in zebrafish wild-type embryos at 48hpf, replicate 2

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: narrowPeak files with peaks called using MACS2 with q<0.01

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were grown at 28°C in E3 medium until desired developmental stage

extract_protocol:
Wild type or mutant embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: Injection of tp53 morpholino was performed at 1-cell stage

value: 48 hpf

value: WT

tag: treatment


title: ATAC-seq in zebrafish wild-type embryos at 48hpf, replicate 1


title: Sample 45


title: Rep2_PHD4_IP


title: Rep2_SET1_IP


title: ATAC-seq in zebrafish wild-type embryos at 48hpf, injected with morpholino against tp53, replicate 2

value: tp53 morpholino


title: Rep2_SET1_input


title: Rep2_PHD4_input


title: ATAC-seq in zebrafish wild-type embryos at 48hpf, injected with morpholino against tp53, replicate 1


title: Sample 44


title: Rep2_PHD2_IP


title: ATAC-seq in zebrafish ctcf mutant embryos at 48hpf, replicate 2

value: ctcf -/-


title: Sample 43


title: Rep2_PHD2_input


title: ATAC-seq in zebrafish ctcf mutant embryos at 48hpf, injected with morpholino against tp53, replicate 2


title: ATAC-seq in zebrafish ctcf mutant embryos at 48hpf, injected with morpholino against tp53, replicate 1


title: Rep2_PHD1_IP


title: GM08505 GFP-BLM

city: New Delhi

first: Sagar

last: Sengupta

address: Aruna Asaf Ali Marg

department: Signal Transduction Laboratory-2

country: India

institute: National Institute of Immunology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed off adaptor sequences and independently aligned using CLC Genomic Workbench 6.5.1 with default setting against miRBase release 19  accounting for a maximum of two gaps or mismatches in each sequence
Differential expression, p-value and fold changes for each gene were determined using CLC Genomic Workbench 6.5.1  with default parameters.
Genome_build: miRBase release 19
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcript per million) values for each miRNA of respective samples

source_name: GM08505 GFP-BLM

growth_protocol: All the cell lines were propagated cell lines 10% Dulbecco’s modified Eagle’s medium supplemented with glutamine and antibiotics in a humidified chamber at 37⁰C, 5% CO2. GM03509 GFP-BLM Clone 4.3.4 and GM03509 GFP Clone 100 were cultuered in 200ug/ml of hygromycin while GM08505 GFP and GM08505 GFP-BLM were cultured in 250ug/ml of G418.

extract_protocol:
RNA was extracted using Trizol and the isolated RNA analyzed s on an Agilent 2100 bioanalyzer for its integrity using the RNA 6000 nano kit (Agilent) to confirm RINs above 8.0. Additionally, the quality of the ribosomal 28 S and 18 S on an agarose gel was used as a measure of integrity and the absorbance at 260/280 nm was used to determine quantity of the extracted RNA.
The small RNAs libraries were constructed using Small RNA v1.5 sample preparation kit according to the manufacturer’s instructions (Illumina, inc., USA.)  Briefly the total RNA (700-800ng) were ligated to 3′ and 5′ RNA adapters. The ligation products were reverse transcribed using Superscript II Reverse Transcriptase and amplified with 12 cycles of PCR. The PCR products constituting the small RNA cDNA libraries were resolved on 6% Novex TBE PAGE Gel and ~150 bp fragments excised. The library was eluted from the PAGE gel and analyzed on Agilent 2100 Bioanalyzer using DNA high sensitivity kit (Agilent Technologies, USA). Sequencing of miRNA libraries (~150bp fragments) were performed using Illumina GAIIX sequencing platform for 36 cycles.

tag: cell line

tag: cell type

value: fibroblasts

value: Bloom Syndrome


title: Rep2_PHD1_input

value: Lister 427

tag: developmental stage


title: GM03509 GFP Clone 100

source_name: GM03509 GFP Clone 100


title: Sample 41


title: GM08505 GFP

source_name: GM08505 GFP


title: Sample 32

value: 3 days after grafting


title: Rep2_EAF6_IP

tag: antibody

value: anti-GFP

value: bloodstream slender form

tag: chromatin factor


title: Rep2_EAF6_input

tag: strain


title: ATAC-seq in zebrafish wild-type embryos at 24hpf, replicate 1

value: 24 hpf


title: Sample 30

tag: tissue


title: Sample 42


title: ATAC-seq in zebrafish ctcf mutant embryos at 24hpf, replicate 2


title: Sample 31


title: Rep2_LCM1_IP


title: GM03509 GFP-BLM Clone 4.3.4

source_name: GM03509 GFP-BLM Clone 4.3.4


title: Control_3 [re-analysis]

value: 15 weeks-old

value: alphaMHC Cre recombinase positive, WT for beta-catenin


title: Wntup_3 [re-analysis]

value: alphaMHC Cre recombinase positive, beta-catenin exon3 deleted-stabilized beta-catenin


title: Control_1 [re-analysis]


title: Sample 26

value: Stem graft junction


title: CoIP_WT_RsmA_R2

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

description:
RNA bound non-specifically
eluted after co-immunoprecipitation with anti-FLAG antibody.

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of reads longer than 11 nt to reference genome using segemehl version 0.2.0 with minimum accuracy 95% (parameters for reademption align: -l 12 -a 95) (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length); Normalization: coverage-tnoar_min_normalized (counts divided by total number of aligned reads and multiplied by the minimum over all libraries) (READemption 0.4.5, Förstner et al., 2014)
Genome_build: Serratia sp. ATCC 39006 (Assembly acc.: GCF_002847015.1_ASM284701v1, Sequence ID: NZ_CP025085.1)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

organism: Prodigiosinella confusarubida

source_name: Serratia sp. ATCC 39006 cells

growth_protocol: RsmA_3xFLAG and WT (untagged) control strains were grown to late exponential (OD600=0.6) and then harvested by centrifugation. Cell pellets corresponding to an OD600 of 60 were resuspended in 1 mL buffer A and harvetsed again by centriguation. Pelletes were snap frozen in liquid nitrogen and stored at -80.

extract_protocol:
RsmA-bound RNAs (eluted RNA) were extracted from beads harboring anti-FLAG immunoprecipitated proteins. For both, untagged and RsmA-3xFLAG co-immunoprecipitated samples, RNA was purified from the bound complexes using Phenol:Chloroform:Isoamylalcohol extraction. Eluted RNA was precipitated overnight at -20°C.
RNA was converted to cDNA using the adapter ligation method by Vertis Biotechnologie.

treatment_protocol: No treatment applied during growth, bacterial lysates used for coIP.

tag: replicate

tag: antibody for coip

value: ANTI-FLAG M2 (Sigma, cat. #F 1804)

tag: epitope tag


title: ATAC-seq in zebrafish ctcf mutant embryos at 48hpf, replicate 1


title: ATAC-seq in zebrafish wild-type embryos at 24hpf, replicate 2


title: Sample 28

value: Pepper:tomato graft junction


title: CoIP_WT_RsmA_3xFLAG_R2

description:
RNA bound to RsmA-3xFLAG
eluted after co-immunoprecipitation with anti-FLAG antibody.


title: CoIP_WT_RsmA_3xFLAG_R1


title: Sample 27


title: Sample 25


title: ATAC-seq in zebrafish ctcf mutant embryos at 24hpf, replicate 1


title: Sample 49

organism: Solanum lycopersicum

source_name: Solanum lycopersicum cv. M82

value: 2 weeks after grafting

value: Tomato:Tomato graft junction


title: Sample 15

value: 24 hours after grafting


title: Rep2_JMJ1_IP


title: Control_2 [re-analysis]

tag: age


title: Sample 50


title: Wntup_1 [re-analysis]


title: Wntup_2 [re-analysis]


title: Rep2_JMJ1_input


title: CoIP_WT_RsmA_R1


title: Sample 13


title: Rep2_HDAC4_IP


title: crzA_GFP_caspofungin_control_1_TCGCGTACT_ChIPMix81

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

description:
crzA_GFP_control_1_GFP
crzA_GFP_control_1

data_processing:
Raw data was aligned to A. fumigatus reference genome using Bowtie2 v2.3.5 tool. Initial 8bp of reads were clipped during mapping step using argument "bowtie2  --trim5 8 --local  "
Normalized the reads depth to 1 million mapped reads using "macs2 bdgopt " command from MACS2 v2.1.1
Converted bedGraph files to bigWig files using UCSC Kent Utils v369 tool "bedGraphToBigWig"
Genome_build: Aspergillus fumigatus Af293 reference genome from AspGD. Version s03-m05-r06
Supplementary_files_format_and_content: bigwig files were generated using UCSC Kent Utils v369; Scores represent normalized read depth to 1 million reads

organism: Aspergillus fumigatus

source_name: cultured colonies

growth_protocol: Conidia (1.10^7) were grown into liquid medium (AMM) for 16 h at 37oC under shaking conditions

extract_protocol:
Chromatin preparation was performed as described by Suzuki et al., 2012
Library preparation was carried out using NEBNext® Ultra II Library Prep kit (Illumina, cat. no. E7645L) according to manufacturer’s protocol

treatment_protocol: Addition of 2  µg/ml of caspofungin for 1 hour

tag: ip tag

value: GFP

tag: chip antibody

value: anti-GFP (ab290, Abcam)


title: crzA_GFP_caspofungin_2_CCTTTACAGT_ChIPMix81

description:
crzA_GFP_HD_2_GFP
crzA_GFP_HD_2


title: Rep2_JMJ2_input

city: Edinburgh

first: Robin

institute: Wellcome Centre for Cell Biology


title: Sample 16


title: Sample 34

value: 5 days after grafting


title: RPMI-8266 scri_2

city: San Francisco

first: Arun

middle: P

last: Wiita

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

institute: University of California San Francisco

description: RPMI8266_scri-VS-RPMI8266_CD38i.DEseq2_Method.GeneDiffExp.xls

data_processing:
For genome mapping, clean reads were mapped to reference genome using HISAT59 with an average of 94.2% mapping across samples.
For gene expression analysis, clean reads were mapped to reference transcripts using Bowtie2 (ref.60) and expression levels calculated using RSEM61.

source_name: MM.1S myeloma cell line

growth_protocol: Cell lines were grown in RPMI-1640 medium and passaged twice a week at 5x10^5 cells/ml

extract_protocol:
After treatment, cell lines were washed with PBS twice, pelleted and flash frozen and frozen cell pellets were sent to BGI Genomics for further processing for RNA Seq
RNA extraction, library preparation, and sequencing were performed at BGI (Shenzhen, China).   RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit

treatment_protocol: CRISPR interference cell lines were generated as described in Ramkumar et al 2020. RPMI-8226 cell lines. They were untreated.  RPMI-8226 cell lines were treated with 25 nM  all-trans retinoic acid (ATRA), 2 uM azacytidine, or 10 nM panobinostat.

value: multiple myeloma cell line


title: Sample 36


title: Rep2_JMJ2_IP

address: Max Born Crescent

value: Lister 427


title: Sample 20

value: 3 days after grafting


title: HiSeq_Method1 trophozoite parasites enriched

value: trophozoite

tag: full-length cdna enrichment

value: enriched

tag: 5' adapter ligation method


title: crzA_GFP_caspofungin_1_TGCGGTTAT_ChIPMix81

description:
crzA_GFP_HD_1_GFP
crzA_GFP_HD_1


title: Sample 14

tag: timepoint

tag: library


title: Sample 29

value: Tomato:pepper graft junction


title: Rep2_HDAC3_IP

value: anti-GFP

value: bloodstream slender form


title: Sample 11

value: Stem graft junction


title: Sample 19


title: crzA_GFP_caspofungin_control_2_TATACCGTT_ChIPMix81

description:
crzA_GFP_control_2_GFP
crzA_GFP_control_2


title: Rep2_HDAC4_input


title: Rep2_LCM1_input


title: Rep2_HDAC3_input


title: Rep2_HDAC2_input


title: Rep2_HDAC2_IP


title: Sample 35


title: Sample 12


title: RPMI-8266 CD38i_2

tag: cell line


title: Sample 17


title: Sample 10


title: Sample 33


title: Rep2_HDAC1_input


title: Rep2_NAT3_IP


title: RPMI-8266 scri_1

tag: cell type


title: Rep2_HDAC1_IP

tag: developmental stage


title: RPMI-8266_DMSO4Aza 2

description: RPMI8266_DMSO4Aza-VS-RPMI8266_Aza.DEseq2_Method.GeneDiffExp.xls

tag: treatment

value: 2 uM azacytidine


title: Sample 3


title: RPMI-8266_Pano1

description: RPMI8266_DMSO4ATRA-VS-RPMI8266_Pano.DEseq2_Method.GeneDiffExp.xls

value: 10 nM panobinostat


title: Sample 4


title: Rep2_NAT3_input

tag: chromatin factor


title: RPMI-8266_Pano2


title: Sample 1


title: Sample 9


title: Sample 18


title: RPMI-8266_DMSO4ATRA_2

description: RPMI8266_DMSO4ATRA-VS-RPMI8266_ATRA.DEseq2_Method.GeneDiffExp.xls

value: 25 nM  all-trans retinoic acid (ATRA)


title: RPMI-8266 CD38i_1


title: Sample 2

value: Tomato:Tomato graft junction