title: HEKGFP output, cell 68

description:
Processed_Data.xlsx, sheet 9 HEKGFP #68
original name: SP09_S188
HEKGFP_output_cell_68.fastq.gz


title: HEKGFP output, cell 66

status: Public on Feb 12 2018

type: SRA

city: South San Francisco

first: Samuel

last: Pollock

state: CA

address: 1 DNA way

department: MPL

country: USA

institute: Genentech

description:
Processed_Data.xlsx, sheet 9 HEKGFP #66
original name: SP09_S186
HEKGFP_output_cell_66.fastq.gz

library_source: transcriptomic

data_processing:
Instructions, scripts, and examples at https://github.com/sbpollock/phage-counting-perl
Create reference library (0-format-indices.pl)
Count each .fastq.gz file against the reference library (1-count-parallel.pl)
Combine and format processed data file (2-format-counts.pl)
Open .txt file in Excel and save as a .xls or .xlsx file
Genome_build: Not applicable here
Supplementary_files_format_and_content: Counts in a ".xls" spreadsheet

molecule: other

organism: Homo sapiens

source_name: M13K07 bacteriophage displaying Fabs on a Herceptin scaffold

extract_protocol:
For cell populations, phage were eluted from cells in 900uL of 0.1M acetic acid for 5mins, cells were spun down 5mins, and 800uL eluent was transferred to 100uL 1M Tris pH 7.5 to neutralize. To the 100uL of neutralized eluent, 1mL of log phase XL-1 bacteria grown up in tetracycline media was added. This tube was shaken at 37C for 20mins, 1E10cfu/mL helper phage was added and shaker at 37C for 20mins, and the infected mix transferred to a 250mL flask containing 30mL of 2xYT+carbenicillin+kanamycin. This flask was shaken 18-20hrs, cells were spun out, and a propagated supernatant boiled in a 96-well PCR plate. For single cell, cells were sorted into individual wells containing 100uL 2xYT media (no elution step) in 96-well plates. 100uL of log phase XL-1 blue bacteria grown in tetracycline was added and propagated by deep well plate at 999rpm, 37C for 24hrs. Work-up was then carried out as above.
To amplify the H3 “barcode” of each phagemid for sequencing, 3µL of boiled propagate and 4µL of 5uM each forward and reverse primers was combined into 43µL of Phusion master mix (New England Biolabs, M0530S) in a 96-well PCR plate (Biorad, HSP9621). Primer design is as follows (shown 5’ to 3’ on both primers, order as shown): AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTGAGGACACTGCCGTCTATTATTGTGCTCGC (forward), CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGACCAGGGTTCCTTGACCCCAGTAGTC (reverse), where NNNNNNNN are substituted with the appropriate dual indices (Nextera Dual Index). The plate was sealed with PCR foil (Excel Scientific, F-96-100) and the complete mix was run on a thermocycler (2˚C/second ramp rate) as follows: step 1_98˚C, 5min; steps 2 to 4_98-60-72˚C, 20-15-15sec; repeat steps 2-4 11 more times; step 5_72˚C,5min; step 6_hold 12˚C. Solid Phase Reverse Immobilization (SPRI) beads were used to purify amplicons (Agencourt AmpureXP beads or similar): 35µL of each amplicon solution was mixed with 65µL ddH2O. 120µL of SPRI beads were added to each well and mixed. The beads were washed twice with 800µL of 80% ethanol, allowed to dry 5-10mins, and eluted in 50µL of water, using either a magnetic stand or a Kingfisher FLEX bead handling system. Samples were run out on 96-well 2% agarose gels to check for the presence of the amplicon band and the absence of primer bands. Samples were combined (2µL per sample or at least 500µL total volume, whichever volume is greater), dried overnight (Genevac, EZ-2 Mk2), re-suspended in 1/10 volume water (i.e. dry 500µL, re-suspend 50µL), and quantified using a nanodrop. The library was then transferred to a 1.7mL low-bind tube (Corning Axygen, MCT-175-L-C) and submitted to a sequencing facility for analysis on a HiSeq4000, along with a custom sequencing primer (order as shown): TGAGGACACTGCCGTCTATTATTGTGCTCGC.

tag: input or output

value: Output

tag: experiment


title: Male_MEF_WT_HiC_Biological_Rep3_Technical_Rep1

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description: Hi-C

library_source: genomic

data_processing:
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8.  The reads were mapped to the mm9 mouse reference genome.  For allele-specific Hi-C analysis, a high quality SNP list for the C57BL6NJ and CastEiJ genomes was generated by using the mm9 annotation from the Mouse Sanger Database, using the HiC-Pro “extract_snps.py” tool.  Next, C57BL6NJ/CastEiJ SNP-masked mm9 reference genome was generated using the bedtools “maskfasta” tool.  Then, allele-specific Hi-C data was analyzed using the HiC-Pro “ALLELE_SPECIFIC_SNP” configuration option.    There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses. The read-depth achieved for each pooled Hi-C dataset supports the generation of genome-wide contact maps at as low as 40kb resolution.
For the Hi-C analysis of endogenous Firre KO with ectopic Firre cDNA insertion MEFs, the Hi-C reads were mapped to a custom mm9 genome with an extra chromosome consisting of the insertion cassette (TRE element, CMV promoter, Firre cDNA and polyA terminator ().  Then, “inter-chromosomal interactions” between the Firre custom chromosome and all the mouse chromosomes were plotted in the DOX- and DOX+ Hi-C datasets.  The regions which displayed consistent “interactions” with the Firre custom chromosome in DOX- and DOX+ samples were determined as Firre cDNA insertion sites.
Genome_build: mm9
Supplementary_files_format_and_content: Processed, iterative corrected sparse Hi-C matrix

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

extract_protocol: Hi-C libraries were generated with the in-situ ligation protocol using the HindIII restriction enzyme.  Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature.  Then, the chromatin was digested with HindIII, end-labelled with biotin-14-dCTP, and in-situ ligation was performed.  Following phenol-chloroform extraction, the biotin was removed from unligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument.  Each Hi-C library was generated in at least two biological replicates from MEFs prepared from at least two distinct mouse embryos.

tag: genotype

value: WT

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: Sex

value: Male


title: Subclone HP biological replicate 2

city: Brisbane

first: Camila

middle: Antonia

last: Orellana

state: Queensland

address: Crn College and Cooper Rds (Bldg 75)

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description: Gene expression SHP vs SLP.xlsx

data_processing:
The reads were trimmed to 75 bases before mapping in order to improve their quality.
TopHat open-source software (version 2.0.12, using Bowtie version 2.2.3.0 and SAMtools version 0.1.19.0), was used with default settings to align the reads to the CHO-K1 genome. A combined file containing the CHO-K1 genomic scaffolds (CriGri_1.0), the mitochondrial sequence (NC_007936.1) and the ERCC standards sequences was used as a reference.
Cufflinks open-source software (version 2.2.1) was used to assemble transcripts, estimate their abundance and tests for differential expression. The annotated version of the CHO-K1 genome last modified on 2014/08/11 was used. Cuffdiff was run using default setting and the frag-bias-correct (for bias detection and correction) and the multi-read-correct (to more accurately weight reads mapping to multiple locations in the genome) options to improve the accuracy of abundance estimates. The genes were classified as differentially expressed if the adjusted p-value (q-value) was lower than 0.05.
Genome_build: A combined file containing the CHO-K1 genomic scaffolds (CriGri_1.0), the mitochondrial sequence (NC_007936.1) and the ERCC standards sequences was used as a reference.
Supplementary_files_format_and_content: Two excel files containing Cuffdiff differential expression analysis

molecule: total RNA

organism: Cricetulus griseus

source_name: Chinese hamster ovary cells

growth_protocol: Separate vials were thawed for each biological replicate and passaged for two weeks prior to bioreactor inoculation. Cells were seeded at 0.5 million cells/mL in a 1L Mini-Bioreactor (Applikon Biotechnologies) with a working volume of 700 mL of EX-CELL® CD CHO Fusion Medium (Sigma Aldrich) containing 25 µM L-Methionine sulfoximine (MSX) as selection. The bioreactor was operated at 125 rpm stirring speed, 37°C, pH 6.9 and dissolved oxygen at 50% air saturation. Glucose concentration was determined using a BioProfile FLEX (Nova Biomedical) and a bolus of 3 g/L of glucose was added to the culture when the extracellular glucose reached 2 g/L, thus maintaining the glucose level between 2 and 5 g/L.

extract_protocol:
For the the subclone high producer (SHP) and subclone low producer (SLP) mRNA-Seq samples were prepared with Agilent's SureSelect Strand Specific RNA Library Preparation Kit for the Illumina platform, according to the manufacturer’s instructions. Libraries were loaded onto the channels of the flow cell at 8 pM concentration, with multiplexing of 6 samples per lane in two different lanes of a Rapid flow cell, performed on a HiSeq 2500 using Rapid reagents and 100 bp paired-end reads.
Five million cells were harvested in the mid-exponential phase from each bioreactor, i.e. three biological replicates per cell line. Cells were centrifuged at 500g for 3 min, and the cell pellet was frozen in dry ice and stored at -80 °C. RNA was extracted from the ice thawed pellet using the RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions for animal cells using spin technology. RNA concentration was measured with a Qubit fluorometer (Life Technologies) and the quality was evaluated with an Agilent 2100 bioanalyzer using a RNA Nano Chip (Agilent Technologies). ERCC ExFold RNA Spike-In Mixes (Life Technologies) were added to the RNA samples to assess the accuracy of measurements of differential gene expression on the platform used. Mix 1 or Mix 2 were added to the different samples to compare the expected versus observed fold-change ratio (Mix 1:Mix 2).
RNA libraries were prepared for sequencing using standard Illumina protocols (described for each sample)

tag: parental strain

value: CHOZN® GS-/-

value: CHO cells

tag: productivity

value: subclone high producer

tag: ercc


title: Male_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep2

description: Hi-C

value: FirreKO


title: Subclone HP biological replicate 1

description: Gene expression SHP vs SLP.xlsx


title: Male_MEF_WT_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C


title: HEKGFP output, cell 71

description:
Processed_Data.xlsx, sheet 9 HEKGFP #71
original name: SP09_S191
HEKGFP_output_cell_71.fastq.gz


title: HEKGFP output, cell 65

description:
Processed_Data.xlsx, sheet 9 HEKGFP #65
original name: SP09_S185
HEKGFP_output_cell_65.fastq.gz


title: Male_MEF_WT_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: HEKGFP output, cell 64

description:
Not processed, insufficient counts
original name: SP09_S184
HEKGFP_output_cell_64.fastq.gz


title: Female_MEF_FirreKO_HiC_Biological_Rep3_Technical_Rep2

description: Hi-C

value: Female


title: G28 MG1655GFP_pD864_3

city: Siena

first: Simone

last: Furini

address: viale Mario Bracci, 16

department: Department of Medical Biotechnologies

country: Italy

institute: University of Siena

data_processing:
paired end sequencing with Illumina HiSeq 2500 Sequencer
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit.
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit.
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene

organism: Escherichia coli

source_name: Bacterial cells

growth_protocol: E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes.

extract_protocol:
170 μl were taken from each of four wells per time point and collected into a fresh tube were 1.360 ml of RNA protection buffer had previously been added. Samples were left for 5 minutes at RT and then centrifuged at 4°C at maximum speed. Supernatant was discarded and pellets frozen at -20°C. RNA extraction was performed using RNeasy Mini Kit from Qiagen [Cat No 74104]. To remove possible traces of genomic DNA contamination, 2 μg of each sample were treated for a second time with DNAseI from Qiagen [Cat No 79254]. Total RNA quality and integrity was assessed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano kit [Cat No 5067-1511]. Samples had an average RIN of 9.5. Enrichment of mRNA was performed using MicrobExpress rRNA removal kit from Thermo Scientific [Cat No AM1905].  Successful rRNA depletion was assessed with analysis on Bioanalyzer. Retrotranscription was then performed starting from 50 ng total enriched mRNA using Tetro cDNA synthesis kit from Bioline [Cat No BIO-65043] and 6 μl of Random Hexamers [Cat No BIO-38028] per reaction. Second cDNA synthesis was performed adding to the first strand synthesis mix 5 μl of Second strand synthesis buffer [Cat No B6117S], 3 μl of dNTPs [Cat No N0446S], 2μl of RNAseH [Cat No M0297L] all from NEB, 2 μl of Polymerase I from Thermo Scientific [Cat No 18010025] and 18 μl of water, per reaction. Samples were incubated at 16°C for 2.5 h. Purification of cDNA was performed using MiniElute PCR purification kit [Cat No 28004] with final elution in 10 μl of DEPC-treated free water. cDNA was quantified using a Qubit fluorometer (Invitrogen).
Library preparation was performed using the Nextera XT kit from Illumina [Cat No FC-131-1096] starting from 1 ng of total cDNA. The original protocol was modified where 3 min tagmentation and 13 cycles of step-limited PCR were used. Ampure beads from Beckman Coulter [Cat No A63880] were used for library purification. Library quality assessment and quantification was performed with Agilent 2100 Bioanalyzer and Agilent high sensitivity DNA analysis kit [Cat No 5067-4626]. Finally all 90 samples were pooled together in the same reaction tube at a final concentration of 1 nM.

treatment_protocol: After 60 minutes into the incubation, the plate was briefly removed so inducer could be added to wells, and this time point was set as time 0. Samples were instead removed from wells at 15 and 60 minutes after induction for processing.

tag: strain

tag: plasmid

tag: synthetic circuit

tag: treatment

value: 60 min after induction with rhamnose


title: G29 DH10BGFP_None_3

value: 15 min


title: G25 MG1655GFP_pLys_3

value: PLYS

value: 60 min after induction with arabinose


title: Female_MEF_FirreKO_HiC_Biological_Rep3_Technical_Rep1

description: Hi-C


title: G26 MG1655GFP_Lux_3

value: Lux


title: Subclone LP biological replicate 1

description: Gene expression SHP vs SLP.xlsx

value: subclone low producer


title: G24 MG1655GFP_pSB1C3_3


title: Female_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep3

description: Hi-C


title: Subclone HP biological replicate 3

description: Gene expression SHP vs SLP.xlsx


title: G22 MG1655GFP_pSB1C3_H3_3


title: HEKGFP output, cell 61

description:
Processed_Data.xlsx, sheet 9 HEKGFP #61
original name: SP09_S181
HEKGFP_output_cell_61.fastq.gz


title: HEKGFP output, cell 63

description:
Processed_Data.xlsx, sheet 9 HEKGFP #63
original name: SP09_S183
HEKGFP_output_cell_63.fastq.gz


title: Female_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C


title: G21 MG1655GFP_pD864_3

value: 15 min after induction with rhamnose


title: Female_MEF_FirreKO_HiC_Biological_Rep1_Technical_Rep2

description: Hi-C


title: HEKGFP output, cell 62

description:
Processed_Data.xlsx, sheet 9 HEKGFP #62
original name: SP09_S182
HEKGFP_output_cell_62.fastq.gz


title: Female_MEF_FirreKO_HiC_Biological_Rep2_Technical_Rep2

description: Hi-C


title: HEKGFP output, cell 59

description:
Processed_Data.xlsx, sheet 9 HEKGFP #59
original name: SP09_S179
HEKGFP_output_cell_59.fastq.gz


title: HEKGFP output, cell 58

description:
Processed_Data.xlsx, sheet 9 HEKGFP #58
original name: SP09_S178
HEKGFP_output_cell_58.fastq.gz


title: G19 MG1655GFP_Lux_3

value: 15 min after induction with arabinose


title: HEKGFP output, cell 60

description:
Processed_Data.xlsx, sheet 9 HEKGFP #60
original name: SP09_S180
HEKGFP_output_cell_60.fastq.gz

value: Output


title: G17 MG1655GFP_pSB1C3_3


title: G18 MG1655GFP_pLys_3


title: Female_MEF_FirreKO_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: G27 MG1655GFP_pD864_LacZ_3

value: LACZ


title: Female_MEF_WT_HiC_Biological_Rep3_Technical_Rep3

description: Hi-C

value: WT

value: Mouse Embryonic Fibroblasts


title: NICD3

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

country: China

institute: Fourth Military Medical University

data_processing: counts and RPKM

source_name: liver sinusoidal endothelial cells

extract_protocol:
Liver sinusoidal endothelial cells were isolated from wide type and NICeCAmice,total RNA was isolated from the cells using the Trizol (invitrogen). The purified library products were evaluated  using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies,USA) and then diluted to 10pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150bp) on HiSeq 3000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: wide type and NICeCA  mice were injected intraperitoneally with Tamoxifen to induced Notch signaling activation

tag: tissue

value: liver

tag: age

value: 7-8 weeks

value: NICeCA


title: G23 MG1655GFP_pLys_M1_3


title: NICD2


title: Female_MEF_WT_HiC_Biological_Rep3_Technical_Rep2

description: Hi-C


title: G16 MG1655GFP_pLys_M1_3


title: HEKGFP output, cell 57

description:
Processed_Data.xlsx, sheet 9 HEKGFP #57
original name: SP09_S177
HEKGFP_output_cell_57.fastq.gz


title: G15 MG1655GFP_pSB1C3_H3_3


title: HEKGFP output, cell 56

description:
Processed_Data.xlsx, sheet 9 HEKGFP #56
original name: SP09_S176
HEKGFP_output_cell_56.fastq.gz


title: CT4

value: wild type


title: G20 MG1655GFP_pD864_LacZ_3


title: CT3


title: HEKGFP output, cell 54

description:
Processed_Data.xlsx, sheet 9 HEKGFP #54
original name: SP09_S174
HEKGFP_output_cell_54.fastq.gz


title: HEKGFP output, cell 55

description:
Processed_Data.xlsx, sheet 9 HEKGFP #55
original name: SP09_S175
HEKGFP_output_cell_55.fastq.gz


title: Female_MEF_WT_HiC_Biological_Rep2_Technical_Rep3

description: Hi-C

value: Female


title: RamDA_mESC_00h_B03

city: Tsukuba

first: Hiroaki

last: Tateno

state: Ibaraki

address: Tsukuba Central 2, 1-1-1 Umezono

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
For RamDA-seq and C1-RamDA-seq data with living cells, fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-l 36 --lowcomplex-pct 74 --homopolymer- pct 74 -k 4' for RamDA-seq and '-L 75 -l 46 -k 4 -q 30' for C1-RamDA-seq. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks -p 4 -k 5 -X 800 --sp 1000,1000'. Uniquely mapped reads were selected using the bamtools ‘filter’ command with the parameters '-isMapped true -tag NH:1' and samtools ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). The transcript-level expression levels were quantified using sailfish (version 0.9.2). The transcript-level expression levels were also calculated using Bowtie2 (version 2.2.6) with the parameters '-k 100 -X 800' and eXpress (version 1.5.1) with the parameter '--no-bias-correct'.
For each scRNA-seq method data with 10 pg of diluted RNA, fastq-mcf (version 1.04.807) was used to trim adapter sequences and generate read lengths of 42 nt with the parameters ‘-L 42 -l 42 -k 4 -q 30 -S’. For comparison, we also prepared R1 reads of rdRNA-seq and paRNA-seq data. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.1) with parameters ‘--dta-cufflinks -p 4 -k 5 --sp 1000,1000’. Uniquely mapped reads were selected using the bamtools (version 2.0.1;) 53 ‘filter’ command with the parameters `-isMapped true -tag NH:1` and the samtools (version 2.0.1)54 ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). Sailfish (version 0.9.2) was used to quantify transcript-level expressions.
For bulk poly(A) and total RNA-seq data, fastq-mcf was used to trim adapter sequences with the parameters ‘-l 50 --lowcomplex-pct 36 --homopolymer-pct 36 -k 4 -S’. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks --rna-strandness RF -k 5 --no-mixed --no-discordant --sp 1000,1000'. Properly (i.e., convergent read pairs) and uniquely mapped reads were selected using the bamtools ‘filter’ command and samtools ‘view’ command with the parameter ‘-q 40’. For genome-guided transcriptome assembly, Cufflinks (version 2.2.1) was used with the parameters ‘--multi-read-correct --frag-bias-correct -M $mask --library-type fr-unstranded’. A GTF file of tRNA and rRNA annotations in GENCODE (vM9) were provided to mask the genome. Cuffcompare was used to annotate transcripts with transfrag class codes with respect to the GENCODE (vM9) annotation. According to the Cuffcompare class codes, we selected (1) unnannotated transcripts with class codes of "i", "o", "u", "x", or "s" and (2) unannotated splicing variant transcripts (‘j’ class (potentially novel isoform)) with at least one unannotated splice junction. We then removed (1) unannotated transcripts with exons located within 100 bp of the tRNA or rRNA annotations in GECODE or RepeatMasker, or pseudogene annotations in GENCODE (‘2wayconspseudos’), and (2) unannotated transcripts with lengths that were not monger than 200 bp. These filtered unannotated gene models were further merged with gene models in GENCODE vM9.
Genome_build: mm10
Supplementary_files_format_and_content: txt, gtf, bigWig

source_name: ES_00h_single cell

growth_protocol: 5G6GR mouse ES cells were used for bulk and single-cell RNA-seq. The cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen). For ribosomal RNA depleted total RNA-seq, depletion of rRNA from 1 µg of ES total RNA was performed by using GeneRead rRNA Depletion Kits (Qiagen). For single-cell RamDA-seq, single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa). For averaged G1-phase cell lysate sample, 180 cells were sorted into 180 µl of the cell lysis buffer and individually divided into 1 μl in a 96-well PCR plate after well-mixing to lyse the cells. The cell lysate solution was stored at -80ºC until use.
For bulk RNA-seq, the libraries were constructed by using a commercial kit (NEBNext Ultra Directional RNA Library Prep Kit for Illumina; NEB) in accordance with the manufacturer's protocol, with slight modifications during the reverse-transcription and PCR steps. SMART-Seq v4 libraries were prepared according to manufacturer's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). For library construction of RamDA-seq and C1-RamDA-seq, refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs". For rRNA-depleted RNA-seq using 1 and 10 ng of diluted total RNA, sequencing libraries were prepared with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to the manufacturer's protocol. C1-SMART-Seq v4 libraries were prepared using Fluidigm C1 with the script "Full-length mRNA Sequencing" was downloaded from Script Hub (https://jp.fluidigm.com/c1openapp/scripthub)in accordance with the manufacturer's protocol. For analyses of plate-to-plate variability (batch effect) of RamDA-seq, we prepared RamDA-seq library DNA by using the advanced method of RamDA-seq (refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs").

treatment_protocol: For the assessment of PrE differentiation, 5G6GR ES cells were cultured in differentiation medium containing 100 mmol/l dexamethasone rather than blasticidin. The cells are cultured for 72 hours.

value: Embryonic stem (ES) cell

tag: sample type

value: MoFlo sorted cell

tag: starting amount

value: single cell

tag: cell cycle phase

value: All phase

tag: method subtype

value: RamDA-seq


title: Female_MEF_WT_HiC_Biological_Rep3_Technical_Rep1

description: Hi-C


title: dpy-7_skn-1_4

city: Gainesville

first: Keith

last: Choe

state: Florida

address: 876 Newell Dr, 321 Bartram Hall

institute: University of Florida

data_processing:
Kallisto for quantification of transcripts
Sleuth for differential abundance analysis
Genome_build: WBcel235
Supplementary_files_format_and_content: .csv files, columns are Wormbase Gene name, Gene name, p-value, q-value, b (log2 estimate of gene expression difference effect size), sample TPM (transcripts per million), fold difference, and log2 of fold difference

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol: Synchronized worms were grown on NGM agar plates at 20 C in one of eight treatment groups.

extract_protocol:
RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher Scientific)
Illumina HiSeq 2000

treatment_protocol: There were eight treatment groups: 51 mM NaCl for 3 h, 300 mM NaCl for 3 h, 300 mM NaCl for 3 h and skn-1(RNAi), 51 mM NaCl for 24 h, 300 mM NaCl for 24 h, 300 mM NaCl for 24 h and skn-1(RNAi), dpy-7 mutant, dpy-7 mutant and skn-1(RNAi)

tag: Stage

value: gravid young adult

value: control

tag: time


title: NICD1

tag: genotype


title: CT1


title: G13 DH10BGFP_pD864_LacZ_3

value: 60 min after induction with rhamnose


title: G11 DH10BGFP_pLys_3

value: PLYS

value: 60 min after induction with arabinose


title: G12 DH10BGFP_Lux_3

value: Lux


title: G14 DH10BGFP_pD864_3


title: G10 DH10BGFP_pSB1C3_3


title: Female_MEF_WT_HiC_Biological_Rep2_Technical_Rep1

description: Hi-C

value: WT

tag: cell type

value: Mouse Embryonic Fibroblasts

tag: Sex


title: Female_MEF_WT_HiC_Biological_Rep1_Technical_Rep2

description: Hi-C


title: HEKGFP output, cell 52

description:
Processed_Data.xlsx, sheet 9 HEKGFP #52
original name: SP09_S172
HEKGFP_output_cell_52.fastq.gz

tag: input or output

value: Output

tag: experiment


title: HEKGFP output, cell 51

description:
Not processed, insufficient counts
original name: SP09_S171
HEKGFP_output_cell_51.fastq.gz


title: G30 DH10BGFP_None_3

tag: strain

value: 60 min


title: Female_MEF_WT_HiC_Biological_Rep2_Technical_Rep2

description: Hi-C


title: dpy-7_skn-1_3


title: G9 DH10BGFP_pLys_M1_3

tag: plasmid


title: Female_MEF_WT_HiC_Biological_Rep1_Technical_Rep1

description: Hi-C


title: dpy-7_skn-1_2


title: HEKGFP output, cell 49

description:
Processed_Data.xlsx, sheet 9 HEKGFP #49
original name: SP09_S169
HEKGFP_output_cell_49.fastq.gz


title: HEKGFP output, cell 50

description:
Processed_Data.xlsx, sheet 9 HEKGFP #50
original name: SP09_S170
HEKGFP_output_cell_50.fastq.gz


title: G8 DH10BGFP_pSB1C3_H3_3

tag: synthetic circuit


title: CHiC E11.5 InvF

city: Berlin

first: Darío

middle: G

last: Lupiáñez

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Base calling with standard Illumina Software
Mapping and filtering of di-tags was performed with the HiCUP pipeline v0.5.8 (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) (parameters: Nofill:1 Format: Sanger  without any size selection). The pipeline used Bowtie2 v2.2.6 for mapping short reads to reference genome (mm9).
Filtered di-tags were further processed with Juicebox command line tools (https://github.com/theaidenlab/juicebox) to bin di-tags (10kb bins) and normalized by KR normalization (Only reads with MAPQ >= 30 were considered). The DNA-capturing step enriches genomic region chr1:71,000,001-81,000,000 on mm9 . Before binning and normalization, di-tags were filtered for the enriched region and mm9 coordinates were shifted by -71,000,001 bp (a custom chromosome file containing only the enriched region on chr1 was used). After binning and normalization, coordinates were shifted back to their original values.
Normalized difference matrices are obtained between the mutant contact matrix and the WT contact matrix.  Specifically, we multiply the matrix corresponding to the mutation by a factor that equalizes the reads count equivalent of the regions that are not involved in the mutation, then we subtract from the mutated matrix the WT matrix. To take into account the genomic distance bias, we normalized the difference matrix by dividing each sub-diagonal by the average WT reads count at its corresponding pairwise genomic distance. Next, in order to identify the statistically significant differences, we only retain the values of the normalized difference matrix falling above two standard deviations of the distributions of values in each sub-diagonal (that corresponds to an average one tail p-value less than 0.1 across genomic distances, over the different samples). In the calculation of the standard deviations, we filter out the points above 96th percentile in the cases where the data are marked by strong outliers. Finally, to correct for finite size effect, we used a higher threshold (four standard deviations) near the edge of the matrix (within the 5% of the matrix size). The same higher threshold is used when the data sample gets smaller, as in the case of genomic distances larger than half of the matrix size.
For visualization CHi-C maps of count values and difference matrices were visualized with the WashU epigenome browser (epigenomegateway.wustl.edu/browser/).
Genome_build: mm9
Supplementary_files_format_and_content: CHi-C maps and substractions in WashU epigenome browser pairwise interaction format

source_name: E11.5 distal limb buds

extract_protocol:
Limbs were re-suspended in Trypsin and incubated for 10 minutes at 37°C. Tissues were disrupted by pipetting and single cells were retrieved using cell strainer and fixed for 10 minutes at room temperature in 10ml (2%PFA, 10%FCS, 1XPBS). Final 140mM glycine was added to stop crosslinking. Cells were then lysed for 10’ at 4°C in  lysis buffer (50mM TRIS pH7.5, 150mM NaCl, 5mM EDTA, 0.5%NP-40, 1.15% TX-100 and 1X Proteinase Inhibitor).
Sheared DNA was then ligated to adaptors and 4 amplification cycles were performed prior to SureSelect hybridization. 700ng of adaptor-ligated DNA was hybridized to the custom probes according to Agilent instructions. Hybridized fragments were then amplified (12 cycles) and products were cleaned using AMPure XP beads. Each sample was sequence on an individual Illumina HiSeq lane following a 100bp paired-end mode.

value: InvF

value: distal limb buds


title: HEKGFP output, cell 48

description:
Processed_Data.xlsx, sheet 9 HEKGFP #48
original name: SP09_S168
HEKGFP_output_cell_48.fastq.gz


title: G7 DH10BGFP_pD864_3

tag: treatment

value: 15 min after induction with rhamnose


title: dpy-7_EV_2


title: CHiC E11.5 DelBs

value: DelBs

tag: tissue


title: dpy-7_EV_1


title: HEKGFP output, cell 53

description:
Processed_Data.xlsx, sheet 9 HEKGFP #53
original name: SP09_S173
HEKGFP_output_cell_53.fastq.gz


title: CHiC E11.5 DelB

value: DelB

tag: age


title: G5 DH10BGFP_Lux_3

value: 15 min after induction with arabinose


title: HEKGFP output, cell 47

description:
Processed_Data.xlsx, sheet 9 HEKGFP #47
original name: SP09_S167
HEKGFP_output_cell_47.fastq.gz


title: CHiC E11.5 WT

description:
Subs_Epha4-WT_vs_DelB_Raw_10kb.WashU.txt
Subs_Epha4-WT_vs_DelBs_Raw_10kb.WashU.txt
Subs_Epha4-WT_vs_InvF_Raw_10kb.WashU.txt


title: HEKGFP output, cell 45

description:
Not processed, insufficient counts
original name: SP09_S165
HEKGFP_output_cell_45.fastq.gz


title: skn-1_NaCl_24h_4

value: 300 mM NaCl

value: 24 hours


title: HEKGFP output, cell 44

description:
Processed_Data.xlsx, sheet 9 HEKGFP #44
original name: SP09_S164
HEKGFP_output_cell_44.fastq.gz


title: skn-1_NaCl_24h_3

value: gravid young adult


title: G4 DH10BGFP_pLys_3


title: dpy-7_EV_3

value: control


title: skn-1_NaCl_24h_2


title: EV_NaCl_24h_2

value: wildtype;control(RNAi)


title: INPUT for H3K27me3 ChIP-seq

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were aligned with Bowtie2 (version 2.2.1) and the following parameters --maxins 1000 --no-mixed --no-discordant
Duplicate Reads were marked with Picard tools
Duplicate Reads and Secondary alignments were removed with samtools
Ezh2 and Runx1 peaks were called using MACS2 (version 2.0.10) and the following parameters --bdg -g mm --keep-dup 9999
H3K27me3 peaks were called using MACS2 (version 2.0.10) and the following parameters --bdg --broad -g mm --keep-dup 9999
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak and broadPeak peak files were generated with MACS2

growth_protocol: EML_C1 was cultured in IMDM medium supplemented with 20% FCS, 2 mM L-glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, 1.5 g/L sodium bicarbonate and 200 ng/ml mSCF.

extract_protocol:
H3K27Me3 ChIP samples were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 60 min, 2 mM DSG and a 60 min 1% FA double fixation protocol was used for Ezh2 and Runx1 antibodies. Fixed chromatin samples were fragmented using a S220 Focused-ultrasonicators (Covaris) for 10 min with 10% duty cycle, 5 intensity, 200 cycle per burst with frequent sweeping mode and constant degassing at 4°C to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 3X with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, de-crosslinked, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. ChIP samples were quantified relative to inputs. A 50 μl aliquot taken from each of 1 ml of sonicated, diluted chromatin before antibody incubation serves as the input, thus the signal from the input samples represents 5% of the total chromatin used in each ChIP.
The library prep was performed on the Apollo system (Wafergen) with the kit PrepX Complete ILMN 32i DNA Library Kit (cat # 400076) and custom adapters.

tag: passage

tag: antibody


title: G2 DH10BGFP_pLys_M1_3

value: PLYS


title: G3 DH10BGFP_pSB1C3_3


title: HEKGFP output, cell 43

description:
Processed_Data.xlsx, sheet 9 HEKGFP #43
original name: SP09_S163
HEKGFP_output_cell_43.fastq.gz


title: INPUT for Ezh2 and Runx1 ChIP-seq


title: EV_NaCl_24h_3


title: HEKGFP output, cell 42

description:
Processed_Data.xlsx, sheet 9 HEKGFP #42
original name: SP09_S162
HEKGFP_output_cell_42.fastq.gz


title: HEKGFP output, cell 41

description:
Processed_Data.xlsx, sheet 9 HEKGFP #41
original name: SP09_S161
HEKGFP_output_cell_41.fastq.gz


title: EV_Con_24h_3


title: HEKGFP output, cell 40

description:
Processed_Data.xlsx, sheet 9 HEKGFP #40
original name: SP09_S160
HEKGFP_output_cell_40.fastq.gz


title: B30 DH10BGFP_None_2


title: Runx1 ChIP-seq Replicate 2

value: Runx1, Abcam, cat no:ab23980, lot:GR184947-1


title: B29 DH10BGFP_None_2

value: 15 min


title: H3K27me3 ChIP-seq Replicate 2


title: H3K27me3 ChIP-seq Replicate 1


title: G1 DH10BGFP_pSB1C3_H3_3


title: HEKGFP output, cell 39

description:
Not processed, insufficient counts
original name: SP09_S159
HEKGFP_output_cell_39.fastq.gz


title: Runx1 ChIP-seq Replicate 1


title: EV_Con_24h_1


title: HEKGFP output, cell 46

description:
Processed_Data.xlsx, sheet 9 HEKGFP #46
original name: SP09_S166
HEKGFP_output_cell_46.fastq.gz


title: skn-1_NaCl_3h_3

value: 3 hours


title: EV_Con_24h_2


title: Ezh2 ChIP-seq Replicate 1

value: Ezh2, Cell Signalling, cat no:5246 , lot:6


title: Ezh2 ChIP-seq Replicate 2


title: B28 MG1655GFP_pD864_2

value: 60 min after induction with rhamnose


title: HEKGFP output, cell 38

description:
Not processed, insufficient counts
original name: SP09_S158
HEKGFP_output_cell_38.fastq.gz

value: Output


title: B26 MG1655GFP_Lux_2

value: Lux

value: 60 min after induction with arabinose


title: HEKGFP output, cell 37

description:
Processed_Data.xlsx, sheet 9 HEKGFP #37
original name: SP09_S157
HEKGFP_output_cell_37.fastq.gz


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ ETPs rep4

data_processing:
Alignment to mm10 genome with transcriptome annotation with Tophat2 (version 2.0.10)
Remove multi-map reads using samtools (version 0.1.19)
Summarise to reads counts with htseq-count (version 0.5.4p5)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

source_name: Early Thymic Precursors

extract_protocol:
100 cells were FACS-sorted directly into lysis buffer
SMARTer; Ramskold et al, Nature Biotechnology 2012: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.

tag: genotype/variation


title: HEKGFP output, cell 36

description:
Processed_Data.xlsx, sheet 9 HEKGFP #36
original name: SP09_S156
HEKGFP_output_cell_36.fastq.gz


title: skn-1_NaCl_3h_2


title: B25 MG1655GFP_pLys_2


title: EV_NaCl_24h_1


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ ETPs rep3


title: skn-1_NaCl_3h_1


title: B24 MG1655GFP_pSB1C3_2


title: B23 MG1655GFP_pLys_M1_2


title: HEKGFP output, cell 35

description:
Processed_Data.xlsx, sheet 9 HEKGFP #35
original name: SP09_S155
HEKGFP_output_cell_35.fastq.gz


title: EV_NaCl_3h_3


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ ETPs rep2


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ Flt3 ITD/+ ETPs rep1


title: HEKGFP output, cell 34

description:
Processed_Data.xlsx, sheet 9 HEKGFP #34
original name: SP09_S154
HEKGFP_output_cell_34.fastq.gz


title: EV_NaCl_3h_2


title: HEKGFP output, cell 33

description:
Processed_Data.xlsx, sheet 9 HEKGFP #33
original name: SP09_S153
HEKGFP_output_cell_33.fastq.gz


title: HEKGFP output, cell 32

description:
Processed_Data.xlsx, sheet 9 HEKGFP #32
original name: SP09_S152
HEKGFP_output_cell_32.fastq.gz


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ ETPs rep4

value: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ ETPs


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ ETPs rep3


title: EV_NaCl_3h_1


title: B21 MG1655GFP_pD864_2

value: 15 min after induction with rhamnose


title: B20 MG1655GFP_pD864_LacZ_2

value: LACZ


title: HEKGFP output, cell 30

description:
Processed_Data.xlsx, sheet 9 HEKGFP #30
original name: SP09_S150
HEKGFP_output_cell_30.fastq.gz


title: B19 MG1655GFP_Lux_2

value: 15 min after induction with arabinose


title: HEKGFP output, cell 31

description:
Processed_Data.xlsx, sheet 9 HEKGFP #31
original name: SP09_S151
HEKGFP_output_cell_31.fastq.gz


title: EV_Con_3h_3


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ ETPs rep2


title: Ezh2 fl/fl Runx1 fl/fl Rag1Cre+ ETPs rep1


title: EV_Con_3h_1


title: Ezh2 fl/fl Runx1 fl/fl ETPs rep4

value: Ezh2 fl/fl Runx1 fl/fl ETPs


title: B18 MG1655GFP_pLys_2


title: HEKGFP output, cell 29

description:
Processed_Data.xlsx, sheet 9 HEKGFP #29
original name: SP09_S149
HEKGFP_output_cell_29.fastq.gz


title: HEKGFP output, cell 28

description:
Processed_Data.xlsx, sheet 9 HEKGFP #28
original name: SP09_S148
HEKGFP_output_cell_28.fastq.gz


title: B22 MG1655GFP_pSB1C3_H3_2


title: B17 MG1655GFP_pSB1C3_2


title: Ezh2 fl/fl Runx1 fl/fl ETPs rep3


title: B15 MG1655GFP_pSB1C3_H3_2


title: Ezh2 fl/fl Runx1 fl/fl ETPs rep2


title: EV_Con_3h_2

value: gravid young adult


title: B14 DH10BGFP_pD864_2


title: Ezh2 fl/fl Runx1 fl/fl ETPs rep1


title: HEKGFP output, cell 27

description:
Processed_Data.xlsx, sheet 9 HEKGFP #27
original name: SP09_S147
HEKGFP_output_cell_27.fastq.gz


title: 03_N2_893_SGkit

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

description: Monosomes were purified using sucrose gradient fractionation and the library was prepared using the library construction protocol of the ARTseq™ Ribosome Profiling Kit (Epicentre)

data_processing:
Library strategy: ribosome profiling
Basecalls performed using RTA v1.17.21.3(sample 5-7) or v1.13.48(other samples). Data converted to FastQ file by bcl2fastq v1.8.4(sample 1-4) or v1.8.3(sample 5-8).
Sequencing adaptors were trimmed using Flexbar v2.5.
rRNA reads were removed using Bowtie2 v2.2.4.
Reads were mapped to reference genome using STAR v2.4. Only unique-mapped reads were kept.
Counting number of reads aligned into CDS regions using costom Julia program.
Calculating RPKM value based on read numbers in CDS regions by 1e+9 * #read / ( #(total CDS reads) * sum_of_CDS_lengths )
Genome_build: WS230
Supplementary_files_format_and_content: tab-delimited text files include CDS-RPKM values for each sample (column) and each coding gene (row).

source_name: Whole-worm

growth_protocol: Egg-prepped C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on peptone rich 2% NGM plates with NA22 for the desired period of time before harvesting

extract_protocol:
Worms were lysed, monosomes purified and RNA was isolated using Tri-reagent (MRC). The RNA from the monosomal fraction was separated using a 15% TBE-Urea Gel (Invitrogen) and the region around 28-30 nucleotides (or the region indicated) excised to isolate Ribosome protected fragments (RPFs). The gel piece was forced through a pierced small tube inside an eppendorf tube by centrifugation and RNA from the gel debris was eluted by overnight incubation in 600 µl cracking buffer (20 mM Tris-HCl (pH 7.9), 1 mM EDTA, 400 mM NH4Acetate, 0.5 % SDS). RNA was precipitated with isopropanol at -80 °C for at least 4 hours (isopropanol precipitation).
RPFs were 3’ dephosphorylated with 10 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer with 40 Units of RNasin for 1 hour at 37 °C. Following isopropanol precipitation, the RNA samples were ligated to 3’ adapters according to the Illumina® TruSeq™ Small RNA Sample Preparation protocol and using the reagents of the kit, then again precipitated with isopropanol. Ligation products were 5’ phosphorylated for 30 minutes at 37 °C with 15 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer, 1 mM ATP and 40 Units of RNasin. Following heat-inactivation of the enzyme for 10 minutes at 70 °C, the RNA was precipitated by isopropanol. Ligation to 5’ adapters, reverse transcription, PCR amplification with barcoded primers and gel-purification of the PCR products were performed using the Illumina® TruSeq™ Small RNA Sample Prep kit. The following barcodes were used: RPIX 2, 4, 6, 7, 12

treatment_protocol: Worms were washed of the plates and subsequently washed three additional times with M9 before extraction of RNA

value: young adult


title: HEKGFP output, cell 26

description:
Not processed, insufficient counts
original name: SP09_S146
HEKGFP_output_cell_26.fastq.gz


title: HEKGFP output, cell 25

description:
Not processed, insufficient counts
original name: SP09_S145
HEKGFP_output_cell_25.fastq.gz


title: HEKGFP output, cell 24

description:
Processed_Data.xlsx, sheet 9 HEKGFP #24
original name: SP09_S144
HEKGFP_output_cell_24.fastq.gz


title: frac_28-35nt

description: For PAGE purification of ribosome-protected fragments, the following region was excised from the gel: 28-35 nucleotides

value: larval stage 4


title: frac_28-30nt

description: For PAGE purification of ribosome-protected fragments, the following region was excised from the gel: 28-30 nucleotides


title: frac_26-34nt

description: For PAGE purification of ribosome-protected fragments, the following region was excised from the gel: 26-34 nucleotides


title: 04_N2_893_GCkit

description: Monosomes were purified using MicroSpin S-400 HR gel filtration columns (GE Healthcare) and the library was prepared using the library construction protocol of the ARTseq™ Ribosome Profiling Kit (Epicentre)


title: frac_25-30nt

description: For PAGE purification of ribosome-protected fragments, the following region was excised from the gel: 25-30 nucleotides


title: B13 DH10BGFP_pD864_LacZ_2


title: 02_N2_893_GCop

description: Monosomes were purified using MicroSpin S-400 HR gel filtration columns (GE Healthcare) and the library was prepared using the library construction protocol described below.


title: B12 DH10BGFP_Lux_2


title: 01_N2_893_SGop

description: Monosomes were purified using sucrose gradient fractionation and the library was prepared using the library construction protocol described below.


title: B11 DH10BGFP_pLys_2

value: PLYS


title: HEKGFP output, cell 23

description:
Processed_Data.xlsx, sheet 9 HEKGFP #23
original name: SP09_S143
HEKGFP_output_cell_23.fastq.gz


title: HEKGFP output, cell 20

description:
Processed_Data.xlsx, sheet 9 HEKGFP #20
original name: SP09_S140
HEKGFP_output_cell_20.fastq.gz


title: HEKGFP output, cell 19

description:
Processed_Data.xlsx, sheet 9 HEKGFP #19
original name: SP09_S139
HEKGFP_output_cell_19.fastq.gz


title: B9 DH10BGFP_pLys_M1_2


title: B10 DH10BGFP_pSB1C3_2


title: HEKGFP output, cell 21

description:
Processed_Data.xlsx, sheet 9 HEKGFP #21
original name: SP09_S141
HEKGFP_output_cell_21.fastq.gz


title: HEKGFP output, cell 18

description:
Processed_Data.xlsx, sheet 9 HEKGFP #18
original name: SP09_S138
HEKGFP_output_cell_18.fastq.gz


title: HEKGFP output, cell 22

description:
Processed_Data.xlsx, sheet 9 HEKGFP #22
original name: SP09_S142
HEKGFP_output_cell_22.fastq.gz


title: B7 DH10BGFP_pD864_2


title: B8 DH10BGFP_pSB1C3_H3_2


title: B16 MG1655GFP_pLys_M1_2


title: B5 DH10BGFP_Lux_2


title: HEKGFP output, cell 16

description:
Processed_Data.xlsx, sheet 9 HEKGFP #16
original name: SP09_S136
HEKGFP_output_cell_16.fastq.gz


title: HEKGFP output, cell 17

description:
Processed_Data.xlsx, sheet 9 HEKGFP #17
original name: SP09_S137
HEKGFP_output_cell_17.fastq.gz


title: HEKGFP output, cell 15

description:
Processed_Data.xlsx, sheet 9 HEKGFP #15
original name: SP09_S135
HEKGFP_output_cell_15.fastq.gz


title: Mouse_ThioMac_RNA_T09-3_EDM_15-07-16

city: La Jolla

first: Jenhan

last: Tao

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Reads from each RNA-Seq sample were aligned to the mm10 build of the mouse genome using STAR.
Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to calculate unnormalized read count (raw_mouse_hepatocyte.tsv and raw_mouse_thiomac.tsv) and RPKM (rpkm_mouse_hepatocyte.tsv and rpkm_mouse_thiomac.tsv) from the gene bodies of RefSeq genes and other analyses in the study. Statistical tests in this study were performed using custom Python scripts.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include a expression text file that contains unnormalized expression values (raw_mouse_hepatocyte.tsv and raw_mouse_thiomac.tsv) as well as normalized (RPKM, rpkm_mouse_hepatocyte.tsv and rpkm_mouse_thiomac.tsv) expression values for each sample (calculated using default HOMER parameters).  All genomic coordinates for mouse samples are relative to the mm10 genome assembly.

molecule: polyA RNA

source_name: thioglycollate elicited macrophage cells

growth_protocol: RPMI-1640 or Hepatozyme (as specified above)

extract_protocol:
RNA was isolated using Trizol and Direct-zol columns (Zymo)
PolyA mRNA was selected from total RNA prior to fragmentation, first strand and second strand synthesis incorporating deoxy-UTP. Following dA-tailing and barcode adapter ligation the product was PCR amplified and subsequently size-selected (223-375 bp) using TBE gel electrophoresis.  The excised library was purified prior to sequencing.

treatment_protocol: Twenty four hours prior to treatment, cells were placed in media supplemented with 10% lipid deficient FBS with 50 uM mevalonate and 10 uM mevastatin. Cells remained in lipid-deficient media for 18-20 hours after addition of ligand

tag: media

value: RPMI + 10% FBS


title: Mouse_ThioMac_RNA_Vehicle-3_EDM_15-07-16

value: thioglycollate elicited macrophage cells

value: Vehicle (DMSO / EtOH)


title: B3 DH10BGFP_pSB1C3_2


title: Mouse_ThioMac_RNA_T09-2_EDM_15-07-16


title: HEKGFP output, cell 12

description:
Processed_Data.xlsx, sheet 9 HEKGFP #12
original name: SP09_S132
HEKGFP_output_cell_12.fastq.gz


title: B1 DH10BGFP_pSB1C3_H3_2


title: B6 DH10BGFP_pD864_LacZ_2


title: R30 DH10BGFP_None_1

value: 60 min


title: Mouse_ThioMac_RNA_T09-1_EDM_15-07-16


title: HEKGFP output, cell 11

description:
Processed_Data.xlsx, sheet 9 HEKGFP #11
original name: SP09_S131
HEKGFP_output_cell_11.fastq.gz


title: Mouse_ThioMac_RNA_Mepip-2_EDM_15-07-16

value: MePipHCA 1 uM


title: Mouse_ThioMac_RNA_Mepip-3_EDM_15-07-16


title: HEKGFP output, cell 14

description:
Processed_Data.xlsx, sheet 9 HEKGFP #14
original name: SP09_S134
HEKGFP_output_cell_14.fastq.gz

value: Output


title: HEKGFP output, cell 10

description:
Processed_Data.xlsx, sheet 9 HEKGFP #10
original name: SP09_S130
HEKGFP_output_cell_10.fastq.gz


title: Mouse_ThioMac_RNA_Vehicle-2_EDM_15-07-16


title: HEKGFP output, cell 9

description:
Processed_Data.xlsx, sheet 9 HEKGFP #9
original name: SP09_S129
HEKGFP_output_cell_9.fastq.gz


title: Mouse_ThioMac_RNA_Vehicle-1_EDM_15-07-16


title: R29 DH10BGFP_None_1

value: 15 min


title: Mouse_ThioMac_RNA_Mepip-1_EDM_15-07-16


title: HEKGFP output, cell 8

description:
Not processed, insufficient counts
original name: SP09_S128
HEKGFP_output_cell_8.fastq.gz


title: HEKGFP output, cell 13

description:
Processed_Data.xlsx, sheet 9 HEKGFP #13
original name: SP09_S133
HEKGFP_output_cell_13.fastq.gz


title: B2 DH10BGFP_pLys_M1_2


title: R27 MG1655GFP_pD864_LacZ_1

value: 60 min after induction with rhamnose


title: B27 MG1655GFP_pD864_LacZ_2


title: R28 MG1655GFP_pD864_1


title: R26 MG1655GFP_Lux_1

value: Lux

value: 60 min after induction with arabinose


title: R25 MG1655GFP_pLys_1


title: Mouse_ThioMac_RNA_GW-2_EDM_15-07-16


title: Mouse_ThioMac_RNA_GW-3_EDM_15-07-16


title: Mouse_ThioMac_RNA_GW-1_EDM_15-07-16


title: HEKGFP output, cell 6

description:
Processed_Data.xlsx, sheet 9 HEKGFP #6
original name: SP09_S126
HEKGFP_output_cell_6.fastq.gz


title: HEKGFP output, cell 5

description:
Processed_Data.xlsx, sheet 9 HEKGFP #5
original name: SP09_S125
HEKGFP_output_cell_5.fastq.gz


title: R24 MG1655GFP_pSB1C3_1


title: Mouse_ThioMac_RNA_DMHCA-3_EDM_15-07-16

value: DMHCA 1 uM


title: R23 MG1655GFP_pLys_M1_1


title: Mouse_ThioMac_RNA_DMHCA-2_EDM_15-07-16


title: Mouse_ThioMac_RNA_DMHCA-1_EDM_15-07-16


title: R22 MG1655GFP_pSB1C3_H3_1


title: Mouse_ThioMac_RNA_Des-3_EDM_15-07-16

value: desmosterol 10 uM


title: HEKGFP output, cell 2

description:
Processed_Data.xlsx, sheet 9 HEKGFP #2
original name: SP09_S122
HEKGFP_output_cell_2.fastq.gz


title: HEKGFP output, cell 7

description:
Not processed, insufficient counts
original name: SP09_S127
HEKGFP_output_cell_7.fastq.gz


title: R21 MG1655GFP_pD864_1

value: 15 min after induction with rhamnose


title: Mouse_ThioMac_RNA_Des-2_EDM_15-07-16


title: HEKGFP single cell input, replicate 3

description:
Processed_Data.xlsx, sheet 9, Input 3
original name: SP09_S111
HEKGFP_single_cell_input_replicate_3.fastq.gz

value: Input


title: HEKGFP output, cell 3

description:
Processed_Data.xlsx, sheet 9 HEKGFP #3
original name: SP09_S123
HEKGFP_output_cell_3.fastq.gz


title: R19 MG1655GFP_Lux_1

value: 15 min after induction with arabinose


title: R20 MG1655GFP_pD864_LacZ_1

value: LACZ


title: HEKGFP output, cell 1

description:
Processed_Data.xlsx, sheet 9 HEKGFP #1
original name: SP09_S121
HEKGFP_output_cell_1.fastq.gz


title: Mouse_ThioMac_RNA_Des-1_EDM_15-07-16


title: HEKGFP single cell input, replicate 1

description:
Processed_Data.xlsx, sheet 9, Input 1
original name: SP09_S109
HEKGFP_single_cell_input_replicate_1.fastq.gz


title: Mouse_Hepatocyte_RNA_Vehicle-2_EDM_15-07-30

source_name: hepatocyte cells

value: hepatocyte cells

value: Hepatozyme + 10%  FBS


title: G6 DH10BGFP_pD864_LacZ_3


title: R18 MG1655GFP_pLys_1

value: PLYS


title: R16 MG1655GFP_pLys_M1_1


title: Neupt11

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Libraries were sequenced using the Nextseq500 platform (Illumina), producing single end reads of 75bp (Utrecht Sequencing Facility). Reads were aligned to the human reference genome GRCh37 using STAR version 2.4.2a. Picard’s AddOrReplaceReadGroups (v1.98) was used to add read groups to the BAM files, which were sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1 using the union mode.
Genome_build: GRCh38
Supplementary_files_format_and_content: [.txt] Raw read counts per gene

source_name: peripheral neutrophils

extract_protocol:
Neutrophils from whole blood leukocytes were sorted based on positive expression of CD16 and negative expression of CD14 (monocytes) and CD41 (platelets attached to neutrophils); sorting was performed using FACSAriaIII (BD). Neutrophils were lysed in Trizol LS (Thermo Fisher) directly after sorting.
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

tag: disease state

value: systemic JIA patient

value: peripheral neutrophils


title: HEKGFP output, cell 4

description:
Processed_Data.xlsx, sheet 9 HEKGFP #4
original name: SP09_S124
HEKGFP_output_cell_4.fastq.gz


title: Mouse_Hepatocyte_RNA_T09-2_EDM_15-07-30


title: P493 MycBACKON output, replicate 3

description:
Processed_Data.xlsx, sheet 6, P493-6 MycBACKON R3
original name: SP05_S77
P493_MycBACKON_output_replicate_3.fastq.gz


title: Neupt10


title: B4 DH10BGFP_pLys_2


title: R15 MG1655GFP_pSB1C3_H3_1


title: Mouse_Hepatocyte_RNA_T09-1_EDM_15-07-30


title: HEKGFP single cell input, replicate 2

description:
Processed_Data.xlsx, sheet 9, Input 2
original name: SP09_S110
HEKGFP_single_cell_input_replicate_2.fastq.gz


title: Mouse_Hepatocyte_RNA_Mepip-2_EDM_15-07-30

value: MePipHCA 1 uM


title: R13 DH10BGFP_pD864_LacZ_1


title: R17 MG1655GFP_pSB1C3_1


title: NeuHC104

value: healthy control


title: P493 MycBACKON output, replicate 4

description:
Processed_Data.xlsx, sheet 6, P493-6 MycBACKON R4
original name: SP05_S78
P493_MycBACKON_output_replicate_4.fastq.gz

value: Output


title: Neupt8


title: R14 DH10BGFP_pD864_1

value: 60 min after induction with rhamnose


title: Mouse_Hepatocyte_RNA_Vehicle-1_EDM_15-07-30

value: Vehicle (DMSO / EtOH)


title: NeuHC082


title: NeuHC085


title: P493 MycOFF output, replicate 4

description:
Processed_Data.xlsx, sheet 6, P493-6 MycOFF R4
original name: SP05_S69
P493_MycOFF_output_replicate_4.fastq.gz


title: P493 MycBACKON output, replicate 1

description:
Processed_Data.xlsx, sheet 6, P493-6 MycBACKON R1
original name: SP05_S75
P493_MycBACKON_output_replicate_1.fastq.gz


title: R11 DH10BGFP_pLys_1

value: 60 min after induction with arabinose


title: R12 DH10BGFP_Lux_1

value: Lux


title: Mouse_Hepatocyte_RNA_GW-2_EDM_15-07-30


title: P493 MycOFF output, replicate 3

description:
Processed_Data.xlsx, sheet 6, P493-6 MycOFF R3
original name: SP05_S68
P493_MycOFF_output_replicate_3.fastq.gz


title: Mouse_Hepatocyte_RNA_GW-1_EDM_15-07-30


title: P493 MycOFF output, replicate 2

description:
Processed_Data.xlsx, sheet 6, P493-6 MycOFF R2
original name: SP05_S67
P493_MycOFF_output_replicate_2.fastq.gz


title: Mouse_Hepatocyte_RNA_DMHCA-2_EDM_15-07-30

value: DMHCA 1 uM


title: P493 MycOFF output, replicate 1

description:
Processed_Data.xlsx, sheet 6, P493-6 MycOFF R1
original name: SP05_S66
P493_MycOFF_output_replicate_1.fastq.gz


title: R10 DH10BGFP_pSB1C3_1


title: R9 DH10BGFP_pLys_M1_1


title: Mouse_Hepatocyte_RNA_DMHCA-1_EDM_15-07-30


title: P493 MycBACKON output, replicate 2

description:
Processed_Data.xlsx, sheet 6, P493-6 MycBACKON R2
original name: SP05_S76
P493_MycBACKON_output_replicate_2.fastq.gz


title: Mouse_Hepatocyte_RNA_Mepip-1_EDM_15-07-30


title: Mouse_Hepatocyte_RNA_Des-2_EDM_15-07-30

value: desmosterol 10 uM


title: P493 MycON output, replicate 4

description:
Processed_Data.xlsx, sheet 6, P493-6 MycON R4
original name: SP05_S65
P493_MycON_output_replicate_4.fastq.gz


title: R8 DH10BGFP_pSB1C3_H3_1


title: R7 DH10BGFP_pD864_1

value: 15 min after induction with rhamnose


title: P493 MycON output, replicate 3

description:
Processed_Data.xlsx, sheet 6, P493-6 MycON R3
original name: SP05_S64
P493_MycON_output_replicate_3.fastq.gz


title: R5 DH10BGFP_Lux_1

value: 15 min after induction with arabinose


title: R6 DH10BGFP_pD864_LacZ_1

value: LACZ


title: HEKCDCP1 ON output, replicate 2

description:
Not processed, insufficient counts
original name: SP09_S50
HEKCDCP1_ON_output_replicate_2.fastq.gz


title: HEKCDCP1 ON output, replicate 3

description:
Processed_Data.xlsx, sheet 5, HEKCDCP1 ON R3
original name: SP09_S51
HEKCDCP1_ON_output_replicate_3.fastq.gz


title: R4 DH10BGFP_pLys_1


title: P493 MycON output, replicate 2

description:
Processed_Data.xlsx, sheet 6, P493-6 MycON R2
original name: SP05_S63
P493_MycON_output_replicate_2.fastq.gz


title: HEKCDCP1 ON output, replicate 1

description:
Processed_Data.xlsx, sheet 5, HEKCDCP1 ON R1
original name: SP09_S49
HEKCDCP1_ON_output_replicate_1.fastq.gz


title: HEKCDCP1 OFF output, replicate 3

description:
Processed_Data.xlsx, sheet 5, HEKCDCP1 OFF R3
original name: SP09_S54
HEKCDCP1_OFF_output_replicate_3.fastq.gz


title: P493 MycON output, replicate 1

description:
Processed_Data.xlsx, sheet 6, P493-6 MycON R1
original name: SP05_S62
P493_MycON_output_replicate_1.fastq.gz


title: R2 DH10BGFP_pLys_M1_1


title: R3 DH10BGFP_pSB1C3_1


title: 80S_7-8h_emb

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

data_processing:
The samples prepared by "small RNA, Barcode" protocol and sequenced on Illumunia Genome Analyser II platform. 3 to 4 samples run in the same channel and each sequence attributed to corresponding sample according to their barcode sequences (first 4 bases) by allowing one mismatch.  The sequences seperated into "fastq" files in the "SampleName_(barcode).fastq" files as raw data. Because in some samples single error in the barcode resulted in the same barcode, sequences with shared barcode were removed from further data. All samples provided sequenced with the same adapter sequence "5'-ATCTCGTATGCCGTCTTCTGCTTGT-3'". The 3' adaptor from the sequences were removed at three steps for each sample; (1) full adaptor sequence used for searching adaptor that allowed insert size smaller than 7 nt. (2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 3 bases permits identifying inserts of up to 29 bases in the samples, (3) Finally the remaining reads are search for not exact matches of the adapter. The first 3 bases of the adapter were searched within the full read sequences and at least 80% of the following bases must be identical to the adapter sequence (max 28 nt). The inserts are given in "fastq" format into "SampleName_0-29_nt_inserts.fastq" files. After trimming of the 3' adaptor remaining sequences are given as with "SampleName_NoAdaptor_inserts.fastq" files. The barcode and 3' adaptor trimming done by an in house-written-scripts in Python. From the "SampleName_0-29_nt_inserts.fastq" files sequences in range of 15-29 nt were seperated. Also from these files, read sequences with more than one "N" or poly(A) were removed and not used for further data analyses. The insert sequences are given in "SampleName_15-29_nt_inserts.txt". Then sequences aligned to the Drosophila melangoaster genome (FB2012_01/dmel_r5.43). In order to align sequences to the Drosophila genome, all chromosome sequences including chrU and mitochondrial genome but not chrUextra were downloaded from flybase (www.flybase.org) and tRNA sequences downloaded fom flybase. 5'-CCA-3' sequences (post-trancriptionally added to mature tRNA, no genomic template for CCA encoded by the genome) appended to mature tRNA and by using "nexalign"(downloaded from http://genome.gsc.riken.jp/osc/english/dataresource/) sequences aligned to both genome and tRNA sequences as; firstly sequences aligned for exact match, then remaning sequences aligned for one error (1 mismatch or 1 insertion or 1 deletion, mindel) and the same alignment done for 2 mismatch and 3 mismatch. Remaning sequences assumed not to be aligned to the genome and grouped as "unmapped", eventhough some sequences may align to exon-exon juctions. The results are plotted in "read-alignments-to-drosophila-genome. xls" file.
Genome Build: FB2012_01/dmel_r5.43
Supplementary_files_format_and_content: There are 4 processed data files formats: (1) Inserts sequence in fastq format, (2) inserts sequences with tab-delimited text files (txt) (insert sequence and read frequency), (3) inserts with no adapters in fastq format, and (4) alignment of the reads to Drosophila genome in Excel format (xls).

organism: Drosophila melanogaster

growth_protocol: Drosophila melanogaster flies expanded on agar, yeast, corn and sucrose medium at 22-25 ˚C. 3-5 days old flies were allowed to lay eggs on 2-3-day-old flies were allowed to lay eggs for 1h on embryo collection plates containing grape juice (0-1h embryos).To collect 7-8h embryos, plates were removed from the cage and incubated at 22-25ºC for 7h. The embryos were gently brushed away from the plates, washed with 0.7% NaCl and 0.1% Triton-X and stored at -80ºC until use.

extract_protocol: 3 replicates from unfractionated total RNAs and fractionated mRNP, 60S, 80S(monosomal) and polysomal RNAs of 0-1h and 7-8h old embryos were mixed in equal amounts and sequenced using Illumina Genome Analyzer by Fasteris (Switzerland).

value: 7-8h old embryo

tag: fraction

value: 80S (monosome)  fraction


title: HEKCDCP1 OFF output, replicate 2

description:
Processed_Data.xlsx, sheet 5, HEKCDCP1 OFF R2
original name: SP09_S53
HEKCDCP1_OFF_output_replicate_2.fastq.gz


title: Poly_7-8h_emb

value: Polysome  fraction


title: mRNP_7-8h_emb

value: mRNP fraction


title: Tot_7-8h_emb

value: Total RNA


title: Mouse_Hepatocyte_RNA_Des-1_EDM_15-07-30

value: hepatocyte cells

value: Hepatozyme + 10%  FBS


title: HEKCDCP1 OFF output, replicate 1

description:
Processed_Data.xlsx, sheet 5, HEKCDCP1 OFF R1
original name: SP09_S52
HEKCDCP1_OFF_output_replicate_1.fastq.gz

value: Output


title: Poly_0-1h_emb

value: 0-1h old embryo


title: 80S_0-1h_emb


title: HEKCDCP1 input, replicate 3

description:
Processed_Data.xlsx, sheet 5, Input R3
original name: SP09_S42
HEKCDCP1_input_replicate_3.fastq.gz

value: Input


title: HeLa (p77-infected) γ-H2AX ChIP-seq

city: beijing

first: XiaLu

last: Li

address: 105 Xisanhuan Beilu

institute: Capital Normal University

description: raw data with 4-nucleotide barcodes TGCT

data_processing:
Barcode splitter: All our libraries had 4nt barcodes at the 5 prime of each reads (ACGT for P77 RNA polymerase II chip-seq, GTAT for PL3.7 RNA polymerase II chip-seq, TGCT for P77 γH2AX chip-seq and CATT for PL3.7 γH2AX chip-seq). We splitted data according to the barcodes. Both P77 RNA polymerase II and γH2AX chip-seq had two replicates. We merged those two replicates into a single file and analyzed them together.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata" Total reads used to map was 27.7M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 18.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 35.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 16M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample. After alignment 21.2M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 15.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 22.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 12.3M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample maped to the genome
Peak calling: Peak calling was performed by MACS and SICER by default parameter except for band width: 200 bps for MACS and Windowsize: 50 bps, Fragment size: 200 bps, Gap size: 150 bps and Evalue for identification of significant islands: 100 for SICER
Wiggle file: The number of ChIP-Seq reads across the genome, in 50 bp non-overlapping bins was summarized and performed rank quantile normalization for P77 and PLL3.7.
Genome Build:
TGCT.HeLa (p77-infected) +-H2AX ChIP-seq.bed: hg18
TGCT.HeLa (p77-infected) +-H2AX ChIP-seq.wig: hg18

source_name: HeLa

growth_protocol: HeLa cells were culture in DMEM medium supplemented with 10% fetal bovine serum.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 250 and 350bp (representing shear fragments between 150 and 250nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: HeLa cells were transduced with EGFP-p77 virus or control pLL3.7 virus in the presence of 8 μg/ml polybrene. 72hr after transduction, cells were subjected to ChIP analysis.

tag: chip antibody

tag: antibody catalog number

tag: antibody vendor

value: Millipore

tag: infection


description: raw data with 4-nucleotide barcodes ACGT

data_processing:
Barcode splitter: All our libraries had 4nt barcodes at the 5 prime of each reads (ACGT for P77 RNA polymerase II chip-seq, GTAT for PL3.7 RNA polymerase II chip-seq, TGCT for P77 γH2AX chip-seq and CATT for PL3.7 γH2AX chip-seq). We splitted data according to the barcodes. Both P77 RNA polymerase II and γH2AX chip-seq had two replicates. We merged those two replicates into a single file and analyzed them together.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata" Total reads used to map was 27.7M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 18.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 35.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 16M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample. After alignment 21.2M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 15.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 22.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 12.3M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample maped to the genome
Peak calling: Peak calling was performed by MACS and SICER by default parameter except for band width: 200 bps for MACS and Windowsize: 50 bps, Fragment size: 200 bps, Gap size: 150 bps and Evalue for identification of significant islands: 100 for SICER
Wiggle file: The number of ChIP-Seq reads across the genome, in 50 bp non-overlapping bins was summarized and performed rank quantile normalization for P77 and PLL3.7.
Genome Build:
ACGT.HeLa (p77-infected) RNA polymerase II ChIP-seq.bed: hg18
ACGT.HeLa (p77-infected) RNA polymerase II ChIP-seq.wig: hg18

value: RNA polymerase II

value: Abcam


title: Dox-treated HCT116-C52 cells

description: raw data with 4-nucleotide barcodes CATT

data_processing:
Barcode splitter: All our libraries had 4 nt barcodes at the 5 prime of each reads (CATT for Dox-treated HCT116-C52 and ACGT for Dox-released HCT116-C52-tTA cells). We splitted data according to the barcodes.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata". Total reads used to map was 9.8M reads for Dox-treated HCT116-C52 and 10M reads for Dox-released HCT116-C52-tTA sample. After alignment 8.3M reads for Dox-treated HCT116-C52 and 8.5M reads maped to the genome.
Peak calling: Peak calling was performed by MACS by default parameter except for band width: 200 bps mfold: 10
Wiggle file: wiggle file was generated by MACS
Genome Build:
C52.Dox.bed: hg18

growth_protocol: HCT116-C52-tTA, were cultured in IMDM medium supplemented with 10% fetal bovine serum.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 200 and 300bp (representing shear fragments between 100 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: HCT116-C52-tTA cells were treated with or without 1ug/ml doxycycline for 48h and subjected to ChIP analysis.

value: abcam

tag: cell line

value: Dox-treated


title: 60S_7-8h_emb

value: 60S fraction


title: HEKCDCP1 input, replicate 2

description:
Processed_Data.xlsx, sheet 5, Input R2
original name: SP09_S41
HEKCDCP1_input_replicate_2.fastq.gz

data_processing:
Instructions, scripts, and examples at https://github.com/sbpollock/phage-counting-perl
Create reference library (0-format-indices.pl)
Count each .fastq.gz file against the reference library (1-count-parallel.pl)
Combine and format processed data file (2-format-counts.pl)
Open .txt file in Excel and save as a .xls or .xlsx file
Genome_build: Not applicable here
Supplementary_files_format_and_content: Counts in a ".xls" spreadsheet

tag: input or output

tag: experiment


title: mRNP_0-1h_emb


title: HEKCDCP1 input, replicate 1

description:
Processed_Data.xlsx, sheet 5, Input R1
original name: SP09_S40
HEKCDCP1_input_replicate_1.fastq.gz


title: LAX7R output, replicate 4

description:
Processed_Data.xlsx, sheet 4, LAX7R R4
original name: SP05_S73
LAX7R_output_replicate_4.fastq.gz


title: Dox-released HCT116-C52-tTA cells

data_processing:
Barcode splitter: All our libraries had 4 nt barcodes at the 5 prime of each reads (CATT for Dox-treated HCT116-C52 and ACGT for Dox-released HCT116-C52-tTA cells). We splitted data according to the barcodes.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata". Total reads used to map was 9.8M reads for Dox-treated HCT116-C52 and 10M reads for Dox-released HCT116-C52-tTA sample. After alignment 8.3M reads for Dox-treated HCT116-C52 and 8.5M reads maped to the genome.
Peak calling: Peak calling was performed by MACS by default parameter except for band width: 200 bps mfold: 10
Wiggle file: wiggle file was generated by MACS
Genome Build:
C52.Release.bed: hg18
C52_Release.wig: hg18

value: Dox-released


title: drug-sensitive (JAP)

data_processing:
The samples pepared by "small RNA, Barcode" protocol and sequenced on Illumunia Genome Analyser II platform. 3 to 4 samples run in the same channel and each sequence attributed to corresponding sample according to their barcode sequences (first 4 bases) by allowing one mismatch.  The sequences seperated into "fastq" files in the "SampleName_(barcode).fastq" files. Because in some samples single error in the barcode resulted in the same barcode, sequences with shared barcode were removed from further data. JNN, JAN and JAP were sequenced with "5'-ATCTCGTATGCCGTCTTCTGCTTGT-3'"  adaptor. The 3' adaptor from the sequences were removed at three steps for each sample; (1) full adaptor sequence used for searching adaptor that allowed insert size smaller than 15 nt. (2) If no adapter sequence was found, in successive steps the last base of the adapter was removed and the sequence was searched at the end of the reads. The minimum adapter size of 3 bases permits identifying inserts of up to 29 bases. (3) Finally, the remaining reads are search for not exact matches of the adapter. The first 3 bases of the adapter were searched within the full read sequences and at least 75% of the following bases must be identical to the adapter sequence (max 28 nt). The inserts are given in "fastq" format into "SampleName_0-29_nt_inserts.fastq" files. After trimming of the 3' adaptor remaining sequences are given as with "SampleName_NoAdaptor_inserts.fastq" files. The barcode and 3' adaptor trimming done by an in-house-written-scripts in Python. From the "SampleName_0-29_nt_inserts.fastq" files sequences in range of 15-29 nt were seperated. Also from these files, read sequences with more than one "N" or Poly(A) were removed and not used for further data analyses. The insert sequences are given in "SampleName_15-29_nt_inserts.txt" files. Then, sequences aligned to the Human Genome (Homo sapiens, hg19/GRCh37). In order to align sequences to the Human Genome, all chromosome sequences downloaded from UCSC  (http://genome.ucsc.edu/) and tRNA sequences downloaded fom flybase GtRNAd (http://gtrnadb.ucsc.edu/) and/or from literature. 5'-CCA-3' sequences (post-trancriptionally added to mature tRNA, no genomic template for CCA encoded by the genome) appended to mature tRNA and by using "nexalign" (downloaded from http://genome.gsc.riken.jp/osc/english/dataresource/) sequences aligned to both genome and tRNA sequences as; firstly sequences aligned for exact match, then remaning sequences aligned for one error (1 mismatch or 1 insertion or 1 deletion, mindel) and the same alignment done for 2 mismatch and 3 mismatch. Remaning sequences assumed not to be aligned to the genome and grouped as "unmapped", eventhough some sequences may align to exon-exon juctions. The results are plotted in "JNN_JAN_JAP_alignments_to_hg19.xlsx" file.
Genome Build: hg19/GRCh37
Supplementary_files_format_and_content: The processed data files are tab-delimited text files with read sequence and read frequency.

source_name: drug-sensitive (JAP)

growth_protocol: Cells cultured at standart RPMI media at 37˚C in 5% CO2 incubator

extract_protocol: From JNN, JAN and JAP cell populations Total RNA isolated by miRVana microRNA isolation kit and RNA treated with TurboDNase kit (Rnase free) to remove genomic DNA contamination. After RNA quality control by Bioanalyser (Agilent 2100), 1 ?g total RNA from each sample sent to Fasteris for small RNA cloning by Illuminia Genome Analyser II. Sample for deep-sequencing prepared by illumina procedure as "small RNA, barcoded" protocol by Fasteris.

treatment_protocol: Cells treated with 8 μg/ml Camptothecin for 4 hour at 37?C in 5% CO2 incubator. Untreated and treated cells were fractionated by magnetic beads conjugated with Annexin-V. From untreated cells "Jurkat Campthotecin Negative Apoptosis Negative" (JNN), and "Jurkat Camptothecin Negative Apoptosis Positive" (JNP), and from campthotecin treated cells "Jurkat Camptotecin Postive Apoptosis Negative" (JAN) and "Jurkat Campthotecin Positive Apoptosis Positive" (JAP) cells obtained by magnetic beads. Then from JNN (Negative Control), JAN(Camptothecin Insensitive) and JAP (Camptothecin Positive) cell pools small RNA were sequenced by Illumina Genome Analyser II platform.

tag: cell type

value: Jurkat T-cell Lymphocyte

value: Camptothecin Treated

tag: apoptosis

value: Apoptosis Positive


title: R1 DH10BGFP_pSB1C3_H3_1

data_processing:
paired end sequencing with Illumina HiSeq 2500 Sequencer
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using TrimGalore version 0.4.1, then mapped to mm8 whole genome using bwa mem version 0.7.12 with default parameters
Numer of reads per gene were counted using Bioconductor Rsubread package v1.12.6
Genome_build: Samples from strain MG1655GFP were mapped to the reference geneome Escherichia coli str. K-12 substr. MG1655, assembly ASM584v2.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit.
Genome_build: Samples from strain DH10BGFP were mapped to the reference geneome Escherichia coli str. K-12 substr. DH10B, assembly ASM1942v1.31 complemented with the GFP sequence, and the sequence of corresponding synthetic circuit.
Supplementary_files_format_and_content: CSV files providing the number of reads mapping to each genomic gene

tag: strain

tag: plasmid

tag: synthetic circuit

tag: treatment

value: 15 min after induction with arabinose


title: insensitive (JAN)

source_name: insensitive (JAN)

value: Apoptosis Negative


title: LAX7R output, replicate 3

description:
Processed_Data.xlsx, sheet 4, LAX7R R3
original name: SP05_S72
LAX7R_output_replicate_3.fastq.gz

extract_protocol:
For cell populations, phage were eluted from cells in 900uL of 0.1M acetic acid for 5mins, cells were spun down 5mins, and 800uL eluent was transferred to 100uL 1M Tris pH 7.5 to neutralize. To the 100uL of neutralized eluent, 1mL of log phase XL-1 bacteria grown up in tetracycline media was added. This tube was shaken at 37C for 20mins, 1E10cfu/mL helper phage was added and shaker at 37C for 20mins, and the infected mix transferred to a 250mL flask containing 30mL of 2xYT+carbenicillin+kanamycin. This flask was shaken 18-20hrs, cells were spun out, and a propagated supernatant boiled in a 96-well PCR plate. For single cell, cells were sorted into individual wells containing 100uL 2xYT media (no elution step) in 96-well plates. 100uL of log phase XL-1 blue bacteria grown in tetracycline was added and propagated by deep well plate at 999rpm, 37C for 24hrs. Work-up was then carried out as above.
To amplify the H3 “barcode” of each phagemid for sequencing, 3µL of boiled propagate and 4µL of 5uM each forward and reverse primers was combined into 43µL of Phusion master mix (New England Biolabs, M0530S) in a 96-well PCR plate (Biorad, HSP9621). Primer design is as follows (shown 5’ to 3’ on both primers, order as shown): AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTGAGGACACTGCCGTCTATTATTGTGCTCGC (forward), CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGACCAGGGTTCCTTGACCCCAGTAGTC (reverse), where NNNNNNNN are substituted with the appropriate dual indices (Nextera Dual Index). The plate was sealed with PCR foil (Excel Scientific, F-96-100) and the complete mix was run on a thermocycler (2˚C/second ramp rate) as follows: step 1_98˚C, 5min; steps 2 to 4_98-60-72˚C, 20-15-15sec; repeat steps 2-4 11 more times; step 5_72˚C,5min; step 6_hold 12˚C. Solid Phase Reverse Immobilization (SPRI) beads were used to purify amplicons (Agencourt AmpureXP beads or similar): 35µL of each amplicon solution was mixed with 65µL ddH2O. 120µL of SPRI beads were added to each well and mixed. The beads were washed twice with 800µL of 80% ethanol, allowed to dry 5-10mins, and eluted in 50µL of water, using either a magnetic stand or a Kingfisher FLEX bead handling system. Samples were run out on 96-well 2% agarose gels to check for the presence of the amplicon band and the absence of primer bands. Samples were combined (2µL per sample or at least 500µL total volume, whichever volume is greater), dried overnight (Genevac, EZ-2 Mk2), re-suspended in 1/10 volume water (i.e. dry 500µL, re-suspend 50µL), and quantified using a nanodrop. The library was then transferred to a 1.7mL low-bind tube (Corning Axygen, MCT-175-L-C) and submitted to a sequencing facility for analysis on a HiSeq4000, along with a custom sequencing primer (order as shown): TGAGGACACTGCCGTCTATTATTGTGCTCGC.


title: LAX7R output, replicate 1

description:
Processed_Data.xlsx, sheet 4, LAX7R R1
original name: SP05_S70
LAX7R_output_replicate_1.fastq.gz


title: Tot_0-1h_emb

tag: age

value: Total RNA


title: control (JNN)

source_name: control (JNN)

value: No Camptothecin


title: LAX7D output, replicate 4

description:
Processed_Data.xlsx, sheet 4, LAX7D R4
original name: SP05_S82
LAX7D_output_replicate_4.fastq.gz

source_name: M13K07 bacteriophage displaying Fabs on a Herceptin scaffold

value: Output


title: LAX7D output, replicate 3

description:
Processed_Data.xlsx, sheet 4, LAX7D R3
original name: SP05_S81
LAX7D_output_replicate_3.fastq.gz


title: LAX7D output, replicate 2

description:
Processed_Data.xlsx, sheet 4, LAX7D R2
original name: SP05_S80
LAX7D_output_replicate_2.fastq.gz


title: LAX7D output, replicate 1

description:
Processed_Data.xlsx, sheet 4, LAX7D R1
original name: SP05_S79
LAX7D_output_replicate_1.fastq.gz


title: dusp2um287/um287;dusp6um286/um286 mutant replicate 3

city: Worcester

first: Jennifer

last: Maurer

state: MA

address: 364 Plantation Street, LRB 870D

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

data_processing:
reads quality check with FastQC
alignment and read counts with RSEM_v1.2.28
Normalized abundance measurements and identification of differentially expressed genes with DESeq2
Genome_build: GRCz10/DanRer7
Supplementary_files_format_and_content: .tsv containing read count tmp values from each replicate, adjusted p-values, and fold change compared to wildtype samples from DEseq2 for all genes detected and selected genes

organism: Danio rerio

source_name: whole 18hpf embryo

growth_protocol: zebrafish egg water maintained at 28°C

extract_protocol:
Total RNA was extracted from pools of dechrionated, deyolked wildtype and dusp2um287/um287;dusp6um286/um286 embryos at 18hpf using the RNeasy Mini Kit (Qiagen).
Three libraries from wildtype embryos and three libraries from dusp2um287/um287;dusp6um286/um286 embryos were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

tag: genotype


title: LAX7D input, MycBACKON input

description:
Processed_Data.xlsx, sheet 4, Input LAX7D + sheet 6, Input MycBACKON
original name: SP05_S74
LAX7D_MycBACKON_input.fastq.gz


title: LAX7R input, MycON+MycOFF input

description:
Processed_Data.xlsx, sheet 4, Input LAX7R + sheet 6, Input MycON
original name: SP05_S61
LAX7R_MycON_MycOFF_input.fastq.gz


title: 60S_0-1h_emb

value: 0-1h old embryo


title: HeLaGFP output, replicate 1

description:
Processed_Data.xlsx, sheet 3, HG1
original name: SP04_S14
HeLaGFP_output_replicate_1.fastq.gz


title: vector_DGE

city: Changsha

first: Wei

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

data_processing:
Raw sequences were transformed into clean tags by data-processing steps using bio-perl scripts, then about 0.22 and 0.24 million non-redundant tags with high qualities were contained in treated and control groups, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contains a table with data matrix seperated by tabs. The table header descriptions are: Tag (tag sequence), CopyNumber (copy number of tags) and TPM (Transcript Per Million)

source_name: embryonic kidney cells

growth_protocol: HEK293 cells were grown in DMEM media containing 10% FBS

extract_protocol:
The total RNA was used for mRNA purification using oligo-dT magnetic beads adsorption, and then oligo-dT was used to guide reverse transcription to synthesize double-stranded cDNA.The generation of 5' ends of tags was recognized by endonuclease NlaIII, which recognizes and cuts off the CATG sites on cDNA.Then, cDNA fragments with 3' ends were purified by magnetic beads precipitation, and Illumina adapter 1 was added to their 5' ends. The junction of Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the 21 bp unique tags with adaptor 1 were purified and ligated to the adaptor 2 to form a cDNA tag library. These adapter-ligated cDNA tags were enriched after 15 cycles of linear PCR amplification. The resulting fragments were purified by PAGE gel electrophoresis. The tag library was then verified using Agilent 2100 and ABI StepOnePlus Real-Time PCR System, and sequenced using the Illumina HiSeq 2000 system according to the manufacturer’s protocols.
Single read - Illumina

treatment_protocol: Overexpression of BRD7 gene

value: human embryonic kidney cell line transformed with adenovirus 5 DNA

tag: tissue

value: kidney

value: wild type


title: Brd7oe_DGE

value: BRD7 overexpression


title: dusp2um287/um287;dusp6um286/um286 mutant replicate 2


title: HeLa output, replicate 2

description:
Processed_Data.xlsx, sheet 3, HeLa 2
original name: SP04_S13
HeLa_output_replicate_2.fastq.gz


title: dusp2um287/um287;dusp6um286/um286 mutant replicate 1


title: vector_ChIP-seq

data_processing:
Raw data was generated and processed through standard Illumina pipeline.
Reads were cleaned by wiping 3' adaptor, empty and low-quality reads, and then were aligned to human genome database hg19 using SOAP 2.21.
Peak-calling using MACS 1.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Wig files for each chromosome were gzipped, separately, and packed into 1 tar file of each lane. Fold enrichment represents reads on peak region against random Poisson distribution with local lambda.

extract_protocol:
Lysates were clarified from sonicated nuclei and the FLAG fusion Brd7 protein-DNA complexes were isolated with mouse-anti-human, Monoclonal ANTI-FLAG® M2 antibody (Sigma Aldrich, Cat# F1804)
Illumina Paired-End DNA Sample Prep kit (Part#1005063) was used to perform end repair, adenylate 3' ends and to ligate adapters.The purified adapter-ligated DNA fragments were then PCR amplified and the products with length of 100bp - 300bp(including adapters) were used for library construction.

tag: antibody


title: LAX7R output, replicate 2

description:
Processed_Data.xlsx, sheet 4, LAX7R R2
original name: SP05_S71
LAX7R_output_replicate_2.fastq.gz


title: wildtype control replicate 2


title: HeLa+HeLaGFP input

description:
Processed_Data.xlsx, sheet 3, Input + sheet 7, P0
original name: SP04_S8
HeLa_HeLaGFP_input_and_library_passage_0.fastq.gz

value: Input


title: HeLa output, replicate 1

description:
Processed_Data.xlsx sheet 3, HeLa 1
original name: SP04_S11
HeLa_output_replicate_1.fastq.gz


title: wildtype control replicate 3


title: HeLa (pLL3.7-infected) RNA polymerase II ChIP-seq

description: raw data with 4-nucleotide barcodes GTAT

data_processing:
Barcode splitter: All our libraries had 4nt barcodes at the 5 prime of each reads (ACGT for P77 RNA polymerase II chip-seq, GTAT for PL3.7 RNA polymerase II chip-seq, TGCT for P77 γH2AX chip-seq and CATT for PL3.7 γH2AX chip-seq). We splitted data according to the barcodes. Both P77 RNA polymerase II and γH2AX chip-seq had two replicates. We merged those two replicates into a single file and analyzed them together.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata" Total reads used to map was 27.7M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 18.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 35.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 16M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample. After alignment 21.2M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 15.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 22.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 12.3M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample maped to the genome
Peak calling: Peak calling was performed by MACS and SICER by default parameter except for band width: 200 bps for MACS and Windowsize: 50 bps, Fragment size: 200 bps, Gap size: 150 bps and Evalue for identification of significant islands: 100 for SICER
Wiggle file: The number of ChIP-Seq reads across the genome, in 50 bp non-overlapping bins was summarized and performed rank quantile normalization for P77 and PLL3.7.
Genome Build:
GTAT.HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq.bed: hg18
GTAT.HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq.wig: hg18

tag: chip antibody

value: RNA polymerase II

value: Abcam


title: wildtype control replicate 1


title: MCF10A/vec

status: Public on Feb 11 2018

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using in-house R scripts
Count data were normalized using "edgeR"
Genome_build: hg19
Supplementary_files_format_and_content: edgeR normalized counts

source_name: Cell line

growth_protocol: Cells were grown in DMEM/F12 (1:1) supplemented with 5% horse serum, 10 ug/ml insulin, 20 ng/ml EGF, 0.1 ug/ml Cholera Toxin and 0.5 ug/ml Hydrocortisone.

extract_protocol:
TRIZOL reagent (Invitrogen) was used to extract total RNA from cells following the manufacturer’s protocols.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
poly(A) RNA-seq following Illumima's recommended protocol

treatment_protocol: The cells tested stably express pBabe vector, pBabe-GFP, pBabe-miR-105, or pBabe-MYC.

tag: transduction

value: pBabe vector


title: HeLa (pLL3.7-infected) γ-H2AX ChIP-seq

description: raw data with 4-nucleotide barcodes CATT

data_processing:
Barcode splitter: All our libraries had 4nt barcodes at the 5 prime of each reads (ACGT for P77 RNA polymerase II chip-seq, GTAT for PL3.7 RNA polymerase II chip-seq, TGCT for P77 γH2AX chip-seq and CATT for PL3.7 γH2AX chip-seq). We splitted data according to the barcodes. Both P77 RNA polymerase II and γH2AX chip-seq had two replicates. We merged those two replicates into a single file and analyzed them together.
Reads mapping: Reads were mapped to the human (hg18) genomes by bowtie with the setting "-n1 -m2 --best --strata" Total reads used to map was 27.7M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 18.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 35.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 16M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample. After alignment 21.2M reads for HeLa (p77-infected) RNA polymerase II ChIP-seq, 15.6M reads for HeLa (pLL3.7-infected)RNA polymerase II ChIP-seq, 22.7M for HeLa (p77-infected) γ-H2AX ChIP-seq and 12.3M reads for HeLa (pLL3.7-infected) γ-H2AX ChIP-seq sample maped to the genome
Peak calling: Peak calling was performed by MACS and SICER by default parameter except for band width: 200 bps for MACS and Windowsize: 50 bps, Fragment size: 200 bps, Gap size: 150 bps and Evalue for identification of significant islands: 100 for SICER
Wiggle file: The number of ChIP-Seq reads across the genome, in 50 bp non-overlapping bins was summarized and performed rank quantile normalization for P77 and PLL3.7.
Genome Build:
CATT.HeLa (pLL3.7-infected) +-H2AX ChIP-seq.wig: hg18
CATT.HeLa (pLL3.7-infected) +-H2AX ChIP-seq.bed: hg18

tag: antibody catalog number

tag: antibody vendor

value: Millipore


title: MCF10A/GFP

tag: cell line

value: pBabe-GFP


title: MCF10A/miR-105


title: HeLaGFP output, replicate 2

city: South San Francisco

first: Samuel

address: 1 DNA way

institute: Genentech

description:
Processed_Data.xlsx, sheet 3, HG2
original name: SP04_S16
HeLaGFP_output_replicate_2.fastq.gz

tag: input or output


title: MCF10A/MYC

value: pBabe-MYC


title: CAF+MDA-MB-231 EV rep2

description:
CAF+MDA-MB-231 EV rep2
X18747_CAF.RNA.231.EV.2.8.29.17_S8_L999_R1_001.fastq.bam.1

source_name: breast cancer associated fibroblasts (CAF)

growth_protocol: CAF cells were grown in Iscove's modified dulbecco's media supplemented with 20% fetal bovine serum.

treatment_protocol: For 2x10e5 recipient CAF cells, 2 μg of EV (based on protein measurement using BCA protein assay kit) resuspended in PBS was added.  RNA was extracted after 48 h.

value: Primary CAF from a human breast tumor

tag: passage

value: MDA-MB-231 EV


title: Brd7oe_ChIP-seq

tag: cell type

value: Monoclonal ANTI-FLAG® M2 antibody (Sigma Aldrich, Cat# F1804)


title: CAF+MCF10A/miR-105 EV rep2

description:
CAF+MCF10A/miR-105 EV rep2
X18745_CAF.RNA.105.EV.2.8.29.17_S6_L999_R1_001.fastq.bam.1

value: MCF10A/miR-105 EV


title: CAF+PBS rep2

description:
CAF+PBS rep2
X18741_CAF.RNA.PBS.2.8.29.17_S2_L999_R1_001.fastq.bam.1

value: PBS


title: CAF+MCF10A EV rep1

description:
CAF+MCF10A EV rep1
X18742_CAF.RNA.vec.EV.1.8.29.17_S3_L999_R1_001.fastq.bam.1

value: MCF10A EV


title: CAF+MCF10A/miR-105 EV rep1

description:
CAF+MCF10A/miR-105 EV rep1
X18744_CAF.RNA.105.EV.1.8.29.17_S5_L999_R1_001.fastq.bam.1


title: CAF+PBS rep1

description:
CAF+PBS rep1
X18740_CAF.RNA.PBS.1.8.29.17_S1_L999_R1_001.fastq.bam.1


title: p300_rn5

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the rn5 genome assembly using Bowtie2 with the default configuration
Peak calling was performed using MACS (Model-based Analysis of ChIP-Seq) (http://liulab.dfci.harvard.edu/MACS) with a p value cut off of 1x e9.
Genome_build: rn5
Supplementary_files_format_and_content: bed files were generated using Macs14

organism: Rattus norvegicus

source_name: Schwann cell

growth_protocol: primary rat schwann cell progenitors were induced to differentiate for 9 hours in the presence of cAMP

extract_protocol:
Lysates were clarified from sonicated nuclei and proteine-DNA complexes were isolated with antibody.
Schwann cells (~20 million cells) were cross-linked in 1% formaldehyde at room temperature for 10 min and then quenched with 125 mM glycine for 5 min. Cells were rinsed, resuspended in lysis buffer (50 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.25% Triton X-100 and 0.5% NP-40 and protease inhibitor cocktail) and incubated on ice for 10 min. Lysates were centrifuged and pellets were resuspended in nuclei washing buffer  (200 mM NaCl, 1 mM EDTA, 1 mM EGTA, 10 mM Tris pH 8.0, and protease inhibitor cocktail) with gentle rocking at 4°C. Nuclei were pelleted and resuspended in 1 ml of sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA and protease inhibitor cocktail). Nuclear suspensions were sonicated with a Covaris S220 sonicator (total time 8 min). Antibody (chromatin: antibody = 4:1) was added to chromatin and incubated at 4°C overnight. Chromatin-protein complex was immunoprecipitated with protein A/G plus agarose beads and washed sequentially, twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 150 mM NaCl), twice with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 500 mM NaCl) and twice with LiCl buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris [pH 8.0]) and once with 1xTE buffer. Immunoprecipitates were then eluted in elution buffer at 65°C for 1 h. Eluted chromatin was subjected to reverse-crosslink and chromatin fragment purification with QIAGEN PCR purification columns. ChIP-Seq libraries were prepared using NEBNext ChIP-Seq Library Prep Kit according to manufacturer’s instructions.

value: Schwann cell

value: p300 (Santa Cruz sc-585)


title: IgG_rn5

value: IgG (Santa Cruz Biotechnology, sc-2027 x)


title: Pro_HDAC3rn5

value: Hdac3 (Santa Cruz Biotechnology, sc-13914)


title: Scr_H3K27acrn5

value: H3k27ac (Abcam, ab4729)


title: H3k27ac_rn5


title: siHdac3_H3k27acrn5


title: diff_HDAC3rn5