title: TS1180K_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

tag: small rna

tag: time point

value: CGA


title: wt M C T0 R2

status: Public on Jan 20 2016

type: SRA

city: State College

first: Michael

middle: J

last: Axtell

state: PA

address: University Park

department: Department of Biology

country: USA

institute: Penn State University

library_source: transcriptomic

data_processing:
3' and 5' adapters were removed with cutadapt ("-m 15 --discard-untrimmed" Martin, 2011).
Low complexity sequences, containing only two different nucleobases, were removed through a customized Perl script.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to verify that in each library the Q score of the 90th percentile of reads was >= 28 across all bases.
The abundance of the unique sequences was obtained with a customized Perl script.
Genome_build: RefGen ZmB73 Assembly AGPv3
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: the first column is the sequence of the unique, non-redundant sRNA read, and the second column is its total raw abundance.

molecule: total RNA

organism: Zea mays

source_name: shoot apical meristematic area

extract_protocol:
Leaf and shoot apical meristematic area samples of four-five plants for each combination of genotype-treatment-sampling time point were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), using "Protocol A" with 750µL of Binding Solution, to recover more of the small-sized RNA, and subjected to On-Column DNase Digestion (SIGMA).
The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina Hiseq2000 platform by the Istituto di Genomica Applicata (Udine, Italy).

tag: tissue

value: shoot apical meristematic area

tag: background strain

tag: genotype

value: wt

tag: treatment

value: control

tag: sampling time point

value: V5/V6 plants after 10 days of treatment

tag: biological replicate


title: Sinorhizobium_medicae_WSM1115_native

city: Berkeley

first: Matthew

middle: James

last: Blow

state: CA

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

library_source: genomic

data_processing:
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 2.0.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Modified sites were grouped into motifs using MotifFinder (v1)2.
Genome_build: As indicated by IMG genome ID in the individual samples section (http://img.jgi.doe.gov/home.html)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage.  (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: motif_summary.csv files contain the genome-wide summary of the methyltransferase recognition motifs discovered in this sample.  (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).
Supplementary_files_format_and_content: motifs.gff files are similar to the modifications.gff files. These files contain information about all sites detected as modified, all locations of a discovered motif (including those which are apparently unmodified), and also the overlap between the modifications and motifs. (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).

molecule: genomic DNA

organism: Sinorhizobium medicae WSM1115

source_name: Bacterial gDNA

extract_protocol:
gDNA was randomly sheared, end repaired, and ligated to blunt end hairpin adapters to form standard SMRTbell templates
SMRT-sequencing

tag: strain

tag: dna treatment

tag: pacbio sequencing chemistry

tag: genome build (img genome id)


title: Sphaerobacter_thermophilus_4ac11_DSM20745_native

organism: Sphaerobacter thermophilus DSM 20745

value: XL / C2


title: Sediminibacter_sp_Hel_I_10_native

organism: Sediminibacter sp. Hel_I_10


title: wt M C T0 R1


title: Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native

organism: Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7


title: TS1300C_CLIP-seq_Huh-7.5_DENV-GFP

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description: Table S1.txt

data_processing:
AGO-CLIP data was processed as described (Moore et al. 2014 Nature Protocols). The deposited CLIP sequences are composed of (i) the index (3 OR 4 nts, see individual samples), (ii) the RL5 sequence (AGGGAGGACGAUGCGG), (iii) a 5N degenerate linker, (iv) the actual read sequence and, depending on read length (iv) a complete or partial RL3 sequence (GTGTCAGTCACTTCCAGCGGATCTCGTATGCCGTCTTCTGCTTG).
Processed reads were aligned to human (hg18) or bovine (BosTau7) host genomes as well as to viral genomes corresponding to the infecting agent using Bowtie or Novoalign (Novocraft). After all mapping, reads were collapsed on coordinates such that only those with sufficiently different degenerate linkers were kept; this distinguished unique binding events from PCR duplicates. For AGO-CLIP data, clustering of AGO-bound regions, annotation and calculations of log2 fold changes was done essentially as described (Luna et al. 2015 Cell). For annotation on cow, BosTau7 GTF annotation were downloaded from the USCS genome table browser and intersected with CLIP-derived clusters. CLIP data was based on 4 replicates per condition.
Quality filtered RNA-seq data were mapped to the cow (bosTau7) genome using Bowtie or Tophat2. The number of reads overlapping each gene (USCS Table Browser and Ensembl annotation) was counted with htseq-count. Expression data was processed essentially as described (Luna et al. 2015 Cell) using the edgeR and limma packages in R with general linear models. For MDBK cells, RNA-seq derived gene expression data was merged on gene name with AGO-CLIP data to allow CLIP-guided representation of changes to gene expression.
Changes to miRNA expression in quadruplicate libraries were calculated using edgeR for miRNAs represented in >=4 libraries, and adjusted p-values (FDRs) were presented.
Genome_build: hg18 or BosTau7
Supplementary_files_format_and_content: Table S1: Virus-aligned AGO-CLIP reads. A concatemerized list of all AGO-CLIP reads aligning to viral positive-strand RNA is given as a BED file. Two additional columns give experiment ID and notes for time course and cell type experiments.
Supplementary_files_format_and_content: Table S3: Abundance of AGO-loaded miRNAs in MDBK cells. The abundance of AGO-loaded miRNAs in MDBK cells is given by seed family. In addition, fraction of total for individual miRNAs is given for four replicates each of MDBK (mock) and MDBK (BVDV infected).
Supplementary_files_format_and_content: Table S4: Summarized AGO-CLIP analysis and related mRNA expression for BVDV and mock infected MDBK cells. The table summarizes AGO-CLIP clusters from analysis of BVDVcp vs. mock infected MDBK cells (four replicates each). For clusters in genic regions with a minimum total biologic complexity (BC) of 4, the peak height (PH) and BC for mock, BVDVcp and total are given. The normalized CLIP PH was calculated by addition of a pseudocount of 1 per condition and dividing by the total library size. The log2 fold change in AGO-CLIP binding was calculated directly from the normalized PH. Gene expression values corresponding to CLIP-defined clusters were calculated from mRNA-seq data in edgeR and logCPM (counts per million), log2 fold change and adjusted p-values (FDR) are given. Additional data include the genic region (CDS, UTR, intron) covering the largest fraction of each cluster, the cluster sequence, and the presence or absence of seed sites (6mer, 7merA1, 7merM8, 8mer) of the 50 most abundant miRNAs in MDBK cells.
Supplementary_files_format_and_content: Table S5: Summarized AGO-CLIP analysis for tinyLNA-17 and mock treated MDBK cells. The table summarizes AGO-CLIP clusters from analysis of tinyLNA-17 vs. mock treated MDBK cells (four replicates each). For clusters in genic regions with a minimum total biologic complexity (BC) of 4, the peak height (PH) and BC for mock, tinyLNA-17 and total are given. The normalized CLIP PH was calculated by addition of a pseudocount of 1 per condition and dividing by the total library size. The log2 fold change in AGO-CLIP binding was calculated directly from the normalized PH. Additional data include the cluster fraction mapping to each genic region (CDS, UTR, intron), the cluster sequence, and the presence or absence of seed sites (6mer, 7merA1, 7merM8, 8mer) of the 50 most abundant miRNAs in MDBK cells.
Supplementary_files_format_and_content: Table S6: Summarized mRNA expression analysis for BVDV and mock infected MDBK cells. The table summarizes RNA expression levels measured by mRNA-seq for mock, BVDVcp or BVDVncp infected MDBK cells, and for miR-17p3,4 transfected MDBK cells infected or not with BVDVcp-m17p3,4 or BVDVncp-m17p3,4. Gene expression values were calculated using general linear models in edgeR and logCPM (counts per million), log2 fold change and adjusted p-values (FDR) are given for pairwise comparisons.

organism: Homo sapiens

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseA digested, clarified by centrifugation, and Argonaute-RNA complexes isolated with pan-Ago 2A8 antibody.
Libraries were prepared as in Moore et al. 2014 Nature Protocols, but with the following modifications: The 2nd PCR step was used to introduce library specific indices that were additionally compatible with MiSeq sequencers using version2 chemistry.

tag: sample subseries

value: Virus AGO-CLIP

tag: virus

value: DENV-GFP

value: Mock

tag: index

value: TCAC


title: TS1180L_CLIP-seq_Huh-7.5_HAV

description: Table S1.txt

value: HAV

value: TCG


title: Ruminococcus_gnavus_AGR2154_native

organism: Mediterraneibacter gnavus AGR2154


title: Thermoanaerobacter_sp_X514_native

organism: Thermoanaerobacter sp. X514


title: TS1438J_CLIP-seq_Huh-7.5_DENV-GFP

description: Table S1.txt

value: GTGC


title: TS1102F_CLIP-seq_Huh-7.5_YFV-asibi

description: Table S1.txt

value: YFV

value: CGA,TCG


title: TS1438I_CLIP-seq_Huh-7.5_VEEV-GFP

description: Table S1.txt

value: VEEV-GFP

value: GCAT


title: Ruminococcus_albus_AD2013_native

organism: Ruminococcus albus AD2013


title: Thiomicrospira_kuenenii_DSM12350_native

organism: Hydrogenovibrio kuenenii DSM 12350


title: rmr6-1 L S T7 R3

source_name: youngest wrapped leaf

value: leaf

value: rmr6-1 mutant

value: salt

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: rmr6-1 L D T7 R3

value: drought


title: TS1288J_CLIP-seq_Huh-7.5_VEEV-GFP

description: Table S1.txt

value: GGCT


title: rmr6-1 L C T7 R3

value: control


title: Pseudomonas_aeruginosa_NCAIM_P_B_001380_native

organism: Pseudomonas aeruginosa NCAIM B.001380


title: rmr6-1 L D+S T0 R3

value: drought plus salt

value: V5/V6 plants after 10 days of treatment


title: TS1468V_CLIP-seq_STAT1-/-_CHIKV-GFP

description: Table S1.txt

value: Virus AGO-CLIP

value: CHIKV-GFP

value: Mock

value: ACTC


title: rmr6-1 L S T0 R3


title: Polycyclovorans_algicola_TG408_native

organism: Polycyclovorans algicola TG408


title: TS1468U_CLIP-seq_STAT1-/-_CHIKV

description: Table S1.txt

value: CHIKV

value: AACC


title: Polaribacter_sp_Hel_I_88_native

organism: Polaribacter sp. Hel_I_88


title: rmr6-1 L C T0 R3


title: rmr6-1 L D T0 R3


title: TS1102J_CLIP-seq_STAT1-/-_CHIKV

description: Table S1.txt

value: AAG,CTT


title: TS1468S_CLIP-seq_Huh-7_CHIKV-GFP

description: Table S1.txt


title: Parabacteroides_distasonis_ATCC8503_native

organism: Parabacteroides distasonis ATCC 8503

value: ATCC 8503


title: Nitriliruptor_alkaliphilus_DSM45188_native

organism: Nitriliruptor alkaliphilus DSM 45188


title: rmr6-1 L D+S T7 R3

value: leaf


title: TS1146D_CLIP-seq_Huh-7_CHIKV-GFP

description: Table S1.txt

value: CAC


title: wt L D T7 R3

value: wt


title: wt L D+S T7 R3

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: wt L S T7 R3

value: salt


title: Methylotenera_versatilis_79_native

organism: Methylotenera versatilis 79


title: wt L C T7 R3


title: TS1102H_CLIP-seq_Huh-7_CHIKV

description: Table S1.txt

value: AGC,GCT


title: TS1438N_CLIP-seq_Huh-7.5_SINV 6hrs

description: Table S1.txt

value: SINV 6hrs

value: TCAC


title: wt L S T0 R3

value: V5/V6 plants after 10 days of treatment


title: TS1468P_CLIP-seq_STAT1-/-_CHIKV-GFP

description: Table S1.txt

value: Virus AGO-CLIP

value: CCGA


title: wt L D+S T0 R3

value: drought plus salt


title: Methylobacter_tundripaludum_21_22_native

organism: Methylobacter tundripaludum 21/22


title: TS1383L_CLIP-seq_Huh-7.5_SINV 6hrs

description: Table S1.txt

value: Mock

value: CTCC


title: Pediococcus_acidilactici_AGR20_native

organism: Pediococcus acidilactici AGR20

value: XL / C2


title: wt L D T0 R3

organism: Zea mays

value: drought


title: TS1438M_CLIP-seq_Huh-7.5_SINV 3hrs

description: Table S1.txt

value: SINV 3hrs

value: TGCA


title: wt L C T0 R3

value: leaf

value: control


title: Meiothermus_ruber_DSM1279_native

organism: Meiothermus ruber DSM 1279


title: Mastigocladopsis_repens_PCC_10914_native

organism: Mastigocladopsis repens PCC 10914


title: rmr6-1 L D+S T7 R2

value: rmr6-1 mutant

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: TS1146C_CLIP-seq_Huh-7_CHIKV

description: Table S1.txt

value: CHIKV

value: GTG


title: TS1300D_CLIP-seq_Huh-7.5_SINV 24hrs

description: Table S1.txt

value: SINV 24hrs

value: AGTG


title: Niabella_soli_JS13_8_DSM19437_native

organism: Niabella soli DSM 19437


title: TS1438K_CLIP-seq_Huh-7.5_SINV 24hrs

description: Table S1.txt

organism: Homo sapiens

value: Virus AGO-CLIP

value: ACCG


title: Lactobacillus_plantarum_AG30_native

organism: Lactiplantibacillus plantarum


title: TS1438P_CLIP-seq_HeLa_CVB-GFP 6hrs

description: Table S1.txt

source_name: HeLa

value: CVB-GFP 6hrs

value: TACG


title: rmr6-1 L S T7 R2

value: salt


title: rmr6-1 L D T7 R2


title: Methylophilus_sp_5_native

organism: Methylophilus sp. 5


title: Methylobacterium_sp_10_native

organism: Methylobacterium sp. 10

value: XL / C2


title: TS1383N_CLIP-seq_HeLa_CVB-GFP 6hrs

description: Table S1.txt

value: Mock

value: GAGG


title: Kangiella_aquimarina_DSM16071_native

organism: Kangiella aquimarina DSM 16071


title: TS1438O_CLIP-seq_HeLa_CVB-GFP 3hrs

description: Table S1.txt

value: CVB-GFP 3hrs


title: Leeuwenhoekiella_sp_Hel_I_48_native

organism: Flavimarina sp. Hel_I_48


title: rmr6-1 L D+S T0 R2

value: leaf

value: drought plus salt

value: V5/V6 plants after 10 days of treatment


title: Lachnospiraceae_bacterium_AC2031_native

organism: Lachnospiraceae bacterium AC2031


title: Psychrilyobacter_atlanticus_DSM19335_native

organism: Psychrilyobacter atlanticus DSM 19335


title: Hydrogenovibrio_marinus_DSM11271_native

organism: Hydrogenovibrio marinus DSM 11271


title: rmr6-1 L S T0 R2

value: rmr6-1 mutant


title: TS1383M_CLIP-seq_HeLa_CVB-GFP 3hrs

description: Table S1.txt

value: GGCT


title: TS1383K_CLIP-seq_Huh-7.5_SINV 3hrs

description: Table S1.txt

value: SINV 3hrs

value: CCGA


title: Halomicrobium_katesii_DSM19301_native

organism: Halomicrobium katesii DSM 19301


title: TS1300E_CLIP-seq_Huh-7.5_Polio-GFP

description: Table S1.txt

value: Polio-GFP


title: rmr6-1 L C T0 R2

value: control


title: wt L D+S T7 R2

value: wt

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: Flexibacter_litoralis_DSM6794_native

organism: Bernardetia litoralis DSM 6794

value: Fx l1, DSM 6794


title: wt L D T7 R2

value: drought


title: TS1293C_CLIP-seq_Huh-7.5_HBV

description: Table S1.txt

value: Virus AGO-CLIP

value: HBV

value: CTAG


title: Exiguobacterium_oxidotolerans_JCM_12280_native

organism: Exiguobacterium oxidotolerans JCM 12280


title: TS1293D_CLIP-seq_Huh-7.5_HBV

description: Table S1.txt

value: Mock

value: GATC


title: TS1293E_CLIP-seq_Huh-7.5_HBV

description: Table S1.txt

value: CGTA


title: Escherichia_coli_O6_K2_H1_CFT073_UPEC_native

organism: Escherichia coli CFT073

value: CFT073 (UPEC)


title: Enterococcus_gallinarum_SKF1_native

organism: Enterococcus gallinarum

value: XL / C2


title: wt L C T7 R2

organism: Zea mays

value: leaf


title: TS1408D_CLIP-seq_Huh-7.5_HCVm122/15

description: Table S1.txt

value: TGCA


title: rmr6-1 L D T0 R2

value: rmr6-1 mutant

value: V5/V6 plants after 10 days of treatment


title: wt L D+S T0 R2

value: drought plus salt


title: TS1408C_CLIP-seq_Huh-7.5_HCVm15/122

description: Table S1.txt

value: CATG


title: Desulfotignum_balticum_DSM7044_native

organism: Desulfotignum balticum DSM 7044


title: TS1438L_CLIP-seq_Huh-7.5_Polio-GFP

description: Table S1.txt

value: Polio-GFP


title: wt L S T0 R2

value: wt

value: salt


title: Fervidobacterium_nodosum_Rt17_B1_native

organism: Fervidobacterium nodosum Rt17-B1


title: wt L D T0 R2

value: drought


title: TS1468H_CLIP-seq_Huh-7.5_HCV-U3

description: Table S1.txt

organism: Homo sapiens

value: Virus AGO-CLIP

value: ACCG


title: wt L C T0 R2

value: control


title: Corynebacterium_aurimucosum_ATCC700975_native

organism: Corynebacterium aurimucosum ATCC 700975


title: Cohnella_panacarvi_Gsoil_349_DSM18696_native

organism: Cohnella panacarvi Gsoil 349


title: TS1468G_CLIP-seq_Huh-7.5_HCV-U3

description: Table S1.txt

value: Mock

value: GTGC


title: wt L S T7 R2

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: rmr6-1 L D+S T7 R1


title: TS1154N_CLIP-seq_Huh-7.5_HCV-U3

description:
Table S1.txt
This library was also submitted as part of GSE64680
GSM1576768

value: CTT


title: Clostridium_thermocellum_ATCC27405_Tet

organism: Acetivibrio thermocellus ATCC 27405

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: rmr6-1 L D T7 R1

value: leaf


title: Desulfovibrio_cf_magneticus_IFRC170_native

organism: Solidesulfovibrio cf. magneticus IFRC170

value: XL / C2


title: rmr6-1 L C T7 R1

value: rmr6-1 mutant


title: Clostridium_phytofermentans_KNHs212_native


title: TS1095D_CLIP-seq_Huh-7.5_HCV-U3

description:
Table S1.txt
This library was also submitted as part of GSE64680
GSM1576766

value: GTG,CAC,AGC


title: Clostridium_thermocellum_ATCC27405_native


title: rmr6-1 L S T0 R1

value: V5/V6 plants after 10 days of treatment


title: Clostridium_methoxybenzovorans_SR3_native

organism: Lacrimispora indolis SR3


title: JL0098.2_CLIP-seq_Huh-7.5_HCVm15

description: Table S1.txt

value: CAC,TCG


title: rmr6-1 L D T0 R1


title: Cellulophaga_algicola_IC166_DSM14237_native

organism: Cellulophaga algicola DSM 14237


title: JL0098.1_CLIP-seq_Huh-7.5_HCVm15

description: Table S1.txt

value: GTG,CGA


title: Bryobacter_aggregatus_DSM_18758_native

organism: Bryobacter aggregatus MPL3


title: rmr6-1 L C T7 R2


title: wt L S T7 R1

value: wt

value: salt


title: wt L D T7 R1

value: drought


title: JL0098.3_CLIP-seq_Huh-7.5_HCVm15

description: Table S1.txt

value: Virus AGO-CLIP

value: AGC,AAG


title: TS1154M_CLIP-seq_Huh-7.5_HCV-U3

description:
Table S1.txt
This library was also submitted as part of GSE64680
GSM1576767

value: Mock

value: AAG


title: wt L D+S T7 R1

value: drought plus salt

value: V5/V6 plants after 10 days of treatment and 7 additional days of recovery


title: Bifidobacterium_infantis_ATCC15697_Tet

organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

value: DNA fragments were treated with Tet-1 according to guidelines for using the WiseGene™ 5-mC Tet1 oxidation kit for SMRT sequencing on the Pacific Biosciences RS (WiseGene LLC., Chicago, IL USA; Item #K004; Pacific Biosciences Inc. Menlo Park, CA USA).


title: Bifidobacterium_infantis_ATCC15697_native


title: JL0098.4_CLIP-seq_Huh-7.5_HCVm15

description: Table S1.txt

value: GCT,CTT


title: Chloroflexus_aggregans_DSM9485_native

organism: Chloroflexus aggregans DSM 9485


title: wt L C T7 R1

value: leaf

value: control


title: rmr6-1 L C T0 R1

value: rmr6-1 mutant


title: JL0110.2_CLIP-seq_Huh-7.5_HCVwt

description:
Table S1.txt
This library was also submitted as part of GSE64680
pool of GSM1576759 + GSM1576760

value: HCVwt

value: CATG,TGCA


title: JL0096.4_CLIP-seq_Huh-7.5_HCVwt

description: Table S1.txt

value: AAG,CTT


title: Arthrobacter_sp_31Y_native

organism: Arthrobacter sp. 31Y

value: XL / C2


title: wt L D+S T0 R1

value: wt

value: V5/V6 plants after 10 days of treatment


title: JL0110.3_CLIP-seq_Huh-7.5_HCVwt

description:
Table S1.txt
This library was also submitted as part of GSE64680
pool of GSM1576761 + GSM1576762

value: Virus AGO-CLIP

value: AACC,GGCT


title: JL0110.1_CLIP-seq_Huh-7.5_HCVwt

description:
Table S1.txt
This library was also submitted as part of GSE64680
pool of GSM1576757 + GSM1576758

value: Mock

value: GTGC,ACCG


title: JL0096.3_CLIP-seq_Huh-7.5_HCVwt

description: Table S1.txt

value: CGA,TCG


title: Anoxybacillus_flavithermus_WK1_DSM2641_native

organism: Anoxybacillus flavithermus WK1


title: Agrobacterium_tumefaciens_C58_Cereon_native

organism: Agrobacterium fabrum str. C58


title: wt L S T0 R1

value: salt


title: wt L C T0 R1


title: TS1330G_CLIP-seq_MDBK_BVDVncp

description: Table S1.txt

organism: Bos taurus

source_name: MDBK

value: BVDVncp

value: ACTC


title: Actinobacillus_succinogenes_130Z_native

organism: Actinobacillus succinogenes 130Z


title: JL0096.2_CLIP-seq_Huh-7.5_HCVwt

description: Table S1.txt

value: AGC,GCT


title: JL0096.1_CLIP-seq_Huh-7.5_HCVwt

description: Table S1.txt

value: GTG,CAC


title: Drought2

status: Public on Jan 19 2016

city: Hobart

first: Xiang

last: LU

state: TAS

address: Private Bag 98

department: Tasmania of Institute Agriculture

country: Australia

institute: University of Tasmania

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM.
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Zea mays subsp. mexicana

source_name: Drought

growth_protocol: Selected plump seeds were washed 3 times with distilled water, then soaked in 75% ethanol and 2% sodium hypochlorite for 10 min and 3 min, respectively, and washed 3 times with distilled water. Sterilized seeds were planted in plastic boxes (54 cm length, 28 cm width and 7 cm height) with soil substrates (Jiffy, Netherlands, http://www.jiffygroup.com/en/substrates/). The boxes were placed in a climate control box (RXZ 500-C, JIANGNAN Instrument) (25℃ under a 10-h light/14-h dark photoperiod, humidity of 60%).

extract_protocol:
Total RNA of 6 samples were extracted by TRIzol® reagent (Invitrogen, Carlsbad, USA) according to the manufacturer's instructions. RNA was purified with the RNase-free DNase I (Takara, Japan) to degrade any possible DNA. The integrity and concentration of the total RNA was identified by agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) and NanoDrop 8000 spectrophotometer (NanoDrop, Wilmington, DE) and checked by running a gel electrophoresis in 1.5% (w/v) agarose gels.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Thirteen days after germination, samples were divided into 3 groups for different treatments: control (no stress); cold treated and drought treated. For cold treatments, seedlings were treated with 4℃ low temperature under the same light condition for 12 h. For drought treatment, seedlings were treated with Hoagland solution mixed with PEG2000 (20%) for 3 h with same light condition. Each sample were selected three seedlings randomly and two replications.

tag: subspecies

value: mexicana

tag: developmental stage

value: Seedling

tag: cultivar

tag: age

value: Thirteen days after germination

tag: stress

value: dry

value: Root, Stem and Leave


title: Drought1

tag: tissue


title: Cold1

source_name: Cold

value: cold


title: Cold2


title: CK1

source_name: Control

value: control


title: CK2


title: CRISPRi, +dox, RepB

city: San Francsico

first: Max

middle: A

last: Horlbeck

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: UCSF

data_processing:
Demultiplexing using Illumina Bcl2Fastq
Reads were aligned to the hg19 genome assembly using the Ensembl 75 reference transcriptome customized to include the GCaMP6f constructs using TopHat2 (v2.1.0) using the following parameters: --library-type fr-firststrand --transcriptome-index --prefilter-multihits
Unaligned reads for CRISPRi and CRIPSRn cell lines were aligned to the appropriate CRISPRi/n transgene sequence and annotation using TopHat2 (v2.1.0) using the following parameters: --library-type fr-firststrand --transcriptome-index --prefilter-multihits
Transcript alignments were counted using SubRead v1.4.6 with the -s 2 flag and otherwise default parameters
For display purposes, alignment counts were incremented with a pseudocount of 0.075 and normalized to reads per million using custom python scripts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

molecule: polyA RNA

source_name: Coriell GM25256

extract_protocol:
RNA was extracted from approximately 10^5 cells with TRIzol reagent
Strand-specific mRNAseq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit

tag: cell line

value: WTC-CRISPRi

tag: sgrna

tag: doxycycline treatment


title: CRISPRi, -dox, RepB


title: CRISPRn, +dox, RepB

value: WTC-CRISPRn


title: WTC, +dox, RepB


title: CRISPRi, sgGcaMP, +dox, RepB

value: sgGCaMP


title: CRISPRi, sgGcaMP, +dox, RepA


title: CRISPRi, +dox, RepA


title: CRISPRi, -dox, RepA


title: wt L D T0 R1

organism: Zea mays

value: leaf

tag: background strain

tag: genotype

value: wt

tag: treatment

value: drought

tag: sampling time point

value: V5/V6 plants after 10 days of treatment

tag: biological replicate


title: CRISPRn, -dox, RepB

organism: Homo sapiens


title: CRISPRi, sgGCaMP, -dox, RepA


title: WTC, +dox, RepA


title: CRISPRn, +dox, RepA


title: WTC, -dox, RepA


title: LC rep3

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

data_processing:
Illumina bcl2fastq 1.8.4 software was used for basecalling.
Sequenced reads were mapped to hg19/GRCh37 whole genome using bwa 0.5.9-r16 with default parameters
Mapped reads where counted for each mRNA of the Ensembl v73 database if a read overlapped the Exon coordinates by at least one base
Raw counts were processed in R using functions of the edgeR library to normalize (calcNormFactors), and calculate logratios and significance using a robust trended dispersion estimate. Counts per Million were calculated using the function cpm from edgeR
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: tab-delimited text file including raw counts and CPM values for each sample as well as the logratios and pValues calculated compairing all LC vs all benign samples

source_name: colorectal biopsy, sigma

extract_protocol:
Biopsies were taken and RNA was immediately harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lymphocytic colitis

tag: medication


title: CRISPRn, -dox, RepA


title: LC rep2


title: LC rep4


title: Ctrl rep2

value: benign


title: Ctrl rep3


title: LC rep1


title: Ctrl rep4


title: CRISPRi, sgGCaMP, -dox, RepB


title: Ctrl rep1


title: WTC, -dox, RepB


title: Input

city: Houston

first: Ross

middle: A.

last: Poché

state: Texas

address: One Baylor Plaza Room T424, Mail Stop 335

department: Department of Molecular Physiology and Biophysics

institute: Baylor College of Medicine

data_processing:
ChIP-Seq reads were mapped to the mm9 assembly (NCBI Build 37) using Torrent Suite (2.0.1) aligner Tmap (0.2.3) (Life Technologies).
ChIP enriched peaks were identified using Homer V4.7 (Heinz et al., 2010) by the default setting. Briefly, a fixed peak size was calculated automatically. In our case, the peak size was 191 bp. The program then scanned the entire genome for 191 bp clusters with the highest density of reads. After all clusters were found, the program compared Ronin ChIP-Seq reads against input control reads. The cutoffs for calling the peaks were read number-enriched at least 4 fold, FDR threshold of 0.001, FDR effective Poisson p-value of 1.3e-6, and minimum read number 6. This process produced 37,360 enriched peaks.
The nearest genes associated to the enriched peaks were annotated using the annotatePeaks function and de novo motif discovery was performed using the findMotifsGenome function in Homer V4.7.
Genome_build: mm9
Supplementary_files_format_and_content: bed format file for genomic cooridinates of Ronin binding sites.

organism: Mus musculus

source_name: retina

extract_protocol:
P0 wild type retinae (CD-1 background) were pooled (>10 each) in ice-cold 1X PBS and immediately processed for chromatin extraction, fragmentation and immunoprecipitation using custom-made antibodies against Ronin G4275 (Zwaka lab, Dejosez et al., 2010), G4275 preimmune serum or normal rabbit IgG (Santa Cruz, sc-2027)
ChIP libraries were constructed using Ion Xpress Plus Fragment Library Kit (Life Technologies).

tag: strain background

tag: genotype/variation

value: Wild type

value: retina

tag: chip antibody

value: normal rabbit IgG (Santa Cruz, sc-2027)


title: Ronin_ChIP-Seq

tag: developmental stage

value: custom-made antibodies against Ronin G4275


title: spleen

city: South San Francisco

first: Melanie

last: Huntley

address: 1 DNA Way

institute: Genentech

data_processing:
Our nine RNA-seq samples derived from a single individual mouse, and two whole genome DNA samples were sequenced on an Illumina HiSeq machine. The fastq sequence files for all RNA-seq samples  were then filtered for read quality (keeping reads where at least 70% of the cycles had Phred scores >= 23), and ribosomal RNA contamination. The remaining reads were then aligned to the mouse reference genome (mm9) using the GSNAP alignment tool. Alignments were produced using the following GSNAP parameters: ``-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap''. These steps, and the downstream processing of the resulting alignments to obtain read counts and RPKMs per gene (over coding exons of RefSeq gene models) are implemented in the Bioconductor package, HTSeqGenie (v 3.12.0). Only uniquely mapped reads were used for further analysis.
Our two DNA samples were processed similarly for quality, and aligned with the following GSNAP parameters specific for whole genome sequence: ``-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap''.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited matrtix file of read counts for each gene (rows) and sample (columns)

source_name: spleen

extract_protocol:
This animal was euthanized by exsanguination with phosphate buffered saline (PBS) and tissues were collected, flash frozen and stored at -80C until further processing. DNA and RNA were extracted with either the All Prep DNA/RNA mini kit (kidney, liver, lung, spleen, testis and thymus), the RNeasy Fibrous tissue mini kit (heart and skin) or the RNeasy Lipid tissue mini kit (brain) according to manufacturers protocol (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 8 weeks

tag: gender

value: male

value: wild type

value: spleen


title: sh1-OHT

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Samples were sequenced on the Illumina Genome Analyzer IIx (GAIIx)
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
The ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina). These files contain only reads that passed "chastity" filtering (flagged with a „N‟, for *NOT filtered* in the sequence identifier line). "Chastity" parameter measures signal contamination in raw data and allows to flag unreliable reads. Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics).
Tophat5 (version 2.0.4) was used for alignment with the following parameters: --bowtie1, --max-multihits 5, --genome- read-mismatches 1 --segment-mismatches 1 --segment-length 19 --splice-mismatches 0 -- library-type fr-firststrand. Gene expression levels and synthetic spike-in RNA (Fragments Per Kilobase of exon per Million fragments mapped, FPKM) were quantified with cufflinks (version 2.0.2), with the following parameters: -N, --library-type fr-firststrand, -u. Further, we used a loess regression to renormalize the FPKM values by using only the spike-in values to fit the loess following the strategy described in Lovén, J. et al. ("Revisiting global gene expression analysis. Cell 151, 476-82 (2012)"). The affy package in R provides a function, loess.normalize, performing loess regression on a matrix of values and allowing to specify which subset of data to use when fitting the loess (see the affy package for further details). The result was a matrix of FPKM values normalized to the control ERCC spike-ins.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each Sample normalized by spikes in

source_name: Primary neonatal human foreskin fibroblasts (HFF)

growth_protocol: Cells were grown in DMEM 10% FBS. To conduct the experiment, cells were serum-starved for 2 days to achieve quiescence and then treated with 4-hydroxytamoxifen (4-OHT).

extract_protocol:
Total RNA was isolated from cultured cells using the GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to manufacturer's instructions.
1 µg of total RNA samples, containing ERCC ExFold RNA Spike-In Mixes (Life Technologies), was used as provided by the user. RNA Integrity Numbers were in the range 8.6 to 9.4 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Cells were treated with 4-OHT 600nM for 8 hours in the absence of serum.

tag: cell type

value: neonatal human foreskin fibroblasts (primary culture cells)

value: transduced with MycER and BPTF-targeting shRNA, not treated with 4-hydroxytamoxifen (4-OHT)


title: sh1+OHT

value: transduced with MycER and BPTF-targeting shRNA, treated with 4-hydroxytamoxifen (4-OHT)


title: testis

source_name: testis

tag: age

tag: tissue

value: testis


title: thymus

source_name: thymus

value: thymus


title: lung

source_name: lung

value: lung


title: Input+OHT

data_processing:
Samples were sequenced on the Illumina Genome Analyzer IIx (GAIIx)
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
The ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina). These files contain only reads that passed "chastity" filtering (flagged with a „N‟, for *NOT filtered* in the sequence identifier line). "Chastity" parameter measures signal contamination in raw data and allows to flag unreliable reads. Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics).
ChIP-seq reads were aligned to the human reference genome (GRCh37/hg19, Feb 2009) with Burrows-Wheeler Aligner (bwa,v0.5.9-r16) allowing 0-1 mismatches. Unique aligned reads were converted to BED format. All ChIP and input samples were normalized randomly to the same number of reads (10,512.988). Furthermore, reads were directionally extended to 300 bp and for each base pair in the genome, the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz (UCSC) genome browser.
MYC binding sites were obtained using MACS (version 2.0.9 20111102, tag:alpha) and parameters: -g 2.7e9; -m 10,30; -q 0.05 and Input+OHT as control.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files for peaks and wiggle files for visualization are provided

extract_protocol:
ChIPed DNA was extracted by phenol-chloroform and isopropanol precipitation.
DNA samples were provided by the user. Input samples correspond to balanced blends of inputs from selected samples. 20ng of DNA, as quantitated by fluorometry, was resolved by electrophoresis and fractions of 50-250bp were extracted. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: Pool of control and Bptf-silenced cells transduced with MycER, treated with 4-hydroxytamoxifen (4-OHT)

value: none (input)


title: shBptf1+OHT-Myc4

value: anti-MYC N262 (Santa Cruz Biotechnology, catalog number sc-764)


title: shNt+OHT

value: transduced with MycER and control shRNA, treated with 4-hydroxytamoxifen (4-OHT)


title: skin

source_name: skin

value: skin


title: kidney

source_name: kidney

value: kidney


title: liver

source_name: liver

value: liver


title: C2C12 DM #B

city: Rome

first: Irene

last: Bozzoni

address: p.le A. Moro 5

department: Biology and Biotechnology

country: Italy

institute: Sapienza University of Rome

data_processing:
Base-calling with Casava
Adapters removal with Cutadapt
head-to-tail splicing detection with FindCirc (Memczak et al., Nature 2013): the two files of each paired end experiment were used as input separately; they were aligned to rRNA with Bowtie2, reads remaining were aligned to reference genome with Bowtie2, reads remaining were used as input to FindCirc.
Genome build: hg19 for human samples; mm9 for mouse samples.
Supplementary_files_format_and_content: FindCirc output

source_name: mouse in vitro differentiated myotubes

growth_protocol: Mouse myoblasts (C2C12, ATCC) were cultured in Growth Medium (GM, DMEM supplemented with 20% FBS, L-Glutammine 2mM and Penicillin/Streptomycin) and induced to differentiation with Differentiation Medium (same as GM with 0.5% FBS). Human myoblasts (9208, Telethon Biobank) were cultured in Growth Medium (GM, DMEM supplemented with 10% FBS, L-Glutammine 2mM, insulin 50 µg/ml, FGFb 25 ng/ml, EGGF 1 ng/ml, Penicillin/Streptomycin) and induced to differentiation with Human Skeletal Muscle Differentiation Medium (DM, Promocell).

extract_protocol:
Qiazol, according to manufacturer instructions, then Ribominus
Illumina Truseq stranded paired end

tag: Sex

value: female

tag: cell line

value: myotube (cell line)

tag: disease status

value: WT


title: C2C12 DM #A


title: brain

source_name: brain

value: 8 weeks

value: male

value: wild type

value: brain


title: C2C12 GM #B

source_name: mouse myoblasts

value: myoblast (cell line)


title: C2C12 GM #A


title: shNt-OHT

value: neonatal human foreskin fibroblasts (primary culture cells)

value: transduced with MycER and control shRNA, not treated with 4-hydroxytamoxifen (4-OHT)


title: RNA-Seq WT Replicate 1

city: Vienna

first: Philipp

last: Rescheneder

address: Dr. Bohr Gasse 9

country: Austria

institute: MFPL

data_processing:
Adapters were clipped with cutadapt
Reads were mapped to the mouse genome with TopHat2 version 2.0.9 using default parameters. Reads with a mapping quality below 20 were discarded.
Htseq-count was used to create a count table taking into account only reads with a mapping quality larger than 20
All annotated transcripts that at least show one mapped read per one million sequenced reads (counts per million) in both replicates were tested for differential expression using edgeR and a FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: TXT containing read counts created by HTSeq-count

source_name: Immortalized murine dermal fibroblasts, passage 34

growth_protocol: Immortalized murine dermal Lap2α+/+ and Lap2α-/- fibroblasts (imMDF) were cultured at 37 °C, 5% CO2 in Dulbecco’s modified Eagles medium (DMEM), supplemented with 10% FCS, 2 mM L-Glutamine, 100 U/ml Penicillin, 100 µg/ml Streptomycin, 0.1 mM non-essential amino acids and passaged at 80-90% confluency

extract_protocol:
10 ng of total RNA (>200 bp) isolated with GeneJET RNA purification kit (Thermo Scientific, Cat.No. K0731), depleted of rRNA (Ribo-Zero Magnetic Kit; epicentre, Cat.No. MRZH116), were fragmented by hydrolysis (40 mM TrisOAc at pH 8.2, 100 mM KOAc, 150 mM MgOAc) at 94°C for 3 min
The sequencing libraries were prepared by the Vienna Biocenter CSF NGS unit using the NEBNext Library Prep Reagent Set for Illumina according to the manufacturer’s instructions (NEB; Cat.No. E6000S) and multiplexed (2 samples/lane)

tag: genotype

value: Lap2alpha +/+

value: fibroblasts

value: dermis


title: RNA-Seq KO Replicate 1

value: Lap2alpha -/-


title: RNA-Seq WT Replicate 2

source_name: Immortalized murine dermal fibroblasts, passage 42


title: RNA-Seq KO Replicate 2


title: shNt+OHT-Myc2

tag: treatment

value: transduced with MycER and control shRNA, treated with 4-hydroxytamoxifen (4-OHT)

value: anti-MYC N262 (Santa Cruz Biotechnology, catalog number sc-764)


title: H3K27me3 KO 12cyc ChIPSeq

data_processing:
Adapters were clipped with cutadapt
Reads were mapped to the mouse genome with bowtie2 version 2.1.0 using default parameters. Reads with a mapping quality below 20 were discarded.
Reads stemming from PCR duplicates were removed and all ChIP read files were downsampled to match the read count of their respective input sample using picard-tools
Regions of enrichment (peaks) were identified EDD (parameters “-b 11 –g 5 –fdr 0.1) version 1.0.2 and SICER version 1.1 (parameters: window size of 1,000bp, a gap size of 3,000bp and a false discovery rate of 0.01)
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing peaks called by EDD or SICER; BigWig files containing log ratios between histone modification ChIP-Seq read counts and respective Input read counts for 500bp bins

source_name: Immortalized murine dermal fibroblasts

extract_protocol:
80-90% confluent cells were fixed with 1% formaldehyde, nuclei were isolated and sonicated with a Diagenode Bioruptor on HIGH setting (30 sec ON/30 sec OFF) for 12 or 30 cycles. Resulting chromatin fragments were immunoprecipitated with respective antibodies. Antibody-chromatin complexes were washed, DNA was eluted, purified  and subsequently used for library preparation. Sequencing was performed on an Illumina HiSeq2000.
The sequencing libraries were prepared from DNA fragments ranging from 100 – 800 bp by the Vienna Biocenter CSF NGS unit (www.csf.ac.at) using the NEBNext Library Prep Reagent Set for Illumina according to the manufacturer’s instructions

tag: sonication cycles

value: 12 cycles

value: H3K27me3 Millipore 07-449


title: H3K27me3 WT 12cyc ChIPSeq


title: H3K9me3 KO 12cyc ChIPSeq

value: H3K9me3 abcam ab8898


title: H3K9me3 WT 12cyc ChIPSeq


title: H3K4me3 KO 12cyc ChIPSeq

value: H3K4me3 Millipore 07-473


title: H3K4me3 WT 12cyc ChIPSeq


title: H3K9Ac WT 12cyc ChIPSeq

value: H3K9Ac Millipore 06-942


title: heart

source_name: heart

value: 8 weeks

value: male

value: heart


title: H3K9Ac KO 12cyc ChIPSeq


title: Lamin B1 WT 12cyc ChIPSeq

value: LaminB1 Proteintech 12987-1-AP


title: Lamin B1 WT 30cyc ChIPSeq

value: 30 cycles


title: Input WT 30cyc DNA


title: LAP2alpha WT 30cyc ChIPSeq

value: Lap2alpha 8C10-1H11, hybridoma supernatant


title: Lamin A/C 3A6 KO 30cyc ChIPSeq

value: LaminA 3A6-4C11, Active Motif 39287


title: Lamin A/C 3A6 WT 30cyc ChIPSeq

value: fibroblasts

value: Lap2alpha +/+


title: Lamin A/C N18 KO 12cyc ChIPSeq

value: dermis

value: Lap2alpha -/-

value: LaminA N18, Santa Cruz sc-6215


title: Lamin A/C N18 KO 30cyc ChIPSeq


title: Lamin A/C 3A6 KO 12cyc ChIPSeq

value: 12 cycles


title: Lamin A/C N18 WT 30cyc ChIPSeq


title: Lamin A/C N18 WT 12cyc ChIPSeq


title: atring1a,b_H3K27me3_ChIPseq_rep2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

data_processing:
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using BOWTIE2.0 for DNA sequencing and TOPHATv2.0.8 for RNA sequencing, both with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, MACS1.4 was used to identify read enriched regions (peaks) and MAnorm was applied to characterize the change of genome-wide H3K27me3 profile. For RNA-seq, HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: In ChIP-seq, peak files was provided; In RNA-seq, read counts for genes (TAIR10) was provided.
Supplementary_files_format_and_content: RNA_seq.deseq.log2fc.p.txt: Contains the ratio between mutant and wild-type for both replicates. The number of read in each gene is counted by DEseq-count.

organism: Arabidopsis thaliana

source_name: 2-week-old seedlings

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
After 2 weeks , seedlings were harvested, frozen in liquid nitrogen, and stored at 80°C for total RNA isolation or directly vacuum-infiltrated with formaldehyde crosslinking solution for ChIP assay.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000 following the manufacturer's instructions (Illumina)

treatment_protocol: No treatment applied.

value: 2-week old seedlings without roots

tag: ecotype

value: Col

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: swn_RNAseq_rep2


title: Input WT 12cyc DNA


title: Input KO 12cyc DNA


title: Col_H3K27me3_ChIPseq_rep2


title: LAP2alpha WT 12cyc ChIPSeq


title: lhp1_6_H3K27me3_ChIPseq


title: clf29swn21_RNAseq_rep2


title: Gillisia_limnaea_R_8282_DSM15749_native

organism: Gillisia limnaea DSM 15749

source_name: Bacterial gDNA

tag: dna treatment

tag: pacbio sequencing chemistry

tag: genome build (img genome id)


title: Input KO 30cyc DNA

tag: chip antibody


title: TS1293F_CLIP-seq_Huh-7.5_HBV

description: Table S1.txt

tag: sample subseries

value: Virus AGO-CLIP

tag: virus

value: HBV

tag: small rna

value: Mock

tag: time point

tag: index

value: GCAT


title: clf29swn21_RNAseq

source_name: Arabidopsis thaliana 2-week-old seedlings

growth_protocol: 16h light, 8h dark, 21°C

extract_protocol:
Chromatin or RNA was extracted from 2-week-old seedlings, using standard protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000 following the manufacturer's instructions (Illumina).

tag: tissue


title: swn_RNAseq

extract_protocol:
After 2 weeks, seedlings were harvested, frozen in liquid nitrogen, and stored at -80°C for total RNA isolation or directly vacuum-infiltrated with formaldehyde crosslinking solution for ChIP assay.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000 following the manufacturer's instructions (Illumina)

tag: genotype/variation

value: swn


title: Col_RNAseq_rep2

value: wild type


title: clf_29_H3K27me3_ChIPseq_rep2


title: atbmi1a,b_H3K27me3_ChIPseq_rep2


title: clf_29_RNAseq_rep2


title: Lamin A/C 3A6 WT 12cyc ChIPSeq

tag: cell type

tag: genotype


title: atring1a,b_RNAseq


title: 9981 DM

description: treated with pccl-myoD-IRES-GFP

source_name: human Duchenne Muscular Dystrophy myotubes (in vitro differentiated with myoD ectopic expression)

tag: Sex

value: male

tag: cell line

value: myotube

tag: disease status

value: DMD


title: 9981 GM

source_name: human Duchenne Muscular Dystrophy myoblasts

value: myoblast


title: lhp1_6_RNAseq

tag: ecotype


title: SG DM

description: treated with pccl-myoD-IRES-GFP


title: MDM Day 7 -UDG

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description:
JS208
HIV lockdown

data_processing:
Reads were trimmed 2 bp on the 5' end for quality. Reads were aligned to the UCSC hg19 genome with HIV virus added as a chromosome using bwa mem. The command to run the alignment: bwa mem <bwaindex (hg19+HIV)> read1.fastq.gz read2.fastq.gz |samtools view -ShuF4 - | samtools sort -o - >bamfile
BAM alignment files were processed to genome coverage in bedGraph format using bedtools
BAM alignment files were processed to deduplicated bamfiles using samtools and piccard.
deduplicated bam alignment files were processed to vcf files using freebayes and vcffilter
BAM alignment files were processed to chimera and discordant alignments using pysam and UNIX
Segmentation analsysis was performed using chimeric and discordant reads and hepG1 segmentation data using bedtools
Genome_build: Hg19 +HIV(virus)
Supplementary_files_format_and_content: bedGraph files
Supplementary_files_format_and_content: VCF files: Contain variant calls (from FreeBayes) for the JS208 and JS215 samples and are produced using the pipeline at: https://github.com/hesselberthlab/stivers-hiv
Supplementary_files_format_and_content: Oligos.xlsx file: Contains all Illumina adaptor and PCR sequences, as well as Lockdown probes used for HIV isolation.

source_name: MDM cells

growth_protocol: Cells were harvested from peripheral blood of donors.  PBMCs were from whole blood ficoll gradient and monocytes were isolated using the Pan monocyte Isolation Kit (Miltenyi Biotec). Monocytes were differentiated into macrophages over 7 d using MDM-20 media containing RPMI 1640, 20% (vol/vol) autologous plasma, 1 ng/mL GM-CSF (BD Biosciences), 1× Hepes, and 1× Glutamine (Gibco). Cultured MDMs were maintained in media containing RPMI 1640 + 10% (vol/vol) dialyzed FBS, 1% Pen/Strep.

extract_protocol:
DNA was isolated using a Qiamp DNA extraction kit(Qiagen) according to manufacturer's protocol.
The isolated DNA was sheared for 12 minutes on a bioruptor with 30sec on 30 sec off.  Sheared DNA was end repaired, a-tailed, and ligated to dual indexed long Illumina adapters.  Libraries were mixed equimolar to 500ng and mixed with 5µg of cot1 and IDT blocking oligos and dried down.  Lockdown probes against HIV in the forward and reverse direction were added in seperate reactions to 3pmol.  Libraries were hybridized for 4 hours at 65˚ then bound to M-270 streptavin beads and washed.  HIV-Lockdown DNA was eluted and samples were split and treated with or without 5U UDG and 10U EndoIV for 2 hours at 37˚.  Samples were then PCRed with short Illumina primers for 22 cycles with Maxima Taq and purified with ampure beads.

treatment_protocol: MDM cells were either mock treated or infected with HIV NL4.3 and incubated for the number of days indicated in the sample name.

value: Monocyte-Derived Macrophage (MDM)

tag: agent

value: HIV NL4.3


title: tfl2_2_RNAseq


title: atbmi1a,b_RNAseq


title: MDM Day 7 +UDG

description:
JS215
HIV lockdown


title: clf_29_RNAseq


title: atring1a,b_RNAseq_rep2


title: Col_RNAseq


title: atbmi1_neg_ChIPseq

tag: chip antibody manufacturer

tag: chip antibody catalog #


title: atring1a,b_neg_ChIPseq

tag: chip antibody


title: atring1a,b_H3K27me3_ChIPseq


title: atbmi1a,b_RNAseq_rep2


title: SG GM


title: 9208 DM #B

source_name: human in vitro differentiated myotubes

value: WT


title: 9208 GM #A

source_name: human myoblasts


title: atbmi1a,b_H3K27me3_ChIPseq


title: 9208 GM #B


title: cko_rep3

data_processing:
Alignment of RNA-Seq data was performed using the bwa version 0.7.6a-r433 analysis pipeline against mouse genome mm9.
HTSeq-count version 0.5.4p3 was used to count read number on gene exons.
Genes differentially expressed between the Control and CKO samples were detected using R bioconductor package ‘DESeq’ version 2.13 and significant differences were called using cutoffs p-value ≤ 0.05; fold change ≥ 1.5 and FDR ≤ 0.10.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read count value for each sample

source_name: RPC-specific Ronin knockout retina

extract_protocol:
Retinae were dissected and total RNA immediately purified using the RNeasy Mini Kit (Qiagen) followed by reverse transcription using the SuperScript III first strand synthesis kit (Invitrogen)
Total RNA was poly-A selected, fractionated (200-500 nucleotide range) and cDNA generated using the Invitrogen SuperScript III reverse transcription kit followed by second strand cDNA synthesis, which was subjected to standard Illumina adaptor ligation and sequencing.

tag: strain background

value: FVB, 129/Sv, SJL/B6, and C57/B6

value: Chx10-Cre::GFP +/tg; Ronin flox/flox

tag: developmental stage

tag: molecule subtype

value: retina

value: polyA enriched RNA


title: tfl2_2_H3K27me3_ChIPseq

value: 2-week old seedlings without roots

value: Col

value: Upstate


title: ctrl_rep3

value: Ronin flox/flox


title: cko_rep1


title: clf_29_neg_ChIPseq


title: Col_neg_ChIPseq


title: ctrl_rep2


title: clf_29_H3K27me3_ChIPseq


title: ctrl_rep1


title: Col_H3K27me3_ChIPseq


title: single cell RNA-seq [NPC3_S41]

status: Public on Jan 18 2016

city: Boston

first: Jean

last: Fan

state: MA

address: 10 Shattuck St 336B

department: Department of Biomedical Informatics

institute: Harvard University

data_processing:
RNA-seq data was aligned using tophat2, read counts were quantified with HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq read counts for each cell were combined and written out into a csv file

source_name: FACS sorted Neural Progenitor Cell

extract_protocol:
Timed-pregnant mice were sacrificed by deep anesthesia followed by cervical dislocation. The embryos were quickly removed and cortical hemispheres were isolated, ganglionic eminences removed, and all pups brains were pooled. Single cells were isolated by gentle trituration in ice-cold phosphate buffered saline containing 2 mM EGTA (PBSE) using P1000 tips with decreasing bore diameter. Cells were then filtered through a 40 uM nylon cell strainer and stained with propidium iodide (PI), a live-dead stain, and fluorescence activated single cell sorting (FACS) was performed selecting for PI negative cells. Samples remained on ice throughout the process and total processing time from cervical dislocation to sorting was limited to 2 hours.
Single cells were sorted directly into cell lysis buffer provided in the Clontech SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing (cat # 634936), and sequencing libraries were generated using the manufacturer’s protocol. Resulting libraries were sequenced on the Illumina® HiSeqTM 2000 sequencing platform.

tag: strain

tag: age

value: Brain, cortex

value: neural progenitor cell


title: single cell RNA-seq [NPC3_S40]

tag: tissue


title: cko_rep2

tag: genotype/variation


title: single cell RNA-seq [NPC3_S44]

tag: cell type


title: single cell RNA-seq [NPC3_S45]


title: single cell RNA-seq [NPC3_S38]


title: 9208 DM #A

value: male


title: single cell RNA-seq [NPC3_S36]


title: single cell RNA-seq [NPC3_S37]


title: tfl2_2_neg_ChIPseq


title: single cell RNA-seq [NPC3_S34]


title: single cell RNA-seq [NPC3_S26]


title: single cell RNA-seq [NPC3_S29]


title: single cell RNA-seq [NPC3_S28]


title: single cell RNA-seq [NPC3_S32]


title: single cell RNA-seq [NPC3_S33]


title: single cell RNA-seq [NPC3_S31]


title: single cell RNA-seq [NPC3_S25]


title: single cell RNA-seq [NPC3_S24]


title: O

city: Philadelphia

first: Arjun

last: Raj

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

description: clone O

data_processing:
Alignments were performed using STAR version 2.3.0e against the BosTau7 genome assembly, with default parameters.
Data was sorted and indexed using samtools.
Counts were assigned using HTSeq using the following options --idattr=gene_id  --mode=union  --stranded=no  --type=exon  --order=name.
Genome_build: bosTau7
Supplementary_files_format_and_content: HTSeq count text files with gene name and transcript count.

source_name: bone marrow derived mesenchymal stem cells

growth_protocol: grown on tissue culture plastic in DMEM + FBS + antibiotics

extract_protocol:
Qiagen microRNeasy, NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra RNA Library Prep Kit for Illumina

tag: clonality

value: clone


title: P

description: clone P

value: bone marrow derived mesenchymal stem cells


title: N

description: clone N


title: Q

description: clone Q


title: single cell RNA-seq [NPC3_S19]


title: single cell RNA-seq [NPC3_S39]


title: single cell RNA-seq [NPC3_S20]


title: single cell RNA-seq [NPC2_S7]


title: single cell RNA-seq [NPC2_S6]


title: M

description: clone M


title: L

description: clone L


title: single cell RNA-seq [NPC3_S23]


title: J

description: clone J


title: single cell RNA-seq [NPC3_S22]


title: single cell RNA-seq [NPC2_S5]


title: K

description: clone K


title: I

description: clone I


title: single cell RNA-seq [NPC2_S25]


title: Het

description: heterogenous population

value: mixed population


title: single cell RNA-seq [NPC2_S23]


title: single cell RNA-seq [NPC2_S22]


title: H

description: clone H


title: G

description: clone G


title: E

description: clone E


title: F

description: clone F


title: single cell RNA-seq [NPC2_S9]


title: single cell RNA-seq [NPC2_S17]


title: single cell RNA-seq [NPC2_S19]


title: single cell RNA-seq [NPC2_S16]


title: D

description: clone D


title: single cell RNA-seq [NPC2_S10]


title: B

description: clone B


title: A

description: clone A


title: single cell RNA-seq [NPC1_S9]


title: single cell RNA-seq [NPC1_S6]


title: C

description: clone C


title: single cell RNA-seq [NPC1_S8]


title: single cell RNA-seq [NPC2_S13]


title: single cell RNA-seq [NPC1_S39]


title: single cell RNA-seq [NPC1_S7]


title: single cell RNA-seq [NPC1_S42]


title: single cell RNA-seq [NPC1_S5]


title: single cell RNA-seq [NPC1_S40]


title: single cell RNA-seq [NPC1_S33]


title: single cell RNA-seq [NPC1_S4]


title: Blimp-1 Knock-out (BlimpKO) rep2, batch 1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained.
Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Ig genes were excluded from the gene-level expression analysis. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least one library.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the 'voom' function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2-FPKM values for each library. EntrezIDs represent NCBI Entrez Gene IDs.
Supplementary_files_format_and_content: GEO_suppl_raw_counts.txt': Includes raw read counts for each gene in each library. The raw read count is the number of mapped reads (or read pairs for paired-end libraries) assigned to each gene. EntrezIDs represent NCBI Entrez Gene IDs.

source_name: Bone marrow, plasma cells, Blimp1 knockout

extract_protocol:
RNA was isolated from ex-vivo sorted Blimp1-GFP+CD138+ plasma cells using the Qiagen RNeasy Micro kit.
Libraries were generated using the Illumina TruSeq RNA sample preparation kit following manufacturer instructions.

tag: strain/background

value: bone marrow

value: plasma cells


title: Blimp-1 Knock-out (BlimpKO) rep1, batch 1


title: single cell RNA-seq [NPC1_S31]


title: single cell RNA-seq [NPC1_S29]


title: Wild type (WT) rep2, batch 1

source_name: Bone marrow, plasma cells, WT

value: wild type


title: single cell RNA-seq [NPC2_S14]


title: Wild type (WT) rep1, batch 1


title: CFPAC1.Control.ELF3

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

description: Chromatin IP against ELF3

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the human hg19 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters, nomodel and bw=300 (except for the H3K27ac of PDACs for which a bw=100 was used). Each IP was compared to input DNA.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

growth_protocol: Iscove's Modified Dulbecco Medium (IMDM) supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol: ChIP lysates were generated from 2-5x10^6 cells for histone marks or 20-40x10^6 cells for transcription factors. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: CFPAC1 clonal cell line

value: Control

tag: antibody

value: Anti-ELF3 (Sigma # HPA003479)


title: single cell RNA-seq [NPC1_S3]


title: single cell RNA-seq [NPC1_S30]


title: CFPAC1.Control.FOXA1

description: Chromatin IP against FOXA1

value: Anti-FOXA1 (Abcam # 23738)


title: single cell RNA-seq [NPC1_S27]


title: single cell RNA-seq [NPC1_S26]


title: CFPAC1.KLF5-KO.FOXA1

description: Chromatin IP against FOXA1

value: CFPAC1 genome-edited clonal cell line


title: CFPAC1.KLF4

description: Chromatin IP against KLF4

value: original PDAC cell line

tag: chip antibody vendor

value: RnD

tag: chip antibody cat.#


title: CFPAC1.KLF6

description: Chromatin IP against KLF6

value: Anti-KLF6 (SCBT # SC-7158)


title: CFPAC1.KLF5-KO.ELF3

description: Chromatin IP against ELF3


title: single cell RNA-seq [NPC1_S2]

value: Brain, cortex


title: single cell RNA-seq [NPC1_S19]

value: neural progenitor cell


title: single cell RNA-seq [NPC1_S20]


title: single cell RNA-seq [NPC1_S16]


title: single cell RNA-seq [NPC1_S32]


title: MRC_5_PD52_1

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava v1.8.2 software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file includes raw counts and RPKM values of each sample

source_name: total RNA extracted from MRC-5 cells

growth_protocol: Cells were cultured as recommended by ATCC in Dulbeccos modified Eagles low glucose medium (DMEM) with L-glutamine (PAA Laboratories, Pasching, Austria), supplemented with 10% fetal bovine serum (PAA Laboratories). Cells were grown under normal air conditions in a 9.5% CO2 atmosphere at 37°C. For sub-culturing, the remaining medium was discarded and cells were washed in 1 x PBS (pH 7.4) (PAA Laboratories) and detached using trypsine/EDTA (PAA Laboratories). Primary fibroblasts were sub-cultured in a 1:4 (= 2 population doublings (PDs)) or 1:2 (= 1 PD) ratio. For stock purposes, cryo-conservation of the cell lines at various PDs were undertaken in cryo-conserving medium (DMEM + 10% FBS + 5% DMSO). Cells were immediately frozen at -80°C and stored for two to three days. Afterwards, cells were transferred to liquid nitrogen for long time storage. Re-freezing and re-thawing was not performed to avoid premature senescence [Honda et al., 2001]. One vial of each of the five different fibroblast cell lines (MRC-5, HFF, BJ, WI-38 and IMR-90) were obtained and maintained in culture from an early PD. On obtaining enough stock on confluent growth of the fibroblasts in 75 cm2 flasks, cells were sub-cultured into three different 75 cm2 flasks (“triplicates”) and were maintained until they were senescent in culture.

extract_protocol:
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.

tag: population doublings

tag: age category


title: single cell RNA-seq [NPC1_S15]


title: MRC_5_PD62_1


title: single cell RNA-seq [NPC1_S14]


title: single cell RNA-seq [NPC1_S28]


title: MRC_5_PD52_2


title: single cell RNA-seq [NPC1_S13]


title: single cell RNA-seq [NPC1_S11]


title: MRC_5_PD42_1


title: single cell RNA-seq [NPC1_S10]


title: MRC_5_PD42_3


title: single cell RNA-seq [NPC1_S12]


title: MRC_5_PD42_2


title: MRC_5_PD62_3


title: MRC_5_PD62_2


title: single cell RNA-seq [NPC1_S18]


title: HFF_PD64_2

source_name: total RNA extracted from HFF cells

value: HFF


title: single cell RNA-seq [NPC1_S1]


title: HFF_PD46_2


title: HFF_PD64_1


title: single cell RNA-seq [NPC1_S17]


title: HFF_PD26_3


title: HFF_PD46_1


title: MRC_5_PD52_3


title: HFF_PD26_2


title: HFF_PD26_1


title: HFF_PD64_3


title: LCL_42

city: San Francisco

first: Kathleen

middle: M

last: Giacomini

address: 1550 4th St, Mission Bay, RH 581

institute: University of California, San Francisco

data_processing:
Insert sizes were estimated using the Picard Tools (v1.79) tools SortSam.jar and CollectInsertSizeMetrics.jar on Bowtie2(v2.0.0-beta7)-generated sam files from a subset of 500,000 paired-end reads per sample (bowtie2 options -q --very-fast --phred33).
Raw reads were mapped to the human genome sequence using Tophat v2.0.6, allowing for four mismatches per 100bp read, a maximum of 6 edit distances per read, and one mismatch in the splice anchor region.
Using Picard Tools, the alignment files were sorted by genomic coordinates, read-group data was added, and duplicate reads were marked and removed.
Transcript structure assembly was performed with Cufflinks (v.2.0.2) on each sample for each tissue type. The Gencode v12 annotation was used as a reference to guide assembly (--GTF-guide); additional parameters included upper-quartile normalization (--upper-quartile-norm), library type (--library-type fr-firststrand), and maximum bundle length (--max-bundle-length 7500000).
Cuffmerge (v2.0.2) was then used to merge all the cufflinks assemblies and the reference annotation into one large set of transcript structures. Splice junctions not present in the reference annotation were required to pass a Shannon entropy score threshold of 2.
The mapped reads for each sample were subsampled down to 20 million using multiple runs of the Picard tool DownsampleSam, and 18 samples per tissue type were selected to create a subsampled dataset. Subsequent steps were performed separatley on both subsampled and non-subsampled datasets.
To calculate the expression level of each gene in each tissue type, Cuffdiff (v2.2.1) was run with default parameters and the option --library-type fr-firststrand on the subsampled read files with 18 samples per tissue type used as ‘replicates’ and the merged set of transcript structures used as the reference annotation. Gene expression for each tissue was calculated by summing all isoforms for a given gene in a given tissue from the isoforms.fpkm_tracking file generated by Cuffdiff. Genes with any isoform with a status of “HIDATA” do not have a calculated FPKM value. Gene expression for each individual was calculated by summing all isoforms for a given gene for each individual from the isoforms.read_group_tracking file generated by Cuffdiff. This file has, for each individual, one value per isoform reported for each gene.
Splice junctions were identified using the JuncBASE package on reads that overlapped protein-coding genes. Only splice junctions with a Shannon entropy score greater than 2 using all subsampled reads were used. Junctions were called non-annotated if they were not present in the Gencode v12 annotation nor in the Ensemble annotation. Reported JuncBASE results were transformed into groups of mutually exclusive junction sets, each with defined length-normalized read counts (reads/100bp) and ‘percent spliced in’ (PSI) values. Complex events (e.g. cassette exon + alternate 3’ splice site) with ambiguously mapped reads and inron retention events were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values by individual and by tissue are reported for 389 pharmacogenes in subsampled and non-subsampled datasets; Percent Spliced In (PSI) values are reported for 389 pharmacogenes by individual in subsampled and non-subsampled datasets.

source_name: Cells - EBV transformed lymphocytes

growth_protocol: Immortalized lymphoblastoid cell lines (LCLs) were grown at 37°C with 5% CO2 in RPMI 1640 media supplemented with 10% FBS, 500 U/ml penicillin/streptomycin, and 2 nmol/L GlutaMAX (Life Technologies).

extract_protocol:
cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2. The corresponding vendor protocol was used for almost all steps (including polyA selection) with a final PCR enrichment using 15 cycles. The protocol was modified to increase fragment size and to yield final libraries containing only the first strand-synthesized product by: (a) reduction of elute-prime-frag treatment time from 8 minutes to 4 minutes (to increase library insert size), (b) second strand synthesis using a mastermix containing dUTP (in place of dTTP) and RNAse H (to remove RNA), and (c) following the final adapter ligation cleanup, libraries were digested with uracil DNA deglycosylase (to remove dUTP-containing second strand product).
Total RNA was isolated from LCLs using the PureLink RNA Mini Kit (Life Technologies).

value: LCLs


title: LCL_38


title: LCL_43


title: LCL_39


title: LCL_44


title: LCL_40


title: LCL_36


title: LCL_35


title: LCL_41


title: LCL_34


title: LCL_33


title: LCL_28


title: LCL_27


title: LCL_26


title: LCL_45


title: LCL_22


title: LCL_23


title: LCL_29


title: LCL_31


title: HFF_PD46_3


title: LCL_21


title: LCL_25


title: LCL_20


title: LCL_32


title: LCL_17


title: LCL_16


title: LCL_30


title: LCL_24


title: LCL_15


title: LCL_9


title: LCL_8


title: LCL_11


title: LCL_37


title: LCL_12


title: LCL_5


title: LCL_6


title: LCL_7


title: LCL_10


title: LCL_13


title: LCL_14


title: LCL_4


title: LCL_2


title: LCL_19


title: LCL_18


title: LCL_3


title: Adipose_25

source_name: Adipose (Subcutaneous)

extract_protocol:
In brief, 0.5-1.0 μg of total RNA was twice selected for mRNA by oligo (dT) and then fragmented by heating. First strand cDNA was synthesized using Superscript III reverse transcriptase and random hexamer primers. After second strand synthesis by DNA polymerase I and with dUTP in place of dTTP, double stranded cDNA was end-repaired and A-tailed prior to ligation of Illumina adaptors including DNA indices. Libraries were made strand-specific by digestion with Uracil-DNA Glycosylase prior to PCR amplification. Bead-based clean-up was incorporated after each enzymatic reaction and libraries were checked by flash gel and Bioanalyzer analysis.
Total RNA was isolated from tissues using TRIzol Reagent.

value: Adipose


title: LCL_1


title: Adipose_10


title: Adipose_18


title: Adipose_17


title: Adipose_23


title: Adipose_19


title: Adipose_15


title: Adipose_21


title: Adipose_14


title: Adipose_20


title: Adipose_12


title: Adipose_22


title: Adipose_4


title: Adipose_6


title: Adipose_16


title: Adipose_5


title: Adipose_24


title: Adipose_11


title: Adipose_13


title: Adipose_7


title: Adipose_2


title: Adipose_8


title: Adipose_3


title: Adipose_9


title: Heart_25

source_name: Heart (Left Ventricle)

value: Heart


title: Heart_24


title: Adipose_1


title: Heart_23


title: Heart_19


title: Heart_16


title: Heart_18


title: Heart_15


title: Heart_12


title: Heart_13


title: Heart_7


title: Heart_11


title: Heart_21


title: Heart_17


title: Heart_4


title: Heart_3


title: Heart_22


title: Heart_5


title: Heart_14


title: Heart_9


title: Heart_1


title: 98-Doxorubicin-uninduced

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

institute: Stanford University

data_processing:
library strategy: Barcode sequencing (Bar-seq)
created a synthetic reference chromosome sequence for each of the expected amplicons. The synthetic reference included Illumina adaptors, library barcode, PCR amplification priming region, PCR barcode, and the gRNA specificity sequence.
merged forward and reverse reads using PEAR version 0.9.4 with default parameters.
resulting FastQ file was mapped against the created synthetic reference using BWA version 0.6.1-r104 with command line  “bwa index [reference]; bwa aln -n3 -o3 -e1 -l22 [reference] [fastq] > [aln]; bwa samse -f [out] [reference] [aln] [fastq] ”
For each of the expected amplicons, we counted the number of perfect matches (flag NM:i:0) from the resulting alignments (Additional data file 8, column “Count_perfect”) that were used in subsequent analyses.
Supplementary_files_format_and_content: Additional data file 8. An Excel spreadsheet that contains sequence read information and raw counts from MiSeq data.

organism: Saccharomyces cerevisiae

source_name: CRISPRi guide RNA library_Doxorubicin-uninduced

growth_protocol: Yeast culturing and sample collection was performed using a cell-screening platform that integrates temperature-controlled absorbance plate readers, plate coolers, and a liquid handling robot. Briefly, 700 µl yeast cultures were grown (+/- a drug and +/- ATc) in 48 well plates at 30oC with orbital shaking in Infinite plate readers (Tecan). To maintain cultures in log phase over many doublings, 23 µls of the culture was removed when it reached an OD of 0.76, added to a well containing 700 µl of media, and then allowed to grow further. After three such dilutions, 600 µls of the culture was collected and saved to a 4oC cooling station (Torrey Pines) when it reached an OD of 0.76. This amounted to approximately 20 culture doublings from the beginning of the experiment. Pipetting events were triggered automatically by Pegasus Software and performed by a Freedom EVO workstation (Tecan).

extract_protocol:
After competitive growth of yeast strains and sample collection, yeast plasmids were purified using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).
Purified plasmids were used as a template for PCR with barcoded up and down sequencing primers that produce a double index to uniquely identify each sample.  PCR products were confirmed by agarose gel electrophoresis. After PCR, samples were combined and bead cleaned with Thermo ScientificTM Sera-Mag Speed Beads Carboxylate-Modified particles.  Sequencing was performed using Illumina MiSeq.

treatment_protocol: In general, drugs were applied at concentrations that inhibit growth by ~20%

tag: grna libraries

tag: growth condition

value: 12.5uM Doxorubicin

tag: index pair

value: TAACG-TGCTAA

value: plasmid DNA


title: 97-Fluconazole-plus ATc

source_name: CRISPRi guide RNA library_Fluconazole-plus ATc

value: 20uM Fluconazole +ATc

value: TAACG-TCGGAT


title: 99-Doxorubicin-plus ATc

source_name: CRISPRi guide RNA library_Doxorubicin-plus ATc

value: 12.5uM Doxorubicin +ATc


title: Heart_8


title: Heart_2


title: 96-Fluconazole-uninduced

source_name: CRISPRi guide RNA library_Fluconazole-uninduced

value: 20uM Fluconazole


title: Kidney_31

source_name: Kidney (Cortex)

value: Kidney


title: Kidney_30


title: 95-4130-1276-plus ATc

source_name: CRISPRi guide RNA library_4130-1276-plus ATc

value: CAGCAG-GTAAC


title: Heart_6


title: Kidney_32


title: Heart_20


title: Heart_10


title: 94-4130-1276-uninduced

source_name: CRISPRi guide RNA library_4130-1276-uninduced

value: CAGCAG-TCGGAT


title: Kidney_28


title: Kidney_29


title: Kidney_21


title: Kidney_19


title: Kidney_24


title: 91-1181-0519-plus ATc

source_name: CRISPRi guide RNA library_1181-0519-plus ATc

value: CTTA-TCGGAT


title: Kidney_18


title: 89-DMSO-plus ATc

source_name: CRISPRi guide RNA library_DMSO-plus ATc

value: 1% DMSO +ATc

value: CTTA-GGATT


title: Kidney_11


title: Kidney_25


title: Kidney_10


title: Kidney_17


title: Kidney_13


title: 90-1181-0519-uninduced

source_name: CRISPRi guide RNA library_1181-0519-uninduced

value: CTTA-TGCTAA


title: Kidney_6


title: 88-DMSO-uninduced

source_name: CRISPRi guide RNA library_DMSO-uninduced

value: 1% DMSO

value: CTTA-GACT


title: 86-Fluconazole-uninduced

value: gene_tiling_18bp & gene_tiling_20bp

value: CTTA-AGGTC


title: Kidney_5


title: 87-Fluconazole-plus ATc

value: CTTA-CCAGGT


title: Kidney_3


title: 85-Rapamycin-plus ATc

source_name: CRISPRi guide RNA library_Rapamycin-plus ATc

value: 2.2nM Rapamycin +ATc

value: CTTA-AACC

value: plasmid DNA


title: Kidney_7


title: Kidney_1


title: Liver_23

source_name: Liver

value: Liver


title: 83-Aureobasidin-A-plus ATc

source_name: CRISPRi guide RNA library_Aureobasidin-A-plus ATc

value: 30nM Aureobasidin-A +ATc

value: ATGAT-GACT


title: Liver_20


title: 82-Aureobasidin-A-uninduced

source_name: CRISPRi guide RNA library_Aureobasidin-A-uninduced

value: 30nM Aureobasidin-A

value: ATGAT-CCAGGT


title: Liver_22


title: Liver_21


title: Liver_19


title: Liver_18


title: Kidney_9

value: Kidney


title: 79-DMSO-plus ATc

value: 1% DMSO +ATc

value: TCGT-GGATT


title: Liver_13


title: 80-Aureobasidin-A-uninduced

value: 20nM Aureobasidin-A

value: ATGAT-AACC


title: Liver_14


title: Liver_15


title: Liver_11


title: Liver_12


title: Liver_9


title: Liver_10


title: 78-DMSO-uninduced

value: 1% DMSO

value: TCGT-GACT


title: Liver_17


title: Liver_8


title: 77-6630449-plus ATc

source_name: CRISPRi guide RNA library_6630449-plus ATc

value: gene_tiling_18bp & gene_tiling_20bp

value: TCGT-CCAGGT


title: Liver_7


title: 76-6630449-uninduced

source_name: CRISPRi guide RNA library_6630449-uninduced

value: TCGT-AGGTC


title: 75-7312221-plus ATc

source_name: CRISPRi guide RNA library_7312221-plus ATc

value: TCGT-AACC


title: 81-Aureobasidin-A-plus ATc

value: 20nM Aureobasidin-A +ATc

value: ATGAT-AGGTC

value: plasmid DNA


title: Liver_6

value: Liver


title: 84-Rapamycin-uninduced

source_name: CRISPRi guide RNA library_Rapamycin-uninduced

value: 2.2nM Rapamycin

value: ATGAT-GGATT


title: Liver_24


title: 74-7312221-uninduced

source_name: CRISPRi guide RNA library_7312221-uninduced

value: GCCGT-GGATT


title: Liver_5


title: Liver_3


title: Liver_4


title: 73-DMSO-plus ATc

value: 1% DMSO +ATc

value: GCCGT-GACT


title: Liver_16


title: Liver_2


title: Liver_1


title: 70-9121982-uninduced

source_name: CRISPRi guide RNA library_9121982-uninduced

value: GCCGT-AACC


title: 71-9121982-plus ATc

source_name: CRISPRi guide RNA library_9121982-plus ATc

value: GCCGT-AGGTC


title: CFPAC1.Control.rep4

description:
processed data file: ZEB1-OE.genes.fpkm_tracking
processed data file: ZEB1-OE.gene_exp.diff

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the human hg19 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 200bp
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 23222703)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Genome_build: hg19 (NCBI build GRCh37), transcripts from Illumina iGenome UCSC hg19
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression comparisons (refer to http://cole-trapnell-lab.github.io/cufflinks/manual/ for details)

growth_protocol: Iscove's Modified Dulbecco Medium (IMDM) supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine, 1% Pen/Strep and 1.5 ug/ml Puromycin

extract_protocol: The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: CFPAC1 cells electroporated with expressing vector pCDH-EF1-MCS-BGH-PGK-GFP-T2A-Puro (SBI #CD550A1) cultured for 48 hours and selected with 1.5 ug/ml of Puromycin for 5 days.

tag: cell line background

value: CFPAC1 cells transfected with empty vector

value: empty vector control


title: CFPAC1.ZEB1_OE.rep2

treatment_protocol: CFPAC1 cells electroporated with expressing vector pCDH-EF1-ZEB1-BGH-PGK-GFP-T2A-Puro cultured for 48 hours and selected with 1.5 ug/ml of Puromycin for 5 days.

value: CFPAC1 cells transfected with ZEB1 expressing vector

value: ectopically expressing ZEB1


title: CFPAC1.ZEB1_OE.rep1


title: CFPAC1.Control.rep3


title: CFPAC1.ELF3-KO.rep1

description:
processed data file: KLF5-KO_and_ELF3-KO.genes.fpkm_tracking
processed data file: KLF5-KO_and_ELF3-KO.gene_exp.diff

treatment_protocol: Isolation of clonal cell line by dilution from CFPAC1 cells electroporated with plasmid ELF3.gRNA-pSpCas9-2A-Puro

value: CFPAC1 genome-edited clonal cell line

value: ELF3-deleted CRISPR-Cas9 clone


title: CFPAC1.Control.rep2

treatment_protocol: Isolation of clonal cell line by dilution from CFPAC1 cells electroporated with plasmid pSpCas9-2A-Puro (px459; Addgene #48139)

value: CFPAC1 clonal cell line

value: wild type clone


title: CFPAC1.ELF3-KO.rep2


title: CFPAC1.KLF5-KO.rep1

treatment_protocol: Isolation of clonal cell line by dilution from CFPAC1 cells electroporated with plasmid KLF5.gRNA-pSpCas9-2A-Puro

value: KLF5-deleted CRISPR-Cas9 clone


title: 69-9125678-plus ATc

source_name: CRISPRi guide RNA library_9125678-plus ATc

value: gene_tiling_18bp & gene_tiling_20bp

value: CGTTGA-GGATT

tag: molecule subtype

value: plasmid DNA


title: CFPAC1.ELF3-KO.rep3


title: CFPAC1.Control.rep1


title: 67-9125678-plus ATc

value: CGTTGA-CCAGGT


title: 65-1181-0519-plus ATc

value: CGTTGA-AACC


title: 66-9125678-uninduced

source_name: CRISPRi guide RNA library_9125678-uninduced

value: CGTTGA-AGGTC


title: PT45P1.rep1

description:
processed data file: PDACs.genes.fpkm_tracking
processed data file: CL-PDACs_vs_QM-PDACs.gene_exp.diff

growth_protocol: RPMI-1640 supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

treatment_protocol: No treatment

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: PANC1.rep2

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: 64-1181-0519-uninduced

value: ACTGCT-GGATT


title: 63-1181-0519-plus ATc

source_name: CRISPRi guide RNA library_1181-0519-plus ATc

value: ACTGCT-GACT


title: HPAF2.rep2

growth_protocol: Eagle's Minimal Essential Medium (EMEM) supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: PANC1.rep1


title: 72-DMSO-uninduced

value: 1% DMSO

value: GCCGT-CCAGGT


title: MiaPaca2.rep2


title: HPAF2.rep1


title: CFPAC1.rep2


title: CFPAC1.KLF5-KO.rep2


title: 68-9125678-uninduced

value: CGTTGA-GACT


title: 62-1181-0519-uninduced

value: ACTGCT-CCAGGT


title: CFPAC1.rep1


title: 61-DMSO-plus ATc

source_name: CRISPRi guide RNA library_DMSO-plus ATc

value: 1% DMSO +ATc

value: ACTGCT-AGGTC


title: CAPAN1.rep2

growth_protocol: RPMI-1640 supplemented with 20% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: 60-DMSO-uninduced

value: ACTGCT-AACC


title: BxPc3.rep2

description: processed data file: PDACs.genes.fpkm_tracking


title: CAPAN2.rep1

growth_protocol: RPMI-1640 supplemented with 15% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep


title: PT45P1.rep2


title: CAPAN2.rep2


title: BxPc3.rep1


title: CAPAN1.rep1


title: 59-1181-0519-uninduced

source_name: CRISPRi guide RNA library_1181-0519-uninduced

value: gene_tiling_18bp & gene_tiling_20bp & mutant18 & mutant20

value: ATGAT-GACT


title: 58-1181-0519-plus ATc

value: ATGAT-CCAGGT


title: 57-Fluconazole-uninduced

source_name: CRISPRi guide RNA library_Fluconazole-uninduced

value: 20uM Fluconazole

value: ATGAT-AGGTC

value: plasmid DNA


title: H3K4me1.CFPAC1.ELF3-KO.rep3

description: Chromatin IP against H3K4me1

value: CFPAC1 genome-edited clonal cell line

value: ELF3-deleted CRISPR-Cas9 clone

tag: chip antibody

value: Abcam


title: MiaPaca2.rep1

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: AsPC1.rep1


title: H3K4me1.CFPAC1.ELF3-KO.rep1

description: Chromatin IP against H3K4me1


title: H3K4me1.CFPAC1.ELF3-KO.rep2

description: Chromatin IP against H3K4me1


title: H3K4me1.CFPAC1.Control.rep1

description: Chromatin IP against H3K4me1

value: CFPAC1 clonal cell line

value: wild type clone


title: H3K4me1.CFPAC1.KLF5-KO.rep2

description: Chromatin IP against H3K4me1

value: KLF5-deleted CRISPR-Cas9 clone


title: 56-Fluconazole-plus ATc

source_name: CRISPRi guide RNA library_Fluconazole-plus ATc

value: 20uM Fluconazole +ATc

value: ATGAT-AACC


title: H3K4me1.CFPAC1.KLF5-KO.rep1

description: Chromatin IP against H3K4me1


title: 54-DMSO-plus ATc

value: 1% DMSO +ATc

value: TCGT-GACT


title: 55-DMSO-uninduced

source_name: CRISPRi guide RNA library_DMSO-uninduced

value: gene_tiling_18bp & gene_tiling_20bp & mutant18 & mutant20

value: 1% DMSO

value: TCGT-GGATT


title: H3K27ac.CFPAC1.ELF3-KO.rep2

description: Chromatin IP against H3K27ac


title: H3K4me1.CFPAC1.Control.rep2

description: Chromatin IP against H3K4me1


title: 51-Doxorubicin-uninduced

source_name: CRISPRi guide RNA library_Doxorubicin-uninduced

value: gene_tiling_18bp & gene_tiling_20bp

value: 12.5uM Doxorubicin

value: TCGT-AACC


title: H3K27ac.CFPAC1.ELF3-KO.rep1

description: Chromatin IP against H3K27ac

value: CFPAC1 genome-edited clonal cell line


title: 50-Doxorubicin-plus ATc

source_name: CRISPRi guide RNA library_Doxorubicin-plus ATc

value: 12.5uM Doxorubicin +ATc

value: GCCGT-GGATT

value: plasmid DNA


title: H3K27ac.CFPAC1.KLF5-KO.rep2

description: Chromatin IP against H3K27ac

value: Abcam


title: AsPC1.rep2

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: PANC1.ZEB1

description: Chromatin IP against ZEB1

value: SCBT


title: CFPAC1.KLF5

description: Chromatin IP against KLF5

value: Millipore


title: H3K27ac.CFPAC1.KLF5-KO.rep1

description: Chromatin IP against H3K27ac

value: KLF5-deleted CRISPR-Cas9 clone


title: CFPAC1.FOXA1

description: Chromatin IP against FOXA1


title: H3K27ac.CFPAC1.Control.rep1

description: Chromatin IP against H3K27ac

value: CFPAC1 clonal cell line

value: wild type clone


title: 46-Rapamycin-plus ATc

source_name: CRISPRi guide RNA library_Rapamycin-plus ATc

value: 10nM Rapamycin +ATc

value: GCCGT-AACC


title: INPUT.CAPAN1

description: Control IP DNA


title: 44-4130-1276-plus ATc

source_name: CRISPRi guide RNA library_4130-1276-plus ATc

value: gene_tiling_18bp & gene_tiling_20bp & mutant18 & mutant20

value: CGTTGA-GACT


title: CFPAC1.ELF3

description: Chromatin IP against ELF3

value: Sigma


title: 47-Rapamycin-uninduced

value: gene_tiling_18bp & gene_tiling_20bp

value: 10nM Rapamycin

value: GCCGT-AGGTC


title: INPUT.MiaPaca2

description: Control IP DNA


title: CFPAC1.IRF1

description: Chromatin IP against IRF1


title: 43-Cantharidin-uninduced

source_name: CRISPRi guide RNA library_Cantharidin-uninduced

value: 10uM Cantharidin

value: CGTTGA-CCAGGT


title: H3K27ac.CFPAC1.Control.rep2

description: Chromatin IP against H3K27ac

value: Abcam


title: CFPAC1.HNF1B

description: Chromatin IP against HNF1B

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: H3K9me3.MiaPaca2

description: Chromatin IP against H3K9me3


title: H3K27ac.CFPAC1.ELF3-KO.rep3

description: Chromatin IP against H3K27ac

value: CFPAC1 genome-edited clonal cell line

value: ELF3-deleted CRISPR-Cas9 clone


title: H3K9me3.PT45P1

description: Chromatin IP against H3K9me3


title: H3K9me3.CFPAC1

description: Chromatin IP against H3K9me3


title: 41-1181-0519-uninduced

value: CGTTGA-AACC

value: plasmid DNA


title: 42-Cantharidin-plus ATc

source_name: CRISPRi guide RNA library_Cantharidin-plus ATc

value: 10uM Cantharidin +ATc

value: CGTTGA-AGGTC


title: 40-1181-0519-plus ATc

value: ACTGCT-GGATT


title: H3K9me3.PANC1

description: Chromatin IP against H3K9me3


title: H3K9me3.CAPAN2

description: Chromatin IP against H3K9me3


title: H3K9me3.HPAF2

description: Chromatin IP against H3K9me3


title: 45-4130-1276-uninduced

source_name: CRISPRi guide RNA library_4130-1276-uninduced

value: gene_tiling_18bp & gene_tiling_20bp & mutant18 & mutant20

value: CGTTGA-GGATT


title: H3K9me3.CAPAN1

description: Chromatin IP against H3K9me3


title: 39-Fluconazole-uninduced

value: 20uM Fluconazole

value: ACTGCT-GACT


title: H3K4me3.PT45P1

description: Chromatin IP against H3K4me3

value: Active Motif


title: H3K4me3.PANC1

description: Chromatin IP against H3K4me3


title: 37-DMSO-uninduced

value: 1% DMSO

value: ACTGCT-AGGTC


title: H3K4me3.CFPAC1

description: Chromatin IP against H3K4me3


title: 38-Fluconazole-plus ATc

value: 20uM Fluconazole +ATc

value: ACTGCT-CCAGGT


title: H3K4me3.HPAF2

description: Chromatin IP against H3K4me3

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: 36-DMSO-plus ATc

value: 1% DMSO +ATc

value: ACTGCT-AACC


title: H3K4me3.CAPAN1

description: Chromatin IP against H3K4me3


title: H3K4me3.MiaPaca2

description: Chromatin IP against H3K4me3


title: H3K4me3.CAPAN2

description: Chromatin IP against H3K4me3


title: H3K4me1.PANC1

description: Chromatin IP against H3K4me1

value: Abcam


title: H3K4me1.PT45P1

description: Chromatin IP against H3K4me1


title: 28-Cerulenin-plus ATc

source_name: CRISPRi guide RNA library_Cerulenin-plus ATc

value: gene_tiling_18bp & gene_tiling_20bp

value: 0.98uM Cerulenin +ATc

value: CTTA-CCAGGT

value: plasmid DNA


title: H3K4me1.HPAF2

description: Chromatin IP against H3K4me1


title: H3K4me1.CFPAC1

description: Chromatin IP against H3K4me1


title: 26-Cerulenin-plus ATc

value: 1.95uM Cerulenin +ATc

value: CTTA-AACC


title: H3K4me1.CAPAN2

description: Chromatin IP against H3K4me1


title: H3K4me1.MiaPaca2

description: Chromatin IP against H3K4me1


title: 27-Cerulenin-uninduced

source_name: CRISPRi guide RNA library_Cerulenin-uninduced

value: 0.98uM Cerulenin

value: CTTA-AGGTC


title: H3K4me1.CAPAN1

description: Chromatin IP against H3K4me1


title: H3K27ac.PANC1

description: Chromatin IP against H3K27ac


title: 24-DMSO-plus ATc

value: ATGAT-GACT


title: H3K27ac.HPAF2

description: Chromatin IP against H3K27ac


title: 25-Cerulenin-uninduced

value: 1.95uM Cerulenin

value: ATGAT-GGATT


title: H3K27ac.CFPAC1

description: Chromatin IP against H3K27ac


title: 23-DMSO-uninduced

value: 1% DMSO

value: ATGAT-CCAGGT


title: H3K27ac.CAPAN2

description: Chromatin IP against H3K27ac

value: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line


title: H3K27ac.MiaPaca2

description: Chromatin IP against H3K27ac


title: 20-0KPI-0099-plus ATc

source_name: CRISPRi guide RNA library_0KPI-0099-plus ATc

value: TCGT-GGATT


title: 19-0KPI-0099-uninduced

source_name: CRISPRi guide RNA library_0KPI-0099-uninduced

value: TCGT-GACT


title: WI_38_Y2

data_processing:
Illumina Casava software was used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

source_name: total RNA extracted from Wi-38 fibroblasts

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

value: Wi-38 fibroblasts


title: WI_38_O1


title: WI_38_O2


title: 18-ST016598-plus ATc

source_name: CRISPRi guide RNA library_ST016598-plus ATc

value: gene_tiling_18bp & gene_tiling_20bp

value: TCGT-CCAGGT


title: WI_38_O3


title: WI_38_Y3


title: WI_38_Y1


title: IMR90_O2

source_name: total RNA extracted from IMR-90 fibroblasts

value: IMR-90 fibroblasts


title: IMR90_O3


title: 16-9150499-plus ATc

source_name: CRISPRi guide RNA library_9150499-plus ATc

value: TCGT-AACC

value: plasmid DNA


title: H3K27ac.PT45P1

description: Chromatin IP against H3K27ac

value: Abcam


title: IMR90_O1


title: IMR90_Y2


title: IMR90_Y3


title: IMR90_Y1