title: eCLIP_MCF10A_B1_input

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

data_processing:
Library strategy: eCLIP-seq
3' barcodes and adapter sequences were removed using standard eCLIP scripts.
Reads were trimmed, filtered for repetitive elements, and aligned to the hg19 reference sequence using STAR.
PCR duplicate reads were removed based on the read start positions and randomer sequence.
Bigwig files for genome browser display were generated based on the location of the second of the paired end reads.
Peaks were identified using encode_branch version of CLIPPER (Lovci et al. 2013) using the parameter -s hg19
Peaks were normalized against size matched input by calculating fold enrichment of reads in IP versus input, and were designated as significant if the number of reads in IP was greater than in the input, with a Bonferroni corrected Fisher exact p-value smaller than 10^–5
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed and bigwig

molecule: nuclear RNA

source_name: MCF10A cells

growth_protocol: MCF10A cells were grown in DMEM/F12 with 5% horse serum, 20 ng/mL EGF, 0.5 µg/mL hydrocortisone, 100 ng/mL cholera toxin, 10 µg/mL insulin, and 1x penicillin/streptomycin

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al. 2016) with minor modifications. Briefly, confluent cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 13 mL of PBS in 15 cm plates; these cells were then spun down, flash frozen in liquid nitrogen, and stored at –80ºC. Nuclear isolation was performed as previously described (Kung et al. 2015), followed by further digestion by Bioruptor, RNase I, and Turbo DNase as specified in the original eCLIP protocol. Overnight immunoprecipitation was performed using 2 mg Protein G Dynabeads per 10 µg antibody, and appropriate antibodies for hnRNP A2/B1 (Abcam ab31645, 9 µg/IP), hnRNP B1 (IBL 18941, 2.5 µg/IP), or IgG (Novus NB810-56910, 5 µg/IP). Following end repair and 3′ adaptor ligation (using X1A and X1B adaptors as previously described), size selection was carried out using Nupage 4-12% Bis-Tris protein gels followed by overnight transfer at 30V to nitrocellulose membranes.
Protein-RNA complexes on nitrocellulose were then digested with Proteinase K (Roche) and reverse transcribed using SuperScript IV (Thermo Fisher). These cDNAs were then prepared for sequencing as described using Illumina TruSeq HT dual indexed primers, and sequenced on an Illumina NextSeq 500 for high-output 2x75 bp run.

tag: antibody vendor

tag: antibody catalog number


title: eCLIP_MCF10A_B1_A

status: Public on Aug 20 2018

type: SRA

country: USA

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

tag: antibody

value: hnRNP B1

value: IBL


title: MycN RNA-seq

city: Lebanon

first: Michael

middle: David

last: Cole

state: NH

address: One Medical Center Drive

department: Genetics

institute: Geisel School of Medicine at Dartmouth

data_processing:
Data was first aligned to the transcriptome using TopHat v2.0.11 with the -G option to flag a gtf comprised of mm9 UCSC refseq genes
Resulting bams were indexed and sorted
Gene expression was quantified using cufflinks v2.2.0 with the -G option to flag a gtf comprised of mm9 UCSC refseq genes
Gene expression values were scaled using a linear scale factor derived from cell count absolute gene expression measurements of 48 genes sampled across multiple expression levels
Genome_build: mm9
Supplementary_files_format_and_content:
fpkm_raw_formatted.txt - cufflinks fpkm values
fpkm_nanoScaled.txt - nanostring scaled fpkm values

molecule: total RNA

organism: Mus musculus

source_name: immortalized MEF cells

growth_protocol: Immortalized mouse embryonic fibroblasts grown in DMEM 10% FBS

extract_protocol:
Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions. Synthetic RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added to each population based on cell number. See manuscript for details.
Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a standard Illumina mRNA-Seq protocol with the following modifications. Briefly, polyadenylated RNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis.

treatment_protocol: Cells containing empty vector, Myc, MycN, or Minimal Myc were treated with adenoviral Cre recombinase followed by 48 recovery before harvest for RNA-seq

tag: cell type

value: Immortalized mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: expressing MycN


title: Myc RNA-seq

value: expressing Myc


title: vector input

description:
ChIP-Seq input whole cell extract control  in mouse embryonic fibroblasts transfected with empty PBMN vector
MEF_PBMN_WCE

library_source: genomic

data_processing:
Reads were aligned to the mm9 genome build using Bowtie version 1.0 with the following command: "bowtie -e 70 -k 1 -m1 -n 2 -p 4 -l 50 --best --sam "
enriched regions were defined using macs1.4.2 with a p-value cutoff of 1e-9
.wig files were produced from macs1.4.2 --wig option
mapped .txt files were produced using a custom script https://github.com/BradnerLab/pipeline/blob/master/bamToGFF_turbo.py that quantifies extended read density at regions in units of reads per base pair per million mapped reads. bamToGFF_turbo.py was called using flags -e 200 -m 1 -r
Genome_build: mm9
Supplementary_files_format_and_content: .wig files of read pile up genome wide. .txt mapped read density at promoters and gene bodies in units of reads per base pair per million mapped reads

molecule: genomic DNA

extract_protocol:
Harvest by Millipore ChIP Lysis Buffer followed by chromatin immunoprecipitation and phenol/chloroform extraction
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Cells containing empty vector (PBMN), Myc, or MycN were passaged equivalently before harvest for ChIP

value: expressing vector


title: vector RNA-seq


title: vector RNAP II ChIP-seq

description:
ChIP-Seq for RNA Pol II in mouse embryonic fibroblasts transfected with empty PBMN vector
MEF_PBMN_RNA_POL2

tag: chip antibody

value: RNA pol II (Abcam ab5408)


title: eCLIP_MCF10A_B1_B


title: eCLIP_MCF7_cytoplasm_input

molecule: cytoplasmic RNA

source_name: MCF7 cells

growth_protocol: MCF7 cells were grown in RPMI supplemeted with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al. 2016) with minor modifications. Briefly, confluent cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 13 mL of PBS in 15 cm plates; these cells were then spun down, flash frozen in liquid nitrogen, and stored at –80ºC. Cellular fractionation was performed as previously described (Wysocka et al. 2001). Each fraction was raised to 1 mL final volume using Buffer D (20 mM HEPES pH 7.5, 210 mM NaCl, 7.5% glycerol, 0.75 mM MgCl2, 0.25 mM PMSF, and 1x proteinase inhibitor) then incubated with TURBO DNase (40U for chromatin sample, 10U for soluble samples) for 30 minutes at 37ºC, then quenched with 10 mM EDTA. Fractions were then further digested with Bioruptor and RNase (but no additional DNase) as specified in the original eCLIP protocol, then immunoprecipitated overnight with antibody to hnRNP B1(IBL 18941, 2.5 µg/IP). Following end repair and 3′ adaptor ligation (using X1A and X1B adaptors as previously described), size selection was carried out using Nupage 4-12% Bis-Tris protein gels followed by overnight transfer at 30V to nitrocellulose membranes.
Protein-RNA complexes on nitrocellulose were then digested with Proteinase K (Roche) and reverse transcribed using SuperScript IV (Thermo Fisher). These cDNAs were then prepared for sequencing as described using Illumina TruSeq HT dual indexed primers, and sequenced on an Illumina NextSeq 500 for high-output 2x75 bp run.


title: eCLIP_MCF10A_A2B1_input


title: MYCN input

description:
ChIP-Seq input whole cell extract control  in mouse embryonic fibroblasts transfected with MYCN vector
MEF_MYCN_WCE


title: eCLIP_MCF7_cytoplasm_IP

description: MCF7_cytoplasm_IP.peaks.inorm.sorted.bed

value: hnRNP A2/B1

value: abcam


title: Minimal Myc RNA-seq

value: expressing Minimal Myc


title: eCLIP_MCF10A_A2B1_A

description: MCF10A_A2B1_AIP.peaks.inorm.enriched.bed


title: eCLIP_MCF7_nucleoplasm_IP

description:
nucleoplasmic RNA
MCF7_nucleoplasm_IP.peaks.inorm.sorted.bed

molecule: other


title: MYC input

description:
ChIP-Seq input whole cell extract control  in mouse embryonic fibroblasts transfected with MYC vector
MEF_MYC_WCE

value: expressing C-Myc


title: MYCN RNAP II ChIP-seq

description:
ChIP-Seq for RNA Pol II in mouse embryonic fibroblasts transfected with MYCN vector
MEF_MYCN_RNA_POL2


title: eCLIP_MCF7_nucleoplasm_input

description: nucleoplasmic RNA


title: eCLIP_MCF7_A2B1_A


title: eCLIP_MCF7_B1_B


title: eCLIP_MCF7_chromatin_input

description: chromatin-associated RNA


title: eCLIP_MCF7_chromatin_IP

description:
chromatin-associated RNA
MCF7_chromatin_IP.peaks.inorm.sorted.bed


title: eCLIP_MCF7_A2B1_input


title: eCLIP_MCF10A_A2B1_B


title: eCLIP_MCF7_B1_input


title: MIA PACa-2 siMLL1 IP H3K4me3

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

state: CA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

description: MIA PaCa-2cells were transiently transfected with siRNA#1 against KMT2D followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (tri-methyl K4)

data_processing:
alignment: Sequencing reads in fastq‐format were aligned to the UCSC hg19 reference genome using BWA (version 0.7.9a bwa mem with default options). Duplicate reads were removed with Picard tools (v. 1.115) MarkDuplicates and were filtered to retain only primary alignments with samtools (v0.1.19, view command with ‐F 0x100 flag).
peak calling: ChIP‐seq peaks were called using HOMER (v4.7) findPeaks using matched input samples with default settings (Poisson pvalue of <= 1E‐4 and fold change >=4.0). For histone marks, the histone option was employed. Further, peaks are annotated using HOMER's annotatePeaks utility using the hg19 annotations database provided with the software.
Genome_build: UCSC hg19 reference genome
Supplementary_files_format_and_content: The processed data files are in bedGraph format and tab-delimited xls format and represent a detailed description of the peak chromosomal coordinates enriched in each sample, peak scores, focus ratio/region size, distance to TSS and detail annotation. Furthermore, all relevant information for the nearest promoter is provided.

source_name: epithelial cells derivef from pancreatic carcinoma

extract_protocol:
Chromatin immunoprecipitation and final DNA purification was carried out using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology)
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, New England BioLabs)

treatment_protocol: MIA PaCa-2 cells were trypsinized and transfected with 50nΜ siRNA for KMT2D or scramble siRNA. Lipofectamine ® RNAiMAX was used as transfection reagent. RNA-Lipofectamine complexes were made in Opti-MEM (serum free). Cells were plated at a 50% confluence in serum and antibiotic-containing media. 24h later double transfection was performed with the same amounts of siRNAs and cells were incubated for 24h before chromatin isolation.

value: MIA PaCa-2 pancreatic cancer cell line

value: Anti-Histone H3 (tri-methyl K4)


title: MIA PaCa-2 siMLL3 IP H3K4me3

description: MIA PaCa-2cells were transiently transfected with siRNA#2 against KMT2D followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (tri-methyl K4)


title: MIA PACa-2 siMLL3 IP H3K4me1

description: MIA PaCa-2cells were transiently transfected with siRNA#2 against KMT2D followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (mono-methyl K4)

value: Anti-Histone H3 (mono-methyl K4)


title: MIA PACa-2 siMLL1 IP H3K4me1

description: MIA PaCa-2cells were transiently transfected with siRNA#1 against KMT2D followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (mono-methyl K4)


title: MIA PaCa-2 sicon 2%input

description: 2% input (sequencing control) for the 2 following  samples: MK2_MLL3_sincon_MLL_IP_H3K4me1 and MK3_MLL4_sicon_MLL_IP_H3K4me3


title: MIA PACa-2 sicon IP H3K4me3

description: MIA PaCa-2cells were transiently transfected with scramble siRNA followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (tri-methyl K4)


title: Tumor_14W_2

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description:
ph505 tumor,after 14 times  transplanted into the adult abdomen weekly
Tum_14W_2

data_processing:
Short read alignment was performed with TopHat 2.0.12 and Bowtie 2.2.3 using --b2-very-sensitive -g 1. For samples 1 to 9 single end and for samples 10-12 paired end alignment was used.
mRNA expression was quantified in R 3.3.1 with counts per million reads located in exonic ranges for each gene normalized to library size using edgeR 3.16.5. The annotations from Ensembl were used.
Genome_build: dm6
Supplementary_files_format_and_content: Abundance of mRNA transcripts in counts per million of library normalized reads

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ph505 tumor transplanted 14 times weekly

growth_protocol: Flies were raised at 25˚C on standard medium

extract_protocol:
Arcturus PicoPure RNA Isolation kit
SMARTSeq2 NexteraXT

tag: tissue

value: ph505 tumor  14 weeks old


title: MIA PACa-2 siMLL1 2%input

description: 2% input (sequencing control) for the 2 following  samples: MK5_MLL7_siMLL1_IP_H34me1 and MK6_MLL8_siMLL1_IP_h3K4me3


title: MIA PACa-2 siMLL3 2%input

description: 2% input (sequencing control) for the 2 following  samples:  MK8_MLL11_siMLL2_IP_H3K4me1 and  MK9_MLL12_siMLL2_IP_H3K4me3


title: Tumor_8W_2

description:
ph505 tumor,after 8 times  transplanted into the adult abdomen weekly
Tum_8W_2

source_name: ph505 tumor transplanted 8 times weekly

value: ph505 tumor  8 weeks old


title: Tumor_4W_2

description:
ph505 tumor,after 4 times  transplanted into the adult abdomen weekly
Tum_4W_2

source_name: ph505 tumor transplanted 4 times weekly

value: ph505 tumor  4 weeks old


title: Tumor_8W_1

description:
ph505 tumor,after 8 times  transplanted into the adult abdomen weekly
Tum_8W_1


title: eCLIP_MCF7_B1_A

value: hnRNP B1


title: 52.S5

city: Aveiro

first: João

middle: André

last: Barbosa

address: Campus Universitário de Santiago

department: Biology Department

country: Portugal

institute: University of Aveiro

data_processing:
Data was trimmed using Trim Galore! version 0.4.4 with the following configurations: trimming of bases with a quality score lower than 30 (-q 30), Illumina adapter sequences removal (--illumina), RRBS mode activation (--rrbs) and a new FastQC report requirement (--fastqc).
The mapping of the samples was performed using Bismark version 0.18.1.
Extraction of methylated calls was performed using Bismark 0.18.1.
Statistical analysis were performed using DSS package, in RStudio version 1.1.383.
Genome_build: GenBank LRGB00000000
Supplementary_files_format_and_content: txt files were generated using RStudio version 1.1.383; The represented scores show the gene code, its position in the genome, the total coverage of the gene and the number of methylated calls for that gene.

organism: Daphnia magna

source_name: DNA

growth_protocol: Six cultures were established in plastic buckets, three for each control (0 g/L NaCl) and salinity (4.1 g/L NaCl) exposures.

extract_protocol:
MasterPure Complete DNA and RNA Purification Kit
DNA was digested using MspI, followed by end repair and adapter ligation using NEBNext Ultra II DNA library kit for Illumina. Methylated NEBNext adapters were used. Bisulfite conversion was done using EZ DNA Methylation Gold kit from Zymo.

treatment_protocol: Cultures were maintained under a temperature of 20 ± 2ºC and a 16hL:8hD photoperiod. Daphnids exposure lasted until the neonates initiating the experiment matured and reached their third brood. All subsequent generations were started with 3rd brood new-born neonates (< 24h old) and maintained in control medium. Tests were conducted until the 4th generation.

tag: gender

value: female

tag: age

value: adult

tag: treatment

value: salinity


title: 54.S14


title: Tumor_14W_1

description:
ph505 tumor,after 14 times  transplanted into the adult abdomen weekly
Tum_14W_1


title: 41.S4


title: 48.S13


title: 55.S21


title: Tumor_4W_1

description:
ph505 tumor,after 4 times  transplanted into the adult abdomen weekly
Tum_4W_1


title: 38.S19


title: 51.S20


title: eCLIP_MCF7_A2B1_B


title: 25.S11


title: 27.S18


title: 36.S12


title: NC-NRCM

city: ShangHai

first: Yuan

last: Tianyou

address: No.1239,SiPing road,YangPu District

country: China

institute: tongji university

description: all.counts.rat.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
mapping to reference genome using hisat2
count counting
Genome_build: GRCh38、rnor6

organism: Rattus norvegicus

source_name: Heart

growth_protocol: All cells were grown  in DMEM supplemented with 10%FBS, 100 U/ml penicillin, 100 μg/ml streptomycin.

extract_protocol:
All cells were washed once by cold PBS  on ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Negative control siRNA and LRP6-targeted siRNA were transfected into the cells corresponding for 72 hours.

tag: transfection

value: negative control siRNA

tag: induced time

value: 72 hour


title: 7.S10

value: control


title: 9.S17


title: eCLIP_invitro_B1_xlink

description:
in vitro transcribed control RNA
B1HA_HAXB1.merged.r2.norm.pos.bw

organism: synthetic RNA

source_name: in vitro transcribed control RNA; xlink

extract_protocol:
Cloning and purification of recombinant hnRNP B1 was performed as previously described (Meredith et al. 2016). HOTAIR and antisense luciferase control RNA (see (Meredith et al. 2016) for sequence details) were in vitro transcribed using the MEGAscript T7 Transcription Kit, treated with TURBO DNase, and purified with RNeasy Qiagen Kit. In a 1:10 RNA:protein molar ratio, 1.2 ug of control or HOTAIR RNA was incubated with recombinant B1 in 100 µL RNA refolding buffer (20 mM HEPES-KOH pH 7.9, 100 mM KCl, 0.2 EDTA pH 8.0. 20% Glycerol, 0.5 mM PMSF, 0.5 DTT) for 20 minutes at room temperature. The mixture was diluted to 250 µL in refolding buffer and UV-crosslinked twice in one well of a 24-well plate at 250 mJ and 254 nm wavelength, with mixing by pipette in between. B1-RNA crosslinked and non-crosslinked samples were treated with 0.1 ng RNase A for 3 minutes at 37ºC and 1200 rpm, then stopped with 200 U Murine RNase Inhibitor (NEB).
Protein-RNA complexes on nitrocellulose were then digested with Proteinase K (Roche) and reverse transcribed using SuperScript IV (Thermo Fisher). These cDNAs were then prepared for sequencing as described using Illumina TruSeq HT dual indexed primers, and sequenced on an Illumina NextSeq 500 for high-output 2x75 bp run.

value: IBL


title: 28.S3


title: eCLIP_invitro_B1_noxlink

description:
in vitro transcribed control RNA
B1HA_HA_B1.merged.r2.norm.pos.bw

source_name: in vitro transcribed control RNA; noxlink


title: 11.S2


title: 3.S1


title: LRP6 KD-NRCM

description: all.counts.rat.txt

value: LRP6-targeted siRNA


title: SIRT6.1-1, RNA-seq RAFi_4_days_2

status: Public on Aug 18 2018

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description:
RNA-seq RAFi_4_days_2
SKMel-239_SIRT6.1-1_Ri_2
CRISPR_RNAseq_Counts_matrix.csv

data_processing:
[Native ChIP-seq] Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10
[XL ChIP-seq] Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 -q0.0005 --keep-dup 1.
[RNA-seq] Reads (100nt, single-end) were aligned using STAR (version v2.4.1c). Transcriptome assemblies and differential expression ratios were performed using featureCount: subread 1.4.6-p2 and voom-limma: 3.26.9. Genes were called downregulated if log2FoldChange≤-1; and Padj<0.05 in the designated comparison. Genes were called upregulated if log2FoldChange≥1; and Padj<0.05 in the designated comparison.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig - aligned reads pileup. csv - gene expression using Voom normalized raw counts

source_name: SKMel-239 SIRT6.1-1

growth_protocol: grown in RPMI supplemented with 10% FBS, penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
RNA for sequencing was processed into Poly A libraries (Illumina)

tag: disease state

value: BRAF metastatic melanoma

value: treated with 2µM of RAFi 4 days


title: SIRT6.1-1, RNA-seq DMSO_1

description:
RNA-seq DMSO_1
SKMel-239_SIRT6.1-1_DMSO_1
CRISPR_RNAseq_Counts_matrix.csv

value: treated with DMSO (1/1000) 4 days


title: SIRT6.1-1, RNA-seq RAFi+MEKi_4_days_1

description:
RNA-seq RAFi+MEKi_4_days_1
SKMel-239_SIRT6.1-1_C_1
CRISPR_RNAseq_Counts_matrix.csv

value: treated with 100nM of RAFi and 1nM of MEKi 4 days


title: SIRT6.1-1, RNA-seq RAFi_4_days_1

description:
RNA-seq RAFi_4_days_1
SKMel-239_SIRT6.1-1_Ri_1
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.2-7, RNA-seq RAFi+MEKi_4_days_2

description:
RNA-seq RAFi+MEKi_4_days_2
SKMel-239_SIRT6.2-7_C_2
CRISPR_RNAseq_Counts_matrix.csv

source_name: SKMel-239 SIRT6.2-7


title: SIRT6.2-7, RNA-seq RAFi+MEKi_4_days_1

description:
RNA-seq RAFi+MEKi_4_days_1
SKMel-239_SIRT6.2-7_C_1
CRISPR_RNAseq_Counts_matrix.csv


title: L-C-B, RNA-seq RAFi+MEKi_4_days_2

description:
RNA-seq RAFi+MEKi_4_days_2
SKMel-239_L-C-B_C_2
CRISPR_RNAseq_Counts_matrix.csv

source_name: SKMel-239 L-C-B

value: L-C-B


title: SIRT6.1-1, RNA-seq DMSO_2

description:
RNA-seq DMSO_2
SKMel-239_SIRT6.1-1_DMSO_2
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.2-7, RNA-seq RAFi_4_days_1

description:
RNA-seq RAFi_4_days_1
SKMel-239_SIRT6.2-7_Ri_1
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.1-1, RNA-seq RAFi+MEKi_4_days_2

description:
RNA-seq RAFi+MEKi_4_days_2
SKMel-239_SIRT6.1-1_C_2
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.2-7, RNA-seq DMSO_2

description:
RNA-seq DMSO_2
SKMel-239_SIRT6.2-7_DMSO_2
CRISPR_RNAseq_Counts_matrix.csv


title: L-C-B, RNA-seq RAFi+MEKi_4_days_1

description:
RNA-seq RAFi+MEKi_4_days_1
SKMel-239_L-C-B_C_1
CRISPR_RNAseq_Counts_matrix.csv


title: 1_TGACCA_R1_RNA

city: Cleveland

first: Jeff

last: Coller

state: Ohio

address: 10900 Euclid Ave., Wood Bldg.  W113

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University School of Medicine

data_processing:
Sequencing was performed with Illumina HiSeq2500
The adaptor sequence (CTGTAGGCACCATCAAT) was removed with Cutadapt
reads aligning to yeast rRNA with Bowtie2 were removed from further analysis
Surviving reads were aligned to the sacCer3 yeast genome with Hisat2, using the Ensembl transcript annotations as a guide
Aligned reads were filtered to remove multi-mapping reads, realigned to transcript space, and assigned to a specific codon corresponding to the A-site of the RPF. RNA-seq reads were quantified with htseq-count.
Genome_build: sacCer3
Supplementary_files_format_and_content: codon_read_counts.tsv contains the number of RPFs over each codon, along with total numbers of each codon in each gene. FPKMs are also included

organism: Saccharomyces cerevisiae

source_name: S. Cerevisiae

growth_protocol: Yeast cells were grown to mid-log phase at 24 C in YPD (pH 6.5) supplemented with 2% glucose and appropriate amino acids

extract_protocol:
Cells were lysed in the presence of cycloheximide, and RPFs were purified from the 80S fraction following sucrose gradient fractionation. Total RNA was fragemented by alkaline hydrolysis.
Following removal of rRNA with Ribo-Zero (Illumina MRZY1324), cDNA libraries were constructed and amplified following Smith et al, 2014

treatment_protocol: No pre-treatment

tag: strain

tag: molecule

value: Total RNA


title: L-C-B, RNA-seq DMSO_2

description:
RNA-seq DMSO_2
SKMel-239_L-C-B_DMSO_2
CRISPR_RNAseq_Counts_matrix.csv


title: L-C-B, RNA-seq DMSO_1

description:
RNA-seq DMSO_1
SKMel-239_L-C-B_DMSO_1
CRISPR_RNAseq_Counts_matrix.csv


title: L-C-B, RNA-seq RAFi_4_days_2

description:
RNA-seq RAFi_4_days_2
SKMel-239_L-C-B_Ri_2
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.2-7, ChIP-H3K4me1

description:
ChIP-H3K4me1
SKMel-239_SIRT6.2-7_H3K4me1

extract_protocol:
Native ChIP was done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: untreated

value: H3K4me1 (Abcam, ab8895)


title: SIRT6.2-7, ChIP-SIRT6

description:
ChIP-SIRT6
SKMel-239_SIRT6.2-7_SIRT6

extract_protocol:
For SIRT6, 50x10^6 cells, were crosslinked with 0.4% PFA for 10 min at RT. ChIP was performed essentially as previously described (Roe, J.S., et al., BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 2015. 58(6): p. 1028-39).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: SIRT6 (Abcam, ab62739)


title: SIRT6.2-7, ChIP-H3K56ac

description:
ChIP-H3K56ac
SKMel-239_SIRT6.2-7_H3K56ac

value: H3K56ac (Abcam, ab76307)


title: SIRT6.2-7, RNA-seq DMSO_1

description:
RNA-seq DMSO_1
SKMel-239_SIRT6.2-7_DMSO_1
CRISPR_RNAseq_Counts_matrix.csv


title: SIRT6.2-7, ChIP-H3K9ac

description:
ChIP-H3K9ac
SKMel-239_SIRT6.2-7_H3K9ac

value: H3K9ac (Abcam, ab10812)


title: SIRT6.2-7, ChIP-H3K27ac

description:
ChIP-H3K27ac
SKMel-239_SIRT6.2-7_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: SIRT6.2-7, ChIP-H3K4me3

description:
ChIP-H3K4me3
SKMel-239_SIRT6.2-7_H3K4me3

value: H3K4me3 (Abcam, ab1012)


title: L-C-B, ChIP-H3K56ac

description:
ChIP-H3K56ac
SKMel-239_L-C-B_H3K56ac


title: L-C-B, ChIP-SIRT6

description:
ChIP-SIRT6
SKMel-239_L-C-B_SIRT6


title: L-C-B, ChIP-H3K27ac

description:
ChIP-H3K27ac
SKMel-239_L-C-B_H3K27ac


title: L-C-B, RNA-seq RAFi_4_days_1

description:
RNA-seq RAFi_4_days_1
SKMel-239_L-C-B_Ri_1
CRISPR_RNAseq_Counts_matrix.csv


title: MIA PACa-2 sicon IP H3K4me1

description: MIA PaCa-2cells were transiently transfected with scramble siRNA followed by chromatin immunoprecitation with antibody against Anti-Histone H3 (mono-methyl K4)

value: MIA PaCa-2 pancreatic cancer cell line

value: Anti-Histone H3 (mono-methyl K4)


title: 9_TGACCA_R1_RPF

value: Ribosome Protected Fragements


title: L-C-B, ChIP-H3K9ac

description:
ChIP-H3K9ac
SKMel-239_L-C-B_H3K9ac


title: SIRT6.2-7, RNA-seq RAFi_4_days_2

description:
RNA-seq RAFi_4_days_2
SKMel-239_SIRT6.2-7_Ri_2
CRISPR_RNAseq_Counts_matrix.csv


title: L-C-B, ChIP-H3K4me3

description:
ChIP-H3K4me3
SKMel-239_L-C-B_H3K4me3


title: human UCB CD34+ YTHDF2 KD 3

status: Public on Aug 17 2018

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the human genome hg38 from UCSC using Tophat 2.0.13 with default parameters. Annotations were from Ensembl 87. Counts of reads on genes were from HTSeq-count with -m intersection-nonempty.
Reads were also aligned to ERCC control sequences and counts tabulated. A scaling factor was calculated based on the median of the ERCC counts for each sample and used for normalization.
Differentially expressed genes were found using the edgeR package (3.18.1) in R (3.4.1). Differentially expressed genes were required to have a BH-adjusted p-value < .05 and a 2-fold change in expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with counts normalized using median ERCC counts for each sample. IDs are ensembl gene ids from Ensembl 87.

source_name: human UCB CD34+ HSPCs

growth_protocol: human UCB cells were cultured with StemSpan medium (StemCell Technologies) supplemented with growth factors interleukin 6(IL-6; 20ng/ml, Peprotech), stem cell factor (SCF; 100ng/ml, Peprotech), Flt3 ligand (FLT3-L; 100ng/ml, Peprotech) and thrombopoietin (TPO; 20ng/ml, Peprotech).

extract_protocol:
CD34+ GFP+ cells were sorted into Trizol.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on a NextSeq in high output mode with 76 base single-end reads.

value: UCB CD34+ HSPCs

tag: genotype

value: YTHDF2 knockdown


title: L-C-B, Input-Native

description:
Input-Native
SKMel-239_L-C-B_Input

value: BRAF metastatic melanoma


title: human UCB CD34+ YTHDF2 KD 2


title: human UCB CD34+ YTHDF2 KD 1


title: human UCB CD34+ wild type 3

value: wild type


title: human UCB CD34+ wild type 2


title: human cord blood CD34+ sample2 m6A

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the human genome hg19 from UCSC using Tophat 2.1.1 with --no-coverage-search.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files normalized by reads per million mapped reads from tophat transcriptome alignment.

source_name: human umbilical cord blood

extract_protocol:
Total RNAs were extracted from freshly isolated human UCB CD34+ cells and chemically fragmented. m6A marked RNAs were isolated with a specific antibody.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on two NextSeq flowcells in high-output mode with 76 base single-end reads.

value: primary umbilical cord blood CD34+ cells

tag: rip antibody

value: EpiMark N6-Methyladenosine Enrichment Kit (NEB E1610S)

tag: sample type

value: IP


title: MPP input 2

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the mouse genome mm10 from UCSC using tophat 2.1.1 with -T (transcriptome only alignment, report in genomic coordinates) and a transcriptome of refseq genes (refgene) from UCSC mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by reads per million mapped reads from tophat transcriptome alignment.

source_name: Bone marrow

extract_protocol:
Total RNAs were extracted from sorted 100K LT-, ST-HSCs and MPPs and chemically fragmented. m6A marked RNAs were isolated with specific antibody.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on two lanes of a NextSeq 500 in high output mode to length 51, single-end.

value: Wild type

value: MPP

value: Input


title: human cord blood CD34+ sample2 input


title: human cord blood CD34+ sample3 m6A


title: ST-HSC input 2

value: ST-HSC


title: human cord blood CD34+ sample3 input


title: ST-HSC input 1


title: LT-HSC m6A 2

value: LT-HSC

value: ANTI-m6A rabbit polyclonal antibody from Synaptic Systems (catalog # 202003)


title: LT-HSC input 1


title: human cord blood CD34+ sample1 input


title: human UCB CD34+ wild type 1


title: YTHDF2 irCLIP-seq replicate 2

description: irCLIP-seq

data_processing:
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the mouse genome mm10 from UCSC using STAR (2.5.2b) with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by reads per million mapped reads from STAR alignment.

source_name: hematopoietic progenitor cell line HPC-7

growth_protocol: HPC-7 cells were cultured with IMDM supplemented with 5%FBS and 100ng/ml mouse SCF.

extract_protocol:
YTHDF2-RNA complex were UV cross-linked and isolated with a specific antibody.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol and sequenced on a Nextseq in high-output mode to generate 76-base single end reads.

tag: cell line

value: Flag antibody (F3165, Sigma)


title: MPP m6A 1


title: YTHDF2 irCLIP-seq replicate 3

description: irCLIP-seq

value: hematopoietic progenitor cell line HPC-7


title: MPP m6A 2


title: MPP input 1


title: Mouse ES cells biological replicate 2, technical replicate 2

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-2b_S6

data_processing:
Library strategy: Tri-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3)
Removal of PCR duplicates, mapping of reads to restriction enzyme fragments, proximity exclusion (if within ~1 kb of viewpoint) (custom scripts)
Calculation of normalized multi-way interaction frequencies with viewpoints (custom scripts)
Processing of interaction frequencies into a contact matrix (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (interacting restriction enzyme fragment1 \t interacting restriction enzyme fragment2 \t sample1_raw_count \t sample2_raw_count \t etc.)

source_name: E14 embryonic stem cells

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Tri-C combines 3C library preparation (NlaIII restriction enzyme) with oligonucleotide capture enrichment that is optimized to detect multiway interactions with viewpoints of interest, as described in detail in the Supplementary Methods of the paper.

treatment_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

value: E14 embryonic stem cell line

tag: viewpoint analyzed

value: a_R2, a_CTCF, b_HS2, b_CTCF


title: Mouse ES cells biological replicate 1, technical replicate 2

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-1b_S3

tag: cell type


title: ST-HSC m6A 1


title: Mouse ES cells biological replicate 2, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-2a_S8


title: Mouse erythroid cells biological replicate 3, technical replicate 3

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-3b_S10

source_name: Primary erythroid cells

value: Ter-119+ cells isolated from phenylhydrazine treated spleen


title: ST-HSC m6A 2


title: Mouse erythroid cells biological replicate 3, technical replicate 2

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-3a_S7


title: Mouse erythroid cells biological replicate 2, technical replicate 2

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-2a_S14


title: Mouse erythroid cells biological replicate 1, technical replicate 2

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-1a_S12


title: LT-HSC m6A 1


title: LT-HSC input 2


title: L-C-B, ChIP-H3K4me1

description:
ChIP-H3K4me1
SKMel-239_L-C-B_H3K4me1

value: L-C-B

value: untreated

value: H3K4me1 (Abcam, ab8895)


title: Mouse ES cells replicate 2; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_ES2

data_processing:
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, as described in Davies et al, Nature Methods, 2016.


title: Mouse ES cells replicate 3; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_ES3


title: human cord blood CD34+ sample1 m6A

value: primary umbilical cord blood CD34+ cells


title: Mouse ES cells biological replicate 3, technical replicate 2

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-3b_S13


title: YTHDF2 irCLIP-seq replicate 1

description: irCLIP-seq


title: Mouse ES cells biological replicate 3, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-3a_S5


title: human bronchial epithelial cells (+SLR14) rep2

city: New Haven

first: Ellen

middle: Flescher

last: Foxman

state: CT

address: 330 Cedar St.

department: Laboratory Medicine

institute: Yale University

description:
Sample 17
mRNA (Total RNA after polyA selection)

data_processing:
The raw reads of RNA-seq experiments were trimmed off sequencing adaptors and low quality reads by btrim
The trimmed reads were mapped to human genome (GRCh37) by tophat2
The counts of reads for each gene were based on Ensembl annotation (release 70)
Differential expression analysis was done by DEseq2[17], which calculated the adjusted p-values.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt file showing FPKM reads

growth_protocol: Primary cells were grown in submerged culture on collagen coated 12 well plates using Bronchial Epithelial Growth Medium (Lonza)

extract_protocol:
RNEasy kit by QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with SLR14 for 1 hr, then incubated at 37C for seven additional hrs prior to RNA isolation.

value: primary bronchial epithelial cells

value: 8hr post-stimulation with RIG-I ligand SLR14


title: Mouse ES cells biological replicate 1, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-1a_S1


title: human bronchial epithelial cells (+SLR14) rep1

description:
Sample 16
mRNA (Total RNA after polyA selection)


title: Mouse erythroid cells biological replicate 3, technical replicate 4

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-3c_S4


title: Mouse erythroid cells biological replicate 2, technical replicate 3

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-2b_S11


title: Mouse erythroid cells biological replicate 1, technical replicate 3

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-1b_S2


title: Mouse erythroid cells biological replicate 3, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-3_S3


title: Mouse ES cells biological replicate 1, technical replicate 3

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
ES-1c_S9


title: Mouse ES cells replicate 3; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_ES3

value: Prom_local_il9r,  Prom_local_mpg, Prom_local_nprl3, Prom_local_snrnp25,  Prom_local_rhbd


title: Mouse erythroid cells biological replicate 1, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-1_S1


title: Mouse erythroid cells biological replicate 2; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_C57-2


title: human bronchial epithelial cells (unstimulated) rep1

description:
Sample 13
mRNA (Total RNA after polyA selection)

value: Unstimulated


title: Mouse ES cells replicate 3; Capture-C viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_ES3


title: Mouse erythroid cells biological replicate 1; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_C57-1


title: human bronchial epithelial cells (unstimulated) rep2

description:
Sample 14
mRNA (Total RNA after polyA selection)


title: Mouse ES cells replicate 1; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_ES1


title: Mouse erythroid cells biological replicate 1; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_C57-1


title: Mouse erythroid cells biological replicate 2; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_C57-2


title: Mouse erythroid cells biological replicate 3; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_C57-3


title: Hi-C erythroid, splenic ter119+ cells, replicate 2

data_processing:
[data processing pipeline] Hi-C data were processed using the HiCPro pipe line (v2.7.5.b).
[read mapping] Reads were aligned to the mm9 reference genome using bowtie2 in HiCPro (global mapping: -k 3 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder; local: same with -L 20).
[read filtering] Reads with more than 2 mappings were discarded
[read pair reconstruction] For reads with two multimapping locations, the nearest, valid HiC fragment pair was reconstructed.
[read pair filtering] Read pairs were filtered for valid Hi-C fragments (HiCPro default settings for HindIII) removing singletons and duplicates.
[merging replicates] All technical replicates were merged.
[building contact matrices] Contact matrices were build from all valid Hi-C fragments (HiCPro) for 20kb bins.
[normalizing contact matrices] Contact matrices were normalized using the ICE normalization in HiCPro.
Genome_build: mm9
Supplementary_files_format_and_content: ICE-normalized intra-chromosomal contact matrices for 20kb bins, technical replicates merged.
Contact matrix format:
chromosome       bin1.coordinate bin2.coordinate normalized_interaction_value
Bin coordinates refer to the left-most coordinate of the respective bin.

source_name: phenylhydrazine treated spleen

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with 1% formaldehyde.
Hi-C (restriction enzyme: HindIII) as described in: Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009 Oct 9;326(5950):289-93. PMID: 19815776   Briefly: cells were crosslinked with formaldehyde; DNA was digested with HindIII; the 5′-overhang was filled, including a biotinylated residue; and the resulting blunt-end fragments were ligated. The resulting DNA sample contains ligation products consisting of fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A Hi-C library was created by shearing the DNA and selecting the biotin-containing fragments with streptavidin beads.

value: phenylhydrazine

value: spleen

value: erythroid cells


title: Mouse ES cells replicate 1; Capture-C, modelling viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
VP_Mod_*viewpoint_analysed*_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP_Mod_ES1


title: Mouse ES cells replicate 2; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_ES2


title: Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_C57-3


title: Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_C57-2


title: Mouse ES cells replicate 1; Capture-C viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_ES1


title: Mouse ES cells replicate 2; Capture-C viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_ES2


title: Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #5

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP5_C57-1


title: Mouse ES cells replicate 3; Capture-C viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_ES3


title: Mouse erythroid cells biological replicate 2, technical replicate 1

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-2_S2


title: Mouse erythroid cells biological replicate 3; Capture-C, local promoters viewpoints

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_C57-3


title: Mouse ES cells replicate 2; Capture-C viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_ES2


title: Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_C57-2


title: Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_C57-1


title: Mouse ES cells replicate 1; Capture-C viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_ES1


title: Mouse ES cells replicate 1; Capture-C viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_ES1

value: VP3_A3_3theta, VP3_A3_5theta, VP3_B3_HS5, VP3_B3_HS6


title: Mouse ES cells replicate 2; Capture-C viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_ES2


title: Mouse ES cells replicate 3; Capture-C viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_ES3


title: Mouse ES cells replicate 1; Capture-C viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_ES1


title: Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_C57-3


title: Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_C57-3


title: Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_C57-2


title: Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #2

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP2_C57-1


title: Mouse ES cells replicate 3; Capture-C viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_ES3


title: Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_C57-1


title: Hi-C erythroid, splenic ter119+ cells, replicate 1


title: Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_C57-2


title: Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #4

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP4_C57-3


title: vESRD_NE50

status: Public on Aug 16 2018

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

data_processing:
Primary analysis of the sequencing data was conducted on Torrent Server using AmpliSeqRNA plugin in Torrent Suite™ Software. The raw read counts of individual transcripts were normalized to total mapped read counts (in million) in the same sample and expressed as RPMR (reads per million mapped reads).
Genome_build: Hg19
Supplementary_files_format_and_content: Excel, transcript expression levels of individual mRNAs and lncRNAs were shown in reads-per-million-mapped-reads (RPMR)

source_name: Human plasma

extract_protocol:
EDTA-treated whole blood samples from individual study subjects were centrifuged at 1,600 g for 10 min at 4 °C, transferred to a new centrifuge tube and centrifuged again at 16,000 g for 10 min to remove any residual blood cells. Plasma samples were stored at -80 °C until the step of RNA extraction. Six ml Trizol LS was mixed with 2 ml plasma sample for 5 min at room temperature (RT), followed by mixing with 1 ml 1-bromo-3-chloropropane, vortexed and incubated at 4 °C for 10 min, centrifuged at 6,000 g for 30 min for phase separation. The aqueous phase layer (~ 4 ml) was transferred into a new 50 ml centrifuge tube, mixed with 40 ul glycogen and 5 ml isopropanol, incubated at -20°C for 15 min, centrifuged at 6,000 g for 30 min at 4 °C. After removal of the supernatant, the pellet was lysed with the mixture of Lysis Solution (300 ml) and miRNA Homogenate Additive (30ml) from mirVana (Thermo Fisher, AM1650) kit, vortexed and fully resuspended, followed by addition of 350 ml isopropanol. The mixture was transferred onto an RNAqueous micro filter cartridge and centrifuged at 10,000 g for 15 sec, washed with 700 ml Wash Solution 1 and centrifuged at 10,000 g for 10 sec, washed again with 500 ml Wash Solution 2/3 and centrifuged at 10,000 g for 1 min. Eight ml of Elution Solution (preheated to 65°C) was applied to the filter and centrifuged 10 sec at 10,000 g to obtain RNA samples. The final step was repeated again and the RNA samples were mixed, quantified using Qubit RNA HS assay kit and stored at -80 °C until RNA sequencing.
(Exploratory cohort) For the plasma transcriptome RNASeq in the exploratory cohort, 10 ng of total plasma RNA samples from individual study subjects was reversed transcribed to cDNA followed by PCR amplification (16 cycles), digestion with FuPa enzyme, ligation (60 minutes) and Ampure cleanup according to the user guide supplied with the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific, PN A26325).  Barcoded libraries were quantitated by Ion Library TaqMan™ Quantitation Kit (Thermo Fisher Scientific, PN4468802) and combined to either 7- or 8- plex pools for sequencing. Sequencing template preparation and Proton P1 chip loading were performed on the Ion Chef™ instrument using the Ion Proton™ Hi-Q ™ Chef kit.
(Validation cohort) For the plasma transcriptome RNASeq in the validation cohort, 10 ng of total plasma RNA samples from individual study subjects was reversed transcribed to cDNA followed by PCR amplification (16 cycles) using predesigned primers targeting 8 candidate lncRNAs and 6 control mRNAs, digestion with FuPa enzyme, ligation (60 minutes) and Ampure cleanup.  Barcoded libraries were quantitated by Ion Library TaqMan™ Quantitation Kit (Thermo Fisher Scientific, PN4468802) and pooled for sequencing. Sequencing template preparation and Proton P1 chip loading were performed on the Ion Chef™ instrument using the Ion Proton™ Hi-Q ™ Chef kit.

tag: cohort

value: Validation cohort

tag: disease state (group)

value: ESRD without CV event


title: Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_C57-3


title: vESRD_NE46


title: Mouse ES cells replicate 3; Capture-C viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_ES3

value: E14 embryonic stem cell line


title: vESRD_NE45


title: Mouse ES cells replicate 1; Capture-C viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_ES1


title: vESRD_NE49


title: Mouse ES cells replicate 2; Capture-C viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_ES2


title: vESRD_NE48


title: Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_C57-2


title: Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #3

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP3_C57-1


title: vESRD_NE44


title: vESRD_NE41


title: vESRD_NE43


title: Mouse ES cells replicate 2; Capture-C viewpoints #1

description:
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file:  See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
VP1_ES2


title: vESRD_NE42


title: vESRD_NE38


title: vESRD_NE35


title: vESRD_NE36


title: vESRD_NE37


title: vESRD_NE39


title: vESRD_NE31


title: no_MMC_fragmented

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Quality trimming with fastq_quality_trimmer (fastx 0.11.2)
Read mapping with READemption (0.4.3) and segemehl (0.2.)
Coverage plote generation with READemtpoin
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wiggle of normalized coverages

organism: Caulobacter vibrioides NA1000

source_name: no_MMC_total bacterial RNA

growth_protocol: Caulobacter crescentus was grown aerobically at 30C in PYE medium

extract_protocol:
RNA was extracted with the HotPhenol method and digested with DNaseI
For the depletion of processed transcripts, equal amounts of RNA were incubated with Terminator 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020) as previously described (Sharma et al., 2010). The transcripts were not fragmented in order to get mainly sequencing reads of the 5'-end of the transcripts. Libraries for Illumina sequencing of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNAs (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis. Equal amounts of RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'-triphosphates were removed by applying tobacco acid pyrophosphatase (TAP) resulting in 5'-monophosphat. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.

treatment_protocol: Samples were collected prior to treatment (OD660 of 0.4) and after 4h of treatment with mitomycinC (0.1 ug/mL)

tag: genotype/variation

value: wild type

tag: internal stock id


title: vESRD_NE33


title: no_MMC_minusTEX


title: vESRD_NE32


title: 4_h_MMC_plusTEX

source_name: 4_h_MMC_total bacterial RNA

tag: treated with

value: 0.1 ug/mL mitomycinC (MMC) for 4hrs


title: vESRD_NE30


title: 4_h_MMC_minusTEX


title: vESRD_NE25


title: vESRD_NE28


title: vESRD_NE26


title: vESRD_NE27


title: vESRD_NE40


title: 4_h_MMC_fragmented


title: vESRD_NE22


title: vESRD_NE24


title: vESRD_NE21


title: vESRD_NE34


title: vESRD_NE18


title: vESRD_NE19


title: vESRD_NE17


title: vESRD_NE29


title: vESRD_NE16


title: no_MMC_plusTEX


title: vESRD_NE13


title: vESRD_NE14


title: vESRD_NE20


title: vESRD_NE12


title: vESRD_NE6


title: vESRD_NE5


title: vESRD_NE9


title: vESRD_NE8


title: vESRD_NE4


title: vESRD_CV49

value: ESRD with CV event


title: vESRD_CV47


title: vESRD_CV50


title: vESRD_CV45


title: vESRD_CV41


title: vESRD_CV34


title: vESRD_CV33


title: vESRD_CV36


title: vESRD_CV39


title: vESRD_CV44


title: vESRD_CV38


title: vESRD_CV32


title: vESRD_NE11


title: vESRD_CV28


title: vESRD_CV25


title: vESRD_CV29


title: vESRD_CV26


title: vESRD_CV27


title: vESRD_CV18


title: vESRD_CV19


title: vESRD_CV22


title: vESRD_CV15


title: vESRD_CV14


title: vESRD_CV21


title: vESRD_CV16


title: vESRD_CV40


title: vESRD_CV24


title: vESRD_CV13


title: vESRD_CV12


title: vESRD_CV11


title: vESRD_CV6


title: vESRD_CV10


title: vESRD_CV7


title: vESRD_CV8


title: vCtrl11

value: Healthy control


title: vESRD_CV4


title: vCtrl12


title: vCtrl13


title: vCtrl10


title: vCtrl9


title: vESRD_CV23


title: vESRD_CV1


title: vCtrl7


title: vCtrl8


title: vESRD_NE3


title: vCtrl6


title: vCtrl5


title: vCtrl3


title: vCtrl2


title: vCtrl4


title: vCKD54

value: CKD


title: vCKD52


title: vCKD39


title: vCKD37


title: vCKD53


title: vCtrl1


title: vCKD36


title: vCKD34


title: vCKD33


title: vCKD26


title: vCKD29


title: vCKD17


title: vCKD19


title: vCKD10


title: nESRD693

value: Initial cohort


title: vCKD5


title: nESRD573


title: vCKD2


title: nESRD574


title: nESRD557


title: nESRD492


title: nESRD518


title: vCKD43


title: nESRD32


title: ESRD25

value: ESRD


title: nESRD16


title: nESRD175


title: ESRD21


title: ESRD18


title: ESRD17


title: ESRD19


title: ESRD13


title: vCKD24


title: vCKD32


title: vCKD13


title: eESRD647


title: ESRD03


title: eESRD612


title: ESRD11


title: eESRD237


title: eESRD450


title: eESRD115


title: eESRD367


title: nESRD544


title: eESRD65


title: Ctrl18


title: eESRD93


title: Ctrl15


title: Ctrl13


title: Ctrl37


title: eESRD5


title: Ctrl12


title: Ctrl04


title: ESRD02


title: Ctrl03


title: Ctrl09


title: Ctrl10


title: Ctrl02


title: CKD8


title: Ctrl01


title: CKD6


title: CKD5


title: CKD7


title: CKD4


title: CKD3


title: CKD1


title: CKD2


title: 293_TUT7_overexp_1

status: Public on Aug 15 2018

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

data_processing:
Illumina bcl2fastq 2.18 software used for basecalling.
Sequence reads were mapped to the hg19 human genome build using STAR 020201, with parameter --outFilterMultimapNmax 1000
Counts for repetitive elements were extracted using Tetranscripts 1.5.1 using option --stranded reverse –mode uniq and gencode.v27.basic.annotation.gtf downloaded from https://www.gencodegenes.org/releases/current.html for genes annotation and hg38_rmsk_TE.gtf downloaded from http://labshare.cshl.edu/shares/mhammelllab/www-data/TEToolkit/TE_GTF/ for repetitive elements annotation
Differential expression analysis was performed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include DESeq2 normalized counts for each sample

source_name: Human Embryonic Kidney Hek293 Flp-IN T-Rex

extract_protocol:
Medium was removed from cells and RNA was extracted using 1 ml TRI-reagent per single well.  RNA was treated with Ambion TURBO DNAse (Life Technologies) according to the producers’ recommendations.
Following DNAse treatment the RNA samples were all supplemented with equal amounts of ERCC RNA spike-in mix (Thermo Fisher Scientific) followed by depletion of rRNA by using Ribo-Zero H/R/M Kit (Epicentre) according to the manufacturer’s protocol. Strand-specific RNA libraries were prepared in triplicate using KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms (KAPA Biosystems) according to the manufacturer’s protocol using 8 mins at 95 °C for RNA fragmentation and 700 μM adapters for amplification. We used 7 cycles of amplification for generation of the libraries. Libraries were analysed by capillary electrophoresis using Bioanalyzer 2100 (Agilent). All libraries were ~250 bp in length (after subtracting 120bp adapter sequences).

treatment_protocol: Hek 293 Flp-In T-Rex cells were used. Cells were transfected with either 99 PUR RPS EGFP or JM101/L1.3 nomarker and plasmids for overexpression of the indicated proteins or siRNA for their depletion. After 3 days cells were tripsinized and transferred to new 6-well plates at 0.2x106 cells per single well, followed by another transfection performed exactly as the first one. Finally, after 6 days from the first transfection with siRNA the cells were used to isolate total RNA

value: Hek293 Flp-IN T-Rex

value: TUT7 overexpression


title: 293_TUT7_overexp_2


title: 293_TUT7_overexp_3


title: 293_TUT7_overexp_control_3

value: TUT7 overexpression control


title: 293_TUT4_overexp_2

value: TUT4 overexpression


title: Ctrl11


title: 293_TUT4_overexp_1


title: 293_TUT7_overexp_control_2


title: 293_TUT7_overexp_control_1


title: 293_TUT4_overexp_control_1

value: TUT4 overexpression control


title: 293_TUT4_overexp_control_3


title: 293_TUT4_overexp_control_2


title: 293_CNTROLKD_2

value: Control of knockdown


title: 293_CNTROLKD_3


title: 293_TUT4TUT7KD_2

value: TUT4 and TUT7 knockdown


title: 293_TUT4TUT7KD_3


title: 293_TUT4TUT7KD_1


title: 293_MOV10KD_3

value: MOV10 knockdown


title: 293_TUT4TUT7MOV10KD_3

value: TUT4, TUT7 and MOV10 knockdown


title: 293_TUT4TUT7MOV10KD_2


title: 293_TUT4TUT7MOV10KD_1


title: 293_CNTROLKD_1


title: 293_MOV10KD_2


title: PA1_TUT7KD_3

source_name: Human embryonic carcinoma cells (PA-1)

value: TUT7 knockdown


title: 293_MOV10KD_1


title: 293_TUT4_overexp_3


title: PA1_TUT7KD_2


title: PA1_TUT7KD_1


title: PA1_TUT4KD_3

value: TUT4 knockdown


title: PA1_TUT4KD_2


title: PA1_TUT4TUT7MOV10KD_3


title: PA1_TUT4TUT7MOV10KD_2


title: PA1_TUT4KD_1


title: PA1_TUT4TUT7MOV10KD_1


title: PA1_TUT4TUT7KD_2


title: PA1_TUT4TUT7KD_4


title: PA1_TUT4TUT7KD_3


title: PA1_CNTROLKD_3


title: PA1_MOV10KD_2


title: PA1_CNTROLKD_1


title: PA1_CNTROLKD_2


title: PA1_MOV10KD_1


title: PA1_TUT4TUT7KD_1


title: 293_MOV10_overexp_3

value: MOV10 overexpression


title: 293_MOV10_overexp_1


title: 293_MOV10_overexp_2


title: WT_c

city: St. Louis

first: Philip

last: Ruzycki

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplier written in python
Alignments performed with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Comparison of gene counts performed with EdgeR 3.17.9, requiring 5 samples to have cpm >= 5
Genome_build: mm10
Supplementary_files_format_and_content: Processed data supplied at RPKM values for each biological sample, and EdgeR calculated comparison metrics (log2 fold-change, p-value, and FDR)

source_name: Retina

extract_protocol:
Retinas were dissected and immediately frozen using dry ice for storage at -80C. Retinas were processed for RNA using the PerfectPure RNA tissue kit (5Prime). Quality was assessed using the Agilent Bioanalyzer, and samples with minimum 8.0 RIN score submitted for library preparation. mRNA was extracted using the DynaI mRNA Direct Kit (Life Technologies).
mRNA was fragmented and reverse transcribed to double stranded cDNA using random primers before the additon of Illumina adaptors. rRNA was depleted using Ribo-Zero (Epicentre).

value: wild type

tag: age


title: WT_b


title: MLL1KO_b

value: MLL1 fl/fl, Chx10-Cre


title: MLL1KO_c


title: WT_a


title: 293_MOV10_overexp_control_3

value: MOV10 overexpression control


title: MLL1KO_a


title: 293_MOV10_overexp_control_1


title: 293_MOV10_overexp_control_2


title: OCT embedded  kidney tumor tissue [283]

city: Cincinnati

first: Kakajan

last: Komurov

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
fastq files received from BGI were used to carry out genomic alignment to the hg19 genome using TopHat run with parameters --library-type fr-firststrand –no-coverage-search
Normalized gene and isoform level expression of the hg19 transcriptome were computed using RSEM using the command rsem-calculate-expression run with the options --paired-end --bowtie2 --forward-prob 0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files that gene/isoform RPKM values for each sample

source_name: OCT embedded  kidney tumor tissue

extract_protocol:
RNA was isolate dfrom 1-10 micro meter thick section of OCT embedded kidney tumor tissue using a QuiagenRNeasy Micro Kiton am Agilent 2200 TapeStation
Stranded(dUTP) poly-A selected library was prepared and sequenced at Beijing Genome Institute (BGI). Paired end sequencing with read length 100bp and read depth of 50M was performed at BGI using Illuminal-HiSeq 4000

tag: disease

value: Renal Clear Cell Carcinoma


title: OCT embedded  kidney tumor tissue [291]


title: OCT embedded  kidney tumor tissue [287]


title: OCT embedded  kidney tumor tissue [277]


title: OCT embedded  kidney tumor tissue [226]


title: PA1_MOV10KD_3


title: OCT embedded  kidney tumor tissue [225]


title: OCT embedded  kidney tumor tissue [215]


title: OCT embedded  kidney tumor tissue [179]


title: OCT embedded  kidney tumor tissue [210]


title: OCT embedded  kidney tumor tissue [49]


title: RNAseq amphioxus Neural Tube replicate 2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Reads were aligned against reference genome using Tophat2 software, and gene models were built using Cufflinks.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), Zebrafish September 2014 (GRCz10/danRer10), Medaka October 2005 (oryLat2).
Supplementary_files_format_and_content: Individual RPKM files (reads per kilobase per million mapped reads) for amphioxus and zebrafish. Complete table of TPM (transcripts per million) for medaka.

organism: Branchiostoma lanceolatum

source_name: neural tube

growth_protocol: Unripe adults were maintained in filtered seawater during one week with one water change per day

extract_protocol: Tissue was dissected in filtered seawater, cut into small pieces with sterile scissors in the lysis buffer and disrupted using a sterile Eppendorf mcro-pestle. RNA was extracted using RNeasy Plus Micro Kit (Qiagen)

tag: developmental stage

value: adult


title: OCT embedded  kidney tumor tissue [110]


title: RNAseq amphioxus Pre-metamorphic stage

source_name: whole embryo

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen)

value: Pre-metamorphic larvae


title: RNAseq amphioxus Muscle replicate 2

source_name: muscle

extract_protocol: Tissue was dissected in filtered seawater, cut into small pieces with sterile scissors in the lysis buffer and disrupted using a sterile Eppendorf mcro-pestle. RNA was extracted using TRIzol® Reagent (Thermo Fisher Scientific)


title: RNAseq amphioxus Male Gonads replicate 2

source_name: male gonads


title: OCT embedded  kidney tumor tissue [94]


title: RNAseq amphioxus 7h replicate 2

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage, and fixed in RNAlater (Thermo Fisher Scientific)


title: RNAseq amphioxus Eggs replicate 2

source_name: eggs

extract_protocol: Tissue was dissected in filtered seawater, cut into small pieces with sterile scissors in the lysis buffer and disrupted using a sterile Eppendorf mcro-pestle. RNA was extracted using RNeasy Mini Kit (Qiagen)

value: egg


title: RNAseq amphioxus Blastula replicate 1

value: Blastula


title: RNAseq amphioxus Gut replicate 2

source_name: gut

extract_protocol: Tissue was dissected in filtered seawater, cut into small pieces with sterile scissors in the lysis buffer and disrupted using a sterile Eppendorf mcro-pestle. RNA was extracted using RNeasy Plus Mini Kit (Qiagen)


title: RNAseq amphioxus 7h replicate 1


title: RNAseq amphioxus 50h replicate 2


title: RNAseq amphioxus 60h replicate 1


title: RNAseq amphioxus 50h replicate 1


title: RNAseq amphioxus 36h replicate 1


title: RNAseq amphioxus Gills replicate 2

source_name: gills


title: RNAseq amphioxus Hepatic replicate 2

source_name: hepatic diverticulum


title: RNAseq amphioxus 32cells replicate 3


title: RNAseq amphioxus 32cells replicate 2


title: RNAseq amphioxus 27h replicate 2


title: RNAseq amphioxus 21h replicate 2


title: RNAseq amphioxus 27h replicate 1


title: RNAseq amphioxus 21h replicate 1


title: RNAseq amphioxus 24h replicate 1


title: RNAseq amphioxus 18h replicate 2


title: RNAseq amphioxus 15h replicate 2


title: RNAseq amphioxus 60h replicate 2


title: RNAseq amphioxus 18h replicate 1


title: RNAseq amphioxus 11h replicate 1


title: RNAseq amphioxus 15h replicate 1


title: RNAseq amphioxus 10h replicate 2


title: RNAseq amphioxus 32cells replicate 1


title: RNAseq amphioxus Eggs replicate 1


title: RNAseq amphioxus Neural Tube replicate 1


title: Tumor_Alb-R26Met_6

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to perform the alignment. Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off when doing methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: mm9

source_name: Liver

extract_protocol:
Control livers and tumors were disected and DNA was extracted from each individual sample using Phenol-chloroform protocol. Then, genomic DNA was used to analyze the DNA methylation profile by the EpiQuest™ Genome-Wide Full Service (Zymo Research Company). This included sample standardization, library preparation, bisulfite conversion, next-generation bisulfite sequencing, and bioinformatics pipeline.
Libraries were prepared from 200-500ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research DNA Clean and Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250bp and 250–350bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, Zymo Research Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Zymo Research, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean and Concentrator™ - Zymo Research, Cat#D4005) for sequencing on an Illumina HiSeq.

value: 50% mixed 129/SV and C57BL6

tag: tissue

value: Liver

value: 70 weeks


title: Tumor_Alb-R26Met_5

tag: strain


title: Tumor_Alb-R26Met_10

value: 62 weeks


title: Tumor_Alb-R26Met_2

value: 66 weeks


title: Tumor_Alb-R26Met_4


title: Tumor_Alb-R26Met_3


title: Control Liver_Alb-R26Met

value: 71 weeks


title: Tumor_Alb-R26Met_1

value: 54 weeks


title: Control_wt_2


title: RNAseq amphioxus Muscle replicate 1


title: Control_wt_1

value: 60 weeks


title: RNAseq amphioxus 11h replicate 2


title: RNAseq amphioxus Gut replicate 1


title: RNAseq amphioxus Gills replicate 1


title: RNAseq amphioxus Female Gonads

source_name: female gonads


title: RNAseq amphioxus Hepatic replicate 1


title: RNAseq amphioxus 8h replicate 2


title: mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 4

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Alignment to hg19 using TopHat 2.0.7 with BowTie 0.12.9 and SamTools 0.1.18
Counts by gene calculated using R/Bioconductor packages GenomicFeatures and GenomicRanges, with Ensembl gene annotations
Normalized counts calculated using DESeq
Differential Gene expression calculated using DESeq (version 1) with treatment as the single variable
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts_100nM_TCDD.txt is a tab-delimited text file containing raw read counts per gene. Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.
Supplementary_files_format_and_content: normalized_counts_100nM_TCDD.txt is a tab-delimited text file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq.  Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.

source_name: MCF-7 breast cancer cells

growth_protocol: 250,000 MCF-7 cells were seeded in 35 mm plates in DMEM supplemented with 10 % FBS for 24 hr, followed by overnight serum-starvation in phenol red-free DMEM

extract_protocol:
Total RNA purification kits from Qiagen (Valencia, CA) were used according to manufacturers instructions
Libraries were prepared from 1 µg of total RNA using a TruSeq RNA Prep Kit (Illumina Inc., San Diego, CA)

treatment_protocol: 6hrs treatment withTCDD

tag: treatment

value: TCDD

tag: concentration


title: Tumor_Alb-R26Met_7

tag: genotype


title: Tumor_Alb-R26Met_8


title: mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 3


title: RNAseq amphioxus Epidermis

source_name: epidermis


title: RNAseq amphioxus Cirri

source_name: cirri


title: mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 2


title: Tumor_Alb-R26Met_9


title: RNAseq amphioxus Blastula replicate 2


title: RNAseq amphioxus 8h replicate 1


title: RNAseq medaka st32 replicate 2

description:
RNA_seq
Olat_bygene_kallisto_tpms.txt.gz

organism: Oryzias latipes

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

extract_protocol: Embryos were suspended in TRIzol reagent (Intron Biotechnology) with chloroform and subsequently treated with TURBO DNA-free (Ambion)


title: RNAseq amphioxus Male Gonads replicate 1


title: RNAseq amphioxus 36h replicate 3


title: RNAseq amphioxus 36h replicate 2


title: mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 1


title: RNAseq zebrafish 72 hpf

organism: Danio rerio

extract_protocol: Embryos were fixed in RNAlater (Thermo Fisher Scientific) and RNA extracted using RNeasy Mini Kit (Qiagen)

value: 72 hpf


title: RNAseq amphioxus 32cells replicate 5


title: RNAseq zebrafish 8 hpf

value: 8 hpf


title: RNAseq medaka st25 replicate 3


title: RNAseq medaka st25 replicate 2


title: RNAseq zebrafish 6 hpf

value: 6 hpf


title: RNAseq medaka st25 replicate 1


title: RNAseq amphioxus 24h replicate 2


title: RNAseq amphioxus 15h replicate 4


title: RNAseq zebrafish 36 hpf

value: 36 hpf


title: RNAseq amphioxus 32cells replicate 4


title: RNAseq medaka st19 replicate 2


title: RNAseq amphioxus 15h replicate 3


title: RNAseq zebrafish 30 hpf

value: 30 hpf


title: RNAseq zebrafish 2 hpf

value: 2 hpf


title: RNAseq medaka st19 replicate 1


title: RNAseq medaka st32 replicate 3


title: RNAseq zebrafish 26 hpf

value: 26 hpf


title: RNAseq medaka st32 replicate 1


title: RNAseq zebrafish 20 hpf

value: 20 hpf


title: Amphioxus Muscle CAGE

data_processing:
Reads were aligned using Bowtie 1.1.2
CTSSs were mapped using CAGEr, and counts normalized to a power law distribution.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession),
Supplementary_files_format_and_content: bedGraph files generated using CAGEr, separately for each strand.

source_name: Muscle

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
nAnT-iCAGE

value: Muscle


title: Amphioxus Hepatic System CAGE

source_name: Hepatic System

value: Hepatic System


title: RNAseq zebrafish 16 hpf

value: 16 hpf


title: RNAseq medaka st16 replicate 3


title: RNAseq zebrafish 48 hpf

value: 48 hpf


title: RNAseq medaka st13 replicate 3


title: RNAseq medaka st16 replicate 1


title: RNAseq zebrafish 12 hpf

value: 12 hpf


title: RNAseq medaka st19 replicate 3


title: Amphioxus Neural Tube CAGE

source_name: Neural Tube

value: Neural Tube


title: RNAseq medaka st13 replicate 1


title: Amphioxus Embryo 15h CAGE

source_name: Embryo 15h

value: Embryo 15h


title: RNAseq amphioxus 10h replicate 1


title: Med17AA_Rapa_lab_RNA

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

institute: Univeristy of Geneva

data_processing:
ForRNA-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For RNA-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For RNA-Seq, reads that mapped to both sacCer3 and 972-h genomes were discarded.
For RNA-Seq, reads were extended by 50 bp
For RNA-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3 and then to total number of uniquely mapped reads in 972-h pombe in the same sample as described in (Hu et al. 2015)
Genome_build: sacCer3, 972-h pombe
Supplementary_files_format_and_content: wig files were obtained using HTSStation (http://htsstation.epfl.ch)

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to mid-log phase before treatment

extract_protocol:
Before extraction, previously 4-tU labeled S.pombe cells were mixed to S.cerevisiae cells to a ratio of 1:6. RNA was extracted with the standard hot phenol method and treated with DNAse I for 15' at room temperature. 4-tU labeled RNA was purified as described in (Baptista, T. 2017; PMID: 28918903)
TruSeq stranded mRNA kit (Illumina)

treatment_protocol: 4-tU labeling was performed as described in (Baptista, T. 2017; PMID: 28918903). After 54 minutes of rapamycin or vehicle treatement 4-tU was added to the cells. Cells were then harvested after 6 minutes of 4-tU labeling.

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 MED17-FRB::HIS3

value: 60 minutes rapamycin, 6 minutes 4-tU labeling


title: Amphioxus Embryo 32 Cell CAGE

source_name: Embryo 32 Cell

value: Embryo 32 Cell


title: RNAseq medaka st11 replicate 2

source_name: whole embryo


title: Tra1AA_Rapa_lab_RNA

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 FRB-TRA1


title: ATACseq amphioxus hepatic replicate 2

description:
ATAC_seq
ATAC_amphioxus_hep_idrpeaks.bed

data_processing:
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), Zebrafish September 2014 (GRCz10/danRer10), Medaka October 2005 (oryLat2)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework

extract_protocol:
Complete hepatic caecum/diverticulum was dissected in filtered seawater, cut into small pieces with sterile scissors in the lysis buffer and disrupted using a sterile Eppendorf mcro-pestle
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: adult


title: ATACseq amphioxus hepatic replicate 1


title: RNAseq medaka st11 replicate 1


title: Amphioxus Female Gonads CAGE

source_name: Female Gonads

value: Female Gonads


title: RNAseq medaka st16 replicate 2


title: ATACseq medaka st32 replicate 2

description:
ATAC_seq
ATAC_medaka_st32_idrpeaks.bed

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


title: ChIPseq amphioxus H3K4me3 8h replicate 2

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS software with default parameters
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession),
Supplementary_files_format_and_content: Called peaks in BED format

source_name: Whole embryo

growth_protocol: Embryos were cultured at 19°C until 8hpf, 15hpf, 36hpf or 60hpf

extract_protocol:
Batches of embryos from six dishes were transferred into a 2mL tube. After a quick centrifugation at 9000 rpm, the seawater was removed and replaced by 1.5mL of fixation solution (1.85% formaldehyde in MOPS-EGTA buffer: 0.1M MOPS pH 7.5, 2mM MgSO4, 1 mM EGTA, 0.5M NaCl). After 15 minutes at room temperature, 155 µL of Glycine 10% was added and the embryos were allowed to naturally sediment. The solution was then gently removed and the embryos were washed five times at 4°C with cold NaPBS (0.9% NaCl, 20 mM sodium phosphate buffer at pH 7.4). After a quick centrifugation at 13,000 rpm, the liquid was removed and the fixed embryos were frozen in liquid nitrogen and subsequently stocked at -80°C. For the chromatin immunoprecipitation, embryos were homogenized and lysed in order to release the chromatin, which was subsequently sonicated in a Bioruptor (Diagenode). Then the sonicated product was incubated with the specific antibody first, and then with Dynabeads (Thermofisher, cat. 10007D). After washing, pulled down chromatin was eluted from the beads and decrosslinked.
Illumina libraries were prepared following manufacturer's instructions.

tag: antibody


title: Gcn5AA_Rapa_lab_RNA

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 GCN5-FRB::HIS3


title: Gcn5AA_Veh_lab_RNA

value: no rapamycin, 6 minutes 4-tU labeling


title: RNAseq medaka st13 replicate 2


title: Amphioxus Embryo 8h CAGE

source_name: Embryo 8h

value: Embryo 8h


title: ATACseq medaka st32 replicate 1

description:
ATAC_seq
ATAC_medaka_st32_idrpeaks.bed


title: ChIPseq amphioxus H3K4me3 8h replicate 1


title: Esa1AA_Veh_lab_RNA

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ESA1-FRB::KanMX


title: ChIPseq amphioxus H3K4me3 36h replicate 1


title: ChIPseq amphioxus H3K4me3 36h replicate 2


title: ATACseq medaka st25 replicate 1

description:
ATAC_seq
ATAC_medaka_st25_idrpeaks.bed


title: ATACseq medaka st19 replicate 2

description:
ATAC_seq
ATAC_medaka_st19_idrpeaks.bed


title: ATACseq zebra shield replicate 1

description:
ATAC_seq
ATAC_zebra_shield_idrpeaks.bed

value: shield


title: ChIPseq amphioxus H3K4me3 15h replicate 1


title: RNAseq medaka st11 replicate 3


title: ChIPseq amphioxus H3K4me3 15h replicate 2


title: Esa1AA_Rapa_lab_RNA


title: ATACseq zebra shield replicate 2

description:
ATAC_seq
ATAC_zebra_shield_idrpeaks.bed


title: ChIPseq amphioxus H3K27me3 8h replicate 1


title: ATACseq medaka st13 replicate 2

description:
ATAC_seq
ATAC_medaka_st13_idrpeaks.bed


title: ATACseq zebra dome replicate 1

description:
ATAC_seq
ATAC_zebra_dome_idrpeaks.bed

value: dome


title: Tra1AA_Veh_lab_RNA


title: ChIPseq amphioxus H3K27me3 36h replicate 2


title: ATACseq medaka st13 replicate 1

description:
ATAC_seq
ATAC_medaka_st13_idrpeaks.bed


title: ATACseq zebra dome replicate 2

description:
ATAC_seq
ATAC_zebra_dome_idrpeaks.bed


title: ATACseq zebra 8 somites replicate 2

description:
ATAC_seq
ATAC_zebra_8som_idrpeaks.bed

value: 8 somites


title: ATACseq medaka st25 replicate 2

description:
ATAC_seq
ATAC_medaka_st25_idrpeaks.bed


title: ATACseq zebra 8 somites replicate 1

description:
ATAC_seq
ATAC_zebra_8som_idrpeaks.bed


title: ChIPseq amphioxus H3K27me3 15h replicate 2


title: ATACseq medaka st11 replicate 2

description:
ATAC_seq
ATAC_medaka_st11_idrpeaks.bed


title: ChIPseq amphioxus H3K27me3 36h replicate 1


title: ATACseq zebra 80% epiboly replicate 2

description:
ATAC_seq
ATAC_zebra_80epi_idrpeaks.bed

value: 80% epiboly


title: ATACseq amphioxus 8h replicate 2

description:
ATAC_seq
ATAC_amphioxus_8h_idrpeaks.bed

extract_protocol:
Embryos were centrifugated at 13000 rpm for 1 min, and then seawater wasa carefully removed. Cells were lysed by gently pipetting in cold lysis buffer
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109