title: tdMEFs at day 12 of reprogramming (rep 3)

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

data_processing:
Paired-end RNA-seq reads were aligned to mouse genome build "mm9" using the program Tophat 2.0.13. Gene annotation (GTF file) used was ENSEMBL version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search  --mate-inner-dist=50 --no-discordant --no-mixed
Aligned reads were  assigned to genes using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Differential expression P-values were calculated using edgeR (Robinson et al., 2010), an R package available through Bioconductor.  Any genes where there were not at least two samples with a CPM (counts per million) value between 0.5 and 5000 were filtered out. The remaining expression values were normalized using "calcNormFactors" in edgeR. P-values for the differential expression between samples were then calculated by edgeR, using a negative binomial distribution for gene expression. Finally, FDR (false discovery rate) for each P-value were calculated by the built-in R function "p.adjust", using the Benjamini-Hochberg method.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq FPKM, CPM (counts per million), and raw count data, tables in Excel format

source_name: reprogrammed tdMEFs at day 12

growth_protocol: tdMEFs were cultured in MEF medium (Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal bovine serum, 0.1 mM nonessential amino acids, and 2 mM Glutamax) in 5 % CO2 and 20 % O2 at 37 °C.

extract_protocol:
Total RNA was extracted using RNeasy Plus mini kit (Qiagen), according to manufacture instruction.
RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN). In this method, the total RNA (50 ng) is reverse-transcribed to synthesize the first-strand cDNA with a combination of random hexamers and a poly-T chimeric primer. The RNA template is then partially degraded by heating and the second-strand cDNA is synthesized using DNA polymerase. The double-stranded DNA is then amplified using single primer isothermal amplification (SPIA). SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′-end of the double-stranded DNA, after which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′-end of the primer by displacement of the existing forward strand. Random hexamers are then used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA amplified cDNA were made using the Ultralow V2 library kit (NuGEN). The RNA-seq libraries were analyzed by Bioanalyzer and quantified by QPCR (KAPA). Three RNA-seq libraries were pooled per lane of paired-end 100 bp sequencing on HiSeq 2500 instrument (Illumina).
RNA-seq with Illumina HiSeq 2500. Each sample was sequenced in two lanes on an Illumina HiSeq 2500.

treatment_protocol: M9-induced neural reprogramming was performed in M9 medium (50% Neural basal, 50% DMEM/F12/Glutamax, 1xN2, 1xB27 without vitamin A, 0.075% BSA, 0.1 mM nonessential amino acids, CHIR99021 3 mM, LDN193189 100 nM, A83-01 0.5 mM, Hh-Ag1.5 0.5 mM, retinoic acid 1 mM, SMER28 10 mM, RG108 10 mM, Parnate 2 mM, bFGF 10 ng/ml) at 5% O2 and 5% CO2 incubator at 37°C.

tag: barcode

value: AAGCCT

value: M9 reprogrammed cells

tag: genetic background

tag: replicate number


title: tdMEFs at day 12 of reprogramming (rep 2)

status: Public on May 12 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: GTGCTT

tag: tissue


title: ciNSLCs (rep 3)

source_name: reprogrammed ciNSLCs

value: AAGAGG


title: ciNSLCs (rep 2)

value: GTCGTA


title: MM401-H3K4me2

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

library_source: genomic

data_processing:
Reads were mapped to mm9 using bowtie with default parameters, only unique mapped reads used to subsequent analysis.
Peaks were called using the Hpeak program
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file for coverage and bed file for called peaks

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: MAF9 (MLL-AF9-transduced mouse bone marrow) cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) + 15% fetal bovine serum (FBS) and supplemented with 10 ng/ml interleukin-3 (IL-3).

extract_protocol:
ChIP experiments were performed using 1E8 cells and 15µl of antibodies per ChIP according to standard protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: MAF9 cells were treated with MM-401 at 20µM for 2 days.DMSO was used as a control treatment; MLL1 flox/flox, ER-Cre+/- cells were treated with 4OHT(400nM) for 2 days. EtOH was used a control treatment.

tag: cell type

value: MLL-AF9  transduced mouse bone marrow cells

tag: agent

tag: antibody


title: tdMEFs at day 4 of reprogramming (rep 2)

source_name: reprogrammed tdMEFs at day 4

value: TGGTGA


title: tdMEFs at day 4 of reprogramming (rep 3)

value: AGTGAG


title: tdMEFs at day 8 of reprogramming (rep 2)

source_name: reprogrammed tdMEFs at day 8

value: GCACTA


title: tdMEFs at day 8 of reprogramming (rep 3)

value: ACCTCA


title: pri-NPCs

source_name: mouse primary embryonic neural progenitor cells

value: GGAGAA

value: mouse cortical neural stem cells from E13.5


title: tdMEFs (rep 2)

source_name: Fsp1-Cre/ROSA26tdTomato-traced tdMEFs

value: AACCAG

value: mouse embryonic fibroblast


title: tdMEFs at day 8 of reprogramming (rep 1)

value: CGTAGA


title: ciNSLCs (rep 1)

value: CACAGT


title: tdMEFs at day 12 of reprogramming (rep 1)

value: TCAGAG


title: SCR029

source_name: mouse neural stem cell line

value: TTGGCA

value: mouse cortical neural stem cells from E15-18 (Millipore); SCR029 cell line


title: Naive E2A/E22 Double Knockout rep2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. The called differentially expressed genes must also have at least 8 FPKMs (fragments per kilobase of exon length per million mapped fragments) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file "Samples_Raw_Counts.txt" includes raw read counts for genes in each library.

source_name: Spleen

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: strain

value: Spleen

value: B cell

tag: genotype/variation

value: E2A/E22 double knockout

tag: protocol

value: naïve


title: tdMEFs at day 4 of reprogramming (rep 1)

value: GAGTCA

value: M9 reprogrammed cells


title: Naïve Wildtype rep2

value: wild type


title: Activated Id3 Knockout rep1

value: Id3 knockout

value: activated


title: Activated Id3 Knockout rep2


title: Naïve Wildtype rep1


title: Naive E2A/E22 Double Knockout rep1


title: Activated Wildtype rep4


title: Activated Wildtype rep3


title: Activated E2A/E22 Double Knockout rep2


title: Activated Wildtype rep2


title: Activated E2A/E22 Double Knockout rep1


title: tdMEFs (rep 1)

value: AGCATG


title: Naive Id3 Knockout rep1


title: Activated Wildtype rep1


title: ChIP_SHAM24_H3K4me1

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

description: chromatin (H3K4me1 enriched)

data_processing:
FastqC was performed. Reads were of good quality.
Reads were aligned to the mm9 genome using bowtie2 with the following parameters: -n 0, -e 40, -m 1, --best
Various additional quality controls were performed: CHANCE (Diaz et al., 2012), phantompeaks (Landt et al., 2012) and fraction of reads in peaks analysis.
Peak finding was performed using MACS1.4.2 with default parameters
Differential binding was tested with the diffbind package in R
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are provided, as well as bigwig files normalised to 10%input. Lastly, we are providing an .xls file containing regions found to be differentially bound by diffbind

source_name: mouse spinal cord microglia

extract_protocol:
Spinal cord microglia were isolated via a Percoll gradient
Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). ChIP-seq libraries were prepared on the automated Wafergen’s Apollo Prep system using a PrepX ILMN 32i 96 sample library kit (400076, Wafergen Biosystems). Libraries were prepared together to avoid batch effects. Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (18 cycles for ChIP) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 40M.

treatment_protocol: SNL mice had their peripheral spinal nerve ligated. SHAM mice only had their nerve exposed but left intact.

tag: gender

value: male

tag: age

value: 6-8 weeks old

tag: injury condition

value: SHAM


title: ChIP_SNL27_10%input

description: 10% input chromatin

value: SNL

value: none, input


title: Naive Id3 Knockout rep2


title: ChIP_SNL27_H3K4me1

description: chromatin (H3K4me1 enriched)


title: RNA_SHAM3

data_processing:
FastQC showed high quality reads. No filtering was performed
Alignment to mouse mm9 (using tophat2, -g 2)
Merging of bam files to combine reads from replicate flow cells
Cufflinks for FPKM (fragments < 150bp were excluded to avoid unreliable quantification for genes significantly shorter than the average fragment size
ht-seq and deseq2 for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files as well as analysis results for cufflinks and deseq2 are provided (.xls)

extract_protocol:
Spinal cord microglia were isolated via a Percoll gradient
Sequencing was performed by the High Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (Oxford University). RNA libraries were prepared using a SMARTer Ultra Low Input HV kit (634820, Clontech). Custom adaptor and barcode tags were used (5'- P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT). Samples were amplified (13 cycles for RNA) and multiplexed in replicate flow cells on an Illumina HiSeq2500 platform to yield 50bp paired-end reads at a depth of at least 20M. All libraries were prepared together to avoid batch effects.


title: ChIP_SNL45_10%input

description: 10% input chromatin


title: ChIP_SHAM35_H3K4me1

description: chromatin (H3K4me1 enriched)


title: RNA_SHAM4


title: ChIP_SHAM24_10%input

description: 10% input chromatin


title: ChIP_SNL45_H3K4me1

description: chromatin (H3K4me1 enriched)


title: 27556-2 (LiaS-K214N)_ES

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

description: isolates are minimally passaged, that is only passaged to the extent required to isolate the bacteria from a normally sterile body site

data_processing:
multiplexed SE libraries were sequenced on an Illumina HiSeq 2500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-Seq reads from clade1 strain MGAS11027 were mapped to reference strain MGAS11027 (GenBank accession number CP013838), clade2 strain(MGAS23530) reads were mapped to reference MGAS23530 (GenBank accession number CP013839), clade3 strain(MGAS26844) reads were mapped to reference MGAS27061 (GenBank accession number CP013840) and subclade3D strains (MGAS27520, MGAS27556, MGAS27556-1(LiaS K214R)) were mapped to a hybrid reference MGAS27061 (MGAS27061 reference with a M1 MGAS5005-like 11kb region ), using Edge-pro v1.3.1(Estimated Degree of Gene Expression for Prokaryotes).
mapping reads from each strain to respective refrence using Edge-pro v1.3.1 yields raw and normalized (RPKM) expression values for each gene.
varible gene content and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
differential expression analysis was perfomed using DESeq2 v1.6.3 runing in R version 3.1.3. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approcah was used to generate fold change values for each gene. Multiple testing correction was performed using Benjamini-Hochberg method.
Supplementary_files_format_and_content: M89_Raw_Normalized_expression.xlsx

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Epicentre)
resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre)

treatment_protocol: at the desired growth stage, mid-exponential OD 600nm 1.0 or early-stationary (2 hours after transition phase), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: clade

value: Subclade3D (SC3D)

tag: isolate

value: invasive infection isolate

tag: growth phase

value: Early-stationary (ES)


title: ChIP_SHAM35_10%input

description: 10% input chromatin


title: 27556-3 (LiaS-K214N)_ES


title: 27556-1 (LiaS-K214N)_ES


title: 27556-3_ES


title: 27556-2_ES


title: RNA_SHAM2


title: 27556-1_ES


title: RNA_SHAM1


title: RNA_SNL4


title: 27520-3_ES


title: RNA_SNL3


title: 27520-2_ES


title: 27520-1_ES


title: RNA_SNL2


title: RNA_SNL1


title: 26844-3_ES

value: Clade3 (C3)


title: 26844-2_ES


title: 26844-1_ES


title: 23530-3_ES

value: Clade2 (C2)


title: 23530-1_ES


title: 27556-2 (LiaS-K214N)_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: 23530-2_ES


title: 11027-1_ES

value: Clade1 (C1)


title: 27556-1 (LiaS-K214N)_ME


title: 27556-1_ME


title: 26844-3_ME


title: 27556-2_ME


title: 26844-2_ME


title: 27556-3_ME


title: 27520-3_ME


title: 27520-2_ME


title: Glycerol-N-limited-1

city: Newcastle upon Tyne

first: Rajesh Reddy

last: Bommareddy

address: Ellision building

department: Health Sciences

institute: Northumbria University

data_processing:
Raw sequence reads were checked for their quality using fastQC and reads were groomed to meet the Sanger-scaled quality values with ASCII offset 33. The groomed paired-end reads were then mapped to the reference genome of R.toruloides NP11  using Tophat2 . The gene and transcript expression levels were estimated and normalized based on FPKM (fragments per kilobase of exon per million fragments mapped) which were estimated using Cufflinks.
Genome_build: Rhodosporidium toruloides NP11 assembly v1.0
Supplementary_files_format_and_content: tab delimited text file is included with FPKM values for each sample

organism: Rhodotorula toruloides

source_name: cell mass

extract_protocol:
Cell mass was withdrawn from the fermentor and flash frozen on liquid nitrogen. RNA was extracted using the RiboPureTM RNA purification kit for yeast (Life technologies, Ambion). 1 ug of RNA was used by the Illumina Truseq kit to prepare sequencing libraries.
RNA libraries were prepared using standard Illumina protocols

value: DSMZ 4444


title: 27520-1_ME


title: Glycerol-N-limited-2


title: PAR-CLIP_diff_GSC_r2

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

data_processing:
Adaptor trimming, custom python script
Genomic alignment with bowtie 0.12.9 --sam -n 1 -l 20 -m 100 --best
Sam to bam conversion , samtools 0.1.9 samtools view -b -S
Sort and index, samtools 0.1.9 samtools sort, samtools index
Binding cluster calling, wavClusteR 2.2.0, R 3.2.0, prob. given by bayes, min. coverage 10 (5) for rep. 1 (2), min. cluster 10
Genome_build: hg19
Supplementary_files_format_and_content: Stranded BED-File of detected binding clusters, scores are log2 cluster coverage scaled to 0-1000

organism: Homo sapiens

source_name: Differentiated Glioma stem cells

extract_protocol:
300e6 differentiated GSC with overnight 4SU incubation were washed once in cold PBS and crosslinked at 365nm and a total energy of 0.15 J/cm2. Cells were scraped and resuspended in cold PBS. After centrifugation at 500 rcf for 5 minutes, pellet was resuspended in lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 5 mM CaCl2, 1 % NP-40) and incubated 15 minutes on ice. Lysate was treated with 20 U/mL Fermentas RNase T1 and 15 U/mL Fermentase RNase free DNase I for 15 minutes at RT and then sonicated for 15 cycles (30 sec on / off) on a Diagenode Bioruptor on high. Lysate was cleared at 21’000 rcf and 4 °C for 10 minutes. IP was performed for 3 hours with 20 ug rabbit pAb MBL Anti-IGF2BP2 (RN008P) preincubated for 1 hour at RT with 100 uL Invitrogen protein A dynabeads. Beads were washed 3 times in lysis buffer and treated with RNase T in 100 uL at 20 U/uL for 15 minutes at RT. After three more lysis buffer and two dephosphorylation buffer washes (50 mM Tris-HCl pH 7.9, 100 mM NaCl, 10 mM MgCl2) RNA was dephosphorylated at 37 °C in 100 uL NEB buffer 3 with 0.5 U / uL CIP for 10 minutes. 500 uL lysis buffer were added for beads to rebind during 10 minutes on ice. Three more lysis buffer washes and two PNK-buffer (70 mM Tris-HCl, pH 7.6, 10 mM MgCl2) washes were followed by phosphorylation with radioactive 32P at 37 °C in 100 uL of PNK buffer with 5 mM DTT, 17 nM (10 uCi) 32P-ATP and 0.5 U/uL PNK. After 30 minutes 5 uM normal ATP were added for additional 5 minutes. 1 mL of lysis buffer was added and beads are allowed to rebind during 10 minutes on ice. Beads were washed 5 times with lysis buffer, boiled in SDS-DTT solution and run on a NuPage Novex 4-12 % bis-tris gel for 1.5 hours at 150 V in MOPS buffer. Gel was imaged for 30 minutes with a phosphorimaging cassette and bands of interest excised. Elution of Protein-RNA complex was performed three times in 400 uL MOPS buffer using d-tube dialyzer midi MWCO 3.5 kDa each for 1 hours at 100 V and 5 minutes at 100 V reversed polarity. All subsequent steps were carried out exactly as described Hafner M. et al 2010.
Library was prepared similary to Illumina small RNA protocol. We adhered to Hafner et al 2010. Library was amplified for 18 cycles during PCR.

tag: cell line

tag: tumor state

value: Differentiated cancer stem cells

tag: growth

value: Withdrawal of growth factors for 7 days in DMEM with 10% FCS on 100ug/mL poly-D-lysine (Sigma) and 15ug/mL laminin (Sigma) coated plates.

tag: treatment

value: Cells were grown overnight in the presence of 100 uM 4-SU

tag: sample type

value: IMP2 bound RNA


title: 26844-1_ME


title: VHIP_Control_28d1hstress_6

city: New York

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: processed data file = VHIP_control_vs_resilient_28day1hstress.diff_list.xlsx,VHIP_control_vs_susceptible_28day1hstress.diff_list.xlsx

data_processing:
Bowtie2, version 2.1.0, parameters: default
TopHat2, version 2.0.9, parameters: --no-novel-juncs --b2-very-sensitive
Cuffdiff, version 2.1.1, parameters: -b path_to/mm9.fa --multi-read-correct
Genome_build: NCBIM37
Supplementary_files_format_and_content: text and excel format with cuffdiff output. Supplementary files are available in a tar archive on the series record.

source_name: adult ventral hippocampus

extract_protocol:
Total RNA was isolated with TriZol reagent (Invitrogen) and purified with RNAeasy micro kits from Qiagen. All RNA samples were determined to have 260/280 and 260/230 values ≥1.8.
RNA integrity was assessed using either an Agilent 2100 Bioanalyzer with the RNA 6000 Nano assay or an Agilent 2200 TapeStation with the R6K ScreenTape (Agilent, Santa Clara, CA). Average RIN values were above 9. Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA). Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with sequencing adaptors. The libraries were then size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing.

treatment_protocol: Please see "Experimental Procedures" from Bagot et al. "Circuit-wide transcriptional profiling reveals region specific gene co-expression networks regulating depression susceptibility " for detailed descriptions of sequencing experiments

tag: tissue

value: brain

tag: brain region

value: adult ventral hippocampus

tag: timepoint

value: 28d +1h stress post CSDS

tag: phenotype

value: control


title: 23530-3_ME


title: Diauxic-2

tag: strain


title: 11027-3_ES


title: PAR-CLIP_diff_GSC_r1


title: Diauxic-1


title: 11027-2_ES


title: 27556-3 (LiaS-K214N)_ME


title: 23530-2_ME


title: PAR-CLIP_GSC_r1

source_name: Glioma stem cells

extract_protocol:
100e6 GSC with overnight 4SU incubation were dissociated mechanically by pipetting vigorously, pelleted at 500 rcf for 5 minutes and washed once in cold PBS. After repeating centrifugation supernatant was removed, cells were resuspended in cold PBS, spread out in a thin liquid sheet on 145mm plates and crosslinked at 365nm and a total energy of 0.36 J/cm2. After centrifugation, pellet was resuspended in lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 5 mM CaCl2, 1 % NP-40) and incubated 15 minutes on ice. Lysate was treated with 20 U/mL Fermentas RNase T1 and 15 U/mL Fermentase RNase free DNase I for 15 minutes at RT and then sonicated for 15 cycles (30 sec on / off) on a Diagenode Bioruptor on high. Lysate was cleared at 21’000 rcf and 4 °C for 10 minutes. IP was performed for 3 hours with 20 ug rabbit pAb MBL Anti-IGF2BP2 (RN008P) preincubated for 1 hour at RT with 100 uL Invitrogen protein A dynabeads. Beads were washed 3 times in lysis buffer and treated with RNase T in 100 uL at 20 U/uL for 15 minutes at RT. After three more lysis buffer and two dephosphorylation buffer washes (50 mM Tris-HCl pH 7.9, 100 mM NaCl, 10 mM MgCl2) RNA was dephosphorylated at 37 °C in 100 uL NEB buffer 3 with 0.5 U / uL CIP for 10 minutes. 500 uL lysis buffer were added for beads to rebind during 10 minutes on ice. Three more lysis buffer washes and two PNK-buffer (70 mM Tris-HCl, pH 7.6, 10 mM MgCl2) washes were followed by phosphorylation with radioactive 32P at 37 °C in 100 uL of PNK buffer with 5 mM DTT, 17 nM (10 uCi) 32P-ATP and 0.5 U/uL PNK. After 30 minutes 5 uM normal ATP were added for additional 5 minutes. 1 mL of lysis buffer was added and beads are allowed to rebind during 10 minutes on ice. Beads were washed 5 times with lysis buffer, boiled in SDS-DTT solution and run on a NuPage Novex 4-12 % bis-tris gel for 1.5 hours at 150 V in MOPS buffer. Gel was imaged for 30 minutes with a phosphorimaging cassette and bands of interest excised. Elution of Protein-RNA complex was performed three times in 400 uL MOPS buffer using d-tube dialyzer midi MWCO 3.5 kDa each for 1 hours at 100 V and 5 minutes at 100 V reversed polarity. All subsequent steps were carried out exactly as described Hafner M. et al 2010.
Library was prepared similary to Illumina small RNA protocol. We adhered to Hafner et al 2010. Library was amplified for 18 cycles during PCR.

value: Cancer stem cells

value: Neurobasal medium (Invitrogen) supplemented with L-glutamine (Glutamax, Gibco), B27 supplement (Invitrogen), N2 supplement (Invitrogen), 20 ng/mL recombinant human EGF (R&D Systems), 20 ng/ml recombinant human FGF2 (R&D Systems).


title: PAR-CLIP_GSC_r2


title: Glucose-N-limited-2


title: 23530-1_ME

value: invasive infection isolate


title: VHIP_Susceptible_28d1hstress_7

description: processed data file = VHIP_control_vs_susceptible_28day1hstress.diff_list.xlsx

value: susceptible


title: ChIP-seq for transcription factor E2A

data_processing:
Sequence reads were mapped to human genome hg19 using the Subread aligner. Only uniquely mapped reads were retained.
E2A binding peaks were identified using MACS2 v2.1.0 program with a p-value cutoff of 1e-5. Genes with binding peaks falling within between 20 kilobases upstream and 5 kilobases downstream of the gene body were considered to be E2A binding targets. NCBI RefSeq human annotation build 37.2 was used to obtain chromosomal coordinates of genes. Binding peaks were assigned to genes using the featureCounts program. Gene symbols were used to match genes in ChIP-seq data with those in RNA-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: A BED file including E2A binding regions
Supplementary_files_format_and_content: A .txt file including E2A binding regions (MACS-generated)

source_name: Human Ramos cell line

extract_protocol:
20 million cells from the human Ramos cell line were crosslinked by the addition of 1% formaldehyde at room temperature for 10 min and quenched with 0.25M glycine followed by sonication and immunoprecipitation with 10 μg of anti-E2A (sc-349; Santa Cruz Technologies).
DNA fragments were blunt-end ligated to the Illumina adaptors, amplified, and sequenced with an Illumina HiSeq Sequencer.

value: Ramos

tag: chip antibody


title: 11027-2_ME


title: 11027-1_ME


title: Glucose-N-excess-1


title: Glucose-N-excess-2


title: 11027-3_ME


title: Glucose-N-limited-1


title: RNAseq round 2 atmorc1/2/4/5/6/7 rep 3

status: Public on May 11 2016

city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

description: 2-3 leaves from an individual plant

data_processing:
RNA-seq: Reads were mapped to the TAIR10 genome with TopHat2 2.0.9 (Kim et al., 2013) including the fr-secondstrand parameter. genomeCoverageBed from bedtools-2.17.0 was used generate coverage tracks (.BedGraph files, incuding the -bg option) from bam files. Note: these tracks are NOT normalised by library size.
genome build: TAIR10
processed data files format and content: BedGraph files. Columns: 1) chromosome 2) start position on chromosome 3) chromosome end position on chromosome 4) number of mapped reads within the defined region

organism: Arabidopsis thaliana

source_name: 3 wk leaves

growth_protocol: 16 hours light 8 hours dark cycle

extract_protocol:
TRIzol (#15596018)
For each library, 2ug of total RNA from a TRIzol extraction of 2-3 leaves from an individual plant was DNase treated (Ambion TURBO DNase AM2238) then depleted for ribosomal RNA using Epicentre RiboZero (MRZPL1224), and strand specific libraries were generated using Epicentre ScriptSeqv2 (SSV21124) according to manufacturers instructions. Round 1 (R1) and Round 2 (R2) were each multiplexed and sequenced on a single lane.

tag: ecotype

value: 3 wk

value: leaf

tag: genotype


title: BSseq atmorc4/7 rep 1

description: 2-3 leaves from an individual plant

data_processing:
Bisulfite-seq: Reads were aligned to the TAIR10 genome using BSMAP 2.89 (Xi and Li, 2009) allowing up to 2 mismatches and only retaining reads that mapped to one location. Methylation ratio are calculated by #C/(#C+#T) at C sites.
genome build: TAIR10
processed data files format and content: Bisulfite-seq: methylation txt files: Output format: tab delimited txt file with the following columns:      1) chromosome      2) coordinate (1-based)      3) strand      4) sequence context (2nt upstream to 2nt downstream in Watson strand direction)      5) methylation ratio, calculated as #C_counts / #eff_CT_counts      6) number of effective total C+T counts on this locus (#eff_CT_counts)               CT_SNP=“no action”, #eff_CT_counts = #CT_counts              CT_SNP=“correct”, #eff_CT_counts = #CT_counts * (#rev_G_counts / #rev_GA_counts)      7) number of total C counts on this locus (#C_counts)      8) number of total C+T counts on this locuso (#CT_counts)      9) number of total G counts on this locus of reverse strand (#rev_G_counts)      10) number of total G+A counts on this locus of reverse strand (#rev_GA_counts)      11) lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.      12) upper bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.

extract_protocol:
Qiagen DNeasy Plant Mini kit (#69106)
For each library, 500ng of genomic DNA from a Qiagen DNeasy Plant Mini kit (#69106) extraction from 2-3 leaves of an individual plant was fragmented with a Covaris S2 instrument, end repaired using KAPA hyper prep kit (#KK8502), bisulphite converted using EZ DNA methylation lightning kit (#D5030)Kit, and amplified during 13 PCR cycles using MyTaq DNA polymerase (Bioline) and Illumina TruSeq PCR primers. The 6 BSseq libraries were multiplexed and sequenced on three lanes.

tag: age


title: BSseq atmorc4/7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc1/2/4/5/6/7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc4/6/7 rep 3

description: 2-3 leaves from an individual plant


title: BSseq atmorc1/2/4/5/6/7 rep 2

description: 2-3 leaves from an individual plant


title: BSseq wt rep 1

description: 2-3 leaves from an individual plant

value: wt


title: RNAseq round 2 atmorc4/6/7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc4/7 rep 3

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc4/6/7 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc4/7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc4/7 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc6 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc6 rep 3

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc6 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 2 wt rep 2

description: 2-3 leaves from an individual plant


title: BSseq wt rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 2 wt rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 2 atmorc1/2/4/5/6/7 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc4/7 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc4/7 rep 3

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc4 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 1 wt rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc7 rep 1

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc4 rep 2

description: 2-3 leaves from an individual plant


title: EC14b

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: biopsy

data_processing:
Quality check of raw reads by FastQC
Tophat v2.0.10 for reads alignment and counts summary
Reads count data were processed using R/Bioconductor "limma" package for RPKM and 'voom' normalization
Batch effect resulted from two library preps were adjusted using "combat" function implemented in R/Bioconductor "sva" package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM followed by ''voom' normalized and batch effect adjusted values

extract_protocol:
clinical demographics: Patients were recruited for the prospective SHARE study at University of Chicago Medical Center and Mayo Clinic Rochester.  Ulcerative colitis patients who underwent total proctocolectomy with IPAA and over the age of 18 were eligible for the study.
sample collection: biopsy via pouchoscopy
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7.
RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit.

tag: patient

tag: diagnosis

value: Ulcerative colitis

tag: prognosis

value: Healthy

value: Prepouch ileum

tag: biopsytime

value: missing

tag: Sex

value: female

tag: ethnicity

value: Caucasian


title: NH64

description: biopsy

value: Normal

value: Ile


title: BSseq atmorc1/2/4/5/6/7 rep 1

description: 2-3 leaves from an individual plant


title: EC13b

description: biopsy

value: Ileal pouch


title: RNAseq round 2 wt rep 3

description: 2-3 leaves from an individual plant


title: EC11b

description: biopsy

value: Pouchitis


title: RNAseq round 1 atmorc4/7 rep 2

description: 2-3 leaves from an individual plant


title: RNAseq round 1 atmorc7 rep 3

description: 2-3 leaves from an individual plant


title: NH65

description: biopsy


title: NH63

description: biopsy

value: FAP


title: RNAseq round 1 wt rep 3

description: 2-3 leaves from an individual plant


title: NH9

description: biopsy

value: male


title: NH55

description: biopsy


title: AF16 rep3

city: Hong Kong

first: Runsheng

last: Li

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Illumina MiSeq with v2 chemistry and software MCS v2.3.0.3 used for basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic, then mapped to to C. briggsae genome (cb4) using CLC genomic workbench 8.0. The genome sequence and gene GFF annotation files were obtained from WormBase (WS250). The cutoff for C. nigoni reads are at least 85% similarity and 80% length while for C. birggsae reads, the cutoff are 90% similarity and 85% length. To de novo annotate putative TEs, RepeatMolder was run with the genome of C. nigoni (cn1, this study) and C. briggsae genome (cb4) as an input, respectively using default parameters. The consensus sequences of TEs produced were used as input to RepeatMasker to annotate all the possible TE loci over the two genomes. RMblast was used in the two annotation pipelines to align genome sequence against possible TEs. For the TE quantification, we mapped all reads from mRNAs against the consensus sequences of as described above using CLC genomic workbench 8.0, with a cutoff of at least 75% similarity and 75 % length.
The unique reads mapped to each genes/TEs were then counted with CLC genomic workbench 8.0. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with R package edgeR.
Genome_build: cb4
Supplementary_files_format_and_content: tab-delimited text files include unique reads mapped values for each sample

organism: Caenorhabditis briggsae

source_name: whole worm

extract_protocol:
300 young adult males were picked for mRNA extraction for each sample for C. briggsae (AF16), C. nigoni (JU1421), ZZY10307 and ZZY10330 with three replicates each. For collection of ZZY10307 and ZZY10330 young adult males, fertile females that carry the introgression were mated with JU1421 males. The male progeny that carry the introgression as judged by the expression of cbr-myo-2::GFP were picked under a fluorescence microscope for mRNA extraction. Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. Illumina’s TruSeq Stranded mRNA Library Preparation Kit was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual

tag: Stage

value: young adult male

tag: genotype/variation

value: wild type C. briggsae

value: fertile


title: AF16 rep2


title: AF16 rep1


title: RNAseq round 1 wt rep 2

description: 2-3 leaves from an individual plant

value: 3 wk

tag: tissue

value: leaf


title: NH7

description: biopsy

value: Ulcerative colitis


title: NH62

description: biopsy


title: NH6

description: biopsy

value: Healthy


title: NH60

description: biopsy

value: Prepouch ileum


title: NH61

description: biopsy

value: missing


title: NH58

description: biopsy


title: NH53

description: biopsy

value: female


title: NH59

description: biopsy

value: Caucasian


title: NH51

description: biopsy


title: NH52

description: biopsy


title: NH56

description: biopsy


title: NH50

description: biopsy


title: NH54

description: biopsy


title: NH47

description: biopsy


title: NH4

description: biopsy


title: NH45

description: biopsy


title: NH48

description: biopsy


title: NH49

description: biopsy


title: NH8

description: biopsy


title: NH41

description: biopsy


title: NH42

description: biopsy


title: NH3

description: biopsy


title: NH44

description: biopsy


title: NH40

description: biopsy


title: NH39

description: biopsy


title: NH37

description: biopsy


title: NH34

description: biopsy


title: NH35

description: biopsy


title: NH38

description: biopsy


title: NH36

description: biopsy


title: NH32

description: biopsy


title: NH30

description: biopsy


title: NH29

description: biopsy

value: Africa American


title: NH2

description: biopsy


title: NH26

description: biopsy


title: NH23

description: biopsy

value: South Indian


title: NH28

description: biopsy

value: Ileal pouch


title: NH21

description: biopsy


title: NH43

description: biopsy


title: NH27

description: biopsy

value: Pouchitis


title: NH19

description: biopsy


title: NH14

description: biopsy


title: NH20

description: biopsy


title: NH15

description: biopsy


title: NH18

description: biopsy


title: NH17

description: biopsy


title: NH13

description: biopsy


title: NH11

description: biopsy


title: NH10

description: biopsy


title: EC16

description: biopsy


title: NH1

description: biopsy


title: EC14

description: biopsy


title: EC13

description: biopsy


title: NH24

description: biopsy


title: EC10

description: biopsy


title: EC11

description: biopsy


title: EC8

description: biopsy


title: NH22

description: biopsy


title: EC12

description: biopsy


title: NH12

description: biopsy


title: EC7

description: biopsy


title: EC5

description: biopsy


title: EC6

description: biopsy


title: EC4

description: biopsy


title: EC2

description: biopsy


title: EC1

description: biopsy


title: EC3

description: biopsy


title: Trop2+ cells E14.5 Squamous Stomach Sample2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: E14.5 embryo

data_processing:
Approximately 25 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38.p4/mm10) using STAR software to generate read alignments for each sample.
Annotations Mus_musculus.GRCm38.79.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTSeq.
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM (count per million) values for each Sample.

source_name: Trop2+ squamous stomach

growth_protocol: Ex vivo cultures: Embryonic stomach and intestine tissue were dissociated and epithelial samples were cultured according to the protocol reported by Sato et al (2010). Specifically, the culture medium used for growing gastric spheroids consisted in Advanced-DMEM/F12 medium supplemented with 2 mM L-Glutamine, N2 and B27 w/o vit.A (Invitrogen), gentamycin, penicillin-streptomycin cocktail, 10 mM HEPES, and 1 mM N acetyl cysteine. Growth factors were added at a final concentration of : 50 ng/ml EGF and 100 ng/ml Noggin (both from Peprotech), and 100 ng/ml CHO-derived R-spondin1 (R&D System). Culture medium was changed each other day and after 5-6 days in culture, spheroids were harvested, mechanically dissociated and replated in fresh Matrigel (BD).                                                                                Isolation of Trop2+ve and Lgr5-GFP+ve cells from fetal stomach and adult pyloric stomach from Lgr5-DTR, after Lgr5 cells ablation, was performed by FACS.   Proximal and distal areas of E14.5 embryos stomach (pool of 12, 18 and 19 embryos from given litter per experiment, n=3 independent experiments), were completely dissociated with the Stem Pro accutase cell dissociation reagent (Thermo electron) at 37°C and passed through a 40-μm nylon cell strainer (Greiner).   For adults Lgr5-DTR, antral glands were isolated as previously described by Barker et al. (Barker et al., 2010). Glands were after incubated in Stem Pro accutase cell dissociation reagent until total dissociation and passed through a 40-μm nylon cell strainer.  Cells from both types of isolation procedures were incubated with fluorochrome-conjugated anti-Trop2-APC antibody, or the relevant isotype control (R&D systems) in PBS-2% BSA-2mM EDTA for 45 min on ice and sorted by using the Facs Aria I (BD Biosciences). Lgr5-GFP+ve cells were directly sorted using the FITC channel. Sorted cells were directly collected for RNA analysis over Qiazol lysis reagent (Qiagen).

extract_protocol:
900 ng of total RNA extracted with the miRNA isolation kit (Ambion, Life Technologies), were checked for quality by Bioanalyzer (Agilent).
TruSeq® Stranded mRNA libraries were prepared for sequencing using standard Illumina protocols.
paired-end libraries 2x 100 bases or 2x 125 bases

treatment_protocol: Adult Lgr5-DTR heterozygous mice were injected with diphetheria toxin (a dose of 50 µg/kg of body weight) at day 1, 2 and 4. Stomach were harvested at day5 for FACS sorting.

tag: strain background

value: mixed

tag: developemental stage/age

value: E14.5 embryo

value: squamous stomach

tag: cell type

value: fetal Trop2 epithelial squamous

tag: passages

value: tissue-sorted cells


title: Trop2+ cells E14.5 Squamous Stomach Sample1

description: E14.5 embryo


title: XXFb151

city: Epalinges

first: Gian-Paolo

last: Dotto

address: Chemin de Boveresses, 155

department: Biochemistry

institute: UNIL

data_processing:
Illumina Casava 1.82
Sequencing quality check, FastQC v0.10.1
Cutting adapter sequences and low quality reads: cutadapt 1.4.1, base quality cutoff 5.
Alignment: Tophat2, v2.0.9
Sorting: picard 1.96
Indexing: sambamba 0.4.7
Alignment statistics: bamtools stats 2.3.0
Reads counting: R package Rsubread v.1.12.6
RNAseq quality check: R package NOISeq v.2.6.0
Batch effect removal: the samples come from 2 batches sequenced at different times, therefore batch effect must be removed in order to correctly assess differential expression across batches. The raw count RPKM matrix has been normalized with the batch effect removal algorithm ComBat. Tool: Rpackage sva v3.10.0, batch effect removal algorithm: ComBat.
Differential gene expression: R package edgeR, v 3.4.2 algorithm: glmFit
Genome_build: GRCh37
Supplementary_files_format_and_content: csv file contains RPKM values for each sample

source_name: Foreskin-derived fibroblasts

growth_protocol: HDFs isolated from foreskin samples by mechanical disruption and collagenase digestion. Cultured for 2 passages in DMEM 10%FBS

extract_protocol:
RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research)
NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® ULTRA RNA Library Prep Kit for Illumina

tag: cell line

value: foreskin HDF

tag: passage

tag: donor's age (years)


title: XXFb150


title: EC15

description: biopsy

tag: age

value: male


title: XXFb149


title: XXFb148


title: XXFb146


title: Trop2+ cells E14.5 Small intestine Sample1

description: E14.5 embryo

source_name: Trop2+ small intestine

value: small intestine

value: fetal Trop2 epithelial intestinal


title: XXFb144


title: XXFb136


title: XXFb145


title: Trop2+ cells E14.5 preglandular Stomach Sample2

description: E14.5 embryo

source_name: Trop2+ glandular stomach

value: glandular stomach

value: fetal Trop2 epithelial glandular


title: Trop2+ cells E14.5 preglandular Stomach Sample1

description: E14.5 embryo


title: mCherry + NL-Dhh1-OE mRNA-Seq

city: Baltimore

first: Aditya

last: Radhakrishnan

state: MD

address: 725 N. Wolfe St., PCTB 704

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

description: rRNA Depleted Total mRNA

data_processing:
Base calling was performed at Johns Hopkins or UC Riverside sequencing core facilities with CASAVA 1.8
Adapter removed with CutAdapt v.1.7.1
Low quality reads removed (Code used available at http://www.github.com/adityaradhakrishnan)
Reads mapping to ncRNA were removed (mapped with Bowtie 1.1.2 using parameters "-Sv 3 -p 4 --best --un Unmapped-*.fastq")
Reads were mapped to yeast genome (mapped with Bowtie 1.1.2 using parameters "-Sm 1 -p 4 --best --strata"
Coverage across genome computed as both counts and reads per million using 3' end mapping (Code used available at http://www.github.com/adityaradhakrishnan)
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Tab-separated text file of reads per kilobase million (RPKM) and counts for all genes under all conditions as well as fixed-step WIG density files for number of mapped counts at every nucleotide in each dataset

organism: Saccharomyces cerevisiae

source_name: Whole Cells

growth_protocol: Cells were grown to an OD of 0.4 in YPD media (or in dropout media in reporter/overexpression conditions as a plasmid selection strategy)

extract_protocol:
For ribosome footprint profiling, lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNase treatment. RNA was extracted using SDS/hot phenol/chloroform. For mRNA-Seq, total RNA was extracted from frozen cells by using SDS/hot phenol/chloroform.
For ribosome footprint profiling, fragments ranging from (15/25)-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, IDT miRNA Cloning Linker 1 was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing. For mRNA-Seq, rRNA was depleted through Ribo-Zero Gold (Yeast) treatment and the remaining RNA was randomly fragmented with light base treatment. Fragments of 20-40 nt were prepared using the above protocol.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Profiling samples were homogenized and lysed with lysis buffer using a freezer mill. Total RNA for mRNA-Seq was extraced from whole cells.

tag: strain

value: Wild-Type (BY4741)

tag: plasmid(s)

value: pAG425-GPD with Dhh1 + pYES-DEST52 with mCherry-3BoxB


title: Dhh1-DQAD-OE mRNA-Seq

description: rRNA Depleted Total mRNA

value: pAG425-GPD with Dhh1-DQAD


title: XXFb133


title: XXFb134

tag: donor's relationship

value: brother of XXFb135


title: Trop2+ cells adult Antrum Sample2

description: Adult (2 month-old) antrum (pool of 2 mice)

source_name: Trop2+ from Lgr5-depleted antrum

value: Adult (2 month-old)

value: antrum (pool of 2 mice)

value: adult Trop2 epithelial glandular


title: XXFb132


title: Dhh1-OE mRNA-Seq (Replicate)

description: rRNA Depleted Total mRNA

value: pAG425-GPD with Dhh1


title: XXFb135

value: brother of XXFb134


title: Trop2+ cells adult Antrum Sample1

value: mixed


title: Dhh1KO Profiling

description: Ribosome Protected mRNA (25-34 nt)

value: Dhh1KO (BY4741)


title: XXFb108

value: foreskin HDF


title: Trop2+ cells E14.5 Small intestine Sample2

description: E14.5 embryo

value: E14.5 embryo

value: tissue-sorted cells


title: Wild-Type Profiling

description: Ribosome Protected mRNA (25-34 nt)


title: XXFb107


title: XXFb103


title: Stomach Spheroids Sample 2

description: E15.5 embryo

source_name: Stomach spheroids

value: E15.5 embryo

value: Stomach

value: ex vivo epithelial progenitors

value: Passage 3 day 2


title: N2 control matched to FBF-2 3

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
Library strategy: CLIP-Seq
PCR duplicates were removed using a random barcode.
The first 9 nucleotides of the read (the random barcode) were removed.
Reads were mapped to the C. Elegans WS235 genome using bowtie2 with the --local parameter or novoalign.
Reads with MAPQ below 20 were removed.
Peaks were called by custom CLIP-seq processing scripts or by the CIMS/CITS methods.
Genome_build: WS235
Supplementary_files_format_and_content: Processed data files are the number of reads mapped to each gene.

organism: Caenorhabditis elegans

source_name: C. elegans with no FLAG tagged protein

growth_protocol: iCLIP was performed on C. elegans grown to early adult phase, 25 hours after L4, on plates.

extract_protocol:
Cells were lysed by ball milling, and libraries prepared by the iCLIP method.
iCLIP

tag: protocol

value: with no FLAG tagged protein


title: Stomach Spheroids Sample 1

description: E15.5 embryo

value: Passage 2 day 6


title: XXFb80


title: KLFb141


title: N2 control matched to FBF-2 2


title: KLFb140


title: KLFb138


title: N2 control matched to FBF-2 1


title: N2 control matched to FBF-1 3


title: KLFb131


title: XXFb118


title: XXFb112


title: KLFb130


title: KLFb127


title: KLFb126


title: N2 control matched to FBF-1 1


title: KLFb120


title: KLFb116


title: N2 control matched to FBF-1 2


title: Stomach Spheroids Sample 3

description: E15.5 embryo


title: FBF-2 CLIP-seq 3

source_name: C. elegans bearing a 3xFLAG tagged FBF-2 integrated as a single copy


title: XXFb105


title: KLFb122


title: KLFb125


title: KLFb113


title: FBF-2 CLIP-seq 2

value: 3xFLAG tagged FBF-2 integrated as a single copy


title: KLFb114


title: KLFb111


title: KLFb110


title: FBF-2 CLIP-seq 1


title: KLFb109


title: FBF-1 CLIP-seq 3

source_name: C. elegans bearing a 3xFLAG tagged FBF-1 integrated as a single copy


title: Lgr5+ cells adult Antrum

description: Adult (2 month-old) antrum (pool of 4 mice)

source_name: Lgr5+ cells from adult antrum

value: Adult (2 month-old)

value: antrum (pool of 4 mice)

value: adult Lgr5 epithelial glandular


title: KLFb101


title: KLFb103


title: FBF-1 CLIP-seq 2

value: 3xFLAG tagged FBF-1 integrated as a single copy


title: FBF-1 CLIP-seq 1


title: KLFb93


title: KLFb97


title: KLFb96


title: KLFb98


title: KLFb79


title: EM3

description:
EM4_vs_EM3_annotated_macs14_peaks-2015-05-29-161244.csv
Nutlin_macs14_peaks.txt

data_processing:
Base calling performed using Casava 1.82
Sequencing quality control: FastQC
Immunoprecipitation qualitiy control PhantomPeak quality tools, CHANCE
Alignment to reference genome (BWA)
Peak calling bassed on MACS
In the post processing we associate each peak to the closest transcription starting sites with ChIPpeakAnno, a Bioconductor R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS peak files contain peaks of the IPd samples relative to the INPUT. csv files contain annotated peaks relative to the INPUT.

source_name: foreskin HDF, Nutlin, INPUT

growth_protocol: Foreskin HDFs cultured in DMEM 10% FBS

extract_protocol:
Crosslinking with formaldehyde, sonication with bioruptor 16 cycles 30" on 30" off. ChIP with p53-DO1 antibody. DNA extracted with phenol/chloroform.
ChIP-seq library was prepared according to manifacturer's suggestion using NEBNext ChIPSEq libraryQ5 Hot Start HiFi PCR Master Mix (NEB inc)

treatment_protocol: Cells treated with Nutlin-3a 10 μM or DMSO for 48h

tag: chip antibody

tag: treatment

value: Nutlin-3a 10 μM


title: KLFb95


title: EM2

description:
EM2_vs_EM1_annotated_macs14_peaks-2015-05-29-160935.csv
DMSO_macs14_peaks.txt

source_name: foreskin HDF, DMSO, IP

value: p53-DO1 (Santa Cruz, catalog# sc126, lot#K2613)

value: DMSO


title: KLFb106

value: foreskin HDF


title: EM1

source_name: foreskin HDF, DMSO, INPUT


title: siUXT_TNF

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
RNASeq and ChIPSeq raw data quality control by FastQC
RNASeq and ChIPSeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2. Cuflinks was used for differential expression gene analysis
ChIPSeq data mapping to hg19 reference genome by bowtie. SICER was used for ChIPSeq peaks calling.
Genome_build: hg19
Supplementary_files_format_and_content: wig file for ChIPSeq signal and txt format file for RNASeq gene expression level in each sample.

growth_protocol: HCT116 cell was cultured in DMEM with 10% FBS supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin(HyClone) at 37°C with %5 CO2.

extract_protocol:
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111). For ChIPSeq chromatin was fragmented into single nucleosome by micrococcal nuclease, and H3K27me1(Millipore Cat. 17-643),H3K27me2(Active Motif Cat. 61435),H3K27me3(Millipore Cat. 17-622 ) ChIP grade antibody were used for ChIP. ChIPed DNA was eluted in TE buffer.
Rubicon ThruPLEX DNA-seq 48D kit was used for RNASeq and ChIPSeq library construction. Brifely, about 100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 15 cycles for each library and gel selection was used for library size selection and purification. For ChIPSeq library construction, 10ng-20ng ChIP eluted DNA was used as initiation and after adaptor ligation, PCR with 15-18 cycles was used to amplify library. Size selection of ChIPSeq library by electrophoresis gel.

treatment_protocol: siRNA was used to knock down UXT and EZH1.

tag: transfection

value: siUXT


title: siUXT_PBS


title: siEZH1_TNF


title: siUXT_H3K27me3

tag: antibody


title: siEZH1_PBS


title: NC_PBS


title: siUXT_H3K27me2


title: KLFb99


title: siUXT_H3K27me1


title: siEZH1_H3K27me2


title: NC_TNF


title: NC_H3K27me3


title: Control Reads (random shear) from iPS cells

city: Bethesda

first: Christophe

middle: E

last: Redon

address: 37 Convent Drive

institute: NIH

description:
iPS sheared DNA
AlliPS_genome
The raw file is the file control to call the peaks for  AS-NS.bam.sorted.bam and PWS-NS-4x.bam.sorted.bam in order to generate AS_IPS_NA and PWS_IPS_NS (narrow peaks)

data_processing:
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.01.
Nascent strand reads were aligned to the hg19 genome assembly
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks

source_name: Induced pluripotent cells

growth_protocol: Cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Illumina Genomic DNA protocol

value: IPS

tag: cell line type

value: cultured normal cell line


title: siEZH1_H3K27me1


title: Nascent strands reads from AS_IPS

description:
PWS_IPS nascent strand DNA
AS_IPS_NS


title: EM4

source_name: foreskin HDF, Nutlin, IP


title: NC_H3K27me2


title: Nascent strands reads from PWS_IPS

description:
APS_IS nascent strand DNA
PWS_IPS_NS


title: Input_ChIPSeq


title: NC_H3K27me1


title: Control Reads (random shear) from K562

description:
K562 sheared DNA
K562_genome
The raw file is the file control to call the peaks for  K562.bam in order to generate K562_NS (narrow peaks)

source_name: Chronic myelogenous leukemia

value: cultured cancer cell line


title: Control Reads (random shear) from U2OS

description:
U2OS sheared DNA
U2OS_genome
The raw file is the file control to call the peaks for  U20S_NS_replicate1.sam.sorted.bam and U20S_NS_replicate2.sam.sorted.bam and to generate U2OS_NS_replicate 1 and U2OS_NS_replicate 2 (narrow peaks)

source_name: Osteosarcoma


title: Nascent strands reads from U2OS_rep1

description:
U2OS nascent strand DNA
U2OS_WT_NS_replicate1


title: Nascent strands reads from U2OS_rep2

description:
U2OS nascent strand DNA
U2OS_WT_NS_replicate2


title: Nascent strands reads from K562

description:
K562 nascent strand DNA
K562_WT_NS


title: siEZH1_H3K27me3


title: KLFb78

source_name: Foreskin-derived fibroblasts


title: AF16 males

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: Small RNAseq

data_processing:
Adapter trimming using the fastX toolkit fastx_collapser module
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed to give only unique sequence, along with read count for each, the using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content:
id number of reads-read count_unique sequence;
for example; 1-350237_TACCCTGTAGATCGAGCTGTGTGT

source_name: 200 individual males

extract_protocol:
RNA was extracted using Trizol according to manufacturers instructions.  RNA was treated with 2ul RppH for 45 minutes at 37C to remove 5' CAP and 5'Triphosphate
Small RNA libraries were constructed using Illumina Truseq SmallRNAseq kit, according to instructions.

tag: developmental stage

value: Adult

tag: fertility

value: YES

tag: genetic background

value: C briggsae


title: JU1421 males

description: Small RNAseq

organism: Caenorhabditis nigoni

value: C nigoni


title: L34Lib46

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

country: Spain

institute: Centro Superior de Investigaciones Científicas

data_processing: Sequencing was performed with the 5500 SOLiD system (Life Technologies, Madrid). Seventy-eight million reads per strain were obtained and short sequences (75bp) were assembled and aligned using a reference S. cerevisiae strain (Saccer2). Values of FPKM (Fragments Per Kilobase of exon per Million fragments mapped) were transformed for the statistical test as log2 (FPKM1/FPKM2) and uploaded on Cuffdiff (Cufflinks V1.3.0, http://cufflinks.cbcb.umd.edu/) where FPKM1 represents data of 12 strain and FPKM2 represent data of 11 strain. The FPKM parameter was used for pair end RNA-Seq experiments, where fragments were sequenced from both ends, providing two reads for each fragment. The Q value, representing significance value for statistical analysis performed through the use of cufflink platform was calculated and significant transcriptome differences were identified

source_name: yeast strain, 30-rep1-12mix

growth_protocol: Single and mixed fermentations, including strain-dye swap, were performed in triplicate. Dominant and non-dominant strains were inoculated reaching the same cell density (0.1 OD) in 10 ml of Nebbiolo natural must (Fig. 1A). Fermentations were carried out at 25°C with continuous shaking. Samples of 1 ml were taken at 3 points of the fermentation. The first sample was taken at the beginning of the exponential growth phase, the second in the middle of the exponential growth phase and the last at the beginning of the stationary phase.

extract_protocol:
The RNA Mini Kit (Qiagen, Madrid) was used following manufacturer’s instructions. RNA quality was checked using the Bioanalyser (Agilent Technologies Spain, Madrid) and samples with good quality RNA, showing 5 as minimum of RNA Integrity Number (RIN) were sequenced
Illumina RNA amplification kit (Thermo-Fisher) was used in order to amplify the low amount of RNA extracted from cells separated by cytometry. Sequencing was performed with the 5500 SOLiD system (Life Technologies, Madrid). Libraries were performed using standard SOLID protocol.

treatment_protocol: Samples were rapidly centrifuged to eliminate the must fractions and RNAlater (Ambion, Monza) was added and immediately frozen in liquid nitrogen. Samples were kept at -80ｰC until flow cytometry separation. Cells were sorted with a MoFlo (Dako cytomation, Glostrup, Denmark) cytometer, on the basis of labels according to fluorescence intensities of the populations. The cytometer was equipped with two lasers: 488nm (for GFP exitation) and 345 nm (for Sapphire exitation). For GFP and Sapphire FL7 570/20 and FL1 530/20 channels were respectively used. Separation was performed with a sorting rate up to 20000 events per second for the time necessary to reach between 500000 and 1000000 cells. Cells were collected in tubes containing PBS buffer and directly put in dry ice to flash freeze them at the exit of the cytometer. Frozen samples were kept at -80ｰC and thawed in ice for the subsequent RNA extraction

tag: time point

tag: single-mixed original culture

value: Mixed culture


title: K37Lib44

source_name: yeast strain, 30-rep2-11mix


title: J50Lib42

source_name: yeast strain, 30-rep3-12

value: Single culture


title: K46Lib45

source_name: yeast strain, 30-rep3-11mix


title: H31Lib36

source_name: yeast strain, 20-rep3-12mix


title: L51Lib48

source_name: yeast strain, 30-rep3-12mix


title: J45Lib40

source_name: yeast strain, 30-rep1-12


title: K32Lib43

source_name: yeast strain, 30-rep1-11mix


title: G33Lib33

source_name: yeast strain, 20-rep3-11mix


title: G16Lib32

source_name: yeast strain, 20-rep2-11mix


title: I42Lib39

source_name: yeast strain, 30-rep3-11


title: L36Lib47

source_name: yeast strain, 30-rep2-12mix


title: I40Lib38

source_name: yeast strain, 30-rep2-11


title: I26Lib37

source_name: yeast strain, 30-rep1-11


title: F8Lib29

source_name: yeast strain, 20-rep1-12


title: F21Lib14

source_name: yeast strain, 20-rep2-12


title: H12Lib34

source_name: yeast strain, 20-rep1-12mix


title: J49Lib41

source_name: yeast strain, 30-rep2-12


title: G13Lib31

source_name: yeast strain, 20-rep1-11mix


title: Gly_mitoRP_15_2

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed .bedGraph file is A-site transformed position data for for 36-40 nt reads on the plus strand as presented in Figure 2d.
processed data file: MitoriboProfiling_RPKmitoM_TlnEfficiency.xlsx
processed data file: TranslationEfficiency_Log2.txt

data_processing:
Base calling was performed on-instrument: MiSeq control/RTA or NextSeq control/RTA2.
3' adaptor sequence was removed using Cutadapt and 5' nt removed except where indicated in processed file descriptions.
Reads mapping to non-coding RNAs were removed by aligning using Bowtie1 to a collection of RNA genes downloaded from Saccharomyces Genome Database. We allowed a 3-nt 3’ mismatch when mapping to tRNAs to account for non-templated CCA addition on mature tRNAs. Remaining reads were then aligned allowing two mismatches using Tophat2.
RNA-seq normalization to spike-ins was performed by dividing the raw read count at each position by the number of spike-in reads in the library (rps, reads per spike-in).
RNA-seq reads were also normalized to total nuclear or mitochondrial mRNA mappers, as were cytoribosome profiling and mitoribosome profiling reads, respectively (rpm, reads per million).
To determine expression values for each gene, rps or rpm values were summed across ORFs and normalized to ORF length (RPKS or RPKM, normalized reads per kilobase). For footprint reads, the first and last five codons were excluded.
Translation efficiency (TE) was calculated by dividing cytoribosome footprint RPKM values by nuclear-mapping RNA-seq RPKM values and mitoribosome footprint RPKM values by mito-mapping RNA-seq RPKM values. If Footprint RPKM value and RNAseq RPKM value = 0: TE = NA. If Footprint RPKM value > 0 and RNAseq RPKM value = 0: TE = inf. *Note no other minimum or maximum value cutoffs set.
For each group of experiments (11-15, 16-19, 20-21) fold-change is calculated compared to the glucose condition. Any gene that that has values of NA, inf, or =< 0.01 in any sample is excluded.
Scripts for measurements described above were written in Python 2.7.5.
Genome_build: Saccharomyces cerevisiae assembly R64 (UCSC: sacCer3)
Supplementary_files_format_and_content: Gene expression data is presented as tab-separated (.txt) or Excel (.xlsx) files. In TranslationEfficiency_Log2.txt, values for mitochondrial genes is the average of two mitoribosome profiling experiments. See associated .xlsx file for individual values.
Supplementary_files_format_and_content: SAMPLE NAMING: Numbering indicates sets of experiments. 11-15: WT cells, Full shift. 11:Glu, 12:Gly15min, 13:Gly1h, 14:Gly3h, 15:Gly. 16-19: Pentamidine drug treatment, 16:Glu(no drug), 17:Gly15min(no drug), 18:Gly15min(+Pent), 19:Gly1h(+Pent). 20-21:rho0 cells, 20:Glu, 21:Gly15min.

source_name: Whole cell lysate

growth_protocol: Yeast cultures were grown to log phase in YPD (2% glucose), pH 5.0 at 30C then collected by filtration, rinsed in YP, pH 5.0, and rapidly resuspended in prewarmed YPGly (3% glycerol), pH 5.0 for collection at indicated timepoints. Alternatively, log phase cultures were diluted to OD600 < 0.06 in YPGly pH5.0 and allowed to grow to log phase (~16 hours). For pet111KO strain, YP Galactose was inoculated at OD600 = 0.06 from an overnight YPD culture and grown to log phase.

extract_protocol:
sample processing: RNaseI treatment, anti-FLAG immunopurification, FLAG elution, RNA isolation by phenol/chloroform extraction, gel purification of 36-42 nt fragments
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

treatment_protocol: Cells were rapidly collected by filtration and flash frozen in liquid nitrogen (except where mitochondria were purified). No drugs were added prior to freezing except Pentamidine where indicated. For Pentamidine treatment, 10 uM was added directly to log phase glucose culture immediately after collection of "Glu" sample. Incubation was continued for 5 minutes, then cells were collected by filtration, rinsed with prewarmed YP + 10 uM Pentamidine, and resuspended in prewarmed YP Gly + 10 uM Pentamidine.

value: YSC052 (S288c with  GAL2+, HAP1+ MIP1[S]G1981A, MRPS17-F)

tag: culture condition

value: YP 3% Glycerol

tag: drug(s) in lysis buffer


title: Gly3h_mitoRP_14_2

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed .bedGraph file is A-site transformed position data for 36-40 nt reads on the plus strand.
processed data file: MitoriboProfiling_RPKmitoM_TlnEfficiency.xlsx
processed data file: TranslationEfficiency_Log2.txt

value: YP 3% Glycerol for 3h


title: F53Lib30

source_name: yeast strain, 20-rep3-12


title: Gly1h_mitoRP_13_2

value: YP 3% Glycerol for 1h


title: Gly_mitoRP_15_1


title: E43Lib28

source_name: yeast strain, 20-rep3-11


title: D17Lib25

source_name: yeast strain, 12-rep3-12mix


title: Gly3h_mitoRP_14_1


title: Gly15m_mitoRP_12_2

value: YP 3% Glycerol for 15 minutes


title: Glu_mitoRP_11_2

value: YP 2% Glucose


title: H15Lib35

source_name: yeast strain, 20-rep2-12mix


title: Hybrid ZZY10330

description: Small RNAseq

source_name: 200 individual males

value: NO

value: C nignoi+X chr introgression C briggsae


title: EC9

description: biopsy

tag: patient

tag: diagnosis

value: Ulcerative colitis

tag: prognosis

value: Pouchitis

tag: tissue

value: Ileal pouch

tag: biopsytime

tag: age

tag: Sex

value: female

tag: ethnicity

value: Caucasian


title: C18Lib22

source_name: yeast strain, 12-rep3-11mix

tag: strain


title: C4Lib20

source_name: yeast strain, 12-rep1-11mix


title: pet111KO_mitoRP

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed file is A-site transformed position datafor 36-40 nt reads on the plus strand as presented in Figure 2d.

value: YP 2% Galactose


title: Gly15min_rho0_RNAseq_21

description:
library strategy: RNA-seq
rRNA-depleted RNA
processed data file: RNAseq_RPKM.txt

extract_protocol:
sample processing: Total RNA was isolated by phenol/chloroform extraction from thawed and precleared lysate after SDS solubilization and Proteinase K treatment. rRNA was depleted with Ribo-Zero Gold kit for yeast. Remaining RNA was randomly fragmented by alkaline hydrolysis and 30-70 nt fragments were gel purified.
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

value: YSC209 (YSC052 rho0)

value: 100 ug/mL cycloheximide


title: E25Lib27

source_name: yeast strain, 20-rep2-11

value: Single culture


title: E7Lib26

source_name: yeast strain, 20-rep1-11


title: Gly1h_mitoRP_13_1

value: YSC052 (S288c with  GAL2+, HAP1+ MIP1[S]G1981A, MRPS17-F)


title: D9Lib24

source_name: yeast strain, 12-rep2-12mix

value: Mixed culture


title: D3Lib23

source_name: yeast strain, 12-rep1-12mix


title: Gly15m_mitoRP_12_1


title: mCherry + NL-Dhh1-DQAD-OE Profiling 2

description: rRNA Depleted Total mRNA

source_name: Whole Cells

value: Wild-Type (BY4741)

tag: plasmid(s)

value: pAG425-GPD with Dhh1-DQAD + pYES-DEST52 with mCherry-3BoxB


title: A54Lib16

source_name: yeast strain, 12-rep3-11


title: Gu_RNAseq_16


title: Gly15min_rho0_cytoRP_21

description:
library strategy: Cytoribo-seq
cytoribosome-associated RNA
processed data file: CytoriboProfiling_RPKM.txt
processed data file: TranslationEfficiency.txt
processed data file: TranslationEfficiency_Log2.txt

extract_protocol:
sample processing: RNaseI treatment, ribosome isolation by pelleting through 1M sucrose cushion, RNA isolation by phenol/chloroform extraction, gel purification of 27-33 nt RNA fragments
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

value: YP 3% Glycerol for 15 minutes


title: NoDrug_mitoRP_5

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed file is list of normalized (reads per million) 5' ends mapping to each exon position along the mitochondrial genome. Plus strand only as all ORFs are on the plus strand.

value: YSC043 (S288c with  GAL2+, HAP1+ MIP1[S]G1981A, IMG1-HA, MRPS17-F)

value: YP 3% Glycerol


title: A1Lib13

source_name: yeast strain, 12-rep1-11


title: Glu_rho0_cytoRP_20

value: YP 2% Glucose


title: C6Lib21

source_name: yeast strain, 12-rep2-11mix


title: BioRep2_mitoRP_10

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed file is list of normalized (reads per million) 5' ends mapping to each exon position along the mitochondrial genome. "39Norm" is all 39 nt (without 5' trimming) reads, used for reading frame analysis. Plus strand only as all ORFs are on the plus strand.
FP10_Mito_mRNA39Norm.wig


title: Glu_mitoRP_11_1


title: B44Lib19

source_name: yeast strain, 12-rep3-12


title: mCherry + NL-Dhh1-OE Profiling

description: Ribosome Protected mRNA (25-34 nt)

value: pAG425-GPD with Dhh1 + pYES-DEST52 with mCherry-3BoxB


title: Gu_cytoRP_16

source_name: Whole cell lysate


title: Gly15min_NoPent_cytoRP_17


title: B29Lib18

source_name: yeast strain, 12-rep2-12


title: BioRep1_mitoRP_9


title: Gly_RNAseq_15

description:
library strategy: RNA-seq
rRNA-depleted RNA
Processed .bedGraph file is coverage data for the plus strand as presented in Figure 2d.
processed data file: RNAseq_RPKS.txt
processed data file: RNAseq_RPKS_Log2.txt
processed data file: RNAseq_RPKM.txt

extract_protocol:
sample processing: Total RNA was isolated by phenol/chloroform extraction from thawed whole cell lysate after SDS solubilization and Proteinase K treatment. rRNA was depleted with Ribo-Zero Gold kit for yeast. Remaining RNA was randomly fragmented by alkaline hydrolysis and 30-70 nt fragments were gel purified.
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.


title: Gly15min_RNAseq_cytoRP_18

value: YP 3% Glycerol + 10 uM Pentamidine for 15 minutes


title: Glu_rho0_RNAseq_20


title: B2Lib17

source_name: yeast strain, 12-rep1-12


title: Gly3h_RNAseq_14

description:
library strategy: RNA-seq
rRNA-depleted RNA
processed data file: RNAseq_RPKS.txt
processed data file: RNAseq_RPKS_Log2.txt
processed data file: RNAseq_RPKM.txt

value: YP 3% Glycerol for 3h


title: Dhh1KO mRNA-Seq (Replicate)

description: rRNA Depleted Total mRNA

value: Dhh1KO (BY4741)


title: Drug_mitoRP_6

description:
library strategy: Mitoribo-seq
mitoribosome-associated RNA
Processed file is list of normalized (reads per million) summed 5' ends mapping to each exon position along the mitochondrial genome. Plus strand only as all ORFs are on the plus strand.

value: 50 ug/mL thiamphenicol, 1mM GMPPNP


title: Gly1h_RNAseq_13

value: YP 3% Glycerol for 1h


title: Dhh1KO mRNA-Seq

description: rRNA Depleted Total mRNA


title: Dhh1KO Profiling (Replicate)

description: Ribosome Protected mRNA (15-34 nt)


title: Gly15min_RNAseq_cytoRP_17


title: A30Lib15

source_name: yeast strain, 12-rep2-11


title: mitoRNAseq

description:
library strategy: RNA-seq
mitochondrial RNA
Processed file is list of normalized (reads per million) 5' ends mapping to each exon position along the mitochondrial genome. "39Norm" is all 39 nt (without 5' trimming) reads, used for reading frame analysis. Plus strand only as all ORFs are on the plus strand.
TotMitoRNaseI_MitoFiltered39.wig

source_name: Purified mitochondria

extract_protocol:
sample processing: RNA was isolated from purified mitochondria by Trizol, randomly fragmented by alkaline hydrolysis, and 36-42 nt fragments were gel purified.
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.


title: Glu_RNAseq_11


title: Gly_cytoRP_15

extract_protocol:
sample processing: RNaseI treatment, 80S monosome isolation on 10-50% sucrose gradient, RNA isolation by phenol/chloroform extraction,  gel purification of 27-33 nt RNA fragments
Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.


title: mCherry + NL-Dhh1-DQAD-OE Profiling 1

description: Ribosome Protected mRNA (25-34 nt)


title: Gly15min_Pent_cytoRP_18


title: Gly1h_cytoRP_13


title: Gly15m_cytoRP_12


title: Wild-Type Profiling (Replicate)

description: Ribosome Protected mRNA (15-34 nt)


title: Dhh1-OE mRNA-Seq

description: rRNA Depleted Total mRNA

value: pAG425-GPD with Dhh1


title: Dhh1-DQAD-OE Profiling

description: Ribosome Protected mRNA (15-34 nt)

value: pAG425-GPD with Dhh1-DQAD


title: Glu_cytoRP_11

value: 100 ug/mL cycloheximide


title: F0H MeDIP

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
The genome sequence of freshwater medaka was used as the reference genome for bowtie alignment.
DiffReps software was employed to identify the differentially methylated regions with a FDR cut-off of 0.01.
Genome_build: Oryzias_latipes release 73 downloaded from ensembl
Supplementary_files_format_and_content: .wig files report peaks

organism: Oryzias melastigma

extract_protocol:
For each group, sperm from 10 male fish were collected by gently pressing the harvested testis and pooled. Sperm genomic DNA was extracted using a DNA extraction kit (MO BIO Ultraclean® Tissue & Cells DNA Isolation Kit, USA).
Extracted DNA was prepared by the Paired-End DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Briefly, DNA was sonicated to fragments of 100-500 bp before the addition of dAs and adaptor ligation. Methylated DNA was then pulled down by an antibody specifically recognizing 5-methylcytosine. The pull-down fraction containing the antibody-5-methylcytosine complex was subjected to column purification (Zymo Research). The purified DNA was next enriched by an adaptor-mediated PCR process. Fragments of 220-232 bp were gel purified with a Gel Extraction Kit (Qiagen).

tag: group

value: Hypoxic group in F0 generation

tag: cell type

value: sperm


title: F0N MeDIP

value: Normoxic group in F0 generation


title: ZZY10330 rep1

source_name: whole worm

extract_protocol:
300 young adult males were picked for mRNA extraction for each sample for C. briggsae (AF16), C. nigoni (JU1421), ZZY10307 and ZZY10330 with three replicates each. For collection of ZZY10307 and ZZY10330 young adult males, fertile females that carry the introgression were mated with JU1421 males. The male progeny that carry the introgression as judged by the expression of cbr-myo-2::GFP were picked under a fluorescence microscope for mRNA extraction. Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. Illumina’s TruSeq Stranded mRNA Library Preparation Kit was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual

tag: Stage

value: young adult male

tag: genotype/variation

value: Mostly C. nigoni genome, with X chromosome syntenic region replaced by C. briggsae X chromosome (from 16.4 M to the end)

tag: phenotype

value: sterile


title: ZZY10307 rep3

value: Mostly C. nigoni genome, with X chromosome syntenic region replaced by C. briggsae chromosome X (from 4.5M to 12.2M)


title: ZZY10330 rep2


title: Dhh1-OE Profiling

description: Ribosome Protected mRNA (25-34 nt)

value: Wild-Type (BY4741)


title: Gly3h_cytoRP_14

value: YSC052 (S288c with  GAL2+, HAP1+ MIP1[S]G1981A, MRPS17-F)

tag: culture condition


title: Gly15m_RNAseq_12

value: YP 3% Glycerol for 15 minutes

tag: drug(s) in lysis buffer


title: Wild-Type mRNA-Seq (Replicate)

description: rRNA Depleted Total mRNA


title: F2H MeDIP

value: Hypoxic group in F2 generation


title: Dhh1-OE Profiling (Replicate)

description: Ribosome Protected mRNA (15-34 nt)


title: ZZY10307 rep1


title: Male small RNA sequence

city: Rongchang

first: Guangxu

last: Ma

state: Chongqing

address: xueyuan road 160#

department: veterinary medicine

country: China

institute: Southwest university

data_processing:
Illumina Casava1.7 software used for basecalling.
software developed by BGI for filtering
Small RNA tags were mapped to reference genome by SOAP, small RNA tags were aligned to  the miRNA precursor/mature miRNA of all plants/animals in miRBase by Tag2miRNA.
Small RNA tags were annoatated by blastall-p blastn these sequences from Rfam and get rid of matched tags from unannotated tags.
Tag2annotation software used for summarize all alignments and annotation.
Supplementary_files_format_and_content: tab-delimited .txt files include miRNA name and raw reads counts of male and female adult toxocara canis samples; .xls files include miRNA name, raw reads counts and normalized miRNA abundance measurements for known and novel miRNA of male and female toxocara canis.

organism: Toxocara canis

source_name: whole body

extract_protocol:
High-quality total RNA were extracted from the entire body of a male and a female adult worms using Trizol reagent (Invitrogen, Carlsbad, CA, USA), respectively.
The RNA yields and qualities were measured spectrophotometrically (eppendorf BioPhotometer 6132). 20 μg RNA from the two samples were size fractionated with Novex 6% TBE-Urea gels (Invitrogen, Carlsbad, CA, USA) and, the fragments of 18-30 nt were ligated with 5’ and 3’ adaptors (Illumina) for reverse transcription. The produced first-stranded cDNA was amplified with small RNA primer set to enrich the libraries

value: Rongchang

tag: developmental stage

value: adult

tag: gender

value: Male

tag: host

value: dog


title: Female small RNA sequence

value: Female


title: WT 6h Refed

status: Public on May 10 2016

first: Youngjung

middle: Rachel

last: Kim

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

data_processing:
RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
Tophat v2.0.4 to map the reads to a mm9 with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Pancreatic islets

extract_protocol:
Isolated primary islets from 3 WT and 3 KR mutant mice after 24 hr-fasted or 24 hr-fasted followed by 6 hr-refeeding were combined per genotype and total RNA isolation was performed using RNeasy Mini Kit (QIAGEN).
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.

tag: protocol

value: Fasted for 48 hours, and refed for 6 hours

tag: genotype

value: WT


title: ZZY10330 rep3


title: F2T MeDIP

value: Transgenerational group in F2 generation

value: sperm


title: KR 48h Fast

value: Fasted for 48 hours

value: KR mutant


title: ZZY10307 rep2

value: young adult male

value: sterile


title: WT_LPM_CR_RNA_Rep1

city: Chapel Hill

first: Shehzad

last: Sheikh

state: NC

address: 5023A Genetic Medicine Building

institute: University of North Carolina - Chapel Hill

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) with GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to blacklisted regions of the mouse genome were removed.
Transcript abundance was estimated by computing RPKM (Mortazavi et al. 2008) using RefSeq gene models aggregated by gene symbol.
genome build: mm9
processed data file format and content: Normalized abundance matrix

molecule: polyA RNA

source_name: Lamina propria macrophages

growth_protocol: WT and Il10−/− mice on a C57BL/6 background and controls were purchased from The Jackson Laboratory (Bar Harbor, ME). GF mice (WT and IL-10−/−) were derived by embryo transplant and maintained at the National Gnotobiotic Resource Center at the University of North Carolina. Lamina propria mononuclear cells were isolated from mouse colon by an enzymatic method and density gradient centrifugation, as described previously (Kobayashi et al. 2014). Splenocytes were isolated as previously described (Steinbach et al. 2015). Lamina propria mononuclear cells and splenocytes were further separated into CD11b+ cells using anti-CD11b microbeads (Miltenyi Biotec, Auburn, CA.

extract_protocol:
RNA was isolated using Qiagen RNeasy Mini Kit (Valencia, CA). This kit uses a column-based DNase treatment to eliminate DNA contamination.
TruSeq libraries were constructed as per manufacturer's recommendations.

value: Wild-type

tag: treatment

value: Conventionally-raised


title: WT_LPM_GF_RNA_Rep1

value: Germ-free


title: KR 6h Refed


title: JU1421 rep2

value: wild type C. nigoni

value: fertile


title: IL10KO_BMM_LPS_RNA_Rep1

source_name: Bone marrow macrophages

growth_protocol: WT and Il10−/− mice on a C57BL/6 background and controls were purchased from The Jackson Laboratory (Bar Harbor, ME). Bone marrow-derived macrophages (BMMs) were harvested, cultured and stimulated as described (Sheikh et al. 2010).

treatment_protocol: Bone marrow-derived macrophages (BMMs) were harvested, cultured and stimulated as described (Sheikh et al. 2010). Cells were stimulated with LPS (100ng/mL) for 4 hours.

value: LPS-stimulated


title: JU1421 rep1


title: Wild-Type mRNA-Seq

description: rRNA Depleted Total mRNA

extract_protocol:
For ribosome footprint profiling, lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNase treatment. RNA was extracted using SDS/hot phenol/chloroform. For mRNA-Seq, total RNA was extracted from frozen cells by using SDS/hot phenol/chloroform.
For ribosome footprint profiling, fragments ranging from (15/25)-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, IDT miRNA Cloning Linker 1 was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing. For mRNA-Seq, rRNA was depleted through Ribo-Zero Gold (Yeast) treatment and the remaining RNA was randomly fragmented with light base treatment. Fragments of 20-40 nt were prepared using the above protocol.

value: Wild-Type (BY4741)


title: JU1421 rep3


title: IL10KO_BMM_Unstimulated_RNA_Rep1

value: Unstimulated


title: WT_BMM_LPS_RNA_Rep2


title: WT_BMM_Unstimulated_RNA_Rep2


title: IL10KO_BMM_LPS_plusIL10_FAIRE_Rep2

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) with GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to more than four locations or overlapped blacklisted regions of the mouse genome were removed. FAIRE-seq signals were quantile normalized along with other data from Il10-/- BMMs
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
genome build: mm9
processed data file format and content: bigWig of quantile-normalized FAIRE-seq signal

extract_protocol:
FAIRE was performed as described previously (Simon 2012).
TruSeq libraries were constructed as per manufacturer's recommendations.

treatment_protocol: Bone marrow-derived macrophages (BMMs) were harvested, cultured and stimulated as described (Sheikh et al. 2010). Cells were pre-treated with IL-10 (10 ng/mL) for 24 hours. Cells were stimulated with LPS (100ng/mL) for 4 hours.

value: IL10-stimulated, LPS-stimulated


title: WT_BMM_LPS_RNA_Rep1


title: IL10KO_BMM_Unstimulated_plusIL10_FAIRE_Rep2


title: IL10KO_BMM_LPS_plusIL10_FAIRE_Rep1


title: IL10KO_BMM_Unstimulated_plusIL10_FAIRE_Rep1


title: WT_BMM_Unstimulated_RNA_Rep1


title: IL10KO_SM_CR_FAIRE_Rep1

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) with GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and allowing 1 mismatch. Reads aligning to more than four locations or overlapped blacklisted regions of the mouse genome were removed.
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
genome build: mm9
processed data file format and content: bigWig of raw FAIRE-seq signal

source_name: Splenic macrophages


title: IL10KO_SM_CR_FAIRE_Rep2


title: WT_SM_CR_FAIRE_Rep1


title: IL10KO_LPM_CR_FAIRE_Rep2


title: IL10KO_LPM_GF_FAIRE_Rep2


title: WT 48h Fast


title: IL10KO_LPM_CR_FAIRE_Rep1


title: IL10KO_LPM_GF_FAIRE_Rep1


title: WT_LPM_CR_FAIRE_Rep2


title: WT_LPM_CR_FAIRE_Rep3


title: IL10KO_BMM_LPS_FAIRE_Rep2


title: IL10KO_LPM_CR_RNA_Rep1


title: WT_BMM_Unstimulated_FAIRE_Rep2


title: IL10KO_LPM_GF_RNA_Rep1


title: WT_LPM_CR_FAIRE_Rep1


title: IL10KO_BMM_LPS_FAIRE_Rep1


title: WT_LPM_GF_FAIRE_Rep1


title: IL10KO_BMM_Unstimulated_FAIRE_Rep1


title: CD_2

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained. High quality reads were aligned to their respective personalized genomes using the SNP-tolerant GSNAP software (Wu and Nacu 2010).
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
genome build: hg19 (customized)
processed data file format and content: bigWig of raw FAIRE-seq signal

source_name: Colonic mucosal biopsy

growth_protocol: CD patients from the adult IBD Center at University of North Carolina were included in this study. A total of 4 samples (2 CD and 2 non-CD controls) were used. Tissue was prepared for FAIRE as previously described (Simon 2012).

value: Crohn's Disease


title: WT_BMM_LPS_FAIRE_Rep2


title: Control_2

value: Control


title: WT_BMM_LPS_FAIRE_Rep1


title: D8 SFRS11 KD

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
The QC of the generated libraries was performed using FastQC. Reads were mapped to hg19 genome using STAR aligner software. Reads with more than 3 mismatches were filtered out. Reads mapped to more than one region in the human genome were also disregarded. The mapped reads have then undergone Differential Splicing Analysis using MATS.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include the exon skipping events detected by MATS.

source_name: BJ Fibroblasts

growth_protocol: BJ fibroblast were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. Human Embryonic Stem Cells (hESCs) and induced Pluripotent Stem Cells (iPSCs) clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromplar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen, 15596-026). Contaminating DNA was removed by DnaseI (Ambion) treatment, and the RNA was further purified using RNeasy column (Qiagen, 74140)
The RNA samples were subject to mRNA selection, fragmentation, cDNA synthesis, and library preparation using a TruSeq RNA Sample Prep Kit (Illumina, RS-122-2001).

treatment_protocol: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with SFRS11 siRNA.

value: SFRS11 Knock-down

tag: cell line

value: BJ


title: WT_LPM_GF_FAIRE_Rep2


title: WT_BMM_Unstimulated_FAIRE_Rep1


title: MCF-7 Spheroid (Replicate 1)

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description:
micro RNA
MCF7_S_1

data_processing:
CLC genomic workbench 7.0
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were aligned to human genome (homo sapiens GRCh 37.57) and known miRNA database (miRBase-19)
Statistical analysis: Bonferroni and FDR corrected
Filtering: Significant, above 2; Kalz test: FDR pvalue <0.05; Kalz test: FC abs value>2
Genome_build: miRBase 19
Supplementary_files_format_and_content: Files containing expression values of miRNAs of monolayer and spheroid MCF-7

source_name: MCF-7 Spheroid

growth_protocol: The monolayer and spheroid MCF-7 cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.

extract_protocol:
Total RNA with retention of small RNAs from the cells were extracted using miRNA easy
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina Tru-seq small RNA

tag: cell source

value: Estrogen-dependent human breast adenocarcinoma

value: Spheroid

tag: culture dimension


title: MCF-7 Monolayer (Replicate 1)

description:
micro RNA
MCF7_P_1

source_name: MCF-7 Monolayer

value: Monolayer


title: IL10KO_BMM_Unstimulated_FAIRE_Rep2

tag: strain


title: Control_1


title: MCF-7 Spheroid (Replicate 3)

description:
micro RNA
MCF7_S_3


title: KP1-sh2-FACS_B [ATAC-seq]

first: William

last: Greenleaf

address: 279 Campus Drive

institute: Stanford University

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line expressing shRNA to Nfib

data_processing:
library strategy: ATAC-seq
Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag.  Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
peak calling was done on the merged ex vivo data (samples 1-27) for the mouse data, or on the merged human cell lines (60-67) with MACS2 with the --nomodel, --broad flags
counts per sample were found within peaks, and differential accessibility was called within each group of samples (ex vivo, cell lines, modified cell lines, and human modified cell lines)
Genome_build: mm9 for mus musculus, hg19 for homo sapiens
Supplementary_files_format_and_content: peak_calls_mm9.nheader.up.bed are the peaks used for all mouse data. Four columns indicate chromosome, start, and end of accessible regions, plus a fourth column giving a unique identifier per peak
Supplementary_files_format_and_content: all_merged.H14_H29_H52_H69_H82_H88_peaks.broadPeak are the peaks used for human data. Standard broadpeak output is given.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)
Supplementary_files_format_and_content: *.bw are bigwig files containing the insertions per base pair, smoothed over 150 bp windows (20bp step size). Sample replicates are merged.

source_name: cell line

growth_protocol: All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS. Primary tumors and metastases were dissected and dissociated using collagenase IV, dispase, and trypsin at 37oC for 30 minutes. After dissociation the samples are continually on ice, in contact with ice-cold solutions, and in the presence of 2mM EDTA and 1U/ml DNase to prevent aggregation, and were FACS sorted for purity.

extract_protocol:
Cells were lysed, incubated with  Tn5 transposase, and purified with Qiagen MinElute kit.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

treatment_protocol: Stable Nfib knockdown cell lines were generated using lentiviral pLKO/PuroR vectors. Inducible and constitutive Nfib expressing human and mouse cells were generated using lentiviral vectors.

tag: tissue/cell type

value: tumor-derived cell line

value: expressing shRNA to Nfib (shNfib)

tag: induced for

value: 2 weeks


title: MCF-7 Monolayer (Replicate 3)

description:
micro RNA
MCF7_P_3


title: MCF-7 Spheroid (Replicate 2)

description:
micro RNA
MCF7_S_2


title: KP1-sh2_counted_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line with expression vector control

value: expressing empty vector (shControl)


title: MCF-7 Monolayer (Replicate 2)

description:
micro RNA
MCF7_P_2


title: D8 SMAD3 KD

treatment_protocol: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with SMAD3 siRNA.

value: SMAD3 Knock-down