title: 14 fuRx

description:
barcode: TCTGA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTGATCGTATGCCGTCTTCTGCTTG
Library 2

value: Asian


title: 13 fuRx

status: Public on Aug 20 2015

type: SRA

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description:
barcode: TCTCC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTCCTCGTATGCCGTCTTCTGCTTG
Library 2

library_source: transcriptomic

data_processing:
Base calling was done using CASAVA versions 1.6 - 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA (Farazi et al. 2011, 71:4443) and other non-coding and coding RNA transcriptomes.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files contain raw, i.e. not-normalized or transformed, miRNA counts based on unique miRNA sequences, or based on precursor clusters and sequence families.

molecule: total RNA

organism: Homo sapiens

source_name: further resolving DTH reaction (4 months after challenge)

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion.  The amount of RNA was assessed by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE).  The quality of extracted RNA was examined using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (2008, 44:3, 2012, 58:164). The libraries for for the serum and plasma samples had the following modifications: 1) the amount of the 10 spiked-in synthetic calibrator oligoribonucleotides was reduced from 0.5 fmol each per 2 µg total RNA input to 0.005 fmol each, 2) the synthetic P32-labeled 19-nt and 24-/35-nt ssRNAs used for size selection were not spiked-into the samples. Note: no calibrator oligoribonucleotides were spiked-in to library 8. The sequences of the 10 used calibrator oligoribonucleotides can be obtained from Hafner et al. 2012 (Methods, 58:164).

treatment_protocol: placebo or diphencyprone (DPCP) gel application

tag: sample id

tag: age

tag: gender

value: Female

tag: race

value: African American

tag: tissue

value: Skin


title: GM18859_H3K4ME3

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

library_source: genomic

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project or imputed using shapeIt and IMPUTE2
ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20, -t 4 and the rest set to defaults)
Peaks were called using MACS2 on merged replicates, subsampled to 50 million single reads. Genome-wide signal tracks (bigWig) were generated using wiggler, also on the subsampled data.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler.

molecule: genomic DNA

source_name: Lymphoblastoid Cell Line

growth_protocol: LCLs were grown to a density of 0.6-0.8 x 10^6/mL in RPMI1640 with 15% fetal bovine serum and 1% PenStrep.

extract_protocol:
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).

treatment_protocol: Cross linking was performed in 1% formaldehyde for 10 minutes at room temperature. Followed by quenching with Glycin with a final concentration of 125mM

tag: cell line

tag: antibody


title: GM18852_H3K27AC


title: GM19127_H3K4ME3


title: GM18913_H3K4ME3


title: GM18859_H3K4ME1


title: 21 pRx

description:
barcode: TCCTA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCTATCGTATGCCGTCTTCTGCTTG
Library 2

source_name: placebo-treated skin at 3 days after challenge timepoint

value: Male


title: Funiculus Epidermis 1

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Alignments performed using TopHat2 (v2.0.13)
Transcript abundances were calculated as Fragments Per Killobase of transcript per Million mapped reads (FPKMs) using the Cufflinks pipeline (v2.2.1)
DESeq (differential expression of RNA-seq data at the gene level, version 1.16.0) was used to determine the relationships between biological replicates and tissue types.
Of the transcripts uniquely present in individual tissue systems (i.e. detected in any epidermis, cortex, and/or vasculature, but not in the WF, a tissue specificity index (I) was calculated according to the following formula modified from Tong et al. (2013) and Yanai et al. (2005):
The lists of Arabidopsis genes were inputted into the online program AgriGO version 1.2 (http://bioinfo.cau.edu.cn/agriGO/) to identify enriched gene ontology (GO) terms against the Arabidopsis genome. A GO term was considered enriched if the log10 p value ≤ -3 (i.e. p ≤ 0.001).
Genome_build: Brassica napus v4.1
Supplementary_files_format_and_content: Fastq files represent raw sequencing data. Cufflinks file contain normalized counts in FPKMs.

organism: Brassica napus

source_name: Funiculus Epidermis

growth_protocol: Plants were grown in Sunshine Mix #1 (Sun Gro Horticulture, Agawam, MA, USA) under long day conditions (16 h light, –100-150 µmol photons  m–2  s–1) at 22ºC with 50-70% relative humidity. Open flowers were pollinated and siliques allowed to develop for 7 days; this corresponds to the globular stage of seed development.

extract_protocol:
RNA was extracted from LMD-collected tissues using the Ambion RNA Aqueous microkit (Life Technologies, Carlsbad, CA, USA) according to manufacturer's instructions
cDNA was amplified with the Ovation RNA-seq V2 kit (NuGEN, San Carlos, CA, USA). The cDNA libraries were then further refined using the Illumina TruSeqTM RNA Sample Preparation v2 kit (Illumina, San Diego, CA, USA) using the low-throughput protocol according to manufacturer’s instructions

tag: cultivar

value: Topaz

tag: line

value: Epidermis


title: 21 dRx

description:
barcode: TCGAT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCGATTCGTATGCCGTCTTCTGCTTG
Library 2

source_name: peak DTH reaction (3 days after challenge)


title: 21 pRes

description:
barcode: TCGCG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCGCGTCGTATGCCGTCTTCTGCTTG
Library 2

source_name: placebo-treated skin at 14 days after challenge timepoint


title: 20 dRes

description:
barcode: TCCGT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCGTTCGTATGCCGTCTTCTGCTTG
Library 2

source_name: resolving DTH reaction (14 days after challenge)


title: GM18855_H3K27AC


title: GM18913_H3K27AC


title: GM19128_H3K4ME1


title: 20 pRes

description:
barcode: TCCAC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCACTCGTATGCCGTCTTCTGCTTG
Library 2


title: 20 dRx

description:
barcode: TCATC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCATCTCGTATGCCGTCTTCTGCTTG
Library 2


title: 16 dRes

description:
barcode: TTGGT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTGGTTCGTATGCCGTCTTCTGCTTG
Library 1


title: GM19101_H3K27AC


title: GM19140_H3K4ME1


title: 16 pRes

description:
barcode: TTACA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTACATCGTATGCCGTCTTCTGCTTG
Library 1


title: GM19092_H3K4ME1


title: 20 pRx

description:
barcode: TCACT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCACTTCGTATGCCGTCTTCTGCTTG
Library 2


title: GM19128_H3K4ME3


title: GM19092_H3K4ME3


title: 21 dRes

description:
barcode: TCTAG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTAGTCGTATGCCGTCTTCTGCTTG
Library 2


title: GM19140_H3K27AC


title: 16 pRx

description:
barcode: TGATG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TGATGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 16 dRx

description:
barcode: TGTGT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TGTGTTCGTATGCCGTCTTCTGCTTG
Library 1


title: 15 dRes

description:
barcode: TATCA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TATCATCGTATGCCGTCTTCTGCTTG
Library 1


title: GM19206_H3K27AC


title: 15 dRx

description:
barcode: TAGAG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TAGAGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 15 pRes

description:
barcode: TAGGA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TAGGATCGTATGCCGTCTTCTGCTTG
Library 1


title: 14 dRes

description:
barcode: TAACG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TAACGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 14 pRes

description:
barcode: TTAAG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTAAGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 14 dRx

description:
barcode: TCTGA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTGATCGTATGCCGTCTTCTGCTTG
Library 1


title: IPCs_1

city: BEIJING

first: Weijun

last: Guan

address: NO.2 YUANMINGYUAN WEST STREET

department: Institute of Animal Science

country: China

institute: Chinese Academy of Agricultrual Sciences

data_processing:
the adaptors were removed from raw data and calculated the reads count and expression value(TPM:Transcripts per million) for each miRNA
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements

organism: Gallus gallus

source_name: IPCs

growth_protocol: MSCs were cultured in L-DMEM (Gibco, USA) supplemented with 10% (v/v) fetal bovine serum (FBS; Biochrom, Germany).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Preparation protocol was used
total RNA samples were size fractionated by 15% PAGE, and the 16-40 nt fractions were collected.
The 5′ and 3′ RNA adaptors were ligated to the RNA, and RNAs of 64–99 nt were isolated by gel elution and ethanol precipitation.
Polymerase chain reaction (PCR) products were purified and small RNA libraries were sequenced using the Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For differentiation of Insulin-producing cells, MSCs were exposed to 1 μM 5-AZA for 18 h before induction. Then MSCs were cultured in low-glucose DMEM and 10% fetal bovine serum supplemented with 0.1 mM β-mercaptoethanol (Sigma) and 1 mM nonessential amino acids (Gibco). On day 6, medium was supplemented with 15 ng/mL activin A (Sigma). On day 7, 10 mM retinoic acid (Sigma) was added. Two days later, medium was replaced with medium supplemented with 1% B27 (Gibco), 10 ng/mL basic fibroblast growth factor (Peprotech, USA), 10 mM nicotinamide and 1% ITS (Gibco) to further encourage differentiation.

tag: cell type

value: IPC


title: 13 dRes

description:
barcode: TCTAG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTAGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 15 pRx

description:
barcode: TAATA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TAATATCGTATGCCGTCTTCTGCTTG
Library 1


title: MSCs_1

source_name: MSCs

value: MSC


title: 13 pRx

description:
barcode: TCCTA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCTATCGTATGCCGTCTTCTGCTTG
Library 1


title: 13 dRx

description:
barcode: TCGAT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCGATTCGTATGCCGTCTTCTGCTTG
Library 1


title: GM19140_H3K4ME3


title: 13 pRes

description:
barcode: TCGCG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCGCGTCGTATGCCGTCTTCTGCTTG
Library 1


title: 12 dRes

description:
barcode: TCCGT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCGTTCGTATGCCGTCTTCTGCTTG
Library 1

value: Caucasian


title: 12 dRx

description:
barcode: TCATC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCATCTCGTATGCCGTCTTCTGCTTG
Library 1


title: 12 pRes

description:
barcode: TCCAC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCCACTCGTATGCCGTCTTCTGCTTG
Library 1


title: Input_LFD8

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

description: Input control

data_processing:
ChIP-seq, RTA 1.8.70.0 software was used for basecall analysis and aligned to the reference genome was performed at a mismatch error rates =<0.05%. CASAVA1.8.2 (Eland_extended used for mapping)
For visualization in the UCSC genome browser read numbers were counted for each ChIP sample and each Input sample using the IGV (Broadinsitute).
Genome_build: MM9
Supplementary_files_format_and_content: Wig files with tag density for 1kb windows.

organism: Mus musculus

source_name: Low fat diet

growth_protocol: High fat or low fat diet treatment of male C57BL/6J mice

extract_protocol:
Chromatin extraction and specific precipitation using anti -H3 or anti -H3K4me1 antibodies, Input served as control
After application of the Illumina ChIP-seq library preparation kit the sample was subjected to Solexa sequencing (Illumina)

treatment_protocol: Spermatozoa extraction of cauda epididymis, pooling of five animals for each experimental group and the biologic replica

tag: cell types

value: spermatozoa

value: male

tag: strain

tag: chip antibody

value: Input control


title: H3K4me1_HFD4

description: ChIP sample

source_name: High fat diet

value: rabbit H3K4me1 antibody (Abcam, ab8895)


title: 12 pRx

description:
barcode: TCACT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCACTTCGTATGCCGTCTTCTGCTTG
Library 1


title: H3K4me1_LFD5

description: ChIP sample


title: Input_HFD7

description: Input control


title: Input_LFD5

description: Input control


title: H3_LFD8

description: ChIP sample

value: rabbit H3 antibody (Abcam, ab1791)


title: Input_HFD4

description: Input control


title: H3_HFD4

description: ChIP sample


title: GM12878_H3K4me3_1.1

description: FG.cell_H3K4Me3_GM78_std_0.0.interactions.fdr-2.bedpe

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project or imputed using shapeIt and IMPUTE2
For ChIP-seq, ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20, -t 4 and the rest set to defaults)
For ChIP-seq, peaks were called using MACS2 on merged replicates, subsampled to 50 million single reads. Genome-wide signal tracks (bigWig) were generated using wiggler, also on the subsampled data.
For HiC, we aligned reads using HICUP, which aligns reads to an in-silico HindIII digested genome in the hg19 assembly. Our HiC-interaction analysis is based on restriction-fragment level resolution. We  obtained the interaction count for each pair of fragments. To estimate the proximity between two restriction fragments A and B we calculated their co-variance as the fraction of fragments that interact with both A and B, normalized by the number of fragments interacting only with A or only with B. The processed data file contains unique interactions, specified with the following entries: i=id of first interaction fragment, j=id of second interaction fragment, x=number of shared interaction partners between fragment i and j, cor=proportion of interaction partners of i and j that are shared between i and j, pos_i=midpoint of fragment i, pos_j=midpoint of fragment j, pair_id=unique identifier for the interaction. The file contains only interactions with an entry for cor > 0.2
For ChIA-PET, data analysis was carried out using software developed in-house, Mango (paper submitted). PETs were trimmed to remove linker sequences.  In addition, only PETs that have the same linker sequences at both ends are kept for further processing.  The resulting reads were aligned to the genome using the Bowtie software suite(Ben Langmead et al., 2009). Duplicate reads were removed that may be due to PCR duplication. MACS2 was used to call binding peaks, which are subsequently used as anchor regions for the detection of interactions in the next step(Zhang et al., 2008). The probability of observing a PET linking any two peaks was modeled as a function of both genomic distance and the read depth of each peak.  Using this model statistical confidence estimates are assigned to interactions. The resulting P-values are corrected to account for multiple hypothesis testing using the Benjamini-Hochberg method and filtered to a user defined false discovery rate (FDR). The processed files are in bedpe format and contain the following entries: chrom1: chromosome of anchor 1, start1:  start position of anchor 1, end1:  end position of anchor 1, chrom2: chromosome of anchor 2, start2: start position of anchor 2, end2: end position of anchor 1, name: unique ID for each interaction, peak1: # of mid range PETs in anchor1, peak2: # of mid range PETs in anchor2, PETs:  # of PETs linking anchor 1 to anchor 2, distance: # the distance in between anchor 1 to anchor 2, P_IAB_distance:  The probability of observing a PET with the distance that these two anchors are separated by. P_combos_distance: The probability of observing two anchors separated by the distance that these two anchors are separated by. P_IAB_depth:  The probability of observing a PET linking two anchors with the same read depths as these two anchors, P_combos_depth: The probability of observing a pair of loci with the same read depths as these two anchors,  p_binom:  # The binomial probability of observing a single PET linking these two loci, P:  # The actual P-value of the interaction (calculated using the binomial distribution), Q: # The P-value after Benjamini-Hochberg correction (for all possible pairs of loci not just once linked by >= 1 PET).
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler.

extract_protocol:
Cells for GM12878 were crosslinked and chromatin prepared for immunoprecipitation with antibodies against Rad21 and H3K4me3, respectively. Immuno-complexes were pulled down with Protein-G dynabeads, marked with biotin and proximity ligated. Biotinylated fragments were pulled down with Streptavidin Dynabeads and libraries prepared for Illumina sequencing.
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).


title: H3_HFD7

description: ChIP sample


title: H3_LFD5

description: ChIP sample


title: hDIS3_PIN_mut_RNA-seq

city: Warszawa

first: Andrzej

last: Dziembowski

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
Basecalls and demultiplexing were performed using CASAVA version 1.8.2
Adapters and reads shorter than 12 nt. and with quality lower than 20 were removed by cutadapt-1.2.1
Reads were mapped  using RUMv2.05_05. The program requires left and right reads to be the same length, so reads has been striped adequately. The information about known transcripts was supplied to the program. It contained i) Gencode v18 transcript data ii) supplemented to Gencode v18 data tRNA coordinates from tRNA scan program iii) previously published PROMPT data which is a set 3kB upstream regions from the selected 2471 genes iv) snoRNA precursors defined by us for intronic snoRNA as regions from the end of the snoRNA to the beginning of the exon.
Only uniquely mapped reads have been counted.
New transcripts were assembled from deeply sequenced libraries from PIN RNB double mutant using Cufflinks v 2.1.1. Reads from three replicates were assembled separately. We applied all default parameters with exception of '--max-bundle-length' increased to 10^7 and '--max-bundle-frags' increased to 10^7. We used cuffmerge from cufflinks package to merge assemblies from the replicates.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample replicate; bedgraph files were generated using RUMv2.05_05; gtf file was generated using cuffmerge from Cufflinks v 2.1.1.

source_name: HEK293 Flip-In T-Rex cell line

growth_protocol: HEK293 Flp-In T-Rex cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Gibco) and penicillin/streptomycin (Sigma-Aldrich) at 37°C in a 5% CO2.

extract_protocol:
RNA was isolated using TRI-Reagent (Sigma-Aldrich)
Total RNA was treated with Turbo-DNAse (Life Technologies), and then rRNA was removed from the samples using Ribo-Zero Kit (Epicentre), according to the manufacturer's protocols. As a control of experiment performance, external RNA (ERCC RNA Spike-In Mix; Life Technologies) was added to the samples. RNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Expression of exogenous genes was induced by addition of doxycycline at a final concentration of 100ng/ml.

tag: variant

value: DIS3D146N + shRNA


title: hDIS3_RNB_mut_RNA-seq

value: DIS3D487N + shRNA


title: CLIP5B 11A9 rep1

status: Public on Aug 19 2015

city: Cambridge

first: Yang

middle: Eric

last: Guo

state: MA

address: 455 Main St

institute: Whitehead Institute MIT

description: immortalized by herpesvirus saimiri strain A11

data_processing:
The cDNA libraries were sequenced (using 50 cycle runs) by the Yale Stem Cell Center Genomics Core; about 100 to 250 million reads were obtained per library. High-quality raw sequencing reads were collapsed and selected for 7mer (seed nt 2-8) binding sites for miR-HSUR4-5p, miR-HSUR4-3p, miR-HSUR5-5p and miR-HSUR5-5p. Reads containing seed binding sites for the miR-HSURs and total reads were mapped to the reference marmoset genome (caljac 3.2) or HVS genome (NCBI Reference Sequence: NC_001350.1) with Bowtie. A maximum of two mismatches were allowed for the alignment. Uniquely aligned reads were then collapsed according to their genomic coordinates unless those reads mapping to the same coordinate had unique degenerate barcodes. This step is important to eliminate PCR duplications, and the resulting uniquely-mapped reads were referred to as Ago-bound mRNA fragments. Overlapping Ago-bound mRNA fragments were assembled into Ago clusters. Seed binding sites of host miRNAs (i.e. top 100 most highly expressed in Δ2A cells) were searched within miR-HSUR clusters to ensure that these clusters represent viral miRNA, not host miRNA, binding sites. Eliminating PCR duplication and Ago cluster assembly were performed using custom tools on Dr. Robert Darnell’s lab server (Rockefeller University). Ago-bound mRNA fragments and Ago clusters were visualized on the UCSC genome browser (http://genome.ucsc.edu).
Genome_build: calJac3
Supplementary_files_format_and_content: UCSC visualization files for Ago-bound mRNA fragments mapped to both the marmoset and HVS genomes

organism: Callithrix jacchus

source_name: HVS infected marmoset T cells

growth_protocol: T cells from common marmoset (Callithrix jacchus) immortalized by wildtype HVS strain A11 (WT cells) or a deletion mutant lacking HSURs 1 and 2 (Δ2A cells) (Murthy et al., 1989) were cultured as described (Cook et al., 2004).

extract_protocol: Please see PMID:24725595 and PMID:19536157

treatment_protocol: About 5 million Δ2A cells were cross-linked with 600 mJ/cm2 UV light (254 nm) on ice, lysed and digested with RNase A. Ago HITS-CLIP was performed in four replicates using two anti-Ago antibodies (clones 2A8 and 11A9 each in duplicates).

value: T cells, Ago bound RNAs

tag: agent

value: herpesvirus saimiri A11


title: hDIS3_WT_RNA-seq

value: DIS3wild type + shRNA


title: CLIP5C 11A9 rep2


title: hDIS3_PAR-CLIP

description: library strategy: PAR-CLIP

growth_protocol: The stable inducible HEK293 Flp-In T-Rex cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco) and penicillin/streptomycin (Sigma Aldrich) at 37°C in a 5% CO2. Cells were cultured in a Petri dish (145 x 20mm) to approximately 80% confluency.

extract_protocol:
Cells were scraped off and centrifuged at 400 x g for 5 min. at 4°C. 5 plates yielded 1 ml of wet cell pellet, which was sufficient for one experiment. Cell pellets were resuspended in lysis buffer, sonicated and centrifuged at 16000 x g for 15 min at 4°C. To obtain RNA of an appropriate size, cleared extracts were treated with 5U/ml of RNAse T1 (Ambion) for 10 min at 22°C with shaking at 150 rpm and cooled on ice for 5 min. Cell lysates containing RNA protein complexes were then mixed with urea at a final concentration of 0.5M and added to 50µl of freshly washed magnetic beads coated with GFP-trap antibodies and were incubated for 1 hour at 4°C with rotation. Co-immunoprecypitation was followed by 3 washes with high salt wash buffer (HS buffer), one wash with low salt wash buffer (LS buffer) and 1 wash with PNK buffer. Beads were resuspended in 50µl of PNK buffer and treated with 35U alkaline phosphatase (NEB) in the presence of RNAse inhibitor (Ribolock; Thermo Scientific) for 20 min at 37°C with shaking at 1100 rpm in Thermomixer (Eppendorf) and immediately washed twice with PNK buffer and twice with ligation buffer. The resulting short RNA fragments, dephosphorylated at their 3’ ends and still crosslinked to proteins, were ligated with a pre-adenylated linker Ra3 (Illumina). The reaction was done by treating with 400U of T4 RNA Ligase 2, truncated (NEB) overnight at 16°C with shaking at 1100 rpm in 50µl of linker ligation buffer in the presence of 20% PEG 400 (Sigma) and 1mM DTT (Sigma). This step was followed by washing once with HS buffer, twice with LS buffer and once with PNK buffer. RNA molecules cross-linked to immunoprecipitated proteins were then radiolabeled at their 5’ ends. Beads were resuspended in 50µl of PNK buffer with 15U of T4 polynucleotide kinase (NEB) and 5µCi [32P]-γ-ATP and incubated at 37°C with shaking at 1100 rpm for 15 min. Then cold ATP was added and the incubation continued for 15 more minutes. Beads with radiolabeled RNA were then washed 4 times with PNK buffer, resuspended in NuPAGE LDS loading buffer (Life Technologies) and incubated for 10 min at 70°C with shaking 1100 rpm to denaturate and release RNAs-RBPs complexes. Then DTT was added to the final concentration of 65mM. RNAs-protein complexes were resolved by size using 4-12% NuPAGE Bis-Tris gel (Life Technologies) in MOPS SDS running buffer (Invitrogen) and transferred from the gel onto Protran Nitrocellulose membrane (Whatman) by wet-blotting (30V, 1h) in a Invitrogen XCell II Blot Module using NuPAGE transfer buffer (Invitrogen) according to the manufacturer's instructions. Membranes were stained with Ponceau S Red (Sigma-Aldrich; 0.1% in 3% acetic acid) and exposed to a phosphoscreen for 30 min. The RNA-protein complexes migrated above the expected MW of the protein, and appeared as a smeary signal. The area of the membrane in which radioactivity appeared was cut into small slices and placed in 400µl of PK buffer. RNAs were released by proteinase K digestion: Proteinase K (BioLine) was added to the samples at a final concentration of 500µg/ml and was incubated at 37°C at 1100 rpm for 1h. The solution containing RNAs was then mixed with phenol:chloroform and shaken at 1100 rpm. Phases were separated by spinning for 5 min at 16000 x g at room temperature. The aqueous layer was mixed with chloroform (1:1), shaken and centrifuged as described above. RNAs were precipitated overnight in the presence of Glycoblue (Ambion), NaAc, pH=5.2, and ethanol. Finally, RNA molecules were purified using magnetic beads (Agencourt AMPure XP; Beckman Coulter) according to the manufacturer's protocol.
RNA libraries were prepared from the obtained RNA using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer's instructions. A cDNA synthesis primer, reverse PCR primer containing user-defined barcode and pre-adenylated linker Ra3 were from TruSeq Small RNA Sample Preparation Kit (Illumina).

treatment_protocol: Expression of exogenous genes was induced by addition of doxycycline at a final concentration of 100ng/ml. Simultaneously, 4-thiouridine (4-sU) was added to the culture medium at a final concentration of 100µM. The 4-sU molecules incorporate into nascent RNA allowing for subsequent photoreactive nucleoside-labelled RNA-protein cross-linking.  After 24 hours cells were washed with ice-cold PBS, irradiated with 0.12J/cm2 of 365nm UV light (CL-1000 UV Crosslinker; UVP).


title: CLIP1B 2A8 rep1


title: CLIP1D 2A8 rep2


title: Lgr5-EGFP positive cells Replicate 2

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Sample Name: Lgr5SC_2

data_processing:
Paired end reads were aligned to the transcriptome using bwaPaired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
genome build: mm10
processed data files format and content: GSE62270_data_counts_Lgr5SC.txt: Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Randomly extracted ex vivo isolated Lgr5 positive cells

growth_protocol: Crypts were isolated from mouse small intestine, pelleted and mixed with Matrigel (BD). After polymerisation of the Matrigel, growth medium (Advanced DMEM/F12, supplemented with Glutamine, Pennicillin/Streptomycin, Hepes, B27-supplement, N-acetylcysteine, human EGF, RspoI and Noggin) was added. Organoids were passed weekly, with dilution of 1:4.

extract_protocol:
Organoids were dissociated into single-cell suspension using TrypleE enzyme mix. The cells were pelleted and resuspended in F12 medium with 5 to 10% serum. Primary cells were harvested from freshly isolated small intestines. Crypts were released using PBS0/EDTA followed by Trypsin dissociation. Single cells were FACS-sorted into 96-well plates, containing 100ul Trizol reagent and 0.03ul of 1:50.000 diluted Spike-In RNA. Total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2ug glycogen.
Single cells were processed using the previously described CEL-seq technique, with a few alterations. A 4bp random barcode as unique molecular identifier (UMI) was added to the primer in between the cell specific barcode and the poly T stretch. RNA pellets were dissolved in primer mix and incubated for 2 minutes at 70 °C. Libraries were sequenced on an Illumina HighSeq 2500 using 50bp paired end sequencing or Illumina NextSeq 500 using 75bp paired end sequencing.

tag: strain/background

tag: genotype/variation

value: small intestinal crypts


title: 14 pRx

description:
barcode: TCTCC
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TCTCCTCGTATGCCGTCTTCTGCTTG
Library 1

tag: sample id

value: Male

value: Asian

value: Skin


title: Lgr5-EGFP positive cells Replicate 1

description: Sample Name: Lgr5SC_1


title: 5 day YFP positive cells Replicate 5

description: Sample Name: YFP5_5d

data_processing:
Paired end reads were aligned to the transcriptome using bwaPaired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
genome build: mm10
processed data files format and content: GSE62270_data_counts_YFPpos.txt: Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Randomly extracted ex vivo isolated 5 day YFP positive cells

value: Lgr5-positive progeny


title: 5 day YFP positive cells Replicate 2

description: Sample Name: YFP2_5d


title: milk clot_D8_rep2

city: Zurich

first: Alexandra

middle: Chloe

last: Title

state: Zurich

address: Otto-Stern-Weg 7

department: Institute of Molecular Heath Sciences

country: Switzerland

institute: ETH Zurich

data_processing:
Illumina Casava-1.8.2 was used for basecalling.
Adapter sequences were trimmed, and the number of occurrences counted in which the first 20 nucleotides of the raw sequence matched the known Mus musculus miRNA sequences present in miRBase (v. 20).
Genome_build: miRBase v.20
Supplementary_files_format_and_content: Tab-delimited text files for each individual sample listing miRNA name, seed sequence, and number of reads detected.

source_name: milk clot, day 8

extract_protocol:
RNA was extracted from ~50 mg milk clot, using miRNeasy kit (Qiagen), following the supplementary protocol for purification of RNA from serum or plasma.
Total RNA was fractionated and size selection for 18-30 nt of length was performed. This was followed by 5' and 3' adapter ligation and amplification using the TruSeq SBS Kit v3. Reads were sequenced on an Illumina HiSeq 2500 (Fasteris, Geneva, Switzerland).

value: wild type

tag: biological material

value: milk clot

tag: day of lactation


title: Pool-and-split control

data_processing:
Paired end reads were aligned to the transcriptome using bwaPaired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: data_counts_*.txt: Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: 96BC.txt: Tab separated data file containing all cell specific barcodes. First column contains barcode number and second column contains barcode sequence.

source_name: Pool-and-split control of 96 Reg4-positive cells

growth_protocol: Crypts were isolated from mouse small inestine, pelleted and mixed with Matrigel (BD). After polymerisation of the Matrigel, growth medium (Advanced DMEM/F12, supplemented with Glutamine, Pennicillin/Streptomycin, Hepes, B27-supplement, N-acetylcysteine, human EGF, RspoI and Noggin) was added. Organoids were passed weekly, with dilution of 1:4.

value: Reg4-positive cells


title: Control Library

source_name: Control Libnrary with randomly extracted intestinal organoid cells, 5 mESCs and 5 MEFs


title: milk clot_D14_rep1

source_name: milk clot, day 14


title: milk clot_D2_rep1

source_name: milk clot, day 2


title: milk clot_D8_rep1


title: milk clot_D2_rep2


title: milk clot_D14_rep2


title: Wild-type GLU 20min (rep2)

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
Illumina index 13
GLU20Rep2

data_processing:
Library strategy: PAT-Seq
All analysis was carried out using Tail Tools version 0.17, available from https://pypi.python.org/pypi/tail-tools/0.17.
Reads were clipped of poly(A) tail and end adaptor sequence.
Reads were aligned using SHRiMP 2.2.3. Where a read had several equal best alignments, one alignment was chosen at random.
Alignments were extended where there truly was a poly(A) sequence in the reference.
Alignments were assigned to genes. The alignment was allowed to be up to 200 bases downstrand of the annotated transcription end point and still be counted as belonging to that gene. From this counts of the number of reads aligning to each gene were produced, and the average poly(A) tail length observed in reads having a poly(A) tail of length at least 4 (not counting what was present in the reference sequence) was calculated.
Genome_build: sacCer3
Supplementary_files_format_and_content: count.csv: Count matrix - read count aligning to each gene.
Supplementary_files_format_and_content: tail.csv: Tail length matrix - average poly(A) tail length observed in reads having a poly(A) tail of length at least 4. At least 10 reads were required for an average to be given. Note that this is probably an underestimate of the poly(A) tail length, as the poly(A) sequence may extend beyond the length of the read.

organism: Saccharomyces cerevisiae

source_name: Wild-type GLU 20min

growth_protocol: The yeast strains BY4741 and Δccr4::KanMX were grown in rich media (2% peptone, 1% yeast extract and 2% glucose) to an OD600 of 0.8 at 30 °C with shaking.

extract_protocol:
Total RNA was extracted from snap frozen cell pellets by hot-phenol extraction. 1 microgram of this was input into the library preperation.
Library construction was by the PAT-seq approach. Breifly this involves a modified the ePAT approach to tagging adenylated RNA to generate libraries suitable for deep sequencing.  Briefly, adenylated RNA is sequence specifically extended by dNTPs using Klenow polymerase and an annealed DNA anchor oligonucleotide. This takes advantage of the native function of DNA polymerase to extend an RNA primer from a DNA template in second strand synthesis. Importantly, any unwanted priming to internal poly(A)-tracts in RNA is avoided by a requirement for 3’ extension in subsequent fragment selection and reverse transcription. No ribosome depletion is necessary. Here, the anchor sequence was compatible with the Illumina index primers and included a 5’ biotin moiety to facilitate handling. In a second step, the 3’ tagged RNA was subject to limited fragmentation by RNase T1. This cleaves RNA after G-residues and ensures that cleavage is only possible within the body of the RNA, not the poly(A)-tract or the DNA sequence of the extended tag. The fragmented RNA was 5’ phosphorylated to allow RNA Ligase 2 mediated ligation of an Illumina compatible splinted-linker to the RNA fragments. Reverse transcription was primed from the anchor sequence. Note: All manipulations after limited fragmentation were performed in association with streptavidin magnetic beads. The cDNA PAT-seq libraries was eluted from beads, size-selected by Urea PAGE and amplified with primers that introduce the features for directional Illumina sequencing and indexing. In samples analysed here, the window of selection was between 120-300 bases. This size range was selected to allow for ≥ 25 bases of 3’UTR sequence to map reads to the genome, the an average yeast poly(A)-tail of ~25 bases (maximum ~90 bases), the majority of reads would contain heterogeneous 5’ sequence of sufficient length to map uniquely to the yeast genome. Note: all reads run in 5’ to 3’ direction from unique sequence into a variable length of poly(A) homopolymers. This means that color balance is preserved and that any low fidelity within the homopolymers is limited to the end of the read.
Cluster Generation: 9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
Sequencing chemistry: 1 x 100bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: To induce a carbon source shift, BY4741 cells were grown overnight in 100 ml rich glycerol/ethanol media (2% peptone, 1% yeast extract, 3% glycerol and 2% ethanol) to an OD600 of 0.8 at 30 °C with shaking. At the start of the experiment 10 ml of culture was harvested, washed in 1ml of icecold dH2O and snap frozen. To induce GAL gene expression 40% galactose was add the culture to a final concentration of 2%. After 10 minutes, 10 ml of culture was harvested and 40% glucose was added to a final concentration of 2%. Additional 10 ml samples were harvested after 10 and 20 minutes of growth in the presence of glucose.

tag: strain backround


title: Wild-type GLU 10min (rep1)

description:
Illumina index 10
GLU10Rep1

source_name: Wild-type GLU 10min


title: Wild-type GLU 20min (rep1)

description:
Illumina index 12
GLU20Rep1


title: 5 day YFP positive cells Replicate 1

description: Sample Name: YFP1_5d

tag: tissue


title: Wild-type GLU 10min (rep2)

description:
Illumina index 11
GLU10Rep2


title: Wild-type GAL (rep1)

description:
Illumina index 8
GALRep1

source_name: Wild-type GAL


title: Wild-type GAL (rep2)

description:
Illumina index 9
GALRep2


title: Lgr5 positive cells Replicate 1 Lane 4

source_name: Randomly extracted Lgr5-positive intestinal cells


title: 5 day YFP positive cells Replicate 4

description: Sample Name: YFP4_5d


title: Reg4-positive cells, Replicate 2, Sample I to III, Lane 2

description: Sample name: Reg8

data_processing:
Paired-end reads obtained by CEL-Seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell-specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics, we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: GSE62270_data_counts_Whole_Organoid_Replicate_1.txt: Processed data for Whole Organoid Replicate 1 Samples (Sample names: Organoid1 to 6). Tab-separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: GSE62270_data_counts_Whole_Organoid_Replicate_2.txt: Processed data for Whole Organoid Replicate 2 (Sample names: Organoid7 to 14). Tab-separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: GSE62270_data_counts_Reg4_positive_cells_Replicate_1.txt: Processed data for Reg4-positive cells Replicate 1 (Sample names: Reg1 to 6). Tab-separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: GSE62270_data_counts_Reg4_positive_cells_Replicate_2.txt: Processed data for Reg4-positive cells Replicate 2 (Sample names: Reg7 to 8). Tab-separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the number of the experiment (the 96-well plate cells were sorted into) and the cell barcode number, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: 96BC.txt: Tab-separated data file containing all cell-specific barcodes. First column contains barcode number and second column contains barcode sequence.

source_name: Randomly extracted Reg4-positive intestinal cells

value: single Reg4-positive intestinal cell


title: Dccr4 cells Log phase (rep3)

description:
Illumina index 5
deltaccr4logRep3

source_name: Dccr4 cells Log phase

value: BY4741 (ccr4::kanMX)


title: Wild-type YPEG (rep1)

description:
Illumina index 6
YPEGRep1

source_name: Wild-type YPEG


title: Lgr5 positive cells Replicate 1 Lane 3


title: Lgr5 positive cells Replicate 1 Lane 2


title: Dccr4 cells Log phase (rep2)

description:
Illumina index 4
deltaccr4logRep2


title: 5 day YFP positive cells Replicate 3

description: Sample Name: YFP3_5d


title: Lgr5 positive cells Replicate 1 Lane 1


title: hDIS3_PIN_RNB_mut_RNA-seq

value: DIS3D146N D487N + shRNA


title: Reg4-positive cells, Replicate 2, Sample I to III, Lane 1

description: Sample name: Reg7


title: Whole Organoid, Replicate 2, Sample IV, Lane 2

description: Sample name: Organoid14

source_name: Randomly extracted cells from whole intestinal organoids

value: wild-type

value: single cell from whole intestinal organoids


title: Dccr4 cells Log phase (rep1)

description:
Illumina index 3
deltaccr4logRep1


title: 7NoD8-25_009

city: new haven

first: James

last: McGrath

state: CT

address: 333 cedar st

department: comparative Medicine

institute: Yale University

description: cl7 (clone7) does not contain the Ctcfl transgene and Doxycycline not present in culture medium

data_processing:
RNA’s were sequenced on an Illumina HiSeq 2000 sequencing system generating 75bp single-end strand-specific reads.
The first 6 and last 2 nucleotides in each read were trimmed using the FASTX toolkit to remove low quality bases.
Trimmed reads were mapped to the mouse reference genome (mm10) with a known transcriptome index (UCSC Known Gene annotation) using Tophat v2.0.8
Differential gene expression analysis was performed with Cufflinks v2.1.1
Pathway analysis was performed using the DAVID program v6.7

source_name: Embryonic stem cells

growth_protocol: ES cells for RNA-Seq studies were cultured in ES medium on MEF’s, and replated in 6 cm tissue culture dishes (Falcon) off of MEF’s for 48 hrs, with and without doxycycline (2µg/ml; Sigma, St Louis MO).

extract_protocol:
Two biological replicates were performed for each of 4 samples (i.e., with and without transgene; with and without doxycycline). Total RNA was isolated with Trizol reagent (Invitrogen, Carlsbad, CA) and chloroform extraction. RNA was precipitated with isopropyl alcohol and washed with 75% ethanol and total RNA was further purified with a Qiagen RNeasy minikit and DNase I digestion (Qiagen Inc. Valencia, CA, USA).
Flow Cell Preparation and Sequencing: Sample concentrations were normalized to 2 nM and loaded onto Illumina version 3 flow cells at a concentration that yields 170-200 million passing filter clusters per lane. Samples were sequenced using 75bp single-end sequencing on an Illumina HiSeq 2000 according to Illumina protocols. The 6 bp index was read during an additional sequencing read that automatically follows the completion of read 1.  Data generated during the sequencing run was simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor sequencing quality in real time.
https://www.neb.com/protocols/2012/09/27/library-preparation-e7330?device=pdf

treatment_protocol: With and without doxycycline

value: mixed

value: Embryonic stem cells

tag: transgene


title: 7NoD8-21_004


title: 7Dox8-25_012

description: cl7 (clone7) does not contain the Ctcfl transgene with  doxycycline present in culture medium


title: Reg4-positive cells, Replicate 1, Sample III, Lane 2

description: Sample name: Reg6


title: 6NoD8-25_006

description: cl6 (clone 6) contains the Ctcfl transgene and Doxycycline not present in culture medium

value: Ctcfl


title: 6Dox8-21_002

description: cl6 (clone 6) contains the Ctcfl transgene with doxycycline present in culture medium


title: Wild-type Log phase (rep2)

description:
Illumina index 2
logRep2

source_name: Wild-type Log phase


title: Whole Organoid, Replicate 2, Sample II, Lane 1

description: Sample name: Organoid9


title: Whole Organoid, Replicate 2, Sample III, Lane 2

description: Sample name: Organoid12


title: Whole Organoid, Replicate 2, Sample I, Lane 1

description: Sample name: Organoid7


title: Whole Organoid, Replicate 1, Sample III, Lane 2

description: Sample name: Organoid6


title: Whole Organoid, Replicate 2, Sample II, Lane 2

description: Sample name: Organoid10


title: Reg4-positive cells, Replicate 1, Sample II, Lane 2

description: Sample name: Reg4


title: Reg4-positive cells, Replicate 1, Sample II, Lane 1

description: Sample name: Reg3


title: Wild-type YPEG (rep2)

description:
Illumina index 7
YPEGRep2


title: Reg4-positive cells, Replicate 1, Sample I, Lane 1

description: Sample name: Reg1


title: 7Dox8-21_005


title: Reg4-positive cells, Replicate 1, Sample III, Lane 1

description: Sample name: Reg5


title: Whole Organoid, Replicate 1, Sample III, Lane 1

description: Sample name: Organoid5


title: Whole Organoid, Replicate 1, Sample II, Lane 2

description: Sample name: Organoid4


title: Wild-type Log phase (rep1)

description:
Illumina index 1
logRep1


title: 6NoD8-21_001


title: 6Dox8-25_007


title: Whole Organoid, Replicate 2, Sample III, Lane 1

description: Sample name: Organoid11


title: Reg4-positive cells, Replicate 1, Sample I, Lane 2

description: Sample name: Reg2


title: Whole Organoid, Replicate 1, Sample I, Lane 2

description: Sample name: Organoid2


title: Whole funiculus 1

source_name: Whole funiculus

value: Topaz

value: Whole funiculus


title: small RNAs from Drosophila melanogaster 0-2h twin12209 mutant embryos

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

country: France

institute: Institut de Genetique Humaine - CNRS

description: RNA-seq

data_processing:
Sequenced reads were stripped of the adapter (TGGAATTCTCGGGTGCCAAG) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch. Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.           Supplementary_files_format_and_content: table of sequences matching release 5 of the genome 100%; indicating sequence and read count.
For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.
For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads.
Genome_build: dm5
Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)

organism: Drosophila melanogaster

source_name: embryos

extract_protocol: RNA was prepared using Trizol (Invitrogen)

treatment_protocol: small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel.

tag: Stage

value: 0-2h embryos

tag: genotype


title: Whole Organoid, Replicate 2, Sample I, Lane 2

description: Sample name: Organoid8

value: small intestinal crypts


title: Whole Organoid, Replicate 1, Sample I, Lane 1

description: Sample name: Organoid1


title: Whole Organoid, Replicate 2, Sample IV, Lane 1

description: Sample name: Organoid13


title: E13.5_Sox9CFP

city: Chicago

first: Danielle

last: Maatouk

address: 303 E. Superior St., Lurie 7-250

institute: Northwestern University

description: Pre-Sertoli cells were collected from the testes of E13.5 mouse embryos (Sox9 Heterozygous male embryos conceived from transgenic homozygous Sox9-ECFP C57BL/6J male mice mated to female CD-1 (Charles River) females)

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Sequenced reads were trimmed to the first 20bp to remove adaptor sequence using custom scripts, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using BWA version 0.6.1-r104 with default indexing (index -a bwtsw) and aln parameters (aln -t 8) to create alignment SAI files.
SAM files were created from the SAI files using bwa samse with default parameters, then filtered for alignments with greater than 4 mismatches using custom scripts.
The SAM files (after filtering for mismatches >4) were converted to BAM format using "samtools view", then sorted via chromosome using "samtools sort", then converted to BED format using "bedtools bamtobed".
Sharp sequence pileups introduced by PCR amplification artifacts or potential misalignments were filtered out to reflect a maximum acceptable read count for a peaks region based on a Poisson distribution.
Genome_build: mm9
Supplementary_files_format_and_content: F-seq (Boyle AP, et al. Bioinformatics 2008; 24(21):2537-2538) was used to generate both base-pair signal Parzen score (wig format - later converted to bigWig) and discrete peaks (bed format) corresponding to DNaseI hypersensitive (DHS) sites.   Final aligned sequences were

source_name: PreSertoli cells

growth_protocol: See SAMPLE descriptions.

extract_protocol:
Mouse tissues (kidney, liver, heart, and brain) were collected from adult B6 mice,flash frozen and then pulverized before use. FACS sorted pre-Sertoli cells were pelleted and resuspended in 250uL of Recovery-Cell Culture Freezing Media (Gibco) and slowly frozen to -80°C before use. Mouse ES and fibroblast cell lines were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations.  All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106) with few exceptions.  Incubation of FACS purified pre-Sertoli cells with low concentrations of exogenous DNaseI enzyme was found to severely degrade the DNA; therefore DNase digestion was performed using endogenous nucleases. Briefly, cells were lysed and incubated at 37°C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).

value: Testes

tag: developmental stage

value: E13.5 embryos


title: Bmal1_kd_ribo_profile_CT22_rep2

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
In order to knockdown Bmal1 expression, 3.0x10^4 cells were seeded per 35 mm plate for the purposes of monitoring. For collection, 5.6x10^5 cells were seeded per 15 cm plate. These cells were grown overnight in complete DMEM without antibiotics, and transfected using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s protocols. A mixture of siRNAs that target Bmal1 (siBMAL1-1 thru siBMAL1-5) was utilized, and 12 picomoles of this mixture was added to each 35 mm plate, and 120 picomoles of siRNA mixture was added to each 15 cm plate. Cells were then synchronized with dexamethasone following transfection as described in the treatment protocol.
library selection: Ribosome profiling (Ribo-seq)

data_processing:
Raw data was aligned to GRCh37/hg19 genome using STAR (v2.3.0e) with default parameters.
RPF reads mapping to gene coding sequences (CDSs) were quantified by running HTSeq (v0.5.4p1) in stranded mode, with default parameters. To assign a single CDS to each gene, the isoforms with the longest CDSs were used for quantification. RNA-seq reads were similarly quantified across the entire length of the transcript. Gene models were taken from the UCSC Known Genes annotation.
Read counts were normalized with DESeq2, using default parameters.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt files contain normalized, gene-level read counts

source_name: U2-OS Cells

growth_protocol: A U2OS human osteosarcoma cell line expressing luciferase under the control of the Per2 promoter was used. Cells were maintained in a humidified 37˚C incubator at 5% CO2 in DMEM (Life Technologies), supplemented with 10% FBS, 4 mM L-glutamine, 50 units/mL penicillin, and 50 μg/mL streptomycin. 2.25x10^6 cells were seeded per 15 cm plate. These cells were grown overnight.

extract_protocol:
Cells in 15 cm plates were treated with 100 μg/mL cycloheximide for 3 minutes at 36˚C, 24.5 hours post-synchronization when luciferase levels were at their nadir. Cells were 80% confluent at the time of collection. All subsequent steps were done on ice. Spent media was aspirated from the plates and the cells were washed with 10 mL of cold PBS before treatment with 790 μL of cold lysis buffer [20 mM Tris, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 1% Triton X-100, and 0.02 units/μL Turbo DNase]. Cells were recovered from the plate using a cell scraper, triturated with a 1.0 mL pipette, and incubated on ice for 10 minutes with occasional mixing. The lysate was then triturated 10 times through a 26 gauge needle and centrifuged at 20,000 g for 10 minutes at 4˚C. Cleared lysate was flash frozen in a dry ice/ethanol bath before storage at -80˚C. Collection of cells was repeated every 2 hours for an entire 24 hour time course.
Frozen cleared lysate was thawed on ice, and RNase I (Life Technologies) was added to 400 μL of cleared lysate to a final activity of 0.75 units/μL. This mixture was incubated for 45 minutes at room temperature with gentle mixing on a tube rotator, and the nuclease was subsequently inactivated by the addition of 20 μL of SUPERase•In (Life Technologies). The digestion was carefully layered onto a 0.9 mL sucrose cushion [20 mM Tris, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 20 units/mL SUPERase•In, 34% sucrose, w/v] in an 11  34 mm polycarbonate ultracentrifuge tube (Beckman Coulter), and centrifuged for 4 hours at 78,000 rpm in a prechilled TLA-100.2 rotor. The ribosome pellet was resuspended in 700 μL of QIAzol lysis reagent and processed according to the Qiagen miRNeasy Quick-Start Protocol. RNA was then isopropanol precipitated from the elution, and resuspended in 5 μL of 10 mM Tris, pH 8.0. RNA samples were run on a 15% TBE-Urea gel (Life Technologies), stained with SYBR Gold, and visualized with a Dark Reader blue light transilluminator (Clare Chemical Research). The 26-34 nt region demarcated by the size selection RNA oligos NI-NI-19 and NI-NI-20 was excised from the gel, and the RPFs were extracted and isopropanol precipitated from the gel fragment. Library generation was performed as described previously, with some modifications. Briefly, RPFs were resuspended in 10 μL of 10 mM Tris, pH 8.0, and dephosphorylated with T4 polynucleotide kinase (New England Biolabs) in the presence of 20 units of SUPERase•In in a final volume of 40 μL. The reaction was incubated for 1 hour at 37˚C, and inactivated for 10 minutes at 70˚C. RNAs were isopropanol precipitated, and ligated to the preadenylated and 3′ blocked cloning Linker-1 (IDT) by incubation with truncated T4 RNA ligase 2 (New England Biolabs) for 2.5 hours at room temperature. Ligated RPFs were isopropanol precipitated and gel purified from a 15% TBE-Urea gel before being reverse transcribed with SuperScript III (Life Technologies), using primer NI-NI-9. The RNA template was then removed by alkaline hydrolysis, and the reverse transcription products were isopropanol precipitated and gel purified. DNA fragments were circularized with CircLigase (Epicentre) in a final volume of 20 μL and reverse transcription products corresponding to rRNAs were removed by subtractive hybridization using MyOne Streptavidin C1 Dynabeads (Life Technologies) and the three biotinylated DNA oligos NI-NI-21, NI-NI-23, and NI-NI-24, which are complementary to the rRNAs with accession numbers NR_003285.2:124-155, NR_003287.1:182-213, and NR_003287.1:1435-1461, respectively. The resulting DNA was precipitated and used as a template for PCR amplification with Phusion polymerase (New England Biolabs) using NI-NI-2 and one of the index amplification primers CJ-NI-4, CJ-NI-6, CJ-NI-12, or CJ-NI-23.

treatment_protocol: To synchronize cells grown overnight, their media was replaced with phenol red free DMEM containing 0.1 mM luciferin and 0.1 μM dexamethasone. Plates were then sealed with sterile vacuum grease (Corning) and incubated in a 36˚C, non-humidified incubator at 5% CO2

tag: cell type

value: osteosarcoma

tag: cell line

tag: replicate

tag: sirna treatment

value: Bmal1 siRNA


title: Bmal1_kd_ribo_profile_CT22_rep1


title: Bmal1_kd_ribo_profile_CT04_rep2


title: Bmal1_kd_ribo_profile_CT18_rep2


title: Bmal1_kd_ribo_profile_CT20_rep2


title: Bmal1_kd_ribo_profile_CT16_rep2


title: Bmal1_kd_ribo_profile_CT12_rep2


title: Bmal1_kd_ribo_profile_CT06_rep2


title: Bmal1_kd_ribo_profile_CT16_rep1


title: Bmal1_kd_ribo_profile_CT14_rep2


title: Bmal1_kd_ribo_profile_CT10_rep2


title: Bmal1_kd_ribo_profile_CT08_rep2


title: Whole Organoid, Replicate 1, Sample II, Lane 1

description: Sample name: Organoid3


title: Individual-nucleotide resolution CLIP and HTS with GFP-Aub in D. melanogaster 0-2h WT embryos- replicate 1

description: iCLIP-Seq as described by König et al. (König et al; Nat Struct Mol Biol 17:909-915, 2010)

data_processing:
.fastq files were adapter 'CACTCGGGCACCAAGGACAGGAATG' clipped using cutadapt. After adapter removal, the first 4 bases (corresponding to random barcode) were trimmed and remaining sequences were mapped on D.melanogaster genome allowing up to 2 mismatches for reads mapping to a single genome location and perfect match for reads mapping to more than one location.                                                               Reads with identical random barcode, strand, identical 5’ and 3’ end coordinates were collapsed.
For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.
For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads.
Genome_build: dm5
Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)

extract_protocol: RNA-protein complexes were transferred to nitrocellulose. After cutting out the region of nitrocellulose containing RNA-Aub complexes, RNAs were removed from the membrane by Proteinase K digestion. The RNAs were reverse transcribed using oligonucleotides that contained two adapter regions separated by a restriction site and a barcode region containing a 3 nt experiment-specific barcode and a 4 nt random barcode to mark individual cDNA molecules. cDNA size selection, circularization and linearization was performed as described earlier (Konig et al., 2010, 2011). Linearized cDNAs were then PCR-amplified using primers complementary to the adaptor regions.

treatment_protocol: embryos were UV-irradiated, six times five minutes at 254 nm in a BIO-LINK

value: UASp-GFP-Aub/  nos-Gal4

tag: antibody

value: rabbit polyclonal anti-GFP (A-6455, Invitrogen)


title: Bmal1_kd_ribo_profile_CT12_rep1


title: Bmal1_kd_ribo_profile_CT10_rep1


title: Bmal1_kd_ribo_profile_CT18_rep1


title: Bmal1_kd_ribo_profile_CT00_rep2


title: small RNAs in complex with Smaug from Drosophila melanogaster 0-2h embryos

description: RIP-seq

data_processing:
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAAT) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch. Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.           Supplementary_files_format_and_content: table of sequences matching release 5 of the genome; indicating sequence and read count.
For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.
For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads.
Genome_build: dm5
Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)

treatment_protocol: after RNA extraction from Smaug immunoprecipitates, small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel.

value: Smaug IP

value: Guinea pig anti-Smaug


title: Bmal1_kd_ribo_profile_CT08_rep1


title: Individual-nucleotide resolution CLIP and HTS with GFP-Aub in D. melanogaster 0-2h oskar54 embryos

treatment_protocol: embryos were UV-irradiated, three times five minutes at 254 nm in a BIO-LINK

value: osk54 UASp-GFP-Aub/  osk54 nos-Gal4


title: Bmal1_kd_ribo_profile_CT02_rep2


title: Bmal1_kd_ribo_profile_CT20_rep1


title: Individual-nucleotide resolution CLIP and HTS with GFP- AubAA (PAZ domain mutant) in D. melanogaster 0-2h WT embryos

value: UASp-GFP-AubAA/+;  nos-Gal4/+


title: hen1-8 mee44 smallRNAseq

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Illumina Casava software used for basecalling.
The raw reads of small RNAs were processed by PERL scripts built in house. Briefly, the raw reads were screened with Illumina’s quality control filter. The reads that passed the filter were separated into different bins according to their barcodes (indexes). The adaptor was trimmed for each read. Reads that match known rRNAs, tRNAs, snRNAs, and snoRNAs were removed. Reads of 20–24 nt were selected as the raw small RNA sequences.
small RNA reads were then mapped to the TAIR10 Arabidopsis genome using Bowtie.any small RNA read that could not be perfectly mapped back to the genome was trimmed one nucleotide at a time from the 3’ end until the remaining sequence was perfectly mapped to the genome. The trimmed 3’ sequence was designated as the “tail” whereas the longest 5’ genome-mapped component (the “head”) was compared to all annotated miRNAs in miRBase to ascertain from which miRNAs they were derived.
Genome_build: TAIR10
Supplementary_files_format_and_content: the first column: read sequence; the second column: read count

organism: Arabidopsis thaliana

source_name: hen1-8 mee44

growth_protocol: Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C.

extract_protocol:
Small RNAs of a desired size range (15–40 nt) were fractionated from 25ug total RNAs by 15% polyacrylamide gel electrophoresis. These small RNAs were sequentially ligated with the 3' and 5' adapters using the Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. A reverse transcription reaction followed by a low cycle PCR was performed to obtain sufficient amounts of products for deep sequencing.
Library was constructed with the Illumina TruSeq-small RNA sample preparation kit per manufacturer’s instructions (Illumina). In brief, gel-purified small RNAs were ligated sequentially to 3’ and 5’ adaptors. Following reverse transcription, PCR amplification of the cDNA resulted in the small RNA library, which was gel-purified and subjected to high throughput sequencing

tag: ecotype

value: Columbia

value: inflorescences

value: hen1-8 mee44


title: hen1-8 heso1-1 smallRNAseq

source_name: hen1-8 heso1-1

value: hen1-8 heso1-1


title: hen1-8 ntp7-1 smallRNAseq

source_name: hen1-8 ntp7-1

value: hen1-8 ntp7-1


title: hen1-8 ntp10-1 smallRNAseq


title: small RNAs from Drosophila melanogaster 0-2h wildtype embryos 2

description: RNA-seq

data_processing:
Sequenced reads were stripped of the adapter (TGGAATTCTCGGGTGCCAAG) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch. Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.           Supplementary_files_format_and_content: table of sequences matching release 5 of the genome with up to 1mm; indicating sequence and read count.
For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.
For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads.
Genome_build: dm5
Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)

value: 0-2h embryos

value: wild type, w1118                                (control of twin12209)


title: small RNAs from Drosophila melanogaster 0-2h wildtype embryos 1

description: RNA-seq

data_processing:
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch. Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.            Supplementary_files_format_and_content: table of sequences matching release 5 of the genome 100%; indicating sequence and read count.
For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs.
For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads.
Genome_build: dm5
Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)

value: wild type, Charolles


title: hen1-8 ntp8-1 smallRNAseq

source_name: hen1-8 ntp8-1

value: hen1-8 ntp8-1


title: Bmal1_kd_ribo_profile_CT14_rep1

value: osteosarcoma


title: WT_ribo_profile_CT22_rep2

description: library selection: Ribosome profiling (Ribo-seq)


title: Bmal1_kd_ribo_profile_CT02_rep1

value: Bmal1 siRNA


title: Bmal1_kd_ribo_profile_CT06_rep1


title: Bmal1_kd_ribo_profile_CT04_rep1


title: Individual-nucleotide resolution CLIP and HTS with GFP-Aub in D. melanogaster 0-2h WT embryos- replicate 3

value: UASp-GFP-Aub/  nos-Gal4


title: Bmal1_kd_ribo_profile_CT00_rep1


title: hen1-8 ntp6-1 smallRNAseq

source_name: hen1-8 ntp6-1

value: hen1-8 ntp6-1


title: hen1-8 smallRNAseq r2


title: Individual-nucleotide resolution CLIP and HTS with GFP-Aub in D. melanogaster 0-2h WT embryos- replicate 2

value: rabbit polyclonal anti-GFP (A-6455, Invitrogen)


title: WT_ribo_profile_CT20_rep2


title: WT_ribo_profile_CT16_rep2


title: hen1-8 ntp5-1 smallRNAseq

source_name: hen1-8 ntp5-1

value: hen1-8 ntp5-1


title: hen1-8 urt1-1 smallRNAseq

source_name: hen1-8 urt1-1

value: hen1-8 urt1-1


title: WT_ribo_profile_CT14_rep2


title: hen1-8 ntp2-1 smallRNAseq

source_name: hen1-8 ntp2-1

value: hen1-8 ntp2-1


title: WT_ribo_profile_CT12_rep2


title: WT_ribo_profile_CT10_rep2


title: WT_ribo_profile_CT08_rep2


title: WT_ribo_profile_CT04_rep2


title: WT_ribo_profile_CT00_rep2


title: WT_ribo_profile_CT20_rep1


title: WT_ribo_profile_CT02_rep2


title: WT_ribo_profile_CT06_rep2


title: WT_ribo_profile_CT18_rep1


title: WT_ribo_profile_CT14_rep1


title: WT_ribo_profile_CT16_rep1


title: WT_ribo_profile_CT22_rep1


title: hen1-8 ntp4-1 smallRNAseq

source_name: hen1-8 ntp4-1

value: Columbia

value: hen1-8 ntp4-1


title: WT_ribo_profile_CT18_rep2


title: WT_ribo_profile_CT12_rep1


title: WT_ribo_profile_CT10_rep1


title: hen1-8 smallRNAseq

value: inflorescences


title: WT_ribo_profile_CT00_rep1


title: WT_ribo_profile_CT04_rep1


title: WT_ribo_profile_CT02_rep1


title: Bmal1_kd_total_RNA_CT22_rep2

description: In order to knockdown Bmal1 expression, 3.0x10^4 cells were seeded per 35 mm plate for the purposes of monitoring. For collection, 5.6x10^5 cells were seeded per 15 cm plate. These cells were grown overnight in complete DMEM without antibiotics, and transfected using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s protocols. A mixture of siRNAs that target Bmal1 (siBMAL1-1 thru siBMAL1-5) was utilized, and 12 picomoles of this mixture was added to each 35 mm plate, and 120 picomoles of siRNA mixture was added to each 15 cm plate. Cells were then synchronized with dexamethasone following transfection as described in the treatment protocol.

extract_protocol:
Cells in 15 cm plates were treated with 100 μg/mL cycloheximide for 3 minutes at 36˚C, 24.5 hours post-synchronization when luciferase levels were at their nadir. Cells were 80% confluent at the time of collection. All subsequent steps were done on ice. Spent media was aspirated from the plates and the cells were washed with 10 mL of cold PBS before treatment with 790 μL of cold lysis buffer [20 mM Tris, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 1% Triton X-100, and 0.02 units/μL Turbo DNase]. Cells were recovered from the plate using a cell scraper, triturated with a 1.0 mL pipette, and incubated on ice for 10 minutes with occasional mixing. The lysate was then triturated 10 times through a 26 gauge needle and centrifuged at 20,000 g for 10 minutes at 4˚C. 150 μL of the cleared lysate was added to 700 μL of QIAzol lysis reagent and stored at -80˚C. Collection of cells was repeated every 2 hours for an entire 24 hour time course. Cleared lysate frozen with QIAzol lysis reagent was processed according to the Qiagen miRNeasy Quick-Start Protocol.
RNA integrity was verified by Bioanalyzer (Agilent Technologies) before library preparation as described according to the TruSeq Stranded Total RNA Sample Prep Kit (Illumina).


title: WT_ribo_profile_CT06_rep1


title: Bmal1_kd_total_RNA_CT20_rep2


title: Bmal1_kd_total_RNA_CT18_rep2


title: Bmal1_kd_total_RNA_CT16_rep2


title: Bmal1_kd_total_RNA_CT14_rep2


title: Bmal1_kd_total_RNA_CT12_rep2


title: Bmal1_kd_total_RNA_CT08_rep2


title: Bmal1_kd_total_RNA_CT10_rep2


title: Bmal1_kd_total_RNA_CT04_rep2


title: Bmal1_kd_total_RNA_CT06_rep2


title: Bmal1_kd_total_RNA_CT02_rep2


title: Bmal1_kd_total_RNA_CT00_rep2


title: Bmal1_kd_total_RNA_CT22_rep1


title: Bmal1_kd_total_RNA_CT20_rep1


title: WT_ribo_profile_CT08_rep1


title: Bmal1_kd_total_RNA_CT18_rep1


title: Bmal1_kd_total_RNA_CT14_rep1


title: Bmal1_kd_total_RNA_CT12_rep1


title: Bmal1_kd_total_RNA_CT16_rep1


title: Bmal1_kd_total_RNA_CT10_rep1


title: Bmal1_kd_total_RNA_CT08_rep1


title: WT_total_RNA_CT22_rep2


title: Bmal1_kd_total_RNA_CT06_rep1


title: Bmal1_kd_total_RNA_CT00_rep1


title: Bmal1_kd_total_RNA_CT02_rep1


title: WT_total_RNA_CT20_rep2


title: WT_total_RNA_CT08_rep2


title: WT_total_RNA_CT04_rep2


title: WT_total_RNA_CT06_rep2


title: OIS input replicate 1

city: Bronx

first: Matthew

middle: Jon

last: Gamble

address: 1300 Morris Park Ave / Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using ELAND  version 1.7.0
significant genomic regions were identified by comparing matched ChIP and input samples with ISOR version 0.4 with the following settings: segmentation_pval(0.01), gap_length(1000)
Genome_build: hg19
Supplementary_files_format_and_content: gappedPeak files are as described (http://genome.ucsc.edu/FAQ/FAQformat.html#format13) the signalValues represent the log2 odds ratio of a segment and the pValue (-log10) represents the significance of the enrichment or depletion. The gaps are regions of at least 1kb with no mapped reads from either the input or ChIP samples; bedGraph files for segments where gaps have been subtracted. The scores represent the log2 odds ratio of each segment.

source_name: IMR90 primary lung fibroblasts_input

growth_protocol: IMR90 (ATCC, CCL-186) primary human fetal lung fibroblast cells were cultured in MEM supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were cross-linked with 1% formaldehyde in PBS at room temperature for 10 min, then quenched in 125 mM glycine in PBS at room temperature for 5 min.  The cells were washed by cold PBS once and were collected by centrifugation and sonication in lysis buffer (50mM Tris pH 7.9, 10 mM EDTA, 1% SDS, 1x protease inhibitor cocktail and 1mM DTT) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation 14,000rpm for 10min at 4 °C, and 20 µl supernatant was used as input for quantitation, the remaining supernatant was diluted 10-fold in dilution buffer (20 mM Tris pH 7.9, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 1X protease inhibitor cocktail and 1mM DTT), and pre-cleared by incubation with protein A-agarose beads at 4°C for 3hr. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions at 4°C overnight with an antibody against macroH2A1, then incubated with protein A-agarose beads at 4°C for 2hr. No antibody negative controls were included for every ChIP experiment. The immuneprecipitated DNA was cleared of protein by digestion with 0.4mg/ml glycogen and proteinase K (2.5U/ml, Roche) in Txn stop buffer (20 mM EDTA, 0.2 M Nacl and 1% SDS) at 37°C for 1 hour. The DNA was then extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and ethanol precipitated.
DNA fragments from ChIP reactions were repaired using T4 DNA Polymerase (NEB) and T4 DNA Polynucleotide kinase (NEB) in T4 DNA ligase buffer (NEB). Next, dA ends were generated by employing Klenow Fragment (3’->5’ exo-, NEB), in Buffer 2 (NEB). Adapter ligation reactions were then set up using indexed adapters and Quick Ligase (NEB). Ligation-mediated PCR was then performed using Phusion High-Fidelity DNA Polymerase (NEB). The libraries were visualized on 2% E-Gel® General Purpose Agarose Gels (Invitrogen). Sequencing for the macroH2A1 ChIPs were performed on an Illumina HiSeq 2500 at the Einstein Epigenomics Core Facility. Sequences reads were mapped to the human genome version hg19 using ELAND version 1.7.0 (Illumina).

treatment_protocol: Cells were infected with retrovirus expressing pBABE-RASV12 and selected with puromycin (1µg/ml) for 14 days

tag: chip antibody

value: none (input)

value: primary fetal lung fibroblast


title: macroH2A1 OIS ChIP replicate 1

source_name: IMR90 primary lung fibroblasts_macroH2A1_IP

value: macroH2A1 (Millipore, 07-219)


title: WT_total_RNA_CT02_rep2


title: WT_total_RNA_CT00_rep2


title: WT_total_RNA_CT22_rep1


title: WT_total_RNA_CT20_rep1


title: WT_total_RNA_CT12_rep2


title: WT_total_RNA_CT16_rep2


title: WT_total_RNA_CT14_rep2


title: WT_total_RNA_CT10_rep2


title: WT_total_RNA_CT18_rep1


title: WT_total_RNA_CT16_rep1


title: WT_total_RNA_CT14_rep1


title: Bmal1_kd_total_RNA_CT04_rep1


title: WT_total_RNA_CT18_rep2


title: WT_total_RNA_CT10_rep1


title: WT_total_RNA_CT12_rep1


title: WT_total_RNA_CT00_rep1


title: WT_total_RNA_CT06_rep1


title: WT_total_RNA_CT02_rep1


title: WT_total_RNA_CT08_rep1


title: WT_BDSF_OtA0800

city: Manassas

first: Monique

last: van Hoek

state: VA

address: Discovery Hall, George Mason Circle

department: School of Systems Biology and National Center for Biodefense and Infectious Diseases

institute: George Mason University

description: genome NC_008601

data_processing:
Sequencing data (fastq) of each samples had been mapped against NC_008601.
Mapped data sets (bam files) had been input into BEDtools to call hits counts on each region defined in NC_008601.gb
Hits counts of samples were used as input of edgeR for differential gene expression analysis.
CPM (count per million), P-value and FDR were calculated using Exact test in edgeR, with bcv as 0.1. FDR <0.05 was considered as significantly different.
Supplementary_files_format_and_content: txt: RPKM, hit counts, CPM, logFC, Pvalue, FDR (txt)

organism: Francisella tularensis subsp. novicida U112

source_name: bacteria

growth_protocol: F. novicida cultures were grown overnight in TSBC in a shaking incubator at 37 C.

extract_protocol:
On the next day, the cultures were centrifuged, and RNA was prepared using a Qiagen RNeasy minikit. DNase I treatment was performed according to the manufacturer’s instructions.
RNA samples were sent to Otogenetics (Norcross, GA, USA) for sequencing.

treatment_protocol: Grown in the presence or absence of 30 uM cis-2-dodecenoic acid (BDSF).

tag: type

value: wild-type

tag: treatment

value: presence of 30 uM cis-2-dodecenoic acid


title: WT_OtA0798

description: genome NC_008601


title: WT_total_RNA_CT04_rep1


title: 10HA2

status: Public on Aug 18 2015

city: Munich

first: Charissa

last: de Bekker

state: Bayern

address: Goethestrasse 31

department: Institute for Medical Psychology

institute: Ludwig Maximilian University

description:
Camponotus castaneus (collected from the wild)
PolyA RNA
Processed data: Camfl1.gene_exp

data_processing:
Mapping to respective parasite and host genomes using TopHat version 2.0.11 and Bowtie version 2.2.2. Default settings, intron length settings: minimum 5, maximum 1000. Microexon-search enabled.
Differential expression using Cuffdiff version 2.2.1. Default settings with bias correction method. Normalization to FPKM.
Genome_build: Camponotus floridanus: CamFlo_1.0 (AEAB00000000.1)
Genome_build: Ophiocordyceps unilateralis s.l. SC16a: LAZP00000000.1
Supplementary_files_format_and_content: Camfl1.gene_exp.diff: cuffdiff output for all Camponotus castaneus reads in this study.
Supplementary_files_format_and_content: Ophio1_1.gene_exp.diff: cuffdiff output for all Ophiocordyceps unilateralis s.l. reads in this study.

organism: Camponotus castaneus

source_name: Head of healthy ant control at 2PM

growth_protocol: Fungal cultures were grown in 250 mL shaking flasks holding 50 mL supplemented insect medium (Grace's insect cell culture media with 10% FBS) shaken at 150 rpm at 28C.

extract_protocol:
Ants and fungal cultures were flash frozen in liquid nitrogen. Ants heads were cut off. The RNA was extracted using TRIzol reagent and subsequently cleaned up with RNeasy MinElute columns (Qiagen).
mRNA-Seq libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina).
Samples were sequenced on an Illumina HiSeq 2500 using 100 x 100 paired-end sequencing in Rapid Run mode.

treatment_protocol: Ants were infected by ways of injection with 1uL of disrupted fungal tissue in Grace's insect medium supplemented with 10% FBS.

value: ant head

tag: time point

tag: sample type

value: healthy ant control


title: 11HA2


title: 7HA10

source_name: Head of healthy ant control at 10AM


title: 9HA10


title: 8HA10


title: clpP untr 3

city: Princeton

first: Mark

last: Brynildsen

state: NJ

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

data_processing:
base-calling was performed with RTA version 1.17.21.3
Split multiplexed single-end sequencing data using a separate index read (standard Illumina TruSeq protocol), reads were mapped to the E. coli MG1655 genome (NCBI NC_000913.3) using TopHat (v2.0.9), and counted for each gene using htseq-count (version 0.6.0) from the HTSeq Python package .
Raw gene counts were analyzed and evaluated for differential expression in R (version 3.1.0) using DESeq2 (version 1.4.5).
Genome_build: NCBI NC_000913.3
Supplementary_files_format_and_content: text files containing the raw counts for each gene; xlsx containing summary DESeq2 output

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: E. coli from a -80°C frozen stock were grown in LB for 4 h (37°C and 250 r.p.m.), and MOPS minimal media (Teknova) + 10 mM glucose for 16 h (37°C and 250 r.p.m.). The overnight culture was inoculated into 20 ml of fresh MOPS + glucose media in a 250 ml baffled shake flask, and grown at 37°C and 250 r.p.m. until OD600 = 0.2. The culture was centrifuged for 3 min at 15,000 r.p.m., resuspended in fresh pre-warmed (37°C) MOPS + glucose, centrifuged for an additional 3 min at 15,000 r.p.m., and again resuspended in pre-warmed MOPS + glucose. The resuspension was delivered to 10 ml fresh pre-warmed (37°C) MOPS + glucose in a stirred, aerobic batch bioreactor to a final OD600 of 0.05.

extract_protocol:
10 min after inoculation & treatment, 3 ml of culture was removed and immediately mixed with 6 ml of RNAprotect Bacteria Reagent (Qiagen). Purification was performed using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. Briefly, after 5 min incubation with the RNAprotect reagent, the sample was centrifuged for 10 min at 5000×g, and the supernatant carefully discarded. Cell pellets were stored at −80 °C until all replicates and conditions for that particular experiment were completed, allowing simultaneous purification of all samples. To eliminate potential DNA contamination, an on-column DNase digestion was performed using RNase-free DNase I (Qiagen).
Half a microgram of total RNA from each sample was subject to ribosomal RNA depletion using RiboZero Bacteria kit (Illumina, CA) and then converted to strand-specific RNA-seq library using the automated Apollo 324TM NGS Library Prep System and associated kits (Wafergen, CA) according to the manufacturer’s protocol, utilizing different DNA barcodes for each library. The libraries were examined on Bioanalyzer (Agilent, CA) DNA HS chips for size distribution, and quantified by Qubit fluorometer (Invitrogen, CA). The 12 RNA-seq libraries were pooled together at equal amounts and sequenced on Illumina HiSeq 2500 in Rapid mode as one lane of single-end 67 nt reads following the standard protocol.

treatment_protocol: Immediately after inoculation of cells into the bioreactor, the culture was either treated with 250 μM DPTA, or an equal volume of only the DPTA solvent (20 μM NaOH) as an untreated control.

tag: genotype/variation

value: [Delta]lpP

tag: treated with

value: 20 μM NaOH (DPTA solvent; untreated control)

value: bacterial liquid cell culture


title: 6Cc5D

description:
Camponotus castaneus (collected from the wild) and Ophiocordyceps unilateralis s.l. strain SC16a
PolyA RNA
Processed data: Camfl1.gene_exp
Processed data: Ophio1_1.gene_exp

organism:
Camponotus castaneus
Ophiocordyceps unilateralis

source_name: Head of infected ant after manipulated biting behavior

tag: tissue

value: ant head and fungal tissue

value: after manipulated biting behavior

value: parasite-host interaction


title: WT untr 1

source_name: wild type_untreated


title: clpP NO 1

source_name: ΔclpP_DPTA treated

value: 250 μM DPTA


title: WT NO 2

source_name: wild type_DPTA treated


title: clpP untr 2


title: clpP untr 1


title: WT NO 3


title: 5Cc4D


title: 4Cc3D


title: 2Cc7L

source_name: Head of infected ant during manipulated biting behavior

value: during manipulated biting behavior


title: WT untr 2


title: 12HA2


title: 3Cc8L


title: 1Cc6L