title: ZUMA-0016 DKO_r3

city: Badalona

first: Miguel

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

data_processing:
Pre-processing. Reads sequences were obtained from the Illumina instruments in fastaQ or qseq format and were pre-processed in different steps in order to remove misleading reads and improve the mapping accuracy. Bases at the 3’ end of the reads with low quality (PHRED score <= 2) were end clipped. The adapters sequence used in the PCR amplification were also removed using iterative searches of 5’ to 3’ fragments. Ambiguous bases (Ns) at both ends of the read were also removed. Finally, reads shorter than 10 bp or with more than 30% of ambiguous bases were filtered out from the analysis.
Mapping. Once trimmed and cleaned, reads were mapped to the human reference genome (build GRCh37/hg19) with Bowtie 0.12.7 using the following parameters: -S –p 8 –v 2 –phred64-quals –best –l 28 –k 2. The value of option v is the number of mismatches allowed.
Post-processing. Once mapped, ambiguous reads (those that are mapped in several genome locations) were disambiguated when the number of mismatches allowed the assignment of a unique position in the human genome with a higher probability, otherwise they were rejected. Reads mapped in unknown chromosome were annotated as chrUn (scaffolds and contigs which could not be placed on chromosomes) and excluded from further analyses. The unambiguous reads (including uniquely mapped reads) were selected for further analysis. The information was stored using the standard SAM/BAM format.
Counting of reads in regions of interest (NSUMA universe) was performed using coverageBed of the bedtools suite 2.16.2
Agilent SurePrint G3 Custom CGH+SNP 2x400K (G4883A) CGH arrays were hybridized for each sample subjected to NSUMA. To detect copy number variations we applied the circular binary segmentation (CBS) algorithm of Olshen and Venkatraman (2004) implemented in the DNAcopy R package. We applied the sundo option to remove change-points detected due to local trends and setting SD=0.5. To detect significant regions we set different thresholds depending on the samples we were comparing based on the distribution of the mean of the segments.
Genome_build: hg19
Supplementary_files_format_and_content: nsuma_reads_all_NSUMA_amplicons.txt: Normalized number of reads by NSUMA amplicon for each sample. The virtual NSUMA universe is thoroughly annotated by the coordinates of the amplicon and the restriction site (SmaI) and by the mapping to its genomic compartment (Alu, CpG Island...).

source_name: DKO cell line

growth_protocol: Three colorectal tumors and their paired non-adjacent normal colonic mucosa as well as the corresponding whole blood DNA were used in this analysis. Samples were obtained from the Hospital Universitari de Bellvitge (Barcelona, Spain) following a protocol approved by the Ethics Committee. Human colon cancer cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA), except DKO {Rhee, 2002 #5501}, generously provided by B. Vogelstein. All cell lines were grown in DMEM:F12 medium plus 10% heat-inactivated FBS, L-glutamine and  pyruvate (Invitrogen)

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer II instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits. Each flow cell ran on the Genome Analyzer IIx contained a PhiX control lane (loaded at a concentration of 4pM) that was used to monitor run quality.

tag: cell type

value: Colon-derived cell line

value: Cell line

value: DKO


title: ZUMA-0015 DKO_r2

status: Public on Sep 08 2015

type: SRA

middle: A.

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell line


title: Day 21 NPC + EC + MSC Plate 2 s2

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

country: USA

institute: Cleveland State University

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Cells were lysed for RNA purification on day21.
131212_multiplexing_Lanes23_E1_NPC_100K_plus_MSCinPeri_plus_EC_D21_minus_2

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment.
Genome Reference: hg19
Supplementary_files_format_and_content: RSEM TPMs (Gene expression levels)

molecule: total RNA

source_name: H1 human embryonic stem cell derived neural progenitor cells, endothelial cells, and mesenchymal stem cells

extract_protocol:
Qiagen Rneasy mini kit with RLT lysis buffer
TruSeq and custom library prep

tag: screening chemicals


title: RN2 Psip1.2474 LT JQ1 50 nM

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

description:
Sample 15
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv

data_processing:
The paired-end and single-read fragments were trimmed on their 5' end (6 cycles PE100, 2 cycles SR50 NEB RNA sample prep protocol)
Adaptors were removed using cutadapt v1.4.2 and reads with a length of less than 18bp in any read of the pair were discarded. (Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, Read2: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT)
The trimmed and adaptor free reads were aligned against rDNA of the respective organism using bowtie2 v2.0.2 for paired-end and bowtie v0.12.5 for single-end reads. (100PE: bowtie2 (v2.0.2) --sensitive-local, 50SR: bowtie v0.12.5 -v 3 -k 1 --tryhard --chunkmbs 256)
The rRNA cleaned paired-end reads were aligned against the transcriptome to estimate the fragment size and the standard deviation of the fragment size using bwa v0.6.2. ( -N 1 -n 1 -a 1000)
The rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-Seq reads using splice junction guidance of a GTF annotation file (mouse: mm10, RefSeq from UCSC, 2012/5/23, human: hg19, RefSeq 2012/11/30) (--segment-mismatches 1 --max-multihits 20 --library-type fr-firststrand --initial-read-mismatches 2, 100PE: --segment-length 25 --mate-inner-dist value from transcriptome alignment --mate-std-dev value from transcriptome alignment; SR50: --segment-length 24)
The uniquely aligning reads were used for counting per gene with htseq-count v 0.6.1p with the overlap-resolution mode option set to 'union' using the processed RefSeq-annotated gene database (supplementary files refseq.hg19.2014_0110.imp.merged.uniq.exons.fulltable.gtf and refseq.mm10.2014_3006.imp.merged.uniq.exons.fulltable.gtf)
genome build: hg19 / mm10
processed data files format and content: Tab-delimited text files containing raw counts and RPKMs for given samples

organism: Mus musculus

source_name: Cell line

extract_protocol:
Cells were harvested, flash frozen on dry ice, and RNA was extracted using RLT plus buffer (Qiagen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA

tag: treatment

value: LT JQ1 50 nM

tag: diagnosis

value: Leukemia


title: ZUMA-0013 DKO_r1


title: RN2 Suz12.909  LT JQ1 50 nM

description:
Sample 14
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: Day 21 NPC + EC + MSC + MG Plate 1 s1

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Cells were lysed for RNA purification on day21.
131227_multiplexing_Lanes7_E2_NPC_100KplusMSCinMSCplusECplusMG_D21_1

source_name: H1 human embryonic stem cell derived neural progenitor cells, endothelial cells, mesenchymal stem cells, and microglia/macrophage precursors


title: JQ1_H3K36me3

description:
Sample 23
processed_data file: mouse_JQ1_H3K36me3.bw

data_processing:
Adaptors of the single-read fragments were removed using cutadapt v1.4.25 and reads with a length of less than 18bp in any read of the pair were discarded.
The remaining reads were aligned to the genome (mouse: mm10) using Bowtie v1.0.0.
Reads with same start and end position on the same strand were removed from the alignment.
Remaining reads were normalized to total mapped reads.
genome build: mm10
processed data files format and content: bigWig files were generated for each individual IP.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: 3d JQ1 25 nM


title: RN2 Suz12.1842 LT JQ1 50 nM

description:
Sample 19
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0014 HCT116_r3

source_name: HCT116 cell line


title: RN2 Ezh2.718 LT JQ1 50 nM

description:
Sample 18
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: Day 21 NPC + EC + MSC Plate 1 s1

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Cells were lysed for RNA purification on day21.
131212_multiplexing_Lanes23_E1_NPC_100K_plus_MSCinMSC_plus_EC_D21_minus_1


title: RN2 Dnmt3a.16 LT JQ1 50 nM

description:
Sample 13
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: RN2 24h JQ1 200 nM

description:
Sample 22
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: RN2 Suz12.909 24h JQ1 200 nM

description:
Sample 12
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0012 HCT116_r2


title: RN2 2h JQ1 200 nM

description:
Sample 21
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv

value: 2h JQ1 200 nM


title: Day 13 NPC Only s3

description:
Human neural progenitor cells cultured on PEG hydrogel for 13 days
131025_multiplexing_Lanes_NPC_Control_3

source_name: H1 human embryonic stem cell derived neural progenitor cells


title: RN2 Suz12.909 DMSO

description:
Sample 11
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv

value: DMSO


title: ZUMA-0010 557 Tumor

source_name: Colon tumor

value: Colon primary tumor matched to normal

value: Colon tumor


title: RN2 DMSO

description:
Sample 20
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: Day 13 NPC Only s2

description:
Human neural progenitor cells cultured on PEG hydrogel for 13 days
131025_multiplexing_Lanes_NPC_Control_2


title: RN2 Suz12.909 2h JQ1 200 nM

description:
Sample 10
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: Input RNA

city: Regensburg

first: Judith

last: Hauptmann

address: Universitaetsstrasse 31

institute: University of Regensburg

description: small RNA sequencing data

data_processing:
HiSeq analysis pipeline: HCS 2.2.38, Casava 1.8.2
The data analysis for obtaining the distribution of insert lengths was performed using custom scripts:
3' adapter-sequences were trimmed. The remaining read sequences between 18 and 28 nt were sorted by length and reads with same length were summed up.
Reads of a specific length were normalized to the sum of all reads between 18 and 28 nt.
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads
Supplementary_files_format_and_content: MS Excel-file; Distribution of insert lengths in the 2 respective libraries

organism: Arabidopsis thaliana

source_name: RKD2 callus

growth_protocol: RKD2-induced cell cultures were cultivated on half strength Murashige and Skoog (MS) medium supplemented with 2% (w/v) sucrose and 30 µg/ml Hygromycin under long day conditions (16 h of light, 8500 lux, 22°C, 60 to 70% humidity).

extract_protocol:
Extracts were prepared in 25 mM HEPES (pH 7.5), 100 mM NaCl, 5 mM EGTA, 2 mM MgCl, 0.05% v/v IGEPAL CA-630, 1 mM DTT, 10% Glycerin, 1x Complete Protease Inhibitor (Roche Applied Science, Mannheim) and 50 µM MG-132. Total RNA was extracted using Trizol Reagent. 3 mg of total protein were subjected to Ago-APP. After incubation for 3 h, the affinity-purfied sample was washed and APP-enriched RNA was extracted by addition of Trizol Reagent to the whole reaction.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

tag: genetic background

value: Col-0 Ecotype

tag: transgene

tag: affinity purification


title: RN2 Psip1.2474 24h JQ1 200 nM

description:
Sample 9
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0007 544 Tumor


title: ZUMA-0002 369 Tumor


title: RN2 Psip1.2474 2h JQ1 200 nM

description:
Sample 8
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: RN2 Psip1.2474 DMSO

description:
Sample 7
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0009 557 Normal Colon

source_name: Normal colon

value: Normal colon matched to tumor

value: Normal colon


title: RN2 Dnmt3a.16 24h JQ1 200 nM

description:
Sample 6
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: RN2 Dnmt3a.16 2h JQ1 200 nM

description:
Sample 5
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0006 544 Normal Colon


title: ZUMA-0003 369 Normal Colon


title: ZUMA-0011 557 Blood

source_name: Blood

value: Whole blood

value: Blood


title: RN2 Ren.713 24h JQ1 200 nM

description:
Sample 3
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: APP-enriched RNA

description: small RNA sequencing data

value: by GST-tagged TNRC6B 599-683 (Ago-APP)


title: RN2 Dnmt3a.16 DMSO

description:
Sample 4
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: 5hmC_IR-1

city: Atlanta

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

description: 5hmC Profiling (hMe-Seal)

data_processing:
library strategy: 5hmC capture (hMe-Seal)
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm9

extract_protocol:
DNA was extracted by phenol/choloroform method.
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method (Song et al, Nature Biotechnology, 2011). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25-50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. [Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology, 29(1): 68-72.]

tag: strain background

value: brain

tag: sample group

value: ischemic injury


title: 5hmC_IR-2

description: 5hmC Profiling (hMe-Seal)


title: ZUMA-0004 369 Blood


title: RN2 Ren.713 2h JQ1 200 nM

description:
Sample 2
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: ZUMA-0008 544 Blood


title: 5hmC_IR-3

description: 5hmC Profiling (hMe-Seal)


title: 5hmC_CTL-1

description: 5hmC Profiling (hMe-Seal)

value: control


title: RN2 Ren.713 DMSO

description:
Sample 1
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: WT2_Output

status: Public on Sep 07 2015

city: Chicago

first: Dali

last: Han

state: IL

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

data_processing:
Raw reads were firstly trimmed for Poly C sequence at 3’ end. Reads shorter than 60bp were discarded. Processed reads were then mapped to the mouse genome (mm9) by bismark v0.8.3, using options -n 1 -l 40 -chunkmbs 512.
The 5fC enriched regions in each output sample were detected by using the model-based analysis of ChIP-seq (MACS) peak-calling algorithm, with the corresponding input AI sample serving as the input control. The numbers of converted (NT) and unconverted cytosines (NC) were further extracted from each output dataset. CpGs with less than 10 reads or 2 converted reads were discarded.
To detect modified CpGs that significantly enriched for 5fC, we used the binomial distribution with parameter N as (NT+ NC) and p as 5fC non-conversion rate (evaluated by spike-in sequence, p = 1.87% & 1.41% for WT replicates, p = 2.01% & 1.42% for KO replicates) to calculate the probability of observing NT or greater C-T conversion by chance. P values were further adjusted by Holm–Bonferroni method. The CpGs with adjusted p.value <0.05 in both replicates samples and located within 5fC enriched region were considered as detected 5fC sites.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files for each dataset was generated by HOMER software. The 5fC sites detected in both wild type(WT) and TDG KO cell lines are also provided.

source_name: mouse embryonic stem cells

growth_protocol: mES cell lines (Tdg -/-, and Tdg fl/fl) were cultured in feeder-free conditions, with 15% FBS, 2mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1x non-essential amino acids, 1,000 units/mL LIF and 1x pen/strp.

extract_protocol:
Fragmented gDNA samples was labeled in a suspension of azido 1,3-indandione (AI) in 100 mM MES buffer (pH 6.0) for 24 h at 37°C, leading to selective and efficient labeling of 5fC. Click chemistry labeling with DBCO-S-S-Biotin (400 mM) was performed for 2 h at 37°C, followed by purification with QIAGEN PCR purification kit.The Dynabeads MyOne Streptavidin C1 (Invitrogen) was used to pull-down the biotin-labelled DNA with minor modifications on the suggested immobilizing procedure for nucleic acids. In brief, a NaOH-solution washing step (incubated in freshly prepared 0.15 M NaOH at room temperature for 10 min) was added following the canonical washing steps (5 times with 1× binding and washing buffer with 0.1% Tween-20). After that, beads were resuspended and incubated in freshly prepared 50 mM DTT to release the 5fC-containing strand for 2 h at 37 °C. Then the supernatant containing the desired DNA was purified with Micro Bio-Spin P-6 Gel Columns (Bio-Rad) to remove DTT.
The fC-CET enriched gDNAs were used directly for library preparation using the TELP protocol. TDT (NEB) enzyme was used to add a poly-dC to allow primer extension of complemwntary strand. MightyAmp DNA Polymerase (TAKARA) was used for one round of on-bead primer extension before PCR amplification. The adaptor-ligated samples were then PCR amplified using NEBNext 2× PCR Master Mix (NEB) and indexed primers (NEB). Libraries were checked using the Agilent 2100 Bioanalyzer DNA 1000 Chip. Two biological replicates of each mESCs were prepared and sequenced, which means that in parallel, two non-enriched input DNAs(Input: preAI), two AI labeled samples (Input: AI) and two pull-down output samples were sequenced simultaneously following the same procedure.

treatment_protocol: Purified mESCs genomic DNAs were fragmented to 100-400bp with NEB dsDNA fragmentas before applied to fC-CET procedures.

tag: strain

value: mES

value: Chemical enriched gDNA

tag: pulldown reagent

value: Dynabeads MyOne Streptavidin C1

tag: genotype/variation

value: Tdg fl/fl


title: DMSO_H3K36me3

description:
Sample 26
processed_data file: mouse_DMSO_H3K36me3.bw

value: Leukemia


title: WT2_AI

value: azido 1,3-indandione (AI) and click chemistry labeled input gDNA

tag: pulldown


title: WT1_preAI

value: Fragmented input gDNA


title: SW48 DNA methylation

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Library strategy: Digital Restriction Enzyme Analysis of Methylation (DREAM)-Seq
GAII Illumina paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*Xma/(c*Xma+Sma)), where c=2.342 was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), MethReads (observed number of reads corresponding to methylated CpG, Xma), UnmethReads (observed number of reads corresponding to unmethylated CpG, Sma), RawMethylation (unadjusted methylation value), AdjMethylation (methylation value adjusted based on the spiked in standards).

source_name: SW48 colon cancer cell line

growth_protocol: SW48 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 500 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

treatment_protocol: untreated cells

tag: tissue of origin

value: colon cancer cell line

tag: disease

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender

value: female


title: Day 13 NPC Only s1

description:
Human neural progenitor cells cultured on PEG hydrogel for 13 days
131025_multiplexing_Lanes_NPC_Control_1


title: WT1_AI

tag: cell line


title: ZUMA-0001 HCT116_r1

tag: cell type

value: Colon-derived cell line

tag: tissue

value: Cell line


title: 5hmC_CTL-3

description: 5hmC Profiling (hMe-Seal)


title: KO2_preAI

tag: treatment

value: Tdg -/-


title: JQ1_H3K27me3

description:
Sample 24
processed_data file: mouse_JQ1_H3K27me3.bw

value: 3d JQ1 25 nM

tag: diagnosis


title: KO2_AI


title: Day 21 NPC + EC + MSC Plate 2 s1

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Cells were lysed for RNA purification on day21.
131212_multiplexing_Lanes23_E1_NPC_100K_plus_MSCinPeri_plus_EC_D21_minus_1

tag: screening chemicals


title: 5hmC_CTL-2

description: 5hmC Profiling (hMe-Seal)

value: brain


title: KO1_preAI


title: KO2_Output


title: KO1_AI


title: 24b_ISRE_plus_combined

city: Cambridge

first: Deborah

middle: T

last: Hung

state: MA

address: 415 Main Street

department: Infectious Disease Initiative

institute: Broad Institute

description:
bacterialCounts.txt
hostCounts.txt
hostTPM.txt

data_processing:
Alignment and quantification of host transcripts was done using RSEM v1.2.3 (Li and Dewey, 2011) using the following command line options: rsem-calculate-expression –paired-end  --calc-ci –estimate-rspd.  Genes were quantified using TPM for normalized expression measurements or raw counts for differential expression analysis.
Bacterial reads were aligned using BWA mem (BWA version 0.7.10-r789, http://bio-bwa.sourceforge.net/) with default settings
An in-house script was used to enumerate bacterial counts from BWA alignments
Genome_build: Samples were aligned to a composite "transcriptome" made by combining the mouse transcriptome generated from the Dec. 2011 (GRCm38/mm10) build of the mouse genome, with release 69 of the mm10 Ensembl gene annotations, the SL1344 genome downloaded from NCBI (NC_017718.1), and a collection of mouse rRNA sequences from the UCSC genome browser (Karolchik et al., 2004).  RSEM v1.2.3 was used to polyAdenylate mouse messenger transcripts using default parameters in rsem-prepare-reference.
Supplementary_files_format_and_content: Host_TPM_table: a table containing TPM values for every ensembl gene(rows) for each single cell (columns).  Host_Counts_table: A table containing raw count values for each Ensembl gene (rows) in each single cell (columns) Bacterial_Counts_table: A table containing raw count values for each NCBI gene (rows) for each sample (columns)

source_name: immortalized bone marrow macrophages infected with Salmonella enterica (SL1344)

growth_protocol: Immortalized bone marrow macrophages were obtained from BEI resources (Manassas, Virginia). iBMMs were transfected with the plasmid pGreenFire1-ISRE, an HIV-based transcription reporter and were maintained in DMEM (Life Technologies, Carlsbad, CA) supplemented with 20%FBS (Life Technologies, Carlsbad, CA), 5% L-glutamine (Life Technologies, Carlsbad, CA) and 25ng/ml recombinant murine m-CSF (R&D Minneapolis, MN). Bacterial cultures were grown overnight in Luria-Bertani (LB) medium at 37°C shaken at 250 rpm, washed with PBS, and stained with pHrodo dye (Life Technologies, Carlsbad, CA) for 1 hour at room temperature in  100mM Sodium Bicarbonate.

extract_protocol:
We used the RNAtag protocol for RNA isolation and construction of libraries of macrophage and bacteria transcripts (Engreitz et al., 2013) with several modifications (see linked article for details)
We used the RNAtag protocol for RNA isolation and construction of libraries of macrophage and bacteria transcripts (Engreitz et al., 2013) with several modifications (see linked article for details)

treatment_protocol: Macrophages were infected with cultures of SL1344 at an MOI of 1:1. After infection cell cultures were spun down for 5 minutes at 250xg.    After a 30 minutes incubation, bacteria were removed by washing with media containing 15ug/ml Gentamicin.  At a given time point, macrophages were lifted from the tissue culture plate and sorted according to GFP fluorescence using FACS.

tag: time after infection (hours)

tag: isre status

value: positive


title: 24b_ISRE_minus_combined

value: immortalized bone marrow macrophages infected with Salmonella enterica (SL1344)

value: negative


title: 24a_ISRE_plus_combined


title: 24a_ISRE_all_combined

value: mixed


title: 24b_ISRE_all_combined


title: T0_ISRE_plus_combined

description:
Most ISRE positive of uninfected cells but not as positive as after infection
bacterialCounts.txt
hostCounts.txt
hostTPM.txt


title: 24a_ISRE_minus_combined


title: T0_ISRE_minus_combined

value: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344


title: WT1_Output

value: mES

value: Chemical enriched gDNA

value: Dynabeads MyOne Streptavidin C1

value: Tdg fl/fl


title: macrophage (exposed to S. enterica LPS) 95

description:
Column G11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt

data_processing:
Alignment and transcript quantification was done using RSEM v1.2.3 (Li and Dewey, 2011) using the following command line options: rsem-calculate-expression –paired-end  --calc-ci –estimate-rspd.  Genes were quantified using TPM for normalized expression measurements or raw counts for differential expression analysis.
Cells containing fewer than 50,000 mapped reads or having fewer than 4,000 detected genes (TPM > 0) were removed from further ananlysis (but are contained in the attached files).
Genome_build: Reads were aligned to the mouse transcriptome generated using rsem-prepare-reference (default parameters), the Dec. 2011 (GRCm38/mm10) build of the mouse genome, and release 69 of the Ensembl mm10 gene annotations.
Supplementary_files_format_and_content: TPM_table: a table containing TPM values for every ensembl gene(rows) for each single cell (columns).  Counts_table: A table containing raw count values for each Ensembl gene (rows) in each single cell (columns)

molecule: polyA RNA

source_name: bone marrow-derived macrophages

growth_protocol: We prepared cultures of bone marrow derived macrophage cells (BMMs) from 6-8 week old female C57BL/6 mice as previously described (Falk et al., 1988). BMMs were maintained in DMEM (Life Technologies, Carlsbad, CA) supplemented with 20%FBS (Life Technologies, Carlsbad, CA), 5% L-glutamine (Life Technologies, Carlsbad, CA) and 25ng/ml recombinant murine m-CSF (R&D Minneapolis, MN). At 5 days of in vitro culture, macrophages were seeded in 6-well non-tissue culture treated plates (5*10^5 cells per plate).

extract_protocol:
Single cells were sorted into individual wells of a 96 well plate containing  5 µl TCL buffer supplemented with 1% 2-mercaptoethanol (Qiagen, Valencia, CA) according to fluorescent phenotype using FACS.  RNA was isolated using 2.2x RNAClean SPRI beads (Beckman Coulter Genomics, Danvers, MA)
To prepare amplified cDNA, we used a slightly modified version of the manufacturer's protocol from the SMARTer Ultra Low RNA Kit ((Clontech, Mountain View, CA) (See linked articule for details).  Fragmentation and library constuction were were done using the Nextera XT kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, with all quantities adjusted the ¼ of the recommended volumes.

treatment_protocol: For coating of latex beads, 30 μg of LPS from S.enterica (Sigma, St. Louis, MO) were incubated at 4°C for 12 hours with 1*10^8 of 1μm yellow-green fluorescent polystyrene latex beads (Sigma, St. Louis, MO). Beads were then extensively washed to remove any free LPS.  Latex beads (coated or uncoated) were used to stimulate cells at an MOI of 1:1.  After allowing 30 minutes for bead uptake, macrophages were washed to remove excess beads

value: bone marrow-derived macrophages

tag: hours after exposure (0 for unexposed)

tag: beads coated with lps?

value: Yes

tag: internalized bead?


title: macrophage (exposed to S. enterica LPS) 92

description:
Column G8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt

tag: strain


title: macrophage (exposed to S. enterica LPS) 94

description:
Column G10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 93

description:
Column G9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 89

description:
Column F11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 91

description:
Column G7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 87

description:
Column F9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: KO1_Output

tag: pulldown reagent

tag: genotype/variation


title: macrophage (exposed to S. enterica LPS) 88

description:
Column F10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 90

description:
Column F12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 86

description:
Column F8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 85

description:
Column F7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 84

description:
Column E12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 82

description:
Column E10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 83

description:
Column E11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 81

description:
Column E9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 80

description:
Column E8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 79

description:
Column E7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 96

description:
Column G12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 76

description:
Column G4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt

value: No


title: macrophage (exposed to S. enterica LPS) 77

description:
Column G5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 78

description:
Column G6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 75

description:
Column G3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 73

description:
Column G1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 74

description:
Column G2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 71

description:
Column F5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 72

description:
Column F6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 70

description:
Column F4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 67

description:
Column F1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 68

description:
Column F2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 60

description:
Column D12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 62

description:
Column E2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 69

description:
Column F3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 61

description:
Column E1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 59

description:
Column D11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: WT2_preAI

value: Fragmented input gDNA

tag: pulldown

value: control


title: macrophage (exposed to S. enterica LPS) 64

description:
Column E4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 55

description:
Column D7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 57

description:
Column D9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 58

description:
Column D10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 54

description:
Column C12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 53

description:
Column C11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 63

description:
Column E3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 56

description:
Column D8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 51

description:
Column C9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 48

description:
Column B12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 47

description:
Column B11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 50

description:
Column C8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 49

description:
Column C7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 52

description:
Column C10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 44

description:
Column B8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 46

description:
Column B10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 43

description:
Column B7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 45

description:
Column B9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 66

description:
Column E6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 42

description:
Column D6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 41

description:
Column D5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 65

description:
Column E5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 40

description:
Column D4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 39

description:
Column D3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 37

description:
Column D1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 38

description:
Column D2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 35

description:
Column C5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 33

description:
Column C3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 31

description:
Column C1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 29

description:
Column B5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 28

description:
Column B4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 27

description:
Column B3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 30

description:
Column B6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 22

description:
Column H10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 23

description:
Column H11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 17

description:
Column H5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 21

description:
Column H9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 15

description:
Column H3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 24

description:
Column H12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 14

description:
Column H2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 16

description:
Column H4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 20

description:
Column H8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 13

description:
Column H1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 26

description:
Column B2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 18

description:
Column H6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 12

description:
Column A12 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 25

description:
Column B1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 34

description:
Column C4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 11

description:
Column A11 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 36

description:
Column C6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 9

description:
Column A9 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 32

description:
Column C2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 10

description:
Column A10 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 7

description:
Column A7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 8

description:
Column A8 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 6

description:
Column A6 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 19

description:
Column H7 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 5

description:
Column A5 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 3

description:
Column A3 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 2

description:
Column A2 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: Day 21 NPC + EC + MSC Plate 1 s2

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Cells were lysed for RNA purification on day21.
131212_multiplexing_Lanes23_E1_NPC_100K_plus_MSCinMSC_plus_EC_D21_minus_2


title: macrophage (exposed to S. enterica LPS) 1

description:
Column A1 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica) 189

description:
Column H9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt

extract_protocol:
Single cells were sorted intp individual wells of a 96 well plate containing  5 µl TCL buffer supplemented with 1% 2-mercaptoethanol (Qiagen, Valencia, CA) according to fluorescent phenotype using FACS.  RNA was isolated using 2.2x RNAClean SPRI beads (Beckman Coulter Genomics, Danvers, MA)
To prepare amplified cDNA, we used a slightly modified version of the manufacturer's protocol from the SMARTer Ultra Low RNA Kit ((Clontech, Mountain View, CA) (See linked articule for details).  Fragmentation and library constuction were were done using the Nextera XT kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, with all quantities adjusted the ¼ of the recommended volumes.

treatment_protocol: Macrophages were treated with GFP labeled S. enterica (strain SL1344 containing the plasmid pFPV25.1) at an MOI of 1:1.  Bacterial cultures were grown overnight in Luria-Bertani (LB) medium at 37°C shaken at 250 rpm, washed with PBS, and stained with pHrodo dye (Life Technologies, Carlsbad, CA) for 1 hour at room temperature in  100mM Sodium Bicarbonate.  After the addition of bacteria, cell cultures were spun down for 5 minutes at 250xg.  After a 30 minutes incubation, bacteria were removed by washing with media containing 15ug/ml Gentamicin

tag: time after salmonella exposure (h)

tag: phrodo positive?

tag: gfp positive?


title: macrophage (exposed to S. enterica) 187

description:
Column G11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt

tag: cell type


title: macrophage (exposed to S. enterica) 188

description:
Column G12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 191

description:
Column H11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 183

description:
Column F11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 186

description:
Column G10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 179

description:
Column E11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 184

description:
Column F12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 182

description:
Column F10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 185

description:
Column G9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 178

description:
Column E10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 190

description:
Column H10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 180

description:
Column E12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 181

description:
Column F9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 176

description:
Column H8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 174

description:
Column H6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 172

description:
Column G8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 173

description:
Column H5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 175

description:
Column H7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 170

description:
Column G6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 171

description:
Column G7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 177

description:
Column E9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 168

description:
Column F8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 166

description:
Column F6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 167

description:
Column F7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 165

description:
Column F5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica LPS) 4

description:
Column A4 of prcessed data file
LPS_TPM_table.txt
LPS_Counts_table.txt


title: macrophage (exposed to S. enterica) 159

description:
Column H3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 160

description:
Column H4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 150

description:
Column F2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 148

description:
Column E4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 162

description:
Column E6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 158

description:
Column H2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 155

description:
Column G3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 147

description:
Column E3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 156

description:
Column G4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 154

description:
Column G2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 153

description:
Column G1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 161

description:
Column E5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 146

description:
Column E2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 192

description:
Column H12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 163

description:
Column E7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 149

description:
Column F1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 140

description:
Column G12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 139

description:
Column G11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 144

description:
Column H12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 142

description:
Column H10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 138

description:
Column G10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 141

description:
Column H9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 137

description:
Column G9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 164

description:
Column E8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 152

description:
Column F4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 145

description:
Column E1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 134

description:
Column F10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 135

description:
Column F11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 131

description:
Column E11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 127

description:
Column D11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 136

description:
Column F12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 128

description:
Column D12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 125

description:
Column D9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 129

description:
Column E9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 126

description:
Column D10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 133

description:
Column F9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 119

description:
Column H7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 122

description:
Column C10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 123

description:
Column C11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 130

description:
Column E10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 120

description:
Column H8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 117

description:
Column H5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 118

description:
Column H6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 116

description:
Column G8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 157

description:
Column H1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 114

description:
Column G6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 151

description:
Column F3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 121

description:
Column C9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 115

description:
Column G7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 112

description:
Column F8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 132

description:
Column E12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 124

description:
Column C12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 111

description:
Column F7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 107

description:
Column E7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 110

description:
Column F6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 109

description:
Column F5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 105

description:
Column E5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 104

description:
Column D8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 143

description:
Column H11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 106

description:
Column E6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 97

description:
Column C5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 96

description:
Column H4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 102

description:
Column D6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 101

description:
Column D5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 100

description:
Column C8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 92

description:
Column G4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 89

description:
Column G1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 95

description:
Column H3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 91

description:
Column G3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 88

description:
Column F4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 93

description:
Column H1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 108

description:
Column E8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 87

description:
Column F3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 90

description:
Column G2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 86

description:
Column F2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 113

description:
Column G5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 85

description:
Column F1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 84

description:
Column E4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 103

description:
Column D7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 99

description:
Column C7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 98

description:
Column C6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 82

description:
Column E2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 79

description:
Column D3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 78

description:
Column D2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 77

description:
Column D1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 94

description:
Column H2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 80

description:
Column D4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 74

description:
Column C2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 75

description:
Column C3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 76

description:
Column C4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 70

description:
Column D10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 65

description:
Column C9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 66

description:
Column C10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 73

description:
Column C1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 68

description:
Column C12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 64

description:
Column B12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 63

description:
Column B11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 83

description:
Column E3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 81

description:
Column E1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 60

description:
Column A12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 59

description:
Column A11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 61

description:
Column B9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 58

description:
Column A10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 62

description:
Column B10 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 72

description:
Column D12 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 54

description:
Column D6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 56

description:
Column D8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 51

description:
Column C7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 57

description:
Column A9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 52

description:
Column C8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 53

description:
Column D5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 67

description:
Column C11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 50

description:
Column C6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 47

description:
Column B7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 49

description:
Column C5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 45

description:
Column B5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 43

description:
Column A7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 480_3.sorted

description:
sortedTPM.txt
sortedCounts.txt

data_processing:
Alignment and transcript quantification was done using RSEM v1.2.3 (Li and Dewey, 2011) using the following command line options: rsem-calculate-expression –paired-end  --calc-ci –estimate-rspd.  Genes were quantified using TPM for normalized expression measurements or raw counts for differential expression analysis.
Genome_build: Reads were aligned to the mouse transcriptome generated using rsem-prepare-reference (default parameters), the Dec. 2011 (GRCm38/mm10) build of the mouse genome, and release 69 of the Ensembl mm10 gene annotations.
Supplementary_files_format_and_content: TPM_table: a table containing TPM values for every ensembl gene(rows) for each single cell (columns).  Counts_table: A table containing raw count values for each Ensembl gene (rows) in each single cell (columns)

extract_protocol:
RNA was extracted from Bulk samples using Qiagen's Rneasy mini kit as per manufacturer's instructions.  Sorted samples were sorted into individual wells of a 96 well plate containing  TCL buffer supplemented with 1% 2-mercaptoethanol (Qiagen, Valencia, CA) using FACS.  RNA was isolated from thee samples using 2.2x RNAClean SPRI beads (Beckman Coulter Genomics, Danvers, MA)
Bulk sample libraries were constructed using the Truseq RNA Sample Preparation kit (Illumina) as per manufacturer's instructions.  Sorted samples were made using a slightly modified version of the manufacturer's protocol from the SMARTer Ultra Low RNA Kit (Clontech, Mountain View, CA) (See linked articule for details).  Fragmentation and library constuction were were done using the Nextera XT kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, with all quantities adjusted the ¼ of the recommended volumes.

treatment_protocol: Macrophages were treated with GFP labeled S. enterica (strain SL1344 containing the plasmid pFPV25.1) at an MOI of 1:25.  Bacterial cultures were grown overnight in Luria-Bertani (LB) medium at 37°C shaken at 250 rpm. After the addition of bacteria, cell cultures were spun down for 5 minutes at 250xg.  After a 30 minutes incubation, bacteria were removed by washing with media containing 15ug/ml Gentamicin

tag: time after salmonella exposure (minutes)

tag: bulk or sorted

value: Sorted


title: macrophage (exposed to S. enterica) 46

description:
Column B6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 69

description:
Column D9 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 44

description:
Column A8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 42

description:
Column A6 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 480_2.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 41

description:
Column A5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 480_1.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 55

description:
Column D7 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 240_3.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 40

description:
Column D4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 169

description:
Column G5 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 240_2.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 38

description:
Column D2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 39

description:
Column D3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 71

description:
Column D11 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 120_3.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: 120_2.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 36

description:
Column C4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 37

description:
Column D1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 240_1.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 34

description:
Column C2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 32

description:
Column B4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 120_1.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: 0_1.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: 480_Bulk_2

description:
total_Bulk_TPM.txt
total_Bulk_Counts.txt

value: Bulk


title: macrophage (exposed to S. enterica) 31

description:
Column B3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 30

description:
Column B2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 33

description:
Column C1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 0_2.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 29

description:
Column B1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 480_Bulk_1


title: 240_Bulk_2


title: macrophage (exposed to S. enterica) 28

description:
Column A4 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 240_Bulk_1


title: macrophage (exposed to S. enterica) 35

description:
Column C3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 27

description:
Column A3 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 120_Bulk_2


title: 0_Bulk_2


title: macrophage (exposed to S. enterica) 26

description:
Column A2 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: 120_Bulk_1


title: 0_Bulk_1


title: macrophage (exposed to S. enterica) 24

description:
Column B12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: 0_3.sorted

description:
sortedTPM.txt
sortedCounts.txt


title: macrophage (exposed to S. enterica) 23

description:
Column B11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 25

description:
Column A1 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 22

description:
Column B10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 21

description:
Column B9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 19

description:
Column B7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 20

description:
Column B8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 15

description:
Column B3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 18

description:
Column B6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 16

description:
Column B4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 13

description:
Column B1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 12

description:
Column A12 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 8

description:
Column A8 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 10

description:
Column A10 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 14

description:
Column B2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 9

description:
Column A9 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 7

description:
Column A7 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 6

description:
Column A6 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 5

description:
Column A5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 3

description:
Column A3 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 4

description:
Column A4 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 2

description:
Column A2 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 17

description:
Column B5 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: gammaH2AX_ChIPSeq Vehicle treated

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

description: Sample 1

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using default settings.
Genome_build: Hg 19
Supplementary_files_format_and_content: Wig files report peaks.

source_name: MCF7 cells

growth_protocol: MCF-7 cells were cultured in DMEM containing 10%FCS. For ChIP-seq study, the cells were cultured in DMEM lacking phenol-red, supplemented with 10% dextran-coated charcoal-stripped FCS for 72 hours. Estrogen (100 nM) or Ethanol  was added and cells were fixed  and sonicated for ChIP after 45 minutes.

extract_protocol:
Lysates were clarified from sonicated nuclei and APOBEC3B--DNA complexes were isolated with antibody.
Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.

tag: agent

value: Vehicle

tag: chip antibody

value: Anti-gamma H2A.X (phospho S139) antibody (Abcam, catalog# ab2893, lot# GR155796-1)


title: gammaH2AX_ChIPSeq Estrogen/H2O2 treated

description: Sample 4


title: gammaH2AX_ChIPSeq Estrogen treated

description: Sample 2

value: Estrogen


title: gammaH2AX_ChIPSeq H2O2 treated

description: Sample 3


title: ma202_L2_TotalRNA_rep2

city: Worcester

first: Isana

last: Veksler-Lublinsky

address: 373 Plantation Street

department: Molecular Medicine

institute: University of Massachusetts Medical School

description: small RNA profiling

data_processing:
Sequencing files in FastQ format were processed using the Fastx toolkit to remove the 3' adapter sequences (CTGTAGGCACCATCAAT) and split  the reads according to the 5' 4 nt barcode sequences.
Reads shorter than 17 nt ang longer then 40 nt were removed.
Reads with identical sequences were combined.
Reads were than aligned to the Caenorhabditis elegans genome (WormBase release WS215) using bowtie with arguments, -v 3 -f -B 1 -a–best –strata
Alignments were then filtered based on the length of the read and the number of mismatches as follows: for sequence lengths 17, 18–19, 20–24, or >24: zero, one, two, or three mismatches were allowed, respectively.
Genome_build: WS215
Supplementary_files_format_and_content: The tab delimeted text files contain unique sequence reads of smallRNA with counts for each sequence.

organism: Caenorhabditis elegans

source_name: Total RNA

growth_protocol: C. elegans culture was performed using standard nematode growth conditions, except the HB101 Escherichia coli strain was used as the food source. All strains were grown at 20 °C. Because of their strong heterochronic phenotypes, alg-1(anti) mutant animals often burst through the vulva during the L4-adult molt (31). Therefore, alg-1(anti) mutations were maintained in a lin-31(n1053) genetic background that impairs vulva development and thereby suppresses the bursting phenotype of alg-1 mutants, while leaving their heterochronic phenotypes intact. The adult-specific col-19::gfp reporter transgene is also present in all of the strains. Therefore, the alg-1(anti) strains used here contain lin-31; col-19::gfp, and in all experiments the wild-type controls were lin-31(n1053); col-19::gfp

extract_protocol:
Whole animal pellets were dounced, the resulting lysates were clarified. Total RNA or RNA that co-immunoprecipitated with anti-ALG-1 antibody was subsequently used for library preparations.
Libraries were prepared according to Gu W, Claycomb J, Batista P, Mello C, Conte D (2011) in Methods in Molecular Biology, eds Hobman TC, Duchaine TF (Humana Press), pp 251–280–280 using the primers appropriate for each sequencing instrument (Illumina GAIIx or Illumina Nextseq500)
Total small RNA or ALG-1 co-immunoprecipitated small RNA

tag: developmental stage


title: WT_L2_TotalRNA_rep2

description: small RNA profiling

value: Wild type


title: macrophage (exposed to S. enterica) 1

description:
Column A1 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: macrophage (exposed to S. enterica) 48

description:
Column B8 of processed data file
s121_p2_TPM_table.txt
s121_p2_Counts_table.txt


title: macrophage (exposed to S. enterica) 11

description:
Column A11 of processed data file
s121_p1_TPM_table.txt
s121_p1_Counts_table.txt


title: ma202_Mixed_IP_rep1

description: small RNA profiling

source_name: RNA immunoprecipitated with ALG-1

value: mixed


title: WT_Mixed_TotalRNA_rep2

description: small RNA profiling


title: ma192_Mixed_IP_rep2

description: small RNA profiling


title: ma202_Mixed_TotalRNA_rep2

description: small RNA profiling


title: ma192_Mixed_TotalRNA_rep2

description: small RNA profiling


title: WT_Mixed_IP_rep2

description: small RNA profiling


title: ma192_Mixed_IP_rep1

description: small RNA profiling


title: ma202_Mixed_IP_rep2

description: small RNA profiling


title: WT_Mixed_IP_rep1

description: small RNA profiling


title: WT_Mixed_IP_rep3

description: small RNA profiling


title: WT_Mixed_TotalRNA_rep3

description: small RNA profiling


title: ma202_Mixed_TotalRNA_rep1

description: small RNA profiling


title: ma192_L2_TotalRNA_rep1

description: small RNA profiling


title: WT_Mixed_TotalRNA_rep1

description: small RNA profiling


title: ma202_L2_TotalRNA_rep1

description: small RNA profiling


title: T0_bacs_combined

description:
Just bacteria
bacterialCounts.txt
N/A
N/A

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica strain SL1344

tag: time after infection (hours)

tag: isre status


title: WT_L2_TotalRNA_rep1

description: small RNA profiling


title: ma192_Mixed_TotalRNA_rep1

description: small RNA profiling


title: mRNA worker sample 5

status: Public on Sep 06 2015

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

data_processing:
Base calling: Cassave 1.8
Alignment of mRNAs: tophat 2.0.9, miRNAs: mirdeep2 2.0.0.5
Counts: htseq 0.5.4p3
Genome_build: Honey bee Apis mellifera genome assembly v4.5 official gene set v3.2
Supplementary_files_format_and_content: For mRNA: Official gene set 3.2 id (GB id), TAB, count; for miRNA, MiRBase ID (or if new, genomic coordinates and strand), TAB, count

organism: Apis mellifera

source_name: L5 worker larvae

extract_protocol:
total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer.
Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip.

value: L5 Larvae

tag: caste

value: Worker

tag: body part

value: Whole body


title: mRNA worker sample 4


title: miRNA worker sample 3


title: miRNA worker sample 4


title: miRNA worker sample 2


title: miRNA worker sample 5


title: mRNA worker sample 3


title: mRNA worker sample 2


title: miRNA worker sample 1


title: miRNA queen sample 5

source_name: L5 queen larvae

value: Queen


title: miRNA queen sample 4


title: miRNA queen sample 2


title: miRNA queen sample 1


title: miRNA drone sample 4

source_name: L5 drone larvae

value: Drone


title: miRNA drone sample 5


title: mRNA queen sample 4


title: miRNA drone sample 3


title: miRNA drone sample 2


title: mRNA queen sample 3


title: miRNA drone sample 1


title: mRNA drone sample 5


title: mRNA drone sample 3


title: mRNA drone sample 4


title: mRNA queen sample 1


title: mRNA drone sample 2


title: schistosomula and adults of Schistosoma japonicum

city: Shanghai

first: Xinye

last: Wang

state: Shanghai

address: 1239 Siping Road

department: Tongji University School of Medicine

country: China

institute: Institute for Infectious Diseases and Vaccine Development

data_processing:
Base calling was performed using the HiSeq Sequencing Control Software.
Filtering standard is that the second lowest CHASTITY value is at least 0.6 in former 25 cycles.
The high quality reads were mapped to the S.japonicum genome of SGST (Data release:Nov 11, 2010) by Tophat (version 2.04)
Then mapped reads were assembled with Cufflinks (version 2.00) to construct unique transcipts sequences and alternative  splicing analysis, using the parameter: -g –b –u –o.
Genome_build: the S.japonicum genome of SGST (Data release:Nov 11, 2010)
Supplementary_files_format_and_content: Fasta file includes sequences of assembled transcripts, and SJ_AS transcript_info.xls provides information of transcripts about FPKM,GO and KEGG annotation.

organism: Schistosoma japonicum

source_name: Whole body of worms

extract_protocol:
The total RNA were extracted from the worms using TRIzol reagent (Invitrogen), following by the RNA purification by Rneasy MiniElute Cleanup Kit (Qiagen), according to the manufacture's protocol.
For mRNA library construction,RNA samples were prepared by using the TruSeq RNA Sample Preparation Kit according to the manufacture’s protocol.

tag: strain

value: Chinese strain

tag: isolation source

value: Poyang Lake

value: schistosomulum and adult


title: mRNA drone sample 1


title: OPC rep2

status: Public on Sep 05 2015

city: Rochester

first: FENG

last: CUI

state: NY

address: One Lomb Memorial Dr.

department: Thomas H. Gosnell School of Life Sciences

institute: ROCHESTER INSTITUTE OF TECHNOLOGY

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to rnor5 whole genome using SHRiMP v2.2.3 with parameters -Q --qv-offset 33 -L ./<indexLocation>/<assemblyName> -N 8 –all-contigs
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. The software used to do this was Rsubread v1.16.1 (Liao et al., Nucleic Acids Research, 2011)
Genome_build: rnor5
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

organism: Rattus norvegicus

source_name: N7746-100 (Life Technologies)

extract_protocol:
RNA samples of the rat neurons, astrocytes and OPCs were prepared by the RNeasy Mini Kit of QIAGEN (Cat. 74104) following the instructions of the Kit. Cells were sheared using the Qiashredder (Cat. 79654). Isolated RNA was quantified using the Thermo Scientific NanoDrop (ND-1000). A total of 250 ng RNA was sent to the UR Genomics Research Center (Rochester, NY) for RNA sequencing using Illumina HiSeq2500 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oligodendrocyte precursor cells

tag: passages

tag: days

value: 8 days before passage and 6 days after passage


title: FFEC

first: Qiuxiang

last: Ma

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology, SIBS,CAS

data_processing:
To get the high quality tags that we used for analysis, we filtered the potentially erroneous tags (only one copy number, only adaptor sequences, or containing unknown sequences "N") to get the clean tags
For mapping the clean tags to reference sequences, a database containing all possible CATG +17 bases length sequences was created using a large collection of cassava ESTs from TIGR (Manihot_esculenta_release_5, containing 5,189 assemblies, 10,214 singletons, released 1 June 2007), cassava ESTs from NCBI (80,631 ESTs, released 25 August 2010), 34,151 predicted cassava transcripts from Phytozome and a 35,400 full-length cDNA RIKEN library. The clean tag expression was normalized to TPM (transcripts per million clean tags).
Mapped genes were locally blasted against the NCBI non-redundant protein database using the blastx program in the blastall package (version 2.2.25), and the top hits were used for gene annotation. Mapped genes were further analyzed with Blast2go to get GO annotations.
Genome_build: cassava ESTs from TIGR and NCBI, predicted cassava transcripts from Phytozome and a 35,400 full-length cDNA RIKEN library
Supplementary_files_format_and_content: files include TPM values for each Sample

organism: Manihot esculenta

source_name: fresh friable embryogenic callus of cassava

growth_protocol: The induced SEs was cultured on GD medium for 2 weeks under in darkness at 26±2ºC. FFEC was initially induced on GD medium at the same condition with SEs,  OFEC was cultured more than 9 months  under 26±2ºC and 16 h/8 h photoperiod, and subcultured  every 3 weeks.

extract_protocol:
Using Oligo (dT) magnetic bead, mRNA was purified from each of the three samples, then Oligo (dT) was used as primer to synthesize cDNA.
The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 105bp  fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS)

treatment_protocol: Samples from three independent replicates were pooled for RNA isolation and library construction.Illumina Gene Expression Sample Prep Kit was used with 6 μg total RNA for the construction of sequencing libraries.

tag: tissue

value: fresh friable embryogenic callus

tag: age

value: initial  induction

tag: cultivar


title: OFEC

source_name: old friable embryogenic callus of cassava

value: old  friable embryogenic callus

value: more than 9 months after induction


title: SEs

source_name: somatic embryos of cassava

value: somatic embryos

value: culture on GD medium  for 2 weeks


title: miRNA queen sample 3


title: mRNA worker sample 1


title: neuron rep2

source_name: A10840-01 (Life Technologies)

tag: cell type

value: neuron