title: Sample 24_ARCA-LUC-TL_CGATG_L001_R1_001

city: Chapel Hill

first: William

middle: F

last: Marzluff

address: 207 Fordham Hall

institute: The University of North Carolina at Chapel Hill

description: Sample 24

data_processing:
Basecalls performed using CASAVA v. 1.8.2
Reads were aligned to hg19 and/or luciferase construct using STAR version 2.3.1n
A custom Perl script was used to identify 3' tails
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing 3' tails were generated using a custom Perl script

source_name: HeLa cells

growth_protocol: HeLa cells were plated at 2X10^5 cells per 10 cm dish. Jurkats were grown to a density of 2.5X10^5 cells/ml

extract_protocol:
Total RNA was extracted with Trizol. Capped RNA was immunoprecipitated with anti-7mG antibody. The antibody used to precipitate the capped mRNAs and then sequence the histone mRNAs in the sample was originally produced by Dr. Ted Munns (Munns et al., 1977; Munns et al., 1979).
Libraries were prepared with Illumina sequnces using two limited rounds of PCR

treatment_protocol: Cells were treated with hydroxyurea at 5 mM [C]. For polysome experiments Jurkats were treated for the specified time with or without pactamycin followed by cycloheximide. Knockdown experiments used either siRNA delivered by lipofectamine or lentivirus containing shRNA.

value: HeLa cells

tag: 3' linker

value: NEB+Ext

tag: sample group

value: Luciferase tetra-loop construct


title: Sample 26_WT_Upf1_00_GGCTA_L001_R1_001

status: Public on Mar 20 2014

type: SRA

state: NC

country: USA

description: Sample 26

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: No dA priming


title: Sample 27_WT_Upf1_20_CTTGT_L001_R1_001

description: Sample 27


title: Sample 22_100-00-siR_S12_L001_R1_001

description: Sample 22

value: Exosome siRNA Pm\Scl-100


title: Sample 17_7mG-dA3_S2_L001_R1_001

description: Sample 17

value: 7mG IP - Combined


title: Sample 15_HUCHXP12_CTTGT_L001_R1_001

description: Sample 15

source_name: Jurkat cells

value: Jurkat cells

value: Polysome Pactamycin


title: Sample 23_100-20-siR_S13_L001_R1_001

description: Sample 23


title: Sample 18_HU00_S4_L001_R1_001

description: Sample 18

value: HU Time course - Controls


title: 30oC. Biol. Replicate 3

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Reads were de-multiplexed. Sequence reads were then mapped against the L. interrogans Copenhageni FIOCRUZ L1-130 reference genome using Segemehl with accuracy set to 100%. To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again. This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Genome_build: RefSeq Genome Accession: PRJNA58065, PRJNA10687 ID: 58065. Leptospira interrogans serovar Copenhageni str. FIOCRUZ L1-130. Nascimento AL et al., "Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis.", J Bacteriol, 2004 Apr;186(7):2164-72.
Supplementary_files_format_and_content: .gr files are provided showing uniquely mapped sequence reads (without normalization). Ready to load into Integrated Genome Browser (IGB). The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the two strands of the Leptospira chromosome

organism: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130

source_name: RNA from bacteria

growth_protocol: Virulent low-passage Leptospira interrogans sv. Copenhageni strain Fiocruz L1-130 was cultivated in vitro under standard conditions at 30C in EMJH medium supplemented with 1% rabbit serum (Pel-514 Freez Biologicals, Rogers, AR) with 100 μg/ml 5-fluorouracil. To obtain L. interrogans in a mammalian host-adapted state, leptospires were cultivated in dialysis membrane chambers (DMCs). Briefly, DMCs were constructed using standard dialysis membrane tubing (Spectra-Por; 8000 MW cut-off). Prior to use, 8-inch strips of dialysis tubing were tied off at one end and then sterilized by boiling for 20 min in sterile water containing 5 mM EDTA, followed by two successive boiling washes in water alone. Dialysis bags were cooled to room temperature and then filled with ~8-9 mls of EMJH medium (supplemented with 10% vaccine-grade bovine serum albumin to maintain osmotic pressure) containing 10^4 organisms per ml. Once filled, the tubing was tied and excess membrane removed from both ends. For implantation, female Sprague-Dawley rats (150-174 g) were anesthetized by intramuscular injection of a mixture of ketamine (50 mg/kg), xylazine (5 mg/kg), and acepromazine (1 mg/kg). Using strict aseptic technique, a DMC was implanted into the peritoneal cavity of each rat. Analgesia (carprofen; 5 mg/kg) was administered on the day of surgery and once the following day. At designated time points (typically 9-10 days postimplantation), rats were euthanized by CO2 narcosis and DMCs recovered. The contents of each chamber were removed by gentle syringe aspiration with an 18G needle; the needle was removed prior to expelling the DMC dialysate into a sterile 15 ml conical bottom tube. Bacteria were enumerated by dark field microscopy immediately following explant using a Petroff-Hausser counting chamber (Hausser Scientific Co., Horsham, PA).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and digested with DNase I
One hundred ng of total RNA was used for library generation according to Illumina standard protocols (TruSeq RNA Sample Preparation Guide, Low-Throughput Protocol, Part # 15008136 Rev. A). cDNAs were normalized using a duplex-specific nuclease (DSN) approach according to the DSN Normalization Sample Preparation Guide, Early Access Protocol, Part # 15014673 Rev. C, which decreases the prevalence of highly abundant transcripts, such as rRNAs.

tag: strain

value: FIOCRUZ L1-130

tag: treatment

value: 30 C in EMJH


title: V6.5_2minFP_#1

status: Public on Mar 21 2014

city: Ithaca

first: Iris

middle: Helene

last: Jonkers

state: NY

address: Biotechnology Building 417

department: Molecular Biology & Genetics

institute: Cornell University

description:
GRO-seq
V6.5_2minFP_Plus.bedGraph
V6.5_2minFP_Minus.bedGraph

data_processing:
All the GRO-seq libraries were sequenced in 50 nt runs on the Illumina HiSeq and split by barcode. Sequences that contained the Illumina adaptor were clipped with the cutadapt tool (https://code.google.com/p/cutadapt/) and remaining sequences were trimmed down to 32-mers, aligned to the ribosomal genome to remove rRNAs, and then aligned uniquely to the mm9 reference genome, with up to 2 mismatches with bowtie (http://bowtie-bio.sourceforge.net/index.shtml).  Replicates were highly correlated and were pooled for further analysis, with exception of one of the 25 min Trp-treated #1 replicate, which suffered from extensive RNA degradation during the library preparation, and was subsequently discarded. Spike-in RNA controls were aligned similarly to a spike-in reference genome.
Sequences that contained the Illumina adaptor were clipped with the cutadapt tool (https://code.google.com/p/cutadapt/) and remaining sequences were trimmed down to 32-mers,
32-Mers were aligned to the ribosomal genome to remove rRNAs, and then aligned uniquely to the mm9 reference genome, with up to 2 mismatches with bowtie (http://bowtie-bio.sourceforge.net/index.shtml).
Replicates were highly correlated and were pooled for further analysis, with exception of one of the 25 min Trp-treated #1 replicate, which suffered from extensive RNA degradation during the library preparation, and was subsequently discarded. Spike-in RNA controls were aligned similarly to a spike-in reference genome.
Instead of using total read counts to normalize between treatments within either the FP or Trp time course, we chose to normalize with the spike-in RNA read counts instead.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph, nascent RNA read density of combined replicates, normalized to spike-in controls for each time course. Split by Plus and Minus strand

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: Cell culturing of the V6.5 mES cell line was done as in (Monkhorst et al., 2008), and drug treatment was performed on pre-plated mES cells, grown for one passage before isolation of nuclei to remove irradiated MEF-feeder cells.

extract_protocol:
Nuclei isolation are performed using standard protocols, in brief, after rinsing the 15 cm2 plates with drug-treated cells, 15 ml cell lysis buffer (10 mM Tris-Cl, pH 7.5, 300 mM Sucrose, 3mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 5 mM DTT, 1 mM PMSF, protease inhibitors) was added to the plates and the cells were scraped off, and spun down at 4°C and 185 xg for 5 min in a GS-6R Beckman swing-bucket centrifuge, after which supernatant was discarded. 5 ml fresh cell lysis buffer was added and cells were dounced 50 times in a 5 ml douncer on ice and spun down at 328 xg for 5 min, after which supernatant was discarded and nuclei were taken up in ~250 μl of glycerol storage buffer (50 mM Tris-Cl, pH 8.3, 40% glycerol, 0.1 mM EDTA, 5 mM MgAc2, 5 mM DTT, 1 mM PMSF, protease inhibitors) and snap frozen.
For each nuclear run-on (NRO), 1e7 nuclei were used. An NRO master mix was added containing nucleotides ATP, GTP, CTP and nucleotide analogue bromo-UTP, as well as sarkosyl and 300 mM KCl to remove all impediments that pause Pol II and prevent NRO and to prevent re-initiation of Pol II. The NRO was performed at 37°C for 5 min, which results in ~100 nt addition to the nascent RNA. Immediately after the NRO, a population of ~100 different in-vitro transcribed Arabidopsis thaliana spike-in RNAs with and without Br-UTP was added to the nascent RNA as a way to assess experimental differences between each library, and to use as a normalization tool between timepoints within each timecourse.  The nascent RNA was fragmented to ~150 nts and NRO BrU-RNA was isolated 3 consecutive times with BrdU-antibody beads (sc-32323, Santa Cruz), with enzymatic TAP and PNK treatments to remove the cap and 3’-phosphate and to add a 5’-phosphate, as well as Illumina adaptor ligations between the BrU-RNA isolation steps. The three consecutive isolation steps lead to an approximate 500.000x enrichment of BrU-RNA over background RNA. BrU-RNA was reverse transcribed, amplified, barcoded and sent for sequencing. Each dataset was done in replicate.

treatment_protocol: Cells were treated with 300nM flavopiridol for 2, 5, 12.5, 25 and 50 min, or with 500nM triptolide for 12.5, 25, and 50 min, or with 0.0125% DMSO for 50min.

tag: cell line

value: treated 2min with 300nM flavopiridol

tag: sample type

value: nascent RNA


title: Sample 20_C2-00-siR_S10_L001_R1_001

description: Sample 20


title: 30oC. Biol. Replicate 1


title: Sample 16_7mG_S1_L001_R1_001

description: Sample 16


title: Sample 21_C2-20-siR_S11_L001_R1_001

description: Sample 21


title: Sample 11_HUCHXP8_ACTTG_L001_R1_001

description: Sample 11


title: Sample 13_HUCHXP10_TAGCT_L001_R1_001

description: Sample 13


title: Sample 14_HUCHXP11_GGCTA_L001_R1_001

description: Sample 14


title: Sample 12_HUCHXP9_GATCA_L001_R1_001

description: Sample 12


title: Sample 10_HUCHXP7_CAGAT_L001_R1_001

description: Sample 10


title: Sample 8_HUCHX_ACAGT_L001_R1_001

description: Sample 8

value: Polysome Control


title: Sample 9_HUCHX6_GCCAA_L001_R1_001

description: Sample 9


title: Sample 5_HUCHX2_CGATG_L001_R1_001

description: Sample 5


title: Sample 6_HUCHX3_TTAGG_L001_R1_001

description: Sample 6


title: Sample 3_D4NONE_GGCTA_L001_R1_001

description: Sample 3

value: Cap analog Luciferase


title: Sample 25_BTH-LUC-TL_ATCAC_L001_R1_001

description: Sample 25


title: Sample 4_HUCHX1_ATCAC_L001_R1_001

description: Sample 4


title: Sample 2_C2NONE_ATCAC_L001_R1_001

description: Sample 2


title: Sample 19_HU20_S5_L001_R1_001

description: Sample 19


title: Sample 1_H2ABNONE_combined_R1

description: Sample 1

value: SOLID Reverse

value: No d(A) priming


title: E26S2

city: Wuhan

first: Jianwei

last: Shan

state: Hubei province

address: shizishan street

department: college of life of science

country: China

institute: huazhong agricultural university

description: Sample 4

data_processing:
Illumina Casava1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using BGI DGE Pipeline
Genome_build: http://www.ncbi.nlm.nih.gov/assembly/304118/
Supplementary_files_format_and_content: text files containing count for each read

molecule: polyA RNA

organism: Solanum tuberosum

source_name: plantlets_short day

growth_protocol: potato plantlets were first grown at longday for 3 weeks, and then half of them were transferred to shortday, half of them were kept grown at longday, samples were taken after before transferred and 2days and 5days later at longday and shortday

extract_protocol:
total RNA were extract (Salzman et al., Plant Molecular Biology Reporter, 1999, 17: 11-17)
libraries were constructed according to instruction of the Illumina Gene Expression Sample Prep Kit

tag: genotype

value: longday for 3 weeks plus 2 d shortday

tag: tissue

value: plantlets


title: E26L2

description: Sample 2

source_name: plantlets_long day

value: longday for 3 weeks plus 2 d longday


title: E26S5

description: Sample 5

value: longday for 3 weeks plus 5 d shortday


title: E26L5

description: Sample 3

value: longday for 3 weeks plus 5 d longday


title: Melanoma

city: Nashville

first: Thomas

last: Andl

state: Tennessee

address: A2310 Medical Center North

department: Department of Medicine

institute: Vanderbilt University Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Quality control checks on raw sequence data from each sample will be performed using FastQC (Babraham Bioinformatics, London, UK).
Raw reads were then imported on a commercial data analysis platform CLCbio (CLCbio, MA, USA).
Adapter trimming was done to remove ligated adapter from 3' end of the sequenced reads with only one mismatch allowed, poorly aligned 3' ends were also trimmed. Sequences shorter than 15 nucleotides length were excluded from further analysis.
Trimmed Reads were then used to extract and count the small RNA which were then annotated with micro RNAs in miRBase release 18 database. Samples were grouped as per their types identifiers and quantification of miRNA abundance was done. Differential expression of miRNA was calculated on the basis of their fold change (default cut-off ≥ ±2.0) between mapped counts observed between individual groups.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Read per million (RPM) values for each Sample ...

source_name: Skin

extract_protocol:
Total RNA, including microRNAs, was isolated from frozen tissue and cell culture with the miRNeasy Mini Kit and from FFPE tissue with the miRNeasy FFPE Kit (Qiagen; Hilden, Germany), according to the manufacturer’s protocols.
Approximately 1ug of total RNA from each sample was taken into small RNA library preparation protocol using NEBNext® Small RNA Library Prep Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer's protocol.

value: Melanoma


title: Sample 7_HUCHX4_TGACC_L001_R1_001

description: Sample 7

value: Jurkat cells

value: NEB+Ext


title: Normal skin

value: Normal skin


title: Merkel cell carcinoma cell line, MS-1

source_name: Cell line

value: Merkel cell carcinoma cell line, MS-1


title: Squamous cell carcinoma (SCC)

value: Squamous cell carcinoma (SCC)


title: MDA_OVOL1&2_1

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
Base Calling: Illumina HiSeq
Quality Control: FastQC
Alignment: Tophat2.0.2 --b2-very-sensitive
Quality Control: FastQC
Abundance Measurement: CuffLinks/CuffDiff2.0.2; UCSC hg19.gtf transcriptome, with -u, -N, --compatible-hits-norm, and -b (relative to the UCSC hg19.fa)
Format Output: Format cufflinks output using a locally derived Perl script
Genome_build: HG19
Supplementary_files_format_and_content: Processed data files are output (.diff files) from CuffDiff.  These are text files, even though the extension is .diff, and we edited the file name to be specific to the relevant CuffDiff run.

extract_protocol:
TruSeq SBS Kit v3; TruSeq PE Cluster Kit v3 - cBot - HS; TruSeq Multiplex Sequencing Primer Box
Rneasy Quiagen

value: MDA

value: breast cancer cells

tag: genotype/variation


title: MDA_OVOL1&2_2


title: Merkel cell carcinoma_1

value: Merkel cell carcinoma


title: 142 Srf WT

city: New Haven

first: Stephanie

last: Halene

state: CT

address: 300 George St. 786E

department: Hematology/YCCC

institute: Yale University School of Medicine

data_processing:
basecalls performed using  Illumina CASAVA-1.8.1 software
reads alignment using tophat-2.0.0.Linux_x86_64
identification of differentially expression using cufflinks-2.0.0.Linux_x86_64
Genome_build: mm10
Supplementary_files_format_and_content: Series supplementary files include FPKM values and test statistics
Supplementary_files_format_and_content: isoform_exp.diff.txt: Transcript differential FPKM
Supplementary_files_format_and_content: gene_exp.diff.txt: Gene differential FPKM
Supplementary_files_format_and_content: tss_group_exp.diff.txt: Primary transcript differential FPKM
Supplementary_files_format_and_content: cds_exp.diff.txt: Coding sequence differential FPKM

source_name: Bone marrow

growth_protocol: primary mouse bone marrow derived neutrophils from Srf WT and KO mice

extract_protocol:
Qiagen RNA extraction protocol
Libraries were prepared according to Illumina’s TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2.

value: WT

value: Mature Gr1 high, 7/4 high, SSC high neutrophils


title: MDA_OVOL1_1


title: Merkel cell carcinoma_2


title: MDA_OVOL1_2


title: 63 Srf KO

value: Srf KO


title: MDA_CTRL_1

value: Control


title: 141 Srf WT


title: MDA_CTRL_2


title: Clone 4L.1.4 non-immune serum

city: La Jolla

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

library_source: genomic

data_processing:
Illumina sequencing of short reads (50 bp) was performed in four lanes of Hiseq 2000 using v2 clustering and sequencing reagents.
Basecalls performed using CASAVA version 1.8.1
Each ChIP sample yielded between 9.6-14.2M reads and were aligned uniquely to the mouse genome (mm9) using bowtie (Langmead et al., 2009).
Bound regions were detected using MACS1.4 (Zhang et al., 2008). Peaks for further analysis were filtered to have FDR % <=5 (number of peaks is 11809 for clone 4L.1.4 and 28166 for MSC21).
Genome_build: mm9
Supplementary_files_format_and_content: MACS1.4 peaks bed files

molecule: genomic DNA

source_name: MSC clone - control

growth_protocol: Mesenchymal cells were extacted from mouse bone marow and grown in Stem Cell media (Stem Cells Tech.).

extract_protocol:
Lysates were clarified from sonicated fixed cells and histone-DNA complexes were isolated with antibody.
Samples were prepared using the ChIP-Seq DNA Sample Prep Kit (illumina, cat#: IP-102-1001) according to manufactures instructions. In the final enrichment step of the protocol 12 cycles were performed to amplify the library. Samples were sequenced on the illumina HiSeq 2000 sequencer on a single read flowcell performing 50 sequencing cycles. Each sample was sequenced on 1 lane of the flowcell.

treatment_protocol: Independent cell samples were grown to confluence and ChIP was perfromed.

value: mesenchymal stem cell (MSC)

tag: culture

value: Clone

tag: chip antibody

value: non-immuned rabbit serum


title: spl rep1

city: shang hai

first: lihua

last: zhao

state: shang hai

address: FengLin road 300#

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequences were transformed into Clean Tags by filtering off empty reads, low-quality tags (containing ambiguous bases), adaptor-only tags, and tags that occurred only once (probably result from sequencing error). The remaining high quality sequences were mapped to the Arabidopsis thaliana genome (TAIR10, ftp://ftp.arabidopsis.org/Genes/TAIR10_genome_release).
For conservative and precise annotation, sequences with perfect homology or only 1-nt mismatch were considered further.
Clean tags aligned to multiple transcripts were excluded from our analysis. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and normalized to TPM (number of transcripts per million clean tags). When multiple types of tags were mapped to the different positions of the same gene, the gene expression levels were represented by the sum of all hit numbers
Genome_build: The remaining high quality sequences were mapped to the Arabidopsis thaliana genome (TAIR10, ftp://ftp.arabidopsis.org/Genes/TAIR10_genome_release)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Arabidopsis thaliana

source_name: ovules with placenta

growth_protocol: Eight-day-old seedlings were transferred to soil with 16-h-light/8-h-dark cycle at 22°C, 70% humidity,and grow up under this condition for 0ne month.

extract_protocol:
Dissected Ovule primordia from the ovaries were collected and stored in Qiagen RNAlater RNA stabilization reagent at 4°C,Total RNA was extracted from the ovule primordia with placenta tissues using the Qiagen RNAeasy Plant Mini kit.6μg of total RNA using Digital Gene Expression Tag Profiling Kit for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: flower

tag: Stage

value: floral buds at stage 10-11

tag: ecotype

value: Colombia

value: SPL-/-


title: spl rep2


title: Basal cell carcinoma

value: Basal cell carcinoma


title: Clone 4L.1.4 H4K20ME1

source_name: MSC clone - H4K20ME1 antibody


title: E26d0

description: Sample 1

value: longday for 3 weeks

value: plantlets


title: MDA_OVOL2_2

value: MDA


title: MSC21 non-immune serum

source_name: MSC population - control

value: Popoulation


title: MDA_OVOL2_1

value: breast cancer cells


title: 65 Srf KO


title: Lymph Node

source_name: Lymph node

value: Lymph Node


title: nhr-62;eat-2 rep1

status: Public on Mar 19 2014

city: Köln

first: Corinna

last: Klein

address: Joseph-Stelzmann-Straße 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: Sample D

data_processing:
Sequencing reads were trimmed to remove adapter sequence using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/)
The trimmed reads were aligned to the C. elegans reference genome (WBcel215.67) using tophat version 1.3 (Trapnell, Pachter & Salzberg 2009) with option −g1 to ensure unique mapping
The number of reads mapping to each Ensemble gene was counted with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count).
Statistical analysis was performed with the bioconductor package Deseq (Anders, Huber 2010).
Significant differentially expressed genes were compiled from the Deseq-result as follows: FDR<0.05, mean normalized count >10 and absolute Foldchange (FC) >1.5.
Genome_build: WBcel215.67
Supplementary_files_format_and_content: htseq-count-table.txt contains non-normalized read counts assigned to genes.

organism: Caenorhabditis elegans

source_name: day 0 adult without bearing eggs

growth_protocol: Worms were grown at 20C on OP50 plates.

extract_protocol:
Total RNA extraction was performed as described in Heestand et al. 2013
Described in Heestand et al. 2013

treatment_protocol: Worms were synchronized by two rounds of bleaching.

tag: strain/genotype


title: eat-2 rep2

description: Sample F


title: nhr-62;eat-2 rep3

description: Sample L


title: MSC21 H4K20ME1

source_name: MSC population - H4K20ME1 antibody


title: WT rep2

value: wild type


title: N2 rep3

description: Sample I


title: eat-2 rep1

description: Sample B


title: nhr-62 rep1

description: Sample C


title: nhr-62;eat-2 rep2

description: Sample H


title: WT rep1


title: nhr-62 rep2

description: Sample G


title: inoculated with diazothrophic bacteria_rep2

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

description: Sample 4

data_processing:
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and  three different databases -  all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing three mismatches with mature miRNAs from miRBase (v19.0). Only reads with match to Zea mays were included in the analysis.
The output of the miRProf contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization
Genome_build: Zea mays v.2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Zea mays

source_name: whole plant

growth_protocol: Herbaspirillum seropedicae provided by EMBRAPA Agrobiology were grown in NFb and JNFb media, respectively, at 30°C. Maize seeds of the variety UENF 506-8 [13] were surface-sterilized for 15 min with a 10% (v/v) solution of a commercial bleach containing 5.25% (w/v) of NaCl and then washed several times with distilled water [14]. Seeds were then soaked overnight in distilled water and germinated at 25°C in wet paper. Seven days after germination the seedlings were moved to 0.5x Hoagland’s solution in a growth chamber at 24°C on 10-h days and left for two weeks. The Hoagland’s solution was renewed every 3 or 4 days. After this period the seedlings were moved to pots with sand and vermiculite (2:1) and left for a week.

extract_protocol:
Total RNA was isolated from whole plants using Trizol (Invitrogen, CA, USA) as described by the manufacturer.
TruSeq Small RNA Sample Prep Kit

treatment_protocol: Fresh overnight Herbaspirillum seropedicae cultures were resuspended in 5 mM MES at pH 5.5 to 1 x 108 cells/mL and 100uL were injected in the stems of plants with a sterile 1 ml hypodermic syringe. Control plants were mock inoculated. Four plants of every variety were inoculated with bacteria suspensions. After seven days of inoculation the plants were analyzed phenotypically and quickly frozen in liquid nitrogen. Colonization was confirmed by plate counting in the same media for all the bacteria.

value: inoculated with Herbaspirillum seropedicae

tag: time

value: seven days cultivation


title: N2 rep2

description: Sample E


title: eat-2 rep3

description: Sample J


title: HUVEC rep2

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

data_processing:
Illumina Casava1.7 software used for basecalling.
fastq-multx -B barcode_withA.txt -b -m 0 lane1_phred33.fastq -o demultiplexed/%.fastq
tophat2 -p 8 -N 2 --read-edit-dist 2 -o tophat_ctrl1 -G ../../../../databases/human/hg19/lncRnas/Noncode_UCSC.gtf /media/media/databases/human/hg19/hg19_refGenome_UCSC HUVEC.fastq
cufflinks -p 6 -o cufflinks_ctr1/ -G /media/media/databases/mouse/hg19/Homo_sapiens.GRCh37.68_ENSEMBLE.gtf -u -b /media/media/databases/mouse/hg19/hg19.fa ../tophat_HUVEC/accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: human umbilical vein endothelial cells

growth_protocol: Third passage HUVEC (bought from Lonza, Basel, Switzerland)

extract_protocol:
Total RNA was isolated with the miRNeasy kit from Qiagen
Illumina TruSeq RNA sample preparation kit

treatment_protocol: Cells were cultivated in EGM medium, containing 10% FCS (Lonza)

value: HUVEC (human umbilical vein endothelial cells)

tag: source

value: multiple donors


title: mm_orthochromatic_3

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome or the murine mm9 genome using TopHat Version 1.3.3 software with default parameters
Reads in every gene were counted using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). Genes with less than 3 samples with >1 read counts/million (cpm) and >1 reads/transcript kb/million reads (rpkm) were called not expressed and were not used in further analysis. The read count data was normalized using the TMM method.21 Differentially expressed genes were identified using the edgeR exact test for the human data, and using an edgeR generalized linear model for the mouse data to accommodate a mouse batch effect.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: Counts per gene and log2 RPKM

source_name: erythroblast

extract_protocol:
Human erythroblasts at each stage of terminal erythroid differentiation were sorted by a combination of cell surface markers for glycophorin A, band 3, and α4 integrin. Murine erythroblasts were sorted from bone marrow using TER119, CD44 and forward scatter as markers. Total RNAs were extracted by RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).  Illumina TruSeq RNA Sample Prep Kit (Part # 15008136) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

tag: surface markers to isolate cells by facs-based methods

value: Ter119 positive, CD44 low and FSC low

value: orthochromatic erythroblast


title: HUVEC rep1


title: N2 rep1

description: Sample A


title: mm_polychromatic_3

value: Ter119 positive, CD44 medium and FSC medium

value: polychromatic erythroblast


title: mm_orthochromatic_1


title: mm_polychromatic_2


title: mm_orthochromatic_2


title: nhr-62 rep3

description: Sample K


title: mm_polychromatic_1


title: mm_basophilic_3

value: Ter119 positive, CD44 high and FSC high

value: basophilic erythroblast


title: mm_basophilic_2


title: hs_orthochromatic_3

value: Cultured CD34+ cells

value: Cord blood

value: GPA positive, Band3 high and alpha 4 integrin negative


title: mm_proerythroblast_3

value: Ter119 low, CD44 high and FSC high

value: proerythroblast


title: mm_basophilic_1


title: hs_orthochromatic_1


title: hs_orthochromatic_2


title: mm_proerythroblast_1


title: mm_proerythroblast_2


title: hs_polychromatic_3

value: GPA positive, Band3 high and alpha 4 integrin medium


title: control_rep2

description: Sample 3

value: control


title: hs_late_basophilic_3

value: GPA positive, Band3 high and alpha 4 integrin high

value: late basophilic erythroblast


title: hs_late_basophilic_1


title: hs_polychromatic_2


title: hs_polychromatic_1


title: hs_late_basophilic_2


title: hs_early_basophilic_3

value: GPA positive, Band3 medium and alpha 4 integrin high

value: early basophilic erythroblast


title: hs_early_basophilic_1


title: hs_proerythroblast_3

value: GPA low, Band3 negative and alpha 4 integrin high


title: hs_early_basophilic_2


title: inoculated_rep2

description:
Saccharum spp.
Sample 4

data_processing:
Quality of the sequences was evaluated by measuring the quality of the reads according to the percentage of bases having a base quality greater or equal than 30 (Q30)
3’ Illumina adapters (CTGTAGGCACCATCAAT) and “N” bases were trimmed
Using the UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) and  three different databases -  all plant t/rRNAs from Rfam, all Arabidopsis tRNAs from The Genomic tRNA Database and all plant t/rRNA sequences from EMBL release - reads with low-complexity (less than 3 different bases) and both sense and antisense matches with t/rRNAs were removed
Detection of conserved miRNAs with UEA sRNA toolkit-Plant version miRProf pipeline was done allowing three mismatches with mature miRNAs from miRBase (v17.0). Only reads with match to Sorghum bicolor were included in the analysis.
The output of the miRProf contains information about unique sequences counts. Counts were normalized in reads per 1 million (RPM) and total reads counts after the final trimming and filtering steps were used for normalization
Genome_build: Sorghum bicolor v1.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Saccharum hybrid cultivar SP70-1143

growth_protocol: Acidovorax avenae subsp. avenae obtained from the Culture Collection of the Instituto Biológico (IBSBF) was grown in NA medium (beef extract 3 g/L; Peptone 5 g/L; NaCl 5 g/L) at 28ºC. In vitro-grown sugarcane plantlets were maintained at 28°C with an irradiance of 60 µmol photons m-2 s-1 and 12 h photoperiod

treatment_protocol: After the development of a root system, vigorous and pathogen-free plants were divided in two halves with a scalpel. One half was inoculated by immersing the root system for 5 minute in a suspension of A. avenae in distilled water (106 CFU mL-1), and then washed twice with distilled water in order to eliminate superficial bacteria. The other half was used as control, immersing the root system in distilled water by 5 minute and then washed twice with distilled water. Inoculated and control plants were transferred to MS medium and kept there for seven days. After this period, whole plants were harvested and examined for bacterial colonization by plate counting.

tag: infection

value: inoculated with Acidovorax avenae subsp avenae

value: seven days cultivation


title: hs_proerythroblast_2

tag: cell type


title: hs_proerythroblast_1

tag: strain


title: IgG Control

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

description: ChIP-seq data with an immunoprecipitated sample using a control IgG

data_processing:
Alignment with bowtie/0.12.8 using mm9 as reference genome and default parameters
Peak calling with macs/1.4.2 using mfold:10,30, pvalue cutoff: 1.00e-05, bandwidth: 300 to generate peak calling model
samtools/0.1.18 and  bedtools/2.15.0 used to interconvert between file formats
Genome_build: mm9 reference assembly
Supplementary_files_format_and_content: bed and wiggle files

growth_protocol: HC11 cells were grown in media RPMI 1640 media suplemented with insulin (5microg/mL), EGF (10microg/mL), and FBS (10%).

extract_protocol:
Cells were scraped and sonicated utilizing Diagenode Bioruptor at High setting and cycling 30 seconds ON, 30 seconds OFF. Ovol2-DNA complexes were isolated with lab generated anti-Ovol2 antibody specific against mouse.
Libraries were prepared according to instructions for BiooScientific NEXTflex ChIP-Seq Library Systems. Specifically, DNA quality and fragment size was assessed by Qubit Sensitivity DNA assay, and the following library preparation steps were achieved with the following mixes: End repair of immunoprecipitated DNA with NEXTflex ChIP End Repair, 3' adenylation NEXTflex ChIP Adenylation mix, Adapter ligation with NEXTflex ChIP-Seq barcode kit containing barcodes to be used. PCR amplification used NEXTflex ChIP Primer Mix supplied in Bioo Scientific NEXTflex ChIP-Seq Barcode kit and amplified for the following program: 2min @ 98C, 30sec @ 98C, 30 sec @ 65C (repeated 16 cycles), 1min @ 72C, 4min @ 72C. Quality of libraries again assesses by Qubit DNA high Sensitivity.

value: Mammary epithelial cells

tag: passage

value: control IgG

tag: vendor/catalog#

value: Santa Cruz/sc-2027

value: Balb/C


title: Ovol2 ChIP

description: ChIP-seq data with an immunoprecipitated sample using an antibody against Ovol2

value: antibody against Ovol2

value: Custom made


title: tolerant 24h

description:
Saccharum spp.
Sample 9

organism: Saccharum hybrid cultivar CTC6

source_name: leaf

growth_protocol: Stalks of sugarcane cultivars, with different drought sensitivities, were provided by the Centro de Tecnologia Canavieira (CTC). Based on chlorophyll and water content measurements, cultivars CTC15, CTC6, SP83-2847 and SP83-5073, and CTC9, CTC13, SP90-1638 and SP90-3414 were considered as drought tolerant and sensitive, respectively. Stalks were planted germinated and grown in 5L pots with a mixture of soil and sand (2:1) in a greenhouse at 28ºC, and irrigated by dripping.

treatment_protocol: After three months, the plants were exposed to drought stress by withholding water for 24hrs. Treated and control roots and shoots were harvested at 0 and 24 hours of treatment, respectively.

tag: treatment

value: 3 months of greenhouse cultivation


title: control_rep2

description:
Saccharum spp.
Sample 3

tag: genotype


title: sensitive 24h

description:
Saccharum spp.
Sample 10

organism: Saccharum hybrid cultivar SP90-3414

value: drought stress by withholding water for 24hrs


title: Euphyllas11

status: Public on Mar 18 2014

city: Harbin

first: Jinjun

last: Gao

state: Heilongjiang

address: Mucai Street

department: Life Sciences

institute: Northeast Agricultural University

data_processing:
Raw sequencing reads of five samples were mixed together to perform the following filtration using a stringent process and subsequent de novo assembly. The adaptor contamination was removed, the reads were screened from the 3’ to 5’ to trim the bases with a quality score of Q<20 using5bp windows and the reads with final length less than 25bp were removed.
De novo transcriptome assembly was performed by Velvet followed by Oases with default settings except for K-mer value (69) to get contigs and transcripts. High quality reads of every sample were remapped to transcripts to get the abundance of transcripts using Bowtie program. Those transcripts with no reads mapped in all five samples were considered error and removed. All the transcripts were searched against Arabidopsis database, for those with no hits were then searched to NCBI nr database with BLAST program (E-value < 1E-5), and the top-hit transcripts were selected as unigenes.
The R package DESeq was performed to get the normalized signal for each unigene with the the number of reads mapped to each unigene as input.
Genome_build: n/a
Supplementary_files_format_and_content: Excel files includes annotation information and expression values generated by DESeq for each samples

organism: Brassica oleracea var. italica

source_name: Euphylla

extract_protocol:
Samples harvested were immediately frozen in liquid nitrogen and total RNA of each sample was isolated using E.Z.N.A. Plant RNA Kit(OMEGA bio-tek, GA) according to the instructions from the manufacturer.
Illumina Miseq library construction was performed according to the manufacturer’s instructions (Illumia, San Diego, CA).

value: Qingxiu

tag: tissue

value: Euphylla

tag: age

value: post germination day 11


title: Cotyledon3

source_name: Cotyledon

value: Cotyledon

value: post germination day 3


title: Cotyledon7

value: post germination day 7


title: Seeds

source_name: Seed

value: Germinated Seed

value: post germination day 0


title: Cotyledon11


title: s9 ddm1_2_dcl1_11

city: Cold Spring Harbor

first: Kate

middle: M

last: Creasey

address: 1 Bungtown Road

department: Plant Sciences

institute: Cold Spring Harbor Laboratory

data_processing: Base call and quality scores were generated using the standard Illumina Pipeline. Bowtie from the open-source Tuxedo suite, allowing for both unique (U) and multiple (M) mapping reads, normalized by reads per million (RPM).

source_name: Arabidopsis stages 9 to 12 inflorescence

growth_protocol: Plants were grown under standard long day growth conditions.

extract_protocol:
Total RNA was isolated from pooled inflorescence tissue (n = 3) and TRIzol (Invitrogen).
Small RNA libraries were constructed using Illumina Tru-Seq Small RNA preparation kit.
NEBNext multiplex small RNA libraries

treatment_protocol: No treatment.

value: plant inflorescence

tag: genotype/variation


title: s6 ddm1_2_dcl1_11


title: s8 ddm1_2


title: s7 col_0


title: srna ddm1-2 rdr6-15


title: rdr6-15 (bisulfite-seq)

description: DNA methylation analysis in Arabidopsis

data_processing:
Base call and quality scores were generated using the standard Illumina Pipeline for Paired-End Reads.
BS-seq reads were trimmed for adaptor sequence and low quality base call, then aligned to ZmB73 4a.53 genome assembly using rmap V2.03  with parameters -Q -v -m 4
Then the C/T counts from aligned BS-seq reads for each cytosine in reference genome were saved in CT count file
Genome_build: TAIR10
Supplementary_files_format_and_content: The CT count files have the first 6 columns the same as bed file, the 7th col is count of C, the 8th col is count of T, the 9th col is the 3 nt in reference genome, the 10th col is the context of cytosine

growth_protocol: Arabidopsis grown on soil under standard long day growth conditions.

extract_protocol: DNA was isolated from pooled inflorescence tissue (n = 3) collected phenol/chloroform extraction. For each library, 1-5 μg of genomic DNA was sheared using a Covaris S220 Adaptive Focused Acoustics ultra sonicator. Libraries were constructed following standard protocol using the NEB Next DNA Sample Prep Master Mix Set 1 (NEB E6040) and Illumina-compatible paired-end adaptors, which had all cytosines, methylated. 50 ng of each library was treated with sodium bisulphite using EZ DNA Methylation-GoldTM Kit (Zymo Research D5005) according to the protocol provided by the manufacturer. For each purified library 5-10 ng of purified library was amplified using Expand High Fidelity PLUS PCR system (Roche 03300242001), which is capable of efficiently amplifying uracil-containing templates. 50 μl reactions contained 200 μM each dNTP, 1 μM primer, 2.5 mM MgCl2  and 2.5 U Expand HiFi enzyme, and were performed according to the manufacturer’s instructions for 18 cycles. Amplified libraries were ran on 2% MetaPhor® agarose (Lonza 50108) gel. Fragments of 220-350 bp were excised from gel and purified using the QIAquick PCR Purification kit (Qiagen 28104). DNA concentrations were quantified on Bioanalyzer (Agilent), diluted to 10 nM and loaded on flow cells to generate clusters.


title: Col-0 (bisulfite-seq)

description: DNA methylation analysis in Arabidopsis


title: ddm1-2 (bisulfite-seq)

description: DNA methylation analysis in Arabidopsis


title: srna ddm1-2


title: ddm1-2 rdr6-15 replicate 2 (bisulfite-seq)

description: DNA methylation analysis in Arabidopsis


title: ddm1-2 rdr6-15 (bisulfite-seq)

description: DNA methylation analysis in Arabidopsis


title: srna rdr6-15


title: srna Col-0


title: ddm1-2 [PARE-seq]

description: Degradome analysis in Arabidopsis to validate microRNA prediction cleavage sites at transposons.

data_processing:
The adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: tag count file

source_name: mix-stage inflorescence

growth_protocol: Arabidopsis grown under standard long day growth conditions.

extract_protocol:
Mix-stage inflorescence (contain majority of unopened flower buds) were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Invitrogen) according to manufacturer's protocol.
PARE: Degradome libraries (PARE) libraries were constructed as previously described (Zhai et al. 2013 PMID: 23810899). The libraries were sequenced on an Illumina HiSeq at the Delaware Biotechnology Institute (Newark, DE).

value: mix-stage inflorescence


title: Col-0 [PARE-seq]


title: rdr6-15 [PARE-seq]


title: rhesus_monkey_heart

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
raw reads were aligned by Tophat v1.2.0
only uniquely-mapped reads are retained
RPKM values were calculated by in-house perl scripts
Genome_build: rheMac2
Supplementary_files_format_and_content: RhesusBase1 Transcript ID, Ensembl Gene ID, RPKM Values, Number of Mapped Reads, Total Length of Exon, The Gene Locus

organism: Macaca mulatta

source_name: heart

extract_protocol:
Total RNA was extracted from 2 rhesus monkey tissues using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies). Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions.
A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

value: heart

tag: gender

value: male

tag: library type

value: strand-specific, dUTP protocal


title: dbr1.Δ _2

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

description:
dbr1_2 (Name in ExpressionTable.txt)
total RNA (rRNA depleted)
Strand specific RNA-Seq

data_processing:
Sequence reads of 49 base length originating from each sample were aligned, using Bowtie 0.12.725, to the S. pombe genome sequence (Ensembl S. pombe, Build EF1, version 13) and to the corresponding exon-exon junctions database. Up to 3 base-pair mismatches were allowed. Reads that matched multiple loci were removed from further analysis, and the resultant alignment files were processed to generate ‘pile-ups’ against each chromosome. Unmapped reads were used for lariat mapping,.
Searches were performed against the genome sequence combined with a dataset of known exon-exon junctions as defined by Ensembl S. pombe, release-13. To ensure that a 49-base read mapped to a splice junction, only the last 43 bases of the first exon and the first 43 bases of the second exon were considered (if the exon exceeded length 43). In this way, reads that overlapped a junction by less than 6 nucleotides were excluded. Reads that matched to more than one junction or elsewhere in the genome were also discarded.
Genome_build: Ensembl S. pombe, Build EF1, version 13
Supplementary_files_format_and_content: Expression table and RPKM summary for all samples in tab-delimited file ExpressionTable.txt (linked as supplementary file on Series record)

organism: Schizosaccharomyces pombe

source_name: S. pombe cells, dbr1.Δ

growth_protocol: Two biological replicates of wild-type (ED668) and dbr1.Δ cultures were grown in YES (yeast extracts plus supplements) media at 32°C till they reached OD600 0.4.

extract_protocol:
Cells were harvested and total RNA was isolated by hot-phenol extraction, and RNA quality was assessed on a Bioanalyzer instrument (Agilent). Total RNA was treated with DNase (Turbo DNA-free by ambion), and thereafter 4 μg was treated with a beta version of Ribo-Zero™ Magnetic Gold Kit (Yeast) to deplete rRNAs.
RNA-seq libraries were prepared from rRNA-free RNA using a strand-specific library preparation protocol based on an early version of the Illumina TruSeq Small RNA Sample Prep Kit. In brief, rRNA-depleted RNA was fragmented to an average size of ~200nt. Fragmented RNA was 3’-de-phosphorylated with Antartic phosphatase and 5’-phosphorylated with polynucleotide kinase; this treatment prepares RNA fragments for subsequent ligation of Illumina RNA adaptors to their 5’ and 3’ ends using a 3’-RNA ligase and a T4 RNA ligase, respectively. First-strand cDNA was produced using a primer specific for the Illumina 3’-adaptor. The library was amplified with 15 PCR cycles using primers specific for the Illumina adaptors and purified using SPRI-beads (Agencourt, Beckman Coulter). Library size distributions and concentrations were determined on a Bioanalyzer (Agilent). RNA-seq libraries were sequenced on an Illumina HiSeq 2000 instrument at the Core Facility of the Huntsman Cancer Institute (University of Utah).


title: E10.5 central neural epithelium

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: E10.5 CNE

data_processing:
RNA-seq data were analyzed by a combination of Bowtie, Tophat, and GeneSpring versions 7.3.1
RNA-seq BAM files generated using the Bowtie-Tophat2 pipeline were analyzed for the expression of known and unknown genes/transcripts using both Cufflinks2 and GeneSpring 12.6. Workflows included filtering to remove duplicate reads, and those with post-aligned read metrics mapping quality below 40, as well as the exclusion of samples that exhibited strong outlier 3’/5’ read distribution ratios.
Transcript/isoform and gene summarized expression tables were filtered to identify entities whose expression was at least 3 FPKM (Cufflinks) or 3 nRPKM (GeneSpring) in at least one sample.
The RNA-seq FPKM table was normalized using a baseline of 1 FPKM (a level of gene expression unlikely to be significant in these assays) followed by global median normalization to give a table of ratio values.
Genome_build: mm9
Supplementary_files_format_and_content: text files containing normalized expression values

source_name: Mouse embryo_E10.5

extract_protocol:
RNA was purified using the ZR RNA MicroPrep kit (Zymo).
RNA-seq was carried out using 50b single end reads on the Illumina Hi-Seq 2500 machine according to Illumina protocols, with read depths > 40 million.

tag: Stage

value: central neural epithelium


title: E10.5 lateral prominence neural epithelium

description: E10.5 LPNE

value: lateral prominence neural epithelium


title: dbr1.Δ _1

description:
dbr1_1 (Name in ExpressionTable.txt) (bioneer strain)
total RNA (rRNA depleted)
Strand specific RNA-Seq


title: Wild-type_2

description:
wt_2 (Name in ExpressionTable.txt)
total RNA (rRNA depleted)
Strand specific RNA-Seq

source_name: S. pombe cells, wt

value: wild-type (ED668)


title: Wild-type_1

description:
wt_1 (Name in ExpressionTable.txt)
total RNA (rRNA depleted)
Strand specific RNA-Seq


title: Col-0  AtGP1 with miRNA construct

value: Col-0 AtGP1 with miRNA construct


title: E10.5 olfactory Pit

description: E10.5 OP

value: olfactory pit


title: E10.5 medial nasal prominence

description: E10.5 MNP

value: medial nasal prominence


title: Stomach mmPCR-Seq R1

city: Stanford

first: Stephen

last: Montgomery

address: 300 Pasteur Lane

institute: Stanford University

description: library strategy: mmPCR-Seq

data_processing:
Aligned samples to reference genome (hg19) with STAR (v2.1.4)
Sorted aligned files (.sam) using Samtools (v0.1.18)
Performed variant calling using Samtools mpileup command
Calculated allelic ratio for each genomic loci by dividing the number of reads mapped to the non-ref allele divided by the total reads per site
Genome_build: hg19
Supplementary_files_format_and_content: Allelic read counts for each genomic loci and corresponding gene tested by mmPCR-Seq

source_name: Stomach

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
mmPCR-Seq libraries were prepared as previously described in Zhang R, et al. (Nature Methods 2013)

value: Stomach


title: E10.5 maxillary arch

description: E10.5 MaxArch

value: maxillayr arch


title: Pancreas mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Pancreas

value: Pancreas


title: ddm1-2 rdr6-15 [PARE-seq]


title: E10.5 mandibular arch

description: E10.5 ManArch

value: mandibular arch


title: Lung mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Lung

value: Lung


title: Skeletal muscle mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Skeletal muscle

value: Skeletal muscle


title: E10.5 lateral nasal prominence

description: E10.5 LNP

value: lateral nasal prominence


title: E9.5 maxillary arch

description: E9.5 MaxArch

source_name: Mouse embryo_E9.5

value: maxillary arch


title: Pancreas mmPCR-Seq R1

description: library strategy: mmPCR-Seq


title: E10.5 dorsal control neural epithelium

description: E10.5 DCNE

value: dorsal control neural epithelium


title: E9.5 mandibular arch

description: E9.5 ManArch


title: E8.5 non-floor plate neural epithelium

description: E8.5 NFP

source_name: Mouse embryo_E8.5

value: non-floor plate neural epithelium


title: Lung mmPCR-Seq R1

description: library strategy: mmPCR-Seq


title: E9.5 cranial mesenchyme

description: E9.5 CranialMes

value: cranail mesenchyme


title: Liver mmPCR-Seq R1

description: library strategy: mmPCR-Seq

source_name: Liver

value: Liver


title: Small intestine mmPCR-Seq R1

description: library strategy: mmPCR-Seq

source_name: Small intestine

value: Small intestine


title: E8.5 mesoderm

description: E8.5 Mesoderm

value: Mesoderm


title: Small intestine mmPCR-Seq R2

description: library strategy: mmPCR-Seq


title: E8.5 floor plate

description: E8.5 Floor Plate

value: floor plate


title: U2OS.CTCF.m

city: New York City

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

description:
Sample 3 (It is simply the merged file of the sequencing data from Samples 1 and 2).
library strategy: PAR-CLIP

data_processing:
Adapters were trimmed & sequences mapped to hg19 with BOWTIE -m40 -v2 --best
Optical/PCR duplicates were removed & reads mapping to repetitive regions (repeatMasker) were removed
bigBed files were generated
Replicate experiments were merged & intersectBed utility was used to map read counts to ensembl annotation
Annotation was filtered for genes that contain at least 5 mapped reads to generate .TXT file
Genome_build: hg19
Supplementary_files_format_and_content: bigBed files containing PAR-CLIP reads & TXT file containing # reads mapping to each gene

extract_protocol:
Whole nuclear lysates (WNL) were obtained by fractionating cytoplasm and nuclei by a standard method (Dunham, 1985), then nuclei were incubated for 10 min at 37ºC in an appropriate volume of CLIP buffer (20 mM HEPES pH 7.4, 5 mM EDTA, 150 mM NaCl, 2% lauryldimethylbetaine) supplemented with protease inhibitors, 20 U/ml Turbo DNase (Life technologies), and 200 U/ml murine RNase inhibitor (New England Biolabs). After clearing the lysate by centrifugation, immunoprecipitations were carried out using 1 mg of WNL, appropriate antibody and protein G-coupled dynabeads (Life technologies) in the same CLIP buffer, ON at 4ºC, after which, contaminating DNA was removed by treating the beads with Turbo DNase (2 U in 20 µl). Then the crosslinked RNA was labeled by successive incubation with 5 U Antarctic phosphatase (New England Biolabs), ligation of a 3′-blocked DNA adapter (100 pmol/μl)  and incubation with 5U T4 PNK (New England Biolabs) in the presence of 10 µCi [γ-32P] ATP (PerkinElmer, MA). Labeled material was resolved on 8% bis-tris gels, transferred to nitrocellulose membranes and visualized by autoradiography.
Libraries were prepared according to Illumina's instructions. Briefly, The band of interest was excised and RNA eluted from the membrane by treatment with proteinase K (Roche, 4 mg/ml) for 30 min at 37 °C and then with proteinase K in the presence of 3.5 M urea for 30 min at 55 °C. After phenol/chloroform extraction, custom-designed 5′ RNA adapters were ligated, the products were size-selected on polyacrylamide gels, and libraries were amplified and sequenced on an Illumina HiSeq 2000 sequencing system.

treatment_protocol: PAR-CLIP was performed as described with some modifications (Bonasio, et al 2013 sub.) Briefly, U2OS cells were grown under standard conditions and pulsed with 400 µM 4-SU (Sigma) for 16–24 h. After washing the plates with PBS, cells were crosslinked with 400 mJ/cm2 UVA (365 nm) using a Stratalinker UV crosslinker (Stratagene, CA).

tag: cell line

value: osteosarcoma U2OS cell line

tag: antibody

value: anti-CTCF (Abcam, cat# ab70303, lot#s GR98618-4 and GR27477-7)


title: Heart mmPCR-Seq R1

description: library strategy: mmPCR-Seq

source_name: Heart

value: Heart


title: Aedes pMos3DB2pBac

city: Pomona

first: Peter

last: Arensburger

state: CA

address: 3801 Watkins Avenue

department: Dept. of Biology

institute: California State Polytechnic University Pomona

library_source: non-genomic

data_processing:
For all libraries, the RAW files were processed using custom written PERL and R scripts (availalbe upon request from the authors) or using software described below.  Processing workflow:
1) remove adapter sequences on 3' end (5' TCGTATGCCGTCTTCTGCTTG  3') sequences without recognizable adapter sequences were discarded from further analysis
2) remove ribosomal degradation products using BLAT aligner (Kent 2002)
3) map the remaining sequences to the the appropiate genome using the alignment program Bowtie (Langmead et al. 2009).  Mapping paramters seed length 30 (-l 30) and up to two mismatches with reference genome (-n 2)
a) for RAW files RNAlib1.fastq, RNAlib2.fastq, RNAlib4.fastq, RNAlib6.fastq, RNAlib10.fastq, RNAlib11.fastq and RNAlib12.fastq mapped to  Aedes agegypti genome assembly (AaegL1) hosted by VectorBase
b) for RAW file RNAlib14.fastq mapped to Drosophila melanogaster assembly BDGP release 5
References:
Kent, W. J. 2002. BLAT---The BLAST-Like Alignment Tool.â? Genome Research 12 (March 20): 656-664. doi:10.1101/gr.229202.
Langmead, B., C. Trapnell, M. Pop, and S.L. Salzberg. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.â? Genome Biol 10 (3): R25.

organism: Aedes aegypti

source_name: whole adult

extract_protocol: Illumina small RNA sample prep kit

value: Orlando

tag: colony transformation line

value: Transformed with sequence containing Mos TIRs and piggyBac transposase

tag: technical replicate number

value: whole organism


title: Heart mmPCR-Seq R2

description: library strategy: mmPCR-Seq


title: Frontal lobe mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Frontal lobe

value: Frontal lobe


title: U2OS.CTCF.b2

description:
Sample 2
library strategy: PAR-CLIP

growth_protocol: U2OS cells were grown under standard conditions

value: anti-CTCF (Abcam, cat# ab70303, lot# GR27477-7)


title: Stomach mmPCR-Seq R2

description: library strategy: mmPCR-Seq

value: Stomach


title: U2OS.CTCF.b1

description:
Sample 1
library strategy: PAR-CLIP

value: anti-CTCF (Abcam, cat# ab70303, lot# GR98618-4)


title: Aedes auto-Hermes257

value: Transformed with an intact Hermes element

value: an intact Hermes element


title: Aedes wild

value: not transformed


title: Frontal lobe mmPCR-Seq R1

description: library strategy: mmPCR-Seq


title: Aedes p3EB2Mos rep2

value: transformed with sequence containing piggyBac TIRs and Mos transposase


title: Cerebellum mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Cerebellum

value: Cerebellum


title: Colon mmPCR-Seq R2

description: library strategy: mmPCR-Seq

source_name: Colon

value: Colon


title: Colon mmPCR-Seq R1

description: library strategy: mmPCR-Seq


title: Aedes p3EB2Mos rep1

value: sequence containing piggyBac TIRs and Mos transposase


title: Liver mmPCR-Seq R2

description: library strategy: mmPCR-Seq

value: Liver


title: Aedes pMosA5D rep2

value: transformed with sequence containing Mos TIRs and Hermes transposase


title: Drosophila auto-Hermes

organism: Drosophila melanogaster

value: csW+


title: Aedes pMosA5D rep1

value: Orlando

value: sequence containing Mos TIRs and Hermes transposase


title: Cerebellum mmPCR-Seq R1

description: library strategy: mmPCR-Seq


title: E8.5 caudal brain neural epithelium

description: E8.5 CBNE

value: caudal brain neural epithelium


title: So_ChIP-seq_rep2

status: Public on Mar 17 2014

city: Houston

first: Feng

last: Wang

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the dm3 genome assembly using The Eland Short Read Aligner
peaks were called using MACS version 1.4
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated using MACS version 1.4

source_name: eye-antennal imaginal disc

growth_protocol: Raised at 25C on standard Drosophila media

extract_protocol:
ChIP protocol (after Jemc and Rebay 2007): imaginal discs were fixed in formaldehyde and homogenized in lysis buffer. Resulting chromatin was sonicated, precleared, and incubated o/n with anti-So (negative control incubated w/o antibody). Chromatin was incubated with protein A beads, eluted, and crosslinks reversed at 65C, and DNA purified with PCR purification kit.
Illumina libraries were generated according to the manufacturer’s sample preparation protocol. Briefly, ~10 ng of DNA was end-repaired using polynucleotide kinase and Klenow. The 5’ ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3’ ends using Klenow exo-nuclease. Illumina Y-shaped index adaptors were ligated to the repaired ends, then the DNA fragments were PCR amplified for 21 cycles and fragments from 200-500 bp were isolated by gel purification. The libraries were quantified using the PicoGreen fluorescence assay and their size distributions determined by the Agilent 2100 Bioanalyzer. Libraries were sequenced on the Illumina Illumina Genome Analyzer IIx as 35-bp single-end reads, following the manufacturer's protocols.

value: eye-antennal imaginal disc

tag: developmental stage

value: wandering 3rd instar larva

tag: chip antibody

value: guinea pig anti-So (from I. Rebay)


title: So_ChIP-seq_neg-ctrl


title: So_ChIP-seq_rep1


title: xf14_sensor_Oxidized

city: Biberach an der Riß

first: Holger

state: Rhineland Palatinate

address: Birkendorfer Str. 65

department: global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Basecalls performed using CASAVA version 1.8.2
Adapter trimming performed using Flexbar version 2.4
Small RNA reads aligned to C. elegans Wbcel215 including additional sequence for GFP_HIS_66 construct.
Read counts for known miRNA and 21U RNA loci obtained using girafe 1.0 Bioconductor package.
Genome_build: WBcel215, additional sequence for GFP_HIS_66 construct.
Supplementary_files_format_and_content: Read assignments to known 21U loci in csv (tab separated). Column names: strand, read ref, chromosome, vread start, read length, corresponding 21U name, corresponding 21U sequence, read start position relative to 21U locus, read end position relative to 21U locus.

source_name: xf14 sensor Oxidized

growth_protocol: C. elegans was cultured on NGM plates with E. coli OP50 as food source

extract_protocol:
RNA was extracted from a synchronized adult population using Trizol (Sigma- Aldrich)
Samples were enriched for small RNAs using the Mirvana kit from Life Technologies. For CIP treated samples 5 ug of small RNAs were treated with 50 U of calf intestine phosphatase (CIP, NEB) at 37C for 1 hour (Gu et al. 2012), followed by Trizol extraction and TAP treatment. One µg of enriched small RNA was size-selected between 15- to 30-nt on 15% TBE-urea gel after treating with 10 U of tobacco acid phosphatase (Epicenter) at 37°C for 2 h to digest 5’ tri- and di-phosphates to mono-phosphates. NebNext small RNA: Small RNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) according to the manufacture’s instruction. In brief, small RNA was first ligated to the 3’ adapter and then the 5’ adapter, both for 1 h at 25°C. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 15 cycles using NEBNext index primers #13-24. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit. Only the fraction containing 135-161 bp was pooled in equal molar ratio. Kamminga2012: Library preparation as described in Kamminga et al., PloS Genetics 8(7):e1002702, 2013.

tag: strain

tag: library prep


title: Wild-type_CIP_TAP

source_name: Wild-type CIP TAP

value: TAP

value: NEBNext small RNA


title: prg-1(pk2298)_TAP

source_name: prg-1(pk2298) TAP


title: prg-1(pk2298)_CIP_TAP

source_name: prg-1(pk2298) CIP TAP

value: CIP-TAP


title: Wild-type_TAP

source_name: Wild-type TAP


title: WT_sensor_TAP

source_name: WT sensor TAP


title: pid-1(xf35)_TAP

source_name: pid-1(xf35) TAP


title: pid-1(xf14)_CIP_TAP

source_name: pid-1(xf14) CIP TAP


title: pid-1(xf36)_TAP

source_name: pid-1(xf36) TAP


title: WT_sensor_Oxidized

source_name: WT sensor Oxidized


title: S+2F

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

description: I

data_processing:
The reads generated were mapped to the D. melanogaster transcriptome using Tophat2. Those that did not map to the transcriptome were then mapped to the genome.
The mapped reads were assigned to features of the D. melanogaster transcriptome using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/).
This count data was then normalized for library size in the DESeq2 package of the BioConductor suite.
Genome_build: Release 5 (BDGP5)
Supplementary_files_format_and_content: Tab-delimited text file is a matrix of normalized counts for all samples.

source_name: fly heads, female, polygamous

growth_protocol: Each population was reared in a common garden for one generation. Emerging virgin flies were separated by sex and held in same-sex groups until RNA extraction.

extract_protocol:
Total RNA was extracted from dissected fly heads from all of the groups using RNAzol (Molecular Research Center, Inc.).
Libraries were generated using Illumina's mRNA-Seq preparation kit.

treatment_protocol: 117 generations of evolution under a mating system manipulation (monogamy vs. polygamy).

value: heads

value: 4 days

tag: Sex

value: female

tag: mating system

value: polygamy


title: S-3F

description: E

source_name: fly heads, female, monogamous

value: monogamy


title: S-2M

description: D

source_name: fly heads, male, monogamous

value: male


title: S+3M

description: L

source_name: fly heads, male, polygamous


title: shFox2-2_r1_RNAseq

city: Cambridge

first: Mohini

last: Jangi

state: MA

address: 500 Main Street

department: Biology

institute: MIT

description: RNAseq, paired-end

data_processing:
Paired-end reads were trimmed of adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATG), collapsed, and aligned to a custom gene annotation using Tophat 2.0.  Abundance estimation and differential analysis were performed using Cufflinks version 2.1.1.
genome build:  mm9

source_name: embryonic stem cells

growth_protocol: Mouse V6.5 ES cells were cultured in DME/HEPES supplemented with 2mM L-glutamine, 100 Units Penicillin, 100 ug Streptomycin, 1X Non-essential amino-acids (Invitrogen), 15% Defined FBS (Hyclone-ES screened), 1000U/ml ESGRO (Chemicon) on gelatinized flasks.

extract_protocol:
Total RNA was extracted using Trizol.
Poly(A) selected RNA was prepared for paired-end sequencing using standard Illumina protocols.

treatment_protocol: ES cells were infected in biological duplicate with lentivirus expressing control (shLuciferase, shGFP) or Rbfox2 (shFox2-1, shFox2-2) shRNAs.  Cells were harvested after 3 days of selection in 1ug/ml puromycin followed by 24 hours in medium containing no puromycin

tag: cell type

value: V6.5 ES cells

tag: lentivirus infection


title: shFox2-2_r2_RNAseq

description: RNAseq, paired-end


title: S+3F

description: K

tag: tissue

tag: age


title: S+2M

description: J


title: S+1M

description: H


title: shFox2-1_r2_RNAseq

description: RNAseq, paired-end


title: S-2F

description: C


title: shFox2-1_r1_RNAseq

description: RNAseq, paired-end


title: pid-1(xf14)_TAP

source_name: pid-1(xf14) TAP

tag: treatment


title: S-3M

description: F


title: xf14_sensor_TAP

source_name: xf14 sensor TAP


title: shGFP_r2_RNAseq

description: RNAseq, paired-end

value: shGFP


title: shGFP_r1_RNAseq

description: RNAseq, paired-end


title: S+1F

description: G


title: shLuc_r2_RNAseq

description: RNAseq, paired-end

value: shLuciferase


title: shLuc_r1_RNAseq

description: RNAseq, paired-end


title: Ncrassa_xylose

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Neurospora crassa OR74A genome (version 12) using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM)  and differential gene expression was determined by DESeq package (v1.5.1).
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Conidia from 10-day-old agar culture were collected and counted by haemocytometer, then inoculated into 1×vogel's salts with 2% carbon source (D-glucose, D-xylose or L-arabinose) and grown for 16-26 hrs at 28 °C with constant light

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: carbon source

value: D-xylose

tag: genotype

value: wild type


title: FHFOX2_iCLIP

description: iCLIP

data_processing:
Sequenced reads were trimmed to remove adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) and collapsed using the FastX toolkit.  Crosslink sites were determined from 5’ terminal nucleotides of contiguously-mapping reads and deletion sites of reads mapping with deletions.
Crosslink sites extended by 12nt on either side were used to generate clusters using the Clipper algorithm (Lovci et al., 2013).  Clusters were filtered for those with FHFOX2 enrichment over UntagFOX2 above a q-value threshold of 0.05 using a binomial test.
genome build:  mm9
processed data file and content:  Single nucleotide crosslink sites in bigwig format (unstranded); significantly enriched binding clusters in bed format

extract_protocol: Cell pellets were resuspended in lysis buffer, partially digested with RNase I, and serially immunoprecipitated with FLAG and HA antibodies.  Radiolabeled protein-RNA complexes were resolved on SDS-PAGE gels and transferred to nitrocellulose.  RNA corresponding to ~20-100nt fragments crosslinked to Untag/FHFOX2 were eluted by proteinase K digestion, ligated to a 3’ linker, and reverse transcribed.  The resulting cDNA was purified on a denaturing polyacrylamide gel, circularized, and amplified for 16 cycles using Illumina-compatible barcoded primers.  PCR product was gel purified on a denaturing polyacrylamide gel.  UntagFOX2 library was amplified for an additional 7 cycles and re-purified.  Samples were pooled and sequenced on the Illumina HiSeq platform.

treatment_protocol: Cells were infected with lentivirus (pSLIK Hygro vector) expressing doxycycline-inducible untagged or FLAG-HA-tagged human RBFOX2 (UntagFOX2, FHFOX2) and selected in 150ug/ml hygromycin for 6 days.  FHFOX2 and UntagFOX2 cells were induced for 24 hours with 1ug/ml doxycycline and crosslinked at 150mJ/cm2, collected, and flash frozen.

value: FLAG-HA-tagged human RBFOX2


title: Ncrassa_glucose_rep2

value: D-glucose


title: Ncrassa_arabinose_rep1

value: L-arabinose


title: Skeletal muscle mmPCR-Seq R1

description: library strategy: mmPCR-Seq

source_name: Skeletal muscle

value: Skeletal muscle


title: Ncrassa_glucose_rep1


title: S-1M

description: B


title: E9.5 epidermal ectoderm

description: E9.5 EE

source_name: Mouse embryo_E9.5

tag: Stage

value: epidermal ectoderm


title: S-1F

description: A


title: OreR_2

status: Public on Mar 15 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Control

data_processing:
Basecalls were performed using CASAVA version 1.8.2
Reads were aligned to dm3 using tophat2 with parameter -g 1 to report unique alignments, and --GTF with transcript definitions from ensembl70.
RPKM values were determined by counting reads on the union of transcripts for each gene and dividing by the length in kb and total number of reads per sample in millions.
Genome_build: dm3
Supplementary_files_format_and_content: RPKM values per gene.

source_name: Wing discs with nota removed

growth_protocol: Males from OreR and UAS-IR lines were crossed with GAL4 line virgin females (genotype: w1118, Bx-GAL4; UAS-dicer2 (Bx-GAL4 also known as MS1096-GAL4, Bloomington 25706). Drosophila larvae were raised at 25°C at low density until the 3rd instar wandering stage.

extract_protocol:
Nota were removed to isolate the knockdown domain of Bx-GAL4. Dissected material was immediately frozen in liquid nitrogen for total RNA extraction in triplicate (QIAGEN RNeasy Mini Kit).
The Illumina TruSeq Stranded mRNA LT kit was used according to manufacturers instructions beginning with 100 ng total RNA.

treatment_protocol: 30 wing discs from the third instar male larvae of each genotype were dissected in Ringer’s solution.

tag: gal4 line

value: Bloomington Stock Number:25706

tag: vdrc transformant id

value: OreR wild type


title: OreR_1

description: Control


title: PFA-6

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

data_processing:
ChIP-seq reads were aligned using the BWA algorithm with removal of redundant reads (Picard Algorithm) likely to represent ChIP-seq PCR library artifacts, yielding uniquely mapped ChIP-seq reads
Peaks were identified using MACS (Version 2) with a p-value cutoff of 0.01. These peaks were identified using MACS2.0 with paired-end (PE) setting, without model fitting, but all other parameters were default MACS settings.
Differential peaks were identified using the R: Bioconductor DiffBind package (p < 0.05) and annotated to the nearest gene +/- 5kb using Cistrome (http://cistrome.org/ap/root).
Genome_build: HG19
Supplementary_files_format_and_content: The processed file contains the bed file representing significant H3K27me3-ChIP-seq peaks (p<0.01). These peaks were identified using MACS2.0 with paired-end (PE) setting, without model fitting, but all other parameters were default MACS settings.

source_name: ependymomas_PFA_H3K27me3 ChIP

extract_protocol:
10-20mg of fresh frozen primary tumour samples were homogenized in 1% Formaldehyde and allowed to incubate at room temperature for 6 – 10 min. Cross-linking was stopped with the addition of 125mM of Glycine, and samples were washed twice with ice-cold PBS containing (1% BSA and 10% FBS). Samples were then sonicated to ~200 bp fragments using a Biorupter (Diagenode). The chromatin immunoprecipitation was then performed using 5 mg of H3K27me3 antibody (C15410069-Diagenode) overnight at 4C as described previously (Lupien et al., Cell 2008).
Following chromatin immunoprecipitation, DNA was quantified using picogreen, and libraries were prepared and barcoded according to NEB NEXT ChIP seq library preparation protocol performed using Agencourt bead purification. This protocol was followed according to NEB instructions.

tag: location

value: Posterior Fossa

value: Primary Ependymoma Tumour

tag: molecular subgroup

value: PFA

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: OreR_3

description: Control


title: CR32027-IR1_2

description: CR32027 knockdown 1


title: CR32027-IR1_3

description: CR32027 knockdown 1


title: CR32027-IR2_1

description: CR32027 knockdown 2


title: CR32027-IR1_1

description: CR32027 knockdown 1


title: CR32027-IR2_2

description: CR32027 knockdown 2


title: PFA-4

tag: chip antibody


title: PFA-2


title: PFA-1


title: Ncrassa_arabinose_rep2

tag: strain


title: PFB-4

source_name: ependymomas_PFB_H3K27me3 ChIP

value: PFB


title: PFB-2


title: input_BV

status: Public on Mar 14 2014

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

data_processing:
ChIP-seq reads were aligned on mm9 genome assembly using bowtie-0.12.8 with "-n 3 -m 1" settings.
2kb binned reads in every 1kb were counted and created BED and WIG files using sql and perl based scripts.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files were created using IGVTools-2.3.5 with "-w 25 -e 250" settings.
Supplementary_files_format_and_content: Bed files were using perl based script.
Supplementary_files_format_and_content: Wig files were using perl based script.

source_name: EpiLC

growth_protocol: ESCs were induced into EpiLCs as described previously (Hayashi et. al., 2011).  1×105 ESCs were cultured in a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore) (16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml; Peprotech), bFGF (12 ng/ml; Invitrogen), and KSR (1 %).  Medium was changed 24 hrs later, and the cells were cultured for another 24 hrs.  The resultant EpiLCs were then cultured under a floating condition by plating 2 x 103 cells in a well of a lipidure coated U-bottom 96-well plate (Thermo Scientific, Waltham, MA) in a GK15+LIF medium in the presence or absence of the cytokines [BMP4 (500 ng/ml), WNT3A (50 ng/ml)].

extract_protocol:
Cells were trypsinized, washed, and collected by centrifugation.  For crosslinking, the pellet was resuspended in PBS containing 1% formaldehyde, incubated for 10 min, and quenched with 125 mM glycine.  The fixed cells were resuspended in 1 ml of cold LB1 (20 mM Tris, 10 mM NaCl, 2.5 mM MgCl2, 0.2% NP-40, and 1 mM PMSF [pH 7.5]), rotated for 10 min at 4 oC, and pelleted by centrifugation at 1,500×g for 5 min.  The pellet was resuspended in 1 ml of LB2 (20 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1 mM PMSF [pH 8.0]) and rotated for 10 min at 4 oC.
The nuclei were pelleted by centrifugation at 1,500×g for 5 min at 4 oC and lysed in 400 ml of LB3 (20 mM Tris, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1mM PMSF).  The lysed nuclei were sonicated using the following conditions: Bioruptor with high power output; 10 cycles (30 s ON and 60 s OFF at 4 oC).
Protein-DNA complexes were immunoprecipitated for 15 hrs at 4 oC using 4 μg of antibodies bound to 50 μl of Dynabeads Protein G (Invitrogen).  Immunoprecipitates were sequentially washed with 200 μl of Low salt buffer (0.1 % SDS, 1 % TritonX100, 2 mM EDTA,20 mM Tris, and 150 mM NaCl [pH 8.0]), High salt buffer (0.1 % SDS, 1 % TritonX100, 2 mM EDTA,20 mM Tris, and 500 mM NaCl [pH 8.0]), RIRA buffer (50 mM HEPES-KOH, 0.5 M LiCl, 1 mM EDTA, 0.5% Na-Deoxycholate, and 1% NP-40 [pH 7.4]), and TE buffer (10 mM Tris and 10 mM EDTA [pH 8.0]).  For collection of the protein-DNA complexes, beads were resuspended with 50 μl of elution buffer (100 mM NaHCO3, 1 % SDS, and 10 mM DTT).  The crosslink for both the immunoprecipitated and input DNA fragments was reversed by incubating at 65 oC for 6 hr.  After Proteinase K digestion, the DNA was purified by using PCR purification Kit (Qiagen), and dissolved with TE buffer.
DNA of between 2000 and 350 bp, purified using an Agencourt AMPureXP Kit, was sequenced on a Life Technologies SOLiD 5500xl platform to generate single-end 50 bp reads.

value: EpiLC

value: Blimp1-mVenus reporter (BV)


title: PFB-1


title: PFB-3


title: 10S

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

description: Column K

data_processing:
FASTQC v0.10.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to carry out preliminary quality control of the 8 FASTQ files.
The 3′ adaptor sequences were trimmed with Cutadapt v1.1 (https://code.google.com/p/cutadapt). After trimming, reads shorter than 18 nucleotides were discarded.
The FASTQ quality filter v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) was applied to trim low quality bases from reads. Phred scores were calculated and reads where at least 50% of the bases had a Phred score of less than 20 were discarded. The filtered reads were further trimmed at their ends to remove low quality bases (Phred score <20). Reads were then aligned to the bovine genome (UMD3.1.) using Novoalign version 2.07.11 (http://www.novocraft.com) using the  “-m” miRNA mode. Only uniquely aligned reads were retained. HTSeq version 0.5.3p3 (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used to annotate uniquely aligned reads using Ensembl (v68) bovine gene and miRNA annotation.
The filtered reads were further trimmed at their ends to remove low quality bases (Phred score <20). Reads were then aligned to the bovine genome (UMD3.1.) using Novoalign version 2.07.11 (http://www.novocraft.com) using the  “-m” miRNA mode. Only uniquely aligned reads were retained. HTSeq version 0.5.3p3 (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used to annotate uniquely aligned reads using Ensembl (v68) bovine gene and miRNA annotation.
Reads were then aligned to the bovine genome (UMD3.1.) using Novoalign version 2.07.11 (http://www.novocraft.com) using the  “-m” miRNA mode. Only uniquely aligned reads were retained. HTSeq version 0.5.3p3 (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) was used to annotate uniquely aligned reads using Ensembl (v68) bovine gene and miRNA annotation.
Genome_build: UMD3.1.68: Ensembl v68 annotation of the UMD3.1 assembly of the bovine genome.
Supplementary_files_format_and_content: Columns with Gene ID, Gene Biotype, Gene name and normalized count data for 8 samples

organism: Bos taurus

source_name: Liver

extract_protocol:
Total RNA enriched for small RNA was extracted from 1mg of frozen tissue from each of the eight samples using the mirVana™ miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol.
Small RNA libraries were constructed at BGI (Shenzhen, China) under contract and sequenced on an Illumina HiSeq2000 platform

value: Severe Negative Energy Balance

tag: breed

value: Holstein Friesian

value: liver

tag: animal


title: 7S

description: Column I


title: Ribosome footprints, WT C. albicans

city: San Francisco

first: Dale

last: Muzzey

address: 1700 4th Street BH403

department: Cellular & Molecular Pharmacology

institute: UCSF

description: ribosomal RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence (CTGTAGGCACCATCAAT)
Trimmed reads were aligned to the diploid genome assembly (build with SNPs and without indels; Muzzey et al., Genome Biology, 2013) using Bowtie v0.12.7 and parameters "-v 0 --all -m 16".
Aligned reads containing SNPs were parsed to their respective alleles ("_A_" or "_B_" files), while reads lacking SNPs were tallied in the "_AandB_" files.
Genome_build: Diploid phased genome (SNPs only; no indels) from Muzzey et al., Genome Biology, 2013
Supplementary_files_format_and_content: wiggle file

organism: Candida albicans

source_name: Whole cells

extract_protocol:
Ribosome profiling: Cells from log-phase cultures were flash frozen in liquid nitrogen. To guard against post-lysis translation in the ribosome-profiling sample, we supplemented the lysis buffer with 50µg/ml GMPPNP and 10µg/ml Blasticidin S (Invivogen). Cells were lysed via mixermilling, and lystates were cleared via centrifugation and then treated with RNase I before loading onto a sucrose gradient and ultracentrifugation. Monosomes were collected, and ribosome-protected mRNAs were extracted with acid phenol and chloroform. RNA-Seq: Cells from log-phase cultures were flash frozen in liquid nitrogen, and mRNA was isolated using acid phenol and chloroform. mRNAs were selected using oligo-dT beads (Invitrogen) and then alkaline fragmented.
Ribosome footprints (FPs) and mRNAs were size-selected on TBE-Urea gels and dephosphorylated prior to ligation with a common linker, rRNA subtraction (FP sample only), and RT on both samples. DNAs were circularized and then amplified by PCR to yield fragments suitable for deep sequencing.


title: RNA-seq, WT C. albicans


title: UntagFOX2_iCLIP

description: iCLIP

data_processing:
Sequenced reads were trimmed to remove adapter sequence (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) and collapsed using the FastX toolkit.  Crosslink sites were determined from 5’ terminal nucleotides of contiguously-mapping reads and deletion sites of reads mapping with deletions.
genome build:  mm9
processed data file and content:  Single nucleotide crosslink sites in bigwig format (unstranded); significantly enriched binding clusters in bed format

tag: cell type

value: V6.5 ES cells

tag: lentivirus infection

value: doxycycline-inducible untagged human RBFOX2


title: PFA-5

organism: Homo sapiens

tag: tissue


title: 8S

description: Column H

tag: treatment


title: PFA-3


title: 3M

description: Column E

value: Mild Negative Energy Balance


title: 4M

description: Column F


title: MAC_CONTROL

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were trimmed to 36 base pairs and mapped against the reference genome (hg19 assembly) using the BWA. Only uniquely placed reads were used for further analysis.
Cisgenome v2.0  was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated transcripts. To avoid transcripts with zero mapped tags to interfere with logarithmic transformation of read counts, 0.1 read was added to each transcript. Raw read counts were normalized to the transcript length and sequencing depth and quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: *.rna files were generated using Cisgenome “rnaseq_countgeneread” command

growth_protocol: Human peripheral blood monocytes were cultured in RPMI 1640 (Cellgro) with 5% human AB serum (Cellgro, Manassa, VA) and 1% penicillin/streptomycin (Gibco) at 37˚C in a humidified incubator with 5% CO2. THP-1 monocytes were cultured in RPMI1640 with 5% fetal calf serum (HyClone) and 1% Penicillin/Streptomycin. For infectious center assay experiments, cells were plated at 7.5 X 10^5 cells / well in 2 mL of cell culture medium to 6-well plates (BD Falcon). To induce THP1 differentiation to monocyte-derived macrophages, cells were treated for 24 hr with phorbol myristate acetate (PMA) (Fisher Scientific) at a concentration of 200 nM. Following the differentiation, the PMA-containing medium was removed and replaced with an equal volume of fresh medium, and the cells were rested for an additional 24 hours.

extract_protocol:
Cells were washed 5x in PBS, and RNA was harvested by extraction with Trizol and purified by RNeasy column elution. RNA quality was ensured by Agilent Bioanalyzer 2100 analysis.
RNA samples were submitted to the Columbia Genome Center for stranded ribominus library preparation.

treatment_protocol: Human peripheral blood mononuclear cell-derived macrophages were infected with HRV16, HRV1A, or mock at an MOI of 10 for 8 hours.

value: monocyte-derived macrophages


title: CR32027-IR2_3

description: CR32027 knockdown 2


title: MAC_HRV16


title: ZL1-Leaf [miRNA]

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: C.annuum Zunla 1

data_processing: Genome_build: Pepper Ref_v1.0 (ASJU00000000)

organism: Capsicum annuum

extract_protocol:
Total RNA for different tissues was isolated from the frozen root samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions
Five libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as previously described, then sequenced on an Illumina HiSeq2000 system.

tag: inbred line

value: Zunla 1

value: Leaves

tag: developmental stage

value: mature leaves


title: 2M

description: Column D


title: ZL1-Flower [miRNA]

description: C.annuum Zunla 1

value: Open flowers

value: fully open flowers


title: ZL1-Fmg [miRNA]

description: C.annuum Zunla 1

value: Fruits

value: mature green fruit


title: ZL1-Stem [miRNA]

description: C.annuum Zunla 1

value: Stems

value: developing stem


title: MAC_HRV1A


title: 11c320-F-Dev5 [mRNA]

description: C.annuum 11c320

extract_protocol:
Different tissues were removed respectively, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from eukaryote . Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeqTM 2000.


title: T803-F-Dev5 [mRNA]

description: C.annuum T803


title: SP3-F-Dev5 [mRNA]

description: C.annuum SP163


title: G16-F-Dev5 [mRNA]

description: C.annuum G16


title: 9S

description: Column J


title: 11c255-F-Dev5 [mRNA]

description: C.annuum 11c255


title: 5M

description: Column G


title: ZL1-F-Dev5 [mRNA]

description: C. annuum Zunla 1


title: ZL1-F-Dev3 [mRNA]

description: C. annuum Zunla 1

value: Fruits with length between 3-4 cm


title: HYL-Stem [mRNA]

description: C. chinense Jacq. HYL

organism: Capsicum chinense

source_name: HYL-Stem

value: HYL

value: Stems of seedlings


title: ZL1-F-Dev6 [mRNA]

description: C.annuum Zunla 1

value: Fruit at breaker (fruit turning red)


title: ZL1-F-Dev4 [mRNA]

description: C. annuum Zunla 1

value: Fruits with length between 4-5 cm


title: HYL-F-Dev8 [mRNA]

description: C. chinense Jacq. HYL

value: Fruit at breaker plus 5 days


title: ZL1-F-Dev1 [mRNA]

description: C. annuum Zunla 1

value: Fruits with length between 0-1 cm


title: ZJ49-F-Dev5 [mRNA]

description: C. annuum Zunla 49

value: Zunla 49


title: HYL-F-Dev5 [mRNA]

description: C. chinense Jacq. HYL


title: HYL-Root [mRNA]

description: C. chinense Jacq. HYL

source_name: HYL-Root

value: Roots

value: Roots of seedlings


title: ZL1-F-Dev2 [mRNA]

description: C. annuum Zunla 1

value: Zunla 1

value: Fruits with length between 1-3 cm


title: HYL-Leaf [mRNA]

description: C. chinense Jacq. HYL

source_name: HYL-Leaf

value: Leaves

value: Leaves of seedlings


title: ZL1-F-Dev9 [mRNA]

description: C. annuum Zunla 1

value: Fruits

value: Fruit at Breaker plus 7 days


title: ZL1-Root [mRNA]

description: C. annuum Zunla 1

value: developing roots


title: HYL-F-Dev6 [mRNA]

description: C. annuum Zunla 1


title: ZL1-F-Dev8 [mRNA]

description: C. annuum Zunla 1


title: ZJ32-Fmg [mRNA]

description: C. annuum Zunla 32

value: Zunla 32

value: mature green fruit


title: ZJ7-F-Dev8 [mRNA]

description: C. annuum Zunla 7

value: Zunla 7


title: ZJ49-F-Dev8 [mRNA]

description: C. annuum Zunla 49


title: ZJ9-F-Dev5 [mRNA]

description: C. annuum Zunla 9

value: Zunla 9


title: ZL1-Flower [mRNA]

description: C. annuum Zunla 1

value: Open flowers


title: ZL1-Bud [mRNA]

description: C.annuum Zunla 1

value: Flower buds

value: Closed flower buds


title: ZL1-F-Dev7 [mRNA]

description: C. annuum Zunla 1

value: Fruit at breaker plus 3 days


title: Chiltepin-F-Dev6 [mRNA]

description: C. annuum var. glabriusculum

organism: Capsicum annuum var. glabriusculum

value: Fruits at breaker (fruit turning red)


title: Chiltepin-Leaf [mRNA]

description: C. annuum var. glabriusculum

source_name: Chiltepin-Leaf

value: Mix leaves from Seedling, Early blooming, Full bloom, and fruit breaker phase


title: ZL1-Stem [mRNA]

description: C.annuum Zunla 1

value: Zunla 1

value: Stems

value: developing stems


title: ZL1-Leaf [mRNA]

description: C.annuum Zunla 1

value: Leaves

value: mature leaves


title: Chiltepin-Flower [mRNA]

description: C. annuum var. glabriusculum

source_name: Chiltepin-Flower

value: Flowers

value: a mix of flowers from unopened flower buds (buds) and fully open flowers


title: GA5362-Set-3-KO-ILC3

status: Public on Mar 13 2014

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: RNA-Seq

data_processing:
Basecalls performed using CASAVA 1.0
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (0.12.7).Uniquely mapped reads were kept for each lane. The last 20 bps of each reads were discarded (due to low sequencing quality) to increase maping rate when running bowtie.
Genome_build: mm9
Supplementary_files_format_and_content: BED

organism: Mus musculus

source_name: ex vivo ILC3s lacking Gata3

growth_protocol: Gata3fl/fl-CreERT2 mice were injected with IL-25 for 3 days. Cells from mesenteric lymph nodes were stained with a cocktail of antibodies to various lineage markers, including antibodies to CD3, CD5, CD45R, CD11b, CD11c, NK1.1, Gr-1, TER119, FcεRI and TCRγ/δ to identify lineage negative (Lin-) cells. Lin- cells were sorted using a FACS Aria and then cultured with IL-7 (10 ng/ml), IL-33 (10 ng/ml) and IL-25 (10 ng/ml) for 5 days. Cells were either treated with 4-OHT or ethanol as a control for 2 days in the presence of IL-7/IL-25/IL-33. Gata3-sufficient (wild type, WT) ILC2s were sorted from ethanol treated samples. Gata3-deficient (Gata3 KO) cells were sorted from 4-OHT treated samples excluding residual T1/ST2-expressing cells. In other experiments (for collecting GA5355, GA5361, GA5360 and GA5362), Gata3fl/fl or Gata3fl/fl-CreERT2 mice were injected with tamoxifen (5mg/mouse). Two to three days later, Lin-Thy1+CD127+Klrg1+ (mostly ILC2s) and Lin-Thy1+CD127+Klrg1-  (mostly ILC3s) were sorted from small intestine lamina propria.

extract_protocol:
RNA-Seq experiments were performed using total RNAs isolated from Gata3-deficient and sufficient ILC2s in duplicate.
100 ng of total RNA was amplified using the Ovation RNA-Seq system V2 kit (NuGEN).  The resulting dsDNA was sonicated to 200-400 bp.  250 ng of sonicated DNA was used to prepare sequencing libraries for multiplex sequencing (Illumina).

value: type 3 Innate lympoid cells (ILC3s)

value: C57BL/6 Gata3fl/fl-CreERT2

tag: in vivo treatment

value: Tamoxifen treatment for 2-3 days

tag: in vitro treatment


title: GA5360-Set-3-WT-ILC3

description: RNA-Seq

source_name: ex vivo ILC3s

value: C57BL/6 Gata3fl/fl


title: GA5361-Set-3-KO-ILC2

description: RNA-Seq

source_name: ex vivo ILC2s lacking Gata3

value: type 2 Innate lympoid cells (ILC2s)


title: GA5355-Set-1-WT-ILC2

description: RNA-Seq

source_name: ex vivo ILC2s