title: WT ZT16 rep1

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Mus_musculus genome GRCm38 using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Ensembl annotation 75.
Gene count tables were imported in R (v. 3.1.1) for normalization (package edgeR, method TMM, Robinson and Oshlack  2010) and transformation (package limma, method voom, Law et al. 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: whole kidney

growth_protocol: The conditional inactivation of the Arntl gene encoding BMAL1 was induced by 2-weeks treatment with doxycycline (DOX, 2 mg/ml in drinking water) of 8-weeks old Bmal1lox/lox/Pax8-rtTA/LC1 mice. Bmal1lox/lox, Pax8-rtTA and LC-1 Cre mice used in this study are inbred strains, bred on the genetic background of the C57BL/6J mouse. The animals were maintained ad libitum on the standard laboratory chow diet (KLIBA NAFAG diet 3800). Before all experiments, mice were adapted to a 12-hour light/ dark cycle.

extract_protocol:
RNA from whole kidneys was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

treatment_protocol: Mice were sacrificed at ZT4 and ZT16 (ZT – Zeitgeber time units; ZT0 is the time of light on and ZT12 is the time of light off).

value: wild-type

tag: time

tag: tissue

value: whole kidney


title: WT ZT16 rep3

status: Public on Jun 01 2016

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype


title: Tumor_N1_R5020_24 Hours_RNAseq

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

country: USA

institute: University of Chicago

description: Processed data file: Tumor N1.csv

data_processing:
The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using TopHat.
Relative expression of transcripts were calculated by subjecting TopHat output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: CSV includes RPKM values for each each of the treatment conditions (E2, R5020 or E2+R5020) versus control treatment. Union of all estrogen and progestin-regulated genes for the respective samples is provided.

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast cancer cells

growth_protocol: Tumor explants: Within one hour of surgery, sliced pieces of tumors were incubated on gelatin sponges for 36 hours in charcoal-stripped serum media. Representative pieces of tumors were in parallel fixed in 4% formalin and subsequently immunohistochemistry for ER and PR protein was performed to assess the status of tumors for these receptors.

extract_protocol:
Hormone-treated explant was homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol: Steroid-deprived tumor explants were treated with 10 nM estradiol, 10 nM R5020 or 10 nM of both the hormones for 24 or 48 hours. Finer details are provided in materials and methods section (Patient tumor explants)

tag: tissue type

value: ER+/PR- Human tumor explants

tag: er/pr status

value: ER+/PR-

tag: drug treatment

tag: hormone exposure time

value: 24 Hours


title: KO ZT4 rep6

value: BMAL1 knock-out


title: KO ZT4 rep4


title: Tumor_N1_E2_24 Hours_RNAseq

description: Processed data file: Tumor N1.csv

value: 10 nM Estradiol


title: RNA-seq Act B cell 14713

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: SuperScript® VILO™ cDNA Synthesis, strand-specific

data_processing:
Peaks were called in the doublecrosslinked E2A ChIP-seq sample with a P value of < 10-10 and in the corresponding singlecrosslinked E2A ChIP-seq sample with a P value of < 10-5 by using the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mature B cell input sample (14951). Second, the overlap of the called double- and single-crosslinked peaks was determined with the Multovl program21 by using a minimal overlap length of one and allowing for all possible overlaps, with the results being parsed and converted to tables with custom-made bash, perl and R scripts. The E2A peaks identified by this overlap analysis were then assigned to target genes as described22. For comparisons of E2A ChIP-seq data between different cell types, we down-sampled all reads before peak calling to the ChIP-seq experiment with the lowest number of aligned reads. Thus, samples 22337 and 22338 (FO B cells), 22331 and 22332 (activated B cells, anti-CD40 plus IL-4, 2 days) were down-sampled to 27.1 million reads, and all other samples such as 22327 and 22328 (activated B cells, LPS, 2 days), 22333 and 22334 (pre-plasmablasts, LPS, 4 days), 22335 and 22336 (plasmablasts, LPS, 4 days) were down-sampled to 15.5 million reads.
Concerning the ATAC-seq data, the DHS sites were identified by peak calling using the MACS 2.0.10 program. The peaks from wild-type and DKO cells were compiled. The peak regions were defined as peak summit ± 500 bp. Peaks were assigned to the genes as described for the ChIP-seq analysis. The read density was calculated as RPKM in each peak.
For analysis of differential gene expression, the number of reads per gene was counted using HTseq version 0.5.3 (ref. 24) with the overlap resolution mode set to ‘union’. The datasets were grouped according to the performed stimulation experiments and analyzed using the R package DESeq2 version 1.4.1 (ref. 25). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. In detail, the following DESeq2 analyses were performed: FO B cell and all anti-CD40 and IL4 stimulation samples were analyzed together considering the genotype, time and genotype over time effects (model design formula: “~ genotype + time + genotype:time”). The genotype over time effect for each day was then tested based on log ratio tests (with a reduced formula of “~ genotype + time). FO B cell and 2 day LPS stimulation data were also grouped and analyzed in the same manner. Three day LPS-stimulated activated B cell (WT and DKO), pre-plasmablast (WT) and plasmablast (WT) samples were considered for sample normalization, dispersion estimation, rlog normalization of the gene counts and the comparison of 3 day LPS-stimulated DKO vs 3 day LPS-stimulated WT activated B cells (Wald test). The 500 most varying rlog normalized counts (option blind) of the 3 day LPS stimulation dataset were used for PCA in Fig. 7d. In general, genes with an adjusted Pvalue < 0.05 and a fold change > 3 as well as a mean RPKM (averaged within conditions) > 3 were called as significantly expressed. Immunoglobulin and T cell receptor genes were filtered from the list of significantly expressed genes and were also disregarded in the RPKM calculations. For the detailed expression analysis of the Igh and Igk loci (Fig. 4 and Supplementary Fig. 8), IghM, IghD, IghG, IghE and IghA were manually curated to provide detailed exon annotations and were split into constant, membrane, secreted, hinge and I exon regions. Ratios between secreted and membrane Igh transcripts were estimated by using the RPKM values of the secreted and membrane regions.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read coverage in reads per million; density bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; text tab delim = RPKM values in ASCII text format tab delimited

source_name: Act B cell

extract_protocol: Rneasy Plus Mini Kit, Dynabeads mRNA purification kit

tag: strain

tag: cell preparation

value: 1-day anti-CD40 rIL-4 stimulation

tag: cell sorting strategy

value: CD19+B220+FSC SSChiGFP- FACS-sorted

tag: chip antibody


title: KO ZT4 rep2


title: Tumor_P8_R5020_24 Hours_RNAseq

description: Processed data file: Tumor P8.csv

value: ER+/PR+ Human tumor explants

value: ER+/PR+


title: WT ZT4 rep5


title: Tumor_P7_R5020_24 Hours_RNAseq

description: Processed data file: Tumor P7.csv


title: Tumor_P7_E2_24 Hours_RNAseq

description: Processed data file: Tumor P7.csv


title: Tumor_P8_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor P8.csv

value: Vehicle


title: WT ZT4 rep3


title: Tumor_P7_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor P7.csv

value: 10nM Estradiol + 10 nM R5020


title: WT ZT4 rep1


title: Non-CML #16-2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

description: RNAseq-SMARTer

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were mapped tomm9 genome using TopHat v2 with default settings.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted
RPKM is calculated in R using counts divided by gene length and then divided by total aligned reads.
Genome_build: mm9
Supplementary_files_format_and_content: Txt. Files including RPKM values

source_name: LTHSC from non-leukemic recipient mice

extract_protocol:
RNA was extracted from lysate of sorted cells using the Qiagen Rneasy Micro Kit (Cat. No. 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted cells

tag: cell type

value: LTHSC

tag: donor mouse genotype

value: SCL-tTA/BCR-ABL

tag: recipient mouse genotype

value: FVBN

tag: recipient mouse leukemia status

value: non-leukemic


title: Tumor_P7_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor P7.csv


title: Non-CML # 1

description: RNAseq-SMARTer


title: Tumor_N1_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor N1.csv


title: CML #14

description: RNAseq-SMARTer

source_name: LTHSC from leukemic recipient mouse

value: leukemic


title: Non-CML # 2

description: RNAseq-SMARTer


title: Tumor_P6_E2+R5020_48 Hours_RNAseq

description: Processed data file: Tumor P6.csv

value: 48 Hours


title: ILC3 NCR+

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Around 30 million reads were generated for each replicate and aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least one library.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. The log2-RPKM (reads per kilobase of exon length per million mapped reads) expression values generated from fitting linear models to genes were used for data analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each gene in each library.

source_name: intestine

extract_protocol:
Total RNA was prepared from purified ILC populations for quantative RT-PCR using an RNeasy mini kit (Qiagen).
cDNA was synthesized from total RNA with OligodT and thermoscript reverse transcriptase (Invitrogen). Real-time PCR was performed using the SensiMix SYBR no-Rox kit (Bioline). Approximately 5 × 10^5 lin– (CD3–CD19–) CD45.2+ cells from each ILC subsets were sorted from the intestines of NCR-FM-, NCR-FM- and NCR+FM+ and one to two biological replicates were generated and subjected to 100bp single end sequencing on an Illumina HiSeq2000 sequencer at the Australian Genome Research Facility (Melbourne, Australia).

value: intestine

value: ILC

value: NCR+


title: CML # 22

description: RNAseq-SMARTer


title: Non-CML #16-1

description: RNAseq-SMARTer


title: CML #13

description: RNAseq-SMARTer


title: Tumor_P6_R5020_48 Hours_RNAseq

description: Processed data file: Tumor P6.csv


title: Tumor_N1_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor N1.csv

value: ER+/PR- Human tumor explants

value: ER+/PR-

value: 24 Hours


title: Tumor_P8_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor P8.csv


title: CML #12

description: RNAseq-SMARTer


title: CML #11

description: RNAseq-SMARTer


title: Tumor_P8_E2_24 Hours_RNAseq

description: Processed data file: Tumor P8.csv

value: 10 nM Estradiol


title: Tumor_P6_E2_48 Hours_RNAseq

description: Processed data file: Tumor P6.csv

value: ER+/PR+ Human tumor explants


title: ILC3 NCR- FM- rep2

value: NCR- FM-


title: Tumor_P6_Vehicle_48 Hours_RNAseq

description: Processed data file: Tumor P6.csv

value: ER+/PR+

value: Vehicle


title: ILC3 NCR- FM+ rep1

value: NCR- FM+


title: Tumor_P5_E2+R5020_48 Hours_RNAseq

description: Processed data file: Tumor P5.csv

value: 10nM Estradiol + 10 nM R5020


title: Tumor_P5_R5020_48 Hours_RNAseq

description: Processed data file: Tumor P5.csv


title: AoSMC replicate 3

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: Small RNAs

data_processing:
Reads were trimmed to remove adaptor sequences.
Inserts longer than 13 bases were mapped to the mouse mm10 genome using Bowtie (with settings –n 0 -m 5 --best  --strata, allowing 0 mismatches and up to 5 genomic loci with a perfect match, {Genome Biol. 2009;10(3):R25, Langmead B, Trapnell C, Pop M, Salzberg SL}).
Reads that mapped to within 50 bp of more than one annotated mouse pri-miR (as defined by miRBase {Kozomara A, Griffiths-Jones S. Nucelic Acids Res 2014 42:D68-D73}), were allotted evenly between these locations.
Reads that fell entirely within established miRbase 3p or 5p miR coordinates, plus or minus 3 bp, were counted as 3p or 5p miRs, respectively. Reads that fell entirely within the range of 35 bp 3’ to 3 bp 5’ of the first base of a 3p miR were counted as 3p moR reads. Those that fell entirely between 3bp 3’ and 35 bp 5’ of the last base of a 5p miR were counted as 5p moR reads. On average each library contained 17.4 million qualifying inserts, of which 13.8 million (79.3%) mapped to one of these four regions, indicating that the large majority of inserts represented miR or moR sequences.
Reads were divided by the number of million reads mapping to these regions in each library to give normalized reads per million reads (RPMR) values.
Genome_build: mm10
Supplementary_files_format_and_content: One Excel (.xlsx) file containing raw read counts, and RPMR normalized read counts, for all known miR regions and for all corresponding moR regions
Supplementary_files_format_and_content: Three .gzip compressed .bdg (bedgraph) files containing read density maps for all mm10 genomic regions that are near any annotated mouse miRbase pri-miR stem loop structure

source_name: Primary aortic smooth muscle cells

growth_protocol: Mouse aortic smooth muscle cells (MAoSMC) were harvested and grown as follows. Briefly, several mouse aortas were obtained sterilely and placed into 100mm dish containing media. The adventia was cleaned off and the aorta was cut horizontally into 10-15 pieces. Each piece was placed into a 6 or 12 well collagen Biocoat plate (Fisher). Explants were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing antibiotics and 10% bovine growth serum (BGS) for 3-7 days. When the well was 50-75% confluent, the explants were removed, and the MAoSMCs were cultured in low glucose phenol red-free DMEM containing antibiotics and 10% fetal bovine serum (FBS).

extract_protocol:
Small RNAs were harvested from mouse aortic smooth muscle cells (AoSMCs), with three biological replicates, using miReasy kits (Qiagen) according to the manufacturer’s instructions.
Small RNA library construction and illumina HiSeq 75bp single read sequencing were performed at the Yale Center for Genome Analysis, using the Illumina TruSeq Small RNA preparation kit, according to manufacturer's instructions.

treatment_protocol: Cells were harvested at near confluence after growth under the protocol above.

value: Primary aortic smooth muscle cells


title: ILC3 NCR- FM- rep1


title: AoSMC replicate 2

description: Small RNAs


title: RNA-seq GC B cell 19475

source_name: GC B cell

value: Wild-type

value: Ex-vivo from SRBC immunized mice, FACS-sorted

value: CD19+Fas+B220+Gl7+ FACS-sorted


title: AoSMC replicate 1

description: Small RNAs


title: Tumor_P5_E2_48 Hours_RNAseq

description: Processed data file: Tumor P5.csv

value: 48 Hours


title: Tumor_P5_Vehicle_48 Hours_RNAseq

description: Processed data file: Tumor P5.csv


title: Tumor_P4_E2+R5020_48 Hours_RNAseq

description: Processed data file: Tumor P4.csv


title: ChIP-Seq input Mature B cell 14951

library_source: genomic

molecule: genomic DNA

source_name: Mature B cell

extract_protocol: phenol-chloroform extraction

value: Ex-vivo, MACS-sorted

value: CD23 MACS-sorted


title: Tumor_P4_R5020_48 Hours_RNAseq

description: Processed data file: Tumor P4.csv


title: MOE high RNA rep2

first: Joanna

last: Burdette

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Oviductal cells

growth_protocol: Outbred CD1 mouse oviductal cells (MOE low) were serially passaged to obtain MOE high cells.

extract_protocol:
Total RNA was extracted from MOELOW (passages 8, 9, & 10) and MOEHIGH (passages 90, 103, & 113) cells using Trizol reagent. Each total RNA sample had ribosomal RNA removed using TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epithelial cells

tag: passages

value: Outbred CD1


title: MOE high RNA rep1


title: Tumor_P4_E2_48 Hours_RNAseq

description: Processed data file: Tumor P4.csv


title: MOE low RNA rep3


title: EpiSC NT RNA-Seq

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

description: Transcriptome sequencing analysis

data_processing:
Illumina GA pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per kilobaseof exon per million fragments mapped (FPKM) were calculated using iIllumina  protocol from chinese BGI company.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: No treatment EpiSCs

growth_protocol: EpiSCs were routinely cultured in serum/IWR1/Y27 condition  (typically 1× 105 cells into a T75 flask) on gelatin-coated tissue culture plate (BD Falcon,USA).

extract_protocol:
Standard illumina RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The NT-EpiSCs were collected after IWR1 and Y27 were withdraw overnight, and IWR1- and Y27-EpiSCs were collected respectively after treatment for 12 h.

value: epiblast stem cells


title: MOE low RNA rep2


title: EpiSC IWR1 RNA-Seq

description: Transcriptome sequencing analysis

source_name: 2 µM IWR1 treated EpiSCs


title: EpiSC Y27 RNA-Seq

description: Transcriptome sequencing analysis

source_name: 0.5 µM Y27 treated EpiSCs


title: ILC3 NCR- FM+ rep2

value: intestine

value: ILC


title: MOE high RNA rep3


title: Tumor_P3_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor P3.csv

value: ER+/PR+ Human tumor explants

value: 24 Hours


title: KO ZT16 rep6

value: BMAL1 knock-out

value: whole kidney


title: MOE low RNA rep1


title: KO ZT16 rep4


title: Tumor_P3_R5020_24 Hours_RNAseq

description: Processed data file: Tumor P3.csv

value: ER+/PR+


title: Tumor_P4_Vehicle_48 Hours_RNAseq

description: Processed data file: Tumor P4.csv

value: Vehicle


title: 14dpa mRNA

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

description:
AxoD14
Axolotl_mRNA_assembly.fa.gz
Axolotl_mRNA_logCPM.txt

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
Reads counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
Trimmed mRNA reads were digitally normalized using khmer (http://khmer-protocols.readthedocs.org/en/v0.8.4/).
Digitally normalized mRNA reads were assembled using Trinity (Haas et al. Nat Protoc. (2013)).
Reads counts per transcript were generated using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: The de novo transcriptome assembly is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per transcript per sample.

organism: Ambystoma mexicanum

source_name: mid-zeugopod

growth_protocol: Axolotls from the Ambystoma Genetic Stock Center (Lexington, KY) were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and PolyA+ mRNA libraries.

treatment_protocol: Forelimbs were amputated with scalpels following anesthesia (0.6mM MS222).

tag: days post amputation

tag: library type

value: mRNA

tag: amputation site

value: mid-zeugopod


title: RNA-seq GC B cell 19476

tag: genotype

value: Wild-type

value: Ex-vivo from SRBC immunized mice, FACS-sorted

value: CD19+Fas+B220+Gl7+ FACS-sorted


title: KO ZT16 rep2

tag: time

tag: tissue


title: 3dpa mRNA

description:
AxoD3
Axolotl_mRNA_assembly.fa.gz
Axolotl_mRNA_logCPM.txt


title: Tumor_P3_E2_24 Hours_RNAseq

description: Processed data file: Tumor P3.csv

tag: tissue type

tag: er/pr status

tag: drug treatment

value: 10 nM Estradiol


title: Tumor_P3_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor P3.csv

tag: hormone exposure time


title: 6dpa mRNA

description:
AxoD6
Axolotl_mRNA_assembly.fa.gz
Axolotl_mRNA_logCPM.txt


title: WT ZT16 rep5

value: wild-type


title: 0dpa mRNA

description:
AxoD0
Axolotl_mRNA_assembly.fa.gz
Axolotl_mRNA_logCPM.txt


title: 14dpa small RNA

description:
AxoD14
Axolotl_microRNA.fa.gz
Axolotl_microRNA_logCPM.txt

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
Reads counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
Trimmed mRNA reads were digitally normalized using khmer (http://khmer-protocols.readthedocs.org/en/v0.8.4/).
Digitally normalized mRNA reads were assembled using Trinity (Haas et al. Nat Protoc. (2013)).
Reads counts per transcript were generated using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: The de novo transcriptome assembly is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Tab-delimited text file with read counts per miRNA per sample.

value: small RNA


title: AND CD4TCell Input Rep3

city: La Jolla

first: Karmel

last: Allison

address: 9500 Gilman Dr

department: Cellur and Molecular Medicine

institute: University of California, San Diego

description:
Gilfillan Chip-Seq
Input for 1uM Chips (Rep3)
processed data file: union_peaks_1um_h3k4me2.txt

data_processing:
ChIP-sequencing reads were mapped to the mm10 genome using Bowtie2, and RNA-sequencing reads were mapped using STAR. Default allowed error rates were used, and only uniquely mapping reads were used in downstream analysis.
Initial processing of aligned data and peak calling was performed using Homer. IDR analysis for ChIP-sequencing replicates was performed using the homer-idr package.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq samples were used to generate an RPKM file with normalized gene expression values by Homer. For ChIP-Seq samples, the union set of peaks was called over all tags, and then tag counts from individual samples were tallied at each called peak using Homer. IDR analysis was used for replicate sets to determine how many of the union peaks to keep.

source_name: Splenic CD4+ T cells

growth_protocol: Spleens from transgenic AND mice were extracted and manually digested. CD11c+ cells were isolated using Miltenyi Biotec Inc. MACS magnetic cell separation with positive selection for CD11c. Subsequently, the CD11c- splenic fraction was used to negatively select for naïve CD4+ T cells using the Miltenyi MACS system.

extract_protocol:
Quoted from GSE42147: "Native chromatin was prepared by lysing CD4+ cells in low salt buffer and digesting with Micrococcal nuclease. Lysates were then sonicated to assist in recovery of oligonucleosomes and adjusted to RIPA immunoprecipitation buffer conditions. Extracts were then incubated overnight with specific antisera prior to immunoprecipitation with protein A & G beads, and recovery of bound DNA using silica column purification." Sodium butyrate added, and library prep as in Gosselin ChIP-Seq.
CD4+ cells were re-isolated from the culture using the Miltenyi MACS system.

treatment_protocol: Peptides were added at indicated concentrations with the CD11c+ and CD4+ cells in DMEM supplemented with 10% Fetal Bovine Serum.

value: spleen

value: CD4+ T cells

tag: strain

value: AND

tag: peptide

value: Combined

tag: timepoint

value: 24 hours


title: Tumor_P2_R5020_24 Hours_RNAseq

description: Processed data file: Tumor P2.csv

value: ER+/PR+ Human tumor explants

value: 24 Hours


title: AND CD4TCell Input H3K4me2 Five Conditions

description:
Gosselin Chip-Seq
Input for five condition Chips (H3K4me2)
processed data file: union_peaks_five_conditions.txt

extract_protocol:
Quoted from GSE62826: "Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles."
CD4+ cells were re-isolated from the culture using the Miltenyi MACS system.

tag: cell type


title: AND CD4TCell Input Rep2

description:
Gilfillan Chip-Seq
Input for 1uM Chips (Rep2)
processed data file: union_peaks_1um_h3k4me2.txt


title: AND CD4TCell Input H3K27Ac Five Conditions

description:
Gosselin Chip-Seq
Input for five condition Chips (H3K27Ac)
processed data file: union_peaks_five_conditions_H3K27Ac.txt


title: 6dpa small RNA

description:
AxoD6
Axolotl_microRNA.fa.gz
Axolotl_microRNA_logCPM.txt


title: AND CD4TCell H3K27Ac 10uM PCC 24h Five Conditions

description:
Gosselin Chip-Seq
processed data file: union_peaks_five_conditions_H3K27Ac.txt

value: 10uM PCC

tag: chip antibody

value: H3K27Ac (Active Motif, cat. no. 39135)


title: Tumor_P1_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor P1.csv

value: ER+/PR+

value: 10nM Estradiol + 10 nM R5020


title: Tumor_P2_E2_24 Hours_RNAseq

description: Processed data file: Tumor P2.csv


title: Tumor_P2_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor P2.csv

value: Vehicle


title: AND CD4TCell H3K27Ac No Peptide 24h Five Conditions

value: No Peptide


title: Tumor_P1_E2_24 Hours_RNAseq

description: Processed data file: Tumor P1.csv


title: AND CD4TCell H3K27Ac 100uM K99A 24h Five Conditions


title: AND CD4TCell H3K27Ac 10uM K99A 24h Five Conditions

value: 10uM K99A


title: Tumor_P1_R5020_24 Hours_RNAseq

description: Processed data file: Tumor P1.csv


title: 0dpa small RNA

description:
AxoD0
Axolotl_microRNA.fa.gz
Axolotl_microRNA_logCPM.txt

value: mid-zeugopod


title: 3dpa small RNA

description:
AxoD3
Axolotl_microRNA.fa.gz
Axolotl_microRNA_logCPM.txt


title: AND CD4TCell Input Rep1

description:
Gilfillan Chip-Seq
Input for 1uM Chips (Rep1)
processed data file: union_peaks_1um_h3k4me2.txt


title: Tumor_P1_Vehicle_24 Hours_RNAseq

description: Processed data file: Tumor P1.csv


title: AND CD4TCell H3K27Ac PCC 24h Rep3

description:
Gilfillan Chip-Seq
processed data file: union_peaks_1um_h3k27ac.txt

value: 1uM PCC

value: H3K27Ac (Abcam, cat. no. ab4729)


title: AND CD4TCell H3K27Ac 0.1uM PCC 24h Five Conditions

value: spleen

value: 0.1uM PCC


title: DN154_TGFbplusIL12_D502_D701

first: Shane

last: Crotty

address: 9420 Athena Circle

institute: La Jolla Institute of Allergy and Immunology

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
RNA-Seq data was mapped against hg19 reference genome using tophat (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome bioinformatics site.
The alignment results (sam files) were converted into bam files and sorted by using samtools.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id).
Genome_build: hg19
Supplementary_files_format_and_content: Excel table, raw counts of sequencing reads per gene generated by HTSeq-count
Supplementary_files_format_and_content: Excel table, raw counts were converted to RPKM vale followed by quantile normalization via R library 'aroma.light'

source_name: PBMC

growth_protocol: Naïve CD4 T cells from 4 or more donors were cultured with the following conditions: beads only (beads), IL-12, activin A, activin A+IL-12, TGFβ, TGFβ+IL-12.

extract_protocol:
Total RNA was purified using miRNAeasy Mini kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent Bioanalyzer (RNA integrity number (RIN) > 8.5; Agilent RNA 6000 Nano Kit, USA) and quantity using ananoliter spectrophotometer (Nanodrop, Thermofisher, USA).
For every sample, 500ng of purified total RNA was prepared into mRNA libraries, according to manufacturer’s instructions, using the Truseq Stranded mRNA Library Prep Kit (Illumina, RS-122-2103).

treatment_protocol: After 3 days of in vitro culture, live CD4+ T cells were sorted by FACS.

tag: cells cultured in vitro with

value: activated naive CD4 T cells


title: DN154_activinplusIL12_D504_D701

value: Activin A+IL12


title: DN154_TGFb_D501_D701

value: TGFb


title: AND CD4TCell H3K27Ac No Peptide 24h Rep3

value: CD4+ T cells

value: AND

value: 24 hours


title: Y&Z pooled spleen B cell day 9 post boost

city: Rochester

first: Martin

last: Zand

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: processed data file: YZXXSE.normalized.txt

data_processing:
CASAVA version 1.7 pipeline was used to call bases, demultiplex indexes, align the first 64 bases of each read to the genome, and count the number of reads aligned with each gene transcript in the mm10 refFlat annotation.
RefSeq gene annotations (mm10 refFlat.txt.gz) were downloaded from UCSC genome broswer and modified to add loci for immunoglobulin heavy chain genes on chromosome 12 (loci in NC_000078.6: Igha:113256204-113260236; Ighd:113407535-113416324; Ighe:113269263-113273248; Ighg1:113326544-113330523; Ighg2b:113304314-113307933; Ighg2c:113287389-113288932; Ighg3:113357442-113361232; Ighm:113418826-113422730).
Base counts per gene (i.e. bases aligned with RefSeq transcripts) were divided by 64 (number of bases used per sequence) to obtain reads per gene.
Reads per gene were divided by the total number of RefSeq reads across all genes to obtain reads per gene per total reads.
Reads per million RefSeq reads (RPM) were obtained by multilying reads per gene per total reads by one million.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted from frozen samples with the Qiagen RNeasy micro kit. Concentrations were determined by UV spectrophotometry (Nanodrop) and integrity of ribosomal RNA was confirmed with an Agilent Bioanalyzer.
Polyadenylated RNA was extracted from total RNA, fragmented, ligated to sequencing and indexing adapters, and PCR amplified using Illumina TruSeq RNA kits as recommended by the kit instructions. Each sample represents the RNA collected from 6 mice. In some cases the RNA from Y and Z pools (3 mice per pool) was mixed prior to sequencing library construction. In other cases the Y and Z pools (3 mice per pool) had separate libraries and indexing adapters and the reads from two libraries were concatenated. The treatment and extraction protocols for Y and Z pools was identical; these pool names are arbitrary identifiers for the convenience of the laboratory.

treatment_protocol: Female 10-12 week old C57BL/6Ntac mice (Jackson Labs) were anesthetized with avertin (100 mg/kg) and immunized intramuscularly in each calf muscle with 2.5 ug/leg purified, whole beta-propiolactone (BPL) inactivated influenza A/New Caledonia/20/99 virus (H1N1). Thirty days later mice were boosted by intramuscular immunization with 10 ug/leg  of undiluted 2006-2007 commercial TIV (Fluzone, Sanofi Pasteur). Mice were euthanized daily at 0 (pre-boost), 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the boost.  Spleens were removed from euthanized mice and placed into the wells of 6 well plates (1 spleen per well) and chopped into small pieces using dissecting scissors. To each well, 3 mL pre-warmed (37°C) IMDM (no supplements; Gibco, Cat:12440-053) containing 0.2 mg.mL TL Liberase (Roche, Cat:05-401-020-001) was added and the plates incubated at 37°C for 20 min. After the incubation 2 mL of IMDM containing 10% heat inactivated FBS (Gibco (HI Clone), 10082) was added to stop the digestion. Cells were further dispersed by pipetting the mixture up and down several times using a 5 mL syringe with a 19 ½ gauge needle. Extraneous tissue was removed by passing the suspension over a 100 μm nylon cell strainer (BD Falcon, Cat:352360). The volume of each single cell suspension (SCS) was brought up to 10 mL with IMDM + 10% FBS and 2.5 mL of each individual SCS removed and pooled into groups (three mice/spleens per group). Pooled SCS were pelleted 1,200 RPM for 10 min. at 4°C. To remove excess RBCs, cell pellets were suspended in a final volume of 2 mL MACS buffer (PBS + 2 mM EDTA + 0.5% BSA) containing 50 μL Ter119 magnetic beads (BD Biosciences, Cat:558536) per 1 x 107 total cells and the mixture incubated in a 4°C refrigerator (not on ice) for 30 min.  Cells bound to the Ter119 beads were removed by placing tubes in an Imag (BD Biosciences, Cat:552311) for 8 min. Unbound cells were transferred to new tubes and washed once with 2 mL MACS buffer. Some of these spleen cells were used for RNA-seq analysis. The remaining cells underwent B cell enrichment with MACS negative selection magnetic beads. Briefly, cells were suspended in 40 μL cold degassed MACS buffer (PBS + 2 mM EDTA + 0.5% BSA) and 10 μL each of the Pan B cell biotin-antibody cocktail (Miltenyi Biotec, Cat:130-095-813) and CD3e-biotin antibody (Miltenyi Biotec, Cat:130¬101¬878) were added per 1 x 107 cells. Antibody/cell mixtures were incubated in a 4°C refrigerator for 10 min followed by addition of anti-biotin Microbeads (Miltenyi Biotec, Cat:130-090-485). Ten mL MACS buffer was added and cells centrifuged at 1,500 10 min. Cell pellets were suspended in 3 mL MACS buffer and separated using LS columns (Miltenyi Biotec, Cat:130-042-401) with a Midi MACS separator (Miltenyi Biotech, Cat:130-042-302). Columns were washed twice and filtrate collected as enriched B cells. For cell lysis and RNA storage, cells were suspended in 350 μL RLT buffer (Qiagen, Cat: 79216). Resuspended samples were immediately loaded onto QIAshredder Columns (Qiagen, Cat:79656) and microcentrifuged at 10,000 RPM for 2 min at 4°C. Filtrate was then transferred into pre-chilled tubes and snap frozen in liquid nitrogen. Samples were stored at -80°C.

value: B cell

value: purified New Caledonia H1N1

value: I.M. legs

value: 2 x 10 ul


title: Y&Z pooled spleen B cell day 8 post boost


title: Y&Z pooled spleen B cell day 10 post boost


title: DN154_activin_D503_D701

value: Activin A


title: AND CD4TCell H3K27Ac K99A 24h Rep3

value: 1uM K99A


title: DN140_6_activinplusIL12_D504_D704


title: AND CD4TCell H3K27Ac PCC 24h Rep2


title: DN140_5_activin_D503_D704


title: Y&Z pooled spleen B cell day 4 post boost


title: Y&Z pooled spleen B cell day 5 post boost


title: DN140_3_IL12_D501_D704


title: Y&Z pooled spleen B cell day 6 post boost


title: AND CD4TCell H3K27Ac K99A 24h Rep2


title: AND CD4TCell H3K27Ac No Peptide 24h Rep1

value: No Peptide


title: DN140_1_beadsonly_D507_D703

value: beads only


title: Y&Z pooled spleen B cell day 2 post boost


title: Y&Z pooled spleen B cell day 1 post boost


title: DN140_4_TGFbplusIL12_D502_D704


title: Y&Z pooled spleen B cell baseline unboosted


title: DN140_2_TGFb_D508_D703


title: DN138_TGFbplusIL12_D504_D703


title: Y&Z pooled spleen B cell day 7 post boost


title: AND CD4TCell H3K4me2 No Peptide 24h Five Conditions

description:
Gosselin Chip-Seq
processed data file: union_peaks_five_conditions.txt

value: H3K4me2 (Millipore, cat. no. 07-030)


title: AND CD4TCell H3K27Ac No Peptide 24h Rep2

value: spleen

value: H3K27Ac (Abcam, cat. no. ab4729)


title: AND CD4TCell H3K4me2 10uM PCC 24h Five Conditions

value: 10uM PCC


title: DN138_IL12_D503_D703

value: activated naive CD4 T cells


title: AND CD4TCell H3K27Ac PCC 24h Rep1

value: 1uM PCC


title: Y&Z pooled spleen day 8 post boost

description: processed data file: YZXXSD.normalized.txt

value: unselected cells


title: Y&Z pooled spleen B cell day 3 post boost


title: DN138_TGFb_D502_D703

value: TGFb


title: DN138_activinplusIL12_D506_D703

value: Activin A+IL12


title: Y&Z pooled spleen day 7 post boost


title: AND CD4TCell H3K4me2 100uM K99A 24h Five Conditions

value: CD4+ T cells

value: AND

value: 24 hours


title: AND CD4TCell H3K27Ac K99A 24h Rep1


title: DN138_activin_D505_D703


title: AND CD4TCell H3K4me2 0.1uM PCC 24h Five Conditions

value: 0.1uM PCC


title: AND CD4TCell H3K4me2 No Peptide 24h Rep3

description:
Gilfillan Chip-Seq
processed data file: union_peaks_1um_h3k4me2.txt


title: DN111_TGFbplusIL12_D506_D702


title: Y&Z pooled spleen day 10 post boost

value: purified New Caledonia H1N1

value: I.M. legs

value: 2 x 10 ul


title: DN138_beadsonly_D501_D703

value: beads only


title: AND CD4TCell H3K4me2 1uM PCC 24h Rep3

value: H3K4me2 (Millipore, cat. no. 07-030)


title: Y&Z pooled spleen day 4 post boost

value: spleen


title: Y&Z pooled spleen day 6 post boost


title: DN111_IL12_D505_D702


title: DN111_TGFb_D504_D702


title: Y&Z pooled spleen day 3 post boost


title: AND CD4TCell H3K4me2 1uM K99A 24h Rep3

value: 1uM K99A


title: Y&Z pooled spleen day 9 post boost


title: Y&Z pooled spleen day 2 post boost


title: AND CD4TCell H3K4me2 10uM K99A 24h Five Conditions

value: 10uM K99A


title: DN111_beadsonly_D503_D702

value: activated naive CD4 T cells


title: Y&Z pooled spleen day 1 post boost


title: AND CD4TCell H3K4me2 No Peptide 24h Rep2

value: No Peptide


title: Y&Z pooled spleen day 5 post boost

value: unselected cells


title: DN111_activinplusIL12_D508_D702


title: Y&Z pooled spleen baseline unboosted


title: AND CD4TCell H3K4me2 1uM K99A 24h Rep2


title: DN105_TGFbplusIL12_D508_D701


title: DN111_activin_D507_D702

value: Activin A


title: AND CD4TCell H3K4me2 1uM PCC 24h Rep1

value: 1uM PCC


title: AND CD4TCell H3K4me2 No Peptide 24h Rep1

value: CD4+ T cells


title: Y&Z pooled lymph node B cell day 8 post boost

description: processed data file: YZXXNE.normalized.txt

source_name: lymph node

treatment_protocol: Female 10-12 week old C57BL/6Ntac mice (Jackson Labs) were anesthetized with avertin (100 mg/kg) and immunized intramuscularly in each calf muscle with 2.5 ug/leg purified, whole beta-propiolactone (BPL) inactivated influenza A/New Caledonia/20/99 virus (H1N1). Thirty days later mice were boosted by intramuscular immunization with 10 ug/leg  of undiluted 2006-2007 commercial TIV (Fluzone, Sanofi Pasteur). Mice were euthanized daily at 0 (pre-boost), 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the boost. Inguinal and popliteal lymph nodes were removed from euthanized mice and pooled (three mice per pool) into wells of a 24 well plate. Each lymph node was mechanically disrupted using two needle nosed forceps to gently tease apart each node, releasing the cells while removing excess fat tissue. To each well, 1 mL pre-warmed (37°C) IMDM (no supplements; Gibco, Cat: 12440-053) containing 0.2 mg/mL TL Liberase (Roche, Cat:05-401-020-001) was added and the plates incubated at 37°C for 20 min. After the incubation 1 mL of IMDM containing 10% heat inactivated FBS (Gibco (HI Clone), 10082) was added to stop the digestion. Cells were further dispersed by pipetting the mixture up and down several times using a 5 mL syringe with a 19 ½ gauge needle. Extraneous tissue was removed by passing the suspension over a 100 μm nylon cell strainer (BD Falcon, Cat: 352360). The resultant single cell suspensions (SCS) were pelleted 1,200 RPM for 10 min. at 4°C. Cells were suspended in 2 mL MACS buffer (PBS + 2 mM EDTA + 0.5% BSA). Some of these lymph node cells were used for RNA-seq analysis. The remaining cells underwent B cell enrichment with MACS negative selection magnetic beads. Briefly, cells were suspended in 40 μL cold degassed MACS buffer (PBS + 2 mM EDTA + 0.5% BSA) and 10 μL each of the Pan B cell biotin-antibody cocktail (Miltenyi Biotec, Cat:130-095-813) and CD3e-biotin antibody (Miltenyi Biotec, Cat:130¬101¬878) were added per 1 x 107 cells. Antibody/cell mixtures were incubated in a 4°C refrigerator for 10 min followed by addition of anti-biotin Microbeads (Miltenyi Biotec, Cat:130-090-485). Ten mL MACS buffer was added and cells centrifuged at 1,500 10 min. Cell pellets were suspended in 3 mL MACS buffer and separated using LS columns (Miltenyi Biotec, Cat:130-042-401) with a Midi MACS separator (Miltenyi Biotech, Cat:130-042-302). Columns were washed twice and filtrate collected as enriched B cells. For cell lysis and RNA storage, cells were suspended in 350 μL RLT buffer (Qiagen, Cat: 79216). Resuspended samples were immediately loaded onto QIAshredder Columns (Qiagen, Cat:79656) and microcentrifuged at 10,000 RPM for 2 min at 4°C. Filtrate was then transferred into pre-chilled tubes and snap frozen in liquid nitrogen. Samples were stored at -80°C.

value: lymph node

value: B cell


title: Y&Z pooled lymph node B cell day 9 post boost


title: DN105_beadsonly_D505_D701


title: DN105_TGFb_D506_D701

value: TGFb


title: AND CD4TCell H3K4me2 1uM PCC 24h Rep2

value: AND

value: 24 hours


title: AND CD4TCell H3K4me2 1uM K99A 24h Rep1


title: Y&Z pooled lymph node B cell day 7 post boost

value: purified New Caledonia H1N1

value: I.M. legs

value: 2 x 10 ul


title: AND CD4TCell RNA No Peptide 24h 0.5uM MEKi

description:
RNA-Seq
processed data file: rpkm.txt

extract_protocol:
Strand-specific RNA-seq libraries were prepared according to Wang et al. with minor modifications: "A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq." PLoS ONE, 2011
CD4+ cells were re-isolated from the culture using the Miltenyi MACS system.

value: spleen

tag: pre-treatment

value: Pre-treatment with the MEK inhibitor 0.5uM Promega U0126 (cat. no. V1121) for thirty minutes at 37ºC.


title: AND CD4TCell RNA 100uM K99A 24h 0.5uM MEKi

description:
RNA-Seq
processed data file: rpkm.txt


title: Y&Z pooled lymph node B cell day 6 post boost


title: DN105_activinplusIL12_D502_D702

value: Activin A+IL12


title: Y&Z pooled lymph node B cell day 4 post boost


title: DN105_IL12_D507_D701

value: activated naive CD4 T cells


title: Y&Z pooled lymph node B cell day 5 post boost


title: AND CD4TCell RNA 10uM PCC 24h 0.5uM MEKi

description:
RNA-Seq
processed data file: rpkm.txt

value: 10uM PCC


title: AND CD4TCell RNA 10uM K99A 24h 0.5uM MEKi

description:
RNA-Seq
processed data file: rpkm.txt

value: 10uM K99A


title: AND CD4TCell RNA 0.1uM PCC 24h 0.5uM MEKi

description:
RNA-Seq
processed data file: rpkm.txt

value: 0.1uM PCC


title: Y&Z pooled lymph node B cell day 3 post boost


title: DN105_activin_D501_D702

value: Activin A


title: Y&Z pooled lymph node B cell day 2 post boost


title: Y&Z pooled lymph node B cell day 10 post boost


title: NA19239_replicate_2_7.5k_Pool

city: Bar Harbor

first: Ryan

last: Tewhey

address: 600 Main Street

institute: Jackson Laboratory

description:
7.5k Oligo Pool
barcode count data
fastq of 3' UTR barcode and residual 5' flanking sequencing

data_processing:
Library strategy: MPRA
Perfect UTR barcode matches were asigned to their respective oligo. Counts for all barcodes asigned to an oligo were summed.
Genome_build: hg19

source_name: lymphoblastoid cell line

growth_protocol: 24 hour growth post-transfection

extract_protocol:
Qiagen Rneasy followed by hybridization pulldown of the GFP transcript.
Illumina Custom Paired-end (TruSeq)

tag: cell line


title: NA19239_replicate_3_7.5k_Pool


title: Y&Z pooled lymph node B cell day 1 post boost


title: Tumor_P2_E2+R5020_24 Hours_RNAseq

description: Processed data file: Tumor P2.csv

source_name: Breast cancer cells

value: ER+/PR+ Human tumor explants

value: ER+/PR+

value: 10nM Estradiol + 10 nM R5020

value: 24 Hours


title: Y&Z pooled lymph node B cell baseline unboosted

value: lymph node

value: B cell


title: AND CD4TCell RNA No Peptide 24h Rep2

description:
RNA-Seq
processed data file: rpkm.txt

value: CD4+ T cells

value: AND

value: No Peptide

value: 24 hours


title: NA19239_replicate_1_7.5k_Pool


title: AND CD4TCell RNA 10uM PCC 24h Rep2

description:
RNA-Seq
processed data file: rpkm.txt

value: spleen


title: NA12878_replicate_4_7.5k_Pool


title: Y&Z pooled lymph node day 10 post boost

description: processed data file: YZXXND.normalized.txt

value: unselected cells

value: purified New Caledonia H1N1

value: I.M. legs

value: 2 x 10 ul


title: Y&Z pooled lymph node day 9 post boost


title: AND CD4TCell RNA 0.1uM PCC 24h Rep2

description:
RNA-Seq
processed data file: rpkm.txt

value: 0.1uM PCC


title: AND CD4TCell RNA 100uM K99A 24h Rep2

description:
RNA-Seq
processed data file: rpkm.txt


title: NA12878_replicate_3_7.5k_Pool


title: NA12878_replicate_1_7.5k_Pool


title: AND CD4TCell RNA No Peptide 24h Rep1

description:
RNA-Seq
processed data file: rpkm.txt


title: HepG2_replicate_5_79k_Pool

description:
79k Oligo Pool
barcode count data
fastq of 3' UTR barcode and residual 5' flanking sequencing

source_name: hepatocellular carcinoma


title: NA12878_replicate_2_7.5k_Pool


title: AND CD4TCell RNA 10uM PCC 24h Rep1

description:
RNA-Seq
processed data file: rpkm.txt

value: 10uM PCC


title: Y&Z pooled lymph node day 6 post boost


title: AND CD4TCell RNA 10uM K99A 24h Rep1

description:
RNA-Seq
processed data file: rpkm.txt

value: 10uM K99A


title: Y&Z pooled lymph node day 7 post boost


title: NA12878_replicate_5_7.5k_Pool


title: Y&Z pooled lymph node day 8 post boost


title: HepG2_replicate_4_79k_Pool


title: Y&Z pooled lymph node day 5 post boost


title: HepG2_replicate_3_79k_Pool


title: AND CD4TCell RNA 100uM K99A 24h Rep1

description:
RNA-Seq
processed data file: rpkm.txt


title: Y&Z pooled lymph node day 4 post boost


title: HepG2_replicate_2_79k_Pool


title: AND CD4TCell RNA 0.1uM PCC 24h Rep1

description:
RNA-Seq
processed data file: rpkm.txt


title: Y&Z pooled lymph node day 3 post boost


title: Input DNA_hP

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM

data_processing:
FastQ files were filtered using fastX toolkit (version 0.0.13.2). The following filters were applied: trimming of nucleotides from the most right position if median quality score across reads smaller than 20 (Phred 33 code); clipping on both side if adapters were identified by fastqc; elimination of reads with more than 20% of nucleotide presenting a quality score below 20
ChIP-sequencing were aligned to the mm9 genome using bowtie 0.12.8. Configuration:maximum number of mismatches = 2; reports max 1 alignment; discard reads with more than 1 alignment
Duplicated reads were removed using samtools rmdup (version 0.1.18)
Peaks were called using MACS (version 1.4.0), with default parameters for Meis1 and Prep1. Only peaks with a p-val below 10e-06 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files generated with bowtie and macs

source_name: Embryonic fibroblast

growth_protocol: Mouse embronic fibroblasts (MEFs) were taken from E14.5 Prep1 hypomorphic embros and cultured in DMEM supplemented with 10% FBS and 2mM L-glutamin. Mefs were passed every 2-3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and  Meis1-DNA  or Prep1-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit, 48 Samples-Set A Box, (part # 15034288).  Briefly, Input DNA (5-10 ng) was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles. The resultant library fragments were ~300 bp. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

value: Prep1 overexpressing cells (hP)

tag: passages

tag: genotype/variation

value: Prep1 hypomorphic


title: HepG2_replicate_1_79k_Pool


title: Input DNA_WT

value: wild-type cells (WT)

value: Prep1 wild-type


title: Y&Z pooled lymph node day 1 post boost

value: lymph node


title: Y&Z pooled lymph node baseline unboosted


title: NA19239_replicate_1_79k_Pool


title: NA19239_replicate_2_79k_Pool


title: AND CD4TCell RNA 10uM K99A 24h Rep2

description:
RNA-Seq
processed data file: rpkm.txt

value: CD4+ T cells


title: Y&Z pooled blood B cell day 10 post boost

description:
YZ10HE
processed data file: YZ XXHE.normalized.txt

source_name: blood

treatment_protocol: Female 10-12 week old C57BL/6Ntac mice (Jackson Labs) were anesthetized with avertin (100 mg/kg) and immunized intramuscularly in each calf muscle with 2.5 ug/leg purified, whole beta-propiolactone (BPL) inactivated influenza A/New Caledonia/20/99 virus (H1N1). Thirty days later mice were boosted by intramuscular immunization with 10 ug/leg  of undiluted 2006-2007 commercial TIV (Fluzone, Sanofi Pasteur). Mice were euthanized daily at 0 (pre-boost), 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the boost. Blood was collected from 9 mice per time point, and blood was saved as 3 pools representing 3 mice per pool (labeled as pools W,Y and Z). Blood was collected by retro-orbital bleed of anesthetized mice into heparinized capillary tubes and aliquoted into polypropylene tubes containing 0.1 mL heparin sulfate (1,000 USP units/ml; Hospira, Cat:0409-27720-02). One mL of HBSS (Gibco, Cat: 14170-112) was immediately added to the tube and the contents gently mixed. Diluted whole blood was then layered onto 4 mL Lympholyte-Mammal (Cedar Lane, Cat: CL5110) in 15 mL canonical tube. Tubes were then centrifuged at 800g for 20 min at RT. Buffy coats were removed and diluted with an equal volume of cold (4°C) HBSS and cells pelleted by centrifugation at 1,200 RPM for 10 min at 4°C. Cells were washed twice with 6 mL MACS buffer (PBS + 2 mM EDTA + 0.5% BSA) by centrifugation at 1,200 RPM for 10 min at 4°C. To remove excess RBCs, cell pellets were suspended in a final volume of 2 mL MACS buffer containing 50 μL Ter119 magnetic beads (BD Biosciences, Cat:558536) per 1 x 107 total cells and the mixture incubated in a 4°C refrigerator (not on ice) for 30 min.  Cells bound to the Ter119 beads were removed by placing tubes in an Imag (BD Biosciences, Cat:552311) for 8 min. Unbound cells were transferred to new tubes and washed once with 2 mL MACS buffer. Some of the resultant PBMCs were used for RNA-seq analysis and some underwent B cell enrichment using MACS negative selection magnetic beads. Briefly, cells were suspended in 40 μL cold degassed MACS buffer (PBS + 2 mM EDTA + 0.5% BSA) and 10 μL each of the Pan B cell biotin-antibody cocktail (Miltenyi Biotec, Cat:130-095-813) and CD3e-biotin antibody (Miltenyi Biotec, Cat:130¬101¬878) were added per 1 x 107 cells. Antibody/cell mixtures were incubated in a 4°C refrigerator for 10 min followed by addition of anti-biotin Microbeads (Miltenyi Biotec, Cat:130-090-485). Ten mL MACS buffer was added and cells centrifuged at 1,500 10 min. Cell pellets were suspended in 3 mL MACS buffer and separated using LS columns (Miltenyi Biotec, Cat:130-042-401) with a Midi MACS separator (Miltenyi Biotech, Cat:130-042-302). Columns were washed twice and filtrate collected as enriched B cells. For cell lysis and RNA storage, PBMC and B cells were suspended in 350 μL RLT buffer (Qiagen, Cat: 79216). Resuspended samples were immediately loaded onto QIAshredder Columns (Qiagen, Cat:79656) and microcentrifuged at 10,000 RPM for 2 min at 4°C. Filtrate was then transferred into pre-chilled tubes and snap frozen in liquid nitrogen. Samples were stored at -80°C.

value: blood

value: B cell


title: NA12878_replicate_5_79k_Pool


title: NA12878_replicate_4_79k_Pool


title: NA12878_replicate_3_79k_Pool


title: Meis1/2_ChIPSeq_WT

value: Meis1/2 (Santa Cruz Biotechnology, sc-10599X, lot# C2912)


title: Y&Z pooled blood B cell day 7 post boost

description:
YZ07HE
processed data file: YZ XXHE.normalized.txt


title: Prep1_ChIPSeq_WT

value: Prep1(N-15X) (Santa Cruz Biotechnology, sc-6245X, lot# F2003)


title: Y&Z pooled blood B cell day 8 post boost

description:
YZ08HE
processed data file: YZ XXHE.normalized.txt


title: Y&Z pooled blood B cell day 6 post boost

description:
YZ06HE
processed data file: YZ XXHE.normalized.txt


title: NA12878_replicate_2_79k_Pool


title: NA19239_replicate_3_79k_Pool


title: Y&Z pooled lymph node day 2 post boost

value: unselected cells


title: D80_HC

first: Pandurangan

last: Vijayanand

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

description:
PolyAtail selected messenger RNA
Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
Bulk RNA-seq data was mapped against the human hg19 reference using TopHat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site. Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Blood PBMCs

growth_protocol: Cells were directly isolated from samples and lysed, no culture were involved.

extract_protocol:
Cells were sorted directly into Trizol LS buffer by Flow cytometry. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012)
Purified total RNA (5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

value: CD3+CD4+CD45RA-CCR7+CD25-CCR4+ T cells

tag: disease group

value: Healthy non allergic


title: Y&Z pooled blood B cell day 5 post boost

description:
YZ05HE
processed data file: YZ XXHE.normalized.txt

value: purified New Caledonia H1N1

value: I.M. legs

value: 2 x 10 ul


title: Y&Z pooled blood B cell day 4 post boost

description:
YZ04HE
processed data file: YZ XXHE.normalized.txt


title: Y&Z pooled blood B cell day 3 post boost

description:
YZ03HE
processed data file: YZ XXHE.normalized.txt


title: D78_HC


title: D77_HC


title: Y&Z pooled blood B cell day 2 post boost

description:
YZ02HE
processed data file: YZ XXHE.normalized.txt


title: D76_HC


title: Y&Z pooled blood B cell day 1 post boost

description:
YZ01HE
processed data file: YZ XXHE.normalized.txt


title: Meis1/2_ChIPSeq_hP


title: Y&Z pooled blood B cell baseline unboosted

description:
YZ00HE
processed data file: YZ XXHE.normalized.txt


title: D75_HC


title: D74_HC


title: Y&Z pooled blood B cell day 9 post boost

description:
YZ09HE
processed data file: YZ XXHE.normalized.txt


title: Y&Z pooled blood PBMC day 9 post boost

description:
YZ09HD
processed data file: YZ XXHD.normalized.txt

value: PBMC


title: D70_HC


title: NA12878_replicate_1_79k_Pool


title: Y&Z pooled blood PBMC day 7 post boost

description:
YZ07HD
processed data file: YZ XXHD.normalized.txt


title: Y&Z pooled blood PBMC day 8 post boost

description:
YZ08HD
processed data file: YZ XXHD.normalized.txt


title: D79_HC


title: D72_HC


title: D69_HC


title: Y&Z pooled blood PBMC day 5 post boost

description:
YZ05HD
processed data file: YZ XXHD.normalized.txt


title: D71_HC


title: D67_HC


title: Prep1_ChIPSeq_hP

value: Prep1 overexpressing cells (hP)


title: Y&Z pooled blood PBMC day 4 post boost

description:
YZ04HD
processed data file: YZ XXHD.normalized.txt


title: D68_HC


title: D66_HC


title: D65_AR

value: Allergic rhinitis


title: Y&Z pooled blood PBMC day 3 post boost

description:
YZ03HD
processed data file: YZ XXHD.normalized.txt


title: Y&Z pooled blood PBMC day 6 post boost

description:
YZ06HD
processed data file: YZ XXHD.normalized.txt


title: Y&Z pooled blood PBMC day 2 post boost

description:
YZ02HD
processed data file: YZ XXHD.normalized.txt


title: D62_AR


title: Y&Z pooled blood PBMC day 1 post boost

description:
YZ01HD
processed data file: YZ XXHD.normalized.txt


title: Y&Z pooled blood PBMC baseline unboosted

description:
YZ00HD
processed data file: YZ XXHD.normalized.txt


title: D73_HC

description:
PolyAtail selected messenger RNA
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: D59_AR


title: D56_AR


title: D55_AR


title: D53_AR


title: D54_AR


title: D64_AR


title: D60_AR


title: D50_AR


title: D63_AR


title: D58_AR


title: Y&Z pooled blood PBMC day 10 post boost

description:
YZ10HD
processed data file: YZ XXHD.normalized.txt


title: D49_AR


title: D51_AR


title: D47_AR


title: D52_AR


title: D48_AR


title: D61_AR


title: D57_AR


title: D45_AR


title: D44_AR


title: D43_AR


title: D42_AR


title: D40_AS

value: Asthmatic


title: D39_AS


title: D38_AS


title: D35_AS


title: D41_AR


title: D33_AS


title: D28_AS


title: D29_AS


title: D30_AS


title: D25_AS


title: D36_AS


title: D22_AS


title: D26_AS


title: D21_AS


title: D20_AS


title: D34_AS


title: D32_AS


title: D31_AS


title: D27_AS


title: D17_AS


title: D46_AR


title: D23_AS


title: D10_AS


title: D19_AS


title: D37_AS


title: D18_AS


title: D16_AS


title: D14_AS


title: D15_AS


title: 5 dpi infected_rep3

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

data_processing:
Image analys+is and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 and 23 was performed while the raw data from 2 sequencing runs (sample 25) and 3 sequencing runs (samples 2, 11-16, 24 and 26) were combined to generate one fastq file and one tsv file each. The generated fastq files were used to calculate average insert sizes and standard deviations for paired end experiments.
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_67) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Danio_rerio.Zv9.67.dna.toplevel / Danio_rerio.Zv9.67.cdna.all.fa (http://www.ensembl.org/info/data/ftp/index.html )
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: zebrafish embryo, M. marinum infected

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich)

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 250 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 2, 4, 6, 8 hours post injection (hpi) and 1, 2, 3, 4, 5 days post injection (dpi) pools of 30 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using QIAZOL reagent.

tag: blood island injection at 28 hpf

value: M. marinum, Mma20 strain 250 cfu

tag: developmental stage rna isolation

value: 5 dpi


title: D11_AS

tag: tissue


title: D09_AS


title: 5 dpi uninfected_rep4

source_name: zebrafish embryo,  not-infected


title: D08_AS


title: 5 dpi uninfected_rep2


title: D07_AS


title: D12_AS


title: 5 dpi infected_rep4


title: D04_AS


title: D06_AS


title: 5 dpi infected_rep1


title: D05_AS


title: 4 dpi infected_rep2

value: 4 dpi


title: 4 dpi uninfected_rep4


title: D24_AS

value: blood


title: 5 dpi uninfected_rep3


title: D01_AS


title: D13_AS


title: 3 dpi infected_rep4

description: R1 raw file was damaged and only includes 9703956 of the original 21069771 reads. R2 file was complete.

value: 3 dpi


title: 4 dpi infected_rep1


title: 4 dpi infected_rep4


title: 3 dpi infected_rep2


title: 3 dpi uninfected_rep2


title: 2 dpi infected_rep4

value: 2 dpi


title: 3 dpi uninfected_rep4


title: 3 dpi infected_rep3


title: 4 dpi uninfected_rep2


title: 2 dpi infected_rep2


title: 4 dpi uninfected_rep1


title: 4 dpi uninfected_rep3


title: D03_AS


title: 2 dpi infected_rep1


title: 5 dpi uninfected_rep1


title: 3 dpi infected_rep1


title: 1 dpi infected_rep4

value: 1 dpi


title: 1 dpi infected_rep3


title: 3 dpi uninfected_rep1


title: 3 dpi uninfected_rep3


title: testes2

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

description: sequencing date: 01/9/2013

data_processing:
Basecalling Illumina RTA 1.17.21.3
demultiplexing (Casava 1.8.2, Illumina)
Alignment to hg19 +18S/28S rRNA using Bowtie39 (v. 2.2.3.0) and splice junction mapper Tophat38 (v.2.0.12)
FPKM coverage for each of 2 testes samples was calcuated based on aligned BAM files using Genomatix Expression Analysis for RNA seq (v3.30126)
Genome_build: hg19
Supplementary_files_format_and_content: Testes-2samples-RPKM.txt - contains FPKM values (Genomatix) for 23180 annotated transcripts (isoform with highest expression)

source_name: testes

extract_protocol:
commerically available Human Testes Total RNA  - Ambion AM7972
Sperm RNA was isolated and purified using a modified RNeasy (Qiagen) protocol and finally the RNA quality assessed for DNA contamination as described in paper
A total of 2 ng of unfractionated input RNA was reverse transcribed and the resulting cDNA amplified using SeqPlex RNA Amplification (Sigma-Aldrich Co.) allowing for the use of samples with low quantity of spermatozoa
Amplified primer dimers were removed prior to library construction using Agencourt AMPure XP (Beckman Coulter) and libraries were constructed with 50 ng of amplified cDNA using Encore NGS Library System I (Nugen, Inc.).
4bp inline Illumina index primers allowed for multiplexing of samples
Paired-end sequencing (2x51  + 6Index) was performed  using an Illumina HiSeq 2500 sequencer

tag: tissue type

value: testes


title: 1 dpi uninfected_rep4


title: 8 hpi infected_rep4

value: 8 hpi


title: 1 dpi uninfected_rep2


title: 8 hpi infected_rep3


title: 1 dpi uninfected_rep3


title: 8 hpi infected_rep2


title: SU070-pHSC-140603.trim

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

description: library strategy: ATAC-seq

data_processing:
ATAC-seq data was processed as previously described (Buenrostro et al., 2015a) with notable exceptions. In brief, reads were trimmed using a custom script and aligned using Bowtie2. To call peaks, data was aggregated by each unique cell type, peak summits were called using MACS2 and filtered using a custom blacklist, as previously described (Buenrostro et al., 2015a).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.

source_name: pHSC

extract_protocol:
ATAC-seq was performed directly from FACS-purified cells
5,000 sorted cells in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed-angle centrifuge. 50 ul transposase mixture (25 ul of 2x TD, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37C for 30 minutes in an Eppendorf ThermoMixer with agitation at 300 RPM. Transposed fragments were purified and amplified as described previously (Buenrostro et al., 2015).

value: acute myeloid leukemia, pre-leukemic hematopoietic stem cell

tag: donorid

tag: sample type

value: primary human leukemia cell from cryopreserved sample


title: 2 dpi infected_rep3


title: 8 hpi uninfected_rep4


title: SU070-LSC-140603.trim

description: library strategy: ATAC-seq

source_name: LSC

value: acute myeloid leukemia, leukmeia stem cell


title: SU070-Leuk-140603.trim

description: library strategy: ATAC-seq

source_name: Blast

value: acute myeloid leukemia, blast cell


title: 8 hpi uninfected_rep3


title: 8 hpi uninfected_rep1


title: 4 dpi infected_rep3


title: 6 hpi infected_rep2

value: 6 hpi


title: 2 dpi uninfected_rep4


title: 2 dpi uninfected_rep2


title: 2 dpi uninfected_rep1


title: testes1

description: sequencing date: 01/9/2013


title: 1 dpi infected_rep2


title: ssmR1

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),

data_processing:
The resulting raw sequence data were subjected to standard data analysis using the pipeline script, ACGT101-miR v4.2 (LC Sciences). First, identical raw sequence reads were clustered into unique families. Mappable sequences from raw sequencing data were obtained and the impurity sequences due to the sample preparation, chemical sequencing and the optical digital resolution of the sequencing detectors were removed. After removing these low quality reads and adaptor sequences, the 16–29 nt mappable reads (filtered unique sequences) were then analyzed by BLAST against Repbase, M. nipponense mRNAs and Rfam to identify rRNA, tRNA, snRNA, snoRNA, mRNA and repeat sequences. The remaining clean reads were aligned against known deuterostoma pre-miRNAs in miRbase 20.0 to determine novelty and species specificity. Due to some overlaps in the size between miRNAs and piwi-interacting RNAs (piRNA), prediction of the secondary structure of individual miRNAs was performed using MFOLD software (Version 2.38, http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form) under the default folding conditions. Multiple sequence alignments were conducted using ClustalW 1.84.
To conduct a comparative genomic analysis of the newly identified miRNAs, the M. nipponense miRNAs were mapped against the genomes of Daphnia pulex, Danio rerio and Homo sapiens with MapMi software using default parameters (Guerra-Assunção et al., 2010). M. nipponense miRNA mature sequences were used as custom sequences to search the M. nipponense transcriptome library (http://www.ncbi.nlm.nih.gov/sra/?term=SRP056408) for target prediction using RNAhybrid v2.2 (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid) with parameter settings defined according to the method reported by Wei et al. (2011). A signal-to noise analysis was performed to estimate the specificity of target prediction (Alves-Junior et al., 2009). First, 10 randomized sequences of each miRNA were generated with the SHUFFLE program from the HMMER package (http://hmmer.janelia.org), maintaining the dinucleotide frequencies of the original miRNAs. The number of predicted targets for these randomly generated miRNAs was compared with the number of predicted targets for the sequenced miRNAs. Specificities and signal-to-noise ratios were calculated for each miRNA, and the averages were defined as the specificity and signal-to-noise ratio of the entire prediction. More specifically, specificity = TP/(TP+FP) and signal-to-noise ratio = (TP+FP)/FP, where TP is the number of true positives and FP is the number of false positives. The targets were extracted using an in-house Python script and annotated using the BLAST2GO database. KEGG annotation was conducted using KAAS software.
Genome_build: EST from NCBI
Supplementary_files_format_and_content: miRNAs prediction results and expression data from microarray experiment and targets function analysis of miRNAs, xls

organism: Macrobrachium nipponense

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA), and then treated with RNase-free DNase I (TianGen, Beijing, China) to remove genomic DNA contamination. The quality of RNA was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Equal amounts of the extracted RNA from the four tissues (gill, hepatopancreas, muscle and hemocytes) were combined to form a single RNA pool. Approximately 20 μg total RNA was ligated with proprietary 5′ and 3′ adaptors developed by Illumina (San Diego, CA, USA) and size-fractionated by 6% Tris/borate/EDTA (TBE)-urea polyacrylamide gel electrophoresis. The 90 base-pair fraction was excised and recovered. The RNA was converted to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen) and subsequently amplified in 15 cycles using Illumina’s small RNA primer set and Phusion High Fidelity polymerase (New England Biolabs, Ipswich, MA, USA). The PCR products were size-fractionated and recovered for sequencing with the Illumina Genome Analyzer IIe according to the manufacturer’s instructions (Illumina).

treatment_protocol: Healthy Oriental River Prawns (wet weights, 1.45–2.86 g) were obtained from a wild population in Lake Tai (Wuxi, (120°13′44″E, 31°28′22″N) China). All the samples were transferred to the laboratory of the Freshwater Fisheries Research Center (Wuxi, Jiangsu, China) and maintained in six 300-liter tanks with aerated freshwater prior to the experiments. The prawns were laboratory acclimated for one week prior to RNA extraction. During acclimation periods, prawns were fed commercial flake food twice daily, and maintained under culture conditions of 22.6 ± 0.5°C, pH 8.2 ± 0.08, DO 6.5 ± 0.2 mg/L, total ammonia-nitrogen 0.08–0.09 mg L−1, and a 14 h light/10 h dark photoperiod.

tag: location


title: 6 hpi uninfected_rep2


title: 6 hpi uninfected_rep3


title: 6 hpi uninfected_rep1


title: 1 dpi infected_rep1


title: 6 hpi infected_rep1


title: 4 hpi infected_rep2

value: 4 hpi


title: 2 dpi uninfected_rep3


title: 8 hpi infected_rep1


title: 1 dpi uninfected_rep1


title: 8 hpi uninfected_rep2


title: 6 hpi infected_rep4


title: 2 hpi infected_rep4

value: 2 hpi


title: 4 hpi uninfected_rep2


title: 6 hpi infected_rep3


title: 2 hpi infected_rep3


title: 2 hpi infected_rep2


title: 2 hpi infected_rep1


title: 4 hpi infected_rep4


title: 6 hpi uninfected_rep4


title: 4 hpi infected_rep1


title: 4 hpi infected_rep3


title: 4 hpi uninfected_rep4


title: 2 hpi uninfected_rep2


title: 4 hpi uninfected_rep3


title: 2 hpi uninfected_rep4


title: 2 hpi uninfected_rep3


title: 4 hpi uninfected_rep1


title: BC9

city: Madrid

first: Angel Mario

middle: Martinez

last: Montes

address: Crta. de la Coruña, km 7,5

department: Mejora Genetica Animal

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA

data_processing:
Sequence reads were analyzed using CLCBio Genomic workbench software (CLC Bio, Aarhus, Denmark).
Quality control analysis was performed using the NGS quality control tool. A hierarchical clustering of the samples was also performed.
Sequence paired-end reads (75bp) were assembled against the annotated Sscrofa10.2 reference genome using the genome, annotated genes and mRNA tracks
Data was normalized by calculating the reads per kilo base per million mapped reads’ (RPKM) for each gene
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: Processed data file includes normalized expression values (RPKM) for all genes in all 10 samples passing the quality control, fold changes and P values for differential expression

organism: Sus scrofa

source_name: Liver

extract_protocol:
Total RNA was extracted using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations and quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). The RNA integrity value (RIN) of the samples ranged between 7.1 and 8.1.
Paired-end libraries with fragments of 300bp were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego CA, USA) for each sample. Multiplex sequencing of the libraries was performed on an Illumina Hi-Seq 2000 (Fasteris SA, Plan-les-Ouates, Switzerland) with three samples per lane, according to the manufacturer’s instructions at CNAG (Centro Nacional de Análisis Genómico) generating paired-end reads of 75 bp.

treatment_protocol: Samples were collected at slaughter, immediately frozen in liquid nitrogen and stored at -80ºC until analyzed

tag: age

tag: Sex

value: male

tag: phenotype

value: low growth and fatness

value: liver


title: BC10


title: BC7


title: 2 hpi uninfected_rep1


title: 4dpa small RNA, rep 2

data_processing:
Reads were adapter clipped and quality filtered using FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) for small RNA, and Trimmomatic (Bolger et al. Bioinformatics (2010)) for mRNA.
Small RNA reads were collapsed reads were collapased using FASTX Toolkit and annotated using miRMiner (Wheeler et al. Evol. Dev. (2009)) and miRBase v. 21 (Kozomara et al. Nucleic Acids Res (2014)).
MicroRNA read counts per sample were analyzed for differentially expression using R/edgeR (Robinson et al. Bioinformatics (2010)).
mRNA reads were mapped to the zebrafish transcriptome (Ensembl v. 76 annotation of zebrafish Zv9 assembly) using RSEM (Li and Dewey BMC Bioinformatics (2011)).
Differentially expressed transcripts were determined using R/edgeR.
Genome_build: zv9
Supplementary_files_format_and_content: Tab-delimited text file with read counts per transcript per sample.

source_name: caudal fin

growth_protocol: Adult Ekkwill (EK) zebrafish were housed and maintained in tanks at 22oC and exposed to a 12:12 hour light:dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) following manufacturer’s protocol.
Illumina TruSeq small RNA and strand-specific PolyA+ mRNA libraries.

treatment_protocol: Caudal fins were amputated with scalpels following anesthesia (0.6mM MS222).

value: caudal fin

tag: days post amputation

tag: library type

value: small RNA


title: 4dpa small RNA, rep 3


title: 0dpa small RNA, rep 3


title: BC3

value: high growth and fatness


title: 0dpa small RNA, rep 2


title: BC4


title: a56.1.leaf.meth.140417

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

data_processing:
Basecalling done using standard Illumina pipelline.
Alignment for DNA-seq done using Bowtie with 2 mismatched allowed for 100 bp reads, 1 mismatch for 50 bp reads. Alignment for RNA-seq was done using Tophat2 allowing for 1 mismatch. Alignment for methyl-seq was done with BSMap, allowing for 2 mismatches. In all cases only uniquely mapping alignments were retained for downstream analysis.
For EMS mapping (both RNA-seq and DNA-seq), mismatches levels were generated using samtools mpileup.
For methyl-seq, methylation ratios were calculated using the python script that is part of the BSMap distribution.
Detail of alignment counting for RNA-seq and DNA-seq can be found in Supplemental Methods of associated manuscript.
Genome_build: TAIR10
Supplementary_files_format_and_content:
"count table" is tab-separated table used to quantify RNA expression over TAIR10 gene models with the following fields ["Gene name", "Length of gene", "Number of overlapping alignments"].
"chromosome count table (csome.txt.gz)" is a tab-separated table used to quantify DNA copy number over binned regions (0-based) of the genome with the following fields ["Chromosome", "Start of bin", "End of bin", "Number of overlapping alignments", "Reads per million per kilobase"].
"mismatch count table (mismatch.txt.gz)" is a tab-separated table used to quantify the number of alignment mismatches at a given position in a library with the following fields ["Chromosome", "Position", "Mismatches", "Matches", "Percent Reference", "ConsensusMismatch"] where "ConsensusMismatch" is the most common mismatch found at a position and "Position" is 1-based genomic position.
"methylation ratio table (ratio.txt.gz)" is a tab-separated table used to quantify cytosine methylation levels at individual cytosine positions. It is the output of the BSMap program and associated python script. It has the following fields ["chromosome", "position", "strand of cytosine", "context of cytosin", "methylation ratio", "Effective number of C or T counts", "Number of C counts", "Total numberof C or T counts", "G counts on reverse strand", "Total G or A counts on the reverse strand", "lower bound of 95% confidence interval of methylation ratio", upper bound of 95% confidence interval of methylation ratio"].

organism: Arabidopsis thaliana

source_name: 3 week-old leaf

growth_protocol: Grown on soil under constant light (22 degrees Celsius)

extract_protocol:
Qiagen Plant DNAesy
Qiagen Epitect followed by Illumina TruSeq

value: atxr5; atxr6

value: 3 week-old leaf

tag: molecule subtype

value: sodium bisulfite-treated DNA


title: BC5


title: BC6


title: BC8


title: EMS_2_129.1.cotyledon.DNA.130602

source_name: cotyledon

growth_protocol: Grown on MS media with no sucrose

extract_protocol:
DNA extraction via, high salt solubilization followed by alcholol precipitation.
Illumina SE DNA prep

value: mbd9-4; atxr5; atxr6

value: cotyledon


title: EMS_2_300.1.cotyledon.DNA.130227

value: atthp1-5; atxr5; atxr6; RAD51pro::GFP transgene


title: BC1


title: atsubtl2.1.leaf.meth.140417

description: Mixed Col/Ws ecotype


title: thp1.1.leaf.meth.140417


title: EMS_2_209.1.cotyledon.DNA.130925

value: atsac3b-5; atxr5; atxr6; RAD51pro::GFP transgene


title: sac3b.1.leaf.meth.140417


title: BC2


title: mbd9.1.leaf.meth.140417


title: 0dpa small RNA, rep 1


title: brca1a56.2.16C.DNA.110202

source_name: sorted 16C nuclei

extract_protocol:
Direct sorting into PicoPure DNA Extraction Kit (Molecular Devices)
Illumina SE DNA prep

value: atbrca1-1; atxr56

value: sorted 16C nuclei


title: Col.1.leaf.meth.140417

value: wildtype


title: a56.1.cotyledon.DNA.110817


title: 4dpa small RNA, rep 1


title: brca1a56.1.16C.DNA.110202


title: a56.1.flower.DNA.110817


title: Col.1.flower.DNA.110817


title: Col.1.cotyledon.DNA.110817


title: EMS_2_37.1.cotyledon.DNA.130105

value: atsac3b-4; atxr5; atxr6; RAD51pro::GFP transgene


title: Col.1.16C.DNA.110202


title: RAD51GFP.1.cotyledon.DNA.130105

value: atxr5; atxr6; RAD51pro::GFP transgene


title: EMS_2_37.GFPpos.1.cotyledon.RNA.121116

extract_protocol:
Trizol extraction
Illumina TruSeq mRNA

value: atsac3b-4/+; atxr5; atxr6; RAD51pro::GFP transgene


title: EMS_2_325.1.cotyledon.DNA.130227

value: at-stubl2-1; atxr5; atxr6; RAD51pro::GFP transgene


title: a56.1.16C.DNA.110202


title: EMS_2_37.GFPneg.1.cotyledon.RNA.121116


title: a56.100Gy.2.seedling.110907

source_name: 10 day old seedling

treatment_protocol: Irradiated with Cesium 137 (100Gy), recovery of 90min

value: 10 day old seedling

tag: treated with


title: Col.1.cotyledon.RNA.121116


title: a56.0Gy.1.seedling.110907

treatment_protocol: Mock irradiation treatment

value: Mock irradiation


title: a56.100Gy.1.seedling.110907

value: Irradiated with Cesium 137 (100Gy), recovery of 90min


title: EMS_2_325.GFPpos.1.cotyledon.RNA.130102

value: at-stubl2-1/+; atxr5; atxr6; RAD51pro::GFP transgene


title: sac3b.2.cotyledon.RNA.140415


title: sac3batxr56.2.cotyledon.RNA.140415

value: atsac3b-3; atxr5; atxr6


title: RAD51GFP.1.cotyledon.RNA.121116


title: mbd9.1.cotyledon.RNA.140415


title: thp1.2.cotyledon.RNA.140415


title: Col.0Gy.1.seedling.110907


title: EMS_2_300.GFPneg.1.cotyledon.RNA.130102


title: EMS_2_325.GFPneg.1.cotyledon.RNA.130102


title: a56.0Gy.2.seedling.110907

value: atxr5; atxr6


title: Col.100Gy.2.seedling.110907


title: atsubtl2.hom.1.cotyledon.RNA.140415

description: Mixed Col/Ws ecotype

value: at-stubl2-2; atxr5; atxr6


title: mbd9a56.1.cotyledon.RNA.140415

value: mbd9-3; atxr5; atxr6

value: cotyledon


title: Col.100Gy.1.seedling.110907


title: thp1a56.1.cotyledon.RNA.140415

value: thp1-1; atxr5; atxr6


title: a56.1.cotyledon.RNA.131202


title: a56.3.cotyledon.RNA.131202


title: EMS_2_300.GFPpos.1.cotyledon.RNA.130102

value: atthp1-5/+; atxr5; atxr6; RAD51pro::GFP transgene


title: a56.3.cotyledon.RNA.140415


title: sac3batxr56.1.cotyledon.RNA.131202


title: Col.0Gy.2.seedling.110907


title: 5 dpi infected_rep2

value: M. marinum, Mma20 strain 250 cfu

value: 5 dpi


title: brca1a56.2.cotyledon.RNA.140415

value: atbrca1-1; atxr56


title: brca1.2.cotyledon.RNA.140415


title: D02_AS

value: blood

tag: cell type

value: CD3+CD4+CD45RA-CCR7+CD25-CCR4+ T cells

value: Asthmatic


title: brca1.1.cotyledon.RNA.131202

tag: genotype/variation


title: Col.3.cotyledon.RNA.140415

value: wildtype


title: Col.2.cotyledon.RNA.140415


title: atsubtl2.het.1.cotyledon.RNA.140415

description: Mixed Col/Ws ecotype

value: at-stubl2-2/+; atxr5; atxr6


title: Col.1.cotyledon.RNA.131202


title: brca1a56.1.cotyledon.RNA.131202


title: Col.0Gy24h.1.seedling.111226

source_name: 11 day old seedling

value: 11 day old seedling

value: Mock irradiation


title: Col.100Gy24h.1.seedling.111226

treatment_protocol: Irradiated with Cesium 137 (100Gy), recovery of 24h


title: sac3b.1.cotyledon.RNA.131202


title: Col.1.flower.RNA.110906

source_name: immature floral bud

value: immature floral bud


title: a56.1.flower.RNA.110906

value: atxr5; atxr6


title: Col.2.flower.RNA.110906


title: Col.3.cotyledon.RNA.131202


title: a56.100Gy24h.1.seedling.111226

value: Irradiated with Cesium 137 (100Gy), recovery of 24h


title: thp1.1.cotyledon.RNA.131202


title: a56.0Gy24h.1.seedling.111226


title: a56.2.cotyledon.RNA.140415


title: nrpe1 Hi-C Rep2

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

data_processing:
Alignment was done by bowtie for each end separately keeping only unique matches. Mapped reads were then paired.
Alignment was done by tophat2 for rna-seq samples and processed by edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: nrpe1 DMRs with long range chromosomal contacts.
Supplementary_files_format_and_content: Chromosome Start End Col-0_Methylation nrpe1_Methylation

source_name: Seedlings

growth_protocol: Long day 2-3 weeks

extract_protocol:
Nuclei were isolated and digested with DPNII overnight. T4 ligase was added in dilute conditions (10ml) and incubated at 16C for 4-6hrs.
Libraries were prepared by the University of Michigan Seqcore.

treatment_protocol: Formaldehyde crosslinking.

value: seedling

tag: genotype

tag: genetic background


title: a56.2.flower.RNA.110906


title: ago4 Hi-C Rep3


title: Col-0 Hi-C Rep2

value: wild type


title: nrpe1 Hi-C Rep3


title: nrpe1 Hi-C Rep1


title: IDH1wt replicate 2

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

data_processing:
Trim Galore (Babraham Bioinformatics) were used in RRBS mode to analyze the quality of the raw data sets (fastq files) and to remove adapter sequence contaminations.
Quality trimmed fastq files (phred score >20) were applied as input data for BSMAP aligner  mapping short reads (50mers) to the murine reference genome (mm9) followed by calling methylation sites (RRBS mode, Lister protocol).
Results from methylation calling were further processed using the R package methylKit 0.9.1. methylKit quantifies, compares and annotates methylation calls (CpG) at single nucleotide and genomic interval levels, respectively.
For clustering of DMRs, the reads were filtered to contain at least one CpG. Only sequences with a coverage of 20 or more reads were included in the analysis. In addition, all sequences that showed no methylation at all were filtered out.
For determination of DMRs logistic regression and the SLIM-adjustment within the methylkit package was used on the filtered dataset and sequences with at least 40 % difference of methylation  were called differentially methylated. For the analysis of DMRs in the vicinity of genes genomic intervals were defined as 500nt windows sliding in steps of 250 nucleotides across the entire genome. The threshold to count for a “CpG” islet is a minimum of 5 CpGs per interval.
To estimate the differential methylation status of samples being analyzed, the overall methylation rate was used to calculate a relative difference among these samples. Genomic intervals (CpG islets) with at least 25% difference in their methylation status were called differentially methylated.
Genome_build: mm9
Supplementary_files_format_and_content: Text files containing differentially methylated regions

source_name: sorted mouse bone marrow cells

extract_protocol: 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with 5mC-methylated Illumina paired end sequencing adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 220 bps insert size were gel-purified (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). Each library was sequenced on a separate lane using an Illumina HiScanSQ instrument with version 2.5 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

tag: strain

tag: tranduction


title: CTL R-2HG replicate2

value: empty vector


title: CTL R-2HG replicate1


title: ORC2 ChIP-seq rep2

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

data_processing:
Libraries sequence reads obtained were aligned to the UCSC human genome assembly hg19 using the Bowtie application (Illumina), allowing no more than two mismatches per sequence.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: genomic DNA

growth_protocol: Human K562 erythroid cells were obtained from American Type Culture Collection (lot no. 4607240) and cultured according to ENCODE procedurses.

extract_protocol:
After pre-clearing with protein A sepharose beads (4C for 1 hours), the chromatin from an equivalent of 5x107 cells was used for immunoprecipitation with an ORC2 antibody (Santa Cruz, sc-28742 or BD Biosciences, bd-6875) or IgG as a control. After 4C overnight incubation, beads were washed, eluted in buffer E (25mM Tris-HCl pH 7.5; 5mM EDTA; 0.5% SDS) and cross-links reversed at 65C with proteinase K for 6 hours.
ChIP libraries were created using 15 cycles of amplification according to the Illumina manufacturer protocol. Libraries were run on a 2% agarose gel, and the 150-450 bp fraction was extracted and purified using DNA gel extraction kit (QIAGEN). To estimate the yield of library and its relative amplification value, library DNA was quantitated using a Nanodrop. Quality of the library was access by qPCR monitoring at known origins (see primers above).

treatment_protocol: Cells were crosslinked in 1% formaldehyde, nuclei isolated and the chromatin shredded by sonication in buffer to obtain chromatin fragments of ~200-300bp. Note that our samples were prepared using the same set of chromatin and procedures as those used for transcription factors mapping and presented on the genome browser as YaleTracks (ENCODE, 2012).

tag: cell line

value: K562 cell

tag: chip antibody

value: ORC2 antibody (Santa Cruz, sc-28742)


title: ago4 Hi-C Rep1

tag: tissue


title: ago4 Hi-C Rep2


title: Col-0 Hi-C Rep3


title: IDH1mut replicate 2


title: ORC2 ChIP-seq rep1


title: ago4 RNA Rep2

description: ago4-1 mutant introgressed into Col-0 background.

data_processing:
Alignment was done by tophat2.
Differential expression was assessed by edgeR compared to Col-0 grown and processed side by side from GSE38464.
Genome_build: TAIR10
Supplementary_files_format_and_content: Differential expression in ago4 compared to Col-0. Log FC, Log CPM, and pvalues for genes.

extract_protocol:
RNA was isolated using the Qiagen Plant RNA kit
Libraries were prepared by the University of Michigan Seqcore.

tag: background strain

value: ago4-1 mutant

tag: developmental stage

value: seedlings


title: ago4 RNA Rep1


title: STZ

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

data_processing:
base-calling:
alignment:Sequenced reads were trimmed for adaptor sequence and mapped to UCSC mouse genome assembly mm9 using novoalign
For each mature miRNA, expression is measured by number of reads located within its genomic location with 10bp flanking regions and scaled to total of 60million reads per sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include  raw count and scaled count for each sample.

source_name: kidney glomeruli from STZ-injected 10-week diaebtic mice

extract_protocol: RNA was extracted using miRNeasy columns (Qiagen, Inc. Valencia, CA) from isolated kidney glomeruli from diabetic or control mice.

value: kidney glomeruli

tag: treatment

value: STZ


title: ago4 RNA Rep3


title: CTR

source_name: kidney glomeruli from age-matched control mice

value: control


title: Plasmid_replicate_5_7.5k_Pool

description:
7.5k Oligo Pool
barcode count data
fastq of 3' UTR barcode and residual 5' flanking sequencing

organism: synthetic construct

source_name: plasmid DNA

extract_protocol:
Qiagen Rneasy followed by hybridization pulldown of the GFP transcript.
Illumina Custom Paired-end (TruSeq)

value: Plasmid DNA


title: IDH1mut replicate 1


title: Col-0 Hi-C Rep1


title: Plasmid_replicate_3_7.5k_Pool


title: Plasmid_replicate_4_79k_Pool

description:
79k Oligo Pool
barcode count data
fastq of 3' UTR barcode and residual 5' flanking sequencing


title: Plasmid_replicate_5_79k_Pool


title: Plasmid_replicate_3_79k_Pool


title: Plasmid_replicate_1_79k_Pool


title: Plasmid_replicate_2_79k_Pool


title: IDH1wt replicate 1