title: Polysome WT Pam3+TDM with GC7

city: Seoul

first: Wook-Bin

last: Lee

address: Shinchon-dong Seodeamun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

description:
mRNA sample from mouse
Polysome_profiling_RNAseq.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were mapped by TopHat with paramters-p 8 -G genes.gtf genome read1.fastq.gz read2.fastq.gz.
Mapped reads were assembled by Cufflinks and FPKM value was calculated by Cufflnorm.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) differentiation, primary bone marrow cells were cultured for 7 d in DMEM supplemented with 20% FBS (Gibco), 50 U/ml penicillin, 50 mg/ml streptomycin, and 20% cultured supernatant from L929 cells.

extract_protocol:
RNAs from cell lysates or polysome fractions were purified with RNeasy mini kit (Qiagen), including a DNase digestion, and were converted to cDNA libraries according to the Illumina TruSeq RNA SamplePrep Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were stimulated with 100 ng/ml Pam3CSK4 and 50 μg/ml TDM, and with or without 125 uM GC7.

tag: strain

value: Bone marrow-derived macrophage

tag: genotype

value: wild type


title: Mincle-KO Pam3

status: Public on Jul 10 2016

type: SRA

description:
mRNA sample from mouse
Total_RNAseq.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

value: Mincle-knock out


title: WT Pam3+TDM with GC7


title: Mincle-KO Pam3+TDM

description:
mRNA sample from mouse
Total_RNAseq.txt


title: Neuron_ASD_AVID_5_20

city: Los Angeles

first: Daniel

middle: H.

last: Geschwind

state: California

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

country: USA

institute: UCLA

data_processing:
Basecalls and demultiplexing: CASAVA version 1.8.2 using default settings
Alignment: TopHat v2.0.5 with default settings except: 1) allowing up to 10 alignments for a given read; 2) expected inner distance between paired reads: 100; 3) alignment is supplied with Homo sapiens GRCh37 gene model annotations
Expression levels: read counts were summarized to Genecode11 gene models using htseq-count version 0.5.4 with intersection-nonempty model option
Genome_build: Human reference genome from the 1000 Genomes Project (human_g1k_v37)
Supplementary_files_format_and_content: tab-delimited text file includes read counts for all the samples

organism: Homo sapiens

source_name: iPSC-derived neurons

growth_protocol: The iPSCs were growing in Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR media (Stem Cell Technologies).

extract_protocol:
Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA).
1000 ng of total RNAs were used for library preparation using Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Differentiation protocol: The iPSC colonies were plated on Matrigel (BD Biosciences)-coated plates and maintained for 5 days in mTSeR media (Stem Cell Technologies). On the fifth day, the media was changed to N2 media [DMEM/F12 media supplemented with 1X N2 supplement (Invitrogen) and 1X B27 supplement (Invitrogen). After 2 days, the colonies were removed from the plate and cultured in suspension as embryoid bodies (EBs) for 2 weeks using NPC media with dorsomorphin during the entire procedure. The EBs were then gently dissociated with accutase (Gibco), plated on Matrigel-coated dishes, and maintained in NBF media (DMEM/F12 media supplemented with 1X N2, 1X B7 supplements, 20 ng/mL FGF2 and 1% penicillin/streptomycin). The rosettes that emerged after 3 or 4 days were manually selected, gently dissociated with accutase, and plated in dishes coated with 10 μg/mL poly-ornithine and 5 μg/mL laminin. This NPC population was expanded using NBF media. To differentiate the NPCs into neurons, the cells were re-plated in the absence of FGF2, with regular media changes every 3 or 4 days.

value: iPSC-derived neurons

tag: patient id

value: AVID

tag: group

value: ASD

tag: iPSc clone

tag: age at biopsy

tag: gender

value: Male

tag: total brain volume

tag: scan age, years

tag: ados total score at biopsy

value: 16 (Fluent Speech - Child/Adolescent)


title: WT Pam3+TDM

description:
mRNA sample from mouse
Total_RNAseq.txt
Polysome_profiling_RNAseq.txt


title: Neuron_ASD_ABLE_3_6

value: ABLE

value: 16 (Pre-verbal/Single Words)


title: WT Pam3

description:
mRNA sample from mouse
Total_RNAseq.txt


title: BZJ_2_T

city: Yangling

first: Sihuan

last: Zhang

state: Shaanxi

address: No. 22 Xinong Road

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

description: treatment group

data_processing:
Illumina CASAVA version1.8+ soft were used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The transcript and unigene assembly was carried out using the short assembly program Trinity methodthen (MG Grabherr, 2011).
The gene expression level was computed by bowtie 0.12.8 soft using single-end mapping method, and further measured by the Reads Per Kilobase of exon model per Million mapped reads value (RPKM), which can be calculated as follow: RPKM=Total exon reads/[mapped read (millions) * exon length (KB)] (Mortazavi et al., 2008).
All assembled unigenes were compared with public database, NCBI non-redundant protein sequences (NR), SWISS-PROTProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), euKaryotic Ortholog Groups (KOG) and Pfam, to make functional annotation by similarity analysis. Sequences alignment using BLAST software.
Genome_build: De novo assembly
Supplementary_files_format_and_content: tab-delimited text files

molecule: polyA RNA

organism: Capra hircus

source_name: Longissimus thoracis

growth_protocol: Five goats were feed on the same fodderand with similar body weight

extract_protocol:
The longissimus thoracis were collected immediately after slaughtering, and were snap-frozen in liquid nitrogen, then stored at -80oC until RNA extraction.Total RNA was extracted from the sample using Trizol reagent (Takara, Dalian, China) according to the manufacturer’s instructions.
RNA samples with a RIN value greater than 8.0 (8.0 out of 10.0), OD260/ OD280 ratio greater than 1.9 and OD260/ OD230 ratio is no less than 1.7 were selected for deep sequencing.The RNA was treated with DNase I for 30 min at 37oC to remove residual DNA. Then enrich and purify mRNA using beads with oligo (dT).The purified mRNA was fragmented to approximately 350 nt fragments using the RNA fragmentation kit. The first strand cDNA was synthesized using purified RNA fragments as template and hexamer primers. After the first strand was synthesized, the buffer (Invitrogen, 20 μL), dNTPs (0.25 mM / μL), RNaseH (0.05 U / μL) and DNA polymerase I (0.5 U / μL) were added to synthesize the second strand cDNA (Zhang et al., 2015). The short cDNA fragments were further purified using the QIAQuick PCR extraction kit (LianChuan Sciences, Hangzhou, China). The samples were then subjected to 3’ end repaired, a single “A” base and an adaptor ligation. Agarose gel electrophoresis was used to filter the suitably sized fragments (350 ± 50 bp), which would be used as the templates for the PCR amplification and RNA-seq library generation. Then the sequencing of the libraries was performed using Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China).

treatment_protocol: The goats in the treatment group were ovariectomized at the beginning of the experiment and the goats in control group were untreated. All the five goats were slaughtered at the 50th day.

tag: sample source

value: ovariectomized goat

tag: breed

value: Hybrid goats (Boer goat(male) and Guan Zhong dairy goat(female))

tag: Sex

value: female

tag: experimental treatment (ovariectomy) age

value: about 5 months old

tag: slaughter age

value: after treatment 50th days


title: Neuron_ASD_ABLE_3_8


title: BZJ_3_N

description: control group

value: normal goat


title: Polysome WT Pam3+TDM


title: BZJ_1_N

description: control group


title: SUIT2_KMT2D siRNA2

status: Public on Jul 09 2016

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

data_processing:
After FASTQ data quality check using FastQC, raw reads were aligned to the reference genome hg19 using Tophat2 to generate sorted BAM files
Number of uniquely aligned reads (mapping quality score q > 10) to the exonic region of each gene were counted using HTSeq based on the Ensembl annotation (version 74). KMT2D and KMT2C siRNA datasets were first analyzed independently. Only genes that achieved at least one count per million (CPM) mapped reads in at least three samples were kept
Read counts were further normalized using the conditional quantile normalization (cqn) method, accounting for gene length and GC content.
Differential expression analysis was then performed using the edgeR package, employing the generalized linear model (GLM) approach, for each siRNA versus its control pairwise comparison, adjusting for baseline differences between the cell lines, with an additive model design as “model.matrix(~cellline+siRNA_treatment)”.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of paired-end reads for all the gene features based on the Ensembl annotation v74

source_name: SUIT2, S32

extract_protocol:
Material for RNA sequencing (RNA-seq) was generated from cells seeded at either 1x105 cells/well (SUIT-2) or 1.6x105 cells/well (PANC-1 and COLO 357) in 6-well plates and transfected for 48 hours. Total RNA was isolated (as above), quantified integrity measured using a RNA 6000 nano assay kit on 2100 BioAnalyser (Agilent). A Ribo-Zero Gold kit (Illumina) was used to deplete rRNA from RNA samples and cDNA libraries were prepared using the TruSeq stranded total RNA library preparation kit (Illumina). Libraries prepared for sequencing were validated on the 2100 BioAnalyzer with a DNA 1000 kit (Agilent) and again after randomizing the samples into seven pools with a high sensitivity DNA analysis kit (Agilent). Paired end sequences (reads) of 100 nt in length were generated using seven lanes of a HiSeq 2000 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment

value: KMT2D siRNA2


title: SUIT2_KMT2C siRNA2

source_name: SUIT2, S34

value: KMT2C siRNA2


title: COLO357_KMT2C siRNA1

value: KMT2C siRNA1


title: COLO357_Control siRNA

value: Control siRNA


title: COLO357_KMT2D siRNA1

value: KMT2D siRNA1


title: COLO357_KMT2D siRNA2


title: COLO357_KMT2C siRNA3

value: KMT2C siRNA3


title: SUIT2_KMT2C siRNA1

source_name: SUIT2, S33


title: PANC1_KMT2D siRNA1

source_name: PANC1, S2


title: PANC1_KMT2C siRNA2

source_name: PANC1, S6


title: PANC1_KMT2C siRNA1

source_name: PANC1, S5


title: COLO357_KMT2C siRNA2


title: SUIT2_KMT2C siRNA3

source_name: SUIT2, S35


title: SUIT2_Control siRNA

source_name: SUIT2, S29


title: PANC1_Control siRNA

source_name: PANC1, S1


title: WT NO

description:
mRNA samples from mouse
Total_RNAseq.txt

tag: strain

value: Bone marrow-derived macrophage

tag: genotype

value: wild type


title: SUIT2_KMT2D siRNA1

source_name: SUIT2, S30


title: NPC_ASD_AERO_3_7

source_name: iPSC-derived neural progenitors

tag: cell type

value: iPSC-derived neural progenitors

tag: patient id

value: AERO

value: ASD

value: Male

value: 20 (Fluent Speech - Child/Adolescent)


title: NA19239-r3-H12

status: Public on Jul 08 2016

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
Processed data files:
reads-raw-single-per-lane.txt
reads-raw-single-per-sample.txt
molecules-raw-single-per-lane.txt
molecules-raw-single-per-sample.txt

data_processing:
We used umitools v2.1.1 (https://github.com/brwnj/umitools/releases/tag/v2.1.1) to remove the 5 bp UMI at the 5' end of the reads.
We used sickle version 1.33 (https://github.com/najoshi/sickle/releases/tag/v1.33) to perform quality trimming of the 3' end of the reads (flag -x). We used the default quality thresholds.
We used Subjunc version 1.5.0-p1 (http://sourceforge.net/projects/subread/files/subread-1.5.0-p1/) to map reads to both human genome hg19 (chromosomes 1-22, X, Y, M) and the ERRC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa). We used the default thresholds and only kept uniquely mapping reads (flag -u).
We used featureCounts version 1.5.0-p1 (http://sourceforge.net/projects/subread/files/subread-1.5.0-p1/) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 82) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
In addition to read counts, we utilized the UMI information to obtain molecule counts for the single cell samples only. We did not count molecules for the bulk samples because they violate the assumptions of the UMI protocol, i.e. they contain too many unique molecules for the 1,024 UMIs to properly tag them all. First, we combined all reads for a given single cell using samtools version 0.1.18-dev (r982:313) (http://sourceforge.net/projects/samtools/files/samtools/0.1.18/). Next, we converted read counts to molecule counts using UMI-tools (https://github.com/CGATOxford/UMI-tools). UMI-tools counts the number of UMIs at each read start position. Furthermore, it accounts for sequencing errors in the UMIs introduced during the PCR amplication or sequencing steps using a "directional adjacency" method. Briefly, all UMIs at a given read start position are connected in a network using an edit distance of one base pair. However, edges between nodes (the UMIs) are only formed if the nodes have less than a 2x difference in reads. The node with the highest number of reads is counted as a unique molecule, and then it and all connected nodes are removed from the network. This is repeated until all nodes have been counted or removed.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are tab-delimited text files which contain the raw counts for all protein-coding genes (Ensembl GRCh37 release 82) and the ERCC spike-in genes. Each row corresponds to a sample. Each column contains either sample metadata or counts for a given gene. The filename denotes the type of counts it contains. "reads" are number of sequences per gene, as per traditional RNA-seq; wherease, molecules are the number of UMIs per gene. "bulk" is sequencing of a population of cells, as per traditional RNA-seq; whereas, "single" is sequencing of single cells. "lane" is the gene counts for a given sample from one lane of sequencing; whereas, "sample" is the sum of the gene counts from all lanes for a given sample.

source_name: LCL-derived iPSC

growth_protocol: Undifferentiated feeder-free iPSCs generated from Yoruba LCLs were grown in E8 medium (Life Tech) (G. Chen et al. 2011) on Matrigel-coated tissue culture plates with daily media feeding at 37 °C with 5% (vol/col) CO2. For standard maintenance, cells were split every 3-4 days using cell release solution (0.5 mM EDTA and NaCl in PBS) at the confluence of roughly 80%. For the single cell suspension, iPSCs were individualized by Accutase Cell Detachment Solution (BD) for 5-7 minutes at 37 °C and washed twice with E8 media immediately before each experiment. Cell viability and cell counts were then measured by the Automated Cell Counter (Bio-Rad) to generate resuspension densities of 2.5 X 105 cells/mL in E8 medium for C1 cell capture.

extract_protocol:
Single cell loading and capture was performed following the Fluidigm manual "Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing Protocol" (PN 100-7168). Briefly, 30 ul of C1 Suspension Reagent was added to a 70-ul aliquot of ~17,500 cells. Five ul of this cell mix were loaded onto 10-17 um C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm), and the chip was then processed on a C1 instrument using the cell-loading script according to the manufacturer's instructions. Using the standard staining script, the iPSCs were stained with StainAlive TRA-1-60 Antibody (Stemgent, PN 09-0068). The capture efficiency and TRA-1-60 staining were then inspected using the EVOS FL Cell Imaging System (ThermoFisher)(supplemental Table X). Immediately after imaging, reverse transcription and cDNA amplification were performed in the C1 system using the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) according to the instructions in the Fluidigm user manual with minor changes to incorporate UMI labeling (Islam et al. 2014). Specifically, the reverse transcription primer and the 1:50,000 Ambion® ERCC Spike-In Mix1 (Life Tech) were added to the lysis buffer, and the template-switching oligos which contain the UMI (5-bp random sequence) were included in the reverse transcription mix. When the run finished, full-length, amplified, single-cell cDNA libraries were harvested in a total of approximately 13 ul C1 Harvesting Reagent and quantified using DNA High Sensitivity LabChip (Caliper). A bulk sample, a 40 ul aliquot of ~10,000 cells, was collected in parallel with each C1 chip using the same reaction mixes following the C1 protocol of "Tube Controls with Purified RNA" (PN 100-7168, Appendix A).
For sequencing library preparation, fragmentation and isolation of 5' fragments were performed according to the UMI protocol (Islam et al. 2014). Instead of using commercial available Tn5 transposase, Tn5 protein stock was freshly purified in house using the IMPACT system (pTXB1, NEB) following the protocol previously described (Picelli et al. 2014). The activity of Tn5 was tested and shown to be comparable with the EZ-Tn5-Transposase (Epicentre). Importantly, all the libraries in this study were generated using the same batch of Tn5 protein purification. For each of the bulk samples, two libraries were generated using two different indices in order to get sufficient material. All of the 18 bulk libraries were then pooled and labelled as the "bulk" for sequencing.

tag: individual

tag: replicate

tag: well

value: LCL-derived iPSC


title: NA19239-r3-bulk

description:
Processed data files:
reads-raw-bulk-per-lane.txt
reads-raw-bulk-per-sample.txt

value: bulk


title: NA19239-r3-H11


title: NA19239-r3-H10


title: NA19239-r3-H07


title: PANC1_KMT2C siRNA3

source_name: PANC1, S7


title: NA19239-r3-H08


title: NA19239-r3-H09


title: PANC1_KMT2D siRNA2

source_name: PANC1, S4


title: NA19239-r3-H06


title: NA19239-r3-H04


title: NA19239-r3-H05


title: NA19239-r3-H02


title: NA19239-r3-H03


title: NA19239-r3-G09


title: NA19239-r3-G07


title: NA19239-r3-G11


title: NA19239-r3-G04


title: NA19239-r3-H01


title: NA19239-r3-G05


title: NA19239-r3-G10


title: NA19239-r3-G03


title: NA19239-r3-G06


title: NA19239-r3-G08


title: NA19239-r3-G01


title: NA19239-r3-F12


title: NA19239-r3-F11


title: NA19239-r3-F10


title: NA19239-r3-F09


title: NA19239-r3-G02


title: NA19239-r3-F08


title: NA19239-r3-F07


title: NA19239-r3-G12


title: NA19239-r3-F06


title: NA19239-r3-F05


title: NA19239-r3-F03


title: NA19239-r3-E10


title: NA19239-r3-E12


title: NA19239-r3-F02


title: NA19239-r3-F04


title: NA19239-r3-E11


title: NA19239-r3-F01


title: NA19239-r3-E06


title: NA19239-r3-E05


title: NA19239-r3-E08


title: NA19239-r3-E09


title: NA19239-r3-E01


title: NA19239-r3-E04


title: NA19239-r3-E02


title: NA19239-r3-D09


title: NA19239-r3-E03


title: NA19239-r3-D08


title: NA19239-r3-D11


title: NA19239-r3-D12


title: NA19239-r3-E07


title: NA19239-r3-D07


title: Neuron_CONTROL_CHAP_1_2

value: iPSC-derived neurons

value: CHAP

tag: group

value: CONTROL

tag: iPSc clone

tag: age at biopsy

tag: gender

tag: total brain volume


title: NA19239-r3-D05


title: Neuron_CONTROL_CHAP_1_5

tag: scan age, years

tag: ados total score at biopsy


title: NA19239-r3-D04


title: NA19239-r3-D03


title: NA19239-r3-D02


title: NA19239-r3-C12


title: NA19239-r3-C10


title: NA19239-r3-C11


title: NA19239-r3-C09


title: NA19239-r3-D10


title: NA19239-r3-C05


title: NA19239-r3-C08


title: NA19239-r3-C06


title: NA19239-r3-C03


title: NA19239-r3-B11


title: NA19239-r3-B12


title: NA19239-r3-B09


title: NA19239-r3-C02


title: NA19239-r3-B06


title: NA19239-r3-B10


title: NA19239-r3-B05


title: NA19239-r3-B04


title: NA19239-r3-B07


title: NA19239-r3-B08


title: NA19239-r3-B02


title: NA19239-r3-D06


title: NA19239-r3-C04


title: NA19239-r3-D01


title: NA19239-r3-B03


title: NA19239-r3-C01


title: NA19239-r3-B01


title: NA19239-r3-A12


title: NA19239-r3-A11


title: NA19239-r3-A10


title: NA19239-r3-A07


title: NA19239-r3-A09


title: NA19239-r3-C07


title: NA19239-r3-A08


title: NA19239-r3-A06


title: NA19239-r3-A03


title: NA19239-r3-A05


title: NA19239-r3-A02


title: NA19239-r2-H12


title: NA19239-r2-bulk


title: NPC_ASD_ABLE_3_8

value: ABLE

value: 16 (Pre-verbal/Single Words)


title: NA19239-r2-H05


title: NA19239-r2-H07


title: NA19239-r2-H03


title: NA19239-r2-H04


title: NA19239-r2-H11


title: NA19239-r2-H09


title: NA19239-r2-H02


title: NA19239-r2-H10


title: NA19239-r2-G12


title: NA19239-r2-G11


title: NA19239-r2-G09


title: NA19239-r2-G06


title: NA19239-r2-G07


title: NA19239-r2-H01


title: NA19239-r2-G04


title: NA19239-r2-G03


title: NA19239-r2-G05


title: NA19239-r2-G10


title: NA19239-r2-H08


title: NA19239-r3-A01


title: NA19239-r2-F12


title: NA19239-r2-H06


title: NA19239-r2-F11


title: NA19239-r2-G02


title: NA19239-r2-F07


title: NA19239-r2-F06


title: NA19239-r2-F08


title: NA19239-r2-F04


title: NA19239-r2-F05


title: NA19239-r2-F02


title: NA19239-r2-E11


title: NA19239-r2-E12


title: NA19239-r2-F01


title: NA19239-r2-F03


title: NA19239-r2-E10


title: NA19239-r2-G01


title: NA19239-r2-E09


title: NA19239-r2-E06


title: NA19239-r2-E03


title: NA19239-r2-E05


title: NA19239-r2-E02


title: NA19239-r2-E01


title: NA19239-r2-F09


title: NA19239-r2-F10


title: NA19239-r2-E08


title: NA19239-r2-E04


title: NA19239-r2-D08


title: NA19239-r2-D12


title: NA19239-r2-D07


title: NA19239-r2-D10


title: NA19239-r2-D05


title: NA19239-r2-D04


title: NA19239-r2-E07


title: NA19239-r2-D06


title: NA19239-r2-D03


title: NA19239-r2-C09


title: NA19239-r2-D01


title: NA19239-r2-C12


title: NA19239-r2-C08


title: NA19239-r2-C11


title: NA19239-r2-C07


title: NA19239-r2-D11


title: NA19239-r2-C06


title: NA19239-r2-C05


title: NA19239-r2-D02


title: NA19239-r2-C04


title: NA19239-r2-C03


title: NA19239-r2-C02


title: NA19239-r2-B12


title: NA19239-r2-D09


title: NA19239-r2-C01


title: NA19239-r2-B11


title: NA19239-r2-B08


title: NA19239-r2-B09


title: NA19239-r2-C10


title: NA19239-r2-B10


title: NA19239-r2-B07


title: NA19239-r2-B06


title: NA19239-r2-B04


title: NA19239-r2-B03


title: NA19239-r2-B05


title: NA19239-r2-B02


title: NA19239-r2-A11


title: NA19239-r2-A10


title: NA19239-r2-A06


title: NA19239-r2-B01


title: NA19239-r2-A05


title: NA19239-r2-A12


title: NA19239-r2-A08


title: NA19239-r2-A07


title: NA19239-r2-A01


title: NA19239-r2-A09


title: NA19239-r1-H11


title: NA19239-r2-A02


title: NA19239-r1-bulk


title: NA19239-r1-H10


title: NA19239-r2-A03


title: NA19239-r1-H08


title: NA19239-r1-H12


title: NA19239-r2-A04


title: NA19239-r1-H09


title: NA19239-r1-H05


title: NA19239-r1-H03


title: NA19239-r1-H06


title: NA19239-r3-A04


title: NA19239-r1-H07


title: NA19239-r1-H02


title: NA19239-r1-G11


title: NA19239-r1-G12


title: NA19239-r1-G08


title: NA19239-r1-H01


title: NA19239-r1-G05


title: NA19239-r1-G10


title: NA19239-r1-G07


title: NA19239-r1-G06


title: NA19239-r1-G03


title: NA19239-r1-G02


title: NA19239-r1-F11


title: NA19239-r1-F10


title: NA19239-r1-G01


title: NA19239-r1-F12


title: NA19239-r1-F07


title: NA19239-r1-F09


title: NA19239-r1-H04


title: NA19239-r1-F08


title: NA19239-r1-F04


title: NA19239-r1-F02


title: NA19239-r1-F01


title: NA19239-r1-E11


title: NA19239-r1-E08


title: NA19239-r1-E09


title: NA19239-r1-G09


title: NA19239-r1-F06


title: NA19239-r1-G04


title: NA19239-r1-E05


title: NA19239-r1-E06


title: NA19239-r1-E03


title: NA19239-r1-E04


title: NA19239-r1-E02


title: NA19239-r1-F05


title: NA19239-r1-E01


title: NA19239-r1-D12


title: NA19239-r1-E07


title: NA19239-r1-F03


title: NA19239-r1-D11


title: NA19239-r1-E12


title: NA19239-r1-D10


title: NA19239-r1-D09


title: NA19239-r1-D07


title: NA19239-r1-D08


title: NA19239-r1-E10


title: NA19239-r1-D05


title: NA19239-r1-D06


title: NA19239-r1-D03


title: NA19239-r1-D02


title: NA19239-r1-D01


title: NA19239-r1-D04


title: NA19239-r1-C12


title: NA19239-r1-C11


title: NA19239-r1-C09


title: NA19239-r1-C10


title: NA19239-r1-C08


title: NA19239-r2-G08


title: NA19239-r1-C07


title: NA19239-r1-C05


title: NA19239-r1-C03


title: NA19239-r1-C04


title: NA19239-r1-C01


title: NA19239-r1-C02


title: NA19239-r1-B10


title: NA19239-r1-B11


title: NA19239-r1-B09


title: NA19239-r1-B08


title: NA19239-r1-B03


title: NA19239-r1-B07


title: NA19239-r1-B01


title: NA19239-r1-B05


title: NA19239-r1-A09


title: NA19239-r1-A12


title: NA19239-r1-B06


title: NA19239-r1-B04


title: NA19239-r1-A10


title: NA19239-r1-A04


title: NA19239-r1-A07


title: NA19239-r1-B02


title: NA19239-r1-A05


title: NA19239-r1-A11


title: NA19239-r1-A01


title: NA19239-r1-A02


title: NA19239-r1-A03


title: NA19239-r1-A08


title: NA19101-r3-bulk


title: NA19239-r1-C06


title: NA19239-r1-B12


title: NA19101-r3-H10


title: NA19101-r3-H08


title: NA19101-r3-H09


title: NA19101-r3-H06


title: NA19101-r3-H07


title: NA19101-r3-H11


title: NA19239-r1-A06


title: NA19101-r3-H04


title: NA19101-r3-H03


title: NA19101-r3-G11


title: NA19101-r3-H05


title: NA19101-r3-H01


title: NA19101-r3-G08


title: NA19101-r3-G12


title: NA19101-r3-G06


title: NA19101-r3-G04


title: NA19101-r3-G05


title: NA19101-r3-G09


title: NA19101-r3-H12


title: NA19101-r3-F12


title: NA19101-r3-F10


title: NA19101-r3-F09


title: NA19101-r3-G02


title: NA19101-r3-G01


title: NA19101-r3-F07


title: NA19101-r3-F06


title: NA19101-r3-H02


title: NA19101-r3-F04


title: NA19101-r3-F05


title: NA19101-r3-F02


title: NA19101-r3-F08


title: NA19101-r3-G10


title: NA19101-r3-G03


title: NA19101-r3-G07


title: NA19101-r3-E11


title: NA19101-r3-E12


title: NA19101-r3-E09


title: NA19101-r3-E08


title: NA19101-r3-E07


title: NA19101-r3-E10


title: NA19101-r3-E04


title: NA19101-r3-E02


title: NA19101-r3-E03


title: NA19101-r3-F11


title: NA19101-r3-E05


title: NA19101-r3-E06


title: NA19101-r3-E01


title: NA19101-r3-D12


title: NA19101-r3-D08


title: NA19101-r3-D10


title: NA19101-r3-D09


title: NA19101-r3-D07


title: NA19101-r3-F03


title: NA19101-r3-D05


title: NA19101-r3-D11


title: NA19101-r3-D04


title: NA19101-r3-D06


title: NA19101-r3-D03


title: NA19101-r3-F01


title: NA19101-r3-D02


title: NA19101-r3-D01


title: NA19101-r3-C12


title: NA19101-r3-C08


title: NA19101-r3-C09


title: NA19101-r3-C07


title: NA19101-r3-C10


title: NA19101-r3-C04


title: NA19101-r3-C05


title: NA19101-r3-C01


title: NA19101-r3-C06


title: NA19101-r3-C11


title: NA19101-r3-C03


title: NA19101-r3-B10


title: NA19101-r3-B08


title: NA19101-r3-B06


title: NA19101-r3-B09


title: NA19101-r3-B05


title: NA19101-r3-B01


title: NA19101-r3-B12


title: NA19101-r3-C02


title: NA19101-r3-A12


title: NA19101-r3-B02


title: NA19101-r3-A11


title: NA19101-r3-B04


title: NA19101-r3-A09


title: NA19101-r3-B03


title: NA19101-r3-A07


title: NA19101-r3-A06


title: NA19101-r3-A02


title: NA19101-r3-A04


title: NA19101-r3-B11


title: NA19101-r3-A01


title: NA19101-r3-B07


title: NA19101-r2-bulk


title: NA19101-r2-H10


title: NA19101-r2-H08


title: NA19101-r2-H12


title: NA19101-r2-H11


title: NA19101-r3-A05


title: NA19101-r2-H07


title: NA19101-r2-H04


title: NA19101-r2-H05


title: NA19101-r3-A10


title: NA19101-r2-H09


title: NA19101-r2-H03


title: NA19101-r2-H02


title: NA19101-r2-H01


title: NA19101-r2-G12


title: NA19101-r2-G11


title: NA19101-r2-G10


title: NA19101-r2-G08


title: NA19101-r2-G09


title: NA19101-r2-H06


title: NA19101-r3-A08


title: NA19101-r2-G07


title: NA19101-r3-A03


title: NA19101-r2-G06


title: NA19101-r2-G05


title: NA19101-r2-G03


title: NA19101-r2-G04


title: NA19101-r2-G01


title: NA19101-r2-F12


title: NA19101-r2-F10


title: NA19101-r2-F08


title: NA19101-r2-F09


title: NA19101-r2-G02


title: NA19101-r2-F02


title: NA19101-r2-F07


title: NA19101-r2-F01


title: NA19101-r2-F03


title: NA19101-r2-F06


title: NA19101-r2-F04


title: NA19101-r2-E03


title: NA19101-r2-E08


title: NA19101-r2-E04


title: NA19101-r2-E05


title: NA19101-r2-E07


title: NA19101-r2-E09


title: NA19101-r2-E01


title: NA19101-r2-F05


title: NA19101-r2-D12


title: NA19101-r2-E12


title: NA19101-r2-D11


title: NA19101-r2-F11


title: NA19101-r2-E11


title: NA19101-r2-D10


title: NA19101-r2-E06


title: NA19101-r2-D09


title: NA19101-r2-D06


title: NA19101-r2-D07


title: NA19101-r2-E02


title: NA19101-r2-D04


title: NA19101-r2-D03


title: NA19101-r2-D02


title: NA19101-r2-C11


title: NA19101-r2-C10


title: NA19101-r2-E10


title: NA19101-r2-D05


title: NA19101-r2-C09


title: NA19101-r2-C06


title: NA19101-r2-B12


title: NA19101-r2-C05


title: NA19101-r2-C03


title: NA19101-r2-C02


title: NA19101-r2-C07


title: NA19101-r2-B09


title: NA19101-r2-C12


title: NA19101-r2-B08


title: NA19101-r2-B10


title: NA19101-r2-D08


title: NA19101-r2-B06


title: NA19101-r2-B07


title: NA19101-r2-B03


title: NA19101-r2-C08


title: NA19101-r2-B02


title: NA19101-r2-B04


title: NA19101-r2-B05


title: NA19101-r2-A12


title: NA19101-r2-D01


title: NA19101-r2-A11


title: NA19101-r2-A10


title: NA19101-r2-A08


title: NA19101-r2-B11


title: NA19101-r2-A07


title: NA19101-r2-C01


title: NA19101-r2-C04


title: NA19101-r2-A06


title: NA19101-r1-H12


title: NA19101-r1-bulk


title: NA19101-r1-H11


title: NA19101-r2-A01


title: NA19101-r1-H10


title: NA19101-r2-A04


title: NA19101-r2-A03


title: NA19101-r1-H08


title: NA19101-r2-A02


title: NA19101-r1-H09


title: NA19101-r1-H05


title: NA19101-r2-B01


title: NA19101-r1-H03


title: NA19101-r1-H04


title: NA19101-r1-H07


title: NA19101-r1-G11


title: NA19101-r1-G12


title: NA19101-r1-H02


title: NA19101-r2-A05


title: NA19101-r1-H01


title: NA19101-r2-A09


title: NA19101-r1-G09


title: NA19101-r1-G10


title: NA19101-r1-H06


title: NA19101-r1-G05


title: NA19101-r1-G06


title: NA19101-r1-G08


title: NA19101-r1-G02


title: NA19101-r1-G01


title: NA19101-r1-G03


title: NA19101-r1-G07


title: NA19101-r1-G04


title: NA19101-r1-F11


title: NA19101-r1-F09


title: NA19101-r1-F07


title: NA19101-r1-F06


title: NA19101-r1-F08


title: NA19101-r1-F12


title: NA19101-r1-F10


title: NA19101-r1-F04


title: NA19101-r1-F02


title: NA19101-r1-E11


title: NA19101-r1-F01


title: NA19101-r1-F03


title: NA19101-r1-F05


title: NA19101-r1-E12


title: NA19101-r1-E07


title: NA19101-r1-E08


title: NA19101-r1-E09


title: NA19101-r1-E05


title: NA19101-r1-E10


title: NA19101-r1-E04


title: NA19101-r1-E06


title: NA19101-r1-E01


title: NA19101-r1-E02


title: NA19101-r1-D12


title: NA19101-r1-E03


title: NA19101-r1-D11


title: NA19101-r1-D08


title: NA19101-r1-D07


title: NA19101-r1-D06


title: NA19101-r1-C10


title: NA19101-r1-C11


title: NA19101-r1-C09


title: NA19101-r1-C04


title: NA19101-r1-B12


title: NA19101-r1-C01


title: NA19101-r1-C08


title: NA19101-r1-C05


title: NA19101-r1-C07


title: NA19101-r1-C03


title: NA19101-r1-C06


title: NA19101-r1-C02


title: NA19101-r1-B10


title: NA19101-r1-B11


title: NA19101-r1-B07


title: NA19101-r1-D05


title: NA19101-r1-B08


title: NA19101-r1-D09


title: NA19101-r1-D04


title: NA19101-r1-D10


title: NA19101-r1-B04


title: NA19101-r1-B03


title: NA19101-r1-D03


title: NA19101-r1-B05


title: NA19101-r1-B02


title: NA19101-r1-C12


title: NA19101-r1-D02


title: NA19101-r1-A12


title: NA19101-r1-D01


title: NA19101-r1-A11


title: NA19101-r1-B01


title: NA19101-r1-A09


title: NA19101-r1-A10


title: NA19101-r1-A07


title: NA19101-r1-A04


title: NA19101-r1-A06


title: NA19101-r1-B09


title: NA19101-r1-A02


title: NA19101-r1-A03


title: NA19101-r1-A08


title: NA19098-r3-bulk


title: NA19098-r3-H12


title: NA19101-r1-A01


title: NA19098-r3-H10


title: NA19098-r3-H11


title: NA19098-r3-H09


title: NA19101-r1-B06


title: NA19101-r1-A05


title: NA19098-r3-H08


title: NA19098-r3-H07


title: NA19098-r3-H05


title: NA19098-r3-H03


title: NA19098-r3-H04


title: NA19098-r3-H02


title: NA19098-r3-H01


title: NA19098-r3-H06


title: NA19098-r3-G12


title: NA19098-r3-G10


title: NA19098-r3-G11


title: NA19098-r3-G08


title: NA19098-r3-G09


title: NA19098-r3-G07


title: NA19098-r3-G05


title: NA19098-r3-G06


title: NA19098-r3-G03


title: NA19098-r3-G02


title: NA19098-r3-F12


title: NA19098-r3-G01


title: NA19098-r3-F10


title: NA19098-r3-F09


title: NA19098-r3-F08


title: NA19098-r3-F07


title: NA19098-r3-F03


title: NA19098-r3-F05


title: NA19098-r3-F02


title: NA19098-r3-F01


title: NA19098-r3-F04


title: NA19098-r3-E11


title: NA19098-r3-E09


title: NA19098-r3-E10


title: NA19098-r3-E08


title: NA19098-r3-E06


title: NA19098-r3-E12


title: NA19098-r3-G04


title: NA19098-r3-E07


title: NA19098-r3-E02


title: NA19098-r3-E05


title: NA19098-r3-E04


title: NA19098-r3-F11


title: NA19098-r3-E03


title: NA19098-r3-D12


title: NA19098-r3-D09


title: NA19098-r3-E01


title: NA19098-r3-D10


title: NA19098-r3-F06


title: HC566 RNA_Seq

city: College Park

first: Antony

middle: Merlin

last: Jose

state: MD

address: Rm 2136, Bioscience Research Building

department: Cell Biology and Molecular Genetics

institute: University of Maryland College Park

data_processing:
Fastq files were mapped to the pTG96FR genome using TopHat2 with and without the --fusion search option.
The inversions and deletions were determined from the junction.bed files that are part of the TopHat2 output files.
The average coverage at inversions and deletions were calculated based after visualizing mapped reads using Integrative Genome Viewer.
Genome_build: Inverted repeat of plasmid pTG96 (pTG96FR)
Supplementary_files_format_and_content: txt file of template pTG96FR, bed files of junctions from mapping with TopHat2, and excel sheet summerizing deletions and inversions detected in transgenic DNA.

organism: Caenorhabditis elegans

source_name: C. elegans with integrated transgene

growth_protocol: The strain was grown at 20C in liquid culture with E. coli strain OP50 as food.

extract_protocol:
Total DNA and total RNA were exracted from worm pellets using standard protocols.
RNA and DNA libraries were prepared as per standard Illumina protocols.
DNA-Seq or RNA-Seq were used as indicated in SAMPLES.

treatment_protocol: Worms were harvested using centrifugation and separated from E.coli using sucrose floatation.

tag: developmental stage

value: Mixed-stage liquid culture


title: HC566 Single read DNA_Seq

library_source: genomic

molecule: genomic DNA


title: NA19098-r3-C11


title: NA19098-r3-D05


title: NA19098-r3-D01


title: NA19098-r3-D04


title: NA19098-r3-D06


title: HC566 Paired-end DNA_Seq_R1_R2


title: NA19098-r3-C10


title: NA19098-r3-D02


title: NA19098-r3-C12


title: gbb11611

first: Jeremy

middle: A

last: Lynch

address: 900 S. Ashland Ave

department: Biological Sciences

institute: UIC

data_processing:
bases were called using RTA (Real-Time Analysis) version 1.12.4.2
Reads were mapped using tophat2 (v2.0.3) and non default parameters: -r 0 -I 10000 --no-novel-juncs
mapped reads were quantitated and assigned to genes with cufflinks (v. 2.0.2) using default parameters
a merged transcriptome used for normalizing gene expression quantification was produced by cuffmerge
differential expression calculated using cuffdiff
Genome_build: nv2clean.fa
Supplementary_files_format_and_content: [_tracking] tab delimited text files contain coverage and FPKM data

organism: Nasonia vitripennis

source_name: 4-7 hour embryos

extract_protocol:
Standard Trizol based methods were used to extract RNA
Libraries were prepared using the Illumina® TruSeq® RNA sample preparation Kit. Library preparation started with 2µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries.

treatment_protocol: Female yellow pupae were injected with either ~2 micrograms of dsRNA of the gene of interest, or with water

value: gbb1 dsRNA injected

tag: tissue

value: embryo

value: late blastoderm


title: NA19098-r3-D03


title: dpp2610

tag: treatment

value: dpp dsRNA injected


title: NA19098-r3-D11


title: NA19098-r3-C08


title: NA19098-r3-C09


title: TollA1611

value: Toll dsRNA injected


title: NA19098-r3-D08


title: NA19098-r3-C06


title: NA19098-r3-C07


title: h2o805

value: water injected


title: NA19098-r3-C05


title: NA19098-r3-D07


title: NA19098-r3-C04


title: TollA2610


title: NA19098-r3-C03


title: NA19098-r3-C01


title: IgG_flower

city: Ithaca

first: Wojciech

last: Pawlowski

state: NY

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the B73 reference genome sequence (release AGPv2) using the Burrows-Wheeler Aligner (BWA).
Data were filtered based on unique mapping.
Peaks were called with the following parameters: bandwidth = 800 bp, shift size = 400 bp.
Genome_build: B73 (release AGPv2)
Supplementary_files_format_and_content: Bed file was generated to represent peaks positions.

organism: Zea mays

source_name: Flower, IgG ChIP

extract_protocol:
Flowers at the zygotene stage of meiotic prophase I were collected from at least twenty maize tassels, fixed in 1% formaldehyde for 10 min, and then quenched in 0.125mM glycine for 5 min.
1.5g of fixed flowers were ground into fine power and homogenized in Chromatin Extraction Buffer A (10 mM Tris-HCl pH 8.0, 0.4 mM sucrose, 10 mM MgCl2, 1 mM PMSF, 5 mM β-mercaptoethanol, 1 tablet of cOmplete Protease Inhibitor Cocktail (Roche, Penzberg, Germany)) for 20 min at 4°C with gentle shaking. The suspension was filtered into a new 50 ml conical tube through 2 layers of Miracloth (EMD Millipore, Billerica, MA, USA), placed in a plastic funnel and centrifuged at 4,000 rpm for 20 min at 4°C. The pellet was resuspended in 1 ml of extraction buffer B (10 mM Tris-HCl pH 8.0, 0.25 M sucrose, 10 mM MgCl2, 1% Triton X-100, 1 mM PMSF, 5 mM β-mercaptoethanol, 1 μg/ml of cOmplete Protease Inhibitor Cocktail) and centrifuged at 14,000 rpm for 10 min. The pellet was resuspended in 500 μl of Extraction Buffer C (10 mM Tris-HCl pH 8.0, 1.7 M sucrose, 2 mM MgCl2, 0.15% Triton X-100, 1 mM PMSF, 5 mM β-mercaptoethanol, 1 μg/ml cOmplete Protease Inhibitor Cocktail), placed on top of 500 μl of Extraction Buffer C cushion and centrifuged at 14,000 rpm for 1 h at 4°C. The nuclei pellet was resuspended in 500 μl Nuclei Lysis Buffer (50 mM Tris–HCl pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF, 1 μg/ml cOmplete Protease Inhibitor Cocktail) to release chromatin.
The resulting chromatin was sonicated into fragments of average length of 500-1000 bp using eight sonicator pulses, five seconds each, and centrifuged at 14,000 rpm for 5 min at 4°C. The supernatant was diluted 10 fold with Dilution Buffer (16.7 mM Tris–HCl pH 8.0, 1.2 mM EDTA, 167 mM NaCl, 1.1% Triton X-100, 1 mM PMSF, 1 μg/ml cOmplete Protease Inhibitor Cocktail) and pre-cleared with Dynabeads Protein A (Invitrogen, Carlsbad, CA, USA). 10 μl of the pre-cleared chromatin was saved as chromatin input control sample. The remaining chromatin was incubated with antibodies overnight at 4°C, and then captured by Dynabeads Protein A. After incubation, beads were washed 5 times in the following buffers: (1) Low Salt Wash Buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), (2) High Salt Wash Buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), (3) LiCl Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and (4) TE Buffer, twice (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted from beads with 200 μl Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 200 mM NaCl, 1% SDS), treated with RNase for 2h at 37°C, deproteinized with Proteinase K for 2h at 45°C, and decrosslinked at 65°C for 8 h. DNA was purified using MinElute PCR Purification Columns (Qiagen, Hilden, Germany). DNA concentration was quantified using Quant-IT dsDNA HS Assay Kit (Invitrogen).

tag: inbred line

tag: genotype/variation

value: wild type

value: flower

tag: chip antibody

value: normal rabbit IgG (custom made)


title: NA19098-r3-B09

tag: cell type

value: LCL-derived iPSC


title: RAD51_flower_input-rep2

source_name: Flower, input


title: RAD51_leaf_rep1_ChIPSeq

source_name: Leaf, RAD51 ChIP

value: leaf

value: ZmRAD51 (custom made)


title: RAD51_leaf_rep2_ChIPSeq


title: NA19098-r3-B11

tag: individual


title: NA19098-r3-B10

tag: replicate


title: RAD51_flower_rep2_ChIPSeq

source_name: Flower, RAD51 ChIP


title: NA19098-r3-B12

tag: well


title: RAD51_flower_rep1_ChIPSeq


title: NA19098-r3-B07


title: NA19098-r3-B08


title: NA19098-r3-B06


title: NA19098-r3-B05


title: NA19098-r3-A11


title: NA19098-r3-C02


title: NA19098-r3-B02


title: RAD51_flower_phs1_ChIPSeq

source_name: Flower, phs1 mutant, RAD51 ChIP

value: phs1 mutant


title: h2o1704


title: NA19098-r3-A10


title: NA19098-r3-A08


title: NA19098-r3-B03


title: NA19098-r3-B04


title: NA19098-r3-B01


title: NA19098-r3-A07


title: RAD51_flower_input-rep1


title: NA19098-r3-A05


title: NA19098-r3-A06


title: NA19098-r3-A04


title: NA19098-r3-A12


title: NA19098-r2-H11


title: NA19098-r2-H10


title: NA19098-r2-bulk

value: bulk


title: RAD51_flower_phs1_input

source_name: Flower, phs1 mutant, input


title: NA19098-r3-A02


title: NA19098-r2-H12


title: NA19098-r2-H08


title: NA19098-r2-H06


title: NA19098-r2-H07


title: NA19098-r2-H09


title: NA19098-r3-A09


title: NA19098-r2-H05


title: NA19098-r2-H01


title: NA19098-r2-H02


title: NA19098-r2-G12


title: NA19098-r2-G11


title: NA19098-r2-H03


title: NA19098-r2-G10


title: NA19098-r2-G09


title: NA19098-r2-G07


title: NA19098-r2-G06


title: NA19098-r2-G08


title: NA19098-r2-G05


title: NA19098-r3-A03


title: NA19098-r3-A01


title: NA19098-r2-G04


title: NA19098-r2-G03


title: NA19098-r2-G01


title: NA19098-r2-G02


title: NA19098-r2-F12


title: NA19098-r2-F08


title: NA19098-r2-F11


title: NA19098-r2-H04


title: NA19098-r2-F04


title: NA19098-r2-F07


title: NA19098-r2-F05


title: NA19098-r2-F03


title: NA19098-r2-F06


title: NA19098-r2-F09


title: NA19098-r2-F01


title: NA19098-r2-E12


title: NA19098-r2-E10


title: NA19098-r2-E06


title: NA19098-r2-E09


title: NA19098-r2-E08


title: NA19098-r2-E11


title: NA19098-r2-F02


title: NA19098-r2-E05


title: NA19098-r2-E04


title: NA19098-r2-E07


title: NA19098-r2-E03


title: NA19098-r2-D11


title: NA19098-r2-E02


title: NA19098-r2-E01


title: NA19098-r2-F10


title: NA19098-r2-D09


title: NA19098-r2-D12


title: NA19098-r2-D08


title: NA19098-r2-D07


title: NA19098-r2-C10


title: NA19098-r2-C12


title: NA19098-r2-D01


title: NA19098-r2-D02


title: NA19098-r2-D03


title: NA19098-r2-D04


title: NA19098-r2-C09


title: NA19098-r2-D06


title: NA19098-r2-C06


title: NA19098-r2-C05


title: NA19098-r2-C08


title: NA19098-r2-C07


title: NA19098-r2-C04


title: NA19098-r2-C03


title: NA19098-r2-D05


title: NA19098-r2-C02


title: NA19098-r2-B10


title: NA19098-r2-C11


title: NA19098-r2-B12


title: NA19098-r2-C01


title: NA19098-r2-D10


title: NA19098-r2-B09


title: NA19098-r2-B06


title: NA19098-r2-B03


title: NA19098-r2-B04


title: NA19098-r2-B07


title: NA19098-r2-B08


title: NA19098-r2-B05


title: NA19098-r2-B02


title: NA19098-r2-B01


title: NA19098-r2-A10


title: NA19098-r2-A09


title: NA19098-r2-A08


title: NA19098-r2-B11


title: NA19098-r2-A02


title: NA19098-r1-bulk


title: NA19098-r2-A05


title: NA19098-r1-H12


title: NA19098-r2-A01


title: NA19098-r2-A04


title: NA19098-r2-A03


title: NA19098-r1-H10


title: NA19098-r1-H07


title: NA19098-r1-H06


title: NA19098-r1-H11


title: NA19098-r1-H08


title: NA19098-r1-H09


title: NA19098-r1-H04


title: NA19098-r1-H02


title: NA19098-r1-H01


title: NA19098-r1-G12


title: NA19098-r1-H05


title: NA19098-r1-H03


title: NA19098-r2-A12


title: NA19098-r2-A11


title: NA19098-r1-G11


title: NA19098-r1-G10


title: NA19098-r2-A06


title: NA19098-r1-G09


title: NA19098-r1-G07


title: NA19098-r1-G06


title: NA19098-r2-A07


title: NA19098-r1-G04


title: NA19098-r1-G03


title: NA19098-r1-G05


title: NA19098-r1-F12


title: NA19098-r1-F10


title: NA19098-r1-F09


title: NA19098-r1-G02


title: NA19098-r1-F08


title: NA19098-r1-F06


title: NA19098-r1-F11


title: WT

city: SHANGHAI

first: Lijie

last: Cui

address: Guilin Road 100

institute: shanghai normal university

data_processing:
Illumina Casava1.7 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
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Unigene Assembly
RPKM result
Genome_build: De novo assembly

organism: Anisodus acutangulus

source_name: root

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: genotype


title: NA19098-r1-F07


title: NA19098-r1-F05


title: NA19098-r1-F04


title: NA19098-r1-F03


title: NA19098-r1-E12


title: NA19098-r1-F01


title: NA19098-r1-E10


title: NA19098-r1-F02


title: NA19098-r1-E09


title: NA19098-r1-G08


title: NA19098-r1-E11


title: NA19098-r1-E07


title: NA19098-r1-E05


title: NA19098-r1-E04


title: NA19098-r1-E08


title: NA19098-r1-E06


title: NA19098-r1-G01


title: NA19098-r1-E03


title: MG19_SEM_H3K27Ac_ChipSeq

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Acute lymphocytic leukemia

growth_protocol: Human B cell precursor leukemia SEM cells reported to carry the t(4;11) MLL-AF4 were purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Cells were maintained under typical conditions in RPMI media with 10% Fetal Bovine Serum at the National Cell Culture Center (NCCC). For location analysis, cells were grown to a density of 0.5 million cells per ml and 99% viability prior to crosslinking with formaldehyde for 20 min.

extract_protocol:
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: cell line

value: SEM

tag: antibody manu.

value: Abcam

tag: antibody catalog


title: NA19098-r1-E02


title: MOLT4_H3K27Ac_15309

source_name: T-ALL

growth_protocol: Maintained as per ATCC guidelines.    RPMI Glutamax, 10% FBS, PS


title: NA19098-r1-E01


title: NA19098-r1-D12


title: H3K27Ac ChIP in Ly1 + DMSO_ChipSeq

source_name: DLBCL

growth_protocol: RPMI 1640+FBS


title: NA19098-r1-D11


title: DLD1_H3K27ac_ChipSeq

source_name: Colon Carcinoma

growth_protocol: RPMI-1640 + GlutaMAX + 10% FBS


title: NA19098-r1-D10


title: BE2C_H3K27AC 2

source_name: Neuroblastoma

growth_protocol: Cells grown in DMEM with 10% FBS. 70% confluent


title: NA19098-r1-D09

source_name: LCL-derived iPSC


title: Loucy_H3K27ac_ChipSeq

growth_protocol: Cells were maintained under typical conditions in RPMI +10% FBS.

value: Loucy


title: NA19098-r1-D08


title: NA19098-r1-D07


title: NA19098-r1-D06


title: NA19098-r1-D04


title: NA19098-r1-D05


title: NA19098-r1-D03


title: NA19098-r1-D01


title: G1_Liver_3 Bis-PCR

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

data_processing:
Bismark (v0.7.12) was used to align RRBS reads to the reference genome mm10, using Bowtie2 (v2.1.0)
Methylation counts for CpG -133 was extracted using Rsamtools from aligned BAM files.
The methylation counts were assigned to either A or C variant
Genome_build: BK000964.3
Supplementary_files_format_and_content: Methylated and Unmethylated Counts for Variant A and Variant C

source_name: Liver

extract_protocol:
Targeted bisulfite PCR-based analysis was performed using the 48.48 layout on the Fluidigm C1 system (Fluidigm, USA), coupled with Illumina MiSeq sequencing. Bisulfite PCR primers were designed using Primer3 (PMID:17485472),
DNA was bisfulite converted (EpiTect, Qiagen) prior to amplification. Amplicons from a single sample were pooled and individually indexed to create a multiplex library prior to sequencing on an Illumina MiSeq instrument using v3 chemistry.
Bis-PCR

tag: Sex

value: M

tag: strain

tag: diet

value: Control

tag: generation


title: G1_Liver_109 Bis-PCR


title: G1_Liver_37 Bis-PCR

value: PR


title: G1_Liver_131 Bis-PCR


title: NA19098-r1-C12


title: G1_Liver_365 Bis-PCR


title: G1_Liver_110 Bis-PCR


title: G1_Liver_376 Bis-PCR


title: NA19098-r1-C11


title: G1_Liver_137 Bis-PCR


title: NA19098-r1-C10


title: G1_Liver_425 Bis-PCR


title: G1_Liver_121 Bis-PCR


title: G1_Liver_152 Bis-PCR


title: G1_Liver_127 Bis-PCR


title: G1_Liver_163 Bis-PCR


title: G1_Liver_167 Bis-PCR


title: NA19098-r1-C08


title: G1_Liver_142 Bis-PCR


title: G1_Liver_166 Bis-PCR


title: NA19098-r1-C05


title: NA19098-r1-C04


title: G1_Liver_111 Bis-PCR


title: NA19098-r1-D02


title: G1_Liver_141 Bis-PCR


title: G1_Liver_165 Bis-PCR


title: NA19098-r1-C01


title: NA19098-r1-B11


title: G1_Liver_118 Bis-PCR


title: NA19098-r1-C09


title: NA19098-r1-B10


title: G1_Liver_120 Bis-PCR


title: NA19098-r1-C02


title: G1_Liver_343 Bis-PCR


title: G1_Liver_442 Bis-PCR


title: G1_Liver_403 Bis-PCR


title: NA19098-r1-B12


title: NA19098-r1-B08


title: NA19098-r1-B09


title: G1_Liver_441 Bis-PCR


title: NA19098-r1-C06


title: G1_Liver_1 Bis-PCR


title: G1_Liver_44 Bis-PCR


title: G1_Liver_43 Bis-PCR


title: NA19098-r1-B06


title: NA19098-r1-B07


title: G1_Liver_42 Bis-PCR


title: NA19098-r1-B05


title: NA19098-r1-B03


title: G1_Liver_30 Bis-PCR


title: NA19098-r1-B04


title: NA19098-r1-B02


title: NA19098-r1-C03


title: G1_Liver_430 Bis-PCR


title: G1_Liver_431 Bis-PCR


title: G1_Liver_429 Bis-PCR


title: NA19098-r1-A12


title: NA19098-r1-A11


title: NA19098-r1-B01


title: Mock IP

city: Boston

first: Peng

last: Du

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

description: RIP RNA

data_processing:
bowtie softare is used to map reads to annotated mRNA in UCSC database and ncRNA in ensembl database with two mismatches permitted, and self-developed perl scripts were used to calculate the reads of each genes
Genome_build: mm9
Supplementary_files_format_and_content: expression_ensembl_ncRNA.txt and expression_UCSC_mRNA.txt provided a matrix table, which contained five columns including the gene's name, cDNA's name, reads number in different samples

source_name: Mock transfected mESC

growth_protocol: Feeder-free gelatin-adapted mouse ESCs were grown in standard culture condition supplemented with LIF and Serum (LIF/Serum)

extract_protocol:
Input or anti-FLAG IP samples were lyzed in Trizol and RNAs were precipitated using Chloroform/Ethanol.
Libraries were prepared according to Illumina's instructions (Low Sample Protocol

value: Mouse embryonic stem cells

tag: passages

tag: rip antibody

value: anti-FLAG M2 Affinity Gel beads (Sigma; A2220; Lot #SLBQ4441V)


title: G1_Liver_421 Bis-PCR


title: NA19098-r1-A10


title: Mock input

description: Ribominus-selected RNA


title: Sperm_RRBS_44 RRBS

data_processing:
Bismark (v0.7.12) was used to align RRBS reads to the reference genome mm10, using Bowtie2 (v2.1.0)
Methylation counts for each CpG were extracted using a custom program (https://bitbucket.org/xboxrob/methylation-extractor). The first 2bp of each read was removed to prevent the filled-in cytosine position being used for methylation calling.
CpGs with less than 10 counts in all samples were removed from analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation and Total Read Counts per CpG

source_name: Sperm

extract_protocol:
RRBS of G1 sperm was performed with modification of published protocols (PMID:21412275). 100 ng of DNA was digested overnight with 20 U of MspI.
Following clean-up and size-selection using Agencourt XP beads, multiplexed sequencing libraries were prepared using the Ovation Ultralow Methyl-Seq Library System by NuGEN (USA)


title: G1_Liver_426 Bis-PCR


title: NA19098-r1-A09


title: Sperm_RRBS_6 RRBS


title: FLAG- mutant Dis3l2 input

description: Ribominus-selected RNA

source_name: FLAG- mutant Dis3l2 transfected mESC


title: G1_Liver_36 Bis-PCR


title: NA19098-r1-A08


title: Sperm_RRBS_7 RRBS


title: NA19098-r1-A07


title: G1_Liver_35 Bis-PCR


title: Sperm_RRBS_35 RRBS


title: Sperm_RRBS_36 RRBS


title: Sperm_RRBS_43 RRBS


title: G1_Liver_424 Bis-PCR


title: FLAG-mutant Dis3l2 IP

description: RIP RNA


title: NA19098-r1-A06


title: Sperm_RRBS_42 RRBS


title: Sperm_RRBS_30 RRBS


title: G1_Liver_435 Bis-PCR


title: Sperm_RRBS_31 RRBS


title: Sperm_RRBS_23 RRBS


title: G1_Liver_378 Bis-PCR


title: Sperm_RRBS_22 RRBS


title: NA19098-r1-A05


title: Sperm_RRBS_8 RRBS


title: NA19098-r1-A04


title: NA19098-r1-A03


title: G1_Liver_436 Bis-PCR


title: G1_Liver_39 Bis-PCR


title: Sperm_RRBS_39 RRBS


title: Sperm_RRBS_24 RRBS


title: adult_male_261 RNA-Seq

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.4 with Bowtie 2 v2.1.0 and samtools v0.1.18 with default settings
Duplicates were filtered using Picard Tools and reads were assigned to a gene using HTSeq
Gene annotation file was downloaded from Tophat website (downloaded on September 25th 2013)
Genome_build: mm10
Supplementary_files_format_and_content: RAW counts per gene

source_name: Adult Liver

extract_protocol:
RNA-seq libraries from adult liver samples were constructed using the Illumina TruSeq Stranded Total RNA Kit, with 1 mg of Total RNA extracted with Qiagen miRNeasy Micro Kit.
All RNA libraries were prepared for sequencing using standard Illumina protocols


title: Sperm_RRBS_1 RRBS


title: adult_male_260 RNA-Seq


title: G1_Liver_24 Bis-PCR


title: adult_male_259 RNA-Seq


title: NA19098-r1-A01


title: G1_Liver_23 Bis-PCR


title: ChIP: H3K27ac_ab4729_SKNAS_012615 [lab: Look-DFCI]

growth_protocol: According to ATCC guidelines

value: SK-N-AS


title: adult_male_247 RNA-Seq


title: G1_Liver_22 Bis-PCR


title: ChIP: H3K27ac_ab4729_PF-382_032615 [lab: Look-DFCI]


title: adult_male_242 RNA-Seq


title: G1_Liver_8 Bis-PCR


title: ChIP: H3K27ac_ab4729_P12-ICHIKAWA_032615 [lab: Look-DFCI]


title: G1_Liver_6 Bis-PCR


title: G1_Liver_434 Bis-PCR


title: G1_Sperm_31 Bis-PCR


title: adult_male_236 RNA-Seq


title: adult_male_235 RNA-Seq


title: ChIP: H3K27ac_ab4729_NGP_012615 [lab: Look-DFCI] 2

value: NGP


title: ChIP: H3K27ac_ab4729_PEER_032615 [lab: Look-DFCI]

value: PEER


title: G1_Sperm_430 Bis-PCR


title: NA19098-r1-A02

value: LCL-derived iPSC


title: adult_male_225 RNA-Seq


title: G1_Sperm_420 Bis-PCR


title: adult_male_224 RNA-Seq


title: G1_Sperm_421 Bis-PCR


title: ChIP: H3K27ac_ab4729_NB1643_012615 [lab: Look-DFCI]


title: HCC827_H3K27Ac

source_name: Non-small cell lung carcinoma

growth_protocol: HCC827 cells were maintained in RPMI 1640 (Cellgro; Mediatech Inc., Herndon, CA) supplemented with 10% FBS, 100 units/mL penicillin, 100 units/mL streptomycin, and 2 mM glutamine.


title: adult_male_222 RNA-Seq


title: G1_Sperm_343 Bis-PCR


title: ChIP:EBC1_H3K27ac_ab4729_062515

growth_protocol: ATCC guidelines


title: G1_Sperm_435 Bis-PCR


title: ChIP: H3K27ac_ab4729_DU.528_032615 [lab: Look-DFCI]


title: G1_Sperm_442 Bis-PCR


title: adult_male_240 RNA-Seq


title: ChIP: H3K27ac_ab4729_CHP134_012615 [lab: Look-DFCI] 2


title: G1_Sperm_403 Bis-PCR


title: adult_male_194 RNA-Seq


title: adult_male_193 RNA-Seq


title: adult_male_185 RNA-Seq


title: ChIP: H3K27ac_ab4729_CHP134_012615 [lab: Look-DFCI] 1


title: G1_Sperm_429 Bis-PCR


title: ChIP: H3K27ac_ab4729_CCRF-CEM_032615 [lab: Look-DFCI]

value: CCRF-CEM


title: adult_male_184 RNA-Seq


title: ChIP: H3K27ac_ab4729_MV411 DMSO_032615 [lab: Look-DFCI]


title: ChIP: H3K27ac_ab4729_BE2C _012615 [lab: Look-DFCI] 2


title: G1_Sperm_441 Bis-PCR


title: G1_Sperm_378 Bis-PCR


title: adult_male_179 RNA-Seq


title: adult_male_176 RNA-Seq


title: G1_Sperm_431 Bis-PCR


title: G1_Sperm_436 Bis-PCR


title: RNASeq ABP1d 2

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
smallRNAs_ABP1d_regions_geo.bed
smallRNAs_ABP1d_vs_WT_regions_geo.bed

data_processing:
Base calling was performed with Illumina Pipeline version 1.5
Solexa Illumina strand-specific small RNA-Seq data for Saccharomyces pombe in ABP1d mutant and wild type control samples were aligned against reference genome (Sanger release 09052011) using Bowtie 0.12.5, allowing 0 mismatches in the read seed. In order to estimate enrichment and depletion in repeated regions (i.e. transposons, rRNA units) in an unbiased manner, all possible sites for multiple hits were considered.
First, significantly enriched regions in small RNA-Seq ABP1d mutant and WT were detected using the enrichedRegions function from the htSeqTools package, using the one tailed option (no control) and a Benjamini Hochbergh pvalue threshold of 0.05, and leaving the other settings as default.
Afterwards, significantly enriched and depleted regions in small RNA-Seq ABP1d mutant against WT (up and down-regulated small RNAs) were detected using the enrichedRegions function from the htSeqTools package, using the two tailed option and a Benjamini Hochbergh pvalue threshold of 0.05, and leaving the other settings as default.
Genome_build: Spombe Sanger 09052011
Supplementary_files_format_and_content: smallRNAs ABP1 and WT BED files include chromosome, start, end, rpkm abundance and BH adjusted pvalue of the identified enriched regions in each sample individually (no control).
Supplementary_files_format_and_content: smallRNAs ABP1_vs_WT BED file include chromosome, start, end, rpkm abundance in ABP1d and WT respectively, and BH adjusted pvalue of the identified regions differentially expressed in ABP1d vs WT.

organism: Schizosaccharomyces pombe

source_name: ABPd

growth_protocol: exponentially growing cells in rich media

extract_protocol:
total RNA extraction by acid phenol protocol
total RNA was quantified by Qubit fluorometer using the Quant-iT RNA Assay Kit (Life Technologies). Using Illumina’s small RNA Sample Prep Kit v1.5, 3’ and 5’ adapters were ligated to 5 µg of total RNA, followed by reverse transcription and 12 cycles of amplification. Amplification products of 125 to 250 nucleotides size selected from a 4% agarose gel and purified. Libraries were quantified by Qubit fluorometer using the Quant-iT DNA HS Assay Kit (Life Technologies). Using Illumina’s Cluster Generation Kit, libraries were subject to cluster generation at 8 pM concentration as one sample per lane. Sequencing-by-synthesis was performed for 38 cycles.
Strand-specific RNA-Seq


title: RNASeq WT 1

description:
smallRNAs_WT_regions_geo.bed
smallRNAs_ABP1d_vs_WT_regions_geo.bed

source_name: WT

value: wild type


title: adult_male_195 RNA-Seq


title: adult_male_175 RNA-Seq


title: RNASeq WT 2


title: adult_female_265 RNA-Seq

value: F


title: G1_Sperm_424 Bis-PCR


title: G1_Sperm_426 Bis-PCR


title: G1_Sperm_434 Bis-PCR


title: adult_female_264 RNA-Seq


title: G1_Sperm_24 Bis-PCR


title: G1_Sperm_23 Bis-PCR


title: adult_male_183 RNA-Seq


title: G1_Sperm_22 Bis-PCR


title: adult_female_263 RNA-Seq


title: G1_Sperm_9 Bis-PCR


title: adult_female_255 RNA-Seq


title: adult_female_249 RNA-Seq


title: ABP1 wt1

description: HA-tagged Abp1

data_processing:
Solexa Illumina ChIP-Seq data for Saccharomyces pombe ABP1 and Input control in wild-type samples were aligned against the reference genome using Bowtie 0.12.5 allowing for 2 mismatches in the read seed. In order to estimate enrichment in repeated regions (i.e. transposons, rRNA units) in an unbiased manner, all possible sites for multiple hits were considered.
Afterwards, strand shift bias and duplicated reads were estimated and removed with the htSeqTools package using the default options.
Significantly enriched regions in ChIP-Seq data were detected with the enrichedRegions function, considering only regions within the IP sample with a coverage above 2.5 times the first quartile, and using a Benjamini Hochberg pvalue threshold of 0.05.
Afterwards the enrichedPeaks function was used to detect significantly enriched peaks (putative binding sites), setting the minimum coverage difference between IP and Input at 200.
Genome_build: Spombe Sanger 09052011
Supplementary_files_format_and_content: BED file includes chromosome, start and end columns of the identified peaks in the Sanger 09052011 SPombe genome. Additional column indicates peak coverage for the IP sample.

source_name: ABP1 wt

growth_protocol: exponentially growing yeast in YES medium

extract_protocol:
Cells were harvested and lysed with a FastPrep cell disrupter (FP120, Bio101 Thermo Savant). DNA was sheared to a range of 250-400bp with a Bioruptor Standard (Diagenode). Monoclonal anti-HA tag antibody [12CA5] (abcam16918) was used to retrieve HA-tagged Abp1 combined with Dynabeads Protein A (Life Technologies). After reversing the crosslinks DNA was purified using phenol-chloroform and precipitated with LiCl and isopropanol
Libraries were prepared using Illumina’s ChIP-Seq Sample Prep Kit

treatment_protocol: formaldehyde was added to the cells at a final concentration of 1% for 15 min then quenching was performed by adding 125mM Glycine

value: HA tag antibody [12CA5] (abcam16918)


title: G1_Sperm_6 Bis-PCR


title: adult_female_254 RNA-Seq


title: G1_Sperm_1 Bis-PCR


title: adult_female_248 RNA-Seq


title: adult_female_221 RNA-Seq


title: G1_Sperm_44 Bis-PCR


title: RNASeq ABP1d 1


title: Input wt1

source_name: Input wt


title: G1_Sperm_43 Bis-PCR


title: adult_female_219 RNA-Seq


title: adult_female_220 RNA-Seq


title: G1_Sperm_42 Bis-PCR


title: adult_female_256 RNA-Seq


title: NA19098-r1-C07


title: adult_female_214 RNA-Seq


title: G1_Sperm_39 Bis-PCR


title: Ssen-veg-SS

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: consists of rep1 and rep2

data_processing:
Illumina 1.5/1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Kabuli chickpea genome (http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip); www.cicer.info/cgi-bin/gb2/gbrowse/kabuli/
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

organism: Cicer arietinum

source_name: Vegetative plants

growth_protocol: Plants were grown in the greenhouse.

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

treatment_protocol: Root tissues were harsvested from the vegetative and reproductive stage plants subjected to control (water) and salinity (irrigated with 80 mM NaCl solution) stresses.

tag: treatment

value: 80 mM NaCl solution


title: G1_Sperm_8 Bis-PCR


title: Ssen-rep-CT

description: consists of rep1 and rep2

source_name: Reproductive plants

tag: genotype/variation

value: water


title: Stol-rep-SS

description: consists of rep1 and rep2


title: Ssen-rep-SS

description: consists of rep1 and rep2


title: adult_female_250 RNA-Seq


title: Pol2Ser5 APB1d

description: genomic DNA

data_processing:
Solexa Illumina ChIP-Seq data for Saccharomyces pombe Pol2Ser5 in wild-type samples and Pol2Ser5 in ABP1d mutant samples, together with their respective Inputs were aligned against the reference genome using Bowtie 0.12.5 allowing for 2 mismatches in the read seed. In order to estimate enrichment in repeated regions (i.e. transposons, rRNA units) in an unbiased manner, all possible sites for multiple hits were considered.
Afterwards, strand shift bias and duplicated reads were estimated and removed with the htSeqTools package using the default options.
Significantly enriched regions in ChIP-Seq data were detected with the enrichedRegions function, considering only regions within the IP sample with a coverage above 2.5 times the first quartile, and using a Benjamini Hochberg pvalue threshold of 0.05.
Afterwards the enrichedPeaks function was used to detect significantly enriched peaks (putative binding sites), setting the minimum coverage difference between IP and Input at 200, and merging adjacent peaks if they were closer than 300bp apart.
Genome_build: Spombe Sanger 09052011
Supplementary_files_format_and_content: BED file includes chromosome, start and end columns of the identified peaks in the Sanger 09052011 SPombe genome. Additional column indicates peak coverage for the IP sample.

source_name: Pol2Ser5 APB1d

extract_protocol:
cells were harvested and lysed with a FastPrep cell disrupter (FP120, Bio101 Thermo Savant). DNA was sheared to a range of 250-400bp with a Bioruptor Standard (Diagenode). For Ser5PolII ChiP-seq we used αPolIIser5 monoclonal antibody (Abcam/ab5131) combined with Dynabeads Protein A (Life Technologies).  After reversing the crosslinks DNA was purified using phenol-chloroform and precipitated with LiCl and isopropanol
Illumina TruSeq RNA Sample Prep Kit, 48 SetA Ref: 15013135 Lot: 6103158. Although this is Chip-DNA, the “TruSeq RNA Sample Prep Kit” has been used for Library Preparation

tag: chip antibody

value: Pol2Ser5 (Abcam/ab5131)


title: G1_Sperm_36 Bis-PCR


title: Stol-rep-CT

description: consists of rep1 and rep2


title: Ssen-veg-CT

description: consists of rep1 and rep2


title: adult_female_211 RNA-Seq


title: adult_female_213 RNA-Seq


title: G1_Sperm_35 Bis-PCR


title: Stol-veg-SS

description: consists of rep1 and rep2


title: G1_Sperm_30 Bis-PCR


title: adult_female_199 RNA-Seq


title: Pol2Ser5 wt2

description: genomic DNA

source_name: Pol2Ser5 wt


title: Stol-veg-CT

description: consists of rep1 and rep2


title: adult_female_197 RNA-Seq


title: Input wt2

description: genomic DNA


title: adult_female_196 RNA-Seq


title: adult_female_189 RNA-Seq


title: Dsen-70d-DS

description: Sample comprises of rep1 and rep2

data_processing:
Illumina 1.5/1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Website available for access of kabuli genome data: http://www.cicer.info/cgi-bin/gb2/gbrowse/kabuli/
Genome_build: Kabuli chickpea genome (http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip)
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

source_name: 70 d plants

treatment_protocol: Root tissues were harsvested from the vegetative and reproductive stage plants subjected to control (water) and drought (water withhelding till transpiration ratio reached 0.2) stress.

tag: condition

value: Drought

tag: days


title: adult_female_188 RNA-Seq


title: Dtol-70d-CT

description: Sample comprises of rep1 and rep2


title: Dtol-70d-DS

description: Sample comprises of rep1 and rep2


title: adult_female_187 RNA-Seq


title: Dsen-50d-DS

description: Sample comprises of rep1 and rep2

source_name: 50 d plants


title: adult_female_181 RNA-Seq


title: adult_female_182 RNA-Seq


title: Dsen-50d-CT

description: Sample comprises of rep1 and rep2


title: adult_female_180 RNA-Seq


title: Dtol-50d-DS1


title: Dtol-50d-CT1


title: Input ABP1d

description: genomic DNA

source_name: Input ABP1d


title: HeLa_Suz12_KD_Rep1

status: Public on Jul 07 2016

middle: E

last: Kingston

state: Massachusetts

address: 185 Cambridge Street

department: Molbio

institute: MGH/Harvard

description: knockdown of control mRNA

data_processing:
Basecalls performed using OLB 1.8
RNA-Sequences were aligned to the hg9 transcriptome using tophat 2.4
EdgeR was uset to compute RPKM values
DNA-Sequences were aligned to the hg19 genome using bwa 0.5.9
For one batch of libraries, ("rep2" RNAseq and ChIP samples) high contamination of a single probe made in parallel for another experiment (chr7:15630900-156311000) was observed and the spike was removed in ChIP files
Aligned and filtered sequences were used to compute input normalized read densities using the SPP software (bw files)
Genome_build: hg19

source_name: Suz12 knockdown

growth_protocol: 1x complete dmem with FBS, gentamycin, 37C, 5% CO2, O2

extract_protocol:
Trizol, cleanup/DNAse with Zymo clean and concentrate,  illumina Truseq to make cDNA
from cDNA or sheared DNA: blunt ends, A-tail, ligate illumina sequencing adapters, PCR with full length/indexed illumina primers

treatment_protocol: nucleofection of 20 pmol siRNA

value: HeLa  F-17

tag: ectopic expression construct

value: murine FLAG-Bmi1 overexpression

tag: cell treatment

value: siRNA knockdown by nucleofection + 48hours growth


title: HeLa_Xist_KD_Rep1

description: knockdown of candidate RNA

source_name: Xist knockdown


title: Dsen-70d-CT

description: Sample comprises of rep1 and rep2

tag: genotype

value: Control


title: HeLa_CAT17_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT17 knockdown

tag: cell line


title: HeLa_SCR_KD_Rep3

description: knockdown of control (scramble)

source_name: SCR knockdown


title: HeLa_CAT13_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT13 knockdown


title: MN_CAT7_KD_Rep2

description: knockdown of control RNA

source_name: CAT7 knockdown in MN

growth_protocol: human ES in mTesR1 differentiated by media change:  grown in 1:1 DMEM/F12 (Life Technologies) and NeuroBasal (Life Technologies),  2 mM glutamax-I (Life Technologies), 1x N2 supplement (Life Technologies), 1x B27 supplement (Life Technologies) 10nM SB431542 (Sigma), 1 μM dorsomorphin (Millipore) and 0.1 μM retinoic acid (RA) (Sigma). Media changed daily

value: H3 ES cells

value: GFP under 9kb murine Mnx1 promoter

value: siRNA knockdown by nucleofection + 72 hrs in neural culture media + Retinoic Acid


title: HeLa_CAT16_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT16 knockdown


title: HeLa_SCR_KD_Rep1

description: knockdown of control (scramble)


title: HeLa_CAT16_KD_Rep2

description: knockdown of candidate RNA


title: HeLa_Bmi1_KD_Rep1

description: knockdown of control mRNA

source_name: Bmi1 knockdown


title: HeLa_CAT7_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT7 Knockdown


title: MN_SCR_KD_Rep2

description: knockdown of control (scramble)

source_name: SCR knockdown in MN


title: Spneumoniae_R6_SECO_t15_rep_1

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

data_processing:
Around 30M reads per replicate were mapped on the S. pneumoniae R6 genome using Bowtie
Reads counts per each gene were obtained using an in-house Perl script
Statistical significance of counts was obtained with the EdgeR package (Bioconductor)
Genome_build: ASM704v1
Supplementary_files_format_and_content: Gene and raw counts in different columns

organism: Streptococcus pneumoniae R6

growth_protocol: Bacteria were grown in AGCH + 0.2% yeast extract + 0.3% sucrose medium until OD620=0.4

extract_protocol:
RNA was extracted with Mini Rneasy columns from Quiagen and treated with DNAse I
1 µg samples of RNA depleted of ribosomal RNA were chemically fragmented. They were 5′ end-tagged cDNA (equivalent to the 3′ end of the original RNA) by random-primed cDNA synthesis. This was followed by 3′-terminal tagging of the cDNA using the Terminal-Tagging Oligo (TTO) which randomly annealed to the cDNA, and served as template for extension by DNA polymerase. The resulting di-tagged cDNAs were purified using the Ampure beads XP system. Enrichment and barcoding of the purified di-tagged cDNAs was done with 15 cycles of PCR. Library size and quantification by qPCR were determined with a 2100 Bioanalyzer Instrument (Agilent Technologies) and Kapa library quantification kit (Kapa Biosystems), respectively. Library sequencing was performed in a NextSeq 500 platform using a 1 x 75 base run. 29.8-35.47 millions of passing filters reads per sample were obtained.

treatment_protocol: Seconeolitsine was added to the culture (8 µM; 0.5 x MIC) and samples were taken at 0, 5 and 15 min

tag: growth phase

value: Exponential

tag: medium

tag: agent

value: Seconeolitsine

tag: time

value: 15 min


title: Spneumoniae_R6_SECO_t5_rep_2

value: AGCH + 0.2% yeast extract + 0.3% sucrose

value: 5 min


title: HeLa_CAT8_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT8 knockdown


title: HeLa_CAT10_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT10 knockdown


title: HeLa_CAT7_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT7 knockdown


title: Spneumoniae_R6_SECO_t15_rep_2


title: Spneumoniae_R6_SECO_t0_rep_2

value: 0 min


title: HeLa_CAT5_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT5 Knockdown


title: HeLa_CAT3_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT3 Knockdown


title: HeLa_FLAG-Bmi1_GRIP

description: GRIP: chromatin extracted and immunoprecipitated; RNAs collected

source_name: FLAG-Bmi1 GRIP

extract_protocol:
reverse crosslink at 65C with ProK, Trizol, cleanup/DNAse with Zymo clean&concentrate 5, cDNA made with NuGEN Ovation FFPE
from cDNA or sheared DNA: blunt ends, A-tail, ligate illumina sequencing adapters, PCR with full length/indexed illumina primers

treatment_protocol: formaldehyde crosslink, nuclear lysis, chromatin extraction by CsCl density gradient, IP

tag: antibody

value: Sigma M8823 anti-FLAG (M2) antibody covalently conjugated to magnetic agarose beads

value: Standard culture media


title: Spneumoniae_R6_SECO_t5_rep_1


title: HeLa_Input_GRIP

description: GRIP input: chromatin extracted and prepared for IP (input)

source_name: GRIP input RNA

treatment_protocol: formaldehyde crosslink, nuclear lysis, chromatin extraction by CsCl density gradient, preparation for IP

value: none (input)


title: Flag-ZNF224

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

data_processing:
Illumina Casava (v. 1.6.0) software used for basecalling.
Sequenced reads were mapped to hg18 genome using CASAVA (v.1.6.0).
The sequence reads were normalized as reads per million per nucleotide (RPM).
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: Tab-delimited text file with bedGraph format.

source_name: HEK293 cell line transfected with Flag-ZNF224, Flag ChIP

growth_protocol: Cells were maintained in Dulbecco's Modified Eagles Medium (DMEM, Hyclone) supplemented with 10% FBS (Fetal bovine serum, Hyclone) and 100 µg/ml penicillin-streptomycin (WelGENE Inc.), at 37°C, 5% CO2.

extract_protocol:
Cells were allowed to crosslink with 1% formaldehyde for 10 minutes at room temperature (RT). To quench the crosslink, 0.125 M glycine was added for 5 minutes at RT. The cell pellets were eluted twice with 10 ml of ice-cold PBS and then incubated with 500 ul of swelling buffer (25mM HEPES, pH 7.8, 1.5mM MgCl2, 10mM KCl, 1mM DTT and 0.1% NP-40) containing a protease inhibitor cocktail (PIC, Roche) for 10 minutes on ice. After centrifugation, the cell pellets were incubated in 200 ul of sonication buffer (50mM HEPES, pH 7.9, 140mM NaCl, 1mM EDTA, 0.1% Na-deoxycholate, 0.1% SDS, 1% Triton X-100 and PIC). The cell lysate was sonicated for 70 seconds (10 sec pulse and 60 sec rest), and DNA lengths were sheared to between 200 and 1,000 bp. The mixture of nucleic acid and protein was incubated with M2 anti-Flag antibody (Sigma Aldrich, cat# F3165, lot# slbl1237v) or normal mouse IgG antibody (Santa Cruz Biotechnology), followed by immunoprecipitation using Protein A and G agarose bead mixture (Invitrogen). The beads were washed in high-salt, low-salt, LiCl and TE buffers. The protein-DNA complexes were separated from the beads by elution buffer (50mM Tris-HCl, pH 8.0, 1mM EDTA, 1% SDS, 50mM NaHCO3) and heated at 65 ℃ for 5 h with protease K to reverse the formaldehyde crosslink. Finally, the DNA was purified with the PCR Clean-up Kit (Promega).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3' ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina's adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries were amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

treatment_protocol: HEK293 cells were transfected with 4ug of FLAG-ZNF224 using lipofectamine 2000 as following the manufacturer's instructions for 24 h.

tag: transfection

value: anti-Flag M2


title: Spneumoniae_R6_SECO_t0_rep_1


title: P.putida (mt-2) treated with m-xylene

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

address: Darwin 3

institute: CNB, CSIC

description: Pseudomonas putida (mt-2)

data_processing:
Basecalls performed using Illumina pipeline version 1.9.
Short reads were aligned to the P. putida genome and pWW0 plasmid genes with the BWA algorithm with default settings for single-ends (Li and Durbin, 2009).
Mapped counts were normalized by trimmed mean of M values (TMM) (Robinson and Oshlack, 2010) using the sample whose 75%-ile (of library-scaled counts) is closest to the mean of 75%-iles as the reference. This is the default normalization method when applying the edgeR method (Robinson and Smyth, 2008) for analyzing gene expression differences by RNA-seq.
Differential expression for each pWW0 transcript was estimated by the method implemented in edgeR software, based on the negative binomial distribution of the reads. For estimating data dispersion, edgeR uses the quantile-adjusted conditional maximum likelihood (qCML) method. In this case, a common dispersion was considered for all samples.
Genome_build: NC_003350.1
Supplementary_files_format_and_content: quantitative_results.txt: Text-tabulated file with raw and normalized quantitative results for each pWW0 transcript analyzed in all samples.

organism: Pseudomonas putida

source_name: P. putida mt-2 culture, m-xylene

growth_protocol: P. putida cultures were routinely grown at 30°C in M9 minimal medium including 6 g/l Na2HPO4, 3 g/l KH2PO4, 1.4 g/l (NH4)2SO4, 0.5 g/l NaCl, 0.2 g/l MgSO4·7H2O and 2.5 ml/l of a trace element solution, with a carbon source as described in "treatment protocol".

extract_protocol:
Total RNAs from m-xylene-treated cells or reference condition were prepared. rRNA was depleted using the RiboZero rRNA removal kit (Epicenter Biotechnologies) for Gram-negative bacteria with a total RNA input of 4 μg. To confirm rRNA removal, we analyzed the samples with the Bioanalyzer system.
RNA libraries were prepared using the TruSeq RNA sample prep kit (Illumina) following the protocol described in the Wiley-Blackwell and Society for Applied Microbiology of TruSeq RNA Sample Preparation Guide, starting at the fragmentation step. The library was validated by running a High Sensitivity DNA chip (Agilent Technologies) on the Bioanalyzer system and quantified by qPCR according to the Illumina Sequencing Library qPCR Quantification Guide, using KAPA SYBR FAST qPCR kit for LC480 (KAPA Biosystems). The libraries were denatured and adjusted to 14 pM prior to generating the clusters as indicated in the Illumina Cluster Generation Guide for a Cluster Station instrument.

treatment_protocol: For induction of TOL catabolic genes during transcriptomics experiments, the P. putida mt-2 strain was precultured overnight in M9 medium with succinate, and bacterial cultures were then diluted 100-fold in the same medium and grown to the exponential phase (OD600 = 0.3-0.5). Samples were then cultured further without additional substrate or exposed to vaporous m-xylene in a flask (2 h). For the C-runout condition, the cells were cultured for 96 h in succinate-supplemented minimal medium. The antibiotics kanamycin (Km) 50 ¹g/ml, ampicillin (Amp) 150 ¹g/ml, streptomycin (Sm) 100 ¹g/ml, chloramphenicol (Cm) 30 ¹g/ml and gentamycin (Gm) 10 ¹g/ml were added to bacterial cultures when necessary.

tag: strain/background

value: m-xylene


title: HeLa_Bmi1_GRIP

source_name: Bmi1 GRIP

value: HeLa  F-17

value: murine FLAG-Bmi1 overexpression

value: Kingston Lab rabbit antiserum targeting Bmi1


title: MLL-Gas7 cell line Rep1

city: Ann Arbor

first: Andrew

middle: G.

last: Muntean

state: Michigan

address: 1301 Catherine St.

department: Pathology

institute: University of Michigan

description: Leukemia cel lines were cultured with IMDM+15%FBS(Stemcell)+1%Pen/Strep+10ng/ml IL3

data_processing:
Basecalls performed using CASAVA-1.8.2
Sequenced reads were aligned to the mm10 genome assembly using Bowtie v2.0.0.7 and TopHat (v2.0.3) with default settings
CPM (Counts per  million) were generated using HTseq
Differential gene expression analysis was performed using the R packge EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include CPM (Counts per million) values for each Sample

source_name: Mouse cell line

growth_protocol: Cells were cultured in IMDM+15%FBS(Stemcell)+1%P/S+10ng/ml IL-3

extract_protocol:
Total RNA was extracted by Qiagen RNeasy Plus Mini Kit and the samples were treated with RNase-free DNase set on RNeasy mini spin columns according to the manufacture's protocols.
TruSeq RNA Sample Prep Kit v2 used in library construction. Oligo(dT) was used in reverse transcription.

tag: strain

tag: cell type

value: leukemia

tag: cell passages

value: Early after cell lines were established


title: MLL-ENL cell line Rep2

value: MLL-ENL


title: MLL-AF9 cell line Rep2


title: MLL-Gas7 cell line Rep2


title: MLL-AF9 cell line Rep1


title: C57BL/6 bone marrow Kit+ cells Rep1

description: Kit+ bone marrow cells were cultured in vitro for 5 days in IMDM+15%FBS(Stemcell)+1% Pen/Strep+10ng/ml IL3+100ng/ml SCF

source_name: C57BL/6 bone marrow

value: Kit+ bone marrow control

value: Cultured 5 days in vitro


title: MLL-AF1p cell line Rep1


title: MN_SCR_KD_Rep1

description: knockdown of control (scramble)

value: H3 ES cells

value: GFP under 9kb murine Mnx1 promoter

value: siRNA knockdown by nucleofection + 72 hrs in neural culture media + Retinoic Acid


title: C57BL/6 bone marrow Kit+ cells Rep2


title: MN_CAT7_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT7 knockdown in MN


title: MLL-AF6 cell line Rep1


title: HeLa_CAT12_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT12 knockdown

value: siRNA knockdown by nucleofection + 48hours growth


title: HeLa_CAT9_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT9 knockdown


title: HeLa_CAT15_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT15 knockdown


title: HeLa_CAT14_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT14 knockdown


title: P.putida (mt-2) C-runout (succinate-96h)

description: Pseudomonas putida (mt-2)

source_name: P. putida mt-2 culture, succinate, 96h (C-runout)

tag: treatment

value: succinate-96h (C-runout)


title: LSCs in Spleen (replicate 2)

city: Aurora

first: Haobin

last: Ye

state: Colorado

address: 12700 East 19th Ave, Room 9122

department: Hematology

institute: University of Colorado

data_processing:
(Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
Quality filter raw read data: Trimmomatic-0.32
Read alignment: SHRiMP_2_2_3
Data normalization and differential expression analysis: cufflinks-2.0.2.Linux_x86_64 (cuffdiff)
Genome build: mm10

source_name: Spleen

growth_protocol: Leukemia cells were transplanted into recipients.

extract_protocol:
Qiagen Rneasy PLUS
Low Input RNA-seq library using Clontech SMARTer chemistry followed by Illumina NexteraXT library construction

treatment_protocol: LSCs were derived from leukemia mice 12 days after transplantation with leukemia cells

tag: age

value: 3 month

tag: gender

value: Female

value: murine model induced by co-expression of human leukemic oncogenes BCR-ABL and NUP98-HOXA9.

value: leukemia stem cells


title: LSCs in Spleen (replicate 3)


title: LSCs in Spleen (replicate 1)


title: HeLa_CAT1_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT1 knockdown

value: HeLa  F-17

tag: ectopic expression construct


title: HeLa_SCR_KD_Rep2

description: knockdown of control (scramble)

source_name: SCR knockdown

value: murine FLAG-Bmi1 overexpression

tag: cell treatment


title: Counterparts for LSCs from normal bone marrow (replicate 3)

source_name: from normal bone marrow


title: MLL-AF6 cell line Rep2


title: MLL-ENL cell line Rep1


title: HeLa_CAT17_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT17 knockdown


title: LSCs in bone marrow (replicate 3)

source_name: bone marrow


title: Counterparts for LSCs from normal bone marrow (replicate 2)


title: HeLa_CAT14_KD_Rep1

description: knockdown of candidate RNA


title: MLL-AF1p cell line Rep2


title: LSCs in bone marrow (replicate 2)


title: HeLa_CAT11_KD_Rep2

description: knockdown of candidate RNA

source_name: CAT11 knockdown


title: HeLa_CAT13_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT13 knockdown


title: Counterparts for LSCs from normal bone marrow (replicate 1)

source_name: normal bone marrow


title: LSCs in peripheral blood (replicate 2)

source_name: peripheral blood


title: HeLa_CAT6_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT6 Knockdown


title: LSCs in bone marrow (replicate 1)


title: HeLa_CAT12_KD_Rep1

description: knockdown of candidate RNA


title: HeLa_CAT1_KD_Rep1

description: knockdown of candidate RNA


title: LSCs in peripheral blood (replicate 3)


title: LSCs in peripheral blood (replicate 1)


title: HeLa_CAT11_KD_Rep1

description: knockdown of candidate RNA


title: HeLa_CAT2_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT2 Knockdown


title: LSCs in gonadal adipose tissue (replicate 2)

source_name: gonadal adipose tissue


title: HeLa_CAT4_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT4 Knockdown


title: 96G5T18

city: Charleston

first: Gary

last: Hardiman

state: SOUTH CAROLINA

address: 135 Cannon Street, Suite 303 MSC835

institute: MUSC

description:
96hrMass
[raw_counts_HG19.txt column] 96hrMass: 1264__96G5T18

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimited raw_counts_HG19.txt is a summary file with raw count data extracted from the blastx alignments to HG19.
Supplementary_files_format_and_content: Each tab-delimited *vs*Cntrl.txt file is standard DEseq2 output for a comparison of treated vs control.  The baseMean column reports a mean of the counts for all the treated vs control samples used in that particular comparison.

organism: Coryphaena hippurus

source_name: whole embryo

growth_protocol: Mahi-mahi broodstock were captured off the coast of Miami, FL using hook and line angling techniques and subsequently transferred to the University of Miami Experimental Hatchery (UMEH) where they were acclimated in 80 m3 fiberglass maturation tanks (typically 5-7 per tank).  Tanks were equipped with recirculating aquaculture systems for water quality and temperature control.  All embryos used in experiments were collected <8 h following a volitional (non-induced) spawn using standard UMEH methods (Stieglitz et al 2012).

extract_protocol:
Thirty pooled embryos or larvae per replicate were homogenized with a Kontes Pellet Pestle Cordless Motor (Sigma-Aldrich, St. Louis, Missouri) in RNAzol (Molecular Research Center, Cincinnati, Ohio). 200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep kit following the protocol described by the manufacturer (Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bulk dilutions were prepared by adding the appropriate volume of slick or source oil HEWAF to 1 µm filtered, UV-sterilized seawater in 5 L glass bottles,  vigorously spinning for several minutes with a stir bar followed by decanting into each of the replicate 1 L glass beakers.   Freshly fertilized embryos were then gently added to each replicate using a glass transfer pipette and each beaker covered with a glass petri dish.  All exposures were static, non-renewal and performed in a temperature controlled environmental chamber at 27°C with a light cycle of 16:8 h light:dark.

tag: tissue

value: whole embryo

tag: developmental stage

tag: stress

value: Mass

tag: concentration


title: LSCs in gonadal adipose tissue (replicate 1)


title: 96G5T16

description:
96hrMass
[raw_counts_HG19.txt column] 96hrMass: 1262__96G5T16


title: 96G5T17

description:
96hrMass
[raw_counts_HG19.txt column] 96hrMass: 1263__96G5T17


title: HeLa_CAT15_KD_Rep1

description: knockdown of candidate RNA

source_name: CAT15 knockdown

tag: cell line


title: Input chromatin ChIPseq

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

description: Low cell number for this ChIP sample meant that there was insufficient material to do an IgG ChIP.

data_processing:
ChIP-seq reads aligned to mm10 using bowtie2 (version 2.0.6) with extra parameters (-k 2 -N 1).
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Peaks were called using macs2 (version 2.0.10).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig – read density profile, BED – peaks file

source_name: embryoid bodies

growth_protocol: ESCs were grown on gelatinized plates (0.1 % gelatin in water) at 37°C and 5 % CO2 in ESC media (Knockout DMEM (Life Technologies) with 15 % FCS (batch-tested for ESC culture; Life Technologies), 2mM L-glutamine (PAA Laboratories), 0.5 % P/S, 0.1mM β-mercaptoethanol (Life Technologies) and 103 U/ml recombinant LIF (ORF Genetics)). Cells were passaged with TrypLE Express dissociation reagent (Life Technologies) every 1-3 days. Differentiations were performed from single cell suspensions as described by Wilkinson AC et al., 2013 Biology Open.  Embryoid bodies were dissociated with TrypLE Express for sorting.

extract_protocol:
Approximately 7x106 FACS-sorted day 5 EB cells per ChIP were cross-linked using formaldehyde to a final concentration of 1%. As samples were pooled from several sorts, isolated nuclei were frozen on dry ice cold isopropanol and stored at -80°C. During the immunoprecipitation step, 4 μl recombinant histone 2B (New England Biolabs) and 1 μl of mouse RNA (Qiagen; diluted 1/5 in IP dilution buffer) were added as carriers, followed by 7 μg of primary antibody
Sequencing libraries were prepared using the TruSeq Kit (Illumina) for high throughput sequencing on an Illumina HiSeq 2500, according to manufacturer’s instructions, with size selection for fragments of 150-400 bp.

value: Runx1-ires-GFP+/Gata1::mCherry+ cells from embryoid bodies after 5 days of differentiation of ES cells towards blood

tag: chip antibody

value: rabbit IgG Sigma I5006


title: 48G5T15

description:
48hrMass
[raw_counts_HG19.txt column] 48hrMass: 1261__48G5T15


title: Gata1 ChIPseq

value: rabbit anti-Gata1, Abcam ab11963, lot I0303


title: A375_shNT_day4_rep2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description: Gene expression 4 days after transfection

data_processing:
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)

growth_protocol: A375 cells were maintained in 10% FBS DMEM

extract_protocol:
Cells were harvested and total RNA was extracted by Thermo RNA kit
The sequencing library was generated by Truseq RNA sample preparation kit according to the instruction
Truseq RNA sample preparation kit V2

treatment_protocol: Cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2, 3, and 4 days after infection

value: melanoma cell line

tag: transfected with

value: lenti-viral based shNT

tag: time point

value: 4 days after transfection


title: 48G5T13

description:
48hrMass
[raw_counts_HG19.txt column] 48hrMass: 1259__48G5T13


title: 48G5T14

description:
48hrMass
[raw_counts_HG19.txt column] 48hrMass: 1260__48G5T14


title: A375_shIno80_day4_rep2

value: lenti-viral based shIno80


title: A375_shIno80_day3_rep2

description: Gene expression 3 days after transfection

value: 3 days after transfection


title: LSCs in gonadal adipose tissue (replicate 3)


title: A375_shNT_day4_rep1


title: 24G5T10

description:
24hrMass
[raw_counts_HG19.txt column] 24hrMass: 1256__24G5T10


title: A375_shIno80_day4_rep1


title: 96G4T9

description:
96hrSlick
[raw_counts_HG19.txt column] 96hrSlick: 1255__96G4T9

value: Slick


title: A375_shNT_day3_rep2


title: 24G5T12

description:
24hrMass
[raw_counts_HG19.txt column] 24hrMass: 1258__24G5T12


title: A375_shNT_day3_rep1


title: HeLa_CAT4_KD_Rep2

description: knockdown of candidate RNA

value: siRNA knockdown by nucleofection + 48hours growth


title: A375_shIno80_day3_rep1