title: 19_HNRPR_B

description: HNRPR

value: lymphoblastoid cell line

value: TGACCA


title: 17_HNRPA2B1_B

status: Public on Dec 01 2014

type: SRA

city: Basel

first: Julien

last: Roux

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

library_source: transcriptomic

data_processing:
Cutadapt (version 1.2.1) was used to trim adapter sequences from RNA-seq reads. Tophat (version 2.0.6) was used to perform gapped alignments of reads to the human reference genome (Ensembl, release 69, October 2012). Ensembl gene model annotations (GFF) were supplied to guide the initial alignment step. Only uniquely mapped reads with less than 3 mismatches to the genome sequence were retained.
The script htseq-count from the package HT-Seq (http://www-huber.embl.de/users/anders/HTSeq/) was used to calculate the number of reads mapped to human genes in each sample (with the options –s no, -m union and -t exon). Gene models were downloaded from the Ensembl database (release 69, October 2012). Gene lengths were downloaded from the Ensembl database (release 69, October 2012), and used to calculate Reads Per Kilobase of exon per Megabase of library size (RPKM).
Genome_build: human reference genome (Ensembl, release 69, October 2012)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: lymphoblastoid cell line

growth_protocol: The human cell line GM19238 was cultured at 5% CO2 and 37°C in RPMI 1640 medium supplemented with 2mM L-glutamine and 15% fetal bovine serum, per Coriell’s recommendations (http://ccr.coriell.org/Sections/Support/Global/Lymphoblastoid.aspx?PgId=213). The medium was also supplemented with 100 IU/mL penicillin and 100 μg/mL streptomycin. Cells were counted and split three times a week to 350,000 cells/mL.

extract_protocol:
RNA from both time points was extracted using the RNeasy Plus 96 kit (Qiagen). The quality and concentration of all RNA samples were measured using the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfections were performed with the Lonza 96-well nucleofector system, using transfection solution SF and transfection program DN-100. On-Target SmartPool siRNAs from Dharmacon were used to knockdown target genes. For each transfection, one million cells were transfected with 50 pmol siRNA. Five independent transfections (biological replicates) were performed for each splicing factor. After transfection, cells were plated in 1 mL of medium in 96‐well plates and incubated for 48 hours. After 48 hours, 500 μL of cell culture were removed for RNA extraction for qPCR, 100 μL of fresh medium was added to each well and plates were incubated for an additional 24 hours. After a total of 72 hours of incubation, the remaining culture was pelleted for RNA extraction for RNA-sequencing library preparation. The control siRNAs consisted of a pool of four siRNAs specifically designed not to target any human or mouse gene. All transfections were conducted in one phase on three separate 96-well plates.

tag: cell type

tag: hapmap individual

tag: condition

value: knockdown

tag: splicing factor targeted

tag: splicing factor targeted (ensembl id)

tag: percentage knockdown (qpcr after 48h)

tag: rin score

tag: multiplexing index sequence

value: GGCTAC

tag: multiplexing index number


title: 22_SYNCRIP_B

description: SYNCRIP

value: SYNCRIP

value: ACTTGA


title: 17_HNRPA2B1_E


title: 21_RNPC2_D

value: CAGATC


title: 20_HNRPH2_G

value: GCCAAT


title: 14_SFRS4_C

value: TAGCTT


title: 20_HNRPH2_D

value: ACAGTG


title: 11_SFRS9_C

value: CGATGT


title: 11_G


title: 14_D


title: 17_C


title: 12_SFRS3_A

value: ATCACG


title: 14_B

value: GTCCGC


title: 12_C


title: 10_F

description: HNRPL

value: HNRPL


title: 10_G

description: HNRPL


title: 11_B

value: CCGTCC


title: 9_D


title: 9_ACIN1_B


title: 7_A

value: ATGTCA


title: 2_G


title: 2_PTBP1_D


title: 7_G


title: 19_G

description: HNRPR

value: HNRPR

value: CTTGTA


title: 2_A

value: lymphoblastoid cell line

value: AGTTCC


title: VCaP Input DNA [ChIP-Seq control]

city: NEW YORK

first: Dimple

last: Chakravarty

state: NY

address: Belfer Research Building 413 E 69 St., New York

department: Pathology

country: USA

institute: Weill Cornell Medical College

library_source: genomic

data_processing:
Sequencing reads were aligned to the reference genome (hg18) using Illumina GERALD (both NCI H660 cell lines and VCaP + E2) or CASAVA 1.8 (VCaP and VCaP ERα) using default parameters
Peak detection for all ChIP-seq experiments was performed with ChIPseeqer (Giannopoulou and Elemento, 2011), using the same parameters for all datasets (i.e., p-value threshold for peaks=10-5, minimum distance between peaks=100bp). For details, please go to: http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_use
Genome_build: hg18
Supplementary_files_format_and_content: BED files of the ERa binding sites locations for the different cell lines

molecule: genomic DNA

source_name: VCaP cell line

growth_protocol: Prostate cell lines were maintained in appropriate medium. VCaP and VCaP ERa expressing cells were maintained in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin streptomycin. NCI-H660 cells were grown in RPMI 1640 supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferrin, 30 nM sodium selenite, 10 nM hydrocortisone, 10 nM 17 beta estradiol, 5% FBS and an extra 2 mM of L-glutamine (for a final concentration of 4 mM).

extract_protocol:
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Brandson), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq Sample Kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments from 200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries for VCaP + E2 and NCI H660 + E2  were sequenced on the Genome Analyzer  II  and for VCaP cells, VCaP ERa + E2 and Sample Input  in a HiSeq 2000.

treatment_protocol: For estrogen treatment experiment,  VCaP and NCI-H660 cells were hormone starved for 48 hours prior to treatment with 10nM of 17 b estradiol (E2) for 14 hours

tag: cell line

value: Prostate cancer cell line

tag: passages

value: 3 to 4

tag: chip antibody

value: none (input)


title: 12_B

value: knockdown

value: ACTGAT


title: VCaP  [ERα_ChIP-Seq]

value: ERα (diagenode, AC-066-100, lot # 001)


title: 7_RBM23_B


title: 10_HNRPL_C

description: HNRPL

value: TTAGGC


title: NG_Seven_days_after_exposure_rep2

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

description: Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine and harvest seven days later

data_processing:
Illumina software used for basecalling.
Sequence reads were trimmed for adaptor sequences and filtered using Galaxy with 100% of all reads having a minimum phred score of 20
Reads were mapped to the  double monoploid DM1-3 516 R44 (DM1-3), Solanum tuberosum Grp. Phureja line (2n=24)
Reference genome was PGSC_DM_v3_2.1.11
Supplementary_files_format_and_content: tab delimited text file with FPKM values

molecule: total RNA

organism: Solanum tuberosum

source_name: Periderm disc with apical meristem

growth_protocol: Commercially grown greenhouse minitubers (cv Atlantic)

extract_protocol:
One to two mm thick disc containing the apical bud was frozen in liquid N2. RNA was isolated using an Ambion RNA extraction kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Atlantic

tag: agent

value: NG

tag: time

value: Seven days


title: NG_Seven_days_after_exposure_rep1

treatment_protocol: Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine


title: NG_Four_days_after_exposure_rep3

description: Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine and harvest four days later

value: Four days


title: NG_One_day_after_exposure_rep1

description: Intact dormant minitubers (3-5 g tuber-1) were injected with 5 ul DMSO +- 10 ug 1-(alpha-ethylbenzy)-3-nitroquanidine and harvested one day later

value: One day


title: NG_One_day_after_exposure_rep2


title: NG_Four_days_after_exposure_rep1


title: No_NG_zero_time_rep3

description: Dormant Minitubers treated with DMSO

value: untreated (no NG)

value: control


title: No_NG_zero_time_rep2

description: Dormant Minitubers treated with DMSO


title: 9_C

value: ATCACG


title: NG_One_day_after_exposure_rep3


title: No_NG_zero_time_rep1

description: Dormant Minitubers treated with DMSO


title: TCRβ68U_3'Partial Bio2 SPARE

city: Newark

first: Pamela

middle: J

last: Green

state: DE

address: 15 Innovation Way

department: Delaware Biotechnology Institute

institute: University of Delaware

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_3'Partial
library strategy: SPARE

data_processing:
[All] base calling was done using bcl2fastq_1.8.3
[RNA-Seq] Sequenced reads were trimmed for adapter sequence and mapped to hg19 whole genome using Tophat v2.0.11, with 1 mismatch, gtf file gencode.v11.annotation.gtf, --no-novel-juncs
[RNA-Seq] Transcript abundance (fpkm) was calculated using Cufflinks V2.2.0 using compatible hits normalization
[PARE, SPARE, C-PARE] Sequenced reads were trimmed for adapter sequence and raw abundance was counted
Genome_build: hg19
Supplementary_files_format_and_content: Transcript abundance (fpkm) reported for RNA-Seq samples.  Trimmed sequence and sequence abundance reported for PARE, SPARE, C-PARE samples.

source_name: HeLa

extract_protocol: SPARE libraries were constructed from poly(A)+ mRNA isolated from 10ug of total RNA.  mRNA was ligated to a 5' RNA adapter using T4 ligase.  The first strand of DNA was synthesized using a TCRβ68 specific RT primer.  PARE libraries were constructed as previously described with modifications.

value: HeLa

tag: stably transfected reporter

tag: transient transfection

tag: library strategy

value: SPARE


title: siGL2+siXRN1 Bio1 SPARE

description:
SPARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1
library strategy: SPARE

value: siGL2 and siXRN1


title: TCRβ68U_Fav1 Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_Fav1
library strategy: SPARE


title: TCRβ68U_5'Partial Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_5'Partial
library strategy: SPARE


title: TCRβ68U_Fav2 Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_Fav2
library strategy: SPARE


title: TCRβ68U_Fav3 Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_Fav3
library strategy: SPARE


title: TCRβ68U_Unfav2 Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_Unfav2
library strategy: SPARE


title: TCRβ68U_wt Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_wt
library strategy: SPARE

treatment_protocol: transiently transfected with TCRβ68U_wt


title: VCaP ERa + E2 [ERα_ChIP-Seq]

source_name: VCaP ERa cell line

value: Prostate cancer cell line overexpressing ERa


title: TCRβ68U_Unfav1 Bio2 SPARE

description:
SPARE libraries from HeLa cells transiently transfected with TCRβ68U_Unfav1
library strategy: SPARE


title: NG_Seven_days_after_exposure_rep3


title: TCRβ68U_3'Partial Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_3'Partial


title: siGL2+siXRN1 Bio2 SPARE

treatment_protocol: stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1


title: TCRβ68U_Unfav1 Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_Unfav1


title: TCRβ68U_Fav3 Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_Fav3


title: TCRβ68U_wt Bio1 SPARE


title: TCRβ68U_Fav1 Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_Fav1


title: TCRβ68U_Fav2 Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_Fav2


title: siUPF1+siXRN1 Bio2 RNA-seq

description:
RNA-Seq libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siUPF1 and siXRN1
Processed data file: isoform_expression.txt

extract_protocol: RNAseq libraries were constructed from poly(A)+ RNA using TruSeq RNA sample prep kit (Illumina)

treatment_protocol: transfected with siRNAs targeting UPF1 and XRN1

value: siUPF1 and siXRN1


title: siSMG6+siXRN1 Bio1 RNA-seq

description:
RNA-seq libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siSMG6 and siXRN1
Processed data file: isoform_expression.txt

treatment_protocol: transfected with siRNAs targeting SMG6 and XRN1

value: siSMG6 and siXRN1


title: siGL2+siXRN1 Bio2 RNA-seq

description:
RNA-Seq libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1
Processed data file: isoform_expression.txt

treatment_protocol: transfected with siRNAs targeting GL2 and XRN1


title: siGL2+siXRN1 Bio1 RNA-seq


title: siUPF1+siXRN1 Bio2 C-PARE

description:
C-PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siUPF1 and siXRN1
library strategy: C-PARE

extract_protocol: C-PARE Libraries were constructed from poly(A)+ mRNA isolated from 300 μg of total RNA as starting material dephosphorylated with calf intestinal alkaline phosphatase (Invitrogen) treatment at 37°C for 1 hr. After terminating the reaction with phenol/chloroform extraction and ethanol precipitation, mRNA was decapped using tobacco acid pyrophosphatase (Epicenter) at 37°C for 1 hr and cleaned with phenol/chloroform extraction and ethanol precipitation.m  RNA was used for PARE library construction as previously described.

value: C-PARE


title: siUPF1+siXRN1 Bio1 RNA-seq


title: siSMG6+siXRN1 Bio2 C-PARE

description:
C-PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siSMG6 and siXRN1
library strategy: C-PARE


title: siSMG6+siXRN1 Bio2 RNA-seq

description:
RNA-Seq libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siSMG6 and siXRN1
Processed data file: isoform_expression.txt


title: siUPF1+siXRN1 Bio2 PARE

description:
PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siUPF1 and siXRN1
library strategy: PARE

extract_protocol: PARE Libraries were constructed from poly(A)+ mRNA isolated from 300 μg of total RNA starting material using Absolute mRNA purification kit (Agilent Technologies). PARE libraries were constructed as previously described (German et al., 2008; German et al., 2009) as modified for Illumina HiSeq platform (Jeong and Green, 2012)

value: PARE


title: siGL2+siXRN1 Bio2 C-PARE

description:
C-PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1
library strategy: C-PARE


title: siGL2+siXRN1 Bio2 PARE

description:
PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1
library strategy: PARE


title: siUPF1+siXRN1 Bio1 C-PARE


title: TCRβ68U_Unfav2 Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_Unfav2


title: siGL2+siXRN1 Bio1 PARE


title: TCRβ68U_5'Partial Bio1 SPARE

treatment_protocol: transiently transfected with TCRβ68U_5'Partial


title: siSMG6+siXRN1 Bio1 C-PARE


title: siGL2+siXRN1 Bio1 C-PARE


title: siUPF1+siXRN1 Bio1 PARE


title: siSMG6+siXRN1 Bio1 PARE

description:
PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siSMG6 and siXRN1
library strategy: PARE


title: ribosome_footprints_4

city: San Francisco

first: Joseph

last: DeRisi

state: CA

address: 1700 4th Street

department: Biochemistry

institute: UCSF

description: library strategy: ribo-seq

data_processing:
Basecalling performed using Casava 1.8.
Sequenced reads were trimmed for linker sequence (CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG). Reads aligning to rRNA ant tRNA sequences were filtered using bowtie 0.12.1. Remaining sequences were uniquely mapped allowing no mismatches to 3D7_derived_W2_genome.fa using bowtie 0.12.1
Wig files were created from bowtie alignments using bowtie 0.12.1 and custom python code.
UTRs were annotated using a Hidden Markov Model on the corresponding mRNA wig files.
Genome_build: PlasmoDB version 7.0 and W2 sequencing (SRP042946)
Supplementary_files_format_and_content: Abundance measurement files are tab delimited and contain 2 columns, one for gene ID and one for RPKM, calculated as described in Mortazavi et al. Nature Methods 2008.
Supplementary_files_format_and_content: Wig files contain normalized read coverage.
Supplementary_files_format_and_content: bed files describe the coordinates for the HMM-discovered UTRs.

organism: Plasmodium falciparum

source_name: P. falciparum parasites

growth_protocol: W2 strain cultures were maintained in Hyperflasks (Corning) in 500 ml RPMIc (RPMI 1640 media supplemented with 0.25% Albumax II (GIBCO), 2 g/l sodium bicarbonate, 0.1 mM hypoxanthine, 25 mM HEPES (pH 7.4), and 50 μg/l gentamycin), at 37°C, 5% O2, and 6% CO2, to maximum 10-15% parasitemia at 5% HC and frequent media changes (at least every 6-8 hours).

extract_protocol:
Cultures were incubated for 5 min in 500 ml 37ºC RPMIc, 100µg/ml cycloheximide (Acros Organics) and harvested by centrifugation for 8 min at 3.65 xg at room temperature. An aliquot was removed and flash frozen in lN2 for total total RNA purification and mRNA-Seq library preparation. RBCs were lysed with ice-cold 0.1% saponin in 1X PBS, 100ug/ml cicloheximide. Parasites were resuspended in ice-cold parasite lysis buffer (15 mM KOAc, 15 mM MgOAc, 10 mM Tris HCl pH 7.4, 0.5 mM DTT, 0.5% Triton X-100, 100 ug/ml cyclohexamide) and dripped into a conical tube filled with, and immersed in, lN2. Frozen cells transferred placed in lN2 pre-chilled chambers and pulverized for 3 min at 15 Hz, on a Retsch MM301 mixer mill. Pulverized cells were thawed on ice and cell debris was removed by centrifugation at 4ºC, 16000 xg for 10 min. The polysome-containing supernatant was treated with 2.88 U/ug Micrococcal nuclease for 30 min at room temperature and immediately loaded onto sucrose gradients. Ribosome footprints were extracted from sucrose gradient monosome peak fractions.
Libraries were prepared as in Ingolia et al. Science 2009

treatment_protocol: Cells were synchronized by two consecutive sorbitol treatments for three generations, for a total of six treatments. Maximum invasion, point at which half of the culture is either rings or schizonts, was defined as hour zero and independent timepoints were harvested 2, 10, 19, 31 and 46 hours later.

tag: Stage

value: Schizonts

tag: strain


title: ribosome_footprints_3

description: library strategy: ribo-seq

value: Late Trophozoites


title: ribosome_footprints_5

description: library strategy: ribo-seq

value: Merozoites


title: ribosome_footprints_2

description: library strategy: ribo-seq

value: Early Trophozoites


title: mRNA_5


title: mRNA_4


title: ribosome_footprints_1

description: library strategy: ribo-seq

value: Rings


title: mRNA_1


title: mRNA_2


title: mRNA_3


title: eye-antennal-imaginal-disc_Grh-GFP

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

country: France

institute: CRCM

description: Grh-GFP ChIP-seq using anti-GFP

data_processing:
cleaning (fastX-clipper)
mapping to Dm3 genome using bowtie2-1.0.0-beta3 (options -q --seed 1 --local)
filtering for mapping quality (minimum 4)
Use MACS2 "callpeak" (options: -g dm --bdg --nomodel) comparing Grh-ChIP to input to produce a Grh-ChIP treated file (_treat_pileup.bdg) and a control file (_control_lamba.bdg) which will be compared with MACS "bdgcmp" (-m ppois -t _treat_pileup.bdg -c _control_lambda.bdg) to create the signal file (grh-vs-input-bdgcmp-pileup_vs_lambda.bw).
Genome_build: Drosophila melanogaster FlyBase version 5
Supplementary_files_format_and_content: The processed file contains Grh-ChIP-seq signal in a bigwig format

organism: Drosophila melanogaster

source_name: eye-antennal discs

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
Lysates were clarified from sonicated chromatin from eye antennal discs and Grh-GFP-DNA complexes were isolated with a GFP antibody.
Libraries were prepared according to Illumina's instructions accompanying the Trueseq DNA library prep.

treatment_protocol: Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest

tag: tissue

value: eye-antennal discs

tag: developmental stage

value: third instar larvae

tag: sample extraction method

value: Hand dissection

tag: genotype

tag: antibody

value: anti-GFP


title: eye-antennal-imaginal-disc_input

description: input

value: CantonS

value: none (input)


title: eye-antennal-imaginal-disc_eya-Gal4_x_UAS-GFP_GFP-positive-cells_2

data_processing:
cleaning (fastX-clipper)
mapping to D. melanogaster genome using TopHat2.0.3 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
filtering (minimum of 1 read per million in 5 samples across the 72) of the raw counts
Normalization of the filtered raw counts using edgeR (version 2.4.6) and DESeq (version 1.6.1) variance-stabilizing transformation in R (version 2.14.0)
Genome_build: Drosophila melanogaster FlyBase version 5
Supplementary_files_format_and_content: RNAseq samples: HT-seq counts on Drosphila Flybase r5.45 annotation; VST normalized count on Drosphila FlyBase r5.45 annotation

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were generated for sequencing using standard Illumina TruSeq protocols

value: eye-antennal disc

value: w1118; P{GMR20C01-GAL4}attP2 x w1118; P{UAS-GFP.nls}8

tag: strain origin

value: Bloomington:48881 X Bloomington:4776


title: siSMG6+siXRN1 Bio2 PARE

tag: cell line

value: HeLa

value: siSMG6 and siXRN1


title: Nt-Xanthi

city: Beijing

first: Zhao

last: Jian-Hua

address: Datun road

country: China

institute: Chinese Academy of Sciences

data_processing:
Remove adaptors, low quality tags as well as contaminants to get clean reads
Map the small RNA tags to genome by SOAP
Genome_build: Nt-Xanthi genome was download from ftp://ftp.solgenomics.net/genomes/
Supplementary_files_format_and_content: tab-delimited text files include clean reads and clones for each Sample

organism: Nicotiana tabacum

source_name: Leaf

growth_protocol: plants were grown in a glasshouse at 25 °C with a 16-h light/8-h dark cycle

extract_protocol:
RNA was isolated from plants using hot-phenol extraction
small RNA library construction and Illumina sequencing was performed by BGI

treatment_protocol: Nt-Xanthi infected with SD-CMVdeltasatRNA, an infectious CMV clone devoid of SD-satRNA.

tag: age

value: five weeks old

tag: treatment

value: mock 10 days

value: Xanthi


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-lab

value: wt; GMR-Gal4 x P{w[+mC]=UAS-lab.M}X2","1

value: GMR-Gal4 X Bloomington:7300


title: eye-antennal-imaginal-disc_m4-Gal4_x_UAS-mam

value: Bloomington:45537 X Bloomington:27743


title: eye-antennal-imaginal-disc_ato-Gal4_x_EP-dip3

value: eye-antennal discs

value: DGRC:105257 X Bloomington:22447


title: eye-antennal-imaginal-disc_eya-Gal4_x_UAS-GFP_GFP-positive-cells

value: third instar larvae

value: Hand dissection


title: eye-antennal-imaginal-disc_m4-Gal4_x_EP-gbsN

value: Bloomington:45537 X Bloomington:17242


title: eye-antennal-imaginal-disc_m4-Gal4_x_EP-danr

value: Bloomington:45537 X Bloomington:32030


title: eye-antennal-imaginal-disc_ato-Gal4_x_EP-dan

value: DGRC:105257 X Bloomington:31841


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-Su(H)

value: wt; GMR-Gal4 x UAS-Su(H)-vp16

value: GMR-Gal4 X  Flybase ID:FBtp0010495


title: eye-antennal-imaginal-disc_ato-Gal4_x_UAS-repo


title: Nt-Xanthi/CMVdeltasatRNA

value: SD-CMVdeltasatRNA infected 10 days

tag: cultivar


title: eye-antennal-imaginal-disc_GMR-gal4_x_UAS-Lim3

value: wt; GMR-Gal4 x AT50

value: GMR-Gal4 X UAS-Lim3


title: eye-antennal-imaginal-disc_hs-Gal4_x_UAS-dfd

value: w; hsGal4[w+] x w[1118]; P{UAS-Dfd.B}W4

value: hs-Gal4 X Bloomington:7299


title: eye-antennal-imaginal-disc_hs-Gal4_x_EP-danr

value: hs-Gal4 X Bloomington:32030


title: eye-antennal-imaginal-disc_GMR-Gal4_x_RNAi-side

value: wt; GMR-Gal4 x VDRC:27049

value: GMR-Gal4 X VDRC:27049


title: eye-antennal-imaginal-disc_lz-Gal4_x_RNAi-soxN

value: eye-antennal discs

value: Bloomington:6314 X Bloomington:25996


title: eye-antennal-imaginal-disc_Gal4-7_x_RNAi-sens2

value: third instar larvae

value: Gal4-7 X Bloomington:27285


title: eye-antennal-imaginal-disc_eye-disc-Gal4_x_RNAi-sens

value: Hand dissection

value: Bloomington:3735 X Bloomington:27287


title: eye-antennal-imaginal-disc_Gal4-7_x_RNAi-tll

value: Gal4-7 X Bloomington:27242


title: eye-antennal-imaginal-disc_Act5-Gal4_x_RNAi-side

value: yw; Act5C-Gal4(25FO1)/CyO, y x VDRC:27049

value: Bloomington:4414 X VDRC:27049


title: eye-antennal-imaginal-disc_Gal4-7_x_slp1

value: Gal4-7 X Bloomington:29354


title: eye-antennal-imaginal-disc_onecut[x652]

value: Thomas J.B.'s Lab [PMID:16613832]


title: eye-antennal-imaginal-disc_lz-Gal_x_RNAi-retn

value: Bloomington:6314 X Bloomington:26309


title: eye-antennal-imaginal-disc_lz-Gal4_x_RNAi-nerfin-1

value: Bloomington:6314 X Bloomington:28324


title: eye-antennal-imaginal-disc_dpp-Gal4_x_RNAi-peb

value: Bloomington:7006 X Bloomington:28735


title: eye-antennal-imaginal-disc_lz-Gal4_x_UAS-lz

value: P{w[+mC]=UAS-mCD8::GFP.L}LL4, y[1] w[*] P{w[+mW.hs=GawB}lz[gal4] x w[*]; P{UAS-lz.B}3

value: Bloomington:6314 X Bloomington:33836


title: eye-antennal-imaginal-disc_GRM-Gal4_x_UAS-lz

value: wt; GMR-Gal4 x w[*]; P{UAS-lz.B}3

value: GMR-Gal4 X Bloomington:33836


title: eye-antennal-imaginal-disc_dpp-Gal4_x_RNAi-CG12071

value: eye-antennal discs

value: Bloomington:7006 X VDRC:101953 (KK library)


title: eye-antennal-imaginal-disc_lz-Gal4_x_UAS-dfd

value: third instar larvae

value: P{w[+mC]=UAS-mCD8::GFP.L}LL4, y[1] w[*] P{w[+mW.hs=GawB}lz[gal4] x w[1118]; P{UAS-Dfd.B}W4

value: Bloomington:6314 X Bloomington:7299


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-gl

value: Hand dissection

value: wt; GMR-Gal4 x y,w,M{eGFP.vas-int.Dm}ZH-2A;+; M {RFP.attP}ZH-86Fb

value: GMR-Gal4 X Basler K.'s Lab (PMID:23583758)


title: eye-antennal-imaginal-disc_hs-Gal4_x_UAS-gl

value: w; hsGal4[w+] x y,w,M{eGFP.vas-int.Dm}ZH-2A;+; M {RFP.attP}ZH-86Fb

value: hs-Gal4 X Basler K.'s Lab (PMID:23583758)

tag: technical replicates pooled together

value: Pooled in the processed data file


title: eye-antennal-imaginal-disc_hs-Gal4_x_UAS-gl_2


title: eye-antennal-imaginal-disc_eye-disc-Gal4_x_RNAi-gl

value: P{w[+mW.hs]=GawB}c701b, w[1118] x UAS-RNAi-gl

value: Bloomington:3735  X VDRC:44524 (GD Library)


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-toy

value: wt; GMR-Gal4 x y[1] w[*]; P{w[+mC]=UAS-toy.C}8

value: GMR-Gal4 X Bloomington:26805


title: eye-antennal-imaginal-disc_Gal4-7_x_UAS-so

value: Gal4-7 X Bloomington:26808


title: eye-antennal-imaginal-disc_dpp-Gal4_x_UAS-so

value: Bloomington:7006 X Bloomington:26808


title: eye-antennal-imaginal-disc_eye-disc-Gal4_x_RNAi-gl_2

value: eye-antennal discs


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-ato

value: wt; GMR-Gal4 x UAS-ato A34 (KNG)


title: eye-antennal-imaginal-disc_ato-Gal4_x_UAS-toy

value: third instar larvae

value: DGRC:105257 X Bloomington:26805


title: eye-antennal-imaginal-disc_hs-Gal4_x_RNAi-eya

value: hs-Gal4 X Bloomington:28733


title: eye-antennal-imaginal-disc_ato-Gal4_x_UAS-Optix

value: Hand dissection

value: DGRC:105257 X Bloomington:26806


title: eye-antennal-imaginal-disc_Kr[lf-1]


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-dac

value: wt; GMR-Gal4 x  UAS-dac [PMID:15242803]

value: GMR-Gal4 X Mardon G.'s Lab [PMID:15242803]


title: eye-antennal-imaginal-disc_Gal4-7_x_RNAi-Lim3

value: Gal4-7 X Bloomington:26227


title: eye-antennal-imaginal-disc_ro-Gal4_x_UAS-oc

value: P{GMR94D11-GAL4}attP2 x w[1118]; P{w[+mC]=UAS-oc.F}RF1

value: Bloomington:47255 X Bloomington:5541


title: eye-antennal-imaginal-disc_aop[ACT.sev]

value: w[*]; P{w[+mW.hs]=sev-yan[ACT]}IVb


title: eye-antennal-imaginal-disc_lz[77a7]


title: eye-antennal-imaginal-disc_peb[1]

value: peb1 v1


title: eye-antennal-imaginal-disc_dfd[r]

value: Dfd[r]


title: eye-antennal-imaginal-disc_sv[spa-pol]

value: sv[spa-pol]


title: eye-antennal-imaginal-disc_rn[roe]

value: rn[roe-1] p[p]


title: eye-antennal-imaginal-disc_ro[1]

value: eye-antennal discs


title: eye-antennal-imaginal-disc_E(spl)[1]

value: e4 E(spl)1


title: eye-antennal-imaginal-disc_FRT-gl[60j]

value: third instar larvae

value: Pooled in the processed data file


title: eye-antennal-imaginal-disc_FRT-gl[60j]2


title: RNA_seq_eye-antennal_imaginal_disc_gl[60j]_rep2_reanalyzed


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-eya

value: wt; GMR-Gal4 x P{w[+mC]=UAS-eya.B.I}55.2","1

value: GMR-Gal4 X Bloomington:5676


title: eye-antennal-imaginal-disc_eye-disc-Gal4_x_UAS-optix

value: Hand dissection

value: Bloomington:3735 X Bloomington:26806


title: eye-antennal-imaginal-disc_dpp-Gal4_x_RNAi-dac

value: Bloomington:7006 X Bloomington:26758


title: eye-antennal-imaginal-disc_sens-Gal4_x_UAS-GFP_GFP-positive-cells

source_name: sens-GFP positive cells

value: Hand dissection of the eye antennal disc + FACS cell sorting

value: w;F2-B [ato-targeted intronic sens enhancer, from Graeme Mardon's paper] x w1118; P{UAS-GFP.nls}8

value: Graeme Mardon [paper] X Bloomington:4776


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-GFP_GFP-positive-cells2

source_name: GMR-GFP positive cells

value: wt; GMR-Gal4 x w1118; P{UAS-GFP.nls}8

value: GMR-Gal4 X Bloomington:4776


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-GFP_GFP-positive-cells


title: RNA_seq_eye-antennal_imaginal_disc_gl[60j]_rep1_reanalyzed


title: eye-antennal-imaginal-disc_sens-Gal4_x_UAS-GFP_GFP-negative-cells

source_name: sens-GFP negative cells

value: w;F2-B x w1118; P{UAS-GFP.nls}8

value: Mardon G.'s Lab [PMID:19004852] X Bloomington:4776


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-GFP_GFP-negative-cells2

source_name: GMR-GFP negative cells


title: eye-antennal-imaginal-disc_eya-Gal4_x_UAS-GFP_GFP-negative-cells

source_name: eya-GFP negative cells

value: w1118; P{GMR20C01-GAL4}attP2  x w1118; P{UAS-GFP.nls}8

value: Bloomington:48881 X Bloomington:4776


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-GFP

value: eye-antennal discs


title: eye-antennal-imaginal-disc_GMR-Gal4

value: third instar larvae

value: wt; GMR-Gal4


title: eye-antennal-imaginal-disc_ato-Gal4


title: eye-antennal-imaginal-disc_GMR27H09-Gal4


title: wing_imaginal_disc_WT_RAL-208_2

source_name: wing discs

value: wing discs

value: Pooled in the processed data file


title: RNA_seq_eye-antennal_imaginal_disc_wild-type [RAL-208]_reanalyzed

value: Hand dissection


title: wing_imaginal_disc_WT_cs

value: Canton S

tag: strain origin:


title: wing_imaginal_disc_WT_RAL-208


title: Larval_brain_WT_RAL-208

source_name: brain

value: brain

value: Bloomington: 25174


title: eye-antennal-imaginal-disc_chp-Gal4_x_UAS-GFP_GFP-positive-cells

source_name: chp-GFP positive cells

value: Hand dissection of the eye antennal disc + FACS cell sorting

value: chp-GFP

value: Published in house construct (PMID:23070853)


title: eye-antennal-imaginal-disc_chp-Gal4_x_UAS-GFP_GFP-negative-cells

source_name: chp-GFP negative cells


title: eye-antennal-imaginal-disc_GMR-Gal4_x_UAS-GFP_GFP-negative-cells

value: wt; GMR-Gal4 x w1118; P{UAS-GFP.nls}8

value: GMR-Gal4 X Bloomington:4776


title: Arapahoe_18C_trimv

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Total small RNA's of wheat cv. Arapahoe at 18C,  infected with Triticum mosaic virus.

data_processing:
Basecalls performed using CASAVA version 1.8.2
Illumina® adapters were removed from the small RNA samples via the cut-adapt tool (version 0.9.5) with a maximum error rate of 15% (-e 15), trimming bases with Phred-like quality scores lower than 45 (-q 45), and removed adapters up to three times (-n 3).
Size distributions of the small RNAs were determined for each sample via a custom in-house Perl script.
Both healthy and virus-infected samples were aligned via bowtie1 (version 0.12.8, Langmead 2009) against the genomes of both the WSMV (GenBank accession number NC_001886) and TriMV (GenBank Accession number FJ669487) to determine the amount of viral origin of small RNAs. The alignment parameters for bowtie1 were as follows: seed length of 25 (-l 25), one mismatch per seed (-n 1), up to 5 alignments per read (-k 5), suppress any read that aligns more than 10 times (-m 10), the best alignments (--best), and valid alignments (--tryhard).
The alignment of the healthy wheat samples against WSMV and TriMV allowed for the removal of host-specific endogenous small RNA in the subsequent analyses, as those small RNAs that did not align to either WSM or TriMV are considered to be originating from the host. Similarly, cross-contamination with the virus in healthy samples was detected and removed. A custom in-house Perl script was developed to target the small RNAs of interest and to generate information on the final length distribution and the nucleotide frequency from the start of the small RNA, as well as coverage information on the virus genomes. As extra filters for the final output, in the case of the healthy samples any read with a non-called base (N) is removed; for the healthy and virus-infected sample reads are size-selected between 18 to 26 nucleotides (inclusive) and reads that have mismatches or indels on the alignment, or that do not align uniquely, are removed. For the samples with the single virus infection any sequences that cross matched between the two viruses are also removed.
Genome_build: n/a
Non-public Draft 5 "Chinese Spring" for wheat, NC_001886 for Wheat streak mosaic virus, FJ669487 for Triticum mosaic virus.
Supplementary_files_format_and_content: Tabular format of small RNA sequence and occurrence count (sequence after adapter removal)

organism: Triticum aestivum

source_name: upper leaves

growth_protocol: Single-leaf seedlings were grown, post-infection, for 16 days in growth chambers at 18C and 27C with a 16h light regime.

extract_protocol:
One gram of fully expanded upper leaves of wheat infected with WSMV, TriMV, WSMV plus TriMV, or healthy plants was ground in liquid nitrogen into a fine powder, followed by addition of 5 ml of TriPure isolation reagent (Roche, Indianapolis, IN). The tissue was ground thoroughly and the extract was transferred to an Oak ridge tube. The mortar was washed with additional 2 ml of TriPure isolation reagent. The extract was vortexed for 30 s, followed by addition of 1.4 ml of chloroform and vortexed for 30 s. This mixture was incubated at room temperature for 10 min, followed by clarification at 12,000 × g for 15 min at 4°C. The total RNA was precipitated from 3 ml aqueous phase by adding an equal volume of isopropanol and incubated at room temperature for 10 min. The RNA was pelleted at 12,000 × g for 10 min at 4°C, and the pellet was washed with 5 ml of 70% ethanol. The air-dried RNA pellet was suspended in 500 ?l of sterile water and stored frozen at -70°C. The amount of total RNA was quantified using a NanoPhotometer (Implene Inc., Westlake Village, CA). Thirty µg of total RNA was denatured in the presence of 47.5% formamide, 0.1X TBE buffer plus 0.015% each of bromophenol blue and xylene cyanol FF at 95ºC for 4 min, followed by incubation on ice for 5 min. Denatured total RNA was separated through a 15% polyacrylamide-urea-TBE gel (Bio-Rad) at 120 V until the bromophenol blue reached the bottom of the gel. The gel slices from just below the center of the xylene cyanol band and extending to three-quarters of the way toward the bromophenol blue band were collected into a 30 ml corex tube containing 5 ml of 0.3 M sodium chloride. The gel slices were crushed into small pieces with a 10 ml syringe piston and incubated in a shaker at 4ºC overnight. The supernatant was collected after centrifugation at 10,000 g for 15 min at 4ºC. Two ml of 0.3 M sodium chloride was added to acrylamide pieces and incubated in a shaker for 1 h at room temperature. The small RNAs were precipitated from the pooled supernatants with the addition of 3 volumes of ice-cold ethanol in the presence of 0.3 M sodium acetate, pH 5.2 and 2 µl of glycogen (Roche), and incubated at -70ºC for 1.5 h. The small RNAs were suspended in 350 µl of 0.3 M sodium chloride, and loaded onto a spin-x-cellulose acetate filter (Sigma-Aldrich, St. Louis, MO). The spin column was centrifuged at 10,000 g for 2 min at room temperature. The small RNAs were precipitated from the elutant by adding 3 volumes of ethanol in the presence of 0.3 M sodium acetate and 1 µl glycogen for 30 min at -70ºC, followed by centrifugation at 12,000 g for 15 min at 4ºC. The RNA pellet was washed with 70% ethanol, and air dried small RNAs pellet was suspended in 10 µl sterile water and stored at -70ºC.
Small RNAs libraries were prepared from gel-eluted small RNAs fractions of total RNA using Illumina TruSeq small RNA Sample Prep Kit (Illumina Inc, San Diego, CA) essentially as described in the manufacturer's instructions. One Illumina TruSeq SR Cluster Generation Kit v5 was used to generate the cluster at one sample per lane. Amplified library was sequenced on Illumina Genome Analyzer IIx using 36-cycle sequencing kit to read 36 nts of sequence from a single end of each insert by standard v8 protocol.

treatment_protocol: Single-leaf seedlings were mechanically infected either mock, with wheat streak mosaic virus, with Triticum mosaic virus, or double infected with both virus species.

value: Arapahoe

value: 16 days post-infection of single-leaf seedlings

tag: infectious agent

value: Triticum mosaic virus  (TriMV)

value: upper leaves


title: Arapahoe_27C_trimv

description: Total small RNA's of wheat cv. Arapahoe at 27C, infected with Triticum mosaic virus.


title: Arapahoe_27C_wsmv

description: Total small RNA's of wheat cv. Arapahoe at 27C, infected with Wheat streak mosaic virus.

value: Wheat streak mosaic virus (WSMV)


title: Mace_27C_wsmv

description: Total small RNA's of wheat cv. Mace at 27C, infected with Wheat streak mosaic virus.

value: Mace


title: RNA_seq_eye-antennal_imaginal_disc_wild-type [CantonS]_reanalyzed

value: eye-antennal discs

value: third instar larvae


title: Mace_18C_wsmv_trimv

description: Total small RNA's of wheat cv. Mace at 18C, double infected with Wheat streak mosaic virus and Triticum mosaic virus.

value: Wheat streak mosaic virus (WSMV) + Triticum mosaic virus  (TriMV)


title: Mace_27C_wsmv_trimv

description: Total small RNA's of wheat cv. Mace at 27C, double infected with Wheat streak mosaic virus and Triticum mosaic virus.


title: Arapahoe_18C_wsmv

description: Total small RNA's of wheat cv. Arapahoe at 18C, infected with Wheat streak mosaic virus.


title: Mace_18C_trimv

description: Total small RNA's of wheat cv. Mace at 18C,  infected with Triticum mosaic virus.


title: Arapahoe_27C_wsmv_trimv

description: Total small RNA's of wheat cv. Arapahoe at 27C,  double infected with Wheat streak mosaic virus and Triticum mosaic virus.


title: Mace_18C_control

description: Total small RNA's of wheat cv. Mace at 18C, mock-infected (healthy control)


title: Mace_27C_control

description: Total small RNA's of wheat cv. Mace at 27C, mock-infected (healthy control)


title: Mace_27C_trimv

description: Total small RNA's of wheat cv. Mace at 27C,  infected with Triticum mosaic virus.


title: endogenous HMW RNA from Dnmt2 mutants, 2-8 days after a single heat shock, female and male, whole body

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description: HMW RNAs (4-10 kb)

data_processing:
base-calling: RTA 1.13.48
pre-processing: pipeline software Casava 1.8.2
filtering of paired-end reads: Shore
mapping: TopHat 1.4.0
average/base coverage calculation: PySam
Genome_build: Dm 3
Supplementary_files_format_and_content: Dnmt2mut_transposon_mapping.txt: list of identifiers and average/base coverage

source_name: whole tissues; Dnmt2 mutants

growth_protocol: Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle

extract_protocol: RNA was extracted from whole animals using Trizol. 30 µg of total RNA per experiment were loaded onto a formaldehyde/agarose gel. RNA was visualized by ethidium bromide staining. Visible high-molecular weight nucleic acids were cut out and electroeluted. RNAs were precipitated using ethanol and further processed for bar-coded RNA sequencing using the TrueSeq RNA sample preparation kit (Illumina). Sequencing of samples was performed on a HighSeq platform (Illumina).

treatment_protocol: 3 day old flies (female and male; 20/20) were heat-shocked (37 C for one hour) in a water bath, followed by a recovery period of 2 to 8 days before extracting total RNA

value: Dnmt2-99 mutant (Schaefer et al., 2010)

value: adult

tag: Sex

value: pooled male and female

value: whole body


title: eye-antennal-imaginal-disc_sens-Gal4_x_UAS-GFP

value: Hand dissection

value: w;F2-B  x w1118; P{UAS-GFP.nls}8

value: Mardon G.'s Lab [PMID:19004852] X Bloomington:4776


title: Arapahoe_18C_wsmv_trimv

description: Total small RNA's of wheat cv. Arapahoe at 18C, double infected with Wheat streak mosaic virus and Triticum mosaic virus.


title: Arapahoe_18C_control

description: Total small RNA's of wheat cv. Arapahoe at 18C, mock-infected (healthy control)


title: Arapahoe_27C_control

description: Total small RNA's of wheat cv. Arapahoe at 27C, mock-infected (healthy control)


title: TG EWAT 1

city: Dallas

first: Kedryn

middle: K

last: Baskin

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern

data_processing:
Data analysis was performed using the software suite TopHat and Cufflink with default settings (Trapnell et al, 2012).
genome build: mm9
Supplementary_files_format_and_content: Tab Delimited Text; Abundance

organism: Mus musculus

source_name: epididymal fat (EWAT)

growth_protocol: Male littermates, 6 weeks old maintainted on normal chow, tissue collected in the ad libitium fed state in the late afternoon

extract_protocol:
Heart ventricles and epididymal fat were removed, flash frozen in liquid nitrogen, and RNA was isolated using Trizol™ according to the manufacturer’s instructions. llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epididymal fat (EWAT)

value: 6 weeks

value: MED13 cardiac transgenic


title: WT EWAT 2

value: wild type


title: WT EWAT 3


title: TG EWAT 2


title: WT EWAT 1


title: TG ventricle 3

source_name: heart ventricles

value: heart ventricles


title: Larval_brain_WT_cs

value: brain

value: Canton S


title: Mace_18C_wsmv

description: Total small RNA's of wheat cv. Mace at 18C, infected with Wheat streak mosaic virus.

value: Mace

value: 16 days post-infection of single-leaf seedlings

value: Wheat streak mosaic virus (WSMV)

value: upper leaves


title: TG ventricle 2


title: TG ventricle 1


title: TG EWAT 3


title: WT ventricle 3


title: WT ventricle 2


title: exp3

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

description: raw data average insert size: 371

data_processing:
Alignment of paired-end reads to mm10 was performed using GSNAP, with 2 mismatches allowed for the full length of the reads.
Mapped unique raw reads that mapped to genes in the RefSeq database were counted using HTSeq and normalized to the total of mapped reads in each condition.
Differential gene expression analysis was performed.  Genes were considered statistically significant if they had p-values less than 0.05 after adjusting for false discovery rate with the Benjamini and Hochberg method {Benjamini:1995ws} in a negative binomial test and showed 1.5 fold-changes between compared conditions.
Genome_build: mm10

source_name: activated beta-catenin mutant_ventral dermis

extract_protocol:
Mice were anesthesized and sacrificed by cervical dislocation.  Hair was clipped and ventral skin dissected from the abdominal wall.  Skin was held in 0.25% trypsin-EDTA at 4C overnight, then incubated at 37C for 45 minutes.  The epidermis was removed to isolating the dermis.  The dermis was flash-frozen, mechanically homogenized, and lysed in Trizol.  RNA was extracted by standard Trizol protocol.
Libraries were prepared in the CWRU Genomics Sequencing Core using TruSeq Stranded Total RNA kit (Illumina, San Diego, CA, USA; RS-122-2301).

treatment_protocol: HoxB6CreERT/+; R26-YFP/+; CatnbΔex3/+ "activated beta-catenin" mice and double-transgenic HoxB6CreERT/+; R26-YFP/+ littermate control mice received tamoxifen (3mg/40 mg maternal weight) at embryonic day 16.5 (E16.5) by maternal gavage.  Mice were born and aged to 3 weeks.

tag: strain background

value: mixed; CD1 and C57BL/6

tag: genotype/variation

value: HoxB6CreERT/+; R26-YFP/+; CatnbΔex3/+

value: 3 weeks

value: ventral dermis


title: exp1

description: raw data average insert size: 362


title: exp2

description: raw data average insert size: 368


title: Pwp1_ChIPSeq

status: Public on Nov 30 2014

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations…
Data were filtered using the following specifications
peaks were called using macs14 version 1.4.2 with the following setting: P.value (1e-4), Enrichment Fold (5), and homer v4.3 with FDR 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bed file include Pwp1 binding sites

source_name: mouse embryonic stem cells

growth_protocol: mES cells (E14.1) were cultured on plates coated with 0.1% gelatin (Millipore) in high-glucose Dulbecco’s modiﬁed Eagle’s medium (DMEM; HyClone) supplemented with 15% ES cell-qualiﬁed fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM non-essential amino acids (NEAAs; Gibco), 0.1 mM 2-mercaptoethanol (Gibco) and 1000 units/ml of LIF (Chemicon).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols at BGI-Shenzhen (sequencing service provider).

tag: cell type

value: mESCs

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog number


title: ctl1

description: raw data average insert size: 375

source_name: control_ventral dermis

value: HoxB6CreERT/+; R26-YFP/+

tag: tissue


title: Input DNA

tag: developmental stage

value: none (input)


title: ctl3

description: raw data average insert size: 366


title: lpxA colistin 2mg 60min R2

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and trimmed for low-quality sequence, using "nesoni clip --quality 10"
Reads were mapped to the ATCC19606 reference using shrimp v2.2.2
Raw feature counts were extract using "nesoni count"
Genome_build: Ab_19606
Supplementary_files_format_and_content: Tables containing raw read counts per CDS feature

organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

source_name: lpxA colistin 2mg 60min

growth_protocol: Experiments to examine the whole-genome transcriptional response of ATCC 19606 to colistin and doripenem alone and in combination were conducted using a one-compartment in vitro PK/PD model to mimic the pharmacokinetics of both antibiotics in patients. Overnight cultures of A. baumannii were sub-cultured 1:100 into 10 mL of cation-adjusted MH broth and grown to an optical density at 600 nm (OD600) of ~0.3. To achieve a starting inoculum of ~108 cfu/mL, 0.8 mL of the early logarithmic phase culture (above) was injected into the central reservoir of the PK/PD model and incubated until OD600 reached ~0.3 with the flow of medium temporarily halted (t = 0). Colistin and/or doripenem were then delivered into the central reservoir (and the medium container for colistin) to achieve constant concentration (0.2 or 2.0 mg/L for colistin) or declining concentration (Cmax 25 mg/L with an elimination t1/2 of 1.5 h for doripenem). Both profiles mirror the clinical PK of these antibiotics. Control samples were grown without the addition of either antibiotic. Samples were collected at 0, 15 and 60 min, for RNA isolation, measurement of viable cells and determination of antibiotic concentrations as described previously. The 19606R strain was also treated with 2.0 mg/L of colistin for 1 h as outlined above for treatment of ATCC 19606.

extract_protocol:
Approximately 75 mL of each culture was transferred to sterile Falcon tubes and cells harvested by centrifugation (4,000 × g for 10 min) at 4°C. The supernatant was removed, and cells were resuspended in 1 mL of RNAlater RNA Stabilization Reagent (Qiagen) and stored at 4°C for up to 4 days. Cell samples, previously resuspended in RNAlater,were centrifuged at 5,000 × g for 10 min, and the supernatant discarded. The pellet was then resuspended in 200 µL of 10 mg/mL lysozyme (Sigma) in TE buffer to which 1 µL Protector RNase Inhibitor (Roche) had been added. The solution was vortex-mixed for 10 sec and incubated at room temperature for 10 min, with further vortex mixing for 10 sec every 2 min. RNA was purified and concentrated using the RNeasy MinElute Cleanup Kit (Qiagen), according to the manufacturer’s RNA cleanup protocol, including an on-column DNase treatment using the RNase-free DNase Set (Qiagen). An additional step was performed after the addition of 700 µL of Buffer RLT to the extracted RNA, as follows; samples were vortex-mixed vigorously and centrifuged at 5,000 × g for 5 min to pellet any precipitate. The supernatant was transferred to a fresh tube and RNA precipitated by the addition of three volumes of ethanol. For further elimination of contaminating DNA, the isolated RNA was treated again with the RNase-free DNase Set (Qiagen), according to the manufacturer’s protocol.
The construction of the cDNA library from purified RNA samples was performed using the Truseq RNA Preparation Kit (Illumina). Ribosomal RNA (rRNA) was removed from the samples using the Ribozero kit (Epicentre). Approximately 300 ng of rRNA-depleted RNA was used as input, following the manufacturer’s protocol (low throughput).

tag: strain


title: CTRL_1

city: Atlanta

first: Benoit

last: Chassaing

state: GA

address: 100 Piedmont Av SE

institute: Georgia State University

data_processing:
Illumina HiSeq Control Software v2.0.12.0, RTA v1.17.21.3 for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 with parameters -p 4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR. 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.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: Intestinal Epithelial Cells_PBS

growth_protocol: Intestinal epithelial cells were purified as follow. Rotavirus chronically infected RAG1-/- mice were sacrificed and small intestine was washed extensively with PBS, cut to 1 cm pieces and incubated with 2 mM EDTA for 30 minutes with shaking. After vortexing, the supernatant was passed through 100 μm cell strainer. The intestinal epithelial cells (IECs) were centrifuged, resuspended in PBS, and counted under microscope.

extract_protocol:
RNAs were extracted using Qiagen RNeasy kit, according to the manufacturer protocol. After purification, RNA concentration and integrity were determined using Biotech Epoch apparatus and agarose gel electrophoresis, respectively. Total RNAs were then used to prepare library for sequencing purpose, using Illumina TruSeq RNA kit, according to the manufacturer protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rotavirus chronically infected RAG1-/-

value: Purified intestinal epithelial cells

value: PBS


title: CTRL_2


title: IL22_2

source_name: Intestinal Epithelial Cells_IL22


title: IL18_1

source_name: Intestinal Epithelial Cells_IL18


title: IL18_IL22_1

source_name: Intestinal Epithelial Cells_IL18+IL22


title: IL18_3


title: IL22_1


title: lpxA control 60min R2

source_name: lpxA control 60min


title: IL22_3


title: colistin 2mg 60min R1

source_name: colistin 2mg 60min


title: IL18_IL22_3


title: colistin 2mg 60min R2


title: WT ventricle 1

value: heart ventricles

value: 6 weeks

tag: genotype

value: wild type


title: IL18_2


title: IL18_IL22_2


title: colistin 2mg 60min R4


title: colistin+doripenem 60min R2

source_name: colistin+doripenem 60min


title: ctl2

description: raw data average insert size: 366


title: colistin 0.2mg 60min R2

source_name: colistin 0.2mg 60min


title: control 60min R3

source_name: control 60min


title: CTRL_3


title: doripenem 15min R2

source_name: doripenem 15min


title: lpxA colistin 2mg 60min R1


title: lpxA control 60min R1


title: colistin 2mg 15min R2

source_name: colistin 2mg 15min


title: control 15min R2

source_name: control 15min


title: doripenem 60min R1

source_name: doripenem 60min


title: control 60min R1


title: colistin 2mg 60min R3


title: colistin 2mg 15min R1


title: colistin 0.2mg 60min R1


title: control 60min R2


title: control 15min R1


title: doripenem 15min R1


title: ATM_TALEN_10ug+Cas9:RAG1B_SRep2

status: Public on Nov 29 2014

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Library strategy: HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: 293T-Embryonic Kidney

growth_protocol: DMEM; 10% Fetal calf serum

extract_protocol:
DNA was extracted overnight at 55degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using either of 2 methods: emulsion PCR (EM-PCR) HTGTS or linear amplification-mediated PCR (LAM-PCR) HTGTS.

treatment_protocol:
CaPO4 transfection
Genomic DNA was collected 48 hours after delivery of nuclease

tag: cell line

value: 293T-Embryonic Kidney

value: WT

tag: nuclease delivery

tag: target locus

value: ATM

tag: extract_protocol (dna fragmentation/blocking methods)

value: Sonication/NdeI

tag: htgts method

value: LAM-PCR


title: ATM_TALEN_10ug+Cas9:RAG1B_SRep3


title: Cas9:RAG1B+ATM_TALEN_3ug_SRep2

value: Sonication/EcoNI


title: Cas9:RAG1B+ATM_TALEN_1ug_SRep1


title: Cas9:RAG1B+ATM_TALEN_100ug_SRep1


title: Cas9:RAG1B+ATM_TALEN_1ug_SRep2


title: colistin+doripenem 60min R1


title: Cas9:RAG1B+ATM_TALEN_10ug_SRep2


title: Cas9:RAG1B+ATM_TALEN_10ug_SRep1


title: Cas9:RAG1B+ATM_TALEN_3ug_SRep1


title: ATM_TALEN_10ug+Cas9:RAG1B_SRep1


title: Cas9:RAG1B+ATM_TALEN_10ug_SRep3


title: ATM_TALEN_3ug+Cas9:RAG1B_SRep3


title: ATM_TALEN_1ug+Cas9:RAG1B_SRep2


title: ATM_TALEN_1ug+Cas9:RAG1B_SRep1


title: Cas9:RAG1B_150ug_SRep2


title: ATM_TALEN_3ug+Cas9:RAG1B_SRep1


title: ATM_TALEN_1ug+Cas9:RAG1B_SRep3


title: Cas9:RAG1B_100ug_SRep2


title: Cas9:RAG1B_100ug_SRep1


title: Cas9:RAG1B_150ug_SRep1


title: ATM_TALEN_3ug+Cas9:RAG1B_SRep2


title: Cas9:RAG1B+ATM_TALEN_100ug_SRep2


title: Cas9:RAG1B+ATM_TALEN_3ug_SRep3


title: Cas9:RAG1B_60ug_SRep2


title: Cas9:RAG1B_60ug_SRep1


title: MYC_TALEN_SRep3

value: MYC

value: Sonication/DraI


title: ATM_TALEN_SRep3


title: ATM_TALEN_SRep2


title: MYC_TALEN_SRep2


title: Cas9:RAG1B+ATM_TALEN_SRep3


title: Cas9:RAG1B+ATM_TALEN_SRep2


title: input2.2_15

city: Jerusalem

first: Alon

last: Appleboim

address: Hebrew University

department: Life Sciences

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
library-strategy: MNase-ChIP-Seq
mapping to S. cerevisiae S288C (release 64) using bowtie2.X with default settings
Read extension to 100bp and summation per bp in genome
Nucleosom calling after smoothing based on local minima/maxima pairs
Maximal level from every time points/Antibodies was collected per nucleosome (window size of 150bp)
each nuc/antibody/time was normalized to its respective input (there are 9 experimental batches) - see CSV file, in log2 ratio to input
failed sequencing libraries were linearly interpolated given adjacent time points
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files containing bp-resolution data after extension of reads and summation; nucs_normed.csv.gz file contains all data, assigned to nucleosomes and normalized to respective input (log2 ratio). First 7 columns describe nucleosome - "nuc_id" is an ordinal number, "chr" is the chromsome number, "center" is the chromsome coordinate of the nucleosome center, "coverage (RPM)" is the reads per million assigned to the nucleosome in the input track from which it was called,  "gene" is the gene name in the corresponding locus (where applicable), "acc"  is the gene accession number (where applicable), and "gene_pos" is the nucleosome position of the nucleosome within the transcribing unit, i.e. -1, +1,+2, etc.

organism: Saccharomyces cerevisiae

growth_protocol: 400 mL wild-type strain (BY4741) cells were grown in YPD medium to mid-log phase (OD600=0.55) with 220 rpm shaking at 30°C

extract_protocol:
Formaldehyde was quenched by 125mM glycine. Cell pellets were then harvested, washed by water, and subjected to beads-beating, MNase digestion, and chromatin immunoprecipitation protocol as previously described in Liu et al (2005)
As described in Blecher-Gonen R et al 2013 (PMID 23429716)

treatment_protocol: final concentration of 1.5 mM diamide

tag: stress

value: diamide

tag: time

value: 15 min

tag: antibody


title: Cas9:RAG1B+Cas9:VEGFA_SRep3


title: input2.2_8

value: 8 min


title: input1.1_0

value: untreated

value: 0 min


title: input1.3_0


title: Cas9:RAG1B+Cas9:EMX1_SRep3


title: Cas9:RAG1B+Cas9:VEGFA_SRep2


title: Cas9:RAG1B+Cas9:VEGFA_SRep1


title: input1.3_60

value: 60 min


title: input2.3_60


title: input1.3_30

value: 30 min


title: input3.2_0


title: input1.3_15


title: input2.3_15


title: Cas9:RAG1B+Cas9:EMX1_SRep1


title: Cas9:RAG1B_A549_SRep2

source_name: A549-Lung Epithelial

treatment_protocol:
Nucleofection
Genomic DNA was collected 48 hours after delivery of nuclease

value: A549-Lung Epithelial


title: input3.2_4

value: 4 min


title: input1.1_30


title: Cas9:RAG1B_A549_SRep1b


title: input1.2_30


title: input2.2_4


title: Cas9:RAG1B_A549_SRep1a


title: input1.1_8


title: input3.1_60


title: Cas9:RAG1B+IR_SRep3

value: 293T-Embryonic Kidney


title: input3.1_8


title: input1.2_15


title: input2.1_30


title: input3.2_8


title: input2.1_15


title: Cas9:RAG1B+IR_SRep2

value: WT


title: Cas9:RAG1B+IR_SRep1


title: input1.1_60


title: input3.2_60


title: input1.3_8


title: Cas9:RAG1B+Cas9:EMX1_SRep2


title: input1.2_60


title: input1.3_4


title: Cas9:RAG1A_OTChr7_SRep3


title: input3.1_4


title: input2.1_0


title: input1.1_4


title: input2.1_8


title: input2.2_0


title: Cas9:RAG1A96hrs_SRep2


title: Cas9:RAG1A_OTChr7_SRep1


title: Cas9:RAG1A96hrs_SRep1


title: input2.3_4


title: input2.3_0


title: Cas9:RAG1A_OTChr7_SRep2


title: input3.1_15


title: input2.1_60


title: input1.2_8


title: input2.2_60


title: input1.2_4


title: Cas9:RAG1A24hrs_SRep1


title: input2.2_30


title: input3.1_0


title: ATM_TALEN_SRep1

value: ATM


title: Cas9n:RAG1A/F_SRep2


title: input1.2_0


title: input1.1_15


title: input2.3_30


title: input3.2_15


title: Cas9n:RAG1A/F_SRep1

value: EM-PCR


title: MYC_TALEN_SRep1

value: LAM-PCR


title: htz1_15

value: anti-htz1 (Active motif, catalog# 39467, lot# 26409001)


title: Cas9n:RAG1A/E_SRep2

value: Sonication/EcoNI


title: htz1_8


title: htz1_0


title: htz1_4


title: htz1_30


title: Cas9n:RAG1A/E_SRep1


title: input2.1_4


title: htz1_60


title: Cas9n:RAG1A/G_SRep5


title: Cas9:RAG1A24hrs_SRep2


title: h4r3me2s_4

value: anti-h4r3me2s (Abcam, catalog# ab5823, lot# GR78124-1)


title: h4r3me2s_8

value: diamide


title: Cas9n:RAG1A/G_SRep4


title: h4r3me2s_30


title: h4r3me2s_0


title: h4r3me2s_15

value: 15 min


title: Cas9n:RAG1A/G_SRep3


title: h4k8ac_15

value: anti-h4k8ac (Millipore, catalog# 07-328, lot# 2075956)


title: h4k8ac_8

value: 8 min


title: h4r3me_15

value: anti-h4r3me (Abcam, catalog# ab17339, lot# GR52461-1)


title: h4k8ac_4


title: h4r3me_60

value: 60 min


title: h4r3me_8


title: Cas9:RAG1D_SRep5


title: Cas9n:RAG1A/G_SRep2


title: Cas9:RAG1D_SRep6


title: Cas9n:RAG1A/G_SRep1


title: h4r3me_4


title: h4r3me_0

value: untreated

value: 0 min


title: Cas9:RAG1D_SRep4


title: h4r3me_30

value: 30 min


title: h4k5ac_8

value: anti-h4k5ac (Millipore, catalog# 07-327, lot# 2019741)


title: h4k8ac_60


title: Cas9:RAG1D_SRep3

value: 293T-Embryonic Kidney

value: WT


title: h4k5ac_4

value: 4 min


title: Cas9:RAG1D_SRep2

value: EM-PCR


title: h4k5ac_15


title: h4k8ac_30


title: h4r3me2s_60


title: Cas9:RAG1C_SRep6

value: LAM-PCR


title: h4k20me_0

value: anti-h4k20me (Abcam, catalog# ab9051, lot# GR79450-1)


title: Cas9n:RAG1A/G_SRep6

value: Sonication/EcoNI


title: Cas9:RAG1D_SRep1


title: h4k5ac_30

value: diamide


title: h4k5ac_60


title: h4k8ac_0


title: h4k5ac_0


title: h4k20me_4


title: h4k20me_8


title: Cas9:RAG1C_SRep4


title: h4k20me_15

value: 15 min


title: h4k20me_30


title: Cas9:RAG1C_SRep3


title: h4k20me_60


title: h4k16ac_8

value: anti-h4k16ac (Millipore, catalog# 07-329, lot# 2073125)


title: h4k16ac_4


title: h4k16ac_0


title: h4k16ac_60


title: h4k12ac_15

value: anti-h4k12ac (Millipore, catalog# 07-595, lot# 2019723)


title: h4k12ac_8

value: 8 min


title: h4k12ac_0


title: h4k16ac_15


title: h4k12ac_4


title: Cas9:RAG1C_SRep1


title: Cas9:RAG1B+MYC_TALEN_SRep2


title: Cas9:RAG1B+MYC_TALEN_SRep3


title: h4k16ac_30


title: h4k12ac_60

value: 60 min


title: Cas9:RAG1B+ATM_TALEN_SRep1


title: Cas9:RAG1B+MYC_TALEN_SRep1


title: h4k12ac_30


title: h3s10ph_4

value: anti-h3s10ph (Millipore, catalog# 04-817, lot# NG1867615)


title: h3s10ph_0

value: untreated

value: 0 min


title: Cas9:RAG1C_SRep5


title: h3s10ph_8


title: h3s10ph_15


title: Cas9:RAG1B+ISceI_SRep3


title: Cas9:RAG1C_SRep2


title: Cas9:RAG1B+ISceI_SRep2


title: h3s10ph_30

value: 30 min


title: h3s10ph_60


title: h3k9ac_0

value: anti-h3k9ac (Abcam, catalog# ab10812, lot# GR68135)


title: Cas9:RAG1B+ISceI_SRep1

value: 293T-Embryonic Kidney

value: WT


title: h3k9ac_15


title: h3k9ac_8


title: Cas9:RAG1B_SRep6


title: h3k9ac_30


title: Cas9:RAG1B_SRep5


title: h3k9ac_60


title: Cas9:RAG1B_SRep2

value: EM-PCR


title: h3k79me3_4

value: 4 min

value: anti-h3k79me3 (Abcam, catalog# ab2621, lot# 361576)


title: Cas9:RAG1B_SRep3

value: Sonication/EcoNI


title: h3k79me3_60

value: diamide


title: Cas9:RAG1B_SRep4


title: h3k79me3_15

value: 15 min


title: h3k79me_0

value: anti-h3k79me (Abcam, catalog# ab2886, lot#s GR64011-1, GR64011-2)


title: h3k79me3_0


title: Cas9:RAG1B_SRep1


title: h3k79me3_30


title: h3k79me_4


title: Cas9:RAG1A_OTChr12+IR_SRep3

value: Sonication/PstI

value: LAM-PCR


title: h3k79me_15


title: h3k79me_8

value: 8 min


title: Cas9:RAG1A_OTChr12+IR_SRep2


title: h3k79me_30


title: h3k9ac_4


title: h3k79me_60

value: 60 min


title: h3k56ac_4

value: anti-h3k56ac (Millipore, catalog# 07-677, lot#s DAM1413945, DAM1462569)


title: h3k56ac_0

value: untreated

value: 0 min


title: Cas9:RAG1A_OTChr12_SRep2


title: Cas9:RAG1A_OTChr12_SRep3


title: h3k56ac_15


title: h3k56ac_30

value: 30 min


title: h3k56ac_60


title: h3k79me3_8


title: h3k4me3_4

value: anti-h3k4me3 (Millipore, catalog# 04-745, lot#s DAM1567816, DAM1606783)


title: Cas9:RAG1A_OTChr12+IR_SRep1

value: 293T-Embryonic Kidney

value: WT


title: Cas9:RAG1A_OTChr12_SRep1


title: h3k4me3_8


title: h3k4me3_0


title: h3k4me3_15


title: h3k4me3_60


title: Cas9:RAG1A_OTChr19+IR_SRep3

value: DAZAP

value: Sonication/ApaLI


title: h3k4me3_30


title: h3k4me2_4

value: 4 min

value: anti-h3k4me2 (Abcam, catalog# ab32356, lot#s GR106705, GR84702)


title: Cas9:RAG1A_OTChr19+IR_SRep1


title: h3k4me2_15

value: diamide

value: 15 min


title: Cas9:RAG1A_OTChr19_SRep3


title: h3k4me2_60


title: h3k4me_0

value: anti-h3k4me (Abcam, catalog# ab8895, lot#s GR46387, GR616306)


title: h3k4me2_30


title: Cas9:RAG1A_OTChr19_SRep1

value: LAM-PCR


title: Cas9:RAG1A+IR_SRep3

value: Sonication/EcoNI


title: h3k56ac_8

value: 8 min


title: h3k4me_8


title: Cas9:RAG1A+IR_SRep2


title: h3k4me_30


title: h3k4me_60

value: 60 min


title: h3k4me2_0

value: untreated


title: Cas9:RAG1A+IR_SRep1


title: Cas9:RAG1A_OTChr19+IR_SRep2


title: h3k4ac_4

value: anti-h3k4ac (Millipore, catalog# 07-539, lot# 2116017)


title: Cas9:RAG1A_SRep5


title: Cas9:RAG1A_SRep4

value: EM-PCR


title: Cas9:RAG1A_SRep6


title: h3k4ac_15


title: h3k4me2_8


title: h3k4ac_30

value: 30 min


title: Cas9:RAG1A_SRep3

value: 293T-Embryonic Kidney


title: h3k4ac_60


title: h3k36me3_0

value: 0 min


title: h3k36me3_8


title: Cas9:RAG1A_SRep2

value: WT


title: h3k4me_4


title: Cas9:RAG1A_SRep1


title: h3k36me3_4


title: h3k4me_15


title: h3k36me3_15


title: h3k4ac_0


title: h3k36me3_30


title: h3k36me2_0

value: anti-h3k36me2 (Abcam, catalog# ab9049, lot# GR75522-1)


title: h3k4ac_8


title: h3k36me3_60


title: h3k36me2_4

value: 4 min


title: h3k36me2_8


title: h3k36me_4

value: anti-h3k36me (Abcam, catalog# ab9048, lot#s GR69672-1, GR81164-1)


title: h3k36me2_30

value: diamide


title: h3k36me_0


title: h3k36me2_60


title: h3k36me_8


title: h3k36me_30


title: h3k27ac_4

value: anti-h3k27ac (Millipore, catalog# 07-360, lot# 2090153)


title: h3k36me_15

value: 15 min


title: h3k27ac_0


title: h3k27ac_8


title: h3k27ac_30


title: h3k36me_60


title: h3k27ac_15


title: h3k23ac_4

value: anti-h3k23ac (Millipore, catalog# 07-355, lot# 27133)


title: h3k23ac_15


title: h3k23ac_8


title: h3k23ac_30


title: h3k18ac_0

value: anti-h3k18ac (Abcam, catalog# ab1191, lot# GR49361-1)


title: h3k36me2_15


title: h3k18ac_4


title: h3k18ac_15


title: h3k23ac_0


title: h3k18ac_30


title: Cas9:RAG1A_OTChr19_SRep2

value: DAZAP

value: Sonication/ApaLI

value: LAM-PCR


title: h3k18ac_60

value: 60 min


title: h3k14ac_4

value: anti-h3k14ac (Millipore, catalog# 07-353, lot# 2073782)


title: h3k14ac_30

value: 30 min


title: h2as129ph_0

value: untreated

value: anti-h2as129ph (Abcam, catalog# ab15083, lot# GR36312-1)


title: h3k14ac_15


title: h3k14ac_60


title: h3k23ac_60


title: h3k14ac_8

value: 8 min


title: h3k27ac_60


title: h2as129ph_4


title: h2as129ph_8


title: h2as129ph_15


title: h2as129ph_60


title: h2as129ph_30


title: h3k14ac_0

value: 0 min


title: h3k18ac_8


title: h2ak5ac_0

value: anti-h2ak5ac (Abcam, catalog# ab45152, lot# GR46560-3)


title: h2ak5ac_8


title: h2ak5ac_15


title: h2ak5ac_30


title: h2ak5ac_60


title: Subject 7 Day 0 APAP overdose

status: Public on Nov 28 2014

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description: healthy

data_processing:
reads were adapter trimmed; length filtered and collapsed by miRDeep2
Genome_build: mirbase version 20
Supplementary_files_format_and_content: text files of counts for miRNAs

extract_protocol:
Serum miRNA was isolated using the miRNeasy Mini Kit (QUIAGEN, CA, USA) Serum samples were recovered from serum-separator tubes following centrifugation of whole blood at 3000xg for 10 minutes at room temperature.
TruSeq Small RNA-Seq Preparation Kit (Illumina, CA, USA)

value: serum


title: Subject 7 Day 7 APAP overdose

description: healthy


title: Subject 7 Day 1 APAP overdose

description: healthy


title: Subject 6 Healthy

description: healthy


title: Subject 8 Day 1 APAP overdose

description: healthy


title: Subject 10 Day 0 APAP overdose

description: healthy


title: Subject 10 Day 3 APAP overdose

description: healthy


title: Subject 12 Day 2 APAP overdose

description: healthy


title: Subject 12 Day 1 APAP overdose

description: healthy


title: Subject 11 Day 1 APAP overdose

description: healthy


title: Subject 12 Day 0 APAP overdose

description: healthy


title: Subject 9 Day 2 APAP overdose

description: healthy


title: Subject 11 Day 0 APAP overdose

description: healthy


title: Subject 12 Day 3 APAP overdose

description: healthy


title: Subject 8 Day 0 APAP overdose

description: healthy


title: h2ak5ac_4

value: diamide

value: 4 min


title: Subject 7 Day 3 APAP overdose

description: healthy


title: Subject 7 Day 4 APAP overdose

description: healthy


title: Subject 5 Healthy

description: healthy


title: Subject 7 Day 6 APAP overdose

description: healthy


title: Subject 4 Healthy

description: healthy


title: Subject 9 Day 0 APAP overdose

description: healthy


title: JDM-RA-18  rep2

city: Leuven

first: Thijs

last: Baens

address: Herestraat 49

country: Belgium

institute: VIB

data_processing:
demultiplex: cassava
tophat
cufflinks v2.0.2
--keep-fasta-order --transcriptome-only --read-realign-edit-dist 0 --mate-inner-dist 200 --mate-std-dev 50
Genome_build: Build37.2

growth_protocol: All Jurkat cells were grown in DMEM-F12 supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was harvested using Trizol reagent and treated with DNaseI.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were untreated or stimulated  for 3 or 18 hrs with 75 ng/ml PMA – 150 ng/ml ionomycin,

value: Jurkat T cell

tag: ectopic expression

tag: p/i stimulation

value: 18 hours P/I


title: Subject 1 Healthy

description: healthy


title: Subject 2 Healthy

description: healthy


title: JDM-RA-0  rep2

value: endogenous MALT1 knock-out


title: JDM-RA-3  rep2


title: JDM-CA-18  rep2

value: wild type MALT1


title: JDM-RA-0  rep1


title: JDM-RA-3  rep1


title: JDM-RA-18  rep1


title: JDM-CA-0  rep2

value: 3 hours P/I


title: JDM-CA-3  rep2


title: RACA-18  rep2


title: RACA-0  rep2


title: JDM-CA-0  rep1


title: JDM-CA-3  rep1


title: MALT1-3  rep2

value: unstimulated


title: MALT1-18  rep2


title: RACA-3  rep2


title: JDM-CA-18  rep1


title: Subject 3 Healthy

description: healthy


title: RACA-0  rep1


title: MALT1-3  rep1


title: MALT1-18  rep1


title: RACA-3  rep1


title: ILC1.Nov82013

status: Public on Nov 27 2014

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Sequenced on HiSeq 2500, base called with CASAVA 1.9
Alignment was done using Tophat 2
Genome_build: n/a
Supplementary_files_format_and_content: mouse genes and counts

source_name: Cell

extract_protocol:
Trizol
RNA-Seq

tag: cell type

value: RAG-2 null


title: RACA-18  rep1


title: iCD8a.Nov82013


title: eat-2(ad1116) Day 1

city: New Delhi

first: Arnab

last: Mukhopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed off adaptor sequences and independently aligned using CLC Genomic Workbench 6.5.1 with default setting against miRBase release 19  accounting for a maximum of two gaps or mismatches in each sequence
Differential expression, p-value and fold changes for each gene were determined using CLC Genomic Workbench 6.5.1  with default parameters.
Genome_build: miRBase release 19
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcript per million) values for each miRNA of respective samples

organism: Caenorhabditis elegans

source_name: whole organism total RNA

growth_protocol: All strains were maintained at 20oC using standard C. elegans techniques

extract_protocol:
RNA was isolated using Trizol (Invitrogen, USA).  Briefly, worms grown on OP50 bacteria,  were washed off the plates with M9 buffer. Then, 0.4 ml of Trizol reagent was added and the worms lysed by vigorous vortexing. RNA was purified by phenol:chloroform:isoamylalcohol extraction and ethanol precipitation. RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. Alternatively, the quality of the ribosomal 28 S and 18 S on an agarose gel was used as a measure of integrity and the absorbance at 260/280 nm was used to determine quantity.
The small RNAs libraries were constructed using  Small RNA v1.5 sample preparation kit  according to the manufacturer’s instructions (Illumina, inc. ,USA.)  Briefly  the total RNA (5µg) were ligated  3' adapter using T4 RNA ligase 2 truncated (NEB)and a 5' adapter using   T4 RNA ligase 2. The ligation products were reverse transcribed using Superscript II Reverse Transcriptase (Life Technologies) and amplified with  PCR (12 Cycle). The PCR  products were purified with electrophoresis of 6% Novex TBE PAGE Gel. The purified cDNA library for each sample was analyzed on Agilent 2100 Bioanalyzer using Agilent DNA high sensitivity kit. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome analyzer IIX for 36 cycles.

tag: genotype/variation

value: Day 1 Adult


title: N2 Day 8

value: wildtype

value: Day 8 Adult


title: eat-2(ad1116) Day 8


title: MALT1-0  rep2


title: Pararge aegeria

status: Public on Nov 26 2014

city: Oxford

first: Peter

middle: W. H.

last: Holland

address: South Parks Road

department: Department of Zoology

country: United Kingdom

institute: University of Oxford

data_processing:
Bowtie index created for each of the Cameraria ohridella and Pararge aegeria genome assemblies
miRDeep2 "mapper.pl" script used to parse fastq to fasta, clip adapters, remove entries with non-canonical letters, collapse reads and map reads to bowtie index
Size selection done on collapsed reads to exclude sequences outside the range of 18-24 nt
miRDeep2 "mirdeep2.pl" script used to predict miRNA hairpins based on processed small RNA reads
Predicted hairpins filtered based on structure and free energy as well as comparisons to existing miRNA data
Genome_build: Cameraria ohridella and Pararge aegeria genome assemblies available in the Oxford Research Data Archive (doi 10.5287/bodleiandury.3)
Supplementary_files_format_and_content: Tab-delimited text files indicating each predicted miRNA precursor sequence as well as sequence and read counts for each of its mature products

organism: Pararge aegeria

source_name: Pararge aegeria whole body

extract_protocol:
TRIzol extraction followed by DNase I digestion
Library construction performed by the Beijing Genomics Institute

value: Embryo, larva, pupa, adult male, adult female

tag: growth

value: Laboratory-reared population

value: whole body


title: 1pmol_NNNNAdaptor

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

description:
Set1
processed data: Set1_miRNAcounts_Fig7_version2.xls

data_processing:
adaptor removal with custom scripts or with cutadapt v. 1.3 allowing 1 mismatch
miRNAs mapped to known input sequences with custom scripts
counts and analysis done with custom scripts
Genome_build: N/A

organism: synthetic construct

source_name: synthetic equimolar miRNA mixture

extract_protocol:
N/A
Libraries were constructed as described in the paper.  In general, a 3' adaptor was ligated to the RNA.  This ligation product was reverse transcribed, and the RT product was purified and circularized.  Circularized RT product was PCR amplified to produce the deep sequencing library.

tag: 5' barcode sequence

value: GGAGCCC

tag: 3' adaptor sequence

value: TGGAATTCTCGGGTGCCAAGG


title: N2 Day 1 WT

description: duplicate of GSM1466687

tag: strain

tag: developmental stage


title: 1pmol_fixedAdaptor

value: TCTACCC


title: daf-2(e1370)

value: Young adult stage


title: N2 Day 1


title: SPY2768_dcr1Δ,clr4re_H3K9me2

city: Boston

first: Gloria

last: Jih

state: MA

address: 240 Longwood Ave, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

description: BARCODE SEQUENCE: GAGTTAAC

data_processing:
Raw reads were separated by barcode and the barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using bowtie with default configurations. Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV)
Genome_build: ASM294v1
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.

organism: Schizosaccharomyces pombe

extract_protocol:
Fixed cells were resuspended in 500 ul lysis buffer (50 mM Hepes-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, and protease inhibitors) and disrupted by bead beating (Mini Beadbeater, Biospec products) for 6x30 sec with 1 ml 0.5 mm glass beads. Tubes were punctured and the flow-through was collected in a new tube by centrifugation. After sonication for 3x20 sec at 40% amplitude (Branson Digital Sonifier), the extract was centrifuged (Eppendorf 5415R) for 15 min at 13000 rpm. Antibody was pre-incubated with washed Dynabeads Protein A, and for each immunoprecipitation, 2 ug antibody coupled to 30ul beads was added to 400 ul soluble chromatin, and lysis buffer was added for a final volume of 600 ul. Samples were rotated for 2h at 4°C, the beads were collected on magnetic stands, and washed 3 times with 1 ml lysis buffer and once with 1 ml TE, and eluted with 100 ul pre-heated buffer (50 mM Tris pH 8.0, 10mM EDTA, 1% SDS) at 65°C for 15 min. The eluate was collected and 150 ul 1xTE/0.67% SDS was added. Input and immunoprecipitated samples were incubated overnight at 65°C to reverse crosslinks, and treated with 50 ug RNase A at 37°C for 1h. DNA was cleaned up with QIAquick PCR Purification Kit (Qiagen).
Libraries for Illumina sequencing were constructed following the manufacturer’s protocols, starting with ∼5 ng of immune-precipitated DNA fragments. Each library was generated with custom-made adapters carrying unique barcode sequence at the ligating end (Wong and Struhl, 2011). Barcoded libraries were mixed and sequenced with Illumina HiSeq2000. Barcodes are 6/8/9 nt in length and should be followed by a T.

tag: media

value: YES


title: SPY2765_ago1Δ,clr4re_H3K9me2

description: BARCODE SEQUENCE: GTCTACAT


title: SPY120_ago1Δ_H3K9me2

description: BARCODE SEQUENCE: ACAGTG


title: MALT1-0  rep1

tag: cell line

value: Jurkat T cell


title: SPY86_dcr1Δ_H3K9me2

description: BARCODE SEQUENCE: TGACCA


title: 50fmol_NNNNAdaptor

value: ATTCACC


title: SPY28_wt_H3K9me2

description: BARCODE SEQUENCE: ATATAGGA


title: SPY5086+tet_H3K9me3

description: BARCODE SEQUENCE: AACACCTAC

value: H3K9me3 (Hattori et al, 2013)

value: YEA + 2.5 ug/mL tetracycline


title: SPY5090_H3K9me3

description: BARCODE SEQUENCE: CCTTTACAG

value: YEA


title: SPY825_clr4Δ_H3K9me2

description: BARCODE SEQUENCE: TTAGGC


title: SPY5090+tet_H3K9me3

description: BARCODE SEQUENCE: GGTCCTTGA


title: SPY5086_H3K9me3

description: BARCODE SEQUENCE: TGCGGTTA


title: SPY5286+tet_H3K9me3

description: BARCODE SEQUENCE: TATACCGT


title: CD11b+.Nov82013

tag: genotype

value: RAG-2 null


title: T-ALL-12

city: New York

first: Hans-Guido

last: Wendel

address: 1275 York Avenue

institute: Sloan Kettering Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg19 genome assembly using Spliced Transcripts Alignment to Reference aligner (STAR)
Data is filtered by removing low quality sequences, and non-uniquely mapping sequences
Differential genes were determined using DESeq, which is a bioconductor pakage to perform differential gene expression based on a negative binomial distribution
Genome_build: hg19

source_name: T cell acute lymphoblastic leukemia

extract_protocol:
Total RNA isolated using Qiagen RNA isolation kit (Qiagen) followd by ribosomal RNA depletion (RbioMinus).
Library preparation and sequencing was done using Illumina Hi-Seq chemistry. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: T cell acute lymphoblastic leukemia


title: SPY5286_H3K9me3

description: BARCODE SEQUENCE: TCGCGTAC


title: 50fmol_fixedAdaptor

value: CGGGACC


title: SPY5285_H3K9me3

description: BARCODE SEQUENCE: GAGTTAAC


title: SPY5090+tet_H3K9me2

description: BARCODE SEQUENCE: GTCTACAT


title: T-ALL-10


title: T-ALL-11


title: T-ALL-7


title: SPY5090_H3K9me2

description: BARCODE SEQUENCE: CGCATTAA


title: SPY5086+tet_H3K9me2

description: BARCODE SEQUENCE: CCATACAC


title: T-ALL-5


title: T-ALL-4


title: T-ALL-2


title: Control-1

source_name: normal thymus

value: normal thymus


title: T-ALL-3


title: Control-4


title: SPY5286_H3K9me2

description: BARCODE SEQUENCE: AACCGTGT


title: SPY5286+tet_H3K9me2

description: BARCODE SEQUENCE: AGGTCAGT


title: SPY5086_H3K9me2

description: BARCODE SEQUENCE: CTCTGTCT


title: Control-2


title: SPY5285+tet_H3K9me2

description: BARCODE SEQUENCE: ATATAGGA


title: Control-3


title: SPY5285+tet_H3K9me3

description: BARCODE SEQUENCE: GCAGCCTC


title: Mouse skeletal muscle control #2

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

description:
mMuscle2
processed data file: 10407R.txt

data_processing:
Human reads were aligned to hg19 plus extended splice junctions and mouse reads were aligned to mm10 plus extended splice junctions using novoalign (2.08.01). Up to 50 alignments were reported for each read. Novoalign was set to trim adapter sequences from reads.
Mouse reads were aligned to mm10 plus extended splice junctions using novoalign (2.08.01). Up to 50 alignments were reported and adapter sequences were trimmed by novoalign.
Splice junction alignments were converted back to genomic space using the USeq (8.7.0) SamTranscriptomeParser application (default settings).
The final alignment files were used in the USeq (8.7.0) DefinedRegionDifferentialSeq application to generate counts per gene, variance stabilized counts, FPKM values and to determine differential expression
Genome_build: hg19 for human, mm10 for mouse
Supplementary_files_format_and_content: tab-delimited files contain raw read counts, normalized counts and FPKM values for each sample

source_name: post-mortem quadriceps sample

extract_protocol:
Qiagen Rneasy mini-kit
Illumina Ribo-Zero

value: mixed SvJ and BL/6

value: skeletal muscle

tag: group

value: control


title: Mouse skeletal muscle control #3

description:
mMuscle3
processed data file: 10407R.txt


title: SPY5285_H3K9me2

description: BARCODE SEQUENCE: CTTGTA


title: Mouse skeletal muscle control #1

description:
mMuscle1
processed data file: 10407R.txt


title: Mouse ASPSCR1-TFE3-induced tumor #5

description:
mASPS5
processed data file: 10407R.txt

source_name: post-mortem tumor sample

value: ASPSCR1-TFE3-induced tumor

value: tumor


title: SPY5081_H3K9me2

description: BARCODE SEQUENCE: GGCTAC


title: Mouse ASPSCR1-TFE3-induced tumor #4

description:
mASPS4
processed data file: 10407R.txt


title: Mouse ASPSCR1-TFE3-induced tumor #3

description:
mASPS3
processed data file: 10407R.txt


title: 30Deg_6hr_NNNN

description:
Set2
processed data: Set2_OneNuc_ColumnAllData_Fig6.csv

source_name: synthetic N24 oligo

value: TCTACCC

value: NNNNTGGAATTCTCGGGTGCCAAGG


title: Mouse ASPSCR1-TFE3-induced tumor #2

description:
mASPS2
processed data file: 10407R.txt


title: T-ALL-6


title: Mouse ASPSCR1-TFE3-induced tumor #1

description:
mASPS1
processed data file: 10407R.txt


title: 30Deg_1hr_fixedAdaptor

value: ACAAGCC

value: TGGAATTCTCGGGTGCCAAGG


title: 30Deg_6hr_fixedAdaptor

value: ATTCACC


title: 22Deg_6hr_fixedAdaptor

value: TGACTCC


title: 30Deg_20min_fixedAdaptor


title: 22Deg_1hr_fixedAdaptor

value: AGCTACC


title: H4 Senes ChIP Rep 3

city: Glasgow

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

description: ChiP-seq of H4 in replicative senescent IMR90 cells

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed using trim galore v0.3.0 with parameter --quality 20 and remaining default settings
Sequenced reads were mapped to hg19 whole genome using bowtie v2.1.0 with parameter -p 15 and remaining default settings
Multimapped reads were removed using samtools 0.1.16 and duplicate reads removed using picard tools v1.98 mark duplicates
Aligned reads normalised by library size, extended to 150bp and converted to bigWig format
USeq 8.6.0 was used to perform HIRA peak finding (normalised to input) with the following steps. BED files converted to Useq Point Format (Tag2Point). Satellite Repeat regions were removed from the dataset (FilterPointData). ScanSeqs used to identify enriched windows (-w 200 -p 150 -f). Enriched Regions Extracted (EnrichedRegionMaker) with 5% FDR and 2 fold change (-i 2,4 -s 13,1)
SICER v1.1 was used to perform histone peak finding (H3.3 was normalised to input, H4K16ac to H4) using redundancy threshold of 1, window size of 200bp, fragment size of 150bp, effective genome fraction of 0.75, gap size of 200bp and R of 0.01.
Differential binding sites for H4K16ac were identified using Diffbind v1.8.3 with the following steps. Reads were counted using an insert length of 150bp and scored using DBA_SCORE_READS_MINUS. Enriched regions were identified using the full library size, DBA_DESEQ method and remaining defaults.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.  peak files were generated with USeq and thresholded at 5% FDR and 2 fold change cutoffs

source_name: Fibroblasts

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 20% (v/v) FBS, 2 mM L-Glutamine, 50 U/ml Pen-Strep and incubated at 37°C in a humidified 5% CO2 and 3% O2 atmosphere. Every 4-5 days the cells were passaged to maintain 40%–90% confluence level until they stopped proliferating through Replicative senescence or oncogene induced senescence

extract_protocol:
Cross-linked cells were solubilized by ultrasound treatment (Bioruptor Diagenode) to generate DNA fragmentation in 150-300 bp range. Protein-DNA complexes were isolated using corresponding antibody pre-immobilized on Dynabeads (Invitrogen).
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®(E6240S). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated using Agencourt AMPure XP beads (Beckman Coulter) and PCR-amplified using Illumina primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were harvested by trypsinization and precipitated by centrifugation. Cells pellets were resuspended in 1% formaldehyde in DMEM and incubated for 5 more minutes. Cross-linking was quenched by adding 1/10 of volume of 1.25 M glycine (125mM final) and incubating for 5 min at room temperature. Media was aspirated and cells were rinsed twice with PBS, scraped into ice-cold PBS supplemented with protease inhibitors (Sigma, P8340) and collected by centrifugation (5 min at 200g, 4°C). Cell pellets were snap frozen in dry ice with ethanol and kept at -70°C before use. For HIRA ChIP IMR90 cells were grown to 80%–90% confluency in 15 cm plates. Three plates (about 20 million cells) were washed with phosphate buffered saline (PBS) and scraped into 6 ml of 10 mM Tris, 30 mM NaCl, 0.1% (v/v) NP40, 3 mM MgCl2 pH 7.5 supplemented with protease (Sigma, P8340) and phosphatase (Sigma, P5726) inhibitor cocktails. Following 10 min incubation on ice the suspension was centrifuged (3 min at 300 g, 4°C) to produce nuclear pellet. This pellet was resuspended in 1ml of benzonase buffer (50 mM Tris pH 7.5, 300 mM NaCl, 0.5% (v/v) NP40, 2.5 mM MgCl2) with protease and phosphatase inhibitors followed by addition of 125 U of benzonase (Sigma, E1014). The lysate was thoroughly mixed and incubated on ice for 30 min. Supernatant was recovered by centrifugation (5 min at 13000 g, 4°C), separated from the pellet and diluted with 1 ml of dilution/stop digestion buffer (50 mM Tris pH 7.5, 100 mM NaCl, 0.5% (v/v) NP40, 15 mM EDTA, protease and phosphatase inhibitors). The resulting lysate was used as chromatin preparation for ChIP.

tag: chip antibody

value: H4 (Millipore 05-858)

tag: cell state

value: senescent


title: H4 Senes ChIP Rep 1


title: Nrl-KO rep7

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

description:
tumour sample
T1X2BX1

data_processing:
MeDUSA
Genome_build: hg19
Supplementary_files_format_and_content: bed files with coordinates of enriched regions

source_name: Osteosarcoma

extract_protocol:
Xenografts extracted and washed in PBS; DNA extracted with Qiagen kit a sper manufacturer's instructions
MeDIP with Diagenode Auto-MeDIP kit; library constructed using NEB reagents

value: PDX

value: osteosarcoma


title: H4 Senes ChIP Rep 2


title: Nrl-KO rep5

description:
tumour sample
T1X2AX1


title: H4 ProlifChIP Rep 2

description: ChiP-seq of H4 in proliferating IMR90 cells

value: proliferating


title: H4 Prolif ChIP Rep 3


title: JBP1-Seq-2

city: Irvine

first: Xueguang

last: Sun

address: 17062 Murphy Ave

institute: zymo research corp

description: JBP1 library

data_processing:
library strategy: JBP1-seq
Using Bowtie 0.12.8 to do alignment against hg19 assembly with --best parameter.
Using MACS to do peak calling with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: BED format and WIG format

source_name: Brain tissue

extract_protocol:
gDNA from human male cerebellum was purified via phenol::chloroform extraction
JBP1-seq protocol published on Genomics 2014

tag: gender

value: male

value: cerebellum

tag: pulldown

value: pull-down of β-glu-5hmC using recombinant JBP1 (biotinylated and conjugated to magnetic beads via biotin-streptavidin interactions)


title: Nrl-KO rep4

description:
tumour sample
T1X2A


title: Nrl-KO rep6

description:
tumour sample
T1X2B


title: Nrl-KO rep3

description:
tumour sample
T1X1


title: H4K16ac Senes ChIP Rep 2

description: ChIP-seq of H4K16ac in replicative senescent IMR90 cells

value: H4K16ac (Abcam ab109463)


title: H4 Prolif ChIP Rep 1


title: H4K16ac Prolif ChIP Rep2

description: ChIP-seq of H4K16ac in proliferating IMR90 cells


title: H4K16ac Senes ChIP Rep 1

value: H4K16ac (Millipore 07-329)


title: H4K16ac Prolif ChIP Rep1


title: Nrl-KO rep1

description:
tumour sample
T2X1X1


title: Nrl-KO rep2

description:
tumour sample
T1P

value: Patient


title: HIRA OIS input DNA

description: corresponding input DNA


title: WT rep2

description:
tumour sample
T2X1


title: WT rep1

description:
tumour sample
T2P


title: 4Deg_18hr_fixedAdaptor

value: ATCTGCC


title: Human skeletal muscle control #2

description:
hMuscle2
processed data file: 10408R.txt

source_name: banked quadriceps sample

value: skeletal muscle

value: control


title: HIRA OIS ChIP

description: ChIP-seq of HIRA in oncogene induced senescent IMR90 cells

value: HIRA (approximately equimolar mixture of WC15, WC19, WC117, WC 119)


title: Human skeletal muscle control #3

description:
hMuscle3
processed data file: 10408R.txt


title: HIRA RS input DNA

description: corresponding input DNA


title: HIRA OIS Control ChIP

description: ChIP-seq of HIRA in OIS control IMR90 cells


title: Human alveolar soft part sarcoma #5

description:
hASPS5
processed data file: 10408R.txt

source_name: banked tumor sample

value: alveolar soft part sarcoma

value: tumor


title: Human skeletal muscle control #1

description:
hMuscle1
processed data file: 10408R.txt


title: HIRA RS ChIP

description: ChIP-seq of HIRA in replicative senescent IMR90 cells


title: JBP1-Seq-1

description: JBP1 library


title: HIRA Prolif input DNA

description: corresponding input DNA


title: Human alveolar soft part sarcoma #2

description:
hASPS2
processed data file: 10408R.txt


title: Human alveolar soft part sarcoma #1

description:
hASPS1
processed data file: 10408R.txt


title: Human alveolar soft part sarcoma #4

description:
hASPS4
processed data file: 10408R.txt


title: Human alveolar soft part sarcoma #3

description:
hASPS3
processed data file: 10408R.txt


title: HIRA Prolif ChIP

description: ChIP-seq of HIRA in proliferating IMR90 cells


title: H3.3 Senes ChIP

description: ChIP-seq of H3.3 in replicative senescent IMR90 cells

value: Anti-HA-H3.3 (Millipore 05904)


title: H3.3 Prolif Input DNA

description: corresponding input DNA


title: H3.3 Prolif ChIP

description: ChIP-seq of H3.3 in proliferating IMR90 cells


title: HIRA OIS Control input DNA

description: corresponding input DNA