title: C1-1771051-168-C02


title: C1-1771051-168-A02

status: Public on Jun 10 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

molecule: polyA RNA

organism: Mus musculus

source_name: corpus callosum

growth_protocol: Wild-type (CD1 or C57BL6) and transgenic mice (5Pdgfratm11(EGFP) Sor/J, Lhx6 Cre RFP and PDGFR-GFP) between post-natal day 21 and 31 of both sexes were used. In the PDGFRa-GFP knock-in mice, H2B-eGFP fusion gene is expressed under the promoter of the oligodendrocyte precursor marker PDGFRa. The Lhx6–Cre transgenic mouse is a BAC transgenic mouse that expresses Cre under transcriptional control of Lhx6. This mouse line was crossed with the Cre-reporter line where tandem-dimer red fluorescent protein (tdRFP) is ubiquitously expressed under the ROSA26 locus. In the BAC transgenic mouse 5HT3aEGFP, EGFP is expressed under control of the Htr3a promoter.

extract_protocol:
Selected CNS regions were dissected in 300µm thick vibratome sections and cut out with scalpel. Tissue was then dissociated into a single cell suspension (described in Zeisel & Munoz-Manchado, Science 2015 Mar 6;347(6226):1138). For the spinal cord, an extra gradient step was used after the strainer and final centrifugation step. The pellet was ressuspended in 2ml Neurobasal-A medium including supplements and transferred onto an Optiprep Density Gradient, which consisted of 3 phases (Bottom phase: 160µl Optiprep + 340µl Neurobasal-A; middle phase: 220µl Optiprep + 1780µl Neurobasal-A; top phase: 75µl Optiprep + 925µl Neurobasal-A). The gradient was then centrifuged at 300g for 10min at 8°C and cells were located between the bottom and the middle phase. Cell suspension in a concentration of 600-1000 cells/μL was used. C1 Suspension Reagent was added in a ratio of 4 μL to every 7 μL cell suspension. 11 μL of the cell suspension mix was loaded on a C1 Single-Cell AutoPrep IFC  microfluidic chip designed for 10- to 17-μm cells, and the chip was then processed on a Fluidigm C1 instrument using the 'mRNA Seq: Cell Load (1772x/1773x)' script (30 min at 4°C).
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: In the stress treatment mice, acute stress was induced injection of 4% PFA into the left paw.

tag: strain

value: PDGFRa-GFP

tag: age

tag: Sex

value: F

tag: treatment

value: No

tag: inferred cell type

value: OPC


title: C1-1771051-167-H07

value: PDGFRa-Cre


title: C1-1771051-167-G11


title: C1-1771051-167-H06


title: C1-1771051-167-D02


title: C1-1771051-167-C02


title: C1-1771051-167-B04


title: C1-1771051-167-G12


title: C1-1771051-167-A07


title: C1-1771051-167-B01


title: C1-1771051-167-E08


title: C1-1771051-167-F06


title: C1-1771051-167-E10


title: C1-1771051-167-E05


title: C1-1771051-168-E11


title: C1-1771051-167-E02


title: C1-1771051-167-D10


title: C1-1771051-165-G09


title: C1-1771051-167-D06


title: C1-1771051-167-A02


title: C1-1771051-167-D05


title: C1-1771051-167-B06


title: C1-1771051-167-D08


title: C1-1771051-167-A11


title: C1-1771051-167-A05


title: C1-1771051-165-H12


title: C1-1771051-165-G03


title: C1-1771051-165-H02


title: C1-1771051-165-H09


title: C1-1771051-165-G07


title: C1-1771051-167-B03


title: C1-1771051-167-D01


title: C1-1771051-165-F12


title: C1-1771051-165-G01


title: C1-1771051-165-E09


title: C1-1771051-165-F02


title: C1-1771051-165-F04


title: C1-1771051-167-A03


title: C1-1771051-165-E04


title: C1-1771051-165-F08


title: C1-1771051-165-F09


title: C1-1771051-165-E10


title: C1-1771051-165-E07


title: C1-1771051-165-E06


title: C1-1771051-165-D10


title: C1-1771051-165-D12


title: C1-1771051-165-D09


title: C1-1771051-165-E03


title: C1-1771051-165-D05


title: C1-1771051-165-D07

value: COP


title: C1-1771051-165-G04


title: C1-1771051-165-C07


title: C1-1771051-165-D04


title: C1-1771051-165-F05


title: C1-1771051-165-D02


title: C1-1771051-165-C10


title: C1-1771051-165-C03


title: C1-1771051-165-A02


title: C1-1771051-165-C05


title: C1-1771051-165-B03


title: C1-1771051-165-B09


title: C1-1771051-165-B07


title: C1-1771051-165-B01


title: C1-1771051-164-G04

source_name: cortex S1


title: C1-1771051-164-H02


title: C1-1771051-164-G11


title: C1-1771051-164-H07


title: C1-1771051-164-H06


title: C1-1771051-164-F11


title: C1-1771051-164-F09


title: C1-1771051-164-F10


title: C1-1771051-164-G01


title: C1-1771051-165-B02


title: C1-1771051-165-A04


title: C1-1771051-164-H03


title: C1-1771051-164-F08


title: C1-1771051-164-F07


title: C1-1771051-164-D08


title: C1-1771051-164-B03


title: C1-1771051-164-D01


title: C1-1771051-164-D03


title: C1-1771051-164-H01


title: C1-1771051-163-H12


title: C1-1771051-163-H08


title: C1-1771051-163-H04


title: C1-1771051-163-G09


title: C1-1771051-163-F06


title: C1-1771051-163-F10


title: C1-1771051-163-C11


title: C1-1771051-163-D02


title: C1-1771051-163-F02


title: C1-1771051-163-C07


title: C1-1771051-163-A04


title: C1-1771051-163-B06


title: C1-1771051-163-G06


title: C1-1771051-163-A06


title: C1-1771051-164-F03


title: C1-1771051-159-H07

value: M


title: C1-1771051-164-E02

value: PPR


title: C1-1771051-164-D06


title: C1-1771051-159-G10


title: C1-1771051-159-G12


title: C1-1771051-159-E05


title: C1-1771051-164-B01


title: C1-1771051-159-D10


title: C1-1771051-159-G03


title: C1-1771051-159-C02


title: C1-1771051-163-G02


title: C1-1771051-159-B05


title: C1-1771051-158-E04


title: C1-1771051-158-H08


title: C1-1771051-159-A09


title: C1-1771051-158-D10


title: C1-1771051-158-B01


title: C1-1771051-158-B09


title: C1-1771051-158-A09


title: C1-1771051-150-F02


title: C1-1771051-150-E11


title: C1-1771051-158-B10


title: C1-1771051-150-F09


title: C1-1771051-150-H08


title: C1-1771051-150-E07


title: C1-1771051-159-F08


title: C1-1771051-150-E02


title: C1-1771051-150-G12


title: C1-1771051-150-D12


title: C1-1771051-150-D04


title: C1-1771051-150-D03


title: C1-1771051-150-G11


title: C1-1771051-159-C06


title: C1-1771051-150-G01


title: C1-1771051-150-C06


title: C1-1771051-150-F07


title: C1-1771051-150-F03


title: C1-1771051-150-C08


title: C1-1771051-150-D09


title: C1-1771051-150-G09


title: C1-1771051-150-F08


title: C1-1771051-150-C07


title: C1-1771051-150-C10


title: C1-1771051-150-B08


title: C1-1771051-150-B11


title: C1-1771051-150-B07


title: C1-1771051-150-C05


title: C1-1771051-150-B03


title: C1-1771051-150-A09


title: C1-1771051-150-A07


title: C1-1771051-150-C04


title: C1-1771051-150-A04


title: C1-1771051-150-A01


title: C1-1771051-147-H10


title: C1-1771051-147-H04


title: C1-1771051-147-H09


title: C1-1771051-150-A02


title: C1-1771051-150-B05


title: C1-1771051-147-F12


title: C1-1771051-147-H03


title: C1-1771051-147-G03


title: C1-1771051-147-G06


title: C1-1771051-147-F06


title: C1-1771051-147-G05


title: C1-1771051-147-F03


title: C1-1771051-150-B06


title: C1-1771051-147-E08


title: C1-1771051-147-E11


title: C1-1771051-147-D10


title: C1-1771051-147-E04


title: C1-1771051-147-D12


title: C1-1771051-147-E05


title: C1-1771051-147-D08


title: C1-1771051-147-D05


title: C1-1771051-147-C10


title: C1-1771051-147-D02


title: C1-1771051-147-D03


title: C1-1771051-147-D01


title: C1-1771051-147-C04


title: C1-1771051-147-C03


title: C1-1771051-147-F07


title: C1-1771051-147-B10


title: C1-1771051-147-B07


title: C1-1771051-147-A09


title: C1-1771051-147-A10


title: C1-1771051-147-A08


title: C1-1771051-146-H08


title: C1-1771051-147-B04


title: C1-1771051-146-H06


title: C1-1771051-146-H11


title: C1-1771051-146-G11


title: C1-1771051-146-G07


title: C1-1771051-146-H05


title: C1-1771051-146-G02


title: C1-1771051-146-G12


title: C1-1771051-146-F08


title: C1-1771051-146-G04


title: C1-1771051-146-G03


title: C1-1771051-146-F09


title: C1-1771051-146-F06


title: C1-1771051-147-C01


title: C1-1771051-146-E11


title: C1-1771051-146-E06


title: C1-1771051-147-B02


title: C1-1771051-146-F07


title: C1-1771051-147-B05


title: C1-1771051-146-E02


title: C1-1771051-146-F03


title: C1-1771051-146-E10


title: C1-1771051-146-E05


title: C1-1771051-146-D02


title: C1-1771051-146-C12


title: C1-1771051-146-F05


title: C1-1771051-146-C04


title: C1-1771051-146-D12


title: C1-1771051-146-E03


title: C1-1771051-146-D10


title: C1-1771051-146-D09


title: C1-1771051-146-B11


title: C1-1771051-146-C09


title: C1-1771051-146-B05


title: C1-1771051-146-B12


title: C1-1771051-146-C01


title: C1-1771051-146-B10


title: C1-1771051-146-A08


title: C1-1771051-146-B02


title: C1-1771051-146-A12


title: C1-1771051-146-D05


title: C1-1771051-146-B08


title: C1-1771051-146-B09


title: C1-1771051-146-A09


title: C1-1771048-208-F03


title: C1-1771048-208-F05


title: C1-1771048-208-E05


title: C1-1771048-208-C10


title: C1-1771048-208-C05


title: C1-1771051-146-A05


title: C1-1771048-208-A12


title: C1-1771048-207-E05


title: C1-1771048-207-D01


title: C1-1771048-207-H01


title: C1-1771048-207-C09


title: H460 Control biological replicate 2

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

country: USA

institute: TULANE UNIVERSITY

data_processing:
Align RNA-Seq reads with STAR
Align unmapped reads from Step 1 with bowtie2
Sort sam files
Merge bam files
Use SAMMatev2.6.1 to generate read counts and wiggle (coverage) files
Perform differential expression testing using EBSeq (100 iterations)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files including ensembl gene ID, gene name, read counts

molecule: total RNA

organism: Homo sapiens

source_name: H460 cells

growth_protocol: Cells were cultured in DMEM plus 10% FBS

extract_protocol:
QIAGEN RNeasy mini Kit
Ribo-depletion: Ambion RiboMinus Eukaryote System v2
Library Preparation: Ion Total RNA-Seq Kit v2
Template Preparation: Ion PI Hi-Q Template OT2 200 Kit
Sequencing: Ion PI Hi-Q Sequencing 200 Kit

treatment_protocol: Transfected with control or NGFR siRNA

tag: cell type

value: non-small-cell lung cancer cell line

tag: cell line


title: C1-1771048-207-C06


title: H460 Control biological replicate 3


title: H460 Control biological replicate 1


title: H460 NGFR knockdown biological replicate 3


title: H460 NGFR knockdown biological replicate 2


title: H460 NGFR knockdown biological replicate 1


title: C1-1771048-207-B11


title: C1-1771048-207-B04


title: H1299 Control biological replicate 2

source_name: H1299 cells


title: H1299 Control biological replicate 3


title: H1299 Control biological replicate 1


title: C1-1771048-208-B05


title: H1299 NGFR knockdown 3 biological replicate 3


title: C1-1771048-207-B02


title: C1-1771048-207-A08


title: H1299 NGFR knockdown 3 biological replicate 1


title: C1-1771048-206-F10


title: C1-1771048-207-C02


title: C1-1771048-206-D11


title: C1-1771048-206-G12


title: C1-1771048-207-A11


title: C1-1771048-207-D05


title: C1-1771048-206-C03


title: C1-1771048-207-C03


title: C1-1771048-206-B11


title: C1-1771048-206-A08


title: C1-1771048-206-G01


title: HT29_RNAseq_48h_T0901317_Rep4

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 female using Tophat and Cufflinks
Sequence counts for each transcript were compiled across all experiments for each time point
Processed data files format and content: Gene transcript sequence counts for all genes across all experiments in each time point
Genome_build: hg19 female

growth_protocol: HT29 cells were grown under recommended growth conditions

extract_protocol:
ChIP-seq was performed as previously described (Reddy et al. Molecular Cell 2013). RNA-seq was performed as previously outlned (Gertz et al. 2012)
Illumina Single End for ChIP-seq, Illumina Paired End for RNA-seq

treatment_protocol: HT29 were treated with DMSO, GW3965 (10uM), T0901317 (10uM) or rosiglitazone (10uM)

value: colorectal adenocarcinoma

tag: agent

tag: time

tag: chip antibody


title: HT29_RNAseq_48h_Rosiglitazone_Rep4

value: Rosiglitazone


title: HT29_RNAseq_48h_Rosiglitazone_Rep2


title: HT29_RNAseq_48h_Rosiglitazone_Rep3


title: HT29_RNAseq_48h_Rosiglitazone_Rep1


title: HT29_RNAseq_48h_T0901317_Rep3


title: C1-1771048-206-A07


title: HT29_RNAseq_48h_T0901317_Rep2


title: C1-1771048-206-A01


title: C1-1771048-205-C09


title: H1299 NGFR knockdown 3 biological replicate 2


title: C1-1771048-205-E03


title: HT29_RNAseq_48h_T0901317_Rep1


title: C1-1771048-206-A06


title: C1-1771048-205-C02


title: HT29_RNAseq_48h_GW3965_Rep3


title: HT29_RNAseq_48h_DMSO_Rep2

value: DMSO


title: HT29_RNAseq_24h_Rosiglitazone_Rep4


title: HT29_RNAseq_24h_Rosiglitazone_Rep3


title: HT29_RNAseq_48h_GW3965_Rep4


title: HT29_RNAseq_24h_Rosiglitazone_Rep1


title: HT29_RNAseq_48h_DMSO_Rep3


title: HT29_RNAseq_48h_DMSO_Rep1


title: C1-1771017-152-E02

source_name: hippocampus CA1

value: pooled male and female


title: C1-1771017-151-C07


title: C1-1771017-152-B09


title: C1-1771017-151-G09


title: HT29_RNAseq_24h_T0901317_Rep4


title: C1-1771017-151-D10


title: C1-1771017-151-H06


title: HT29_RNAseq_24h_T0901317_Rep2


title: HT29_RNAseq_24h_T0901317_Rep3


title: HT29_RNAseq_24h_Rosiglitazone_Rep2


title: C1-1771017-151-A11


title: HT29_RNAseq_24h_GW3965_Rep4


title: HT29_RNAseq_24h_GW3965_Rep3


title: C1-1771017-151-F05


title: HT29_RNAseq_48h_GW3965_Rep2


title: C1-1771017-151-A09


title: HT29_RNAseq_48h_GW3965_Rep1


title: HT29_RNAseq_24h_GW3965_Rep2


title: HT29_RNAseq_24h_T0901317_Rep1


title: HT29_RNAseq_24h_GW3965_Rep1


title: HT29_RNAseq_24h_DMSO_Rep3


title: HT29_RNAseq_24h_DMSO_Rep4


title: C1-1771017-151-A04


title: HT29_RNAseq_24h_DMSO_Rep2


title: C1-1771017-037-G07


title: JunD_DMSO_Rep2

library_source: genomic

data_processing:
ChIP-seq and ChIP input control FASTQ files were aligned to hg19 female genome using Bowtie
Peak Calling was performed using MACS peak caller
Processed data files format and content: bed  (Chromosome number, start position, stop position)
Genome_build: hg19 female

molecule: genomic DNA

value: ctrl

value: anti-JunD (Santa Cruz, sc-74)


title: H3K36me3_48h_GW3965_Rep1

description: Peaks with this histone modification were not called since it is found in gene bodies and does not make a canonical "binding" site.

value: anti-H3K36me3 (Abcam, ab9050)


title: C1-1771017-037-A08


title: C1-1771017-037-F08


title: C1-1771017-151-A06


title: RNA_Pol2_48h_GW3965_Rep2

value: anti-RNA Pol2 (Abcam, ab5408)


title: RNA_Pol2_48h_GW3965_Rep1


title: H3K36me3_48h_GW3965_Rep2


title: RNA_Pol2_24h_GW3965_Rep1


title: C1-1771017-037-D11

value: PDGFRa-GFP


title: HT29_RNAseq_24h_DMSO_Rep1


title: JunD_DMSO_Input_ctrl

value: none (input)


title: JunD_DMSO_Rep1


title: H3K36me3_DMSO_Rep2


title: RNA_Pol2_DMSO_Rep2


title: RNA_Pol2_DMSO_Rep1


title: C1-1771017-036-B11

value: F

value: No


title: C1-1771017-037-C07


title: H3K36me3_DMSO_Rep1


title: RNA_Pol2_48h_Rosiglitazone_Rep1


title: RNA_Pol2_24h_Rosiglitazone_Rep2


title: C1-1771017-036-G01


title: RNA_Pol2_24h_Rosiglitazone_Rep1


title: C1-1771017-036-F06


title: miR-25 antagomir RNA seq sample 1

city: Reno

first: Binghai

last: Zhao

state: helongjiang

address: No.3 Tongxiang Street

department: physiology

country: China

institute: Mudanjiang Medical University

description: AAinh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 genome by Tophat2, assembled by cufflink
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflink and differential expression by cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text files include FPKM values for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from cells and tissues using TRIzol (Invitrogen, Shanghai, China) according to the manufacturer’s instructions.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext RNA Library Prep Kit for Illumina following manufacturer’s recommendations (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.   The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq 4000 PE Cluster Kit (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 4000 platform (Novogene, Beijing, China) and 150bp paired-end reads were generated

tag: tissue

value: kidney

value: 9 weeks

value: miR-25 antagomir


title: H3K27ac_and_Pol2_GW3965_Input_ctrl_Rep2


title: C1-1771017-036-C01


title: RNA_Pol2_24h_GW3965_Rep2


title: C1-1771017-034-D09

value: M


title: miR-25 antagomir RNA seq sample 3

description: AAinh


title: C1-1771017-036-B06


title: H3K27ac_and_Pol2_Rosiglitazone_Input_ctrl_Rep2


title: H3K27ac_and_Pol2_Rosiglitazone_Input_ctrl_Rep1


title: HT29_RNAseq_48h_DMSO_Rep4


title: RNA_Pol2_48h_Rosiglitazone_Rep2


title: C1-1771017-035-C06


title: H3K27ac_and_Pol2_GW3965_Input_ctrl_Rep1


title: C1-1771017-034-A10


title: C1-1771017-034-B07


title: wild type RNA seq sample 2

description: AAwt

value: control


title: miR-25 angomir RNA seq sample 2

description: AAover

value: miR-25 angomir


title: C1-1771017-033-H03

value: OPC


title: H3K27ac_and_Pol2_DMSO_Input_ctrl

value: colorectal adenocarcinoma

value: DMSO


title: H3K27ac_48h_Rosiglitazone_Rep2

value: Rosiglitazone

value: anti-H3K27ac (Abcam, ab4729)


title: wild type RNA seq sample 3

description: AAwt


title: C1-1771017-034-A08


title: miR-25 angomir RNA seq sample 3

description: AAover


title: H3K27ac_48h_Rosiglitazone_Rep1


title: miR-25 antagomir RNA seq sample 2

description: AAinh


title: H3K27ac_48h_GW3965_Rep1


title: miR-25 angomir RNA seq sample 1

description: AAover


title: C1-1771017-032-H07

value: pooled male and female

value: PPR


title: C1-1771017-033-B11

value: PDGFRa-GFP


title: H3K27ac_24h_Rosiglitazone_Rep2


title: H3K27ac_24h_GW3965_Rep1


title: H3K27ac_24h_Rosiglitazone_Rep1


title: C1-1771017-033-F01


title: wild type RNA seq sample 1

description: AAwt


title: C1-1771017-032-H05


title: wt_2_IP

city: Bangalore

first: Avantika

last: Lal

address: GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

data_processing:
Reads were trimmed for quality using Trimmomatic-0.32 with a cutoff quality score of 20
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected. Files were coverted to .bam format using samtools. The MACS 2.1.0 software was used to call peaks. Peaks overlapping in both replicates were selected for further analysis.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .narrowPeak files output by MACS, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial cells

growth_protocol: Cells were grown at 37°C, 200 rpm in M9 glucose, for 16 hours (stationary phase).

extract_protocol:
Cross-linked cells were harvested by centrifugation, washed thrice with ice-cold TBS (pH 7.5), resuspended in 1 ml lysis buffer [10 mM Tris (pH 8.0), 20% sucrose, 50 mM NaCl, 10 mM EDTA, 20 mg/ml lysozyme and 0.1 mg/ml RNase A] and incubated at 37°C for 30 min. After lysis, 3 ml immunoprecipitation (IP) buffer [50 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% sodium dodecyl sulphate (SDS) and PMSF (final 1 mM)] was added and the DNA sheared to an average size of ~250 bp using a Bioruptor (Diagenode). Insoluble cellular matter was removed by centrifugation for 10 min at 4°C. An 800 μl aliquot was incubated with 20 μl Protein A/G UltraLink Resin (Pierce) on a rotary shaker for 45 minutes at room temperature. The supernatant was removed and incubated with mouse monoclonal antibody (Neoclone cat. no. WP009) and 30 μl Protein A/G UltraLink Resin (pre-incubated with 1mg/ml BSA in TBS), on a rotary shaker at room temperature for 90 min. Samples were washed once with IP buffer, twice with IP buffer + 500 mM NaCl, once with wash buffer [10 mM Tris (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet P-40 and 0.5% sodium deoxycholate] and once with TE (pH 7.5). Immunoprecipitated complexes were eluted in 100 μl elution buffer [10 mM Tris (pH 7.5), 10 mM EDTA and 1% SDS] at 65°C for 20 min. Immunoprecipitated samples and the sheared DNA from the Bioruptor were uncrosslinked in elution buffer containing 0.8 mg/ml Pronase at 42°C for 2 h followed by 65°C for 6 h. DNA was purified using the phenol-chloroform method.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Formaldehyde was added to a final concentration of 1%. After incubation for 20 minutes, glycine was added to a final concentration of 0.5 M and incubated for 5 minutes.

tag: genotype

value: MG1655 wild-type

value: RpoS (Neoclone cat. no. WP009)


title: wt_2_input


title: wt_1_input


title: C1-1771017-033-F08

value: No


title: C1-1771017-032-G09


title: ssrS_1_IP

data_processing:
Reads were trimmed for quality using Trimmomatic-0.32 with a cutoff quality score of 20
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected.
Files were coverted to .bam format using samtools
The MACS2 software was used to call peaks.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .narrowPeak files output by macs2, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start

value: MG1655 del ssrS


title: C1-1771017-034-D02


title: H3K27ac_24h_GW3965_Rep2


title: C1-1771017-032-H08


title: H3K27ac_DMSO_Rep2

value: ctrl


title: H3K27ac_48h_GW3965_Rep2


title: wt_1_IP


title: C1-1771017-032-H04


title: H3K27ac_DMSO_Rep1


title: PPARG_48h_Rosiglitazone_Input_ctrl

value: none (input)


title: LXRA_2h_GW3965_Input_ctrl


title: wts149 d9 3b.RNAseq

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

country: France

institute: CRCM

description: wts d9 3b

data_processing:
cleaning (fastq-mcf)
mapping to D. melanogaster genome r 6.03 using TopHat2.0.11 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 6.03 from FlyBase
Genome_build: Drosophila melanogaster FB6
table of counts (From HT-seq)

organism: Drosophila melanogaster

source_name: wing imaginal disc

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

extract_protocol:
RNA was extracted using RNAeasy mini spin kit (Qiagen).
Quality control, library preparation and sequencing were performed by Genomic Technologies Facility at the Center for Integrative Genomics, University of Lausanne.

treatment_protocol: Wandering third instar larvae were collected and wing imaginal discs were isolated by dissection for each genotype on the day indicated (day 5 or 9). Dissection tools and surfaces were prepared with RNAseAway (Ambion.) Discs were dissected from larvae and transferred into RNAse-free 1xPBS on ice.

tag: developmental stage

value: third instar wandering larvae

tag: dissection

value: Hand dissection

value: ubxflp:FRT82B wts149 clones in Minute background

tag: time point


title: wts149 d9 1b.RNAseq

description: wts d9 1b


title: PPARG_2h_Rosiglitazone_Input_ctrl


title: wts149 d9 3a.RNAseq

description: wts d9 3a


title: C1-1771017-032-G06

value: OPC


title: C1-1771017-032-E07


title: C1-1771017-032-F02


title: wts149 d5 3b.RNAseq

description: wts d5 3b


title: C1-1771017-032-E11


title: C1-1771017-032-E03


title: C1-1771017-032-G05


title: wts149 d9 2a.RNAseq

description: wts d9 2a


title: ssrS_1_input

data_processing:
Reads were trimmed for quality using Trimmomatic-0.32 with a cutoff quality score of 20
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected.
Files were coverted to .bam format using samtools
The MACS 2.1.0 software was used to call peaks.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .narrowPeak files output by MACS, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start


title: LXRB_48h_GW3965_Input_ctrl

value: colorectal adenocarcinoma


title: wts149 d9 2b.RNAseq

description: wts d9 2b


title: wts149 d5 2b.RNAseq

description: wts d5 2b


title: wts149 d9 1a.RNAseq

description: wts d9 1a


title: C1-1771017-032-E02


title: C1-1771017-032-D11


title: PPARG_48h_Rosiglitazone_Rep2

value: anti-PPARG (Santa Cruz, sc-7273)


title: wts149 d5 3a.RNAseq

description: wts d5 3a


title: PPARG_2h_Rosiglitazone_Rep2

value: Rosiglitazone


title: wts149 d5 2a.RNAseq

description: wts d5 2a


title: LXRA_48h_GW3965_Input_ctrl


title: C1-1771017-032-D07


title: C1-1771017-032-D05


title: wts149 d5 1b.RNAseq

description: wts d5 1b


title: LXRA-FLAG_48h_GW3965_Rep2

value: anti-FLAG (Sigma, F1804)


title: C1-1771017-032-D04

value: pooled male and female


title: LXRA-FLAG_48h_GW3965_Rep1


title: LXRB_2h_GW3965_Input_ctrl


title: wts149 d5 1a.RNAseq

description: wts d5 1a


title: PPARG_48h_Rosiglitazone_Rep1


title: C1-1771017-032-D03

value: PPR


title: LXRA-FLAG_2h_GW3965_Rep2


title: C1-1771017-032-C02

value: PDGFRa-GFP


title: LXRA-FLAG_2h_GW3965_Rep1


title: 82B d5 2b.RNAseq

description: X82B d5.d6 2b

value: ubxflp:FRT82B clones in Minute background


title: 82B d5 3a.RNAseq

description: X82B d5.d6 3a


title: 82B d5 2a.RNAseq

description: X82B d5.d6 2a


title: C1-1771017-032-B10


title: C1-1771017-032-B08


title: 82B d5 1b.RNAseq

description: X82B d5.d6 1b


title: PPARG_2h_Rosiglitazone_Rep1


title: LXRB_48h_GW3965_Rep2

value: anti-NR1H2 (Active Motif, 61178)


title: LXRB_2h_GW3965_Rep1


title: LXRB_2h_GW3965_Rep2


title: 82B d5 1a.RNAseq

description: X82B d5.d6 1a


title: C1-1771017-032-B02

value: No


title: 392_pb

city: Detroit

first: Wen

last: Qu

state: MI

address: 275 E. Hancock Ave., Room  291.1

department: Pharmacology

institute: Wayne State University

description:
Sample 158; 12392
processed dat afile: tedatapb_qnorm.txt

data_processing:
Tophat2 (V2.0.8) was used to map reads against the known Drosophila Melanogaster (UCSC/dm3) transcriptome
The transcript assembly tool Cufflinks and differential expression tool Cuffdiff were utilized for gene discovery and comprehensive expression analysis of RNA-seq data
After the Cufflink pipeline, we assembled all the expression data and quantiled normalized to the overall average empirical distribution across all samples first, then across all genes.
Genome_build: dm3
Supplementary_files_format_and_content: column headers: gene list, row names: sample list

source_name: Pb-treated_fly head

growth_protocol: All the fly stocks were reared at 25° C in 35ml vial containing standard Drosophila 10 ml medium.

extract_protocol:
50 heads of adult male flies (5-10 days old) in each of the 79 strains were collected and TruSeq Cluster RNA sample prep kit from Illumina was used to prepare the samples.
1μg of RNA was used after RNA isolation. The High Sensitivity D1K ScreenTape on the Agilent TapeStation instrument and quantitative PCR on the QuantStudio 12K Flex were used to make sure the quality of library.
RNA expression analyses were performed with 50 cycle paired-end RNA-seq on the Hiseq2000™ instrument from Illumina.

treatment_protocol: To mimic lead-poisoning, medium was mixed with 250μM PbAc for lead-containing medium or 250 μM NaAc for control.

value: Drosophila Synthetic Population  (sub) A2

tag: fly/stock id

value: 5-10 days

tag: sample group

value: Pb-treated


title: C1-1771017-032-A09

tag: strain


title: 385_pb

description:
Sample 157; 12385
processed dat afile: tedatapb_qnorm.txt

tag: age


title: C1-1771017-032-A07

tag: Sex


title: 82B d5 3b.RNAseq

description: X82B d5.d6 3b

value: third instar wandering larvae


title: C1-1771017-032-C01

tag: treatment


title: 382_pb

description:
Sample 156; 12382
processed dat afile: tedatapb_qnorm.txt


title: MR49F_3G_MDV3100-JQ1

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

data_processing:
Quality trimmed V16D samples to 50bp length using seqtk version 1.0-r63-dirty
Tophat version 2.0.9 for alignment
Cufflinks version 2.1.1 for transcript assembly
Htseq-counts v0.5.4p3 for transcript-level counts assembly
Genome_build: hg19
Supplementary_files_format_and_content: fpkm files represent transcript-level FPKM expression values; count files represent gene-level read count values per sample

source_name: Prostate Cancer Cell Line

growth_protocol: MR49F were cultured in RPMI-1640 (Hyclone #SH30027.01) + 10% FBS without MDV3100 for 72 hours prior to plating. 200,000 MR49F cells per well were plated in triplicate in 6-well plates. Cells were grown for 24 hours to approximately 50% confluence in RPMI-1640 + 10% FBS without MDV3100 (a total of 96 hours without MDV3100). The media was then replaced with RPMI-1640 + 10% charcoal-stripped serum without MDV3100 and incubated for 72  hours

extract_protocol:
TriZol+CHCl3
Agilent SureSelect Stranded RNAseq

treatment_protocol: The media was then replaced with RPMI-1640 + 10% charcoal-stripped serum (CSM) + 10uM MDV3100 or 500nM JQ1 or 1nM DHT or 0.1% DMSO, 0.1% ethanol vehicle. Cells were harvested at 24 hours post-treatment for total RNA in Trizol


title: MR49F_3E_JQ1


title: MR49F_3F_DHT-JQ1


title: C1-1771017-031-H03

tag: inferred cell type


title: 377_pb

description:
Sample 155; 12377
processed dat afile: tedatapb_qnorm.txt


title: MR49F_3C_MDV3100


title: 369_pb

description:
Sample 154; 12369
processed dat afile: tedatapb_qnorm.txt


title: MR49F_3B_DHT


title: LXRB_48h_GW3965_Rep1

tag: cell type


title: 315_pb

description:
Sample 153; 12315
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-031-G02


title: C1-1771017-031-F08


title: MR49F_3A_Mock

tag: cell line


title: 313_pb

description:
Sample 152; 12313
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-031-F05


title: MR49F_2G_MDV3100-JQ1


title: MR49F_2F_DHT-JQ1


title: C1-1771017-031-E11


title: 312_pb

description:
Sample 151; 12312
processed dat afile: tedatapb_qnorm.txt


title: MR49F_2E_JQ1


title: 303_pb

description:
Sample 150; 12303
processed dat afile: tedatapb_qnorm.txt


title: 301_pb

description:
Sample 149; 12301
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-032-A06


title: C1-1771017-031-E05


title: MR49F_2C_MDV3100


title: C1-1771017-031-D10


title: C1-1771017-031-C07


title: 280_pb

description:
Sample 147; 12280
processed dat afile: tedatapb_qnorm.txt


title: MR49F_2B_DHT


title: MR49F_2A_Mock


title: 271_pb

description:
Sample 145; 12271
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-G04


title: C1-1771017-031-C05


title: MR49F_1G_MDV3100-JQ1


title: MR49F_1F_DHT-JQ1


title: C1-1771017-031-F06


title: C1-1771017-030-F12


title: 264_pb

description:
Sample 144; 12264
processed dat afile: tedatapb_qnorm.txt


title: 260_pb

description:
Sample 143; 12260
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-F11


title: 258_pb

description:
Sample 142; 12258
processed dat afile: tedatapb_qnorm.txt


title: MR49F_1C_MDV3100


title: MR49F_1B_DHT


title: C1-1771017-030-F09


title: 284_pb

description:
Sample 148; 12284
processed dat afile: tedatapb_qnorm.txt


title: MR49F_1A_Mock


title: C1-1771017-030-F02


title: C1-1771017-030-F01


title: V16D_VEH_3

growth_protocol: MR49F and V16D cells were cultured in RPMI-1640 (Hyclone #SH30027.01) + 10% FBS without MDV3100 for 72 hours prior to plating. 300,000 MR49F or V16D cells per well were plated in triplicate in 6-well plates. Cells were grown for 24 hours to approximately 50% confluence in RPMI-1640 + 10% FBS without MDV3100 (a total of 96 hours without MDV3100)

treatment_protocol: The media was then replaced with RPMI-1640 + 10% FBS with 10uM MDV3100 or 0.1% DMSO vehicle. Cells were harvested at 24 hours post-treatment for total RNA in Trizol

value: Vehicle


title: C1-1771017-030-E12


title: 272_pb

description:
Sample 146; 12272
processed dat afile: tedatapb_qnorm.txt


title: 236_pb

description:
Sample 139; 12236
processed dat afile: tedatapb_qnorm.txt


title: V16D_VEH_2


title: C1-1771017-030-E08


title: V16D_VEH_1


title: 203_pb

description:
Sample 138; 12203
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-E06


title: MR49F_1E_JQ1


title: 202_pb

description:
Sample 137; 12202
processed dat afile: tedatapb_qnorm.txt


title: V16D_MDV_3

value: Enzalutamide-Treated


title: 200_pb

description:
Sample 135; 12200
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-E01

value: OPC


title: V16D_MDV_2


title: V16D_MDV_1


title: 201_pb

description:
Sample 136; 12201
processed dat afile: tedatapb_qnorm.txt


title: 180_pb

description:
Sample 134; 12180
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-D06


title: C1-1771017-030-D11


title: 248_pb

description:
Sample 141; 12248
processed dat afile: tedatapb_qnorm.txt


title: 179_pb

description:
Sample 133; 12179
processed dat afile: tedatapb_qnorm.txt


title: 243_pb

description:
Sample 140; 12243
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-C09


title: MR49F_veh_2


title: MR49F_veh_3


title: MR49F_veh_1


title: C1-1771017-030-D02


title: 177_pb

description:
Sample 132; 12177
processed dat afile: tedatapb_qnorm.txt


title: MR49F_MDV_3


title: C1-1771017-030-B04


title: C1-1771017-030-B03


title: 157_pb

description:
Sample 130; 12157
processed dat afile: tedatapb_qnorm.txt


title: 159_pb

description:
Sample 131; 12159
processed dat afile: tedatapb_qnorm.txt


title: MR49F_MDV_2


title: C1-1771017-030-A12


title: 154_pb

description:
Sample 129; 12154
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-B02


title: MR49F_MDV_1


title: 149_pb

description:
Sample 128; 12149
processed dat afile: tedatapb_qnorm.txt


title: 145_pb

description:
Sample 127; 12145
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-A10


title: C1-1771017-030-A09


title: 142_pb

description:
Sample 125; 12142
processed dat afile: tedatapb_qnorm.txt


title: 143_pb

description:
Sample 126; 12143
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-029-H12

value: F


title: 135_pb

description:
Sample 124; 12135
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-030-A07


title: C1-1771017-029-H07


title: 127_pb

description:
Sample 121; 12127
processed dat afile: tedatapb_qnorm.txt


title: 123_pb

description:
Sample 120; 12123
processed dat afile: tedatapb_qnorm.txt


title: 120_pb

description:
Sample 119; 12120
processed dat afile: tedatapb_qnorm.txt


title: 131_pb

description:
Sample 122; 12131
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-029-F07


title: 115_pb

description:
Sample 117; 12115
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-029-G01


title: C1-1771017-029-F03


title: 117_pb

description:
Sample 118; 12117
processed dat afile: tedatapb_qnorm.txt


title: rpoS_LS_2

data_processing:
Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected and the number of reads mapping to each gene was computed using custom scripts.
These  counts were fed into the DESeq package in Bioconductor to estimate differential expression between the mutants and the wildtype.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Tab-delimited text file; genes in rows and samples in columns; each entry corresponds to the number of reads mapping to the given gene in the given sample.

growth_protocol: M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen), following the manufacturer's protocol. Total RNA was treated with DNAse I (Invitrogen, Cat No. 18068-015) according to the manufacturer's protocol. Further precipitation of RNA and ribosomal RNA cleanup was achieved by Ambion MICROBExpress bacterial mRNA purification Kit (cat. no. AM1905) according to the manufacturer's protocol. The RNA was finally suspended in 10 μL RNAse free water.
Libraries for Illumina HiSeq 1000 sequencing using the Truseq kit were prepared using protocols recommended by the manufacturer.

treatment_protocol: Overnight cultures in M9 glucose were inoculated into 100 mL fresh M9 glucose to a final OD600 of 0.02. The flasks were incubated at 37 °C with shaking at 200 rpm. Cells were collected by centrifugation at the early exponential (OD600 ~0.3), mid-exponential (OD600 ~0.8), transition to stationary (OD600 ~1.6), stationary (16 hrs, OD600 ~2), and late stationary (48 hrs, OD600 ~1.6) phases of growth.

value: del rpoS

tag: growth phase

value: Late Stationary


title: 113_pb

description:
Sample 116; 12113
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-029-E07


title: C1-1771017-029-E02


title: rpoS_LS_1


title: C1-1771017-030-A03


title: rsdssrS_LS_2

value: del rsd; del ssrS


title: C1-1771017-029-D10


title: C1-1771017-029-E01


title: C1-1771017-029-D09


title: 100_pb

description:
Sample 113; 12100
processed dat afile: tedatapb_qnorm.txt


title: 109_pb

description:
Sample 115; 12109
processed dat afile: tedatapb_qnorm.txt


title: 99_pb

description:
Sample 112; 12099
processed dat afile: tedatapb_qnorm.txt


title: rsdssrS_LS_1


title: C1-1771017-029-D05


title: ssrS_LS_2

value: del ssrS


title: C1-1771017-029-E10


title: ssrS_LS_1


title: rsd_LS_2

value: del rsd


title: 98_pb

description:
Sample 111; 12098
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-029-A07

value: PDGFRa-GFP


title: C1-1771017-029-A09


title: 134_pb

description:
Sample 123; 12134
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-028-H09


title: 88_pb

description:
Sample 108; 12088
processed dat afile: tedatapb_qnorm.txt


title: 96_pb

description:
Sample 110; 12096
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-028-G10


title: rsd_LS_1


title: 104_pb

description:
Sample 114; 12104
processed dat afile: tedatapb_qnorm.txt


title: 90_pb

description:
Sample 109; 12090
processed dat afile: tedatapb_qnorm.txt


title: 87_pb

description:
Sample 107; 12087
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-028-G05


title: wt_LS_2

value: Wild-type


title: 85_pb

description:
Sample 106; 12085
processed dat afile: tedatapb_qnorm.txt


title: rpoS_S_2

value: Stationary


title: C1-1771017-028-F08

value: No


title: rsdssrS_S_2


title: C1-1771017-028-E12

value: PPR


title: C1-1771017-028-G03


title: 79_pb

description:
Sample 103; 12079
processed dat afile: tedatapb_qnorm.txt

value: Drosophila Synthetic Population  (sub) A2

value: 5-10 days


title: C1-1771017-028-E08


title: wt_LS_1


title: 83_pb

description:
Sample 105; 12083
processed dat afile: tedatapb_qnorm.txt

value: Pb-treated


title: rsdssrS_S_1


title: 75_pb

description:
Sample 102; 12075
processed dat afile: tedatapb_qnorm.txt


title: ssrS_S_2


title: rpoS_S_1


title: 74_pb

description:
Sample 101; 12074
processed dat afile: tedatapb_qnorm.txt


title: C1-1771017-028-E01


title: C1-1771017-028-E03


title: 71_pb

description:
Sample 100; 12071
processed dat afile: tedatapb_qnorm.txt


title: ssrS_S_1


title: rsd_S_2


title: C1-1771017-028-D09


title: C1-1771017-028-D03


title: wt_S_2


title: 69_pb

description:
Sample 99; 12069
processed dat afile: tedatapb_qnorm.txt


title: 64_pb

description:
Sample 97; 12064
processed dat afile: tedatapb_qnorm.txt


title: 65_pb

description:
Sample 98; 12065
processed dat afile: tedatapb_qnorm.txt


title: 81_pb

description:
Sample 104; 12081
processed dat afile: tedatapb_qnorm.txt


title: 53_pb

description:
Sample 92; 12053
processed dat afile: tedatapb_qnorm.txt


title: ssrS_TS_2

value: Transition to Stationary


title: rsd_S_1


title: ssrS_TS_1


title: 41_pb

description:
Sample 90; 12041
processed dat afile: tedatapb_qnorm.txt


title: wt_S_1


title: 63_pb

description:
Sample 96; 12063
processed dat afile: tedatapb_qnorm.txt


title: rsd_TS_1


title: 37_pb

description:
Sample 88; 12037
processed dat afile: tedatapb_qnorm.txt


title: wt_TS_2


title: wt_TS_1


title: 31_pb

description:
Sample 85; 12031
processed dat afile: tedatapb_qnorm.txt


title: 36_pb

description:
Sample 87; 12036
processed dat afile: tedatapb_qnorm.txt


title: rpoS_TS_2


title: 34_pb

description:
Sample 86; 12034
processed dat afile: tedatapb_qnorm.txt


title: rpoS_TS_1


title: 62_pb

description:
Sample 95; 12062
processed dat afile: tedatapb_qnorm.txt


title: rsdssrS_TS_2


title: 61_pb

description:
Sample 94; 12061
processed dat afile: tedatapb_qnorm.txt


title: 60_pb

description:
Sample 93; 12060
processed dat afile: tedatapb_qnorm.txt


title: rsdssrS_TS_1


title: 49_pb

description:
Sample 91; 12049
processed dat afile: tedatapb_qnorm.txt


title: 17_pb

description:
Sample 82; 12017
processed dat afile: tedatapb_qnorm.txt


title: rsd_TS_2


title: rpoS_ME_2

value: Mid-Exponential


title: 392_ctrl

description:
Sample 79; 12392
processed dat afile: tedatacon_qnorm.txt

source_name: control_fly head

value: control


title: 385_ctrl

description:
Sample 78; 12385
processed dat afile: tedatacon_qnorm.txt


title: rsd_ME_1


title: 23_pb

description:
Sample 84; 12023
processed dat afile: tedatapb_qnorm.txt


title: wt_ME_2


title: 369_ctrl

description:
Sample 75; 12369
processed dat afile: tedatacon_qnorm.txt


title: rsdssrS_ME_2


title: wt_ME_1


title: 377_ctrl

description:
Sample 76; 12377
processed dat afile: tedatacon_qnorm.txt


title: 315_ctrl

description:
Sample 74; 12315
processed dat afile: tedatacon_qnorm.txt


title: 313_ctrl

description:
Sample 73; 12313
processed dat afile: tedatacon_qnorm.txt


title: 22_pb

description:
Sample 83; 12022
processed dat afile: tedatapb_qnorm.txt


title: 382_ctrl

description:
Sample 77; 12382
processed dat afile: tedatacon_qnorm.txt


title: rsdssrS_ME_1


title: rsdssrS_EE_1

value: Early Exponential


title: 38_pb

description:
Sample 89; 12038
processed dat afile: tedatapb_qnorm.txt


title: Co-culture replicate 3, 48 hours after heterotroph addition

city: Cambridge

first: Steven

last: Biller

state: MA

address: 15 Vassar St, MIT 48-424

department: Civil and Environmental Engineering

institute: MIT

data_processing:
Low quality sequence removed using quality_trim (CLCbio) using default parameters
Alignment of paired-end reads to references using the Burrows-Wheeler Aligner V0.7.12
Number of aligned read pairs mapping in the sense orientation to each ORF determined using Python scripts and the samtools package (0.1.19), method after: "Anders, S., Pyl, P. T., & Huber, W. (2014). HTSeq–A Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England)."
Genome_build: NCBI accessions CP000095 and JXRW01000000
Supplementary_files_format_and_content: tab-delimited text file with the number of reads mapping to each ORF for all timepoints and replicates, as well as associated annotation data

organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A

source_name: Bacterial culture

growth_protocol: Prochlorococcus cells were grown in natural seawater-based PRO99 media under constant light

extract_protocol:
Culture samples added to cold RNAlater at each timepoint, cells collected onto a 0.2µm filter, and total RNA extracted with the mirVana kit (Ambion)
Strand-specific RNAseq library construction starting with 100ng of total RNA using the dUTP second-strand approach; duplex-specific normalization was performed to reduce ribosomal RNA content in each sample

treatment_protocol: The heterotroph Alteromonas MIT1002 was added to one set of biological replicates, at a ~equal cellular abundance to Prochlorococcus. Equivalent amounts of media alone were added to the axenic controls.

value: NATL2A (P. marinus), MIT1002 (A. macleodii)

tag: timepoint

value: 48 hours after heterotroph addition


title: rsd_EE_2


title: 6_pb

description:
Sample 81; 12006
processed dat afile: tedatapb_qnorm.txt


title: ssrS_ME_1


title: 1_pb

description:
Sample 80; 12001
processed dat afile: tedatapb_qnorm.txt


title: Co-culture replicate 2, 24 hours after heterotroph addition

value: 24 hours after heterotroph addition


title: rpoS_ME_1

value: del rpoS


title: rsd_ME_2

value: del rsd


title: 280_ctrl

description:
Sample 68; 12280
processed dat afile: tedatacon_qnorm.txt


title: Co-culture replicate 3, 12 hours after heterotroph addition

value: 12 hours after heterotroph addition


title: rsd_EE_1


title: 271_ctrl

description:
Sample 66; 12271
processed dat afile: tedatacon_qnorm.txt


title: Sample_213

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences.
Paired-end fastq-files of two separate runs for each sample were aligned separately using TopHat v2.0.1.1.
BAM files from both alignments were merged using samtools to obtain a single BAM alignment file for each sample.
mRNA quantification was performed according to RefSeq Transcripts - 2014-07-30 using Partek® Genomics Suite® (PGS) software v6.6©.
Raw read counts were normalized by DESeq2 method.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes DESeq2 normalized expression values for each sample.

source_name: blood

growth_protocol: Cells were isolated from peripheral blood

extract_protocol:
Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit v2 was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+ T cells

tag: subpopulation


title: ssrS_ME_2

value: del ssrS


title: rsdssrS_EE_2

value: del rsd; del ssrS


title: rpoS_EE_2


title: Sample_210


title: rpoS_EE_1


title: Co-culture replicate 2, 6 hours after heterotroph addition

value: 6 hours after heterotroph addition


title: Co-culture replicate 1, 6 hours after heterotroph addition


title: Co-culture replicate 2, 12 hours after heterotroph addition


title: ssrS_EE_1


title: Co-culture replicate 1, 48 hours after heterotroph addition


title: Co-culture replicate 2, 48 hours after heterotroph addition


title: Co-culture replicate 3, 24 hours after heterotroph addition


title: 303_ctrl

description:
Sample 71; 12303
processed dat afile: tedatacon_qnorm.txt

value: Drosophila Synthetic Population  (sub) A2


title: ssrS_EE_2


title: 301_ctrl

description:
Sample 70; 12301
processed dat afile: tedatacon_qnorm.txt

value: 5-10 days


title: 312_ctrl

description:
Sample 72; 12312
processed dat afile: tedatacon_qnorm.txt


title: wt_EE_2

value: Wild-type


title: wt_EE_1


title: Co-culture replicate 2, 4 hours after heterotroph addition

value: 4 hours after heterotroph addition


title: Co-culture replicate 3, 4 hours after heterotroph addition


title: Co-culture replicate 1, 24 hours after heterotroph addition


title: 272_ctrl

description:
Sample 67; 12272
processed dat afile: tedatacon_qnorm.txt


title: 236_ctrl

description:
Sample 60; 12236
processed dat afile: tedatacon_qnorm.txt


title: 203_ctrl

description:
Sample 59; 12203
processed dat afile: tedatacon_qnorm.txt


title: Sample_202

value: Naive


title: 202_ctrl

description:
Sample 58; 12202
processed dat afile: tedatacon_qnorm.txt

value: control


title: Co-culture replicate 1, 4 hours after heterotroph addition


title: 264_ctrl

description:
Sample 65; 12264
processed dat afile: tedatacon_qnorm.txt


title: 201_ctrl

description:
Sample 57; 12201
processed dat afile: tedatacon_qnorm.txt


title: Sample_201


title: 260_ctrl

description:
Sample 64; 12260
processed dat afile: tedatacon_qnorm.txt


title: 284_ctrl

description:
Sample 69; 12284
processed dat afile: tedatacon_qnorm.txt


title: Co-culture replicate 3, 6 hours after heterotroph addition


title: 200_ctrl

description:
Sample 56; 12200
processed dat afile: tedatacon_qnorm.txt


title: 258_ctrl

description:
Sample 63; 12258
processed dat afile: tedatacon_qnorm.txt


title: Sample_205


title: Co-culture replicate 1, 12 hours after heterotroph addition


title: Sample_208


title: Sample_207


title: Sample_212


title: Sample_206


title: 243_ctrl

description:
Sample 61; 12243
processed dat afile: tedatacon_qnorm.txt


title: Sample_198


title: 179_ctrl

description:
Sample 54; 12179
processed dat afile: tedatacon_qnorm.txt


title: 180_ctrl

description:
Sample 55; 12180
processed dat afile: tedatacon_qnorm.txt


title: Sample_204


title: Co-culture replicate 3, 2 hours after heterotroph addition

value: 2 hours after heterotroph addition


title: 248_ctrl

description:
Sample 62; 12248
processed dat afile: tedatacon_qnorm.txt


title: Sample_199


title: 177_ctrl

description:
Sample 53; 12177
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 3, 48 hours after heterotroph addition

organism: Prochlorococcus marinus str. NATL2A


title: Axenic replicate 3, 24 hours after heterotroph addition


title: Axenic replicate 1, 48 hours after heterotroph addition


title: Axenic replicate 2, 48 hours after heterotroph addition


title: Co-culture replicate 2, 2 hours after heterotroph addition

value: NATL2A (P. marinus), MIT1002 (A. macleodii)


title: 157_ctrl

description:
Sample 51; 12157
processed dat afile: tedatacon_qnorm.txt


title: Sample_195


title: 154_ctrl

description:
Sample 50; 12154
processed dat afile: tedatacon_qnorm.txt


title: 159_ctrl

description:
Sample 52; 12159
processed dat afile: tedatacon_qnorm.txt


title: Sample_193


title: Axenic replicate 1, 24 hours after heterotroph addition


title: Sample_194


title: 149_ctrl

description:
Sample 49; 12149
processed dat afile: tedatacon_qnorm.txt


title: Sample_200


title: Axenic replicate 2, 12 hours after heterotroph addition


title: Axenic replicate 3, 12 hours after heterotroph addition


title: Axenic replicate 1, 12 hours after heterotroph addition


title: Axenic replicate 2, 6 hours after heterotroph addition


title: Axenic replicate 2, 24 hours after heterotroph addition


title: Co-culture replicate 1, 2 hours after heterotroph addition


title: 131_ctrl

description:
Sample 43; 12131
processed dat afile: tedatacon_qnorm.txt


title: 145_ctrl

description:
Sample 48; 12145
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 1, 4 hours after heterotroph addition


title: 143_ctrl

description:
Sample 47; 12143
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 3, 6 hours after heterotroph addition


title: 135_ctrl

description:
Sample 45; 12135
processed dat afile: tedatacon_qnorm.txt


title: 117_ctrl

description:
Sample 39; 12117
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 2, 2 hours after heterotroph addition


title: 134_ctrl

description:
Sample 44; 12134
processed dat afile: tedatacon_qnorm.txt


title: 142_ctrl

description:
Sample 46; 12142
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 3, 4 hours after heterotroph addition


title: Sample_196


title: 127_ctrl

description:
Sample 42; 12127
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 2, 4 hours after heterotroph addition


title: Axenic replicate 3, 12 hours before heterotroph addition

value: 12 hours before heterotroph addition


title: 109_ctrl

description:
Sample 36; 12109
processed dat afile: tedatacon_qnorm.txt


title: 104_ctrl

description:
Sample 35; 12104
processed dat afile: tedatacon_qnorm.txt


title: 120_ctrl

description:
Sample 40; 12120
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 1, 6 hours after heterotroph addition


title: Axenic replicate 3, 2 hours after heterotroph addition


title: fvb-8wk-miRNAseq-rep3

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

institute: Albert Einstein College of Medicine

data_processing:
Sequences ranging from 17 - 27 bases (the size of mature microRNAs) are aligned to genomic and RefSeq libraries using Bowtie.
Sequences that align to annotated regions of the genome are compared with known microRNAs in miRBase. A hit is defined as an aligned sequence that overlaps at least 50% with coordinates of a miRBase-defined microRNA.
Genome_build: mm9

source_name: fvb-mammary-gland

extract_protocol:
Mammary tissue was snap-frozen, later total RNA was extracted with miRNeasy (Qiagen).
Total RNA was used to create small RNA libraries using Illumina trueseq small RNA KIT Version 1.

value: FVB

tag: genotype/variation

tag: Stage

tag: time

tag: tissue

value: mammary gland


title: Axenic replicate 2, 12 hours before heterotroph addition


title: fvb-12wk-miRNAseq-rep3


title: Axenic replicate 1, 2 hours after heterotroph addition


title: Co-culture replicate 3, 12 hours before heterotroph addition


title: fvb-6wk-miRNAseq-rep3


title: 115_ctrl

description:
Sample 38; 12115
processed dat afile: tedatacon_qnorm.txt


title: pymt-10wk-miRNAseq-rep3

source_name: pymt-early-carcinoma-tumor

value: MMTV-PyMT

value: early carcinoma tumor


title: 123_ctrl

description:
Sample 41; 12123
processed dat afile: tedatacon_qnorm.txt


title: pymt-8wk-miRNAseq-rep3

source_name: pymt-adenoma/MIN-tumor

value: adenoma/MIN tumor


title: SiR-tai-L2

description:
day10
SiR-tai-L2_S13

data_processing:
cleaning (fastq-mcf)
mapping to D. melanogaster genome r_5.45 using TopHat2 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
Genome_build: Drosophila melanogaster dm3

source_name: leg imaginal disc

extract_protocol:
RNA was extracted using RNAeasy mini spin kit (Qiagen).
Quality control, library preparation and sequencing were performed by VIB Nucleomics Core Facility (Leuven, BE)

treatment_protocol: Wandering third instar larvae were collected and eye-antennal, leg, and wing imaginal discs were isolated by dissection for each genotype on the day indicated. Dissection tools and surfaces were prepared with RNA-Zap(Sigma). Discs were dissected from 35-50 larvae and transferred into RNAse-free 1xPBS on ice. In each genotype replicate 1 and replicate 2 represent independent dissections.

tag: developmental time point

value: third instar wandering larvae

value: Hand dissection

tag: genotype

value: UAS-scrib-RNAi, UAS-Ras[v12]/UAS-tai-TRiP[GL00514]-RNAi; hh-Gal4, UAS-GFP/+


title: 99_ctrl

description:
Sample 33; 12099
processed dat afile: tedatacon_qnorm.txt

value: Drosophila Synthetic Population  (sub) A2

tag: fly/stock id

tag: sample group


title: 98_ctrl

description:
Sample 32; 12098
processed dat afile: tedatacon_qnorm.txt

tag: strain

tag: age

value: 5-10 days


title: fvb-10wk-miRNAseq-rep3


title: pymt-6wk-miRNAseq-rep3

source_name: pymt-hyperplasia-mammary-gland

value: hyperplasia mammary gland


title: 113_ctrl

description:
Sample 37; 12113
processed dat afile: tedatacon_qnorm.txt


title: Axenic replicate 1, 12 hours before heterotroph addition


title: fvb-12wk-miRNAseq-rep2


title: SiR-tai-EA1

description:
day10
SiR-tai-EA1_S9

source_name: eye-antennal imaginal disc


title: 100_ctrl

description:
Sample 34; 12100
processed dat afile: tedatacon_qnorm.txt


title: 96_ctrl

description:
Sample 31; 12096
processed dat afile: tedatacon_qnorm.txt


title: SiR-tai-EA2

description:
day10
SiR-tai-EA2_S10


title: 87_ctrl

description:
Sample 28; 12087
processed dat afile: tedatacon_qnorm.txt


title: pymt-12wk-miRNAseq-rep2

source_name: pymt-late-caricnoma-tumor

value: late caricnoma tumor


title: 88_ctrl

description:
Sample 29; 12088
processed dat afile: tedatacon_qnorm.txt


title: fvb-8wk-miRNAseq-rep2


title: SiR-stat-L2

description:
day8
SiR-stat-L2_S4_R1_001

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-Stat92E-TRiP[HMS00035]-RNAi


title: Co-culture replicate 2, 12 hours before heterotroph addition


title: 85_ctrl

description:
Sample 27; 12085
processed dat afile: tedatacon_qnorm.txt

value: control


title: Co-culture replicate 1, 12 hours before heterotroph addition


title: pymt-10wk-miRNAseq-rep2


title: SiR-stat-L1

description:
day8
SiR-stat-L1_S3_R1_001


title: 83_ctrl

description:
Sample 26; 12083
processed dat afile: tedatacon_qnorm.txt


title: pymt-8wk-miRNAseq-rep2


title: 90_ctrl

description:
Sample 30; 12090
processed dat afile: tedatacon_qnorm.txt


title: fvb-6wk-miRNAseq-rep2


title: 81_ctrl

description:
Sample 25; 12081
processed dat afile: tedatacon_qnorm.txt


title: fvb-10wk-miRNAseq-rep2


title: 79_ctrl

description:
Sample 24; 12079
processed dat afile: tedatacon_qnorm.txt


title: fvb-12wk-miRNAseq-rep1


title: 74_ctrl

description:
Sample 22; 12074
processed dat afile: tedatacon_qnorm.txt


title: pymt-6wk-miRNAseq-rep2


title: SiR-sdi-EA2

description:
day8
SiR-sdi-EA2_S6

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-kay-TRiP[HMS00254]-RNAi


title: 75_ctrl

description:
Sample 23; 12075
processed dat afile: tedatacon_qnorm.txt


title: SiR-stat-EA2

description:
day8
SiR-stat-EA2_S5_R1_001


title: SiR-sdi-L1

description:
day8
SiR-sdi-L1_S7

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-sd-TRiP[JF02514]-RNAi


title: pymt-12wk-miRNAseq-rep1


title: SiR-kay-EA2

description:
day10
SiR-kay-EA2_S9_R1_001


title: 69_ctrl

description:
Sample 20; 12069
processed dat afile: tedatacon_qnorm.txt


title: SiR-sdi-EA1

description:
day7 & 8
SiR-sdi-EA1_S5


title: pymt-10wk-miRNAseq-rep1


title: SiR-6272-L2

description:
day8
SiR-6272-L2_S15_R1_001

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-CG6272-TRiP[HMS00057]-RNAi


title: 71_ctrl

description:
Sample 21; 12071
processed dat afile: tedatacon_qnorm.txt


title: fvb-10wk-miRNAseq-rep1

value: FVB


title: pymt-8wk-miRNAseq-rep1

value: mammary gland


title: SiR-6272-L1

description:
day8
SiR-6272-L1_S14_R1_001


title: fvb-8wk-miRNAseq-rep1


title: 65_ctrl

description:
Sample 19; 12065
processed dat afile: tedatacon_qnorm.txt


title: fvb-6wk-miRNAseq-rep1


title: 63_ctrl

description:
Sample 17; 12063
processed dat afile: tedatacon_qnorm.txt


title: SiR-sdi-L2

description:
day7 & 8
SiR-sdi-L2_S8


title: 64_ctrl

description:
Sample 18; 12064
processed dat afile: tedatacon_qnorm.txt


title: SiR-6272-EA2

description:
day8
SiR-6272-EA2_S17_R1_001


title: pymt-6wk-miRNAseq-rep1

value: MMTV-PyMT


title: 62_ctrl

description:
Sample 16; 12062
processed dat afile: tedatacon_qnorm.txt


title: hh-SiR-W2

description:
day11
hh-SiR-W2_S23

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-luci-RNAi


title: 61_ctrl

description:
Sample 15; 12061
processed dat afile: tedatacon_qnorm.txt


title: 49_ctrl

description:
Sample 12; 12049
processed dat afile: tedatacon_qnorm.txt


title: 53_ctrl

description:
Sample 13; 12053
processed dat afile: tedatacon_qnorm.txt


title: hh-SiR-EA2

description:
day11
hh-SiR-EA2_S2


title: hh-SiR-W1

description:
day9
hh-SiR-W1_S22


title: 60_ctrl

description:
Sample 14; 12060
processed dat afile: tedatacon_qnorm.txt


title: 38_ctrl

description:
Sample 10; 12038
processed dat afile: tedatacon_qnorm.txt


title: hh-SiR-EA1

description:
day9
hh-SiR-EA1_S24


title: hh-luci-W2

description:
day5
hh-luci-W2_S12

value: hh-Gal4, UAS-GFP/UAS-luc-RNAi


title: hh-luci-W1

description:
day5
hh-luci-W1_S1

value: third instar wandering larvae


title: 37_ctrl

description:
Sample 9; 12037
processed dat afile: tedatacon_qnorm.txt


title: hh-luci-L2

description:
day5
hh-luci-L2_S21

value: Hand dissection


title: hh-luci-L1

description:
day5
hh-luci-L1_S20


title: 34_ctrl

description:
Sample 7; 12034
processed dat afile: tedatacon_qnorm.txt


title: 31_ctrl

description:
Sample 6; 12031
processed dat afile: tedatacon_qnorm.txt


title: pymt-12wk-miRNAseq-rep3


title: 17_ctrl

description:
Sample 3; 12017
processed dat afile: tedatacon_qnorm.txt


title: 23_ctrl

description:
Sample 5; 12023
processed dat afile: tedatacon_qnorm.txt


title: SiR-6272-EA1

description:
day8
SiR-6272-EA1_S16_R1_001


title: hh-luci-EA1

description:
day5
hh-luci-EA1_S18


title: 22_ctrl

description:
Sample 4; 12022
processed dat afile: tedatacon_qnorm.txt


title: 41_ctrl

description:
Sample 11; 12041
processed dat afile: tedatacon_qnorm.txt


title: hh-SiR-L1

description:
day9
hh-SiR-L1_S3


title: SRL_EA_RNA-seq

data_processing:
cleaning (fastX-clipper -M15)
orphan reads were removed
mapping to D. melanogaster genome using TopHat2.3 (default parameters + -r200 option)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: RNAseq samples: tophat2 alignments in bigwig format and ht-seq gene counts on Drosphila FB5.45 annotation

extract_protocol:
RNA was extracted using RNAeasy mini spin kit (Qiagen).
Quality control, library preparation and sequencing were performed by MD Anderson Sequencing and Microarray facility

treatment_protocol: 50-60 wandering third instar larvae were collected and eye-antennal imaginal discs were isolated by dissection for each genotype (due to developmental delays, for different genotypes wandering stage was reached at different time points). Dissection tools and surfaces were prepared with RNAseAway (Ambion.) Discs were dissected from larvae and transferred into RNAse-free 1xPBS on ice.

tag: developmental stage

value: third instar wandering larvae (11 days AEL)

value: y,w,eyflp;act>y+>Gal4, UAS-GFP/UAS-Ras[V12]; FRT82 e, tub-GAL80/FRT82  e scrib[2


title: SRB_EA_RNA-seq

value: third instar wandering larvae (6 days AEL)

value: y,w,eyflp/UAS-BSK[DN];act>y+>Gal4, UAS-GFP/UAS-Ras[V12]; FRT82 e, tub-GAL80/FRT82  e scrib[2


title: SB_EA_RNA-seq

value: y,w,eyflp/w, UAS-Bsk[DN];act>y+>Gal4, UAS-GFP/+; FRT82 e, tub-GAL80/FRT82  e scrib[2


title: Scrib-_wing_RNA-seq

value: w/+;;FRT82 e scrib[2]/scrib[1]


title: SRE_EA_RNA-seq

value: third instar wandering larvae (7 days AEL)


title: BskDN_EA_RNA-seq

value: y,w,eyflp/w, UAS-Bsk[DN];act>y+>Gal4, UAS-GFP/+; FRT82 e, tub-GAL80/FRT82


title: Nucleosomes_rep1

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

description:
mononucleosomal-DNA
Replica1 of mononucleosomal-DNA

data_processing:
SNS: Sequenced reads were aligned to LmjF.6.0 whole genome using bowtie v1.0.0 with parameters  -v 3 -m 5 -k 1 --best
SNS: Paired-reads were convert into single-reads and duplicates were removed with bedTools v2.7.0
SNS: Peaks were called applying MACS2 v2.1.0.20140616 with parameters callpeak -nomodel -extsize 150
SNS: Peak summits were extended 400bp (in F4 peaks) or 600bp (in F5 peaks) to both sides with custom shell scripts
MN: Sequenced reads were aligned to LmjF.6.0 whole genome using RUbioSeq (Rubio-Camarillo et al., 2013) which applies BWA and then Samtools v0.1.19 to convert the output to BAM file
MN: Aligned reads were filtered to delete those incoherent pairs (with large distance between them, aligned in diferent chromosomes, etc) and converted to a NUCwave input format. These steps were performed with custom Perl and Shell scripts
MN: Nucleosome ocuppancy profiles were generated applying NUCwave (Quintales et al., 2015) and converting the resulting WIG file to bigWig
Genome_build: LmjF.6.0
Supplementary_files_format_and_content: bigWig files with density of each sample; bed files with SNS called peaks (ORIs) and nucleosomes defined by both paired reads (MNnucleosomes)

organism: Leishmania major strain Friedlin

source_name: Culture

growth_protocol: Promastigote cells were grown in M199 medium by standard conditions

extract_protocol:
Nuclei were digested with MNase yielding a 80:20 mono:dinucleosomes ratio. Mononucleosomal-DNA was excised from 2,5% agarose gels and purified with Wizard® SV Gel and PCR Clean-Up System
Each protocol is detailed in the SAMPLES section
DNA libraries were prepared for sequencing using Illumina standard protocols

treatment_protocol: Nuclei were released by careful lysis followed by sucrose cushion purification

value: Promastigote

value: exponential phase


title: Nucleosomes_rep2


title: 36_ctrl

description:
Sample 8; 12036
processed dat afile: tedatacon_qnorm.txt

value: Drosophila Synthetic Population  (sub) A2

value: 5-10 days

value: control


title: control_EA_RNA-seq

value: third instar wandering larvae (5 days AEL)

value: y,w,eyflp;act>y+>Gal4, UAS-GFP/+; FRT82 e, tub-GAL80/FRT82


title: SNS_F5

description:
short DNA replication intermediates
Replica of SNS corresponding to the fraction F5

data_processing:
Library strategy: SNS-Seq
SNS: Sequenced reads were aligned to LmjF.6.0 whole genome using bowtie v1.0.0 with parameters  -v 3 -m 5 -k 1 --best
SNS: Paired-reads were convert into single-reads and duplicates were removed with bedTools v2.7.0
SNS: Peaks were called applying MACS2 v2.1.0.20140616 with parameters callpeak -nomodel -extsize 150
SNS: Peak summits were extended 400bp (in F4 peaks) or 600bp (in F5 peaks) to both sides with custom shell scripts
MN: Sequenced reads were aligned to LmjF.6.0 whole genome using RUbioSeq (Rubio-Camarillo et al., 2013) which applies BWA and then Samtools v0.1.19 to convert the output to BAM file
MN: Aligned reads were filtered to delete those incoherent pairs (with large distance between them, aligned in diferent chromosomes, etc) and converted to a NUCwave input format. These steps were performed with custom Perl and Shell scripts
MN: Nucleosome ocuppancy profiles were generated applying NUCwave (Quintales et al., 2015) and converting the resulting WIG file to bigWig
Genome_build: LmjF.6.0
Supplementary_files_format_and_content: bigWig files with density of each sample; bed files with SNS called peaks (ORIs) and nucleosomes defined by both paired reads (MNnucleosomes)

extract_protocol:
Nuclei were lysed and DNA was purified by phenol/cloroform extraction. DNA was denaturated (boiling) and size fractionated through a sucrose gradient centrifugation and fractions containing the sizes of interest (F4 and F5) were digested three times with lambda-exonucleasa. Finally, ssDNA was converted into dsDNA prior library preparation
Each protocol is detailed in the SAMPLES section
DNA libraries were prepared for sequencing using Illumina standard protocols


title: RasV12_EA_RNA-seq

value: y,w,eyflp;act>y+>Gal4, UAS-GFP/UAS-Ras[V12]; FRT82 e, tub-GAL80/FRT82


title: SNS_F4

description:
short DNA replication intermediates
Replica of SNS corresponding to the fraction F4


title: genomicDNA_Ctrl

description:
genomic DNA
Genomic DNA from a late culture phase used as a control during SNS peak calling

extract_protocol:
Nuclei were lysed and DNA was purified by phenol/cloroform extractions and ethanol precipitation
Each protocol is detailed in the SAMPLES section
DNA libraries were prepared for sequencing using Illumina standard protocols

value: stationary phase


title: Pdx1LaxZ/+;Oc1+/-_panc_RNASeq_e15.5_3

status: Public on Jun 09 2016

city: Philadelphia

first: Diana

middle: Elena

last: Stanescu

state: PA

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

description: Pdx1-Oc1 double heterozygous embryos

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome to obtain transcript quantitation.
Raw read counts were used for differential expression analysis using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: xls file with fold changes and false discovery rate <0.10
Supplementary_files_format_and_content: xls file with raw read counts

source_name: mouse pancreatic progenitos

extract_protocol:
Embryos at e15.5 were dissected in cold PBS, the pancreas was isolated and placed in Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols, TruSeq® RNA sample preparation kit V2 (Illumina, CA), according to the manufacturers protocol

value: Mouse pancreata

value: embryonic day e15.5

value: mixed background


title: Pdx1LaxZ/+;Oc1+/-_panc_RNASeq_e15.5_4

description: Pdx1-Oc1 double heterozygous embryos


title: Pdx1LaxZ/+;Oc1+/-_panc_RNASeq_e15.5_2

description: Pdx1-Oc1 double heterozygous embryos


title: 6_ctrl

description:
Sample 2; 12006
processed dat afile: tedatacon_qnorm.txt


title: Pdx1LaxZ/+;Oc1+/-_panc_RNASeq_e15.5_1

description: Pdx1-Oc1 double heterozygous embryos


title: Oc1+/-_panc_RNASeq_e15.5_2

description: Oc1 heterozygous embryos


title: Oc1+/-_panc_RNASeq_e15.5_1

description: Oc1 heterozygous embryos


title: 1_ctrl

description:
Sample 1; 12001
processed dat afile: tedatacon_qnorm.txt


title: Pdx1LacZ/+_panc_RNAseq_e15/5_3

description: Pdx1 heterozygous embryos


title: Oc1+/-_panc_RNASeq_e15.5_3

description: Oc1 heterozygous embryos


title: Pdx1LacZ/+_panc_RNAseq_e15/5_2

description: Pdx1 heterozygous embryos


title: Control_panc_RNASeq_e15.5_3

description: control


title: Pdx1LacZ/+_panc_RNAseq_e15/5_1

description: Pdx1 heterozygous embryos


title: Control_panc_RNASeq_e15.5_4

description: control


title: Control_panc_RNASeq_e15.5_2

description: control


title: Control_panc_RNASeq_e15.5_1

description: control


title: hh-SiR-L2

description:
day11
hh-SiR-L2_S4

value: third instar wandering larvae

value: Hand dissection

value: UAS-scrib-RNAi, UAS-Ras[v12]/+; hh-Gal4, UAS-GFP/ UAS-luci-RNAi


title: Pdx1LaxZ/+;Oc1+/-_panc_RNASeq_e15.5_5

description: Pdx1-Oc1 double heterozygous embryos


title: Hoxa9_Meis1-control1

city: New York

first: Noushin

last: Farnoud

state: NY

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Institite

data_processing:
Raw RNASeq reads (.fastq) files were aligned to mouse assembly mm10 using STAR
The number of uniquely mapped reads overlapping with each RefSeq transcript was counted with featureCounts
We used DESeq to evaluate the differences in expression upon loss of Jmjd1c in Hoxa9/Meis1 leukemia
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with normalized read counts per gene for all samples

source_name: Mouse bone marrow cells

growth_protocol: Cells were maintained in RPMI-1640 with 10% FBS and 1% penicillin/streptomycin supplemented with 10ng/ml IL3

extract_protocol:
Trizol
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

value: bone marrow cells


title: Hoxa9_Meis1-control2


title: LSK Jmjd1c2

data_processing:
raw RNASeq reads (.fastq) files were pre-processed using trimgalore version 0.2.8 (with default parameters)
The high-quality reads were aligned to mouse assembly mm10 using STAR version  v2.3.0.e0
The number of reads per gene was calculated using Htseq version 0.6.1p1 using the "union" mode to handle reads that overlap more than one gene.
Differential expression analysis was performed using DESeq version 1.18.0.
The DESeq output was filtered for significant genes based on the following threshold: false dicovery rate (FDR) <10%
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw read counts per gene for all samples

extract_protocol:
Trizol
Libraries were prepared by first using SMARTer® Ultra™ Low RNA Kit according to manufacture's instruction followed by  Illumina® Paired-End Sample Preparation Kit  according to Illumina's instructions accompanying the Kit.


title: LSK Jmjd1c1


title: Hoxa9_Meis1-Jmjd1c3


title: LSK Jmjd1c3


title: Hoxa9_Meis1-control3


title: LSK control2


title: LSK control3


title: ChIP-Seq MLL_AF9-Jmjd1c2

data_processing:
Sequence reads were aligned to genome assembly mm9 using Bowtie2 with default parameters.
Wiggle (wig) files were generated using a custom pipeline.
.tdf files created with the toTDF command of the igvtools package
Genome_build: mm9
Supplementary_files_format_and_content: wig

extract_protocol:
ChIP using H3K9me2 Abcam antibody ab1220 Lot# GR138716-1
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit.

tag: sample type

value: Jmjd1c f/f MLL-AF9-GFP CRE

tag: chip antibody


title: ChIP-Seq MLL_AF9-Jmjd1c3

tag: cell type


title: LSK control1


title: ChIP-Seq MLL_AF9-control1

value: Jmjd1c primary leukemia cells


title: ChIP-Seq MLL_AF9-control3

value: Jmjd1c f/f MLL-AF9-GFP MIT


title: RNA-Seq MLL_AF9-Jmjd1c4

data_processing:
raw RNASeq reads (.fastq) files were pre-processed using trimgalore (with default parameters)
The high-quality reads were aligned to mouse assembly mm9 using TopHat
The number of reads per gene was calculated using Htseq using the "union" mode to handle reads that overlap more than one gene.
Differential expression analysis was performed using EdgeR version 3.8.5
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with raw read counts per gene for all samples


title: ChIP-Seq MLL_AF9-control2


title: ChIP-Seq MLL_AF9-Jmjd1c1

value: Jmjd1c -/-MLL-AF9-GFP SSC


title: RNA-Seq MLL_AF9-Jmjd1c3


title: RNA-Seq MLL_AF9_Jmjd1c1


title: Pdx1LacZ/+_panc_RNAseq_e15/5_4

description: Pdx1 heterozygous embryos


title: Hoxa9_Meis1-Jmjd1c1


title: RNA-Seq MLL_AF9_cntrl3


title: RNA-Seq MLL_AF9_cntrl2


title: LSK control4


title: RNA-Seq MLL_AF9_cntrl4


title: Hoxa9_Meis1-Jmjd1c2


title: RNA-Seq MLL_AF9_cntrl1


title: click-ChIP-seq_MEF_2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Streptavidin purified DNA from PARP-1 8-Bu(3-yne)T-ADP-ribosylated chromatin in nuclei

data_processing:
The ChIP-seq reads were aligned to the mm9 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to  “bed” files for all analyses
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: MEF, click-ChIP-seq

growth_protocol: PARP-1 knockout MEFs expressing analog-senstive PARP-1 were cultured in DMEM supplemented with 10% fetal bovine serum, penicillin, and streptomycin containing 1 µg/mL puromycin

extract_protocol:
PARP-1 ChIP-seq:  Following mock ADP-ribosylation in intact nuclei from MEFs, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.  Click-ChIP-seq:  Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads.  Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C.  DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation
After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: MEFs were harvested in cold PBS and collected by centrifugation.  The cells were swollen in Nuclei Isolation Buffer (10 mM HEPES, pH 8.0, 2 mM MgCl2, 3 mM CaCl2, 300 mM sucrose, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) and the nuclei were released by the addition of 0.65% NP-40 with moderate vortexing.  Following collection by centrifugation, the nuclei were resuspended in PARP Reaction Buffer (30 mM Tris•HCl, pH 7.5, 10 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 0.01% NP-40, 0.05 mM EDTA, 20% glycerol, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) containing 250 μM 8-Bu(3-yne)T-NAD+ for 30 minutes at 25°C with occasional gentle mixing to allow ADP-ribosylation to occur in the isolated nuclei.

value: mouse embryonic fibroblasts


title: RA_hip_4

city: La Jolla

first: Gary

middle: S

last: Firestein

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Data was demultiplexed using Illlumina’s CASAVA software
Raw read quality was evaluated using FastQC.
Adapter and low quality bases below a quality score of 15 were trimmed from raw RNA-seq reads using Cutadapt.After trimming, reads with less than 30bp were further discarded.
The remaining reads were aligned to human reference genome hg19 using STAR (2.3.0) and assembled and quantified by HTSeq (0.5.4p5).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include log2(count) values for each Sample.

source_name: RA_hip_fibroblast-like synoviocytes

extract_protocol:
Total RNA was extracted and the quality of all samples was evaluated using an Agilent Bioanalyzer. The samples had an average RNA Integrity Number (RIN) of 9.4 with a minimum of 7.5. Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina with an input of 400 ng RNA.
Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cell.

tag: subject status

value: rheumatoid arthritis (RA) patient

value: hip

value: Fibroblast-like synoviocytes


title: RA_hip_3


title: ChIP-seq_Input_MEF_1

description: ChIP Input DNA from MEF cells

source_name: MEF, Input


title: BJAB-LANA

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

data_processing:
The libraries were run on Illumina Hi-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Genomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome database sequence to calculate the RPKM values of cellular gene using CLC Workbench
Relative abundance of the viral genes in LANA expressing cells were determined in refrence to the control cells
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence
Supplementary_files_format_and_content: csv files with abundance measurements

source_name: BJAB-expressing KSHV LANA

growth_protocol: BJAB cells were grown in RPMI medium with 10% FBS

extract_protocol:
Total RNA was extracted from BJAB expressing LANA-GFP or GFP
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Cells were transduced with lentiviral vector expressing LANA GFP or GFP vector and selected with puromycin for pure population of cells

tag: cell line

value: BJAB

value: Burkitt lymphoma cell line


title: BJAB-control

source_name: BJAB-control cells


title: PARP-1_ChIP-seq_MEF_2

description: ChIP-enriched DNA from MEF cells

source_name: MEF, PARP-1


title: ChIP-seq_Input_MEF_2

description: ChIP Input DNA from MEF cells


title: click-ChIP-seq_MEF_1


title: RNA-Seq MLL_AF9_Jmjd1c2


title: click-ChIP-seq_Input_MEF_2

description: click-ChIP-seq Input DNA from Sonicated Nuclei


title: click-ChIP-seq_Input_MEF_1


title: RA_hip_1


title: RA_hip_2


title: RA_knee_1

source_name: RA_knee_fibroblast-like synoviocytes

value: knee


title: RA_knee_4


title: RA_knee_2


title: RA_knee_3


title: RA_knee_5


title: DOX WiNTRLINC1 KD replicate 2

city: Vari

first: Pantelis

last: Hatzis

state: Attiki

address: 34 Fleming Str

department: Molecular Biology and Genetics

country: Greece

institute: Biomedical Sciences Research Center 'Alexander Fleming'

description: Colon epithelial adherent cells

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence using cutadapt software and mapped to hg19 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html).
Tags overlapping the Ensembl GRCh37 human exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene.

source_name: DOX WiNTRLINC1 KD

growth_protocol: Cells were grown for three days at 37 C, 5% CO2 in DMEM standard growth medium, 10% FBS reaching a maximum confluency of 50 % before harvesting

extract_protocol:
Trizol
For RNA-Seq experiments, the isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.

treatment_protocol: KD treated samples were grown for three days in conditions described above in the presence of doxycycline (final concentration of 1ug/ml). Control cells were grown as KD cells without doxycycline addition.

tag: tissue source

value: Duke's type B adenocarcinoma of the colon

value: Derivatives of Ls174 colon cancer cells

value: inducible shRNAs against the ASCL2

tag: treated with

value: 1ug/ml doxycycline


title: CON WiNTRLINC1 WT replicate 2

description: Colon epithelial adherent cells

source_name: CON WiNTRLINC1 WT

tag: genotype/variation


title: input H1299 cells knock down for Mdm2

city: Montpellier

first: Laetitia

middle: Karine

last: Linares

address: 208 rue des apothicaires

institute: INSERM

data_processing:
Basecalls performed using Illumina hiseq2000
Alignment performed using Map with Bowtie for Illumina (version 1.1.2)
ChIP-seq reads were aligned to the human genome hg19
peaks were called using MACS (version 1.0.1)
Genome_build: hg19
Supplementary_files_format_and_content: bed and wig files were generated using MACS (verseion1,0,1)

growth_protocol: H1299 cells are grown at 37°C in Dulbecco’s modified medium supplemented with 10% Fetal Bovine Serum, glutamax, pyruvate and 4.5g/l D-glucose under 5% CO2, 100% saturated H2O incubator.

extract_protocol: Input and immunoprecipitated DNA were purified and prepared for Illumina sequencing following their standard protocol

treatment_protocol: Cells are transfected by lipofectamine Reagent with PCDNA empty vector or PcDNA-Mdm2 Delta AD. Or cells are infected with retrovirus expressing shMdm2 or sh scramble. Cells are trypsinized, counted and crosslinked with 1% formaldehyde/1% paraformaldehyde for 5 minutes. Nuclei were then isolated and lyzed. Chromatin was sheared by sonication to fragments below 500 nucleotides. Sonicated chromatins were immunoprecipitated with Mdm2 antibody (N20, santa cruz)

value: Input

value: lung carcinoma


title: PARP-1_ChIP-seq_MEF_1

description: ChIP-enriched DNA from MEF cells


title: input H1299 cells overexpressing Mdm2 Delta AD


title: ChIP Mdm2 In H1299 cells knock down for Mdm2

value: Mdm2 ChIP

value: anti-Mdm2 N20 (Santa Cruz, catalog# sc-813, lot# JO412)


title: ChIP Mdm2 In H1299 cells overexpressing Mdm2 Delta AD


title: DOX WiNTRLINC1 KD replicate 1

description: Colon epithelial adherent cells


title: CON WiNTRLINC1 WT replicate 1

description: Colon epithelial adherent cells


title: DOX ASCL2 KD replicate 1

description: Colon epithelial adherent cells

source_name: DOX ASCL2 KD

value: inducible shRNAs against the WNTRLINC1


title: DOX ASCL2 KD replicate 2

description: Colon epithelial adherent cells


title: CON ASCL2 WT replicate 2

description: Colon epithelial adherent cells

source_name: CON ASCL2 WT


title: CON ASCL2 WT replicate 1

description: Colon epithelial adherent cells


title: RNA-seq_PARP-1KD_MCF7_1

description: oligo(dT)-purified RNA

data_processing:
Trimmed human GRO-seq reads were aligned to the human reference genome (hg19) using the bwa aligner {Li and Durbin, 2009} with default settings (uniquely aligned, 2 mismatches allowed, and 19 bp seed sequence).  The 5’-most base pair from each read was used in all analyses, with no more than 2 duplicates allowed at any genomic location. RNA-seq reads were mapped to the hg19 human genome using Tophat and converted to bed files.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: RNA-seq in MCF7 cells with shRNA-mediated knockdown of PARP-1

growth_protocol: MCF-7 cells were maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum containing 0.5 μg/mL puromycin and 800 μg/mL G418.

extract_protocol:
GRO-seq: MCF-7 cells were washed three times with ice-cold PBS and then resuspended for swelling in ice-cold Hypotonic Lysis Buffer [10 mM Tris•HCl, pH 7.4, 0.5% NP-40, 10% Glycerol, 3 mM CaCl2, 2 mM MgCl2, and 1 mM DTT containing 1x protease inhibitor cocktail (Sigma-Aldrich) and 4 units/mL SUPERase-In (Ambion)].   The swollen cells were collected by centrifugation at 1000 RCF for 10 min at 4°C and then resuspended in 1.5 ml of lysis buffer and pipetted up and down through a narrow opening tip 30 to 50 times to lyse the cells and release the nuclei.  The nuclei were collected by centrifugation and washed once with 1 mL of Hypotonic Lysis Buffer.  After a final collection by centrifugation, the resulting pellets of nuclei were resuspended in 500 μL of Freezing Buffer (50 mM Tris•HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 4 units/mL of SUPERase-In per mL), counted, frozen in liquid nitrogen in 100 μL aliquots containing 5 x 106 nuclei, and stored at -80°C until use. RNA-seq: Following 3 hours of treatment, RNA was harvested using QIAGEN RNeasy Kit.
GRO-seq: Nuclear run-on and GRO-seq library preparation were performed as previously described {Core, 2008;Hah, 2011}.  Briefly, nuclear run-on reactions were performed for ~100 bases in the presence of sarksoyl (to prevent reengagement of RNA polymerases), rNTPs, α32P-CTP, and 5-bromo-UTP.  The nascent RNAs were isolated, hydrolyzed to ~100 bases, and enriched using α-BrdUTP antibody-conjugated agarose beads (Santa Cruz).  The bound RNAs were washed several times and eluted.  The 5’ RNA cap was removed and the ends were repaired in preparation for adapter ligation.  Small RNA adapters were ligated to the 5’ end, followed by another bead binding enrichment using α-BrdUTP antibody-conjugated agarose beads.  These steps were repeated using a 3’ adapter.  The resulting RNAs were reverse transcribed, amplified using PCR, and analyzed by high throughput sequencing using an Illumina 1G Genome Analyzer. RNA-seq: RNA was prepared for sequencing as previously described (Sun, M. et al. Mol. Cell 2015).

treatment_protocol: GRO-seq: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum. RNA-seq: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum and 1 µg/mL Doxycycline for 4 days prior to treatment with DRB or vehicle (DMSO) treatment for 3 hours prior to RNA harvest.

value: human breast cancer cells

tag: gender

value: female


title: RNA-seq_PARP-1KD_MCF7_2

description: oligo(dT)-purified RNA


title: RNA-seq_LucKD_DRB_MCF7_1

description: oligo(dT)-purified RNA

source_name: RNA-seq in MCF7 cells with shRNA-mediated knockdown of Luciferase as a control with 3 hours 100 µM DRB treatment


title: NELF-EKD_VEH_GFP_PolII_1

data_processing:
The ChIP-seq reads were aligned to the mm9 or hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for all analyses
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: bed

source_name: NELF-E Knockdown, vehicle, GFP, PolII

growth_protocol: MCF-7 cells were grown in culture as previously described (Hah et al. Cell 2011). PARP-1 knockout MEFs expressing analog-senstive PARP-1 were cultured in DMEM supplemented with 10% fetal bovine serum, penicillin, and streptomycin containing 1 µg/mL puromycin.

extract_protocol:
PARP-1 ChIP-seq:  Following mock ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.  Click-ChIP-seq:  Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads.  Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C.  DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation. All Other ChIP-seq:  Cells were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.
After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: MCF-7 Cells were grown in (1) MEM supplemented 1 µg/mL doxycycline for four all four days, (2) MEM with charcoal stripped calf serum for three days, and (3) vehicle (DMSO) or DRB (100 µM) containing medium (1:1000 dilution of DMSO) for 1 hour prior to their crosslinking with 1% formaldehyde in PBS. Crosslinking was quenched with 0.1 M Glycine after 10 minutes at room temperature, and cells were harvested with cold PBS for sonication (200-500 bp) and chromatin immunoprecipitation.  MEFs were harvested in cold PBS and collected by centrifugation.  The cells were swollen in Nuclei Isolation Buffer (10 mM HEPES, pH 8.0, 2 mM MgCl2, 3 mM CaCl2, 300 mM sucrose, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) and the nuclei were released by the addition of 0.65% NP-40 with moderate vortexing.  Following collection by centrifugation, the nuclei were resuspended in PARP Reaction Buffer (30 mM Tris•HCl, pH 7.5, 10 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 0.01% NP-40, 0.05 mM EDTA, 20% glycerol, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) containing 250 μM 8-Bu(3-yne)T-NAD+ for 30 minutes at 25°C with occasional gentle mixing to allow ADP-ribosylation to occur in the isolated nuclei.

value: PolII


title: RNA-seq_LucKD_MCF7_2

description: oligo(dT)-purified RNA

source_name: RNA-seq in MCF7 cells with shRNA-mediated knockdown of Luciferase as a control


title: NELF-EKD_VEH_flagNELF-Emutant_PolII_2

source_name: NELF-E Knockdown, vehicle, flagNELF-Emutant, PolII


title: NELF-EKD_VEH_flagNELF-Emutant_PolII_1


title: NELF-EKD_VEH_flagNELF-Ewildtype_PolII_1

source_name: NELF-E Knockdown, vehicle, flagNELF-Ewildtype, PolII


title: RNA-seq_LucKD_DRB_MCF7_2

description: oligo(dT)-purified RNA


title: NELF-EKD_VEH_GFP_PolII_2


title: NELF-EKD_VEH_flagNELF-Ewildtype_FLAG_1

source_name: NELF-E Knockdown, vehicle, flagNELF-Ewildtype, FLAG

value: FLAG


title: NELF-EKD_VEH_flagNELF-Emutant_FLAG_2

source_name: NELF-E Knockdown, vehicle, flagNELF-Emutant, FLAG


title: NELF-EKD_VEH_flagNELF-Ewildtype_PolII_2


title: NELF-EKD_VEH_GFP_FLAG_1

source_name: NELF-E Knockdown, vehicle, GFP, FLAG


title: NELF-EKD_VEH_flagNELF-Emutant_FLAG_1


title: NELF-EKD_VEH_GFP_NELFE_2

source_name: NELF-E Knockdown, vehicle, GFP, NELFE

value: NELFE


title: NELF-EKD_VEH_GFP_FLAG_2


title: NELF-EKD_VEH_flagNELF-Ewildtype_IgG_1

source_name: NELF-E Knockdown, vehicle, flagNELF-Ewildtype, IgG

value: IgG


title: NELF-EKD_VEH_flagNELF-Emutant_IgG_2

source_name: NELF-E Knockdown, vehicle, flagNELF-Emutant, IgG


title: NELF-EKD_VEH_GFP_NELFE_1


title: NELF-EKD_VEH_flagNELF-Ewildtype_IgG_2


title: RNA-seq_LucKD_MCF7_1

description: oligo(dT)-purified RNA


title: NELF-EKD_VEH_GFP_IgG_1

source_name: NELF-E Knockdown, vehicle, GFP, IgG


title: NELF-EKD_VEH_GFP_IgG_2


title: NELF-EKD_VEH_flagNELF-Emutant_IgG_1


title: PARP-1KD_VEH_HDAg-S_PolII_2

source_name: PARP-1 Knockdown, vehicle, HDAg-S, PolII


title: A549_MEP50kd_3

city: Bronx

first: David

last: Shechter

address: 1300 Morris Park Ave

department: Biochemistry

description:
biological replicate 3
total RNA, rRNA depleted

data_processing:
Trim Galore for removal of AGATCGGAAGAGC TruSeq Indexed Adapters
Mapping to hg19 with STAR aligner
gene counts determined with htseq-count
DESeq2 and edgeR differential expression analysis
Genome_build: hg19

source_name: A549 lung adenocarcinoma MEP50 shRNA knockdown

growth_protocol: RPMI and 10% FBS

extract_protocol:
Total RNA extraction with Rneasy kit (Qiagen)
Stranded ribrary construction after depletion of rRNA with riboerase

treatment_protocol: Stable depletion with shRNA under selection with 1ug/ml puromycin

tag: knockdown

value: MEP50 knockdown

value: A549 lung adenocarcinoma


title: A549_MEP50kd_2

description:
biological replicate 2
total RNA, rRNA depleted


title: PARP-1KD_VEH_HDAg-S_PolII_1