title: P2-SFTPC scRNA-seq_30


title: P2-SFTPC scRNA-seq_31

status: Public on Oct 02 2017

type: SRA

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Single P2-SFTPC+ cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq-1.8.4 software was used to demultiplex data and convert BCL files from HiSeq2500 systems running RTA versions 1.18.64 to standard FASTQ file formats for downstream analysis.
Sequenced reads were mapped to hg19 whole genome using illumin ELAND v2 with 'eland_rna' mode.
The tags uniquely aligned to the genome region with permissive two base mismatches were counted with normalization to the reads per million tags per kilobase mRNA (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

molecule: total RNA

organism: Homo sapiens

source_name: SFTPC+ cells

growth_protocol: CPMhigh progenitor cells were induced from iPSCs via ventralized anterior foregut andodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days, Step 2: SB431542 and Noggin for 4 days, Step 3: CHIR99021, BMP4 and ATRA, Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days.  P0 SFTPC+ cells were induced from CPMhigh progenitor cells by forming alveolar organoids (AO) via three-dimensional coculture with human fetal lung fibroblasts. P2 and P5 SFTPC+ cells were obtained from P2 and P5 AO which were derived from once and four-times passaged SFTPC+ cells by forming AO, respectively.

extract_protocol:
Single cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) .
The first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

tag: cell type

value: hiPSC-derived SFTPC+ cells

tag: passages


title: P2-SFTPC scRNA-seq_28


title: P2-SFTPC scRNA-seq_33


title: P2-SFTPC scRNA-seq_37


title: P2-SFTPC scRNA-seq_26


title: P2-SFTPC scRNA-seq_27


title: P2-SFTPC scRNA-seq_25


title: P2-SFTPC scRNA-seq_21


title: P2-SFTPC scRNA-seq_17


title: P2-SFTPC scRNA-seq_13


title: P2-SFTPC scRNA-seq_14


title: P2-SFTPC scRNA-seq_19


title: P2-SFTPC scRNA-seq_16


title: P2-SFTPC scRNA-seq_20


title: P2-SFTPC scRNA-seq_22


title: P2-SFTPC scRNA-seq_36


title: P2-SFTPC scRNA-seq_23


title: P2-SFTPC scRNA-seq_24


title: P2-SFTPC scRNA-seq_18


title: P2-SFTPC scRNA-seq_10


title: P2-SFTPC scRNA-seq_9


title: P2-SFTPC scRNA-seq_11


title: P2-SFTPC scRNA-seq_6


title: P2-SFTPC scRNA-seq_15


title: P2-SFTPC scRNA-seq_5


title: P2-SFTPC scRNA-seq_4


title: P2-SFTPC scRNA-seq_3


title: dm3.wingDiscs.k4m1.yf

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 and dm3 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: dm3, hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: wing imaginal discs from 3rd instar larvae

growth_protocol: HCT116 cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Wildtype HCT116 and MLL4-ΔCT cells were infected with lentiviral vector (pSin) expressing either a minimal MLL4 SET domain (WT-MLL4), a catalytic-dead SET domain (C/A-SET), or just empty-vector, and selected in Puromycin (1ug/ml) for 24 hours. Cells were harvested  84 hours after infection for RNA extraction and ChIP-sequencing.

tag: tissue

tag: strain

tag: chip antibody

value: anti-H3K4me1 (homemade, rabbit polyclonal)


title: dm3.wingDiscs.k4m3.wt

value: wing imaginal discs from 3rd instar larvae

value: trr[1] ;; trr-WT

value: anti-H3K4me3 (homemade, rabbit polyclonal)


title: dm3.wingDiscs.k4m3.ca


title: dm3.wingDiscs.k4m3.yf


title: P2-SFTPC scRNA-seq_1


title: P0-SFTPC scRNA-seq_42

description: Single P0-SFTPC+ cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.


title: dm3.wingDiscs.k27ac.wt

value: anti-H3K27ac (CST, D5E4, Rb mAb #8173)


title: dm3.wingDiscs.k4m1.wt


title: P2-SFTPC scRNA-seq_7


title: P0-SFTPC scRNA-seq_41


title: P2-SFTPC scRNA-seq_8


title: P0-SFTPC scRNA-seq_43


title: dm3.wingDiscs.k27ac.yf


title: dm3.wingDiscs.input.k4m13.yf


title: dm3.wingDiscs.input.k27ac.yf


title: dm3.wingDiscs.input.k27ac.wt


title: dm3.wingDiscs.k27ac.ca


title: dm3.wingDiscs.k4m1.ca


title: dm3.wingDiscs.input.k4m13.wt


title: dm3.wingDiscs.input.k4m13.ca


title: dm3.wingDiscs.RNAseq.yf.rep2


title: dm3.wingDiscs.input.k27ac.ca


title: P0-SFTPC scRNA-seq_39


title: P2-SFTPC scRNA-seq_2


title: P0-SFTPC scRNA-seq_40


title: dm3.wingDiscs.RNAseq.yf.rep1


title: dm3.wingDiscs.RNAseq.wt.rep1


title: P0-SFTPC scRNA-seq_38


title: dm3.wingDiscs.RNAseq.wt.rep2


title: P0-SFTPC scRNA-seq_37


title: P2-SFTPC scRNA-seq_12


title: dm3.wingDiscs.RNAseq.T80.GAL4.wt.rep1

value: UAS_LacZ_RNAi x T80_Gal4


title: dm3.wingDiscs.RNAseq.ca.rep2


title: P0-SFTPC scRNA-seq_36


title: dm3.wingDiscs.RNAseq.T80.GAL4.wt.rep2


title: dm3.wingDiscs.RNAseq.ca.rep1


title: P0-SFTPC scRNA-seq_35


title: P0-SFTPC scRNA-seq_34


title: dm3.brains.trr.yf.rep1

source_name: total brains

value: Total brains from adult flys (2-4 days post-eclosion)

value: anti-TRR-NT (homemade, rabbit polyclonal)


title: dm3.brains.trr.yf.rep2


title: P0-SFTPC scRNA-seq_33


title: HeLa_Control_AMO_8hr_IgG_ChIP

city: Philadelphia

first: Christopher

middle: Conrad

last: Venters

state: Pennsylvania

address: 415 Curie Boulevard

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were trimmed of adapter sequences using TrimGalore, and thenwere aligned to the reference genome (UCSC, hg19) using TopHat by default parameters.
Reads with multiple alignments were filtered for downstreat analysis.
FPKMs for RNA-seq were generated using GFold with default parameters.
PCPAed genes were called using a Fisher's Exact test on both terminal exon reads vs. primary exon reads and pre-mRNA quartile 1 vs quartile 4. Benjamini-Hochberg multiple testing was done with an adjusted p-value < 0.01.
Internal, non-genomic 3' poly(A) reads were extracted from odT selected RNA-seq were extracted by selecting non-hg19 aligned reads from Bowtie with a 3' poly(A) stretch >= 10 nucleotides. These A stretches were then trimmed with Cutadapt, and the read was realigned to the genome.
Peaks for ChIP-seq were generated with MACS using the IgG as the background for subtraction.
Metagene plots were generated with CGAT. For ChIP-seq, the aboslute distance around the TSS and TES was used, and the intervening sequence was scaled to 2kb. For 3'-poly(A) reads in RNA-seq, CGAT was used with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: PCPA detection files for each RNA-seq sample are from GFold in tab-delimited text files, and 3' poly(A) sites are in BigWig format. Peaks for the RNA pol II ChIP-seq are from MACS in BED files.

source_name: Human Carcinoma Cells

growth_protocol: Cells grown in DMEM supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
Cells were harvested and then crosslinked with 1% Formaldehyde. Nuclei were chemically isolated and then lysed, then sheared using a sonicator. The resulting sample was cleared using dynabeads, and polII-DNA complexes were isolated with the antibody.
Libraries were prepared according to instructions accompanying the TruSeq ChIP sample preparation kit from Illumina (# IP-202-1012). Briefly, the overhanging DNA ends were blunted using exonuclease, and then the 3' end was adenylated to prevent improper ligation. The adapters were then ligated, and the library was amplified.

treatment_protocol: Cells transfected with antisense morpholino to control or U1 using Neon system for 4 or 8 hours.

tag: cell line

value: HeLa

value: PV

tag: transfection

value: Control

value: Normal mouse IgG (Santa Cruz Biotechnology sc-2025)


title: dm3.brains.trr.wt.rep2


title: dm3.wingDiscs.RNAseq.RNAi.T80.GAL4.rep2

value: UAS_Trr_RNAi x T80_Gal4


title: dm3.brains.trr.input.trr.lpt.yf.rep2


title: dm3.wingDiscs.RNAseq.RNAi.T80.GAL4.rep1


title: P0-SFTPC scRNA-seq_32


title: dm3.brains.trr.input.trr.lpt.wt.rep2


title: P0-SFTPC scRNA-seq_31


title: HeLa_U1_AMO_8hr_PolII_ChIP

value: Pol II N-terminus (Santa Cruz Biotechnology sc-899x)


title: dm3.brains.trr.input.trr.lpt.ca.rep2


title: HeLa_U1_AMO_8hr_IgG_ChIP


title: dm3.brains.trr.ca.rep2


title: dm3.wingDiscs.RNAseq.RNAi.en.GAL4.rep1

value: UAS_Trr_RNAi x engrailed_Gal4


title: dm3.brains.trr.ca.rep1


title: HeLa_Control_AMO_8hr_PolII_ChIP


title: dm3.wingDiscs.RNAseq.RNAi.en.GAL4.rep2


title: dm3.brains.lpt.yf.rep2

value: anti-LPT (homemade, rabbit polyclonal)


title: dm3.brains.trr.wt.rep1


title: P0-SFTPC scRNA-seq_29

value: hiPSC-derived SFTPC+ cells


title: dm3.brains.lpt.wt.rep2


title: P0-SFTPC scRNA-seq_28


title: HeLa_U1_AMO_8hr_Labeled_rRNA_odT_selection

description:
nascent polyA mRNA
U1AMO_15nmol_odT_selection.polyA_sites.bw

extract_protocol:
Total RNA extracted using trizol, polyA mRNA extracted using Rneasy Kit, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the Nugen kits. Briefly, RNA was converted to cDNA using the Ovation RNA-seq System and starting with 100ng RNA. cDNA was amplified using SPIA protocol recommended by Nugen Kit. Libraries for RNA-seq were prepared from the amplified cDNA using Encore NGS Library System I.


title: dm3.brains.lpt.ca.rep2


title: dm3.brains.k4m3.yf.rep1


title: dm3.brains.k4m3.ca.rep2


title: dm3.brains.k4m3.yf.rep2


title: dm3.brains.k4m3.wt.rep2


title: P0-SFTPC scRNA-seq_25


title: P0-SFTPC scRNA-seq_26


title: P0-SFTPC scRNA-seq_27


title: P0-SFTPC scRNA-seq_24


title: dm3.brains.k4m2.yf.rep2

value: anti-H3K4me2 (homemade, rabbit polyclonal)


title: dm3.brains.k4m3.ca.rep1


title: P0-SFTPC scRNA-seq_30


title: dm3.brains.k4m2.yf.rep1


title: P0-SFTPC scRNA-seq_23


title: dm3.brains.k4m2.wt.rep1


title: P0-SFTPC scRNA-seq_22


title: dm3.brains.k4m2.ca.rep2


title: dm3.brains.k4m1.yf.rep2

value: anti-H3K4me1 (homemade, rabbit polyclonal)


title: dm3.brains.k4m2.wt.rep2

value: trr[1] ;; trr-WT


title: dm3.brains.k4m2.ca.rep1


title: dm3.brains.k4m1.wt.rep2


title: dm3.brains.k4m1.yf.rep1


title: P0-SFTPC scRNA-seq_20


title: dm3.brains.k4m1.ca.rep2


title: P0-SFTPC scRNA-seq_19


title: dm3.brains.k4m3.wt.rep1

value: anti-H3K4me3 (homemade, rabbit polyclonal)


title: dm3.brains.k27ac.yf.rep2

value: anti-H3K27ac (CST, D5E4, Rb mAb #8173)


title: dm3.brains.k27ac.yf.rep1


title: dm3.brains.k27ac.wt.rep1


title: dm3.brains.k27ac.ca.rep2


title: P0-SFTPC scRNA-seq_18


title: dm3.brains.k27ac.ca.rep1


title: P0-SFTPC scRNA-seq_17


title: P0-SFTPC scRNA-seq_14


title: P0-SFTPC scRNA-seq_16


title: dm3.brains.input.k27ac.k4m123.wt.rep2


title: dm3.brains.RNAseq.yf.rep2


title: P0-SFTPC scRNA-seq_21


title: dm3.brains.k27ac.wt.rep2


title: Tumor tissue from HCD mice, number 3

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

country: China

institute: Eastern Hepatobiliary Surgery Hospital

description:
HCD-3
Tumor tissue from HCD mice were harvested and total RNA were extracted

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat (version:2.0.9)
Gene abundance measurements were generationed and normalized using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Mus musculus

source_name: melanoma

growth_protocol: B16F10 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with high cholesterol diet.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

tag: diet

value: HCD

tag: treatment

value: B16F10 cells were subcutaneously injected into the right flanks of mice

value: Tumor tissue in C57BL/6J mice


title: dm3.brains.RNAseq.wt.rep2

value: Total brains from adult flys (2-4 days post-eclosion)


title: dm3.brains.k4m1.wt.rep1


title: dm3.brains.RNAseq.yf.rep1


title: P0-SFTPC scRNA-seq_12


title: P0-SFTPC scRNA-seq_13


title: dm3.brains.input.trr.wt.rep1


title: dm3.brains.RNAseq.ca.rep2


title: dm3.brains.RNAseq.ca.rep1


title: dm3.brains.input.k27ac.k4m123.wt.rep1


title: Tumor tissue from HCD mice, number 1

description:
HCD-1
Tumor tissue from HCD mice were harvested and total RNA were extracted


title: P0-SFTPC scRNA-seq_11


title: Tumor tissue from ND mice, number 3

description:
ND-3
Tumor tissue from ND mice were harvested and total RNA were extracted

growth_protocol: B16F10 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with normal diet.

value: ND


title: dm3.brains.RNAseq.wt.rep1


title: dm3.brains.k4m1.ca.rep1


title: P0-SFTPC scRNA-seq_15


title: P0-SFTPC scRNA-seq_10


title: Tumor tissue from HCD mice, number 2

description:
HCD-2
Tumor tissue from HCD mice were harvested and total RNA were extracted


title: Tumor tissue from ND mice, number 2

description:
ND-2
Tumor tissue from ND mice were harvested and total RNA were extracted


title: P0-SFTPC scRNA-seq_9


title: Tumor tissue from ND mice, number 1

description:
ND-1
Tumor tissue from ND mice were harvested and total RNA were extracted


title: P0-SFTPC scRNA-seq_8


title: P0-SFTPC scRNA-seq_7


title: P0-SFTPC scRNA-seq_5


title: P0-SFTPC scRNA-seq_6


title: TCCTGAGCTCTCTCCG [[H4]] C76-3

city: Miami

first: Nirupa

last: Chaudhari

state: FL

address: 1600 NW 10th Ave

department: Physiology & Biophysics

institute: University of Miami Miller School of Medicine

description: Isolated geniculate ganglion neuron from C1 Fluodigm chip.

data_processing:
Base-calling was performed using HiSeq Control Software 2.2.58.
Data was demultiplexed and BCL files converted to FASTQ using bcl2fastq 2.17.1.14.
Alignments and quantification were performed using the RUM package v2.0.5_06 (Grant et al, Bionformatics, 2011) at the University of Pennsylvania Next Generation Sequencing Core. Using this pipeline, reads were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences. The RUM software package aligned the sequences to the mm9 genome/transcriptome using Bowtie and Blat. The RUM package then quantified Fragments Per Kilobase of transcript per Million (FPKM) mapped reads for each transcript in each cell.
Genome_build: mm9
Supplementary_files_format_and_content: GEO-ID_Dvoryanchikov_2017_All_Transcripts_Read_Counts.txt: txt file containing read counts for all transcripts in all cells. Value of 1 in best.rep column represents best representative transcript. Nonzero.counts column calculates how many cells had a count of at least 1.
Supplementary_files_format_and_content: GEO-ID_Dvoryanchikov_2017_Datatable_FPKM.txt: Tab-delimited text file containing FPKM values for best representative transcripts for all sequenced neurons.

source_name: Geniculate ganglion

extract_protocol:
Geniculate ganglia (≈900 neurons) were rapidly dissected from six 8-12 week-old C57BL6J mice of both sexes and placed in Ca-Mg-Free Hank’s Balanced Salt Solution (HBSS, ThermoFisher 14170161) at room temperature. All 12 ganglia were sequentially digested, first with 1 ml of 40u/ml Papain with NaHCO3 and l-cysteine at 37°C for 13 min, followed by 4mg/ml Collagenase Type 2, 4.7mg/ml Dispase Type 2 at 37 °C for another 13 min. Enzymes were Papain (Worthington #LS003126, Collagenase (Worthington, # LS004174) and Dispase (Roche 04942078001). Ganglia were washed with Tyrode’s buffer (in mM: 135 NaCl, 5 KCl, 2 CaCl2, 1 MgCl2, 10 HEPES, 5 NaHCO3, 10 glucose, 10 pyruvate, adjusted to pH 7.4 (318-323 mOsM) to remove enzymes and transferred into 40μl fresh Tyrode’s solution. Under visual guidance on a stereomicroscope, ganglia were gently triturated 3-5 times each with a 200μm diameter and then a 140μm fire-polished glass pipet. Large debris was removed by gravity filtering the suspension through a ≈35μ cell sieve (Corning 352235) into 1ml Tyrode’s buffer in a 15mm cell culture well. At this stage, the suspension still included significant quantities of axon fragments and glial cells. The cell suspension was gently swirled by hand such that neurons remained concentrated at the center of the well while glial cells and axon fragments dispersed centrifugally to the periphery and could be carefuly withdrawn in 700μl. This manual separation was repeated 8-10 times with 700μl of fresh Tyrode’s buffer at each iteration. Total time for ganglion dissociation and neuronal enrichment was ≈60 min. Cell viability was assessed in an aliquot of each final preparation by trypan blue exclusion on a Countess Automated Cell Counter (ThermoFisher). Two independent cell suspensions (on separate days) that displayed neuronal viability of 93% and 96% respectively (and 50%≤ viability of satellite cells ≤ 12μm in diameter) were used for subsequent steps. The suspension included ≈ 350 cells /μl in a neuron: glia ratio ≥1.5. Each cell suspension was loaded onto a primed Fluidigm C1 System (located in the University of Miami CFAR Core). Capture was on a Fluidigm integrated fluidics circuits (IFC) for large cells (“17-25μm”, Fluidigm 100-5761) exactly according to manufacturer’s instructions. After completion of the run, all capture sites on the chip were examined microscopically and photographed. From a total of 192 sites on two IFCs, we rejected 68 that contained more than one cell or in which captured neurons showed blebs or membrane ruffling. Captured neurons ranged from 19-40μm in diameter.
Synthesis of cDNA libraries and sequencing were performed at the Next-Generation Sequencing Core (NGSC) at the University of Pennsylvania. An Illumina Nextera XT DNA library preparation protocol, modified for single-cell mRNA sequencing of cDNAs acquired on the C1 system was used. Each single cell library was barcoded during synthesis, libraries were pooled (median length before fragmentation was 900bp) and single-end sequenced for a total depth of 250x10^6 reads for the pool, running on a single lane on an Illumina HiSeq 2500 (High Output Mode) system. Sequence data were processed through the NGSC’s standard RUM pipeline for genome alignment, junction calling, and feature quantification. Reads were mapped against mouse transcriptome (mm9) using Bowtie and genome using Bowtie and Blat and converted to Fragments per kilobase of exon per million reads mapped (FPKM) values.

value: Geniculate ganglion

value: Neuron

tag: age

value: 8-12 weeks


title: P0-SFTPC scRNA-seq_3


title: P0-SFTPC scRNA-seq_1


title: TCCTGAGCCGTCTAAT [[G4]] C54-3


title: TCCTGAGCCTAAGCCT [[F4]] C35-3


title: P0-SFTPC scRNA-seq_2


title: TCCTGAGCGTAAGGAG [[C4]] C61-1


title: TCCTGAGCCTCTCTAT [[A4]] C08-1


title: TCCTGAGCACTGCATA [[D4]] C76-1


title: TAGGCATGTATCCTCT [[B6]] C36-1


title: TAGGCATGCTAAGCCT [[F6]] C38-3


title: TAGGCATGACTGCATA [[D6]] C80-1


title: TAGGCATGCTCTCTAT [[A6]] C11-1


title: TAGGCATGGTAAGGAG [[C6]] C63-1


title: TAGGCATGTCTCTCCG [[H6]] C79-3


title: neural progenitor ataxia 2

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using R version 3.1.1 with package Rsubread 1.14.2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the protocol from Mortazavi et al, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and RPKM values for all samples (no log2 transform).

source_name: neural progenitor

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: neural progenitor

tag: disease state

value: Ataxia Telangiectasia


title: neural progenitor control 3

value: Normal


title: neural progenitor control 2


title: neural progenitor control 1


title: neural progenitor ataxia 3


title: TAGGCATGCGTCTAAT [[G6]] C57-3


title: iPSC ataxia 2

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: iPSC ataxia 3


title: neural progenitor ataxia 1


title: iPSC control 2


title: TAAGGCGATCTCTCCG [[H1]] C69-3


title: TCCTGAGCTATCCTCT [[B4]] C30-1


title: TAAGGCGAGTAAGGAG [[C1]] C55-1


title: iPSC control 1


title: TAAGGCGATATCCTCT [[B1]] C25-1


title: P0-SFTPC scRNA-seq_4

value: hiPSC-derived SFTPC+ cells


title: TAAGGCGACTCTCTAT [[A1]] C05-1


title: TAAGGCGACTAAGCCT [[F1]] C30-3


title: TAAGGCGACGTCTAAT [[G1]] C49-3


title: TAAGGCGAACTGCATA [[D1]] C73-1


title: TCCTGAGCAAGGAGTA [[E4]] C06-3


title: iPSC ataxia 1


title: TAGGCATGAAGGAGTA [[E6]] C10-3


title: iPSC control 3


title: TAAGGCGAAAGGAGTA [[E1]] C01-3


title: GTAGAGGACTCTCTAT [[A10]] C22-1


title: GTAGAGGACTAAGCCT [[F10]] C44-3


title: GTAGAGGACGTCTAAT [[G10]] C65-3


title: GGACTCCTTCTCTCCG [[H5]] C78-3


title: GTAGAGGATCTCTCCG [[H10]] C91-3


title: GTAGAGGATATCCTCT [[B10]] C44-1


title: GGACTCCTCTAAGCCT [[F5]] C36-3


title: GGACTCCTCTCTCTAT [[A5]] C10-1


title: GGACTCCTTATCCTCT [[B5]] C35-1


title: GTAGAGGAACTGCATA [[D10]] C84-1


title: GTAGAGGAAAGGAGTA [[E10]] C21-3


title: GTAGAGGAGTAAGGAG [[C10]] C68-1


title: GGACTCCTCGTCTAAT [[G5]] C55-3


title: GGACTCCTAAGGAGTA [[E5]] C09-3


title: GGACTCCTACTGCATA [[D5]] C77-1


title: GCTCATGATCTCTCCG [[H11]] C92-3


title: GCTCATGACTAAGCCT [[F11]] C45-3


title: GCTCATGATATCCTCT [[B11]] C49-1


title: GCTCATGACGTCTAAT [[G11]] C67-3


title: GCTCATGACTCTCTAT [[A11]] C23-1


title: GCTCATGAGTAAGGAG [[C11]] C69-1


title: GCTCATGAACTGCATA [[D11]] C86-1


title: CTCTCTACGTAAGGAG [[C7]] C64-1


title: GCTCATGAAAGGAGTA [[E11]] C22-3


title: CTCTCTACTATCCTCT [[B7]] C37-1


title: GGACTCCTGTAAGGAG [[C5]] C62-1


title: CTCTCTACCGTCTAAT [[G7]] C60-3


title: CTCTCTACACTGCATA [[D7]] C81-1


title: CTCTCTACAAGGAGTA [[E7]] C15-3


title: CGTACTAGTCTCTCCG [[H2]] C73-3


title: CTCTCTACCTCTCTAT [[A7]] C17-1


title: CGTACTAGGTAAGGAG [[C2]] C58-1


title: CGTACTAGTATCCTCT [[B2]] C28-1


title: CTCTCTACCTAAGCCT [[F7]] C40-3


title: CGTACTAGCTCTCTAT [[A2]] C06-1


title: CGAGGCTGTCTCTCCG [[H8]] C82-3


title: CGTACTAGAAGGAGTA [[E2]] C03-3


title: CTCTCTACTCTCTCCG [[H7]] C80-3


title: CGAGGCTGCTAAGCCT [[F8]] C41-3


title: CGAGGCTGCGTCTAAT [[G8]] C61-3


title: CGTACTAGCGTCTAAT [[G2]] C50-3


title: ATCTCAGGTCTCTCCG [[H12]] C95-3


title: CGAGGCTGTATCCTCT [[B8]] C39-1


title: ATCTCAGGCTCTCTAT [[A12]] C24-1


title: ATCTCAGGCTAAGCCT [[F12]] C46-3


title: ATCTCAGGTATCCTCT [[B12]] C51-1


title: CGTACTAGACTGCATA [[D2]] C74-1


title: CGAGGCTGAAGGAGTA [[E8]] C17-3


title: ATCTCAGGCGTCTAAT [[G12]] C68-3


title: ATCTCAGGACTGCATA [[D12]] C95-1


title: CGAGGCTGACTGCATA [[D8]] C82-1


title: AGGCAGAATCTCTCCG [[H3]] C74-3


title: ATCTCAGGAAGGAGTA [[E12]] C23-3


title: CGTACTAGCTAAGCCT [[F2]] C32-3


title: AGGCAGAAGTAAGGAG [[C3]] C59-1


title: CGAGGCTGGTAAGGAG [[C8]] C65-1


title: AGGCAGAATATCCTCT [[B3]] C29-1


title: AGGCAGAACTAAGCCT [[F3]] C33-3


title: AGGCAGAACTCTCTAT [[A3]] C07-1


title: CGAGGCTGCTCTCTAT [[A8]] C19-1


title: AGGCAGAACGTCTAAT [[G3]] C53-3


title: ATCTCAGGGTAAGGAG [[C12]] C71-1


title: AGGCAGAAACTGCATA [[D3]] C75-1


title: AAGAGGCATCTCTCCG [[H9]] C83-3


title: AGGCAGAAAAGGAGTA [[E3]] C05-3


title: AAGAGGCATATCCTCT [[B9]] C43-1


title: AAGAGGCAGTAAGGAG [[C9]] C67-1


title: AAGAGGCAAAGGAGTA [[E9]] C20-3


title: CsA2

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

data_processing:
The quality of the reads was verified using FASTQC version 0.11.4
All reads were aligned to the T. urticae genome using the two-pass alignment mode of STAR 2.5.0a with a maximum intron size set to 20 kb. Resulting BAM files were subsequently sorted on read name by using SAMtools 0.1.19.
Read counts per gene using the most recent T. urticae annotation (version of June 23, 2016) were then obtained using the default settings of HTSeq 0.6.0 with the “STRANDED” flag set to “yes” and the “feature” flag set to “exon”
Genome_build: Grbić, M. et al. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479, 487–92 (2011).
Supplementary_files_format_and_content: Tab-delimited text file includes read counts (HTSeq) for each sample. Gene IDs are found at http://bioinformatics.psb.ugent.be/orcae/overview/Tetur

organism: Tetranychus urticae

source_name: complete organism

growth_protocol: The T.urticae JP-R strain was maintained on potted bean plants, Phaseolus vulgaris L. var. Prelude, sprayed with 200 mg a.i. cyenopyrafen L-1 (STARMITE, 30% SC) until run-off. For the week prior to collection of RNA, the strain was maintained on bean plants without cyenopyrafen selection pressure. About 30 3-5 day old adult females were transferred to the upper (adaxial) side of a 9 cm2 square-cut kidney bean leaf discs placed on wet cotton wool. About 600 mites (20 leaf disks with mites) were used for each treatment (DEF, DEM, PBO or CsA) and for the controls (FORM, CON). After spraying, leaf disks were placed in a climatically controlled room at 26°C, 60% RH with a 16:8h light:dark photoperiod.

extract_protocol: Total RNA was extracted from about 100 adult female mites using the RNeasy mini kit (Qiagen, Belgium) with four-fold biological replication for each treatment (PBO, DEF, DEM, CsA) and the controls (FORM, CON).

treatment_protocol: Synergists were dissolved in a mixture of N,N-dimethylformamide and emulsifier W (alkylarylpolyglycolether, 3:1 w/w, respectively) and subsequently diluted with deionized water 100-fold. Used concentrations; PBO (1000 ppm), DEF (500 ppm), DEM (2000 ppm) and CsA (50 ppm). Leaf discs were sprayed at 1 bar pressure in a Cornelis spray tower with 650µl spray fluid (1.56 ± 0.04mg fluid deposit cm-2) containing one of the synergists (DEF, DEM, PBO, CsA) or formulation (FORM; N,N-dimethylformamide and emulsifier W (3:1 w/w) diluted in deionized water 100-fold) only. Unsprayed mites (CON) served as an additional control. Next, leaf disks were placed in a climatically controlled room at 26°C, 60% RH with a 16:8h light:dark photoperiod. After 24 hours, living mites were scored and collected for RNA extraction.

tag: Stage

value: female adult

value: JP-R

tag: synergists

value: CsA


title: CsA3


title: AAGAGGCACTCTCTAT [[A9]] C20-1


title: CsA4


title: AAGAGGCACTAAGCCT [[F9]] C42-3


title: AAGAGGCACGTCTAAT [[G9]] C63-3


title: AAGAGGCAACTGCATA [[D9]] C83-1


title: DEM1

value: DEM


title: DEM4


title: DEF4

value: DEF


title: DEM2


title: DEM3


title: CsA1


title: DEF2


title: DEF1


title: C3682

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description: nascent RNA

data_processing:
Library strategy: PRO-Seq
We removed exact duplicate reads and trimmed a 6bp random hexamer at the 5' end of each read.
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format.
Genome_build: canFam3
Supplementary_files_format_and_content: PRO-seq data are provided in standard bigWig and raw fastq formats.

organism: Canis lupus familiaris

source_name: Canine fetal gonads, day 39

extract_protocol:
Gonads were isolated by dissection of fetal tissues.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

tag: developmental stage

value: day 39 embryo

value: gonads

tag: Sex

value: female

tag: genotype


title: C3681

description: nascent RNA


title: PBO2

value: PBO


title: PBO4


title: PBO3


title: C3641

description: nascent RNA


title: PBO1


title: FORM4

value: FORM


title: C3640

description: nascent RNA

value: male


title: C3639

description: nascent RNA


title: FORM2


title: FORM1


title: C3556

description: nascent RNA


title: CON4

value: control


title: DEF3


title: 6mA-IP_rep1

city: Guangzhou

first: Minghui

last: He

address: International Biotech Island

department: Bioinformatics Department

institute: Forevergen Biosciences Co., Ltd

data_processing:
Base calling was performed using CASAVA version 1.8.2 (illumina)
DNA IP-seq reads were trimmed for adaptor sequence and mapped to human genome using BWA (v0.7.12) by default parameters.
Peaks were called using MACS2 (v2.1.1) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using MACS2

source_name: peripheral blood mononuclear cell

extract_protocol:
Genomic DNA was extracted using Qigen DNA Extract Kit (Cat#). Lysates were harvested  from sonicated genomic DNA  Immunoprecipitated with 6mA antibody
Libraries were constructed according to manufacturer’s instructions of NEB Next DNA library prep kit (EE7370L ). Briefly, Harvested DNA was ligated to adaptor using NEB Next DNA library prep kit. Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X10 platform and 150bp paired-end reads were generated.

value: peripheral blood mononuclear cell

tag: antibody

value: m6A (N6-methyladenosine) (Synaptic Systems. Cat. No. 202 003)


title: CON2


title: A1114

description: nascent RNA


title: CON1

treatment_protocol: Synergists were dissolved in a mixture of N,N-dimethylformamide and emulsifier W (alkylarylpolyglycolether), 3:1 w/w, respectively, and subsequently diluted with deionized water 100-fold. Used concentrations; PBO (1000 ppm), DEF (500 ppm), DEM (2000 ppm) and CsA (50 ppm). Leaf discs were sprayed at 1 bar pressure in a Cornelis spray tower with 650µl spray fluid (1.56 ± 0.04mg fluid deposit cm-2) containing one of the synergists (DEF, DEM, PBO, CsA) or formulation (FORM; N,N-dimethylformamide and emulsifier W (3:1 w/w) diluted in deionized water 100-fold) only. Unsprayed mites (CON) served as an additional control. Next, leaf disks were placed in a climatically controlled room at 26°C, 60% RH with a 16:8h light:dark photoperiod. After 24 hours, living mites were scored and collected for RNA extraction.


title: HSUR 2-negative sample IP 3

status: Public on Oct 01 2017

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_Control_IP.txt
11581X24

data_processing:
Reads were aligned to marmoset genomic sequence (calJac3), Saimiriine herpesvirus 2 (Genbank: X64346.1) and splice junction sequences using Novoalign (2.08.03), allowing up to 50 alignments.  Splice junction sequences were created with USeq (v8.8.8) MakeTranscriptome using CalJac3 Ensembl build 80 and X64346.1 gene annotations.
The resulting alignment file was processed with the USeq SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive or low quality alignments.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq DefinedRegionDifferentialSeq application was used to count the number of reads aligning to each gene.
DESeq (v1.4.5) was used to detect gene count differences between HSUR2_IP and Control_IP or HSUR2_IP and HSUR2_input
Genome_build: cj3 and X64346.1
Supplementary_files_format_and_content: tab-delimited files containing read counts, log2 fold changes and -10 * log10(adjusted p-value) for each gene.

molecule: polyA RNA

organism: Callithrix jacchus

source_name: Herpesvirus saimiri-transformed T cells

growth_protocol: HVS-infected Marmoset T cells were grown at at density of 500,000-1 million cells/ml in RPMI 1640 medium supplemented with 20% FBS, 100 Units of penicllin, 100 µg/ml streptomycin, 1 mM of sodium pyruvate, 2 mM glutaMAX and 0.001% b-mercaptoethanol.

extract_protocol:
Total RNA was extracted with TRIzol following the manufacturer's protocol (Invitrogen).  Poly A+ RNA was selected with oligo-dT magnetic beads following the manufacturer's protocol (New England Biolabs). Ten percent of each sample was saved as input and stored in TRIzol.  Crosslinked-HSUR 2-mRNA complexes were captured with HSUR 2 antisense oligonucleotide and magnetic streptavidin beads (MPG PureBioTech).  Bound RNA was released from the beads with TRIzol.  Inputs and HSUR 2 pull down samples were purified and crosslinks were reversed before proceeding directly to library preparation.
Illumina's TruSeq Stranded mRNA LT kit

treatment_protocol: Three independent samples of 60 million HVS-infected marmoset T cells each were transfected with GFP antisense oligonucleotide and three independent samples of of 60 million HVS-infected cells were transfected with HSUR 2 antisense oligonucleotide to deplete the levels of HSUR 2.  After 24 hours, each sample was crosslinked with psoralen at 254 nm for one hour at 4°C.  Samples were then lysed with 6 M guanidium hydrochloride, 0.8% SDS & proteinase K and incubated at 65°C for one hour.  One milliliter of TRIzol was added to each sample and stored at -80°C.

value: Cj319  T

value: Transformed with HVS strain A11

tag: development  stage

value: Adult

tag: sample type

value: IP


title: DOT-T1E_LB2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

description: processed data files: T1E_LB.xlsx

data_processing:
We use Rockhopper for alignment and the complete analysis of data
Genome_build: NC_018220 and NC_000913
Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition
Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2
Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2
Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2
Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2

organism: Pseudomonas putida

extract_protocol:
Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 6mA-IP_rep2

tag: tissue


title: DOT-T1E_LB1

description: processed data files: T1E_LB.xlsx

tag: strain


title: HSUR 2-negative sample IP 1

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_Control_IP.txt
11581X22


title: HSUR 2-positive sample IP 3

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
HSUR2_IP_vs_Control_IP.txt
11581X21


title: HSUR 2-negative sample IP 2

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_Control_IP.txt
11581X23


title: HSUR 2-positive sample IP 2

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
HSUR2_IP_vs_Control_IP.txt
11581X20


title: HSUR 2-positive sample input 3

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
11581X15

value: input


title: HSUR 2-positive sample IP 1

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
HSUR2_IP_vs_Control_IP.txt
11581X19


title: HSUR 2-positive sample input 2

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
11581X14


title: HSUR 2-positive sample input 1

description:
polyA RNA crosslinked to viral HSUR 2 ncRNA
HSUR2_IP_vs_HSUR2_input.txt
11581X13


title: FORM3

value: female adult

value: JP-R


title: GFP RNAi regenerating trunks day 4

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

description: 3 RNAi feeds, amputated 3 days after final feed, and RNA-extracted at appropriate timepoint from regenerating trunk fragment

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Head and tail regeneration enriched genes were determined by comparing the Smed-Bcatenin1(RNAi) regenerating time points (days 1,2,3,4,5 and 6 post amputation) to timepoint matched apc(RNAi) regenerating time points by the DEseq2 test using RNAseq raw counts. This procedure includes normalization, and differentiation expression tests. A total of 5886 transcripts were significantly upregulated between the Smed-Bcatenin1(RNAi) and apc(RNAi) conditions when using an adjusted p-value < 0.05, FDR < 0.05 and >=20 counts over the time course (average).
Differentially expressed genes identified by DESeq2 analysis were then compiled and their 6-day readcounts were normalized against matched control(RNAi) time points to normalize expression in terms of gene expression versus control regenerating animals. This was done for both Smed-Bcatenin1(RNAi) and apc(RNAi) conditions across all timepoints (days 1, 2, 3, 4, 5 and 6).
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt

organism: Schmidtea mediterranea

source_name: Wildtype animals

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol: All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.

treatment_protocol: Animals were fed 3 times control(RNAi), apc(RNAi), or Smed-Bcatenin1(RNAi) every 3 days. Animals were amputated 3 days following their final feed. RNA was extracted from >5 regenerating tail fragments at days 1, 2, 3, 4, 5 and 6 post amputation. In total, 54 samples (3 RNAi conditions with 6 time points, biologically replicated 3 times) were sequenced to a depth of >43 million reads per mixed sample.

value: Asexual CIW4

value: Regenerating trunk fragments

value: Control RNAi


title: GFP RNAi regenerating trunks day 6


title: GFP RNAi regenerating trunks day 3


title: C3557

description: nascent RNA

value: day 39 embryo

value: gonads


title: GFP RNAi regenerating trunks day 2


title: CON3


title: GFP RNAi regenerating trunks day 1


title: Bcat RNAi regenerating trunks day 5

value: Bcat RNAi


title: Bcat RNAi regenerating trunks day 6


title: Bcat RNAi regenerating trunks day 2


title: Bcat RNAi regenerating trunks day 3


title: Bcat RNAi regenerating trunks day 4


title: APC RNAi regenerating trunks day 5

value: APC RNAi


title: APC RNAi regenerating trunks day 4


title: APC RNAi regenerating trunks day 2


title: APC RNAi regenerating trunks day 1


title: APC RNAi regenerating trunks day 3


title: GFP RNAi regenerating trunks day 5


title: p65 null MEFs

city: Columbus

first: Denis

last: Guttridge

address: Biomedical Research Tower, 460 West 12th Avenue

institute: The Ohio State University

data_processing:
Base calls were made using tools for HiSeq 4000 which include HCS3.3.376, RTA2.7.6 and bcl2fastq2-v2.16
Spliced transcripts were aligned using Star 2.4 with UCSC genome and annotation data for the mm10 assembly.
HOMER was used to create tag directories and quantify gene expression.
edgeR utilized by HOMER was used to determine differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: p65wt_p65null_raw_counts.txt contains non adjusted integer counts analyzed by HOMER.

source_name: Mouse embryonic fibroblasts

extract_protocol:
RNA was harvested using Trizol reagent from cells in culture. Illumina Hiseq 4000  was used with 1 mg of RNA for construction of sequence library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Immortalized mouse embryonic fibroblasts


title: p65 WT MEFs


title: Ataxin7_tc_2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: total chromatin

data_processing:
Base Calls were performed using CASAVA version 1.8.2
Reads were aligned to Drosophila genome dm3 with bowtie using the following parameters: -v 2 --best --strata -k 1 -m 3
Enrichment analysis was performed using macs2 to find peaks using default parameters with ip as treatment and total chromatin as control
Genome_build: dm3
Supplementary_files_format_and_content: BED fles of peak locations determined by macs2

source_name: 1-3 hr embryo

growth_protocol: Drosophila melanogaster was grown on standard medium at 25°C.

extract_protocol:
Embryos were fixed in 1.8% formaldehyde for 15 min at room temperature. Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Embryos were homogenized in buffer A1 (15 mM HEPES at pH 7.5, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5% TritonX-100, 0.5 mM DTT) (0.1g embryos/1ml A1). The chromatin pellet was washed three times with 5ml buffer A1 and once with 5ml buffer A2 (15 mM HEPES at pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroyl sarcosine). The chromatin was sonicated in 250μL of buffer A2 (0.1g embryos/250ul A2) seven times for 10 sec (0.9s on/0.1s off for 10 times) at 30% power. After centrifugation at 14,000 rpm for 10 min at 4°C, 250 μL of clarified soluble chromatin was used for ChIP as described previously (Huang et al. 2014). The antibodies used for ChIP included 10 μg of rabbit α-Sgf11, 20 μg of rabbit α-Ada2b, 20 μg of rabbit α-Spt3, 20 μg of rabbit α-Non-stop, 3 μg mouse α-pol2(4H8) (ab5408, Abcam).
For ChIP-seq library preparation, 10ng ChIP DNA and WCE DNA were used with the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies).  Post amplification size selection was performed on all libraries using a Pippin Prep (Sage Science).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina HiSeq 2500 instrument as 50-bp single read.

treatment_protocol: Stage 4-6 embryos were collected at 25°C and embryo stage confirmed microscopically.

value: 1-3 hr embryo

value: Ataxin-7 mutant

tag: replicate

tag: ip target

tag: epitope


title: tc_1839_2

description: total chromatin


title: KO_Oil Brep2 Trep2

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: KO Oil

data_processing:
Basecalls were provided by Torrent Suite (version 4.0.2)
Reads were mapped to mm10 using STAR (version 2.5.1b), with an mm10-derived index, and the following parameters: outFilterType (BySJout), outFilterMultimapNmax (20), alignSJoverhangMin (8), alignSJDBoverhandMin (1), outFilterMismatchNmax (999), alignIntronMin (20), alignIntronMax (1000000), alignMatesGapMax (1000000), twopassMode (Basic), sjdboverhang (100)
Overlap with genes was determined using the function “summarizeOverlaps” from the R package “GenomicAlignments” (version 1.8.4), with Ensembl release 84 as a reference.
FPKM (fragments per kilobase of exon per million reads) values were derived from the gene overlap data, using the function “fpkm” from the R package “DESeq2” (version 1.12.4).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file containing FPKM values generated using DESeq2 (version 1.12.4) and Ensembl release 84

source_name: HSC

extract_protocol:
Freshly isolated HSCs were sorted into Trizol and total RNA was extracted per manufacturers instructions.
Ion Torrent Libraries were constructed using cDNA generated with NuGEN Ovation 2 protocol.  After Covaris shearing, Ion Torrent libraries were made with the KAPA Library Preparation Kit (KK8301) per manufacturers instructions.

treatment_protocol: 2 month old male mice (Esr1fl/fl and Esr1fl/fl;Mx1-Cre) were treated with Poly(I:C ) intraperitoneally every other day for a total of 6 treatments.  Upon reaching 3 months of age, Poly(I:C) treated mice were then treated injected with 100 microliters of corn oil containing 2 micrograms of oestradiol.

value: bone marrow

value: 3 months


title: KO_Oil Brep2 Trep1

description: KO Oil


title: KO_E2 Brep2 Trep1

description: KO E2


title: tc_1907_1

description: total chromatin


title: Ataxin7_tc_1

description: total chromatin


title: tc_1839_1

description: total chromatin


title: WT_E2 Brep2 Trep2

description: WT E2


title: WT_Oil Brep2 Trep2

description: WT Oil


title: KO_E2 Brep1 Trep2

description: KO E2


title: ubH2B_ip_1839_2

description: ubH2B ip

value: mouse α-ubH2B  (17-650)

value: Lys120 ubiquitination site


title: WT_E2 Brep2 Trep1

description: WT E2


title: Bcat RNAi regenerating trunks day 1

tag: treatment


title: APC RNAi regenerating trunks day 6


title: ubH2B_ip_1907_1

description: ubH2B ip


title: ubH2B_ip_1839_1

description: ubH2B ip


title: WT_E2 Brep1 Trep2

description: WT E2

tag: age


title: KO_Oil Brep1 Trep1

description: KO Oil


title: H3K9ac_Ataxin7_ip_2

description: H3K9ac ip

value: rabbit α-H3K9ac (ab4441)

value: ARTKQTAR(Ac)KSTG-C


title: WT_E2 Brep1 Trep1

description: WT E2


title: WT_Oil Brep1 Trep2

description: WT Oil


title: WT_Oil Brep1 Trep1

description: WT Oil


title: H3K9ac_Ataxin7_ip_1

description: H3K9ac ip


title: H3K14ac_Ataxin7_ip_2

description: H3K14ac ip

value: rabbit α-H3K14ac (ab52946)

value: Lysine 14ac of Histone H3


title: H3_Ataxin7_ip_2

description: H3 ip

value: rabbit α-H3 (ab1791)

value: Histone H3 aa 100 to the C-terminus


title: H3K14ac_Ataxin7_ip_1

description: H3K14ac ip


title: WT_Oil Brep2 Trep1

description: WT Oil


title: H2B_ip_1907_1

description: H2B ip

value: rabbit α-H2B (ab1790)

value: C-terminus of  Histone H2B


title: H3_Ataxin7_ip_1

description: H3 ip


title: H2B_ip_1839_1

description: H2B ip


title: ada2b_ip_1839_2

description: ada2b ip


title: tc_1749_2

description: total chromatin

value: wild type


title: ada2b_ip_1907_1

description: ada2b ip


title: H2B_ip_1839_2

description: H2B ip


title: KO_Oil Brep1 Trep2

description: KO Oil


title: ubH2B_ip_1749_2

description: ubH2B ip


title: KO_E2 Brep1 Trep1

description: KO E2


title: ubH2B_ip_1749_1

description: ubH2B ip


title: tc_1749_1

description: total chromatin


title: wt_tc_1

description: total chromatin


title: wt_tc_2

description: total chromatin


title: H3K14ac_wt_ip_2

description: H3K14ac ip


title: H3K14ac_wt_ip_1

description: H3K14ac ip


title: H3K9ac_wt_ip_1

description: H3K9ac ip


title: H3K9ac_wt_ip_2

description: H3K9ac ip


title: H3_wt_ip_1

description: H3 ip


title: H2B_ip_1749_2

description: H2B ip


title: H3_wt_ip_2

description: H3 ip


title: H2B_ip_1749_1

description: H2B ip


title: FRT_1846_3

data_processing:
Base Calls were performed using CASAVA version 1.8.2
Reads were aligned to Drosophila genome dm3 with tophat v2.0.13 using -g 1 and --library-type fr-firststrand and gene models in gtf format from Ensembl 78
Reads were quantified on reduced transcripts from genes in Ensembl 78 using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version edgeR_3.14.0 using the count of mapped reads on the intervals for each gene.
Genome_build: dm3
Supplementary_files_format_and_content: rpkm.txt text file of expression values per sample in RPKM format.

source_name: ovary

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), with biological triplicates for each genotype.
Illumina libraries were generated using the TruSeq Stranded RNA kit.

treatment_protocol: For germline clone analyses, larvae were heat-shocked for 2 hr at 37°C for two consecutive days starting from the second day after hatching. Females were conditioned with yeast for 2–3 d before ovary dissection.

value: ovary

tag: experiment

value: wt


title: FRT_1846_2


title: K1 dmMLE-wt replicateB

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
5’-barcode: CGGCG, 3’-barcode: YRRY
K1_dmMLE-wt_combined_dm3.bed
K1_dmMLE-wt_combined_dm3.bw
K1_dmMLE-wt_jamm_dm3.narrowPeak
K1_dmMLE-wt_peakachu_dm3.gff
K1_dmMLE_wt_combined_gaps_dm3.bed/.bigWig

data_processing:
Barcodes and random tags were extracted using custom fastqpl scripts (Horton P. fastapl – a utility for versatile and easy processing of fasta format data (and fastqpl for fastq files). F1000Posters 2011, 2:1197 (poster)).
Adapters were trimmed and the library was demultiplexed using Flexbar (v2.32).
Possible readthroughs into the barcoded regions were removed by clipping 10 and 5 nt from the 3’-ends of first and second mate reads.
Reads were mapped to dm3 using bowtie2 (v2.2.0) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant and –maxins=200, only uniquely mapped reads were kept.
Uniquely mapped reads were used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013))
Crosslinking events from mid (M) and low (L) size fractions were combined for each biological replicate.
Combined crosslinked nucleotides of both replicates, extended by 5 nt up- and downstream, were used to create binding profiles in bigWig format.
Peaks were called with JAMM (version 1.0.7rev1, parameters "-d y -t paired -b 50 -w 1 -m normal") on the two replicates for the respective pulldown condition as foreground and the eGFP pulldown condition as background.
Peaks were called with PEAKachu (version 0.0.1alpha2, parameters "--pairwise_replicates -m 0") on the two replicates for the respective pulldown condition as foreground and the two replicates of eGFP pulldown condition as background. All crosslinked nucleotides were extended by 5 nt up- and downstream prior to peak calling to enable shape-based detection of candidate peaks.
Gapped alignments were determined using HMMSplicer (v 0.9.5) with parameters "runHMM.py -g dm3 -c FALSE -w 5 -k 2000 -d TRUE -r FALSE -p 8" for each size fraction of each replicate.
PCR duplicates were removed from HMMSplicer alignments using random barcodes. For multiple alignments at the same position with similar random barcodes (Hamming distance < 2), only the alignment with highest HMMSplicer score was kept.
The resulting alignments of size fractions and replicates were combined and filtered to retain only gapped alignments that do not correspond to canonical splice sites.
The gaps between the split-reads were extracted using a custom script.
Genome_build: dm3
Supplementary_files_format_and_content: bed files of crosslinking events with random tag in name column and number of merged PCR-duplicates in score column. bed files combining crosslinking events of size fractions and replicates. bigWig profiles of combined crosslinking events. JAMM peaks in narrowPeak format. PEAKachu peaks in gff format. Bed files of gapped alignments (gaps_dm3.bed/gaps_dm3.bigWig).

extract_protocol:
The cells are rinsed with PBS and crosslinked with 0.15mJ/cm2 UV-C light. After crosslinking, the cells are pelleted by centrifugation, snap-frozen in liquid nitrogen and kept at -80˚C until use. Cells are lysed with 0.5mL of lysis buffer, mildly sonicated and immunoprecipitated with anti-FLAG beads for 1hr at ˚C. The beads are washed with lysis buffer and bound material is eluted with 3xFLAG peptide (250µg/mL). The eluate is then incubated with MyONEC1 beads to collect biotinylated target protein, after which the beads are washed with high-stringency buffers (0.1%SDS, 1M NaCl, 0.5% LiDS, 0.5M LiCl and 1% SDS, 0.5M LiCl) to aggressively remove non-specific interactors. 3’-linkers are then ligated with T4 RNA Ligase 1, excess adapters are washed away and 3’-tagged, cross-linked RNA is released with proteinase K digestion and column purification (Zymo DNA Clean & Concentrator).
Reverse transcription is carried out with SuperScript III and barcoded reverse-transcription primers. After reverse transcription, relevant samples are mixed and the cDNA is separated on a 6% 6M Urea PAA gel. Size fractionated cDNA is then processed essentially as described in the iCLIP protocol to generate sequencing libraries (König, J. et al. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J. Vis. Exp. (2011). doi:10.3791/2638). uvCLAP reads contain two custom barcodes adjacent to the 5'- and 3'-adapters. The 5 nt 5'-barcodes are flanked by 5 random nt according to the pattern NNNTTTTTNN (N: random nucleotide, T: barcode nucletide) and specify the pulldown condition. The 5 nt semi-random 3'-barcodes DRYYR and DYRRY (D: not C, R: purine, Y: pyrimidine) are used to distinguish the two replicates of each experiment. The 5'-barcodes are located at the first 10 nucleotides of the first mate reads. The read pairs align forward/reverse, thus the reverse complement of the 3'-barcodes is located at the first 5 nucleotides of the second mate reads.

tag: expression vector

value: dmMLE-wt

tag: clip antibody

value: Anti-FLAG M2 Magnetic Beads (M8823 Sigma)


title: FRT_1846_1


title: nonstop_1846_3

value: nonstop


title: K1 dmMLE-wt replicateA

description:
5’-barcode: CGGCG, 3’-barcode: RYYR
K1_dmMLE-wt_combined_dm3.bed
K1_dmMLE-wt_combined_dm3.bw
K1_dmMLE-wt_jamm_dm3.narrowPeak
K1_dmMLE-wt_peakachu_dm3.gff
K1_dmMLE_wt_combined_gaps_dm3.bed/.bigWig


title: K1 dmMLE-K replicateB

description:
5’-barcode: AGAAT, 3’-barcode: YRRY
K1_dmMLE-K_combined_dm3.bed
K1_dmMLE-K_combined_dm3.bw
K1_dmMLE-K_jamm_dm3.narrowPeak
K1_dmMLE-K_peakachu_dm3.gff
K1_dmMLE_K_combined_gaps_dm3.bed/.bigWig

value: dmMLE-K


title: K1 dmMLE-K replicateA

description:
5’-barcode: AGAAT, 3’-barcode: RYYR
K1_dmMLE-K_combined_dm3.bed
K1_dmMLE-K_combined_dm3.bw
K1_dmMLE-K_jamm_dm3.narrowPeak
K1_dmMLE-K_peakachu_dm3.gff
K1_dmMLE_K_combined_gaps_dm3.bed/.bigWig


title: nonstop_1846_2


title: K1 dmMLE-KHR replicateB

description:
5’-barcode: GAGGT, 3’-barcode: YRRY
K1_dmMLE-KHR_combined_dm3.bed
K1_dmMLE-KHR_combined_dm3.bw
K1_dmMLE-KHR_jamm_dm3.narrowPeak
K1_dmMLE-KHR_peakachu_dm3.gff
K1_dmMLE_KHR_combined_gaps_dm3.bed/.bigWig

value: dmMLE-KHR


title: FRT_1799_3


title: nonstop_1846_1


title: K1 dmMLE-HR replicateA

description:
5’-barcode: TCACG, 3’-barcode: RYYR
K1_dmMLE-HR_combined_dm3.bed
K1_dmMLE-HR_combined_dm3.bw
K1_dmMLE-HR_jamm_dm3.narrowPeak
K1_dmMLE-HR_peakachu_dm3.gff
K1_dmMLE_HR_combined_gaps_dm3.bed/.bigWig

value: dmMLE-HR


title: K1 dmMLE-GET replicateB

description:
5’-barcode: GCTGA, 3’-barcode: YRRY
K1_dmMLE-GET_combined_dm3.bed
K1_dmMLE-GET_combined_dm3.bw
K1_dmMLE-GET_jamm_dm3.narrowPeak
K1_dmMLE-GET_peakachu_dm3.gff
K1_dmMLE_GET_combined_gaps_dm3.bed/.bigWig

value: dmMLE-GET


title: K1 control replicateA

description:
5’-barcode: GTATG, 3’-barcode: RYYR
K1_control_combined_dm3.bed
K1_control_combined_dm3.bw
K1_control_combined_gaps_dm3.bed/.bigWig

value: eGFP


title: FRT_1799_2


title: ataxin7_1799_3


title: ataxin7_1799_2


title: K1 dmMLE-HR replicateB

description:
5’-barcode: TCACG, 3’-barcode: YRRY
K1_dmMLE-HR_combined_dm3.bed
K1_dmMLE-HR_combined_dm3.bw
K1_dmMLE-HR_jamm_dm3.narrowPeak
K1_dmMLE-HR_peakachu_dm3.gff
K1_dmMLE_HR_combined_gaps_dm3.bed/.bigWig


title: K1 control replicateB

description:
5’-barcode: GTATG, 3’-barcode: YRRY
K1_control_combined_dm3.bed
K1_control_combined_dm3.bw
K1_control_combined_gaps_dm3.bed/.bigWig


title: K1 dmMLE-GET replicateA

description:
5’-barcode: GCTGA, 3’-barcode: RYYR
K1_dmMLE-GET_combined_dm3.bed
K1_dmMLE-GET_combined_dm3.bw
K1_dmMLE-GET_jamm_dm3.narrowPeak
K1_dmMLE-GET_peakachu_dm3.gff
K1_dmMLE_GET_combined_gaps_dm3.bed/.bigWig


title: ada2b_1764_2


title: ataxin7_1799_1


title: Total RNA from BFTC 905/CTL cell line

city: Chia-Yi

first: Yu Ming

last: Chuang

address: 168 University Road,Min Hsiung

department: Department of Biomedical Science

country: Taiwan

institute: National Chung Cheng University

description: BFTC 905 bladder cancer cell line which the ANGPTL4 expression is low.

data_processing:
Illumina MiSeq used for basecalling.
CLC Genomics Workbench 8.5.1 software was used.
The raw reads were cleaned by trimming of adaptor sequences.
Sequenced reads were mapped to hg19 genome using CLC Workbench default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: fastq files were generated by Illumina MiSeq

source_name: bladder cancer cell line

growth_protocol: BFTC 905 cells were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were incubated at 37C under a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA was extracted from each sample using TRIzol reagent.

treatment_protocol: BFTC 905 cells were either transfected with pcDNA3.1-myc-His (-) A or plasmid overexpressing ANGPTL4. Stable clones were selected using medium containing 400ug/ml G418.

tag: cell line

value: BFTC 905

tag: transfection

value: pcDNA3.1 (vector control)


title: FRT_1799_1

tag: genotype


title: FRT_1764_3


title: ada2b_1764_3


title: Total RNA from BFTC 905/ANGPTL4 cell line

value: plasmid overexpressing ANGPTL4


title: ada2b_1764_1


title: nonstop_1190_1

source_name: stage 5 embryos

treatment_protocol: Embryos were collected for 2h and aged 1h at 25°C. Stage 5 embryos were hand sorted.

tag: developmental stage

value: stage 5 embryos

value: non-stop


title: ataxin7_1013_3


title: FRT_1764_2


title: ataxin7_1013_2


title: K1 dmMLE-KHR replicateA

description:
5’-barcode: GAGGT, 3’-barcode: RYYR
K1_dmMLE-KHR_combined_dm3.bed
K1_dmMLE-KHR_combined_dm3.bw
K1_dmMLE-KHR_jamm_dm3.narrowPeak
K1_dmMLE-KHR_peakachu_dm3.gff
K1_dmMLE_KHR_combined_gaps_dm3.bed/.bigWig


title: nonstop_1190_3


title: nonstop_1190_2


title: ataxin7_1013_1


title: oreR_1013_3

value: oreR


title: Mouse_Macrophage_RAW_LPS_3

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

country: United Kingdom

institute: University of Bath

data_processing:
Human sequencing data was aligned against human reference genome hg38 using Tophat2: tophat --library-type fr-firststrand <reference_genome.gtf> -1 <forward_strand.fa> -2 <reverse_strand.fa> -o <output.sam>. Mouse sequencing data was aligned against mm10 using Hisat2: hisat2 -q --dta --rna-strandness FR –x <reference_genone.gtf> -1 <forward_strand.fa> -2 <reverse-strand file.fa> –S <output.sam>.
Output SAM files were then sorted and converted to BAM files (samtools sort -@ 8 –o output.bam output.sam) and indexed (samtools index –b output.bam) in Samtools
Differential expression of protein coding genes and lncRNAs in human macrophages and epithelium (Gencode v23 - human macrophages and epithelium.txt) and mouse RAW cells (Gencode m12 - mouse macrophages.txt) was assessed with the geometric option (DESeq) in Cuffdiff v2.2.1.3 using a significance threshold of q <0.05: cuffdiff --FDR=0.05 --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled -u <reference_genome.gtf> <control_1.bam>,<control_x.bam> <activated_1.bam>,<activated_x.bam> -o <output_file_name>using Cuffdiff (V2.2.1.2)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values for each group and differential expression between groups

extract_protocol:
RNA was extracted from cells using the Rneasy kit which included on on-column Dnase treatment. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LPS


title: Mouse_Macrophage_RAW_LPS_2


title: Mouse_Macrophage_RAW_Control_4

value: media


title: Mouse_Macrophage_RAW_Control_3


title: Mouse_Macrophage_RAW_LPS_1


title: oreR_1013_1


title: tc_1632_1

description: Processed data file: polII_1632_1.bed

source_name: total chromatin

value: 1-3 hr embryo


title: Mouse_Macrophage_RAW_Control_1


title: Mouse_Macrophage_RAW_Control_2


title: spt3_ip_1530_2

description: Processed data file: spt3_1530_2.bed

source_name: spt3 ip

tag: antibody

value: full length


title: H3K14pr_F2

city: Neuherberg

first: Robert

last: Schneider

address: Ingolstaedter strasse 1

department: Institute of Functional Epigenetics

institute: Helmoltz Zentrum Muenchen

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Wig files were generated using an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Liver, fasted, H3K14pr ChIP

extract_protocol:
Livers were crosslinked in situ with 1% formaldehyde for 5 min at RT based on Chaya and Zaret (2003) protocol. Chromatin was isolated using NEXON protocol (Arrigoni et al., 2015).
ChIP-seq libraries prepared according to Illumina protocols.

treatment_protocol: C57BL/6J male mice were fed normally or fasted for 48h.

tag: strain/background

tag: gender

value: Male

value: Liver

value: Fasted

tag: chip antibody


title: H3K14bu_F2

source_name: Liver, fasted, H3K14bu ChIP

tag: tissue


title: polII_ip_1188_2

description: Processed data file: polII_1188_2.bed

source_name: pol II ip

tag: replicate

value: CTD repeat YSPTSPS (phospho S5)


title: spt3_ip_1760_2

description: Processed data file: spt3_1760_2.bed


title: tc_1760_2

description: Processed data file: ada2b_1760_2.bed


title: oreR_1013_2


title: ada2b_ip_1760_2

description: Processed data file: ada2b_1760_2.bed

source_name: ada2b ip


title: Input_F2

source_name: Liver, fasted, input


title: polII_ip_1632_1

description: Processed data file: polII_1632_1.bed


title: H3K9ac_F2

source_name: Liver, fasted, H3K9ac ChIP


title: FRT_1764_1

value: ovary

value: wt


title: tc_1530_3

description: Processed data file: ada2b_1530_3.bed


title: spt3_ip_1530_1

description: Processed data file: spt3_1530_1.bed


title: H3K14bu_F1


title: Mouse_Macrophage_RAW_LPS_4

tag: cell type


title: H3K14pr_F1


title: H3K9ac_F1


title: tc_1530_2

description: Processed data file: ada2b_1530_2.bed


title: tc_1188_2

description: Processed data file: polII_1188_2.bed


title: ada2b_ip_1530_2

description: Processed data file: ada2b_1530_2.bed

tag: epitope


title: Input_F1

tag: treatment


title: H3K14bu_R2

source_name: Liver, re-fed, H3K14bu ChIP

value: Re-fed


title: anti_Brd4cachexia_JQ1+

city: Milan

first: Giuseppina

last: Caretti

address: Via Celoria 26

country: Italy

institute: University of Milan

description: ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
peaks were called using MACS2 ( Zang et al, 2008) with the default options for broad peak calling
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample

source_name: adult skeletal muscle

growth_protocol: Muscles from 10 weeks old control and C26-tumor bearing mice were isolated after sacrifice; samples were promptly frozen with liquid nitrogen and kept at -80C.

extract_protocol:
Frozen tissues were pulverized in Covaris tissue TUBEs (Covaris 520001) using a chilled hammer on a cold metallic block, in dry ice. Powdered tissue was resuspended in PBS, cross-linked in 1% formaldehyde for 15 minutes. After blocking crosslink with 0.125M glycine for 5 minutes and washes with PBS plus protease and phosphatase inhibitors, pellet was resuspended in Farnham buffer (5 mM PIPES pH 8.0; 85 mM KCl; 0.5% NP-40) and briefly homogenized with a tissue homogenizer.   Cells were subsequently lysed in RIPA buffer (1x PBS; 1% NP-40; 0.5% sodium deoxycholate; 0.1% SDS). 100mg of starting tissue was used for each antibody. Chromatin was sonicated to fragments length of approximately 0.5Kb and immunoprecipitated with 3.5µg of BRD4 antibody. Immunoprecipitation procedures were performed as in Proserpio et al., 2013.
For ChIPSeq,  10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with  Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol.

treatment_protocol: Tumor-bearing mice received 105 C26 colon carcinoma cells in PBS by dorsal s.c. injection. Animals were then randomized and divided into 3 groups: Control (mice without tumor cell inoculation, treated with vehicle), C26+(-)-JQ1-20 (C26-bearing mice, 20 mg/kg body weight of the inactive JQ1 enantiomer), C26+(+)-JQ1-20 (C26-bearing mice, 20 mg/kg body weight of the active JQ1 enantiomer)

value: adult skeletal muscle

tag: age

value: 10 weeks

tag: strain

value: Balb/c


title: Input_muscle_cachexia_JQ1+

description: ChIP-seq


title: tc_1530_1

description: Processed data file: ada2b_1530_1.bed


title: Input_muscle_cachexia

description: ChIP-seq


title: H3K9ac_R2

source_name: Liver, re-fed, H3K9ac ChIP


title: anti_Brd4_control

description: ChIP-seq


title: Input_muscle_control

description: ChIP-seq


title: nonstop_ip_1924_2

description: Processed data file: nonstop_1924_2.bed

source_name: nonstop ip

value: rabbit-anti-nonstop


title: tc_1924_1

description: Processed data file: nonstop_1924_1.bed


title: Input_R2

source_name: Liver, re-fed, input


title: ada2b_ip_1530_3

description: Processed data file: ada2b_1530_3.bed


title: 10_WT_LipidA_rep2_6h

city: los angeles

first: Prabhat

middle: Kumar

last: Purbey

state: California

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

data_processing:
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle. RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-unstranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to stimulation.

extract_protocol:
total RNA was biochemically purified as previously described (Bhatt et al, Cell 2012). Cells were resuspended in TriReagent and RNAs were purified using Rneasy columns (Qiagen).
All mRNA libraries were generated using the Illumina Truseq v.2 kit with a few modifications: strand specific libraries were generated using the dUTP method. Briefly, the second strand cDNA was synthesized in the presence of dUTP. Prior to library amplification, the second strand was degraded with dUTPase. Few libraries were genearted using TruSeq Stranded mRNA Library Prep  Kit as per manufacturere's instructions.

value: bone marrow

value: macrophage

value: wildtype

tag: stimulus

value: LipidA

tag: time point (h)


title: nonstop_ip_1924_1

description: Processed data file: nonstop_1924_1.bed

value: 1-3 hr embryo


title: tc_1924_2

description: Processed data file: sgf11_1924_2.bed


title: 07_WT_LipidA_rep2_0.5h


title: H3K14bu_R1


title: H3K14pr_R1

source_name: Liver, re-fed, H3K14pr ChIP


title: 09_WT_LipidA_rep2_2h


title: 08_WT_LipidA_rep2_1h


title: H3K9ac_R1


title: 04_WT_LipidA_rep1_2h


title: sgf11_ip_1924_2

description: Processed data file: sgf11_1924_2.bed

source_name: sgf11 ip

value: full length


title: 05_WT_LipidA_rep1_6h


title: ada2b_ip_1530_1

description: Processed data file: ada2b_1530_1.bed


title: 06_WT_LipidA_rep2_0h

value: no-stimulation


title: H3K14pr_R2

value: Male

value: Liver


title: tc_1377_2

description: Processed data file: sgf11_1377_2.bed


title: 03_WT_LipidA_rep1_1h


title: Input_R1


title: 01_WT_LipidA_rep1_0h


title: sgf11_ip_1377_2

description: Processed data file: sgf11_1377_2.bed


title: anti_Brd4_cachexia

description: ChIP-seq


title: 02_WT_LipidA_rep1_0.5h


title: 48h fasted3

description: Processed data file: S14203_genesdiff_wo5.xlsx

data_processing:
Reads were mapped onto the mm9 assembly of mouse genome using Tophat v2.0.10 (Kim et al., 2013) and the bowtie2 v2.1.0 aligner (Langmead et al., 2012).
Quantification of gene expression was performed using HTSeq v0.5.4p3 (Anders et al., 2015) using gene annotations from Ensembl release 67.
Read counts were normalized across libraries with the method proposed by Anders and Huber (2010).
Comparisons of interest were performed using the method proposed by Love et al. (2014) implemented in the DESeq2 Bioconductor library (DESeq2 v1.0.19). Resulting p-values were adjusted for multiple testing using the Benjamini and Hochberg (1995).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: S14203_genesdiff.xlsx: Excel spreadsheet with normalized read counts and log2 fold change comparison between re-fed and fasted mouse livers.

source_name: Liver, fasted

extract_protocol:
Trizol reagent was used to extract total RNA from homogenized liver tissue.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 48h Fasted


title: 48h fasted2


title: tc_1377_1

description: Processed data file: sgf11_1377_1.bed

source_name: total chromatin


title: EL4 CTCF-motif KO Pol II ChIP-Seq

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: ChIP-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed from further analysis in each library.
We identified peak of ChIP-Seq using MACS and calculated the RPKM of each gene in RNA-seq
Using our 3e Hi-C data, the topological domain were identified based on the the approach in Dixon et al., 2012.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph: plan text file. The four columns are chrom, start position, end position, data value.

growth_protocol: The R1 murine ES cells were cultured on feeder coated dishes in ES-qualified DMEM supplemented with various growth factors as described previously (Hu et al., 2013a). For generation of Th2 cells, naïve CD4+ T cells were isolated from the lymph nodes of C57BL/6 mice from the Jackson Laboratory (JAX) by staining with Pacific Blue-anti-CD62L, APC-anti-CD4, APC-Cy7- anti-CD44 and PE-anti-CD25 and sorting for CD4+CD25-CD62LhiCD44low population by FACSAria (BD Biosciences) as described before (Hu et al., 2013b). For Th2 condition induction, the cytokine and antibody cocktail containing IL-4 (5000U/ml), IL-2 (100U/ml), anti-IFNγ (10μg/ml) and anti-IL-12 (10μg/ml) was added to the cell culture and two rounds of polarization were performed (Hu et al., 2013b). EL4 cells were cultured in DMEM (Gibco Invitrogen) supplemented with 50 IU/mL penicillin and 50μg/mL streptomycin (Gibco Invitrogen) and 10% heat inactivated calf serum (Sigma, USA). Cultures was maintained by replacement of fresh medium every 3 days, and carefully kept cell density between 1 X 105 and 1 X 106 cells/ml.

extract_protocol:
For generating ChIP-Seq libraries, chromatin extracts were prepared by sonication of cells following crosslinking with 1% formaldehyde for 10min at room temperature. The ChIP was performed with 1 ug specific antibodies as described (Barski et al., 2007) and ChIP-Seq libraries were prepared using indexing primers as described (Hu et al., 2013a). RNA-Seq libraries using polyA RNA isolated from both the WT and KO cells were prepared as described (Chepelev et al., 2009).
Murine R1 ES cells and in vitro inducted Th2 cells were cross-linked with 1% formaldehyde for 10min at room temperature. 10 X106 cells were lysed by resuspending in 10ml lysis buffer (10mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP40; 10μl protease inhibitors (Sigma)) and incubation at 4°C with rotation for one hour. The cells were then treated with 400 μl 1xNEB cutsmart buffer + 0.1% SDS at 65°C for 10 minutes, followed by addition of 44μl 10% Triton X-100 to quench SDS. Chromatin was subsequently digested with 20 Units CviQ I (NEB), and 20 Units CviA II (NEB) at 25°C for 20 minutes, then 20 Units Bfa I (NEB) at 37°C for 20 minutes. The reaction was stopped by washing the cells twice with 600 ul wash buffer (10mM NaCl, 1mM EDTA, 0.1% triton-100). Then the samples were processed as the Hi-C protocol (Lieberman-Aiden et al., 2009) with modifications briefly described below. The DNA ends were blunted and labeled with biotin by Klenow enzyme in the presence of dCTP, dGTP, dTTP, biotin-14-dATP, followed by 3C ligation using T4 DNA ligase. After reverse crosslinking, the DNA was fragmented to 300-500 bp by sonication with a Bioruptor sonicator (Diagenode UCD-200). The samples were treated with T4 DNA polymerase to remove biotin labels at the DNA ends. The remaining biotinylated DNA fragments were then captured using Dynabeads MyOne Streptavin C1 Beads (Invitrogen) by incubating for 30 minutes at RT with rotation. The DNA on beads was end-repaired, followed by A-addition and ligation to the Illumina Paired End Adaptors as described previously. Following PCR-amplification of the libraries, DNA fragments from 300 to 600 bp were purified from 2% agarose gel and sequenced on HiSeq2000.

treatment_protocol: Genome Editing was carried out by CRISPR/Cas9 system (Cong et al., 2013). The CRISPR/Cas9 plasmid pairs were nucleofected by using Nucleofector Kit V according to the manufacturer’s instructions (Lonza). One plasmid expressing pGreenpuro was also co-transfected. After 24 hours, the cells were selected in fresh medium with 6mg/ml puromycin (Sigma). After 72 hours, limiting dilution was performed and selection was continued for 8–12 days. Individual clones were picked and genomic DNA was extracted by following the manufacturer’s instructions (Redextract-N-AMP tissue kit, SIGMA). Genotyping was done by using locus-specific PCR primers under the following PCR conditions: 98°C for 30 s; 35 cycle (98°C for 10 s, 60°C for 30 s, 72°C for 35 s); 72°C for 5 min; hold at 4°C. PCR products were run on 2% agarose gel. Positive clones were expanded for further experiments.

tag: cell line


title: 48h fasted1


title: EL4 CTCF-motif KO CTCF ChIP-Seq

description: ChIP-seq


title: EL4 WT H3K27ac ChIP-Seq

description: ChIP-seq


title: sgf11_ip_1377_1

description: Processed data file: sgf11_1377_1.bed


title: EL4 CTCF-motif KO Input

description: ChIP-seq


title: Refed3

source_name: Liver, re-fed


title: Refed2


title: EL4 WT Pol II ChIP-Seq

description: ChIP-seq


title: Trpv1- Nodose neurons_2 (Trpv1-tdTomato selection)

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

data_processing:
Basecalls performed using CASAVA-1.8.2
Sequenced reads were aligned to the mm10 genome assembly using TopHat v2.0.9 and Bowtie v2.1.0.0 with default settings
Raw gene counts were generated using HTseq
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for each sample

source_name: vagal C-fiber neurons

extract_protocol:
From each jugular/nodose ganglion complex of the mouse, the most rostral (jugular) and the most caudal (nodose) portion were used. The ganglia were enzymatically dissociated. Individual capsaicin-sensitive (capsaicin selection) /Trpv1-positive (Trpv1-tdTomato selection) nodose and jugular neurons were collected into the pipette under the microscope. cDNA synthesis was performed using SMARTer Ultra Low Input RNA Kit v3 following manufacturer’s protocol (Clontech). Cells were used directly as starting material without RNA extraction to avoid extra loss of RNA.
Illumina paired-end DNA sequencing library was generated using Low Input Library Prep Kit v2 following manufacturer’s protocol (Clontech)

value: Trpv1- Nodose neurons

value: Trpv1-tdTomato mice


title: Trpv1- Nodose neurons_1 (Trpv1-tdTomato selection)


title: Refed1

value: Re-fed


title: Nodose neurons_1 (Capsaicin selection)

value: Capsaicin-sensitive nodose neurons


title: Nodose neurons_2 (Capsaicin selection)


title: Trpv1+ Jugular neurons_1 (Trpv1-tdTomato selection)

value: Trpv1+ Jugular neurons


title: E13.5 WlsShhCre trachea replicate 2

city: Cincinnati

first: Debora

last: Sinner

state: OH

address: 3333 Burnet Ave

department: Neonatology and Pulmonary Biology

institute: CCHMC

description:
M4
Tracheomalacia_E13.5_all_raw-counts

data_processing:
paired reads were aligned against mm9 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Deseq was used to normalize .bam files
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include Raw counts andRead Density

source_name: embryonic mouse trachea

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
Total RNA was isolated from dissected trachea using Trizol (Life Technologies)
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

value: trachea

tag: development stage

tag: genotype/variation

value: WlsShhCre


title: Trpv1+ Jugular neurons_2 (Trpv1-tdTomato selection)


title: Trpv1+ Nodose neurons_1 (Trpv1-tdTomato selection)

value: Trpv1+ Nodose neurons


title: T_wt_Day4

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

data_processing:
ChIP-seq
Bowtie1.0.0
To estimate the fragment size distribution of the libraries and determine the maximum length cutoff, we performed an initial mapping of a limited number of reads using the options -y -m 1 -S -I 100 -X 500
The final mapping was performed using the same options and the determined maximum length parameter (-X).
Paired-end reads from the sam file were combined into a single bed file by generating the original fragment using a custom perl script and .wig files were generated using BEDtools version 2.23.0
RNA-seq
TopHat2, 2.0.8--mate-inner-dist 250 --mate-std-dev 100 -g 1 --library-type fr-secondstrand
BEDtools version 2.23.0, converted into bigwig
to calculate FPKM: Cufflinks 2.1.1 -u --no-effective-length-correction -b
Genome_build: mm10
Supplementary_files_format_and_content: ChIPseq resultes are represented in BigWig files. RNAseq results are given in FPKM values, listed in an Excel file

source_name: T_positiveFACSsorted cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 20,00 T positive cells were FACS sorted directly into RLT RNA Lysis buffer (Qiagen) and RNA extarcted according to the manufactureres protocol.
Libraries for ChIP-seq were constructed accoording to the Illumina TrueSeq ChIP Sample Preparation Kit. Libraries for RNA-seq were constructed according to the ScriptSeq v2 Complete (Mouse/Human/Rat) Low Input Kit (Illumina/Epicenter)

treatment_protocol: Feeder cells were removed from mESCs by serial plating and mESCs were aggregated by the hanging drop method overnight in ESC medium (40 cells per μL, 5μL per drop). The next day, embryoid bodies were washed thoroughly with Advanced DMEM (Gibco #12491015), and plated onto tissue culture dishes coated with fibronectin (1:100 dilution in 1x PBS, Calbiochem #341631) in serum-free medium (SFM, 1:1 Neurobasal:F12/DMEM (Gibco), 2mM L-glutamine (Gibco), 50U/mL penicillin; 50μg/mL streptomycin (Lonza), 0.5x B-27 supplement, serum-free (Gibco), 0.5x N-2 supplement (Gibco), 0.05% Albumin, bovine Fraction V (7.5%; Sigma-Aldrich), 0.001% 1-thioglycerol (Sigma-Aldrich)) containing recombinant BMP4 (20ng/mL, R&D Systems) for 18 hours. After 18 hours, SFM+rBMP4 was removed and replaced with SFM with 40ng/mL rWNT3A (R&D Systems) and 40ng/mL rFGF8 (R&D Systems) for the remainder of the differentiation.

value: Tpos cells in vitro diff FACS

tag: Stage

value: Day 4 in vitro diff


title: T_Y88A_Day4


title: Trpv1+ Nodose neurons_2 (Trpv1-tdTomato selection)


title: E13.5 WlsShhCre trachea replicate 1

description:
M3
Tracheomalacia_E13.5_all_raw-counts


title: E13.5 control trachea replicate 2

description:
C4
Tracheomalacia_E13.5_all_raw-counts

value: control


title: EL4 WT Input

description: ChIP-seq


title: EL4 CTCF-motif KO H3K27ac ChIP-Seq

description: ChIP-seq


title: EL4 WT CTCF ChIP-Seq

description: ChIP-seq


title: 15_WT_6G_6h_pp53

data_processing:
ChIP-seq libraries were sequenced on an Illumina HiSeq 2000.
ChIP-seq fastq files were mapped using Bowtie2. Only the uniquely mapped reads were kept for further analysis.
Uniquely aligned reads were peak-called using the Homer suite with a FDR threshold of 0.01.
Called peaks were annotated to the nearest Refseq ID, mm9 build
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample was generated using Homer and represent the read coverage at each genomic position

growth_protocol: Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 6 days prior to irradiation experiment.

extract_protocol:
Purified nuclei from BMDMs were lysed and chromatin was sheared using a Misonix-3000 microtip prior to immunoprecipitation with anti-IRF1, anti-IRF3, or anti-p-p53 antibodies
libraries were constructed using Kapa's LTP Library Preparation kit according to manufactuer's instruction.

treatment_protocol: Chromatin samples from 0,1, 2, and 6 h post irradiation were used for Chromatin IP with anti IRF1 and IRF3 antibodies.  For p-p53 ChIP, chromatin from 0, 0.5, 1, 2 and 6 h post irradiation were used.

tag: genotype

value: wildtype

value: bone marrow

value: macrophage

tag: irradiation

value: Irradiated

tag: antibody


title: 13_WT_6G_1h_pp53

tag: time point


title: 12_WT_6G_0.5h_pp53

tag: tissue


title: E11.5 WlsShhCre trachea replicate 2

description:
M2
Tracheomalacia_E11.5_all_raw-counts


title: E11.5 WlsShhCre trachea replicate 1

description:
M1
Tracheomalacia_E11.5_all_raw-counts


title: Jugular neurons_2 (Capsaicin selection)

value: Capsaicin-sensitive jugular neurons


title: 14_WT_6G_2h_pp53


title: 10_Inputmix_pp53

value: INPUT (none)


title: 09_WT_6G_6h_IRF3


title: 07_WT_6G_1h_IRF3


title: 11_WT_0_pp53


title: Jugular neurons_1 (Capsaicin selection)


title: 06_WT_0_IRF3


title: 08_WT_6G_2h_IRF3


title: E11.5 control trachea replicate 2

description:
C2
Tracheomalacia_E11.5_all_raw-counts


title: E11.5 control trachea replicate 1

description:
C1
Tracheomalacia_E11.5_all_raw-counts


title: 04_WT_6G_2h_IRF1


title: 05_WT_6G_6h_IRF1


title: T_Y88A_TS12

data_processing:
ChIP-seq:
Bowtie1.0.0
To estimate the fragment size distribution of the libraries and determine the maximum length cutoff, we performed an initial mapping of a limited number of reads using the options -y -m 1 -S -I 100 -X 500
The final mapping was performed using the same options and the determined maximum length parameter (-X).
Paired-end reads from the sam file were combined into a single bed file by generating the original fragment using a custom perl script and .wig files were generated using BEDtools version 2.23.0
RNA-seq:
TopHat2, 2.0.8--mate-inner-dist 250 --mate-std-dev 100 -g 1 --library-type fr-secondstrand
BEDtools version 2.23.0, converted into bigwig
to calculate FPKM: Cufflinks 2.1.1 -u --no-effective-length-correction -b
Genome_build: mm10
Supplementary_files_format_and_content: ChIPseq resultes are represented in BigWig files. RNAseq results are given in FPKM values, listed in an Excel file

tag: strain background

value: T_Y88A (mutant)

value: Tpos cells embryo FACS


title: T_Y88A_TS13

tag: cell type


title: 01_Input_IRF1-IRF3


title: 249.NRF2_rep2_24h

data_processing:
RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
All aligned reads were imported to SeqMonk. The mRNA expression was calculated by totaling all uniquely aligned exonic reads. The raw reads were converted to RPKM by dividing the reads by the cDNA length and the total number of uniquely mapped reads in the sample.
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

value: 6Gray Ionizing Radiation


title: E13.5 control trachea replicate 1

description:
C3
Tracheomalacia_E13.5_all_raw-counts


title: 03_WT_6G_1h_IRF1


title: 245.NRF2_rep2_0.5h


title: 246.NRF2_rep2_1h


title: 247.NRF2_rep2_2h


title: 244.NRF2_rep2_0

value: No-radiation


title: 243.WT(Nrf2)_rep2_24h


title: T_Y88A_H3K27Ac_ChIPseq

source_name: Early mesodermal enriched

value: ES derived mesodermal enriched

tag: chip antibody

value: Anti-Histone H3K27ac antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: T_ChIPseq

value: wild type

value: brachyury (N-19) Antibody

value: Santa Cruz


title: 248.NRF2_rep2_6h

tag: strain


title: wt_TS12/TS13


title: T_Y88A_H3K27me3_ChIPseq

value: H3K27me3 polyclonal antibody

value: Diagenode


title: 236.NRF2_rep1_6h

value: bone marrow

tag: stimulus


title: 240.WT(Nrf2)_rep2_1h

value: macrophage

value: wildtype

tag: time point (h)


title: T_het_H3K27me3_ChIPseq

value: wild type control (T_het)


title: 237.NRF2_rep1_24h


title: 241.WT(Nrf2)_rep2_2h


title: 242.WT(Nrf2)_rep2_6h


title: 239.WT(Nrf2)_rep2_0.5h


title: 235.NRF2_rep1_2h


title: 02_WT_0_IRF1

value: Irradiated


title: T_Y88A_H3K4me3_ChIPseq

value: T_Y88A (mutant)

value: Anti-Histone H3K4me3 antibody


title: T_het_H3K27Ac_ChIPseq


title: 234.NRF2_rep1_1h

value: 6Gray Ionizing Radiation


title: 233.NRF2_rep1_0.5h


title: 230.WT(Nrf2)_rep1_6h


title: 232.NRF2_rep1_0

value: No-radiation


title: AIDTET_WT3 ERRBS

city: New York

first: Francine

middle: E.

last: Garrett-Bakelman

address: 413 East 69th street, BRB 1426

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to mm9 using a whole genome bismark alignment software approach with a maximum of 2 mismatches in a directional manner allowed. Only uniquely aligned reads were retained. Reads which pass filter were considered for mapping. If both matched reads pass filter, the last base of R2 was compared to the first base of R1 (one base overlap); the base with the best quality score was retained and R1 was concatenated to R2 for use in alignment.
methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base (Cs and Ts).
Genome_build: mm9; NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (base) covered

source_name: bone marrow

growth_protocol: Not applicable

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis, cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina Tru-seq adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads

treatment_protocol: Not applicable

value: LSK


title: 229.WT(Nrf2)_rep1_2h


title: 228.WT(Nrf2)_rep1_1h


title: AIDTET_WT2 ERRBS


title: 227.WT(Nrf2)_rep1_0.5h


title: 238.WT(Nrf2)_rep2_0


title: AIDTET_WT1 ERRBS


title: 225.P53_rep2_24h


title: AIDTET_KO2 ERRBS

value: Aid+/-


title: 226.WT(Nrf2)_rep1_0


title: AIDTET_KO1 ERRBS


title: 219.WT(p53)_rep2_24h


title: 222.P53_rep2_1h


title: 223.P53_rep2_2h


title: AIDTET_WT2 RNA-Seq

data_processing:
Raw reads were aligned to the mm9 genome using STAR RNA-seq aligner (v 2.4.0f1) with default parameters and using Gencode M1 transcriptome assembly
RNAseq counts were annotated by using subread (v 1.4.5-p1) featureCounts
Genome_build: mm9 (NCBIM37) using Gencode M1 transcriptome assembly

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis, cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) per manufacturer's recommendations


title: 224.P53_rep2_6h


title: 221.P53_rep2_0.5h


title: 217.WT(p53)_rep2_2h


title: AIDTET_WT1 RNA-Seq


title: 220.P53_rep2_0


title: AIDTET_KO3 RNA-Seq


title: 216.WT(p53)_rep2_1h


title: AIDTET_KO2 RNA-Seq


title: 231.WT(Nrf2)_rep1_24h


title: T_het_H3K4me3_ChIPseq

value: ES derived mesodermal enriched

value: Abcam


title: 214.WT(p53)_rep2_0


title: AIDTET_KO1 RNA-Seq


title: 213.P53_rep1_24h


title: 212.P53_rep1_6h


title: 211.P53_rep1_2h


title: 210.P53_rep1_1h


title: 209.P53_rep1_0.5h


title: 218.WT(p53)_rep2_6h


title: 000183Y

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

data_processing:
TopHat was used for mapping of RNA-Seq data, and Cufflinks version 2.1.1 was used for quantifying the expression level of each gene as fragments per kilobase of exon per million fragments (FPKM) with default parameters.
The differentially expressed genes were identified using Cuffdiff version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

source_name: B220+Gr1–cKit+ bone marrow cells

extract_protocol:
Total RNA was prepared by using Sepasol-RNA I Super G (nacalai tesque) and 80 ng of total RNA was used for further steps. Isolation of poly(A)-tailed RNA and library construction were performed using Sureselect Strand Specific RNA Sample Prep Kit (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B220+Gr1–cKit+ bone marrow cells


title: 000181Y


title: 208.P53_rep1_0


title: 000184Y


title: 215.WT(p53)_rep2_0.5h


title: 000177Y


title: 000178Y


title: 202.WT(p53)_rep1_0


title: 201.WT_100uM-NAC_6G_6h

description: samples1-5 are no treatment control for this set

value: 100uM NAC + Ionizing Radiation


title: 206.WT(p53)_rep1_6h


title: 204.WT(p53)_rep1_1h


title: 000180Y


title: 203.WT(p53)_rep1_0.5h


title: 205.WT(p53)_rep1_2h


title: 199.WT_100uM-NAC_6G_1h