title: Input Day 5 Repl_3

city: Bellinzona

first: Samuele

last: Notarbartolo

address: Via Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Data processing was run on the Fish the ChIPs automated pipline (Barozzi, I., Termanini, A., Minucci, S. & Natoli, G. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data. Biol Direct 6, 51 2011).
Alignment: Bowtie
Peak calling: MACS 1.4
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: Processed data included in the submission are: Excel files (.merge.xlsx) containing peaks genomic coordinates, MACS p-value, FDR and fold enrichmnt; tiled data files (.tdf) files for ChIP-seq data graphical visualization in the Integrative Genome Viewer software

source_name: primary Th17 lymphocytes

growth_protocol: T cells were cultured in RPMI-1640 medium supplemented with 1% (v/v) glutaMAX™-I, 1% (v/v) non-essential amino acids, 1 mM sodium pyruvate, 50 μM bmercaptoethanol, penicillin (50 U/ml), streptomycin (50 μg/ml), 1% (v/v) kanamycin (all from Gibco, Life Technologies) and 5% (v/v) human serum (Swiss Blood Center Basel) (hereafter referred as complete medium). 500 U/ml IL-2 (produced in house from IL-2T6 culture supernatants) was added to the culture medium for long term cultures. Single T cell clones were isolated by limiting dilution in 384-well plates (0.65 cells/well) and expanded with allogeneic irradiated (45 Gy) feeders (2.5 x 104/well) and phytohemagglutinin (PHA, 1 μg/ml; Remel) in IL-2- (500 U/ml) containing complete medium.

extract_protocol:
ChIP was performed as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013). Briefly, 20-50 x 106 cells were fixed in 1% formaldehyde (Sigma-Aldrich) for exactly 10 min at RT under rotation. Crosslinking reaction was quenched by the addition of 125 mM Tris-HCl pH 7.6 for 5 min at RT. Cells were washed 3 times with ice-cold PBS. The cell pellet was then resuspended in RIPA buffer (without Triton X-100) supplemented with protease inhibitors (Halt™ Protease Inhibitor Cocktail, Thermo Scientific) and frozen at -80°C. Chromatin was sheared with a Bioruptor® Plus bath sonicator (Diagenode) applying the following settings: 5 x 10 cycles 30 sec ON and 60 sec OFF, high intensity, at 4°C. Every 10 cycles samples were mixed and briefly spun down. The shearing of DNA into 200-300 bp fragments was evaluated by electrophoresis on a 1.5% agarose gel. Prior to IP, 1% Triton X-100 was added to the sample and an aliquot was stored at -20°C as input control. Antibody-bound Protein G dynabeads™ (Life Technologies) were added to each sample (10 μg c-MAF antibody per sample) and immunoprecipitation was performed overnight at 4°C on a rotating wheel. The day after, dynabeads were thoroughly washed: 6 times with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), then twice with RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% 1% Na-Deoxycholate), twice with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-Deoxycholate), and once with TE buffer. ChIP DNA was eluted with direct elution buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS) and subjected to RNAse A and proteinase K treatment before overnight de-crosslinking at 65°C. Finally, de-crosslinked DNA was purified with SPRI magnetic beads and eluted in 10 mM Tris-Cl pH 8.0. ChIP DNA was quantified by picogreen on a Qubit 2.0 device.
ChIP-seq libraries were prepared as previously described (Blecher-Gonen, R. et al. Nat. Protoc. 8, 539-554. 2013).

treatment_protocol: Resting Th17 cells were stimulated with plate-bound antibodies to CD3 (156 ng/cm2, clone: TR66) and CD28 (156 ng/cm2 clone: CD28.2, BD Biosciences). Recently-activated cells were stimulated in CD3 and CD28 antibody-coated plates for 48 hours, and left in culture in uncoated plates for additional 3 days. On Day 5 they were re-stimulated for 2 hours with plate-bound CD3 and CD28 antibodies.

value: primary Th17 lymphocytes

value: Pool of expanded Th17 clones

tag: activation state

value: recently-activated


title: Input Day 0 Repl_3

status: Public on Sep 12 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type

value: resting


title: Th17-IL-10+ Day 5 c-MAF ChIP Repl_3


title: Th17-IL-10+ Day 0 c-MAF ChIP Repl_3


title: H22786/5283_gas_L1.D707

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com) and RSEM method,  and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text matrix files include RSEM raw values and normalized values.
Supplementary_files_format_and_content: rsem_gcounts* files: gene raw count matrix with rsem method
Supplementary_files_format_and_content: rsem_gnorm* files: gene normalized count matrix with rsem method
Supplementary_files_format_and_content: rsem_icounts* files: isoform raw count matrix with rsem method
Supplementary_files_format_and_content: rsem_inorm* files: isoform normalized count matrix with rsem method

molecule: total RNA

organism: Mus musculus

source_name: gastrocnemius skeletal muscle

extract_protocol: Wild type (C57BL6/J – C57n:C57mt and C3H/HeN - C3Hn:C3Hmt) and MNX (C57n:C3Hmt and C3Hn:C57mt) mouse were weaned with Chor diet and continued with Chow or changed to high-fat diet from 6 to 12-13 weeks of age. RNA samples were isolated from white adipose tissues collected from epididymal (eWAT) and inguinal (iWAT) fat, representing visceral and subcutaneous fat depots, respectively with RNeasy kit (Qiagen).

tag: genotype

value: C3H wt

tag: diet

value: Chow

value: gastrocnemius skeletal muscle


title: H31243/4111_ingfat_L1.D702_506

source_name: inguinal white adipose tissues

value: High Fat Diet

value: inguinal white adipose tissues


title: H31243/2102_epifat_L1.D706_504

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: Input Day 0 Repl_2


title: H22786/3207_ingfat_L3.D702


title: H22786/3208_epifat_L5.D706


title: Input Day 5 Repl_2


title: H22786/3206_gas_L1.D710


title: H22786/3202_ingfat_L4.D710

value: C57 wt


title: H22786/3204_epifat_L5.D710


title: H22786/3206_ingfat_L3.D701


title: H22786/3202_gas_L2.D705


title: Th17-IL-10+ Day 5 c-MAF ChIP Repl_2


title: Th17-IL-10– Day 0 c-MAF ChIP Repl_2


title: Th17-IL-10– Day 5 c-MAF ChIP Repl_2


title: Input Day 5 Repl_1


title: H22786/3109_ingfat_L4.D702


title: H22786/3204_ingfat_L3.D706


title: H22786/3204_gas_L1.D711


title: H22786/3201_ingfat_L4.D703


title: H22786/3202_epifat_L6.D702


title: H22786/3206_epifat_L5.D704


title: Th17-IL-10– Day 5 c-MAF ChIP Repl_1


title: Input Day 0 Repl_1


title: Th17-IL-10– Day 0 c-MAF ChIP Repl_1


title: H22786/3104_ingfat_L3.D705


title: H22786/3103_gas_L1.D701


title: H22786/3201_gas_L2.D710


title: H22786/3103_epifat_L5.D709


title: H22786/3102_ingfat_L3.D704


title: Th17-IL-10+ Day 0 c-MAF ChIP Repl_1


title: H22786/3110_gas_L2.D706


title: H22786/3207_epifat_L5.D705


title: Th17-IL-10+ Day 0 c-MAF ChIP Repl_2


title: H22786/3105_gas_L1.D702


title: H22786/2207_gas_L2.D709


title: H22786/2207_ingfat_L4.D701


title: H22786/2206_gas_L2.D708


title: H22786/2209_epifat_L6.D706


title: H22786/2208_epifat_L6.D705


title: H22786/2203_gas_L1.D709


title: H22786/2201_epifat_L5.D708


title: H22786/2203_ingfat_L3.D712


title: H22786/2207_epifat_L6.D704


title: H22786/2108_gas_L2.D704


title: H22786/2109_ingfat_L4.D709


title: Th17-IL-10+ Day 5 c-MAF ChIP Repl_1


title: H22786/2108_ingfat_L4.D708


title: H22786/2106_epifat_L5.D711


title: H22786/2105_ingfat_L4.D711


title: H22786/2105_gas_L2.D707


title: H22786/2212_epifat_L6.D701


title: H22786/2107_gas_L2.D703


title: H22786/2201_ingfat_L3.D703


title: H22786/2206_epifat_L6.D703


title: H22786/2103_ingfat_L3.D711


title: E9.5_Heart_Dgcr8 cKO_rep2

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

country: China

institute: Tsinghua University

data_processing:
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, Clean reads were mapped to mouse genome (mm9) using BWA software.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files of gene names and FPKM values for each sample.

source_name: E9.5_Heart_Dgcr8 cKO

extract_protocol:
Total RNA was extracted using TRIZOL and treated with RNase free DNase.
RNA library was prepared following the instruction of SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing（Clontech）

tag: strain background

tag: genotype/variation

value: Mesp1Cre/+; Dgcr8-/-

tag: age

value: Embryonic day 9.5

value: heart


title: E9.5_Heart_Dgcr8 cKO_rep1


title: H22786/2103_gas_L1.D708


title: H22786/2101_epifat_L5.D707


title: E9.5_Heart_WT_rep2

value: wild type


title: H22786/3102_gas_L1.D712


title: H22786/2108_epifat_L6.D712


title: E8.5_Heart_WT_rep1

value: Embryonic day 8.5


title: E9.5_Heart_WT_rep1


title: E8.5_Heart_Dgcr8 cKO_rep1

source_name: E8.5_Heart_Dgcr8 cKO


title: E8.5_Heart_WT_rep2


title: H22786/2106_ingfat_L4.D707


title: H3K9me2 caa39_3

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

country: France

institute: Aix-Marseille Université

data_processing:
Checking sequence quality with FASTQC (0.11.5)
Adaptator trimming with trimmomatic (0.36)
sequences were aligned with bowtie 2 (2.2.9) againt TAIR10.31 and filtered with bamtools filter (2.4.0) to remove sequence with a MapQuality below 20. Finally MarkDuplicate (2.8.1) was used to remove PCR duplicate
Peak calling with diffReps-nb (1.55.2)
BamCoverage (2.4.1) was used to create bigwig files for visualization
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files

organism: Arabidopsis thaliana

source_name: 6 day-old aerial parts

growth_protocol: Seeds are stratified for 3 days at 4°C in darkness before transfer to growth chamber for 6 days  (16hL/8hD: 8 am-12 pm, ~80 µE, ~65% humidity, ~21°C). Media: Murashige and Skoog (MS) 1/2, 1% sucrose, 0,4% phytagel or 0.8% Agar

extract_protocol:
Two hundred 6 day-old seedlings were used per biological replicates. Seedlings were quickly harvested using a cat hair comb, root material was cut-off and the remaining photosynthetic material was fixed with 1% formaldehyde for 9 minutes. Crosslinking was quenched by addition of glycine at 125 mM final concentration and 5 minutes incubation, washed twice in ddH2O and the excess water was drained using kimwipes. Plant material was then ground in liquid nitrogen, resuspended in extraction buffer 1 (0.4M Sucrose, 10mM Tris pH8, 10 mM MgCl2, 5mM β-Mercaptoethanol and protease inhibitor), filtered with four layers of miracloth and centrifuged 20 minutes at 4000 rpm, 4°C. The pellet was resuspended in extraction buffer 2 (0.25M Sucrose, 1% Triton X100, 10mM Tris pH8, 10 mM MgCl2, 5mM β-Mercaptoethanol and protease inhibitor) and centrifuged 10 minutes, 13000 rpm, 4°C. The pellet was resuspended in 300 µL extraction buffer 2 and layered on top of 300 µL extraction buffer 3 (1.75M Sucrose, 0.15% Triton X100, 10mM Tris pH8, 2 mM MgCl2, 5mM β-Mercaptoethanol and protease inhibitor) and centrifuged at 13000 rpm for 1h, 4°C. The resulting pellet was resuspended in 130 µL of nuclear lysis buffer (50mM Tris pH8, 10 mM EDTA, 1% SDS and protease inhibitor) and sheared using a Bioruptor for 10 cycles, high settings, 30 sec ON/60 sec OFF, twice. Then, the sheared chromatin was diluted ten times in ChIP dilution buffer (1.1% Triton X100, 16.7mM Tris pH8, 1.2mM EDTA, 167mM NaCl and protease inhibitor). In parallel, 10 µL protein G Dynabeads® were washed twice in ChIP dilution buffer and incubated either with 2 µg of mouse IgG (Sigma), anti-H3K27me3, anti-H3K9m2, anti-MAT or anti-GFP during 2h at 4°C under gentle agitation. Antibody-conjugated beads were washed twice with 100 µL ChIP dilution buffer and 400 µL of input was submitted to IP for 4h or at 4°C under gentle agitation. Immunocomplexes were washed twice with each following buffer, 5 minutes, 4°C, gentle agitation, in that order: low salt wash buffer (150mM NaCl, 0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris pH8), high salt wash buffer (500mM NaCl, 0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris pH8), LiCl wash buffer (250mM LiCl, 1% Igepal CA-630, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris pH8), TE buffer (10mM Tris pH8, 1mM EDTA). Immunocomplexes were then eluted twice with 100 µL elution buffer (100mM NaHCO3, 1% SDS), 15 minutes at 65°C, agitation. The 200 µL eluate was reversed crosslinked by adding 16 µL of 2.5M NaCl and incubating at 65°C overnight and DNA was purified using phenol/chloroform extraction. A 40 µL aliquot of input was reversed crosslinked and purified in parallel. DNA was quantified using Qubit® dsDNA HS assay kit (ThermoFischer Scientific).
TruSeq ChIP Library Preparation kit

tag: antibodies

value: H3K9me2 (abcam ab1220)


title: E9.5_Heart_WT_miRNA_rep2

description: heart

data_processing:
Clean reads were mapped to mouse genome (mm9), using miRDeep2
Genome_build: mm9
Supplementary_files_format_and_content: Excel files of gene names and read count for each sample.

extract_protocol:
Total RNA was extracted using TRIZOL and treated with RNase free DNase.
TruSeq® Small RNA Library Prep Kit, Illumina

treatment_protocol: Total RNA of E9.5 heart were extracted with TRIZOL, miRNA deep sequencing were performed in using Illumina Hiseq 2500, SE50 (RIBOBIO, http://www.ribobio.com/), producing over 10 million reads from each sample. Clean reads were mapped to mouse genome (mm9), using miRDeep2

tag: strain


title: H3K9me2 wt_3


title: H3 wt_2

value: H3 (abcam ab1791)


title: E9.5_Heart_WT_miRNA_rep1

description: heart


title: Input chromatin wt_2


title: H3 wt_1


title: H3 caa39_2


title: H3K9me2 caa39_2


title: Input chromatin caa39_2


title: H3 caa39_1


title: Input chromatin caa39

data_processing:
Checking sequence quality with FASTQC (0.11.5)
Adaptator trimming with trimmomatic (0.36)
sequences were aligned with bowtie 2 (2.2.9) againt TAIR10.31 and filtered with bamtools filter (2.4.0) to remove sequence with a MapQuality below 20. Finally MarkDuplicate (2.8.1) was used to remove PCR duplicate
Peak calling with diffReps-nb (1.55.2)
BamCoverage (2.4.1) was used to create bigwig files for visualization
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files, Excel file containing gene and TE transcript quantification in the mutant versus the wt

value: caa39 mutant


title: Input chromatin wt

value: Wild type


title: E9.5_Dgcr8-cKO+miR-541_rep2

description: cultured heart cells

data_processing:
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to mm10 genome using STAR.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files of gene names and FPKM values for each sample.

growth_protocol: Dgcr8 cKO heart cells were dissociated into very small clusters, and cultured in vitro in a chemical defined medium

treatment_protocol: In vitro cultured Dgcr8 cKO heart cells were transfected with miR-541-5p and NC miRNA 24 hrs after plating, and total RNA were collected 48 hrs after transfection

tag: transfected with

value: miR-541 mimics

value: cultured heart cells


title: H3K27me3 caa39 2

value: H3K27me3 (abcam ab6002)


title: H3K27me3 caa39 1


title: E9.5_Dgcr8-cKO+NC-miRNA_rep2

description: cultured heart cells

value: NC miRNA


title: E9.5_Dgcr8-cKO+miR-541_rep1

description: cultured heart cells


title: H3K9me2 caa39

data_processing:
Checking sequence quality with FASTQC (0.11.5)
Adaptator trimming with trimmomatic (0.36)
sequences were aligned with bowtie 2 (2.2.9) againt TAIR10.31 and filtered with bamtools filter (2.4.0) to remove sequence with a MapQuality below 20. Finally MarkDuplicate (2.8.1) was used to remove PCR duplicate
BamCoverage (2.4.1) was used to create bigwig files for visualization
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files, Excel file containing gene and TE transcript quantification in the mutant versus the wt


title: H3K9me2 wt


title: E8.5_Heart_Dgcr8 cKO_rep2


title: caa39-0-2

data_processing:
Trimming of library adapters with fastQC (0.10.1) and reads with a Phred Quality score>20 and lenght > 30 bases were kept
Alignement with Bowtie 2 against TAIR10 transcriptome with one isoform per gene
Quatification with edgeR (1.12.0)
Quantification of transposable element transcripts unsing Tetranscripts (Jin et al, 2015) with prior alignement against TAIR10_TE.gtf. Multi-read alignement allowed.
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files, Excel file containing gene and TE transcript quantification in the mutant versus the wt

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen®, Hilden, Germany) according to the supplier’s instruction
TruSeq Stranded mRNA SamplePrep Guide 15031047 D protocol (Illumina®, California, U.S.A.)


title: caa39-0-3


title: H3K9me2 wt_2


title: WTCol0-0-3


title: caa39-0-1


title: E9.5_Dgcr8-cKO+NC-miRNA_rep1

description: cultured heart cells


title: WTCol0-0-2


title: WTCol0-0-1


title: 29C

city: Cambridge

first: Erel

last: Levine

state: Massachusetts

address: 52 Oxford St

department: Physics

institute: Harvard University

data_processing:
FASTQ files were processed with a stringent quality filter (All bases Q>27, roughly 60% of reads) and required to have the expected restriction site scars on each end (TATG from NdeI at the 5' end, GGATC from BamHI at some position near the end of the sequence, less than 1% discarded).
Unique sequences were  collected and counted from each index. Sequences were aligned to the wild-type RyhB sequence in order to determine the position of substitutions, insertions and deletions.
Read count tables were normalized to estimate sorted cells per variant in each pool. The sum of these counts for a single sample is the total sorted cells per variant, which is used to estimate quantitative error.
Sorted cells per variant in each pool is normalized to convert to the fraction of flow cytometry events from each sort gate. Matrix multiplication of this frequency table with phi_j gives mean fluorescence for each variant as in Peterman & Levine, 2016.
Error model is fitted from the two replicates at 37C to estimate RMS error which decreases as the total number of sorted cells per variant increases
Genome_build: CP009273 (E. coli)
Supplementary_files_format_and_content: tab-delimited text files include frequency tables, total sorted cells per variant, and estimates of mean fluorescence, fold repression, and error inferred from the sort-seq data. Also sort-seq assay summary that contains details from the sort-seq assay needed to infer fluorescence from raw sequencing data, in tab-delimited text files.

organism: Escherichia coli

source_name: Cultured bacteria

growth_protocol: For all fluorescence experiments including sort-seq, cultures were inoculated and incubated 37 C overnight, and then diluted 32,000-fold into 48-well plates with 0.8 mL media and inducers. Media is M63 minimal media supplemented with 0.5% glucose and 0.1% casamino acids. Inducers are 1.0 mM IPTG and 10 ng/mL aTc. Plates were incubated at different temperatures, shaking in an ELMI DOS-20S plate shaker (250 RPM, 20 mm amplitude) to ensure adequate aeration of the cultures. Bacteria were grown for at least 9 generations to allow enough time to reach steady state fluorescence, and harvested in exponential phase with absorbance between 0.1-0.2 OD600.

extract_protocol:
Sorted bacterial cells were grown overnight and plasmid DNA was extracted containing enriched RyhB variant sequences.
Cycle-limited PCR was used to amplify the region containing sRNA variant sequences. These products were digested with BamHI and NdeI. dsDNA adapters with BamHI and NdeI overhangs were ligated. Finally, flow cell binding sequences and barcode sequences were appended by cycle-limeted PCR. Samples were pooled in proportion to the number of sorted cells represented in each sample.

treatment_protocol: Bacterial cells, carrying a target reporter plasmid and a plasmid carrying a library of sRNA variants, were sorted according to the ratio of GFP/RFP fluorescence. Sort gates and number of sorted cells per gate are contained processed files such as 33C_summary.txt.

value: BW-RI delta-ryhB

tag: temperature


title: H3K27me3 wt 2


title: 25C


title: 21C


title: 33C


title: H3K27me3 wt 1


title: 37C rep 1


title: 37C rep 2


title: Ctl_10w_2

status: Public on Sep 11 2018

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D)
Genome_build: rn5
Supplementary_files_format_and_content: read counts were obtained for each sample for RNAseq data

organism: Rattus norvegicus

source_name: pancreatic islets

growth_protocol: Dams and offspring had ad libitum access to water and standard chow. Control litters were culled to 8 to equilibrate nutrient availability during laction.

extract_protocol:
Islets were isolated via ductal collagenase perfusion and digestion followed by histopaque gradient centrifugation. RNA was islolated using Trizol and Qiagen RNeasy mini kits
Only RNA with RNA Integrity Numbers greater than 7 were used. RNA-Seq libraries were made using the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold

treatment_protocol: Bilateral uterine artery ligation performed at embryonic day 18 to restrict growht of fetuses.

value: Sprague Dawley

tag: condition

value: Control


title: IUGR_10w_3

value: IUGR


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(ΔCBM) 3

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: text file includes raw expression counts

source_name: stable PGC-1α-KD C2C12 myoblasts

growth_protocol: Mouse C2C12 myoblasts were cultured in Dulbecco´s Modified Eagle´s Medium (DMEM; Gibco) containing 15% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was extracted using Trizol (Ambion).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next-generation sequencing library construction following the manufacturer’s protocols. Briefly, poly(A)+ RNA was purified from 200 ng of total C2C12-cell RNA using oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed using random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. The resulting double-stranded cDNA was then subjected to end repair and 3´-end adenylation. Illumina adaptors were ligated to both cDNA ends. Adapted cDNA was purified using Ampure beads and PCR-amplified using primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500 base-pairs. Amplified libraries were hybridized to the Illumina single-end flow cell and further amplified using the cBot (Illumina, San Diego, CA). Single-end reads of 100 nucleotides were generated for each sample using HiSeq2500v4 (Illumina).

treatment_protocol: To generate C2C12 MBs in which PGC-1α was stably knocked-down, HEK293T cells were transiently transfected with VSV-G plasmid (Addgene, 8454) and pCG-gag-pol (Ulm et al., 2007) and, respectively, MISSION shRNA pLKO.1-puro vector for PGC-1α (TRCN0000234017: CCGGTCCAGTAAGCACACGTTTATTCTCGAGAATAAACGTGTGCTTACTGGATTTTTG; Sigma) or pRetroSuper-GFP-shRNA  (Brummelkamp et al., 2000). C2C12 MBs were transduced using the resulting viral supernatants (MOI of 1) supplemented with 2 µg/ml of hexadimethrine bromide (Sigma). After 24 hr, cells were selected for resistance to 2 mg/ml of puromycin (Gibco), and resistant cells were pooled. WT or PGC-1α-KD myoblasts were transiently transfected with the indicated plasmids using Lipofectamine 2000 (Life Technologies) and harvested 32-hr later.

tag: transfection

value: plasmid encoding FLAG-tagged PGC-1α lacking its CBM


title: IUGR_10w_1


title: Ctl_10w_3


title: Ctl_2w_2


title: IUGR_2w_1


title: IUGR_2w_3


title: Ctl_10w_1


title: Ctl_2w_1


title: IUGR_2w_2


title: Ctl_2w_3


title: PGC-1α-KD C2C12 + FLAG 2

value: plasmid encoding for FLAG alone


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(ΔCBM) 1


title: PGC-1α-KD C2C12 + FLAG 1


title: WT C2C12 + FLAG 1

source_name: C2C12 myoblasts


title: 500 µM-ZnO-nano replicate 3

status: Public on Sep 10 2018

city: Brookings

first: Jose

middle: L.

last: Gonzalez

state: SD

address: Agricultural Hall

department: Plant Science

institute: South Dakota State University

data_processing:
The raw .bcl (base call ) files were converted into demultiplexed fastq files with Casava 1.8.2
Quality score in CLC Genomics Workbench is based on phred scale using Mott-trimming algorithm. Quality scores from the sequencer converted to error probability (P error = 10 Q/-10) and compared with the limit (Limit – Perror).
Expression values for each Transcript Assemblies in each sample were calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM) (Mortazavi et al., 2008) in order to normalize for transcript length and depth of each library.
Transcript assemblies are blastx searched against Arabidopsis thaliana database and mapped with their Gene ontology annotations.
Transcript assemblies were tested for gene enrichment using CLC Genomics workbench. Gene expression data obtained after statistical analysis was overlayed onto biological pathways using MapMan.
Genome_build: De novo transcriptome assembly
Supplementary_files_format_and_content: Total of six tab-delimited text files which contain Contig Identifiers and RPKM values for each sample.

organism: Spinacia oleracea

source_name: Root

growth_protocol: Spinach (Spinacea oleracea) N1L1 seeds were germinated, grown in a greenhouse on sand culture, and watered with DI water as needed.   After three weeks, the plants were transferred to pots containing standard nutrient solution ZnSO4 2 µM and grown in the greenhouse under light/temperature conditions then set to acclimate for three weeks (four leaf stage).  The nutrient solution was changed twice a week.   The pots consisted of 500 ml hydroponic nutrient solution in an aluminum foil-covered 1 L plastic pot, with the plant held in place with non-absorbent cotton, through a floating disk of Styrofoam.

extract_protocol:
Fresh root tissue samples were collected for genomic analysis one day before harvest from plants in the 500 µM treatments and flash frozen in liquid nitrogen and stored at -80 °C.Total RNA extracted from three biological replicated root tissue samples from each treatment 500 µM-ZnO-nano and 500 µM-ZnO-bulk using the Trizol reagent.  RNA-Seq libraries were constructed using the TruSeq RNA Sample Preparation Kit.
The multiplexed libraries were loaded onto one lane of an 8-lane flowcell for cluster formation and sequenced on an Illumina HiSeq2000 with TruSeq SBS sequencing kits version 3.

treatment_protocol: After the acclimation period, the treatments were begun and lasted another three weeks.  For the treatment nutrient solutions, each pot was filled with 500 ml stock nutrient solution (minus Zn).  Each of the nine Zn treatments solutions were prepared separately; a volume of 0.5 ml of the appropriate Zn solution was then added to each pot followed by agitation of the solution to ensure dispersal of the Zn throughout the solution.

value: ZnO-nano

value: root

value: four leaf stage


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(ΔCBM) 2


title: 500 µM-ZnO-bulk replicate 1

value: ZnO-bulk


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(WT)  3

value: plasmid encoding FLAG-tagged WT PGC-1α


title: day 3 of MESP1- rep1

status: Public on Sep 09 2018

description:
homozygote
cultured cells
day3_nc_genes.Rpkm_tracking

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg19 genome using Tophat2.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: hg19
Supplementary_files_format_and_content: merged text files include FPKM values for all  Samples

source_name: cultured cells

growth_protocol: Undifferentiated hESCs was cultured in Pseasy medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase.
RNA library was prepared following the instruction of TruSeq™ RNA Sample Preparation kit (Illumina)

treatment_protocol: For monolayer based cardiomyocyte differentiation, we employed a protocol published by Lian et al (Yan et al., 2013).  On day 3 and day 5 of differentiation, MESP1-mTomato positive and negative cells were sorted.

tag: cell line

value: H9 ESC line

tag: passages

tag: differentiation time

value: day 3

tag: differentiated/sorted cell type


title: day 5 of MESP1- rep1

description:
homozygote
cultured cells
day5_nc_genes.Rpkm_tracking

value: day 5


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(WT)  1


title: hESC rep2

description:
homozygote
cultured cells
hes_2_genes.Rpkm_tracking


title: day 3 of MESP1+ rep2

description:
homozygote
cultured cells
day3_2_genes.Rpkm_tracking


title: day 3 of MESP1+ rep1

description:
homozygote
cultured cells
day3_1_genes.Rpkm_tracking


title: WT C2C12 + FLAG 3


title: day 5 of MESP1+ rep1

description:
homozygote
cultured cells
day5_1_genes.Rpkm_tracking


title: IUGR_10w_2


title: P21 PvCre;Tom_1

city: Stockholm

first: Francois

last: Lallemend

state: Stockholm

address: Tomtebodavägen 16

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: A few neurons still had glial cells attached to the cell body.Glial cells associated genes could easily be discarded from the analysis .

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
For P17, P21 and P33 datasets, samples were dissected and processed to contain both spiral ganglion and vestibular ganglion neurons. The vestibular ganglion neurons, which can easily be distinguished from spiral ganglion neurons (notably they do not express Prox1 but express Pcp4 and other markers), were removed from the data set to be analyzed in a future study.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include individual counts aligning to each gene per cell

molecule: polyA RNA

source_name: Spiral ganglion neurons

extract_protocol:
Spiral ganglia were dissected and collected in Leibovit’z L-15 medium (Life technologies) on ice. Then the spiral ganglia (SG) were incubated in papain–DNAse solution (1.5 ml of papain at 1 mg/ml, 0.5 ml of DNAse at 0.1%) for 35 min (for P3 samples) or 25 min (for Adult samples) at 37 °C, shaking at 700 RPM. After spinning down the samples at 400 RCF for 10 min, the supernatant was removed and replaced by Dulbecco’s modified Eagle’s medium (DMEM) F-12 (Life technologies). SG were physically triturated using 3 different sizes of pipettes previously coated with 0.2% bovine serum albumin until the solution homogenized. The cell suspension was then filtered through 70 μm cell strainer (BD Biosciences) to remove clusters of cells. Single fluorescence positive cells were sorted by FAC sorting into individual wells of 384-well plates containing lysis buffer. Plates containing single cells were frozen immediately on dry ice and stored at -80 °C. We used 6 animals (12 cochleae) per experiment.
RNA libraries were prepared according to Smart-seq2 protocol.

value: PvCre;Tom

tag: developmental stage

value: Spiral ganglion neurons


title: P3 PvCre;Tom

tag: cell type


title: day 5 of MESP1- rep2

description: cultured cells

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg19 genome using Tophat2.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: hg19
Supplementary_files_format_and_content: merged text files include FPKM values for all  Samples.

growth_protocol: Undifferentiated hESCs was cultured in homemade E8 medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase.
RNA library was prepared following the instruction of SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing（Clontech）

value: human embryonic stem cell line


title: WT C2C12 + FLAG 2


title: PGC-1α-KD C2C12 + FLAG-PGC-1α(WT)  2


title: P17 PvCre;Tom


title: 500 µM-ZnO-bulk replicate 3

tag: tissue

tag: genotype


title: 500 µM-ZnO-bulk replicate 2


title: PGC-1α-KD C2C12 + FLAG 3


title: 500 µM-ZnO-nano replicate 2


title: 500 µM-ZnO-nano replicate 1


title: day 5 of MESP1+ rep2

description:
homozygote
cultured cells
day5_2_genes.Rpkm_tracking


title: hESC rep1

description:
homozygote
cultured cells
hes_1_genes.Rpkm_tracking


title: retina_rep3_20

status: Public on Sep 08 2018

city: Bethesda

first: Steven

last: Coon

state: MD

address: 10 Center Dr; Room 8S261A

department: NICHD

institute: National Institutes of Health

data_processing:
Trim low quality reads and adapters using Trimmomatic software
Mapping trimmed reads to human reference genome using TopHat software
Transcript assembly and quantification using Cufflinks software
Genome_build: Ensembl WASHUC2.0
Supplementary_files_format_and_content: Pineal_retina_36_samples_23352_transcripts_count.txt
Supplementary_files_format_and_content: Pineal_retina_36_samples_23352_transcripts_FPKM.txt

organism: Gallus gallus

source_name: 20 time point

extract_protocol:
Total RNA was extracted using TRIzol, followed by clean-up with an RNeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One-day-old (Gallus domesticus) were obtained from Hyline International, Inc. and entrained to a 12 h light : 12 h dark cycle of illumination for 9 days. The light cycle was switched to L:D 0: 24 (constant darkness) on day 10. Sampling was initiated immediately at the beginning of the subjective day.

tag: time point

value: retina


title: P33 PvCre;Tom

tag: genotype/variation


title: P21 PvCre;Tom_2


title: J0

city: Montreal

first: Katrina

last: Podsypanina

state: QC

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

description: RNA from all (breast) cells

data_processing:
Alignment of short reads on the mm9 genome was performed using TopHat version 1.4.1.
Gene expression values were subsequently estimated using Cufflinks version 1.3.0 (Trapnell, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with FPKM values.

source_name: MG: undissociated mammary gland tissue (3 samples combined)

extract_protocol:
total RNA was cleaned up using RNeasy column (74104, Qiagen) followed by on-column DNase treatment using RNase-free DNase set (79254, Qiagen). Poly-T capture beads were used to isolate mRNA  (Illumina TruSeq RNA Sample Preparation kit).
cBot system was used to produce clonal clusters and sequencing was performed at the McGill University and Genome Quebec Innovation Center using the Illumina HiSeq 2000 platform.

tag: strain background

value: FVB

tag: sample group

value: intact mammary gland


title: P3 EphA4-GFP


title: retina_rep3_08

source_name: 08 time piont

growth_protocol: One-day-old (Gallus domesticus) were obtained from Hyline International, Inc. and entrained to a 12 h light : 12 h dark cycle of illumination for 9 days. The light cycle was switched to L:D 0: 24 (constant darkness) on day 10.


title: J1

description: RNA from cells able to seed in the lung; cells from the lung (J1 stands for "jour 1" in lung)

source_name: LCC: FACS-isolated mammary cells of GFP mice or FACS isolated DDAO-stained mammary cells from FVB mice (15 experiments,  42 lungs, 455880 cells)

value: mammary cells that colonize lungs following intravenous delivery


title: Cd29

description: Subpopulation of mammary cells after FACS that is enriched for lung colonizing cells.

source_name: E-Int29-Hi: FACS-isolated EpCAM-Int and CD29-Hi (3 samples combined)

value: a subset of the dissociated mammary cells that contains lung colonizing subset


title: retina_rep3_16

source_name: 16 time point


title: pineal_rep3_16

value: pineal


title: day 3 of MESP1- rep2

description: cultured cells


title: retina_rep3_00

source_name: 00 time point


title: pineal_rep3_12

source_name: 12 time piont


title: pineal_rep3_04

source_name: 04 time piont


title: pineal_rep3_08


title: retina_rep2_20


title: retina_rep2_08


title: pineal_rep3_20


title: pineal_rep3_00


title: retina_rep2_00


title: pineal_rep2_20


title: retina_rep2_16


title: retina_rep2_12


title: pineal_rep2_16


title: retina_rep1_16


title: pineal_rep2_00


title: retina_rep1_12


title: pineal_rep2_04


title: pineal_rep2_12


title: retina_rep1_20


title: pineal_rep2_08


title: retina_rep3_04


title: retina_rep3_12


title: retina_rep1_00


title: retina_rep1_08


title: pineal_rep1_16


title: retina_rep1_04


title: pineal_rep1_20


title: retina_rep2_04


title: pineal_rep1_12


title: hac1/5+INA

status: Public on Sep 07 2018

city: Seoul

first: Hongshi

last: Jin

address: Gwanak_599 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
After total RNA extraction, mRNA was enriched by using oligo-(dT) magnetic beads. By adding fragmentation buffer, mRNA was interrupted to short fragments (about 200 bp), then the first strand cDNA was synthesized using random hexamer primers using the mRNA fragments as templates. Buffer, dNTPs, RNase H, and DNA polymerase I were added to sythesize second strand cDNAs. Double-strand cDNAs were purified with QiaQuick PCR extraction kit (QIAGEN) and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments. The adaptor-ligated fragments were purified by agrose gel electrophoresis and enriched by PCR amplification. Then, the library products were sequenced via Illumina HiSeq™ 2000.
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bp were allowed in the alignment.
Gene expression level was calculated by using RPKM method (Reads per kb per million reads).
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: .txt files including RPKM values for each sample

source_name: hac1/5+INA, leaves

growth_protocol: Plants were grown under 100 μmol m-2 s-1 cool white fluorescent lights at 22°C in short days (SD).

extract_protocol:
Total RNAs were isolated using Tri Reagent (MRC) and purified with RNeasy Mini Kit (QIAGEN) (OD260/280 ratio of 1.8 to 2.2).
RNA libraries were prepared by BGI using standard Illumina protocols.

treatment_protocol: 4-week-old plants grown under SD were sprayed with water or 300 µm INA for 12h before havest.

value: hac1-2 hac5-2 mutant

tag: treatment

value: INA

value: leaf


title: hac1/5

source_name: hac1/5, leaves

value: water


title: Input

data_processing:
Basecalls were performed by BGI.
ChIP-seq reads were aligned to the Arabidopsis Col-0 genome using SOAP2 aligner.
BWA was used for genome alignment after evaluating performance.
Candiate peak region was defined using MACS version 1.4.2 (Model-based analysis for ChIP-seq). Dynamic Possion Distribution was used to calculate the p-value of specific region based on unique mapped reads, and the region was defined as a peak when p-value < le-05.
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: The whole-genome peak region was generated by MACS version 1.4.2. Results for peak location and peak length are stored in wiggle (wig) files.

source_name: Col, leaves

extract_protocol:
Chromatin was isloated from sonciated nuclei, and immune complexes were immunoprecipitated with anti-H3Ac antibody (Millipore 06-599). ChIPed DNAs were eluted using MinElute PCR Purification Kit (QIAGEN). 12 ng of ChIPed DNAs were pooled from 6 independent experiments.
Libraries were prepared by Beijing Genomics Institute (Hong Kong) following standard Illumina protocol.

tag: chip antibody

value: wild type


title: H3Ac Col

description: Col leaves after 12hr water treatment

value: Anti-H3Ac (Millipore, catalog# 06-599, lot# 2370129)


title: H3Ac hac1/5

description: hac1-2 hac5-2 leaves after 12hr water treatment


title: H3Ac hac1/5+INA

description: hac1-2 hac5-2  leaves after 12hr INA treatment


title: H3Ac npr1-1

description: npr1-1 leaves after 12hr water treatment

source_name: npr1-1, leaves

value: npr1-1 mutant


title: H3Ac npr1-1+INA

description: npr1-1 leaves after 12hr INA treatment

source_name: npr1-1+INA, leaves


title: H3Ac Col+INA

description: Col leaves after 12hr INA treatment

source_name: Col+INA, leaves


title: npr1-1


title: npr1-1+INA


title: Col+INA


title: Col


title: CD4low rep2

status: Public on Sep 06 2018

city: ShangHai

first: Chao

last: Wang

address: 1954HuaShan road

institute: Shanghai Jiao Tong University

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg19 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Text generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj and text file with read counts.

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA LT V2 Sample Prep Kit(Illumina, Sandiego) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood

value: CD4lowHLA-G+ T cells


title: lung from control group, rep1

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

institute: Yangzhou University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two group were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: lung from mock-infected mouse

extract_protocol:
The mouse lungs were homogenized in TRIzol (Invitrogen, CA, US) using the MagNA Lyser system (Roche) according to the manufacturer’s instructions. RNA was further purified using the miRNeasy minikit (Qiagen) based on the manufacturer’s instructions. The purity of the RNA samples was verified spectroscopically, and RNA quality was assessed using Agilent Bioanalyzer 2100 (Cui et al., 2014). Only samples with an RNA integrity number greater than 8 were used. rRNA was depleted from 1 mg of total RNA using RiboZero (Illumina).
cDNA libraries were prepared from the remaining RNA, without poly (A) selection, using the TruSeq Stranded RNA LT kit (Illumina) following the TruSeq stranded total RNA sample preparation guide provided by the vendor (RS-122-9007DOC). The libraries underwent cluster generation using TruSeq PE Cluster Kit v3-cBot-HS and 100 cycles of paired-end sequencing using TruSeq SBS Kit v3-HS (Illumina) and an Illumina HiSeq 2000 sequencer using standard Illumina protocols

tag: strain

value: BALB/c

value: lung

tag: age

value: 6-week old


title: CD4low rep1


title: lung from control group, rep2


title: lung from GS10 group, rep2

source_name: lung from GS10-infected mouse


title: lung from GS10 group, rep1


title: lung from GS10 group, rep3


title: fleQ_L1

city: Wuxi

first: Yuzhou

state: Jiangsu

address: 1800 Lihu Avenue

department: School of Biotechnology

institute: Jiangnan University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean reads were aligned to reference sequences with SOAPaligner/SOAP2
Reads per kilobase transcriptome per million mapped reads(RPKM) were calculated
Results of gene expression include gene expression levels and differential expression analysis.
Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis were performed.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Pseudomonas putida

source_name: FleQ_mutant_planktonic culture

growth_protocol: For transcriptome analysis, overnight cultures of P. putida strains KT2442 or △fleQ were diluted 100 times into 50 ml LB medium and grown at 30°C to the early exponential phase with OD600 around 1.3.

extract_protocol:
Total RNA was prepared using the Qiagen RNeasy Total RNA kit.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000

treatment_protocol: Cells from cultures were harvested by addition of the same volume of RNA-protect buffer and centrifugation.

value: fleQ mutant

tag: cell density


title: lung from CK10 group, rep3

source_name: lung from CK10-infected mouse


title: lung from CK10 group, rep1


title: KT2442_L1

source_name: KT2442_planktonic culture

value: wild-type


title: PFL_E11_WT_H3K27ac

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Proximal forelimb mouse E11.5 WT_H3K27ac ChIPseq

data_processing:
Demultiplexed ChIP-seq reads were mapped onto the mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
The ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016).
All analysis was done with Dr. Denis Duboule lab Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the normalized 1x depth coverage
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the normalized 1x depth coverage

source_name: Forelimb

extract_protocol:
Micro-dissected most proximal and distal tip domains of E11.5 forelimb buds from wild type CD1 mice were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 20 minutes at room temperature, washed at least three times with cold PBS containing protease inhibitor and stored at -80°C. Pools of fifty pairs of wild type proximal or distal forelimb buds were used for each ChIP. The samples were treated with lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl and protease inhibitor) for 10 min on ice, followed by RIPA buffer (TE with 140 mM NaCl, 0.1% deoxycholate, 0.1% SDS, 1% TritonX-100 and protease inhibitor) and fragmented to a range of 200-500 bp by a Biorupter sonication device (Diagenode). PierceTM Protein A/G magnetic beads (88803, Thermo Scientific) were conjugated with each antibody in blocking buffer (PBS, 0.5% Tween20, 0.5% BSA and protease inhibitor) for 4 hrs at 4°C and washed with blocking buffer. Chromatin was incubated with the prepared protein A/G beads overnight at 4°C with rotation. 20 µg of anti-RAR (sc-773X, Santa Cruz) and 3 µg of H3K27ac (ab4729, Abcam) were used for each immunoprecipitation. Samples were washed 6 times with RIPA buffer, twice with RIPA/500 mM NaCl buffer, twice with LiCl wash buffer (TE, 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholate) and twice with TE, followed by eluted in direct elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl and 0.1% SDS). Cross-links were reversed overnight at 65°C and ChIPed DNA was treated with RNase A and proteinase K, and purified by phenol chloroform extraction.
For ChIP-seq, at least 5 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

tag: tissues

value: Proximal forelimb buds

tag: antibody


title: PFL_E11_WT_RAR

description: Proximal forelimb mouse E11.5 WT_RAR ChIPseq

data_processing:
Demultiplexed ChIP-seq reads were mapped onto the mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
The ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016).
All analysis was done with Dr. Denis Duboule lab Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the normalized 1x depth coverage

value: RAR (Santa Cruz sc-773X, Lot. B2414)


title: ATAC-seq G1 rep3

status: Public on Sep 05 2018

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description:
ATAC-seq with synchronized G1 T98G cells, rep3
processed data file:
ATAC-seq_processed_data.txt

data_processing:
Basecalls performed using HiSeq Control and Real-Time Analysis Software
Reads were aligned to hg19 using Rbowtie through the R package QuasR. For chromatin fraction sequencing and input, default parameters were used.  For ATAC-seq, adapter sequences were first trimmed using cutadapt.  Subsequently, one bp was trimmed from the 3' end of each read, as bowtie1 will not align perfectly overlapping forward and reverse reads. Default parameters for mapping paired-end reads were used with the QuasR package in the R environment, except for:  alignmentParameter="-m 3 -k 1 --best --strata --maxins 2000 --tryhard"
Mitochondrial reads were removed from ATAC-seq bam files using samtools: (ex..) samtools idxstats G1_rep1.bam | cut -f 1 | grep -v chrM | xargs samtools view -b G1_rep1.bam > G1_rep1_NoMito.bam
Peaks in ATAC-seq datasets were called using macs2 and subsequently merged for G1 an mitotic datasets. The following command parameters were used in macs2: -f BAM -g hs --nomodel --broad
Reads were counted in peaks and scaled down to the smallest library size before comparison.
Genome_build: hg19
Supplementary_files_format_and_content: Text file is tab-delimited containing merged ATACseq peak locations, scaled counts for each replicate, average log2(M/G1) for each peak as well as the standard deviation for this change. "NoMito" means no mitochondrial sequence included. Wig files are provided for the Chromatin fraction sequencing samples.

growth_protocol: DMEM supplemented with 10% FCS and 2.5mM L-glutamine.  Cells were passaged every 2-3 days, depending on density

extract_protocol:
For input and chromatin fractions, nuclear prep was carried out followed by sonication to solubilize chromatin. Crosslinks were reversed overnight at 65⁰ and DNA was was isolated by phenol/chloroform followed by ethanol precipitation
ATAC-seq libraries were prepared as described in Buenrostro 2015.  Input and chromatin fractions were prepared using the NEBnext kit as per manufacturers intstructions.

treatment_protocol: G1 synchronization was achieved by serum starvation for 72 hours.  Sphase synchronization was obtained by serum starvation for 72 hours followed by a 22 hour release into 20% serum media. Mphase populations were enriched by starvation for 48 hours, followed by a 36 release into nocodazole containing media.  Mitotic cells were harvested by shaking.

tag: cell cycle stage

tag: cell line

value: glioblastoma

tag: platform

value: HiSeq


title: ATAC-seq Mphase rep3_HiSeq

description:
ATAC-seq with synchronized M-phase T98G cells, rep3
processed data file:
ATAC-seq_processed_data.txt

value: Mitosis

tag: cell type


title: ATAC-seq Mphase rep1_HiSeq

description:
ATAC-seq with synchronized M-phase T98G cells, rep1
processed data file:
ATAC-seq_processed_data.txt


title: ATAC-seq Mphase rep2_HiSeq

description:
ATAC-seq with synchronized M-phase T98G cells, rep2
processed data file:
ATAC-seq_processed_data.txt


title: DFL_E11_WT_RAR

description: Distal forelimb mouse E11.5 WT_RAR ChIPseq

value: Distal forelimb buds


title: ATAC-seq G1 rep1

description:
ATAC-seq with synchronized G1 T98G cells, rep1
processed data file:
ATAC-seq_processed_data.txt


title: Input rep1

description: Input chromatin sequencing of T98G cells, rep1

data_processing:
Library strategy: Chromatin fraction sequencing
Basecalls performed using HiSeq Control and Real-Time Analysis Software
Reads were aligned to hg19 using Rbowtie through the R package QuasR. For chromatin fraction sequencing and input, default parameters were used.  For ATAC-seq, adapter sequences were first trimmed using cutadapt.  Subsequently, one bp was trimmed from the 3' end of each read, as bowtie1 will not align perfectly overlapping forward and reverse reads. Default parameters for mapping paired-end reads were used with the QuasR package in the R environment, except for:  alignmentParameter="-m 3 -k 1 --best --strata --maxins 2000 --tryhard"
Mitochondrial reads were removed from ATAC-seq bam files using samtools: (ex..) samtools idxstats G1_rep1.bam | cut -f 1 | grep -v chrM | xargs samtools view -b G1_rep1.bam > G1_rep1_NoMito.bam
Peaks in ATAC-seq datasets were called using macs2 and subsequently merged for G1 an mitotic datasets. The following command parameters were used in macs2: -f BAM -g hs --nomodel --broad
Reads were counted in peaks and scaled down to the smallest library size before comparison.
Genome_build: hg19
Supplementary_files_format_and_content: Text file is tab-delimited containing merged ATACseq peak locations, scaled counts for each replicate, average log2(M/G1) for each peak as well as the standard deviation for this change. "NoMito" means no mitochondrial sequence included. Wig files are provided for the Chromatin fraction sequencing samples.

value: Unsynchronized


title: DFL_E11_WT_H3K27ac

description: Distal forelimb mouse E11.5 WT_H3K27ac ChIPseq

value: wild type


title: Chromatin Fraction rep2

description: Chromatin fraction sequencing of T98G cells, rep2


title: Input rep2

description: Input chromatin sequencing of T98G cells, rep2


title: Chromatin Fraction rep1

description: Chromatin fraction sequencing of T98G cells, rep1


title: lung from control group, rep3

tag: tissue


title: D267ALI14

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: Sample prepared 14 days after air-liquid interface

data_processing:
The Cell Ranger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger command used to produce output directory for each sample was executed using --cells=1000 and --transcriptome based on human genome release.GRCh37.p13
Cell Ranger aggregated dataset has been produced with default normalization method based on mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: HDF5: cellranger filtered gene / barcode matrix.

source_name: Human nasal turbinates cells

growth_protocol: HAECs were cultured as described in Marcet et al. (Nature Cell Biology, 2011).

extract_protocol:
Cells were incubated with 0.10% protease type XIV from Streptomyces griseus in HBSS for 4 hours at 4°C degrees. Cells were  detached from the Transwells by pipetting and then transferred to a microtube. 50 units of DNase I per 250µl, were directly added and cells were further incubated at room temperature for 10 min. Cells were washed in 500 µL HBSS 10% Fetal Bovine Serum then in 500 µL HBSS before being mechanically dissociated through a 26G syringe (4 times). Finally, cell suspensions were filtered through a Scienceware® Flowmi™ Cell Strainer (40µm porosity), then centrifuged (150g for 5 min) and resuspended in 500 µL of cold HBSS. Cell concentration measurements were performed and 1500 cells were used for single-cell sequencing.
Single cell RNA-Seq libraries were made following the User Guide for v2 Chemistry (https://support.10xgenomics.com/single-cell/sample-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry). Library was sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 57bp Read 2 (transcript), and 8bp i7 sample barcode for each scRNA-Seq library.

treatment_protocol: Cells were induced to differentiate at the air-liquid interface for 14 days as described in Marcet et al. (Nature Cell Biology, 2011).

value: nasal airway epithelium

value: nasal turbinates cells

tag: time

value: 14 days


title: KT2442_st

tag: genotype


title: ATAC-seq G1 rep2

description:
ATAC-seq with synchronized G1 T98G cells, rep2
processed data file:
ATAC-seq_processed_data.txt


title: Uninfected A549 cells, replicate 1

city: New York

first: Harm

middle: van

last: Bakel

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
After adapter removal with cutadapt (Martin, 2011) and base quality trimming to remove 3’ read sequences if more than 20 bases with Q < 20 were present, paired-end reads were mapped to the human (hg38) reference genome using STAR (Dobin et al., 2013) and gene count summaries were generated using featureCounts (Liao et al., 2014). Raw read counts were then combined into a numeric matrix, with genes in rows and experiments in columns and used as input for differential gene expression analysis with the Bioconductor Limma package (Ritchie et al., 2015) after multiple filtering steps to remove low-expressed genes. First, gene counts were converted to FPKM (fragments per kb per million reads) using the RSEM package (Li et al., 2011) with default settings in strand specific mode and only genes with expression levels above 1 FPKM in at least 50% of samples were retained for further analysis. Additional filtering removed genes with less than 50 total reads across all samples or less than 200 nucleotides in length. Finally, normalization factors were computed on the filtered data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom (Law et al., 2014) mean-variance transformation in preparation for Limma linear modeling. Data was fitted to a design matrix containing all sample groups and pairwise comparisons were performed between sample groups. eBayes adjusted P-values were corrected for multiple testing using the Benjamin-Hochberg (BH) method and used to select genes with significant expression differences.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing the Gene ID, raw counts and the normalized Log2 count per million reads.

source_name: Cells

growth_protocol: A549 cells were infected by the indicated viruses at an MOI of 2 for indicated hours.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions, adding 600 μls RLT Buffer and 6 μls of B-mercaptoethanol to each sample.
One ug of DNase-treated RNA was depleted of rRNAs using the Ribo-Zero Gold rRNA  Removal Kit (Human/Mouse/Rat) according to the manufacturer’s instructions and purified  post-depletion with 1.6X volume AMPure XP beads. Barcoded directional RNA-Seq libraries  were then prepared using the TruSeq Directional Library Prep kit (Illumina), per kit  instructions. PCR products were purified with 1.8X volume AMPure XP beads and fragments  of 300-500 bp were size-selected using BluePippin 2% M1 gels (Sage Scientific). Afterwards,  libraries were sequenced on the Illumina HiSeq 2500 platform in a 100 bp single-end read run  Format.

tag: infection

value: Uninfected A549 cells


title: PR8 NS1-SUMO infected A549 cells, 12 hours post-infection, replicate 2


title: PR8 NS1-SUMO infected A549 cells, 6 hours post-infection, replicate 2


title: Uninfected A549 cells, replicate 2


title: PR8 NS1 infected A549 cells, 12 hours post-infection, replicate 2


title: PR8 NS1 infected A549 cells, 6 hours post-infection, replicate 2


title: PR8 NS1 infected A549 cells, 12 hours post-infection, replicate 1


title: PR8 NS1-SUMO infected A549 cells, 12 hours post-infection, replicate 1


title: EAE5_R9_Unpolarized

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

description:
EAE5_R9
Processed data file: counts.txt
Processed data file: cpm.txt

data_processing:
Basecalling was performed using RTA 1.18.61.
bcl files were converted to fastq using CASAVA 1.8.2.
Fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b).
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1).
Prior to differential gene expression analysis, low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis were performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw transcript counts ("counts.txt") and counts per million ("cpm.txt").

source_name: Spinal Cord

growth_protocol: Transgenic mice were aged to 6 weeks of age under specific pathogen-free conditions and subsequently Experimental Autoimmune Encephalmyelitis (EAE) was induced.

extract_protocol:
Mice were sacrificed and spinal cords were isolated and transferred to ice-cold PBS (Sigma-Aldrich). Tissue was then cut in small pieces and digested in RPMI containing 2% fetal calf serum (Sigma-Aldrich), 25mM HEPES (Sigma-Aldrich), DNase I (10ng/ml, StemCell Technologies) and Collagenase D (0.8mg/ml, Roche) for 30 min at 37°C. Reaction was stopped by addition 1:100 dilution of a 0.5M EDTA (Sigma-Aldrich) solution. Suspension was filtered through 70 µm cell strainers (Falcon) and resuspended in a 30% solution of Percoll (Sigma-Aldrich). After 30 min of gradient centrifugation at 10.800 r.p.m., the top (myelin) and lower (red cells) layers were removed and the remaining solution was filtered through 70µm cell strainers (Falcon) before further analysis. Cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next, ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease-free water. Purity and integrity of the RNA were assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: Active EAE was induced in adult mice by injecting 400μg of purified recombinant MOG (N1-125) in complete Freund's adjuvant (containing 10mg/ml Mycobacterium tuberculosis H37 Ra, Sigma-Aldrich). At day 0 and 2, 400ng of pertussis toxin (Sigma-Aldrich) was administered intraperitoneally.

tag: strain/background

tag: genotype/variation

value: Arginase-YFP x iNOS-tdTomato

value: Unpolarized

tag: tissue derivation

value: Spinal Cord


title: EAE5_R8_Tomato

description:
EAE5_R8
Processed data file: counts.txt
Processed data file: cpm.txt

value: Tomato+


title: EAE3_R8_Tomato

description:
EAE3_R8
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE5_R6_EYFP

description:
EAE5_R6
Processed data file: counts.txt
Processed data file: cpm.txt

value: YFP+


title: EAE3_R9_Unpolarized

description:
EAE3_R9
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE4_R7_Double_Positive

description:
EAE4_R7
Processed data file: counts.txt
Processed data file: cpm.txt

value: YFP+ Tomato+


title: EAE2_R8_Tomato

description:
EAE2_R8
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE3_R6_EYFP

description:
EAE3_R6
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE3_R7_Double_Positive

description:
EAE3_R7
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE4_R9_Unpolarized

description:
EAE4_R9
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE4_R6_EYFP

description:
EAE4_R6
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE5_R7_Double_Positive

description:
EAE5_R7
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE2_R7_Double_Positive

description:
EAE2_R7
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE2_R9_Unpolarized

description:
EAE2_R9
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE2_R6_EYFP

description:
EAE2_R6
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE4_R8_Tomato

description:
EAE4_R8
Processed data file: counts.txt
Processed data file: cpm.txt


title: EAE1_R9_Unpolarized

description:
EAE1_R9
Processed data file: counts.txt
Processed data file: cpm.txt


title: PR8 NS1 infected A549 cells, 6 hours post-infection, replicate 1


title: EAE1_R8_Tomato

description:
EAE1_R8
Processed data file: counts.txt
Processed data file: cpm.txt


title: lung from CK10 group, rep2

value: BALB/c

value: lung

value: 6-week old


title: EAE1_R7_Double_Positive

description:
EAE1_R7
Processed data file: counts.txt
Processed data file: cpm.txt


title: PR8 NS1-SUMO infected A549 cells, 6 hours post-infection, replicate 1


title: EAE1_R6_EYFP

description:
EAE1_R6
Processed data file: counts.txt
Processed data file: cpm.txt


title: 12_CNS_microglia

description:
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

data_processing:
Basecalling was performed using RTA 1.18.61.
bcl files were converted to fastq using CASAVA 1.8.2.
Fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b).
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1).
Prior to differential gene expression analysis, low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis were performed using the limma/voom pipeline (limma version 3.30.8).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_Matrix.txt").

source_name: CNS

value: CD11b-high CD45-low microglia

value: CNS


title: 08_CNS_microglia


title: 11_CNS_microglia


title: 10_CNS_microglia


title: 09_CNS_microglia


title: 06_Blood_Ly6c_high_monocytes

source_name: Blood

value: CD45-positive CD115-positive Ly6c-high monocytes

value: Blood


title: 05_Blood_Ly6c_high_monocytes


title: 07_CNS_microglia


title: B6_P3_Unpolarized

data_processing:
Basecalling was performed using RTA 1.18.61
bcl files were converted to fastq using CASAVA 1.8.2
fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b)
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1)
Prior to differential gene expression analysis low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_Matrix.txt").

growth_protocol: Transgenic mice were aged to 6 weeks of age under specific pathogen free conditions and subsequently Experimental Autoimmune Encephalmyelitis (EAE) was induced.

extract_protocol:
Mice were sacrificed and spinal cords were isolated and transferred to ice-cold PBS (Sigma-Aldrich). Tissue was then cut in small pieces and digested in RPMI containing 2% fetal calf serum (Sigma-Aldrich), 25mM HEPES (Sigma-Aldrich), DNase I (10ng/ml, StemCell Technologies) and Collagenase D (0,8mg/ml, Roche) for 30 min at 37°C. Reaction was stopped by addition 1:100 dilution of a 0.5M EDTA (Sigma-Aldrich) solution. Suspension was filtered through 70 µm cell strainers (Falcon) and resuspended in a 30% solution of Percoll (Sigma-Aldrich). After 30 min of gradient centrifugation at 10.800 r.p.m., the top (myelin) and lower (red cells) layers were removed and the remaining solution was filtered through 70µm cell strainers (Falcon) before further analysis. Cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

tag: strain background

value: spinal cord

tag: cell markers


title: 04_Blood_Ly6c_high_monocytes


title: 02_Blood_Ly6c_high_monocytes


title: 01_Blood_Ly6c_high_monocytes


title: B6_P2_Tomato+ YFP+ cells

value: Tomato+ YFP+ cells


title: Control Sciatic nerve

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling
equenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (genes.fpkm tracking)

source_name: control Sciatic nerve

extract_protocol:
Sciatic nerves were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent. Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mixed

tag: development stage

value: control


title: B1_P1_YFP+ cells

value: Arginase-YFP x iNOS-tdTomato

value: YFP+ cells


title: MP_RNA1

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

data_processing:
Adapter sequences were trimmed by Trimmomatic 0.32
RNA-seq reads were aligned by Tophat 2 with default settings
Gene counts were generated with HTSeq
Differential Analysis was performed with edgeR
Genome_build: mm9
Supplementary_files_format_and_content: Compressed text file shows RPKM values.

source_name: Lin- bone marrow

growth_protocol: Bone marrow cells were lineage depleted and cultured in IL3, SCF and IL6 for 7 days

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Mini Kit, and on-column DNase treated
Library was prepared with Illumina TruSeq RNA Prep Kit

value: untransformed myeloid progenitors (MP)

tag: days in culture

tag: culture condition

value: Myeloid

value: Lin- bone marrow


title: MP_Aldh1a3_4C

data_processing:
Library strategy: 4C-seq
Different samples were demultiplexed using the in-line barcode sequences.
Reads were mapped to the mm9 assembly using BWA 0.7.10. Only uniquely mapped reads were kept.
Library size was normalized to 10 million per sample
Read counts were generated by mapping the normalized reads to a HindIII-DpnII restriction map of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files contain normalized read count per restriction unit for display on UCSC browser.

growth_protocol: Bone marrow cells were lineage depleted and retrovirally transduced with MIGR1-HA-HOXA9-ER and MIGR1-Flag-MEIS1 viruses. Cells were cultured in myeloid culture condition after transduction.

extract_protocol:
Chromatin was extracted from 1% formaldehyde-fixed cells. DNA was digested with HindIII, ligated and digested again with DpnII. Primers with Illumina adaptors and sequencing primer were used to amplify the library. Different samples were in-line barcoded for multiplexed sequencing.
Primers with Illumina adaptors were used to amplify the library.

tag: viral transduction

value: Stem cell (10ng/mL IL3, 10ng/mL IL6 100mg/mL SCF)


title: Ptip-DD_H3K4me1

description: High percentage adapter contamination

data_processing:
Adapter sequences were trimmed by Trimmomatic 0.32
ChIP-seq reads were aligned by BWA 0.7.10 with default settings
Peaks were called using MACS version 1.4 with parameters -g mm --bw 300 --pvalue 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files generated by MACS, including genome coordinate of peaks detected, fold enrichment and FDR

source_name: GFP+ bone marrow

growth_protocol: Bone marrow cells were lineage depleted and retrovirally transduced with MIGR1-HA-HOXA9(MIGR1-HA-HOXA9-ER) and MIGR1-Flag-MEIS1 viruses. Cells were cultured in myeloid or B cell culture condition after transduction.

extract_protocol:
Lysates were collected from sonicated cells. Chromatin fragments were isolated with antibody, RNase treated and column purified.
Libraries were generated using Illumina ChIP-seq Library Preparation Kit

tag: chip antibody

value: H3K4me1 (Abcam ab8895)

value: GFP+ bone marrow


title: HOXA9in_Aldh1a3_4C

value: HMM cells with HOXA9 inactivation

value: Myeloid (10ng/mL IL3) + 4OHT wash off


title: Ptip-DD_Input

description: High percentage adapter contamination


title: Ptip-FF_Input

description: High percentage adapter contamination


title: HMB_Input

value: HOXA9/MEIS1-transformed proB lymphoblasts (HMB cells)

value: B cell (5ng/mL IL7, 5ng/mL Flt3L)


title: Ptip-FF_H3K4me1

description: High percentage adapter contamination


title: HMB_HA

value: HA (Abcam ab9110


title: HMB_H3K27me3

value: H3K27me3 (Millipore 07-449)


title: HMB_H3K4me1


title: 03_Blood_Ly6c_high_monocytes

value: CD45-positive CD115-positive Ly6c-high monocytes

value: Blood


title: Tsc1cKO sciatic nerve

source_name: Tsc1cKO sciatic nerve

value: mixed


title: HOXA9in_Input


title: HOXA9in_CEBPA

value: C/EBP α (Santa Cruz sc-61 X)


title: MP_RNA2


title: HOXA9in_H3K4me1


title: HMM_MLL3/4

value: HOXA9/MEIS1-transformed myeloblasts (HMM cells)

value: Myeloid (10ng/mL IL3) + 100nM 4OHT

value: MLL4 #3 (Ge lab)


title: HOXA9in_MLL3/4

value: Lin- bone marrow


title: HMM_Input


title: HMM_Aldh1a3_4C

value: Myeloid


title: HMM_H3K27ac

value: H3K27ac (Abcam ab4729)


title: HMM_H3K4me1_1

value: H3K4me1 (Abcam ab8895)


title: HMM_H3K4me1_2


title: MP_CEBPA

value: untransformed myeloid progenitors (MP)

value: Stem cell (10ng/mL IL3, 10ng/mL IL6 100mg/mL SCF)


title: MP_Input


title: MP_H3K4me1


title: prdm14_puro_pgclc2

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

description:
DamID
processed data file:
prdm14_matada_pgclc_average.bedgraph

data_processing:
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline.
Processed data from the damidseq_pipeline software in bedgraph format were used for peak calling with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised fold enrichment of Dam-OCT4 or Dam-PRDM14 fusion protein over dam-alone.  Processed files are provided as averaged bedgraphs

source_name: Primordial germ cells

extract_protocol:
gDNA was extracted using the QuiAmp® DNA Micro. The gDNA was digested with DpnI, adaptors were ligated and then digested with DpnII and pcr amplified.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed with AlwI digestion.  Sonicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

tag: media

value: BMP4, BMP8, SCF, EGF and LIF

tag: flox cassette

value: PuroR

value: Primordial germ cells


title: HMB_H3K27ac

tag: cell type

value: HOXA9/MEIS1-transformed proB lymphoblasts (HMB cells)

value: B cell (5ng/mL IL7, 5ng/mL Flt3L)

tag: tissue


title: dam_puro_pgclc3


title: prdm14_puro_pgclc3


title: prdm14_puro_pgclc1


title: E13KO_ATAC_3

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

description: Genomic DNA of region accessible to Tn5 transposase

data_processing:
Libraries are sequenced by Illumina HiSeq 2000 and 2500.
Raw reads are alligned to mouse genome version mm10 though Tophat 2 (RNA-seq) or Bowtie 2 (ATAC-seq, ChiP-seq)
Gene count data are generated using Htseq count function.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, .bedgraph

source_name: Epidermis

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension. Epidermal cells isolated by FACS of GFP positive cells. Dermal cells isolated by FACS through CD140a antibody staining.
SMARTer Directional cDNA Library Construction Kit and NEBNext® Ultra™ Directional RNA Library Prep Kit ; ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013; ChiP-seq, protocol described in Wang et al., RNA, 2013.

tag: age

value: Embryonic day 13

value: Epidermis

tag: genotype

value: {delta}Np63 -GFP KI-KO


title: E13KO_ATAC_2


title: p63ChiP

source_name: cultured keratinocytes cell

value: cultured keratinocytes

value: Wild type

value: P63 antibody, Cell Signaling, #4892


title: dam_puro_pgclc2


title: HMM_CEBPA

value: HOXA9/MEIS1-transformed myeloblasts (HMM cells)

value: Myeloid (10ng/mL IL3) + 100nM 4OHT

value: C/EBP α (Santa Cruz sc-61 X)

value: Lin- bone marrow


title: E13KO_ATAC_1


title: OffDox_4

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) number of introns and exons; (9) length (sum of feature lengths, e.g. introns and exons); (10) read count (sense strand); (11) density (RPK) – count/length; (12) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: Subcutaneous tumor grown from KCip53-1_OffDox

growth_protocol: Immunocompromised (NSG) animals 8-10 weeks of age were used for all subcutaneous or orthotopic tumor growth experiments. For subcutaneous tumors, 500,000 cells were injected in a 200uL solution of 50% Matrigel and 50% RPMI media. Each mouse was implanted subcutaneously with two tumors, and tumor growth was recorded at least 3X weekly until tumors reached a 1.5cm diameter.

extract_protocol:
Tissue from subcutaneous tumors was collected in lysis buffer for RNA extraction. RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA Universal kit according to the manufacturer’s instructions.
PolyA+, non strand specific libraries were prepared by the University of Michigan Sequencing Core, and all samples were sequenced on an Illumina HiSeq 4000.

treatment_protocol: Doxycycline was administered in the drinking water (0.2g/L in a 5% sucrose solution) and changed every 3-4 days.

tag: host strain

value: Immunocompromised (NSG) mouse

tag: cell line used for tumor growth

value: KCip53-1 mouse pancreatic cancer cell line

value: Subcutaneous tumor grown from KCip53-1 cell line

tag: doxycycline treatment time (days)

tag: doxycycline removal time (days)

tag: doxycycline concentration (g/l)


title: dam_puro_pgclc1

value: BMP4, BMP8, SCF, EGF and LIF

value: PuroR


title: dam_puro_esc1_10000

description:
DamID
processed data file: prdm14_esc_10000cells_new.bedgraph

source_name: Embryonic stem cells (2i)

value: 2i and LIF

value: GFP

value: Embryonic stem cells


title: prdm14_puro_esc1_10000


title: E13het_ATAC_2

value: Embryonic day 13

value: Epidermis

value: {delta}Np63 -GFP KI-Het


title: E13het_ATAC_3


title: OffDox_2


title: OffDox_1


title: MP_H3K27ac

tag: strain

value: untransformed myeloid progenitors (MP)

value: Stem cell (10ng/mL IL3, 10ng/mL IL6 100mg/mL SCF)

value: H3K27ac (Abcam ab4729)


title: OffDox_3


title: Dox_4

source_name: Subcutaneous tumor grown from KCip53-1_Dox


title: prdm14_puro_esc3

description:
DamID
processed data file:
prdm14_matada_esc_average.bedgraph


title: Dox_3


title: prdm14_puro_esc2


title: prdm14_puro_esc1


title: Dox_2


title: Dox_1


title: E9het_ATAC_2

value: Embryonic day 9


title: NoDox_4

source_name: Subcutaneous tumor grown from KCip53-1_NoDox


title: dam_puro_esc2


title: NoDox_2


title: NoDox_3


title: dam_puro_esc1


title: NoDox_1


title: E15_KO_2

description: genes.tsv

data_processing:
Libraries are sequenced by Illumina HiSeq 4000.
Raw reads are processed
Cell Ranger software from 10x Genomics and Seurat from Satija Lab
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes tsv file and filtered and filtered gene-barcode matrices

source_name: Embryonic skin

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension.
Sing cell 3' Reagent kits from 10x Genomics

value: Embryonic day 15

value: <delta>Np63 -GFP KI-KO


title: oct4_gfp_epilc2

description:
DamID
processed data file:
oct4_matada_epilc_average.bedgraph

source_name: Epiblast-like stem cells

value: FGF2 and ActivinA

value: Epiblast-like stem cells


title: E15_KO_1

description: genes.tsv


title: E15_HET

description: genes.tsv

value: <delta>Np63 -GFP KI-Het


title: oct4_gfp_epilc1


title: E9het_ATAC_3


title: dam_gfp_epilc2


title: dam_puro_esc3


title: E15_WT

description: genes.tsv

value: WT


title: dam_gfp_epilc1


title: E13_WT

description: genes.tsv


title: E13_HET

description: genes.tsv


title: oct4_gfp_esc1

description:
DamID
processed data file:
oct4_matada_esc_average.bedgraph


title: dam_gfp_esc2


title: E13_KO_2

description: genes.tsv


title: oct4_gfp_esc3


title: oct4_gfp_esc2


title: dam_gfp_esc1


title: OLN2-1

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

data_processing:
Read Cleaning: Reads were cleaned in R using ShortRead::TrimEnds, removing bases from each end until the remainging read has bases p-values all over 0.1.  Afterwards reads shorter than 25bp were removed.
Read Alignment: Reads were aligned to the TAIR10 genome using Tophat2 using default parameters except -g 1, specifying to only retain reads with one valid alignment
Read Counting: Reads were counted in R using GenomicAlignments::summarizeOverlaps with the TAIR10 gff as input and the counting mode of 'union'
FPKM calculations: psuedo-counts (generated from edgeR's library size normalization) were divided by the gene length (in kb) found in the TAIR 10 gff.
Differential Expression: Differential expression was carried out using edgeR with the global coefficient of variation.  Genes with less than 50 counts in any biological replicate had their log2 fold changes set to zero, along with genes with absolute log2 fold changes less than 0.5
Genome_build: TAIR10
Supplementary_files_format_and_content: raw_read_counts.txt is a tab delimated text file with genes along the rows and libraries across the columns.  Each column is named by the sample which it belongs to followed by a underscore and the lane of the illumina chip which the reads were obtained.  Genes are represented by their AGI numbers.  The value for each gene-sample combination is the non-normalized feature counts obtained from summarizeOverlaps

source_name: opt3-2 leaf tissue

growth_protocol: Seedlings were plated on 1/4 strength MS media and stratified at 4C in the dark for 48hr.  Seedlings grew on the plates for 11d before being transferred to minimal hydroponic media for 22 days.  Hydroponic media was airated with a bubble stone.  Plants were grown in a growth chamber with 16 hours light and 8 hours dark with 40% RH and XC.

extract_protocol:
RNA was first isolated by pulverizing 3-4 plants with a LN2 cooled mortar and pestle.  A Qiagen RNeasy Plant Kit was used to isolate RNA.  DNA was digested using Ambion Turbo DNase.  All protocols were followed according to manufacturers protocol
cDNA libraries were constructed using Illumina TruSeq kits according to manufacturers protocol

treatment_protocol: Plants were transferred from minimal media to minimal media with 20uM CdCl2 for 72 hours before being harvested.  Treatment and harvest were both performed at 11:00am.

value: Leaf

tag: treatment

value: Replete media

tag: biological replicate

tag: technical replicate


title: OLN1-2


title: OLN1-3


title: OLN1-1


title: OLN2-3


title: ORN3-2

source_name: opt3-2 root tissue

value: Root


title: OLN2-2


title: ORN3-3


title: ORN3-1


title: ORN2-2


title: ORN2-3


title: E13_KO_1

description: genes.tsv


title: ORN2-1


title: ORN1-3


title: dam_gfp_esc3

value: 2i and LIF

value: GFP

value: Embryonic stem cells


title: OLN3-3


title: ORN1-1


title: CLN2-3

source_name: Columbia-0 leaf tissue


title: CLN2-1


title: CLN2-2


title: CLN1-3


title: CLN1-1


title: OLN3-1


title: CLN1-2


title: CRN3-2

source_name: Columbia-0 root tissue


title: CRN3-1


title: SUM149 cell line treated with DMSO Replicate 4

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing:
RNASeq reads were aligned to the hg19 genome assembly using STAR 2.4.0h1 with default parameters except for --outSAMattributes NH HI AS nM XS . The output was sorted .BAM files
Alternative splicing detection and quantification was done using EventPointer with the following parameters: Reference Transcriptome = Affymetrix HTA 2.0 Mapping File .gtf and Alpha = 2
Genome_build: hg19
Supplementary_files_format_and_content: RawCounts, FPKMs

source_name: SUM149 cell line treated with DMSO

growth_protocol: All cell lines were grown according to the suppliers’ recommendation

extract_protocol:
Total RNAs were isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer's protocol
RNAseq was performed in the Center for Cooperative Research in Biosciences (CICBiogune) using the Illumina HiSeq2000 sequencing technology, HiSeq Flow Cell v3 and TruSeq SBS Kit v3. 2ug of RNA of each sample was sent for this purpose. The run type was strand specific, multiplexed with paired-end reads of 100 nucleotides each. The amount of RNA for hybridization and validation purposes was 5 ug.

treatment_protocol: To induce splicing events, cells were grown to ~70% confluence and treated with 1µM CX-4945  or DMSO during 12 hours in a total of 5 replicates per condition

tag: cell line

value: Triple Negative Breast Cancer Cell Line

tag: agent

value: DMSO


title: SUM149 cell line treated with DMSO Replicate 5


title: SUM149 cell line treated with DMSO Replicate 3


title: CRN2-2


title: OLN3-2


title: SUM149 cell line treated with DMSO Replicate 2


title: CLN3-3


title: CRN2-1


title: CRN2-3


title: SUM149 cell line treated with DMSO Replicate 1


title: CRN1-3


title: CRN1-2


title: ORN1-2


title: SUM149 cell line treated with CX4945 Replicate 5

source_name: SUM149 cell line treated with CX4945


title: SUM149 cell line treated with CX4945 Replicate 4


title: CRN3-3


title: CRN1-1


title: SUM149 cell line treated with CX4945 Replicate 3


title: SUM149 cell line treated with CX4945 Replicate 2


title: SUM149 cell line treated with CX4945 Replicate 1


title: MDA468 cell line treated with DMSO Replicate 4

source_name: MDA468 cell line treated with DMSO


title: MDA468 cell line treated with DMSO Replicate 1


title: MDA468 cell line treated with DMSO Replicate 3


title: MDA468 cell line treated with DMSO Replicate 2


title: MDA468 cell line treated with CX4945 Replicate 5

source_name: MDA468 cell line treated with CX4945


title: MDA468 cell line treated with CX4945 Replicate 4


title: MDA231 cell line treated with DMSO Replicate 5

source_name: MDA231 cell line treated with DMSO


title: MDA231 cell line treated with DMSO Replicate 2


title: MDA231 cell line treated with DMSO Replicate 3


title: MDA468 cell line treated with CX4945 Replicate 2


title: MDA231 cell line treated with DMSO Replicate 1


title: MDA231 cell line treated with DMSO Replicate 4


title: MDA468 cell line treated with CX4945 Replicate 1


title: MDA231 cell line treated with CX4945 Replicate 5

source_name: MDA231 cell line treated with CX4945


title: MDA231 cell line treated with CX4945 Replicate 3


title: MDA231 cell line treated with CX4945 Replicate 4


title: MDA231 cell line treated with CX4945 Replicate 1


title: MDA468 cell line treated with DMSO Replicate 5


title: MDA231 cell line treated with CX4945 Replicate 2


title: MDA468 cell line treated with CX4945 Replicate 3