title: CMC-_Rep2

data_processing:
Sequenced reads were trimmed for low-quality reads, adaptor sequences, and inline barcodes(10 random bases after the barcode added during the library construction at the 5' end of inserted sequences).
Trimmed reads were mapped with Bowtie2 to the human rRNA reference.
PCR duplications were removed according to the inline barcodes.
Misincorporation information were analyzed based on translated Pileup files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include numbers of miscorporation events of different types at each site on the reference

extract_protocol:
Total RNA was extracted with TRIzol.
For dephosphorylation of 3' end, RNA fragments on C1 beads were first treated by FastAP enzyme and then by T4 PNK enzyme. 3' RNA linker ligation was performed with T4 RNA Ligase 1 high concentration. To remove excess adaptors, samples were washed five time, and then heated at 95 ℃ for 5 min to elute RNAs from beads followed by ethanol precipitation. Subsequently, the RNA was reverse transcribed with RT DNA primer, followed by ExoSAP treatment and cleanup with MyONE Silane beads. The cDNA product was subjected to 5' ligation with a second adaptor performed by T4 RNA Ligase 1 high concentration. cDNA ligated with 5' linker was purified by Silane beads and amplified by Index Primers, followed by cleanup and size-selection of PCR products using AMPure XP beads. Libraries were sequenced on Illumina HiSeq X Ten with double end reads.


title: CMC+_Rep2

status: Public on Oct 03 2017

type: SRA

city: Beijing

first: Chengqi

last: Yi

address: 5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin and grown at 37 ℃ with 5% CO2.

tag: genotype

value: wild type


title: Mdl_0_No_KDE_rep1

city: Berkeley

first: Heather

middle: Marie

last: Jensen

state: California

address: 1 Cyclotron Road, Mailstop 978-4110K

country: USA

institute: Lawrence Berkeley National Laboratory

description: Biorep analysis

library_source: genomic

data_processing:
Library strategy: BAR-Seq
log2 fitness values for bar-coded strains processed using the published FEBA analysis method with "Time0_control" as Time0; Wetmore et. al (2015) mBio;open access code available at https://bitbucket.org/berkeleylab/feba
Supplementary_files_format_and_content: Excel file includes log2 fitness (bar code abundance) values for each bar-coded gene disruption.  Time0_control is the sample used as the initial abundance of each barcode (i.e.,  would have a 0 value in all fields).

molecule: genomic DNA

organism: Escherichia coli BW25113

source_name: E. coli BW25113 transposon library (TnLib)

growth_protocol: Grown and induced in 0.42mL EZ rich + 1% glucose + kanamycin + chloramphenicol in 48 well plates at 30degC for 6 hours

extract_protocol:
Sorted cells were pelleted, and genomic DNA was purified using the Qiagen DNeasy Blood and Tissue Kit.
Barcodes were amplified as described in Wetmore (2015). In brief, barcodes were amplified using Q5 DNA polymerase with a common primer and indexed primer. Amplicons were checked with gel electrophoresis and purified using the Zymo Clean and Concentrator kit. Finally, concentrations were measured with Qubit HS assay, and samples were multiplexed.

treatment_protocol: Cells were sorted by FACS according to GFP signal intensity.

tag: tnlib

value: TnLib/mdlB-GFP

tag: iptg (mm)

tag: sorting gate

value: No GFP


title: Lep_0_No_KDE_rep1

description: Biorep analysis

value: TnLib/lepI-GFP


title: Lep_0_No_KDE_rep2

description: Biorep analysis


title: CMC-_Rep1


title: Yid_0_No_KDE_rep1

description: Biorep analysis

value: TnLib/yidC-GFP


title: Cyo_0_No_KDE_rep1

description: Biorep analysis

value: TnLib/cyoB-GFP


title: Gst_0_No_KDE_rep1

description: Biorep analysis

value: TnLib/gstA-GFP


title: Cyo_200_No_rep5

description: Bar codes in sorted sample


title: Cyd_100_No_rep4

description: Bar codes in sorted sample

value: TnLib/cydB-GFP


title: CMC+_Rep3


title: Cyd_100_Low_rep4

description: Bar codes in sorted sample

value: Low GFP


title: Gst_0_No_KDE_rep2

description: Biorep analysis


title: Cyo_200_Low_rep5

description: Bar codes in sorted sample


title: CMC-_Rep3


title: Cyd_0_No_KDE_rep2

description: Biorep analysis


title: Yid_200_Low_rep2

description: Bar codes in sorted sample


title: Cyd_100_High_rep4

description: Bar codes in sorted sample

value: High GFP


title: CMC+_Rep1


title: Cyo_200_High_rep5

description: Bar codes in sorted sample


title: Yid_200_High_rep2

description: Bar codes in sorted sample


title: Mdl_200_High_rep2

description: Bar codes in sorted sample


title: Mdl_0_No_KDE_rep2

description: Biorep analysis


title: Mdl_200_Low_rep2

description: Bar codes in sorted sample


title: Mdl_200_No_rep2

description: Bar codes in sorted sample


title: Mdl_100_Low_rep1

description: Bar codes in sorted sample


title: Cyd_100_High_rep3

description: Bar codes in sorted sample


title: Cyo_200_No_rep4

description: Bar codes in sorted sample


title: Yid_200_High_rep1

description: Bar codes in sorted sample


title: Cyo_200_Low_rep4

description: Bar codes in sorted sample


title: Cyd_100_Low_rep3

description: Bar codes in sorted sample


title: Lep_100_High_rep2

description: Bar codes in sorted sample


title: Gst_400_High_rep2

description: Bar codes in sorted sample


title: Yid_200_Low_rep1

description: Bar codes in sorted sample


title: Lep_100_Low_rep2

description: Bar codes in sorted sample


title: Mdl_200_High_rep1

description: Bar codes in sorted sample


title: Mdl_100_Low_rep3

description: Bar codes in sorted sample


title: Mdl_200_No_rep1

description: Bar codes in sorted sample


title: Lep_100_No_rep2

description: Bar codes in sorted sample


title: Cyd_100_No_rep3

description: Bar codes in sorted sample


title: Cyd_100_No_rep2

description: Bar codes in sorted sample


title: Cyd_100_High_rep2

description: Bar codes in sorted sample


title: Cyo_200_No_rep3

description: Bar codes in sorted sample


title: Cyd_100_Low_rep2

description: Bar codes in sorted sample


title: Gst_400_Low_rep2

description: Bar codes in sorted sample


title: Mdl_100_High_rep2

description: Bar codes in sorted sample


title: Cyo_200_High_rep3

description: Bar codes in sorted sample


title: Cyo_200_Low_rep3

description: Bar codes in sorted sample


title: Cyo_50_High_rep3

description: Bar codes in sorted sample


title: Cyo_50_Low_rep3

description: Bar codes in sorted sample


title: Lep_100_High_rep1

description: Bar codes in sorted sample


title: Mdl_100_High_rep3

description: Bar codes in sorted sample


title: Cyo_200_High_rep4

description: Bar codes in sorted sample


title: Mdl_200_Low_rep1

description: Bar codes in sorted sample


title: Lep_100_Low_rep1

description: Bar codes in sorted sample


title: Lep_100_No_rep1

description: Bar codes in sorted sample


title: Gst_400_Low_rep1

description: Bar codes in sorted sample


title: Gst_400_High_rep1

description: Bar codes in sorted sample


title: Cyd_100_Low_rep1

description: Bar codes in sorted sample


title: Cyd_100_High_rep1

description: Bar codes in sorted sample


title: Cyo_50_High_rep2

description: Bar codes in sorted sample


title: Cyo_200_No_rep2

description: Bar codes in sorted sample


title: Cyo_200_Low_rep1

description: Bar codes in sorted sample


title: Cyd_0_No_KDE_rep1

description: Biorep analysis


title: Cyd_100_No_rep1

description: Bar codes in sorted sample


title: Cyo_50_High_rep1

description: Bar codes in sorted sample


title: Cyo_50_Low_rep2

description: Bar codes in sorted sample


title: Cyo_200_High_rep1

description: Bar codes in sorted sample


title: Set1YF

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

country: France

institute: INSERM

description: Nascent RNA immunoprecipitated with Set1 mouse monoclonal antibody, prepared in lab, Nagy et al, 2002.

data_processing:
Library strategy: CRAC-seq
Sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al 2012).
The 3’ adaptor is clipped with Cutadapt and the resulting insert is quality trimmed from the 3’ end using Trimmomatic rolling mean clipping (bolger et al 2013)
Read counts were normalized relative to reads derived from an S. pombe spike that was added to S. cerevisiae cells before the crosslinking step. The S. pombe spike cells contain a non-relevant protein tagged with the same HTP tag that was co-purified with the S. cerevisiae
The reads were mapped to the R64 genome (sgd) using bowtie2.
Genome_build: R64 genome (Saccharomyces cerevisiae )
Supplementary_files_format_and_content: Wig files providing read coverage for all samples. All wigs are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: crosslinked tagged Set1-YF11 mutant

growth_protocol: For all datasets, 2L of yeast cells expressing PTH-Set1 were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) .

extract_protocol:
The detailed extract protocol is described in the experimental procedures of the article. PTH-Set1 was isolated by three purification steps, two of which in denaturing conditions. The RNA crosslinked to Set1 was submitted to adaptors ligation, isolated and reverse transcribed.
Between half to ¾ of the cDNA solution was used to performed multiple PCR reactions in individual 25 µl reactions containing 1/10 of the whole cDNA reaction for 13 cycles under standard conditions. The PCR reactions were pooled and treated with 200 U of Exonuclease I (NEB)/ml   for 1 hour at 37°C. DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sequenced using  Illumina technology (NextSeq 500).

treatment_protocol: Cells were submitted to UV crosslink in Megatron for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

tag: background strain

tag: genotype/variation


title: Set1rep1

source_name: crosslinked tagged Set1, replicate1


title: Set1NoCLK

source_name: Non crosslinked tagged Set1


title: Cyo_200_No_rep1

description: Bar codes in sorted sample


title: PTH-vector

description: PTH-vector

data_processing:
Libraries were sequenced on a mid-output flow cell (130M clusters) using the NextSeq® 500/550 High Output v2 150 cycles kit (Illumina)
ChIP-Seq data quality was assessed using FastQC tool
ChIP-seq reads were aligned to the sacCer3 genome assembly using BFAST alignment tool with default parameters
Data were filtered using the following specifications: Only uniquely mappable reads (non secondary alignment) were considered to create BedGraphs with a normalization to 10 million mapped reads for each sample.
Genome_build: sacCer3 (Saccharomyces cerevisiae )
Supplementary_files_format_and_content: Bigwig files were converted from BedGraph using bedGraphToBigWig tool. The bedGeaph files were generated first using Homer makeUCSCfile tool (only uniquely mappable reads were considered)

source_name: PTH-vector

growth_protocol: Yeast strains were grown in Yeast extract-Peptone-Dextrose (YPD) (1% yeast extract, 2% peptone and 2% dextrose) media at 30◦C.

extract_protocol:
Cells were lysed using glass beads. Lysates were sonicated, clarified and Set1-DNA complexes were isolated with a set1 monoclonal antibody 166 (Nagy et al, 2002) that recognizes a Set1 epitope between residues 700 and 761.
Library were prepared from fragmented DNA using the Chip-seq MicroPlex Library Preparation Kit v2 samples preparation (Diagenode) according to manufacturer’s instructions.

value: no transfected Set1

tag: chip antibody

value: W303-1A  (Rothstein RJ, 1983)


title: Cyo_50_Low_rep1

description: Bar codes in sorted sample


title: PTH-Set1 YF-AA

description: PTH-Set1 Y-271 F-272 /AA


title: PTH-Set1 deltaNSET

description: PTH-Set1 deltaNSET

source_name: PTH-Set1 deltaNSET

value: Set1 deltaN


title: PTH-Set1 deltaRRM deltaNSET

description: PTH-Set1 deltaRRM deltaNSET

source_name: PTH-Set1 deltaRRM deltaNSET

value: Set1 deltaN, deltaRRM


title: PTH-Set1 deltaRRM

description: PTH-Set1 deltaRRM

source_name: PTH-Set1 deltaRRM

value: Set1 deltaRRM


title: PTH-Set1 FL

description: PTH-Set1 Full Length

source_name: PTH-Set1 Full Length

value: wildtype Set1


title: Input PTH-Set1 FL

description: Input PTH-Set1 Full Length

source_name: Input PTH-Set1 Full Length


title: Input PTH-Set1 YF-AA

description: Input PTH-Set1 Y-271 F-272 /AA

source_name: Input PTH-Set1 Y-271 F-272 /AA


title: control_dental pulp cells

city: Vancouver

first: Mary

last: MacDougall

address: 2329 West Mall

country: Canada

institute: UUniversity of British Columbia

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were aligned with TopHat version 2.0.8 with parameters --library-type fr-unstranded -r 150
FPKM values were calculated with Cufflinks version 2.1.1 with parameters -g -L -b -u
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the FPKM values, log2 fold change, p-/q-values output from Cuffdiff

source_name: dental pulp cells

extract_protocol:
Total RNA from CCD-011 and control pulp cells were isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CCD and control dental pulp cells with the same passage unmber were cultured in 6-well plates with growth medium.

tag: tissue resource

value: sex-age matched unaffected healthy individual (CCD07)

tag: tissue

value: tooth

tag: cell type

value: dental pulp cells


title: Cyo_200_High_rep2

description: Bar codes in sorted sample


title: Cyo_200_Low_rep2

description: Bar codes in sorted sample


title: Set1rep2

source_name: crosslinked tagged Set1, replicate2


title: larval_T3_INPUT

city: Oxford

first: Yoshinori

last: Tomoyasu

state: Ohio

address: 700E High St

department: Biology

institute: Miami University

description:
genomic input
larval_INPUT_merged_q10.bw.gz

data_processing:
Illumina TruSeq adapter sequences were removed from reads using Trimmomatic (v0.32)
The first eight bases (index sequence) were removed and reads were aligned to the Tribolium genome (v3) using Bowtie2 (v2.2.3)
For bigWig files, sam files were converted to bam files, sorted, duplicates removed, and alignments with a quality score less than ten removed, and replicate files merged using samtools (v0.1.12a). The merged bam alignments were converted to bigWig format by normalizing to sequencing depth using deepTools (v2.5.2) and visualized in IGV (v2.3)
For narrowPeak (bed) files, sam files were converted to bam files and sorted using samtools (v0.1.12a), then peaks were called on each FAIRE-seq replicate using both input files as control using MACS2 (v2.1.1.20160309)
Genome_build: Tcas3
Supplementary_files_format_and_content: FAIRE processed data files are in bigWig format showing FAIRE signal normalize to sequencing depth, and narrowPeak (bed) format, showing peaks called on FAIRE signal versus input.

organism: Tribolium castaneum

source_name: last-instar larval T3 segment

growth_protocol: last-instar larvae were selected based on enhancer-trap activity of pu11. Elytron discs (T2) or hindwing discs (T3) were dissected out along with lateral epidermis.

extract_protocol: 1-100ng DNA was prepared for sequencing on an Illumina Hi-Seq 2000 machine at the UNC High-Throughput Sequencing Facility.

treatment_protocol: dissected samples were fixed for 30 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb.

tag: strain

tag: developmental stage

value: last-instar larvae

value: T3 lateral epidermis

tag: internal index

value: TGCTTCAT


title: larval_T2_INPUT

source_name: last-instar larval T2 segment

value: T2  lateral epidermis

value: CGCCCACT


title: larval_T3_FAIRE_Rep3

description:
FAIRE-seq
larval_T3_FAIRE_merged_q10.bw.gz

treatment_protocol: dissected samples were fixed for 30 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: T3  lateral epidermis

value: ACAGTTGT


title: larval_T3_FAIRE_Rep2

value: TCAGGACT


title: Mig1_YPM_None_4

city: Singapore

first: Norman

last: Pavelka

address: 8A Biomedical Grove, Immunos Building, Level 4

department: Singapore Immunology Network

country: Singapore

institute: Agency for Science, Technology and Research

data_processing:
Mapping to C albicans SC5314 genome (version A21 s02 m08 r09) with STAR (version 020201)
Number of assigned reads was counted using featureCounts
ANOVA analysis performed using R
Genome_build: C albicans SC5314 version A21 s02 m08 r09

organism: Candida albicans

source_name: in vitro culture

growth_protocol: 37 °C, 150 rpm. 50ml of culture in 200ml flask

extract_protocol:
Centrifugation. Flash frozen in liquid nitrogen. Protocol from Cottier et al., 2015
Illumina protocol

tag: strain/genotype

tag: media

value: YPM

tag: treatment


title: SC5314_YPM_Acetic_4

value: Acetic acid


title: Mig1_YPM_Butyric_4

value: Butyric acid


title: larval_T3_FAIRE_Rep1

value: GTTAATCT


title: SC5314_YPM_Butyric_4


title: larval_CNS_FAIRE_Rep2

description:
FAIRE-seq
larval_CNS_FAIRE_merged_q10.bw.gz

source_name: last-instar larval brains

growth_protocol: brains were dissected from  last instar larvae

treatment_protocol: dissected samples were fixed for 20 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: brain

value: TGACCA


title: Mig1_YPD_None_4

value: YPD


title: larval_T2_FAIRE_Rep2

description:
FAIRE-seq
larval_T2_FAIRE_merged_q10.bw.gz

value: CCCGTCGT


title: larval_T2_FAIRE_Rep3

value: GCTCTTGT


title: larval_CNS_FAIRE_Rep1

value: last-instar larvae

value: TTAGGC


title: Mig1_YPD_Acetic_4


title: 48hr_FAIRE_Rep2

description:
FAIRE-seq
48hr_FAIRE_merged_q10.bw.gz

source_name: 48 - 72 hour embryos

growth_protocol: Following a pre-clearing step, embryos were collected for 24 hours and then aged at 30C until the designated time

treatment_protocol: staged samples were fixed for 30 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: Georgia I

value: 48 - 72 hours after egg laying

value: whole embryo

value: GTATG


title: SC5314_YPD_Butyric_4


title: SC5314_YPM_None_4


title: 48hr_FAIRE_Rep1

description:
FAIRE-seq
48hr_FAIRE_merged_q10.bw.gz

value: CAGGA


title: 24hr_FAIRE_Rep2

description:
FAIRE-seq
24hr_FAIRE_merged_q10.bw.gz

source_name: 24 - 48 hour embryos

value: 24 - 48 hours after egg laying

value: CCAGT


title: SC5314_YPD_Acetic_4

value: Acetic acid


title: SC5314_YPD_None_4


title: CCD-011_dental pulp cells

value: CCD patient with allelic RUNX2 deletion (CCD-011)

value: tooth

value: dental pulp cells


title: Mig1_YPM_Acetic_3

value: YPM


title: Mig1_YPM_Butyric_3

value: Butyric acid


title: 24hr_FAIRE_Rep1

description:
FAIRE-seq
24hr_FAIRE_merged_q10.bw.gz

value: CTCAC


title: Mig1_YPM_Acetic_4


title: Mig1_YPM_None_3


title: 0hr_FAIRE_Rep2

description:
FAIRE-seq
0hr_FAIRE_merged_q10.bw.gz

source_name: 0 - 24 hour embryos

value: 0 - 24 hours after egg laying

value: AAGTT


title: Mig1_YPD_Butyric_4

value: YPD


title: larval_T2_FAIRE_Rep1

value: last-instar larvae

value: T2  lateral epidermis

value: AGATGGTT


title: Mig1_YPD_Butyric_3


title: 0hr_FAIRE_Rep1

description:
FAIRE-seq
0hr_FAIRE_merged_q10.bw.gz

value: Georgia I

value: whole embryo

value: GCACA


title: Mitotic drought experiment, nine days water deprivation, 4 week old Col-0, biological rep3

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Raw sequencing reads were quality controlled and trimmed using Trim Galore! (v0.3.7), Cutadapt (v1.9), and FastQC (v0.11.2)
Reads were then aligned to TAIR10 using the Bismark aligner (v0.14.5) with the flags --bowtie1 -n 2, -l 20 (bowtie v1.1.2).
Methylated cytosines were extracted, at single cytosine resolution, from aligned reads using the Bismark methylation extractor with default parameters.
The proportion of genome-wide CG, CHG, and CHH methylation was determined as mean methylation across reads at single cytosine resolution (.bed) and across 100 bp windows (.100bp.bed) for genome wide comparisons.
Genome_build: TAIR10
Supplementary_files_format_and_content: 100bp.bed: genome wide mean methylation summarised into 100bp windows. Column headers are as follows: Chromosome, position, length, Proportion methylated C, Number of  C's methylated, Number of C's unmethylated, Total C's, Number of C's in region.
Supplementary_files_format_and_content: .bed: mean methylation at single cytosines. Separate files have been produced for each sequence of DNA methylation: CG, CHG, and CHH.
Supplementary_files_format_and_content: .cov: coverage files giving proportion methylation, counts methylated, and counts unmethylated for single cytosines. Separate files have been produced for each sequence of DNA methylation: CG, CHG, and CHH.

organism: Arabidopsis thaliana

source_name: 4 week old Col-0

growth_protocol: Plants grown on soil, with approximately 3g/L osmocote fertilizer, under a 12-hour photoperiod of 100-150μ mol photons m-2 s -1, 20 (±0.5) °C, and 55 (±5) % RH.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit (Limburg, Netherlands), as per the manufacturer’s instructions. 100-200 ng of fragmented (Covaris) and purified gDNA was bisulfite converted using the Zymo DNA-Gold bisulfite conversion kit (Zymo Research; CA, USA)
Whole genome bisulfite sequencing libraries were constructing using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences; MI, USA) as per the manufacturer’s instructions.

treatment_protocol:
For excess-light treatments, exposure to approximately 10X growth irradiance (1000 μ mol photons m-2 s-1) was applied using a mixture of 250W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON-T 250W E E40 SL/12) providing a source of ‘warm’ light (similar to sunlight). This was applied for one hour repeated thrice daily at 9:30 am, 1:30pm, and 5:30 pm.
For lineages exposed to drought, stress was applied twice every generation. The first was applied at 2 weeks of age, which involved saturating to field capacity on day 0 and subsequently withholding watered for 2 weeks. Plants were then watered and allowed to recover for 5 days. The drought treatment was repeated following recovery, however, this time for only 12 days to minimise plant death. Plants were then watered until rosette leaf senescence and the appearance of dried, mature siliques for seed harvesting following ABRC guidelines.

tag: age

value: 4 weeks old

value: whole rosette

tag: stress

tag: ecotype


title: SC5314_YPM_Acetic_3

value: Acetic acid


title: SC5314_YPM_Butyric_3


title: Mig1_YPD_None_3


title: SC5314_YPM_None_3


title: Mitotic drought experiment, Unstressed, 4 week old Col-0, biological rep3

value: unstress


title: Mitotic drought experiment, nine days water deprivation, 4 week old Col-0, biological rep1


title: Mitotic drought experiment, Unstressed, 4 week old Col-0, biological rep2


title: SC5314_YPD_Acetic_3


title: Mitotic drought experiment, Unstressed, 4 week old Col-0, biological rep1


title: 20uM G47_2

city: shanghai

first: cheng

last: luo

address: zuchongzhi road 555

institute: shanghai institute of material medica

data_processing:
Tophat2 with default parameters
Samtools for sorting
Cufflinks with default parameters
Cuffdiff with default parameters
Cuffmerge with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files including FPKM for each Sample

growth_protocol: MV4-11 default culture protocol

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20uM G47 added directly to the dish The detailed method described in related paper

tag: cell line

value: Peripheral Blood

value: 10 years

tag: Sex

value: male


title: SC5314_YPD_Butyric_3

value: Butyric acid


title: 20uM G47_1


title: DMSO control_2


title: SC5314_YPD_None_3


title: TMO5_Distal_rep1

city: Gent

first: Jos

last: Wendrich

address: Technologiepark 71

department: PSB

country: Belgium

institute: VIB-UGent

description:
TMO43
TMO4.3 barcode: TGTGAA
processed data file:
TMO5_Distal.fpkm.txt

data_processing:
Differential expression was calculated using, Bowtie, Tophat, Cufflinks, and CuffDiff
Genome_build: TAIR10
Supplementary_files_format_and_content: "fpkm" files contain normalized expression values from respective cell population, showing test_id, gene_id, gene accession number, locus location and fpkm value; "total" files contain normalized expression values, -log2 fold changes and q-values comparing the different cell populations showing: gene accession number, gene name/symbol, gene description (title) fpkm values is different populations, -log2 fold changes and q-values comparing the different populations.

source_name: protoplasted root meristem cells

extract_protocol:
Total RNA was extracted from fluorescent activated cell-sorted cells, using QIAGEN Rneasy micro kit.
RNA-seq libraries were created using NuGEN Ovation ultralow Library Systems kit.

value: root meristematic xylem


title: TMO5_Medial_rep2

description:
TMO72
TMO7.2 barcode: CACCTC
processed data file:
TMO5_Medial_fpkm.txt


title: TMO5_Distal_rep2

description:
TMO73
TMO7.3 barcode: GTGGCC
processed data file:
TMO5_Distal.fpkm.txt


title: TMO5_Medial_rep1

description:
TMO42
TMO4.2 barcode: GTGTTA
processed data file:
TMO5_Medial_fpkm.txt


title: Mig1_YPM_Butyric_2

value: YPM


title: Mig1_YPM_Acetic_2


title: Mig1_YPD_Acetic_3

value: YPD


title: DMSO control_1


title: TMO5_Proximal_rep2

description:
TMO71
TMO7.1 barcode: ACAAAC
processed data file:
TMO5_Proximal_fpkm.txt


title: Cyto_p53-_4

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institute

data_processing:
RNAseq reads were mapped to the human reference genome using Bowtie with parameters -m 1 -n 2 -l 28 --chunkmbs 1000
The rpkmforgenes script (cf. Ramskold et al. (2009) PLoS computational biology, 5, e1000598.) was used to quantify gene expression (with options -readCount, -fulltranscript and -onlycoding). Raw read counts are provided here.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited file containing raw reads counts for each sample

growth_protocol: HCT-116 p53+/+ and HCT-116 p53-/- and MCF7 ATCC HTB-22™ cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum 1% penicillin/streptomycin and 1% L-glutamine (Gibco, Life Technologies).

extract_protocol:
RNA was extracted using Tri-reagent® and further purified with RNAeasy MinElute Cleanup Kit (Qiagen) according to manufacturer’s recommendations.
Smart-seq2 was performed as described in Picelli S et al. Nature protocols, 9, 171-181 (2014) using 10 ng (when possible, otherwise less) of RNA as starting material. Prior to sequencing, all RNAseq libraries were adjusted to a concentration of 10 nM and then pooled.

treatment_protocol: Cells were serum-starved for 16 hours.

tag: cell line background

tag: p53 status

tag: rna type

value: cytosolic RNA

tag: gradient preparation method

tag: replicate identifier

tag: sample identifier


title: Mig1_YPM_None_2


title: Cyto_p53+_4


title: TMO5_Proximal_rep1

description:
TMO41
TMO4.1 barcode: CACACA
processed data file:
TMO5_Proximal_fpkm.txt

tag: strain

tag: tissue


title: Mig1_YPD_Acetic_2


title: Mitotic drought experiment, nine days water deprivation, 4 week old Col-0, biological rep2


title: Poly_Opt_p53-_4

value: polysome-associated RNA

value: Optimized non-linear gradient


title: SPT_Distal_rep3

description:
SPT53
SPT5.3 barcode: ACACGA
processed data file:
SPT_Distal_fpkm.txt

value: SPT

value: root meristem


title: SPT_Distal_rep2

description:
SPT43
SPT4.3 barcode: CCTCGG
processed data file:
SPT_Distal_fpkm.txt


title: Mig1_YPD_Butyric_2


title: SC5314_YPM_Acetic_2


title: Mig1_YPD_None_2


title: Poly_Lin_p53+_4

value: Linear gradient


title: SPT_Medial_rep3

description:
SPT52
SPT5.2 barcode: TTCGCT
processed data file:
SPT_Medial_fpkm.txt


title: Poly_Lin_p53-_4


title: Cyto_p53-_3


title: SPT_Medial_rep2

description:
SPT42
SPT4.2 barcode: AAGACG
processed data file:
SPT_Medial_fpkm.txt


title: SPT_Distal_rep1

description:
SPT23
SPT2.3 barcode: GGACCC
processed data file:
SPT_Distal_fpkm.txt


title: SC5314_YPM_None_2


title: SPT_Medial_rep1

description:
SPT22
SPT2.2 barcode: CCTTCA
processed data file:
SPT_Medial_fpkm.txt


title: SC5314_YPM_Butyric_2


title: SC5314_YPD_Acetic_2


title: SPT_Proximal_rep3

description:
SPT51
SPT5.1 barcode: GGATGT
processed data file:
SPT_Proximal_fpkm.txt


title: Poly_Opt_p53+_3


title: Cyto_p53+_3


title: SPT_Proximal_rep2

description:
SPT41
SPT4.1 barcode: TTCAGC
processed data file:
SPT_Proximal_fpkm.txt


title: Poly_Opt_p53-_3


title: SC5314_YPD_None_2


title: Poly_Lin_p53-_3


title: SPT_Proximal_rep1

description:
SPT21
SPT2.1 barcode: AAGGGA
processed data file:
SPT_Proximal_fpkm.txt


title: Mig1_YPM_Acetic_1


title: PUB25_Distal_rep3

description:
PUB33
PUB3.3 barcode: ACACGA
processed data file:
PUB25_Distal_fpkm.txt


title: Poly_Lin_p53+_3


title: Poly_Opt_p53+_4


title: Mig1_YPM_Butyric_1


title: Cyto_p53-_2


title: Cyto_p53+_2


title: Mig1_YPD_Acetic_1


title: Poly_Opt_p53-_2


title: PUB25_Medial_rep3

description:
PUB32
PUB3.2 barcode: TTCGCT
processed data file:
PUB25_Medial_fpkm.txt


title: PUB25_Distal_rep1

description:
PUB13
PUB1.3 barcode: GGACCC
processed data file:
PUB25_Distal_fpkm.txt


title: Mig1_YPD_None_1


title: PUB25_Medial_rep2

description:
PUB22
PUB2.2 barcode: AAGACG
processed data file:
PUB25_Medial_fpkm.txt


title: Poly_Opt_p53+_2


title: SC5314_YPD_Butyric_2


title: PUB25_Medial_rep1

description:
PUB12
PUB1.2 barcode: CCTTCA
processed data file:
PUB25_Medial_fpkm.txt


title: Poly_Lin_p53+_2


title: Mig1_YPD_Butyric_1


title: Poly_Lin_p53-_2


title: Cyto_p53-_1


title: PUB25-Proximal_rep3

description:
PUB31
PUB3.1 barcode: GGATGT
processed data file:
PUB25_Proximal_fpkm.txt


title: SC5314_YPM_Butyric_1


title: SC5314_YPM_Acetic_1


title: PUB25-Proximal_rep2

description:
PUB21
PUB2.1 barcode: TTCAGC
processed data file:
PUB25_Proximal_fpkm.txt


title: PUB25-Proximal_rep1

description:
PUB11
PUB1.1 barcode: AAGGGA
processed data file:
PUB25_Proximal_fpkm.txt


title: SC5314_YPM_None_1


title: SC5314_YPD_Acetic_1


title: Cyto_p53+_1


title: Poly_Opt_p53-_1


title: SC5314_YPD_Butyric_1


title: Poly_Opt_p53+_1


title: Mig1_YPM_None_1


title: PUB25_Distal_rep2

description:
PUB23
PUB2.3 barcode: CCTCGG
processed data file:
PUB25_Distal_fpkm.txt


title: Poly_Lin_p53-_1


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep5

value: 4 weeks old

value: repeated drought stress


title: Poly_Lin_p53+_1


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep3

value: whole rosette


title: Day 15_CD47+_C

city: Boston

first: Anjali

last: Jacob

state: MA

address: 670 Albany St., 2nd Floor, CReM-232

department: Center for Regenerative Medicine

institute: Boston University School of Medicine

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensembl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: Hg19
Supplementary_files_format_and_content: Voom transformed abundance measurement, log2 scaled.

source_name: RUES2 ESCs

extract_protocol:
Illumina TruSeq RNA Sample Preparation Kit v2
The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina cBot using Illumina TruSeq Paired-End Cluster Kit. Each sample was sequenced four per lane on the Illumina HiSeq 2500 to generate more than 30 million single end 100-bp reads.

tag: developmental stage

value: Day 15 in-vitro differentiation

tag: culture media

value: 9 days Chir, Bmp4, retinoic acid (CBRa)

tag: isolation method

value: sorted CD47hi/CD26lo, enriched for NKX2-1+ cells


title: Day 15_CD47+_B


title: Day 15_CD47+_A


title: 21 wk fetal_D

source_name: lung explant

value: lung explant

tag: cell type

value: distal alveolar epithelial progenitors

value: gestational week 21

value: overnight in Waymouth's media

value: enriched for epithelial cells by overnight culture


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep1

tag: age


title: G5 progeny, control conditions, 4 week old Col-0, biological rep4

tag: stress

value: control conditions


title: G5 progeny, control conditions, 4 week old Col-0, biological rep5

tag: ecotype


title: wt.rep2.me

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Raw .fastq files were mapped to the reference genome (NC000913.2) using BWA (version 0.7). Mapped reads were then converted to read count per gene using bedtools (version 2).  In the case of Ion torrent data .bam files were converted using BWA.
Resulting read count matrix was used as input for the differntial expression analysis in edgeR (version 3.12.1).
Genome_build: Escherichia coli (NC000913.2)
Supplementary_files_format_and_content: .txt (log2 fold change values, p-values)

organism: Escherichia coli

source_name: cells

growth_protocol: Cells were inoculated from overnight grown culture in Lysogeny Broth (LB) and then harvested in the early exponential growth phase and mid exponential growth phase.

extract_protocol: NEXTflexRapid Directional RNA-Seq library kit

treatment_protocol: RNA was extracted from the harvested cells using Trizol reagent. Depending upon the concentration of total RNA, sample were treated with Dnase and ribocleanup was given according to the instruction manual.

tag: srain

tag: growth phase

value: Mid exponential

tag: genotype

value: wildtype


title: wt.rep1.me


title: 21 wk fetal_C


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep2


title: G5 progeny, control conditions, 4 week old Col-0, biological rep6


title: 21 wk fetal_B


title: cya.rep2.me

value: cya mutant background


title: G5 progeny, control conditions, 4 week old Col-0, biological rep2


title: SC5314_YPD_None_1

tag: strain/genotype

tag: media

value: YPD

tag: treatment


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep6


title: Day 35 Tomato neg_A

value: Day 35 in-vitro differentiation

value: 20 days Chir, Kgf, DCI (CK+DCI)

value: sorted SFTPC-tdTomato reporter negative cells


title: cya.rep1.me


title: G0 progeny, 1 week repeated excess light stress, 4 week old Col-0, biological rep3

value: 4 weeks old

value: whole rosette

value: 1 week repeated excess light stress


title: Day 35 Tomato neg_C


title: Adult AEC2_C

source_name: lung

value: lung

value: alveolar epithelial type II cells

value: 77 years

value: sorted HT2-280 antibody positive cells


title: crpfis.rep2.me

value: crpfis mutant background


title: G5 progeny, control conditions, 4 week old Col-0, biological rep1


title: HG3

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: ATAC-seq

data_processing:
Raw reads were quality checked using FastQC version v0.10.1. NG2 sample was excluded from the advanced analysis due to the low mapping rate.
Nextera primers were trimmed from raw reads using cutadapt, version 1.0 with parameters –O 5 –m 30 –q 15, and the trimmed reads were aligned to the mm10 genome using Bowtie 1.0.0 with activation of “-m 1” so only unique reads were allowed
The mapping results in SAM were converted to BAM and sorted by coordinates using samtools, version 0.1.19 and the mapping statistics were extracted using Picard, version 1.90.
Peak calling was performed using MACS2 version 2.1.0 with default parameters. Affinity-based differential binding analysis and annotation were performed using DiffBind, version 1.12.3, and ChIPpeakAnno, version 3.0.0. The R package DiffBind employs edgeR for differential analysis, utilizing TMM (trimmed mean of M values) to account for sequence depth to normalize the read counts between samples in differential peak calling analysis.
Data visualization was performed by normalizing the merged HG BAM file to the merged NG BAM file through random downsampling.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files are provided as processed data files. NG2 sample was excluded from the advanced analysis due to low mapping rate.

organism: Mus musculus

source_name: AVM cells 25mM Glucose

growth_protocol: Atrioventricular cushion mesenchymal cells were made and provided by Dr. Kai Jiao's laboratory (Peng et al, Cardiovascular research. 2016;112(2):532-542). Immortalized AVM cells were grown and maintained in DMEM (Dulbecco’s modified Eagle’s medium; ThermoFisher Scientific) media with 5.5mM D-glucose (Normoglycemia, NG), L-Glutamine, sodium pyruvate and supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin at 37°C in 5% CO2-chamber.

extract_protocol:
54,000 AVM cells cultured in NG and HG for 48hrs were used for ATAC-sequencing. Similar to Buenrostro et al. (Nat Methods. 2013 Dec;10(12):1213-8), unfixed AVM cells were lysed and immediately transposed using Nextera DNA library preparation kit (FC-121-1030, Illumina) followed by column purification with MinElute Reaction cleanup kit (Qiagen).
ATAC-seq libraries were generated from transposed and amplified DNA using Nextera index primers. The quality of the libraries was assessed using Agilent Bioanalyzer High Sensitivity DNA analysis kit and sent for 50bp paired-end sequencing on Illumina HiSeq 2000 platform to Epigentek Group Inc. (Farmingdale, NY).

treatment_protocol: AVM cells were cultured in normal glucose (NG, 5.5mM) and high glucose (HG, 25mM) for 48 hrs.

value: H- 2Kb-tsA58 transgenic

value: AV cushion mesenchymal cells

tag: passage

tag: glucose status

value: high glucose


title: Day 35 Tomato neg_B


title: G5 progeny, repeated drought stress, 4 week old Col-0, biological rep4

value: repeated drought stress


title: G0 progeny, 1 week repeated excess light stress, 4 week old Col-0, biological rep2


title: crpfis.rep1.me

value: Mid exponential


title: HG1

description: ATAC-seq

tag: strain


title: NG3

description: ATAC-seq

source_name: AVM cells 5.5mM Glucose

value: normal


title: G0 progeny, 1 week repeated excess light stress, 4 week old Col-0, biological rep1

tag: tissue


title: crp.rep2.me

value: crp mutant background


title: Adult AEC2_B

tag: developmental stage

value: 62 years


title: G5 progeny, control conditions, 4 week old Col-0, biological rep3

value: control conditions


title: Adult AEC2_A

value: 43 years

tag: culture media


title: Day 35 SFTPCTomato+_C

value: Day 35 in-vitro differentiation

value: 20 days Chir, Kgf, DCI (CK+DCI)

tag: isolation method

value: sorted SFTPC-tdTomato reporter positive cells


title: NG2

description: ATAC-seq

tag: cell type


title: Day 35 SFTPCTomato+_B


title: wt.rep2.ee

value: Early exponential

value: wildtype


title: crp.rep1.me


title: G0 progeny, 1-hour excess light stress, 4 week old Col-0, biological rep3

tag: age

value: 4 weeks old

value: whole rosette

value: 1-hour excess light stress


title: NG1

description: ATAC-seq

value: H- 2Kb-tsA58 transgenic

value: AV cushion mesenchymal cells


title: wt.rep1.ee


title: Day 35 SFTPCTomato+_A


title: G0 progeny, 1-hour excess light stress, 4 week old Col-0, biological rep2

tag: stress


title: HG2

description: ATAC-seq

value: high glucose


title: G0 progeny, 1-hour excess light stress, 4 week old Col-0, biological rep1

tag: ecotype


title: serp0316 deletion strain of S. epidermidis 1457_rep3

city: Shanghai

first: Xiaofei

last: Wang

address: Room 1103, Zhidao building, Dong'an Road, Xuhui district, Shanghai

department: Shanghai Medical College

institute: Fudan 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 whole genome（version:ATCC 35984）using TopHat（version:2.0.9).
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 genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: the referance geneome is Staphylococus epidermidis  (https://www.ncbi.nlm.nih.gov/genome/?term=RP62a)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: polyA RNA

organism: Staphylococcus epidermidis

extract_protocol:
Total RNA of SE1457, △phoU1 and △phoU2 were isolated using the RNeasy Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. Briefly, the bacterial cultures (10h) were centrifuged at 5,000 x g for 5 min, then the pellets were washed twice in 0.9% saline. The culture was homogenized using 0.1 mm Zirconia-silica beads in a Mini-Bead beater (Biospec, Bartlesville, OK, USA) at 4800 rpm for 40 sec at 1 min intervals on ice for 5 times. The RNA extracted using the silica-based filter was purified by phenol-chloroform-isoamyl alcohol and precipitated with absolute ethanol.
RNA samples of SE1457, △phoU1 and △phoU2 were treated with RNase-free DNase I (Takara) to prevent contamination with genomic DNA. The RNA quality was evaluated with the BioAnalyzer 2100 system (Agilent technologies, Deutschland GmbH). Ribosomal RNA was removed with the RiboZero rRNA removal kit, which is for gram-positive organisms prior to sequencing analysis. After depletion of the rRNA, fragmented RNA was used as a template for PCR with random primers. The cDNA libraries were prepared by using the mRNA-seq Sample Prep kit (Illumina). The concentration of the cDNA was measured by Qubit 2.0 Fluorometer, the fragment size (200–300 bp) verified on a BioAnalyzer 2100 system, and amplified using an Illumina cBot and sequenced on an Illumina HiSeq 2500 for 51 cycles according to manufacturer protocols.

treatment_protocol: Overnight culture of SE1457, △phoU1 and △phoU2 were diluted (1:200) to the fresh Tryptone soy broth medium and and incubated for 10h with shaking at 220 rpm. Then the bacteria cell were collected by centrifugation at 12,000×g.

value: phoU2 deletion

value: Stationary  phase (10 h)


title: serp0316 deletion strain of S. epidermidis 1457_rep2


title: cya.rep2.ee

tag: srain

value: cya mutant background


title: 21 wk fetal+DCI_C

value: lung explant

value: distal alveolar epithelial progenitors

value: gestational week 21

value: 4 days Dexamethasone, cAMP, IBMX (DCI)

value: enriched for epithelial cells by overnight culture, RNA isolated from DCI-cultured cells


title: 21 wk fetal+DCI_B


title: G0 progeny, unstressed, 4 week old Col-0, biological rep5

value: unstress


title: cya.rep1.ee

tag: growth phase

value: Early exponential


title: G0 progeny, unstressed, 4 week old Col-0, biological rep4


title: 21 wk fetal+DCI_A


title: crpfis.rep2.ee

tag: genotype

value: crpfis mutant background


title: G0 progeny, unstressed, 4 week old Col-0, biological rep3

value: 4 weeks old


title: crpfis.rep1.ee


title: Day 0 PSCs_C

value: pluripotent stem cell

value: mTeSR1 (StemCell Technologies)

value: cultured cells


title: serp0956 deletion strain of S. epidermidis 1457_rep1

value: phoU1 deletion


title: serp0956 deletion strain of S. epidermidis 1457_rep3


title: crp.rep2.ee

value: crp mutant background


title: Day 0 PSCs_A


title: crp.rep1.ee


title: G0 progeny, unstressed, 4 week old Col-0, biological rep1

value: whole rosette


title: The parent strain (the control strain)_rep3

source_name: Staphylococus epidermidis 1457

value: S. epidermidis 1457

value: wildtype (parental)

value: Stationary  phase (10 h)


title: shDnmt3a_2

first: Sona

last: Kang

state: CA

address: 316 Morgan Hall

department: Nutritional Sciences and Toxicology

institute: UC Berkeley

data_processing:
De-multiplexing was performed with bcl2fastq v2.17.1.14
Reads were aligned to the mm9 reference genome with TopHat v2.0.14 with the parameters -M --GTF mm9.gtf –mate-inner-dist fragment_size
PCR duplicates and low quality reads were filtered out using Picard 2.2.4 and samtools 0.1.19
Reads were assigned to genes using featureCounts 1.4.6 and a custom meta-annotation derived from mm9 that merges together overlapping transcripts
Differential expression analysis was performed with edgeR using a standard approach to pair-wise comparisons with no confounding factors as described in the edgeR manual
Genome_build: mm9
Supplementary_files_format_and_content: counts.tsv contains raw counts for each gene in all 12 samples. UCSC gene ids, official gene symbols, and gene lengths are provided for each gene.

source_name: 3T3-L1 adipoyctes

growth_protocol: 3T3-L1 preadiopocytes were differentiated with Dexamethasone (1uM), IBMX (0.5mM), and Insulin (5ug/ml) from day 0-2.  Insulin was added for additional 2 days.

extract_protocol:
RNAs were extracted using Rneasy kit from Qiagen following manufacturer's protocol.
mRNA was purified from 100 ng of total RNA using the Ribo-Zero Magnetic Gold Kit (catalog MRZG126, Illumina) per manufacturer instructions. Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122-2001, Illumina) according to the manufacturer’s protocol starting with the EPF step.

treatment_protocol: On day 8, mature adipocytes were  transduced with lentivirus containing titled construct for two days. After 4 days of transduction, cells were harvested for RNA extraction.

tag: cell line

value: mature adipoyctes

value: Dnmt3a knockdown


title: shDnmt3a_3


title: fis.rep2.me

value: Mid exponential

value: fis mutant background


title: serp0316 deletion strain of S. epidermidis 1457_rep1

value: phoU2 deletion


title: Ad-YAP-S127A-2

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCh38.p2 (hg38) + Gencode-23 Annotation
Supplementary_files_format_and_content: raw count matrix in tab-delimited text file, one column for each sample

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 80% confluent HUVECs were transfected with non-targetting siRNA pool (siNC, GE Dharmacon, #D-001810-10)  or siGenome YAP1 siRNA pool (siYAP1, GE Dharmacon, #M-012200) using Lipofectamine 2000 for 48 hours, n=3. In the overexpression experiment, 80% confluent HUVECs were infected with control adenovirus (Ad-NC) or YAP-S127A catalytically active adenovirus (Ad-YAP-S127A, gifted by Prof. Junichi Sadoshima, New Jersey Medical School, NJ) for 48 hours, n=2.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: passage 3 to passage 5

tag: transfected/infected with

value: YAP-S127A catalytically active adenovirus (Ad-YAP-S127A)


title: shDnmt3a_1

tag: treatment


title: The parent strain (the control strain)_rep2


title: The parent strain (the control strain)_rep1


title: scr_3

value: scramble

value: control


title: Ad-YAP-S127A-1

tag: passage


title: Ad-NC-2

value: control adenovirus (Ad-NC)


title: SE1457△phoU2-3

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 whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
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 genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: the referance geneome is ATCC 35984
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: serp0316 deletion strain of S. epidermidis 1457

extract_protocol:
Total RNA of SE1457, △phoU1 and △phoU2 were isolated using the RNeasy Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. Briefly, the bacterial cultures (6h) were centrifuged at 5,000 x g for 5 min, then the pellets were washed twice in 0.9% saline. The culture was homogenized using 0.1 mm Zirconia-silica beads in a Mini-Bead beater (Biospec, Bartlesville, OK, USA) at 4800 rpm for 40 sec at 1 min intervals on ice for 5 times. The RNA extracted using the silica-based filter was purified by phenol-chloroform-isoamyl alcohol and precipitated with absolute ethanol.
RNA samples of SE1457, △phoU1 and △phoU2 were treated with RNase-free DNase I (Takara) to prevent contamination with genomic DNA. The RNA quality was evaluated with the BioAnalyzer 2100 system (Agilent technologies, Deutschland GmbH). Ribosomal RNA was removed with the RiboZero rRNA removal kit, which is for gram-positive organisms prior to sequencing analysis. After depletion of the rRNA, fragmented RNA was used as a template for PCR with random primers. The cDNA libraries were prepared by using the mRNA-seq Sample Prep kit (Illumina). The concentration of the cDNA was measured by Qubit 2.0 Fluorometer, the fragment size (200–300 bp) verified on a BioAnalyzer 2100 system, and amplified using an Illumina cBot and sequenced on an Illumina HiSeq 2500 for 51 cycles according to manufacturer protocols.

treatment_protocol: Overnight culture of SE1457, △phoU1 and △phoU2 were diluted (1:200) to the fresh Tryptone soy broth medium and and incubated for 6h with shaking at 220 rpm. Then the bacteria cell were collected by centrifugation at 12,000×g.

value: log-phase (6 h)

value: serp0316 deletion strain


title: fis.rep2.ee

value: Early exponential


title: scr_2


title: serp0956 deletion strain of S. epidermidis 1457_rep2

value: phoU1 deletion


title: SE1457△phoU2-2

value: serp0316 deletion strain of S. epidermidis 1457


title: G0 progeny, unstressed, 4 week old Col-0, biological rep2

value: 4 weeks old

value: whole rosette

value: unstress


title: Ad-NC-1


title: Day 0 PSCs_B

value: pluripotent stem cell

value: mTeSR1 (StemCell Technologies)

value: cultured cells


title: scr_1

value: mature adipoyctes


title: SE1457△phoU2-1


title: siYAP1-3

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: passage 3 to passage 5

value: YAP1 siRNA pool (siYAP1)


title: Dnmt3a_pCDH_3

value: Dnmt3a overexpression


title: SE1457△phoU1-3

source_name: serp0956 deletion strain of S. epidermidis 1457

value: serp0956 deletion strain


title: Dnmt3a_pCDH_2


title: SE1457△phoU1-2

value: serp0956 deletion strain of S. epidermidis 1457

value: log-phase (6 h)


title: siYAP1-2


title: Dnmt3a_pCDH_1


title: fis.rep1.me

value: Mid exponential

value: fis mutant background


title: SE1457△phoU1-1


title: siNC-3

value: non-targetting siRNA pool (siNC)


title: GFP_pCDH_3

value: control


title: siNC-1


title: SE1457-2

value: S. epidermidis 1457

value: The parent strain( the control strain).

value: wild type


title: SE1457-3


title: siNC-2


title: SE1457-1


title: GFP_pCDH_2


title: GFP_pCDH_1


title: Casein Control Treatment

status: Public on Oct 02 2017

city: Columbia

first: Alan

last: Parrish

state: Missouri

address: MA415 MSB, 1 Hospital Drive

department: Medical Pharmacology & Physiology

institute: University of Missouri

data_processing:
A mRNA-focused, barcoded library was generated using the TruSeq kit and analyzed using the HiSeq 2000 platform from Illumina.
Sequencing yielded ~7.5 Gb of data, corresponding to around 30 million 50-base reads per sample across the whole transcriptom.
Reads were aligned against the rat genome (Rattus norvegicus RGSC3.4; Ensemble) and analyzed using Bowtie, TopHat and Cufflinks software.
Differential expression values defined as fragments per kilobase of transcript per million mapped reads (FPKM) with a false discovery-correct p-value equal or lower than 0.05 were considered significant.
Genome_build: Rattus norvegicus RGSC3.4
Supplementary_files_format_and_content: Excel spreadsheet including the soy vs. control genes and Ensemble description that were considered significant.

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Kidneys were removed and flash frozen in liquid nitrogen.  RNA was extraced using the RNeasy kit with on column DNase digestion.  Illumina TruSeq was used with 5 µg total RNA to construct the libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 16 month F344 rats where obtained from the NIA colony.  Rats were fed a casein control diet or a 14% soy diet for 4 months.

value: Kidney

value: 20 months

tag: diet

value: Casein control


title: fis.rep1.ee

value: Early exponential


title: HeLa_Control_AMO_8hr_Labeled_odT_selection

first: Christopher

middle: Conrad

last: Venters

state: Pennsylvania

address: 415 Curie Boulevard

department: Biochemistry and Molecular Biophysics

description:
nascent polyA mRNA
cAMO_15nmol_odT_selection.polyA_sites.bw

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

source_name: Human Carcinoma Cells

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

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

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

value: HeLa

tag: strain

value: PV

tag: transfection

value: Control

tag: chip antibody


title: HeLa_U1_AMO_8hr_Labeled_rRNA_depletion

description:
nascent total RNA
U1AMO_8hr_rRNA_depletion.PCPAed_genes.txt

extract_protocol:
Total RNA extracted using trizol, total mRNA extracted using Ribozero kit, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the KAPA kit (#KK8400). Briefly, RNA was fragmented using MgCl2+ and heat, then converted into cDNA using a strand-specific synthesis method with dUTP. cDNA was A-tailed, and adapters were ligated. The library was then amplified, and any adapter dimers were removed with SPRI beads.


title: HeLa_U1_AMO_4hr_Labeled_rRNA_depletion

description:
nascent total RNA
U1AMO_4hr_rRNA_depletion.PCPAed_genes.txt


title: FF-SFTPC_scRNA-seq_78

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

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

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

source_name: hiPSC-derived SFTPC+ cells

growth_protocol: Fibroblast-free (FF) SFTPC+ cells were induced from isolated CPM-high progenitor cells on day 21 by forming aggregates on non-adherent cell culture plates for 2 days and subsequent Matrigel-embedded three-dimensional culture for 5 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF, Y27632, CHIR99021, and SB431542 WITHOUT using human fetal lung fibroblasts.

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

value: hiPSC-derived SFTPC+ cells induced under fibroblast-free condition

tag: isolation date

value: day 28


title: FF-SFTPC_scRNA-seq_77


title: FF-SFTPC_scRNA-seq_76


title: siYAP1-1

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: passage 3 to passage 5

value: YAP1 siRNA pool (siYAP1)


title: FF-SFTPC_scRNA-seq_74


title: FF-SFTPC_scRNA-seq_75


title: FF-SFTPC_scRNA-seq_72


title: FF-SFTPC_scRNA-seq_73


title: FF-SFTPC_scRNA-seq_71


title: FF-SFTPC_scRNA-seq_70


title: FF-SFTPC_scRNA-seq_67


title: FF-SFTPC_scRNA-seq_66


title: FF-SFTPC_scRNA-seq_68


title: FF-SFTPC_scRNA-seq_69


title: FF-SFTPC_scRNA-seq_65


title: Soy Treatment

tag: tissue

value: 14% soy


title: FF-SFTPC_scRNA-seq_59

tag: cell type


title: FF-SFTPC_scRNA-seq_64


title: FF-SFTPC_scRNA-seq_63


title: HeLa_Control_AMO_4hr_Labeled_rRNA_depletion


title: FF-SFTPC_scRNA-seq_58


title: FF-SFTPC_scRNA-seq_55


title: FF-SFTPC_scRNA-seq_54


title: HeLa_Control_AMO_8hr_Labeled_rRNA_depletion


title: FF-SFTPC_scRNA-seq_62


title: FF-SFTPC_scRNA-seq_60


title: FF-SFTPC_scRNA-seq_61


title: FF-SFTPC_scRNA-seq_51


title: FF-SFTPC_scRNA-seq_56


title: FF-SFTPC_scRNA-seq_57


title: FF-SFTPC_scRNA-seq_53


title: FF-SFTPC_scRNA-seq_49


title: FF-SFTPC_scRNA-seq_46


title: FF-SFTPC_scRNA-seq_45


title: FF-SFTPC_scRNA-seq_52


title: FF-SFTPC_scRNA-seq_48


title: FF-SFTPC_scRNA-seq_42


title: FF-SFTPC_scRNA-seq_41


title: FF-SFTPC_scRNA-seq_40


title: FF-SFTPC_scRNA-seq_43


title: FF-SFTPC_scRNA-seq_38


title: FF-SFTPC_scRNA-seq_37


title: FF-SFTPC_scRNA-seq_39


title: FF-SFTPC_scRNA-seq_34


title: FF-SFTPC_scRNA-seq_33


title: FF-SFTPC_scRNA-seq_36


title: FF-SFTPC_scRNA-seq_32


title: FF-SFTPC_scRNA-seq_35


title: FF-SFTPC_scRNA-seq_31


title: FF-SFTPC_scRNA-seq_50


title: FF-SFTPC_scRNA-seq_30


title: FF-SFTPC_scRNA-seq_29


title: FF-SFTPC_scRNA-seq_47


title: FF-SFTPC_scRNA-seq_26


title: FF-SFTPC_scRNA-seq_25


title: FF-SFTPC_scRNA-seq_27


title: FF-SFTPC_scRNA-seq_24


title: FF-SFTPC_scRNA-seq_28


title: FF-SFTPC_scRNA-seq_23


title: FF-SFTPC_scRNA-seq_44


title: FF-SFTPC_scRNA-seq_22


title: FF-SFTPC_scRNA-seq_21


title: FF-SFTPC_scRNA-seq_17


title: FF-SFTPC_scRNA-seq_18


title: FF-SFTPC_scRNA-seq_16


title: FF-SFTPC_scRNA-seq_15


title: FF-SFTPC_scRNA-seq_20


title: FF-SFTPC_scRNA-seq_14


title: FF-SFTPC_scRNA-seq_11


title: FF-SFTPC_scRNA-seq_9


title: FF-SFTPC_scRNA-seq_12


title: FF-SFTPC_scRNA-seq_8


title: FF-SFTPC_scRNA-seq_10


title: FF-SFTPC_scRNA-seq_7


title: FF-SFTPC_scRNA-seq_4


title: FF-SFTPC_scRNA-seq_5


title: FF-SFTPC_scRNA-seq_3


title: FF-SFTPC_scRNA-seq_2


title: Individual 54. Fulani. Infected, Lymphocyte. RNA-Seq

city: Stockholm

first: Ann-Kristin

last: Östlund-Farrants

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

description:
count_table.txt
P2044_131

data_processing:
Quality of raw sequencing reads was checked using FastQC/0.11.2
Reads were filtered using timmomatic/0.32, and reads with quality below 20 (within 4-base sliding window) and/or shorter than 36bp were removed
Star/2.4.1c was used to align reads to reference genome Homo_sapiens.GRCh38-.dna.primary_assembly.fa using annotation Homo_sapiens.GRCh38.83 .gtf
FeatureCounts/1.5.0 from subread.1.4.5 was used to count fragments in exon regions, counts from multiple lanes were added.
MultiQC(0.3.1) to aggregate results from multiple samples
Genome_build: Homo_sapiens.GRCh38-.dna.primary_assembly.fa
Supplementary_files_format_and_content: tab-delimited text file including count values for each sample

source_name: Peripheral blood mononuclear cells from 18ml venous whole blood

extract_protocol:
Venous whole blood (approximately 18ml) was collected from study participants, and peripheral blood mononuclear cells (PBMCs) were purified by Ficoll-Paque density centrifugation. CD14+ monocytes were isolated with EasySep CD14 positive selection kit according to manufacturer’s instructions (Stem Cell Technologies) CD14+ monocytes and the remaining CD14- cells (lymphocytes) were stored in RNAprotect Cell Reagent (Qiagen) at -80C. Total DNA and RNA were extracted from CD14+ and CD14- cells with AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions .
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup in RapidHighOutput mode

tag: ethnic group

value: Fulani

tag: individual

tag: cell population

value: CD14- lymphocytes

tag: ID


title: FF-SFTPC_scRNA-seq_19


title: Individual 53. Fulani. Infected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_132


title: Individual 47. Fulani. Infected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_121


title: Individual 60. Fulani. Uninfected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_136


title: Individual 49. Fulani. Uninfected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_124


title: Individual 51. Fulani. Uninfected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_201


title: Individual 54. Fulani. Infected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_102

value: CD14+ monocyte


title: FF-SFTPC_scRNA-seq_1


title: Individual 57. Fulani. Uninfected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_123


title: Individual 60. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_110


title: Individual 59. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_106


title: FF-SFTPC_scRNA-seq_13


title: Individual 51. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_202


title: Individual 43. Fulani. Uninfected, Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_119


title: Individual 57. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_109


title: Individual 53. Fulani. Infected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_101


title: Individual 43. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_117


title: FF-SFTPC_scRNA-seq_6


title: Individual 24. Mossi. Infected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_134

value: Mossi


title: Individual 5. Mossi. Infected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_125


title: Individual 39. Mossi. Infected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_133


title: Individual 35. Mossi. Uninfected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_130


title: Individual 33. Mossi. Uninfected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_128


title: Individual 20. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_105


title: Individual 7. Mossi. Uninfected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_126


title: Individual 2. Mossi. Uninfected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_120


title: Individual 39. Mossi. Infected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_114


title: Individual 24. Mossi. Infected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_112


title: Individual 5. Mossi. Infected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_113


title: Individual 7. Mossi. Uninfected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_103


title: Individual 2. Mossi. Uninfected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_107


title: Individual 8. Mossi. Uninfected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_115


title: Individual 49. Fulani. Uninfected, Monocyte. RNA-Seq

description:
count_table.txt
P2044_104


title: CPM-high-day14 scRNA-seq_76

description:
Single " CPM-high-day14" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.
CPM-high-day14_scRNA-seq_RPKM.txt

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

source_name: CPM-high cells

growth_protocol:
CPM-high-day14 cells were induced from iPSCs with the three-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days, Step 2: SB431542 and Noggin for 4 days, Step 3: CHIR99021, BMP4 and ATRA, Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days.
CPM-high-day21 cells were induced from iPSCs via ventralized anterior foregut endodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days, Step 2: SB431542 and Noggin for 4 days, Step 3: CHIR99021, BMP4 and ATRA, Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days.
CPM-high cells were induced from iPSCs via ventralized anterior foregut endodermal (VAFE) cells with the four-step treatment; Step 1: Activin, sodium butyrate, and CHIR99021 for 6 days, Step 2: SB431542 and Noggin for 4 days, Step 3: CHIR99021, BMP4 and ATRA, Step 4: CHIR99021, FGF10, KGF and DAPT for 7 days.  Alveolar organoids (AO) were generated from CPM-high progenitor cells via three-dimensional coculture with human fetal lung fibroblasts. P0-AO-day5 EpCAM+ cells were isolated using EpCAM-based cell sorting 5 days after starting AO formation.

tag: cell types

value: hiPSC-derived CPM-high cells

tag: time

value: isolated on day 14


title: CPM-high-day14 scRNA-seq_77


title: CPM-high-day14 scRNA-seq_74


title: Individual 28. Mossi. Uninfected. Monocyte. RNA-Seq

description:
count_table.txt
P2044_111


title: CPM-high-day14 scRNA-seq_72


title: CPM-high-day14 scRNA-seq_73


title: CPM-high-day14 scRNA-seq_75


title: CPM-high-day14 scRNA-seq_71


title: CPM-high-day14 scRNA-seq_67


title: CPM-high-day14 scRNA-seq_70


title: CPM-high-day14 scRNA-seq_66


title: CPM-high-day14 scRNA-seq_65


title: Individual 8. Mossi. Uninfected. Lymphocyte. RNA-Seq

description:
count_table.txt
P2044_122


title: CPM-high-day14 scRNA-seq_63


title: CPM-high-day14 scRNA-seq_68


title: CPM-high-day14 scRNA-seq_62


title: CPM-high-day14 scRNA-seq_64


title: CPM-high-day14 scRNA-seq_60


title: CPM-high-day14 scRNA-seq_61


title: CPM-high-day14 scRNA-seq_78


title: CPM-high-day14 scRNA-seq_57


title: CPM-high-day14 scRNA-seq_56


title: CPM-high-day14 scRNA-seq_55


title: CPM-high-day14 scRNA-seq_54


title: CPM-high-day14 scRNA-seq_53


title: CPM-high-day14 scRNA-seq_52


title: CPM-high-day14 scRNA-seq_51


title: CPM-high-day14 scRNA-seq_50


title: CPM-high-day14 scRNA-seq_47


title: CPM-high-day14 scRNA-seq_48


title: CPM-high-day14 scRNA-seq_69


title: CPM-high-day14 scRNA-seq_49


title: CPM-high-day14 scRNA-seq_44


title: CPM-high-day14 scRNA-seq_46


title: CPM-high-day14 scRNA-seq_42


title: CPM-high-day14 scRNA-seq_43


title: CPM-high-day14 scRNA-seq_39


title: CPM-high-day14 scRNA-seq_41


title: CPM-high-day14 scRNA-seq_40


title: CPM-high-day14 scRNA-seq_59


title: CPM-high-day14 scRNA-seq_45


title: CPM-high-day14 scRNA-seq_36


title: CPM-high-day14 scRNA-seq_34


title: CPM-high-day14 scRNA-seq_35


title: CPM-high-day14 scRNA-seq_58


title: CPM-high-day14 scRNA-seq_37


title: CPM-high-day14 scRNA-seq_33


title: CPM-high-day14 scRNA-seq_30


title: CPM-high-day14 scRNA-seq_38


title: CPM-high-day14 scRNA-seq_27


title: CPM-high-day14 scRNA-seq_28


title: CPM-high-day14 scRNA-seq_29


title: CPM-high-day14 scRNA-seq_26


title: CPM-high-day14 scRNA-seq_25


title: CPM-high-day14 scRNA-seq_24


title: CPM-high-day14 scRNA-seq_31


title: CPM-high-day14 scRNA-seq_22


title: CPM-high-day14 scRNA-seq_23


title: CPM-high-day14 scRNA-seq_20


title: CPM-high-day14 scRNA-seq_19


title: CPM-high-day14 scRNA-seq_17


title: CPM-high-day14 scRNA-seq_16


title: CPM-high-day14 scRNA-seq_14


title: CPM-high-day14 scRNA-seq_11


title: CPM-high-day14 scRNA-seq_15


title: CPM-high-day14 scRNA-seq_32


title: CPM-high-day14 scRNA-seq_18


title: CPM-high-day14 scRNA-seq_10


title: CPM-high-day14 scRNA-seq_12


title: CPM-high-day14 scRNA-seq_9


title: CPM-high-day14 scRNA-seq_5


title: CPM-high-day14 scRNA-seq_6


title: CPM-high-day14 scRNA-seq_8


title: CPM-high-day14 scRNA-seq_13


title: CPM-high-day14 scRNA-seq_4


title: CPM-high-day14 scRNA-seq_2


title: CPM-high-day14 scRNA-seq_3


title: CPM-high-day14 scRNA-seq_21


title: P0-AO-day5 EpCAM+ scRNA-seq_81

description:
Single " P0-AO-day5 EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.
P0-AO-day5_EpCAM+_scRNA-seq_RPKM.txt

source_name: EpCAM+ cells

value: hiPSC-derived EpCAM+ cells

value: isolated on day 26


title: P0-AO-day5 EpCAM+ scRNA-seq_82


title: P0-AO-day5 EpCAM+ scRNA-seq_80


title: P0-AO-day5 EpCAM+ scRNA-seq_79


title: P0-AO-day5 EpCAM+ scRNA-seq_78


title: P0-AO-day5 EpCAM+ scRNA-seq_77


title: P0-AO-day5 EpCAM+ scRNA-seq_76


title: P0-AO-day5 EpCAM+ scRNA-seq_75


title: P0-AO-day5 EpCAM+ scRNA-seq_74


title: P0-AO-day5 EpCAM+ scRNA-seq_73


title: P0-AO-day5 EpCAM+ scRNA-seq_70


title: CPM-high-day14 scRNA-seq_7


title: P0-AO-day5 EpCAM+ scRNA-seq_72


title: P0-AO-day5 EpCAM+ scRNA-seq_69


title: P0-AO-day5 EpCAM+ scRNA-seq_68


title: P0-AO-day5 EpCAM+ scRNA-seq_71


title: P0-AO-day5 EpCAM+ scRNA-seq_66


title: P0-AO-day5 EpCAM+ scRNA-seq_61


title: P0-AO-day5 EpCAM+ scRNA-seq_63


title: CPM-high-day14 scRNA-seq_1


title: P0-AO-day5 EpCAM+ scRNA-seq_67


title: P0-AO-day5 EpCAM+ scRNA-seq_59


title: P0-AO-day5 EpCAM+ scRNA-seq_64


title: P0-AO-day5 EpCAM+ scRNA-seq_55


title: P0-AO-day5 EpCAM+ scRNA-seq_57


title: P0-AO-day5 EpCAM+ scRNA-seq_58


title: P0-AO-day5 EpCAM+ scRNA-seq_54


title: P0-AO-day5 EpCAM+ scRNA-seq_60


title: P0-AO-day5 EpCAM+ scRNA-seq_49


title: P0-AO-day5 EpCAM+ scRNA-seq_47


title: P0-AO-day5 EpCAM+ scRNA-seq_46


title: P0-AO-day5 EpCAM+ scRNA-seq_45


title: P0-AO-day5 EpCAM+ scRNA-seq_44


title: P0-AO-day5 EpCAM+ scRNA-seq_56


title: P0-AO-day5 EpCAM+ scRNA-seq_41


title: P0-AO-day5 EpCAM+ scRNA-seq_62


title: P0-AO-day5 EpCAM+ scRNA-seq_43


title: P0-AO-day5 EpCAM+ scRNA-seq_39


title: P0-AO-day5 EpCAM+ scRNA-seq_42


title: P0-AO-day5 EpCAM+ scRNA-seq_38


title: P0-AO-day5 EpCAM+ scRNA-seq_37


title: P0-AO-day5 EpCAM+ scRNA-seq_36


title: P0-AO-day5 EpCAM+ scRNA-seq_35


title: P0-AO-day5 EpCAM+ scRNA-seq_33


title: P0-AO-day5 EpCAM+ scRNA-seq_51


title: P0-AO-day5 EpCAM+ scRNA-seq_52


title: P0-AO-day5 EpCAM+ scRNA-seq_32


title: P0-AO-day5 EpCAM+ scRNA-seq_34


title: P0-AO-day5 EpCAM+ scRNA-seq_48


title: P0-AO-day5 EpCAM+ scRNA-seq_29


title: P0-AO-day5 EpCAM+ scRNA-seq_28


title: P0-AO-day5 EpCAM+ scRNA-seq_30


title: P0-AO-day5 EpCAM+ scRNA-seq_31


title: P0-AO-day5 EpCAM+ scRNA-seq_27


title: P0-AO-day5 EpCAM+ scRNA-seq_53


title: P0-AO-day5 EpCAM+ scRNA-seq_40


title: P0-AO-day5 EpCAM+ scRNA-seq_26


title: P0-AO-day5 EpCAM+ scRNA-seq_23


title: P0-AO-day5 EpCAM+ scRNA-seq_24


title: P0-AO-day5 EpCAM+ scRNA-seq_22


title: WT_H3K4me3

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 and dm3 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: dm3, hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
Supplementary_files_format_and_content: For select bigWig files, spike-in normalized bigWig files are also provided. Spike-in normalization factors were computed using the number of reads mapped to the human (H) and drosophila (D) genomes for the wildtype (W) and mutant (M) conditions using the following equation: (DM/HM) / (DW/HW).  Spike-in normalization factors for samples HCT-caSET-H3K4me1-170416, HCT-caSET-H3K4me1-170418, HCT-wtSET-H3K4me1-170416, HCT-wtSET-H3K4me1-170418, CT84-caSET-H3K4me1-170416, CT84-caSET-H3K4me1-170418, CT84-wtSET-H3K4me1-170416, CT84-wtSET-H3K4me1-170418 are 0.670, 0.606, 3.767, 3.061, 0.831, 0.767, 5.659, and 6.075, respectively.

source_name: v6.5 mouse embryonic stem cells

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

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

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

value: v6.5 mouse embryonic stem cells

tag: genotype/variation

value: WT v6.5 mouse embryonic stem cells

value: anti-H3K4me3 (homemade, rabbit polyclonal)


title: P0-AO-day5 EpCAM+ scRNA-seq_21


title: WT_H3K4me1

value: anti-H3K4me1 (homemade, rabbit polyclonal)


title: WT_H3K27ac

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


title: P0-AO-day5 EpCAM+ scRNA-seq_50


title: WT_ESC_RNA_2


title: Mll34dSET_H3K4me3_2

value: MLL3 and MLL4 double-SET domain-deletion clone #2


title: P0-AO-day5 EpCAM+ scRNA-seq_19


title: WT_H3K4me2

value: anti-H3K4me2 (homemade, rabbit polyclonal)


title: Mll34dSET_H3K4me3_1

value: MLL3 and MLL4 double-SET domain-deletion clone #1


title: Mll34dSET_input2


title: WT_input


title: WT_ESC_RNA_1


title: Mll34dSET_input1


title: P0-AO-day5 EpCAM+ scRNA-seq_15


title: P0-AO-day5 EpCAM+ scRNA-seq_17


title: Mll34dSET_H3K4me2_2


title: P0-AO-day5 EpCAM+ scRNA-seq_65


title: P0-AO-day5 EpCAM+ scRNA-seq_18


title: Mll34dSET_H3K4me2_1


title: P0-AO-day5 EpCAM+ scRNA-seq_20


title: Mll34dSET_H3K4me1_2


title: P0-AO-day5 EpCAM+ scRNA-seq_16


title: P0-AO-day5 EpCAM+ scRNA-seq_14


title: P0-AO-day5 EpCAM+ scRNA-seq_25


title: P0-AO-day5 EpCAM+ scRNA-seq_13


title: Mll34dSET_H3K4me1_1


title: P0-AO-day5 EpCAM+ scRNA-seq_12


title: Mll34dSET_H3K27ac_1


title: Mll34dSET_H3K27ac_2


title: Mll34dSET_ESC_RNA_4


title: P0-AO-day5 EpCAM+ scRNA-seq_11


title: Mll34dSET_ESC_RNA_3


title: Mll34dSET_ESC_RNA_1


title: P0-AO-day5 EpCAM+ scRNA-seq_8


title: P0-AO-day5 EpCAM+ scRNA-seq_5


title: P0-AO-day5 EpCAM+ scRNA-seq_4


title: P0-AO-day5 EpCAM+ scRNA-seq_9


title: P0-AO-day5 EpCAM+ scRNA-seq_6


title: P0-AO-day5 EpCAM+ scRNA-seq_2


title: P0-AO-day5 EpCAM+ scRNA-seq_1


title: P0-AO-day5 EpCAM+ scRNA-seq_3


title: Th9 IRF8flfl CD4cre day2 B

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

description: rRNA depleted RNA

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm10 reference genome
Cufflink was applied
Genome_build: mm10
Supplementary_files_format_and_content: Tabular

source_name: Naive T cells from spleen and nodes

growth_protocol: CD4 T naive cells were isolated from C57/Bl6 Wt and CD4cre IRF8flox mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates

extract_protocol:
Total RNA was extracted from 300,000 CD4+ T cells with Trireagent by following manufacturer protocol. Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit for RNAseq or mRNA purified thanks to NEB kit
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Th1 differentiation was induced with IL-12 (10ng/ml) in presence of IL-4 blocking antibody for 1 or 2 days. Th2 differentiation was induced with IL-4 (10ng/ml) in presence of IFNγ blocking antibody for 1 or 2 days. Th9 differentiation was induced with IL-4 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ blocking antibody for 1 or 2 days. Th17 differentiation was induced with IL-6 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ and IL-4 blocking antibodies for 1 or 2 days. Treg differentiation was induced with TGF-β (4ng/ml) in presence of IFNγ and IL-4 blocking antibodies for 1 or 2 days.

tag: age

value: 7 weeks

tag: genotype

value: CD4cre IRF8flox

value: CD4 T cells


title: Th9 IRF8++ CD4cre day2 B

description: rRNA depleted RNA

value: CD4cre IRF8++


title: Th9 IRF8flfl CD4cre day2 A

description: rRNA depleted RNA


title: Th9 IRF8++ CD4cre day2 A

description: rRNA depleted RNA


title: Th9 IRF8flfl CD4cre day1 B

description: rRNA depleted RNA


title: Th9 IRF8++ CD4cre day1 B

description: rRNA depleted RNA


title: Th9 IRF8flfl CD4cre day1 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_87

description:
Single " CPM-high-day21" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.
CPM_high_day21_scRNA-seq_RPKM.txt

value: isolated on day 21


title: CPM_high_day21 scRNA-seq_86

value: hiPSC-derived CPM-high cells


title: Th9 IRF8++ CD4cre day1 A

description: rRNA depleted RNA


title: Treg WT day 2 B

description: rRNA depleted RNA

value: Wild-type


title: CPM_high_day21 scRNA-seq_85


title: Treg WT day 2 A

description: rRNA depleted RNA


title: P0-AO-day5 EpCAM+ scRNA-seq_10

value: hiPSC-derived EpCAM+ cells


title: Mll34dSET_ESC_RNA_2


title: P0-AO-day5 EpCAM+ scRNA-seq_7

value: isolated on day 26


title: CPM_high_day21 scRNA-seq_84


title: CPM_high_day21 scRNA-seq_83


title: Th17 WT day 2 B

description: rRNA depleted RNA


title: Th17 WT day 2 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_82


title: Th9 WT day 2 B

description: rRNA depleted RNA


title: Th2 WT day 2 B

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_78


title: CPM_high_day21 scRNA-seq_80


title: CPM_high_day21 scRNA-seq_81


title: Th2 WT day 2 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_77


title: CPM_high_day21 scRNA-seq_75


title: Treg WT day 1 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_74


title: Treg WT day 1 B

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_76


title: Th1 WT day 2 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_73


title: CPM_high_day21 scRNA-seq_71


title: Th9 WT day 1 B

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_72


title: Th17 WT day 1 A

description: rRNA depleted RNA


title: Th17 WT day 1 B

description: rRNA depleted RNA


title: Th9 WT day 1 A

description: rRNA depleted RNA


title: Th2 WT day 1 B

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_70


title: CPM_high_day21 scRNA-seq_68


title: Th2 WT day 1 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_69


title: Th9 WT day 2 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_67


title: CPM_high_day21 scRNA-seq_79


title: Th1 WT day 2 B

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_66


title: Th1 WT day 1 A

description: rRNA depleted RNA


title: CPM_high_day21 scRNA-seq_65


title: Th2 WT IP with ETV6 antibody

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with Bowtie2 on mm10 reference genome
MACS was applied
MACS files were used on the NEBULLA website
Genome_build: mm10
Supplementary_files_format_and_content: BED

growth_protocol: CD4 T naive cells were isolated from C57/Bl6 Wt mice. Differentiation was induced in RPMI culture medium complemented with 10% FBS,1% antibiotics in CD3/CD28 coating plates

extract_protocol:
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 300,000 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies by using the Active Motif's ChIP IT Kit by following manufacturer's instructions
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: Th9 differentiation was induced with IL-4 (20ng/ml) and TGF-β (2ng/ml) in presence of IFNγ blocking antibody for few hours, Th2 differentiation was induced with IL-4 (10ng/ml) in presence of IFNγ blocking antibody for few hours,


title: Th9 WT IP with Ig anti rabbit antibody


title: Th2 WT IP with IRF8 antibody


title: CPM_high_day21 scRNA-seq_64


title: CPM_high_day21 scRNA-seq_63


title: Th9 WT IP with Ig anti goat antibody


title: Th9 WT Input


title: CPM_high_day21 scRNA-seq_62


title: Th9 WT IP with BATF antibody


title: Th1 WT day 1 B

description: rRNA depleted RNA


title: Nuclease-free water rep 4

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

country: Germany

institute: MPI für Herz- und Lungenforschung

data_processing:
bcl2fastq 2.0 software tool was used for signal processing and demultiplexing
The RNA-Seq analysis was performed with the CLC Genomics Workbench V9.5.1 “RNA-Seq analysis” tool and mapped against the mouse reference genome (mmGRCm38.p3) to generate expression tables for every sample
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. In short the value was calculated as follows: RPKM = total exon read count / mapped reads [millions] * exon length [kb]
Genome_build: mmGRCm38.p3
Supplementary_files_format_and_content: files are in csv format and contain the RPKM values

source_name: lung tissue

extract_protocol:
Mice were euthanized with pentobarbital for P6 or with isoflurane for P14. Thoracic cavity was opened and lungs were perfused through the heart with PBS. Lung were placed in RNAlater (Qiagen) overnight in 4°C and then transferred to -80°C. Lungs were homogenized with Precellys 24 homogenizer. Total RNA was extracted with peqGOLD Total RNA kit following the manufacturer’s instructions.
Library preparation was performed with the TruSeq Stranded mRNA HT technology High Sample (HS) according to the manufacturer´s protocol

treatment_protocol: Saline (daily treatment) group was treated via i.p. injection (25µl/g) daily from the postnatal day (P)1 to P13. Scramble antagomiR controls: Scrambled 1 (Custom miRCURY™ LNA Inhibitor probe, batch number 184196, Exiqon) and Scrambled 2 (Custom miRCURY™ LNA Inhibitor probe, New scramble control design, Exiqon) were applied at P1 and P3, by i.p. injection (10 mg/kg) dissolved in nuclease-Free Water (Ambion). Nuclease-Free Water (Ambion) was applied via i.p injection at P1 and P3 at (10µl/g). At P14 mice from Saline (daily treatment), Scrambled 1, Scrambled 2, Water and Untreated groups were sacrificed. Tamoxifen (Sigma-Aldrich) was applied at P1 and P2, by i.p. injection (0.4 mg; 25 µl) dissolved in Miglyol. Migloyl was applied at P1 and P2 at 25 µl via i.p. injection. Saline (treatment day 1+2) was applied at P1 and P2 at 25 µl via i.p. route. At P6 mice from Tamoxifen, Migloyl and Saline (treatment day 1+2) treatment groups were sacrificed.

value: lung

value: post natal day 14

tag: treatment

value: Nuclease-free water (10µl/g, P1,P3)


title: Saline (treatment day 1+2) rep 4

value: post natal day 6

value: Saline (25µl, P1-P2)


title: Th9 WT IP with IRF8 antibody


title: Th9 WT IP with IRF4 antibody


title: Scrambled 2 rep 4

value: Scrambled 2 (10 mg/kg, P1,P3)


title: CPM_high_day21 scRNA-seq_59


title: CPM_high_day21 scRNA-seq_54


title: CPM_high_day21 scRNA-seq_57


title: CPM_high_day21 scRNA-seq_58


title: CPM_high_day21 scRNA-seq_53


title: Untreated rep 4

value: Untreated


title: CPM_high_day21 scRNA-seq_56


title: CPM_high_day21 scRNA-seq_60


title: Th9 WT IP with ETV6 antibody


title: Th9 WT IP with PU.1 antibody


title: CPM_high_day21 scRNA-seq_61


title: CPM_high_day21 scRNA-seq_51


title: CPM_high_day21 scRNA-seq_52


title: CPM_high_day21 scRNA-seq_55


title: Migloyl rep 4

value: Migloyl (25µl, P1-P2)


title: CPM_high_day21 scRNA-seq_50


title: CPM_high_day21 scRNA-seq_48


title: CPM_high_day21 scRNA-seq_47


title: Nuclease-free water rep 2


title: Nuclease-free water rep 3


title: Tamoxifen rep 4

value: Tamoxifen (25µl, P1-P2)


title: CPM_high_day21 scRNA-seq_49


title: CPM_high_day21 scRNA-seq_46


title: Tamoxifen rep 3


title: Tamoxifen rep 1


title: Tamoxifen rep 2


title: CPM_high_day21 scRNA-seq_44


title: Saline (treatment day 1+2) rep 3


title: Saline (treatment day 1+2) rep 2


title: CPM_high_day21 scRNA-seq_41


title: CPM_high_day21 scRNA-seq_43


title: CPM_high_day21 scRNA-seq_42


title: CPM_high_day21 scRNA-seq_40


title: Nuclease-free water rep 1


title: Saline (treatment day 1+2) rep 1


title: Scrambled 1 rep 3

value: Scrambled 1 (10 mg/kg, P1,P3)


title: Scrambled 1 rep 4


title: CPM_high_day21 scRNA-seq_39


title: Scrambled 1 rep 2


title: CPM_high_day21 scRNA-seq_37


title: CPM_high_day21 scRNA-seq_36


title: Scrambled 1 rep 1


title: Scrambled 2 rep 3


title: CPM_high_day21 scRNA-seq_45


title: Scrambled 2 rep 1


title: CPM_high_day21 scRNA-seq_32


title: CPM_high_day21 scRNA-seq_33


title: Untreated rep 3


title: Untreated rep 1


title: Scrambled 2 rep 2


title: CPM_high_day21 scRNA-seq_38


title: CPM_high_day21 scRNA-seq_31


title: CPM_high_day21 scRNA-seq_35


title: CPM_high_day21 scRNA-seq_30


title: Sailne daily rep 4

value: Saline (25µl/g, daily)


title: CPM_high_day21 scRNA-seq_34


title: Sailne daily rep 3


title: CPM_high_day21 scRNA-seq_29


title: CPM_high_day21 scRNA-seq_28


title: Saline daily rep 2


title: CPM_high_day21 scRNA-seq_27


title: Saline daily rep 1


title: Migloyl rep 3


title: Miglyol rep 2


title: Untreated rep 2


title: CPM_high_day21 scRNA-seq_24


title: CPM_high_day21 scRNA-seq_25


title: CPM_high_day21 scRNA-seq_21


title: CPM_high_day21 scRNA-seq_20


title: CPM_high_day21 scRNA-seq_17


title: CPM_high_day21 scRNA-seq_19


title: CPM_high_day21 scRNA-seq_18


title: CPM_high_day21 scRNA-seq_23


title: CPM_high_day21 scRNA-seq_22


title: CPM_high_day21 scRNA-seq_15


title: CPM_high_day21 scRNA-seq_12


title: CPM_high_day21 scRNA-seq_13


title: CPM_high_day21 scRNA-seq_11


title: Migloyl rep 1


title: CPM_high_day21 scRNA-seq_8


title: CPM_high_day21 scRNA-seq_7


title: CPM_high_day21 scRNA-seq_26


title: CPM_high_day21 scRNA-seq_6


title: CPM_high_day21 scRNA-seq_5


title: CPM_high_day21 scRNA-seq_3


title: CPM_high_day21 scRNA-seq_4


title: CPM_high_day21 scRNA-seq_16


title: CPM_high_day21 scRNA-seq_2


title: CPM_high_day21 scRNA-seq_14


title: CPM_high_day21 scRNA-seq_1


title: CPM_high_day21 scRNA-seq_10


title: P5-SFTPC scRNA-seq_66

description: Single P5-SFTPC+ cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

source_name: SFTPC+ cells

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

value: hiPSC-derived SFTPC+ cells

tag: passages


title: P5-SFTPC scRNA-seq_64


title: P5-SFTPC scRNA-seq_65


title: P5-SFTPC scRNA-seq_63


title: CPM_high_day21 scRNA-seq_9

value: isolated on day 21


title: P5-SFTPC scRNA-seq_62


title: P5-SFTPC scRNA-seq_59


title: P5-SFTPC scRNA-seq_61


title: P5-SFTPC scRNA-seq_55


title: P5-SFTPC scRNA-seq_60


title: P5-SFTPC scRNA-seq_49


title: P5-SFTPC scRNA-seq_57


title: P5-SFTPC scRNA-seq_58


title: P5-SFTPC scRNA-seq_50


title: P5-SFTPC scRNA-seq_53


title: P5-SFTPC scRNA-seq_52


title: P5-SFTPC scRNA-seq_54


title: P5-SFTPC scRNA-seq_48


title: P5-SFTPC scRNA-seq_51


title: P5-SFTPC scRNA-seq_46


title: P5-SFTPC scRNA-seq_47


title: P5-SFTPC scRNA-seq_45


title: P5-SFTPC scRNA-seq_43


title: P5-SFTPC scRNA-seq_44


title: P5-SFTPC scRNA-seq_56


title: P5-SFTPC scRNA-seq_41


title: P5-SFTPC scRNA-seq_40


title: P5-SFTPC scRNA-seq_38


title: P5-SFTPC scRNA-seq_37


title: P5-SFTPC scRNA-seq_39


title: P5-SFTPC scRNA-seq_36


title: P5-SFTPC scRNA-seq_35


title: P5-SFTPC scRNA-seq_34


title: P5-SFTPC scRNA-seq_42


title: P5-SFTPC scRNA-seq_33


title: P5-SFTPC scRNA-seq_32


title: P5-SFTPC scRNA-seq_25


title: P5-SFTPC scRNA-seq_29


title: P5-SFTPC scRNA-seq_28


title: P5-SFTPC scRNA-seq_26


title: P5-SFTPC scRNA-seq_31


title: P5-SFTPC scRNA-seq_24


title: P5-SFTPC scRNA-seq_21


title: P5-SFTPC scRNA-seq_23


title: P5-SFTPC scRNA-seq_19


title: P5-SFTPC scRNA-seq_22


title: P5-SFTPC scRNA-seq_18


title: P5-SFTPC scRNA-seq_17


title: P5-SFTPC scRNA-seq_13


title: P5-SFTPC scRNA-seq_11


title: P5-SFTPC scRNA-seq_16


title: P5-SFTPC scRNA-seq_30


title: P5-SFTPC scRNA-seq_12


title: P5-SFTPC scRNA-seq_10


title: P5-SFTPC scRNA-seq_14


title: P5-SFTPC scRNA-seq_15


title: P5-SFTPC scRNA-seq_20


title: P5-SFTPC scRNA-seq_6


title: P5-SFTPC scRNA-seq_27


title: P5-SFTPC scRNA-seq_9


title: P5-SFTPC scRNA-seq_7


title: P5-SFTPC scRNA-seq_8


title: P5-SFTPC scRNA-seq_5


title: P5-SFTPC scRNA-seq_3


title: P2-SFTPC scRNA-seq_42

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


title: P5-SFTPC scRNA-seq_2


title: P5-SFTPC scRNA-seq_1


title: P2-SFTPC scRNA-seq_43


title: P2-SFTPC scRNA-seq_44


title: P2-SFTPC scRNA-seq_38


title: P5-SFTPC scRNA-seq_4


title: P2-SFTPC scRNA-seq_39


title: P2-SFTPC scRNA-seq_35


title: P2-SFTPC scRNA-seq_41


title: P2-SFTPC scRNA-seq_45


title: P2-SFTPC scRNA-seq_40


title: P2-SFTPC scRNA-seq_34


title: P2-SFTPC scRNA-seq_32


title: P2-SFTPC scRNA-seq_29