title: t13_t11_bM

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
liquid culture
Processed_data_rpkm_t13595.txt
Processed_data_rpkm_t13595.txt

data_processing:
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: 1280.1984_Staphylococcus_aureus GenBank: JAAFYP000000000.1             42 rc    DNA     linear   BCT 09-FEB-2020
Genome_build: 1428.155_Bacillus_thuringiensis Genbank: JAAFYT000000000.1
Genome_build: 571.31_Klebsiella_oxytoca GenBank: JAAFYN000000000.1             59 rc    DNA     linear   BCT 09-FEB-2020
Genome_build: 1280.1985_Staphylococcus_aureus GenBank: JAAFYO000000000.1             37 rc    DNA     linear   BCT 09-FEB-2020
Supplementary_files_format_and_content: Tab delimited text file

source_name: chronic wound

growth_protocol: Bacterial isolates were grown in RPMI liquid medium and RPMI agar

extract_protocol:
Immediately after obtaining the cell pellet, 100 µl of killing buffer was added. Mechanical cell disruption was carried out with a Teflon vessel and a disruption ball filled with liquid N2 and pre-cooled in liquid N2 . The resulting cell powder was resuspended in 4 ml of lysis solution by repeated pipetting and transfer into 1 ml aliquots. Subsequently, one volume of acid phenol solution was added to cell lysate, and mixed on a tube shaker. Centrifugation and supernatant transfer into a new tube were followed by the addition of one volume acid phenol solution. This procedure was repeated twice; first by the addition of one volume chloroform/IAA and then by the addition of  Na-Acetate and isopropanol for overnight precipitation. RNA extraction was carried out by centrifugation at 4°C, where the pellet was washed twice with 80% ethanol, dry at room temperature, and dissolved in nuclease-free water. DNase Digestion and RNA clean-up (Qiagen, Hilden, Germany) were performed following manufacturer’s protocol. RNA concentration was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and RNA quality assessment was carried out by Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA) and the manufacturer’s recommended protocol.

treatment_protocol: Main cultures  were started in water bath under constant shaking (80–85 rpm) at 37ºC in 120 mL pre-warmed RPMI medium. The monocultures were initiated with an OD600 of 0.05 while co-cultures were inoculated with an OD600 of 0.025 of each isolate to a total of 0.05. Samples were collected at mid-exponential phase (2-2.5 h, OD600 ±0.5) and at 90 min within the stationary growth phase (4-5 h, OD600 ±1.0). To mimic biofilm conditions, serial dilutions were performed with monocultures or mixed cultures of t111, t13595, Bt plus Ko, and these were plated onto RPMI agar and incubated at 37 ºC for 24 hr to form a homogeneous plate with coalescent individual colonies.

tag: strain

value: spa type t13595

value: S. aureus t13595 + S. aureus t111 co-culture, exponential phase

tag: origin

value: clinical isolate

tag: collection date

tag: reference genome name

tag: eference genome


title: t13_t11_aS

status: Public on Feb 22 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Staphylococcus aureus

tag: condition

value: S. aureus t13595 + S. aureus t111 co-culture, stationary phase


title: Brain-F-Y

city: Beijing

first: Shuai

last: Ma

address: No.15, Da Tun road

country: China

institute: Chinese Academy of Sciences

description: Single-Nucleus RNA

data_processing:
Sequences from the microfluidic droplet platform were de-multiplexed and aligned using CellRanger version 2.2.1, available from 10x Genomics with default parameters.
Genome_build: rat6.0
Supplementary_files_format_and_content: tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
The organs and tissues were isolated from young, old, and calorie-restricted (CR) SD rats. Pooled samples of 2 to 3 rats were quickly minced into ∼1 mm3 pieces on ice with scissors in cold 1× PBS (Sigma-Aldrich) and transferred into 15-ml centrifuge tubes, rinsed twice with cold 1× PBS and then incubate with the same volume of dissociation buffer with the addition of trypsin-EDTA (0.125%) at 37°C for 1 hr (Han et al., 2018a, b).
sc/snRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3′ Gel Bead and Library V2 Kit.

tag: Stage

value: Y-AL

tag: tissue

value: Brain


title: t13_t11_aM


title: t13_Klox_bS

value: S. aureus t13595 + K. oxytoca co-culture, stationary phase


title: t13_Klox_bM

value: S. aureus t13595 + K. oxytoca co-culture, exponential phase


title: PRF_MPRA_plus1

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

description: frameshifting library integrated in the AAVS1 locus (single copy per cell)

library_source: genomic

data_processing:
base-calling (Illumina)
mapping to the designed sequence libraries with custom Python scripts (will be provided as part of the published manuscript)
identifying reads coming from synthesis errors vs those that perfectly match the library sequence ("wt")
For each variant, obtain the distribution across expression bins (by identifying the bin specific barcode incorporated during PCR amplification from genomic DNA)
In the case of RNA, determine the number and fraction of reads that might constitute cryptic splicing events
Supplementary_files_format_and_content: csv, contains the sequences of the library and the computed splicing ratios/splicing values

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 cells with integrated reporter construct

growth_protocol: 37deg Celsius, 5% CO2

extract_protocol:
NucleoSpin RNA II kit (MACHEREY-NAGEL), SuperScript® III First-Strand Synthesis System (Thermo Fisher Scientific) for RNA samples, DNeasy Blood & Tissue Kit (Qiagen) for genomic DNA samples
PCR to amplify the reporter library, library preparation following Illumina protocols for Truseq. End repair, poly A addition, adaptor ligation, enrichment.
Sequencing of PCR amplicons (from cDNA or genomic DNA)

value: 1 AAVS1 site mutated

tag: cell line


title: Brain-M-CR

description: Single-Nucleus RNA

value: O-CR


title: PRF_MPRA_minus1


title: t13_bS

value: S. aureus t13595 + B. thuringiensis co-culture, stationary phase


title: t13_Klox_aM


title: t13_bM

value: S. aureus t13595 + B. thuringiensis co-culture, exponential phase


title: t13_Bathu_bS


title: WAT-F-O

description: Single-Cell RNA

source_name: WAT

value: O-AL

value: White adipose tissue


title: t13_Klox_aS


title: Brain-M-O

description: Single-Nucleus RNA


title: t13_Bathu_aM

value: S. aureus t13595 monoculture, exponential phase


title: t13_Bathu_aS

value: S. aureus t13595 monoculture, stationary phase


title: WAT-F-CR

description: Single-Cell RNA


title: Brain-M-Y

description: Single-Nucleus RNA


title: t13_Bathu_bM


title: t13_aS


title: PRF_MPRA_stopvector


title: t13_aM


title: MN2-KO-4R_S3_R1_001

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
Base calls and Illumina adaptors trimming performed using bcl2fastq v2.18. Clontech adaptors trimming performed with CLC 9.
Raw reads were aligned to the mouse genome (mm9) using TopHat (v2.0.11).
Gene counts were generated using FeatureCounts (v1.6.2). Data preprocessing was done using the edgeR package from Bioconductor (v3.8).
Genome_build: mm9
Supplementary_files_format_and_content: Raw read counts from FeatureCounts.

organism: Mus musculus

source_name: FACS-sorted GFP+ MECs

growth_protocol: we transcriptionally profiled 3 pairs of contralateral glands engrafted with either WT.EGFP+ or Adamts18-/-.EGFP+ epithelia using RNA-seq

extract_protocol:
RNA was extracted from GFP+ FACS-sorted cells using miRNeasy Mini Kit (Qiagen).
Libraries were prepared in 2 steps and were sequenced on Illumina NextSeq 500 instrument with single-end reads of 85 bp.

tag: genotype

value: Adamts18 KO

value: mammary gland

tag: cell type

value: FACS-sorted GFP+ MECs


title: MN3-WT-4L_S6_R1_001

value: Adamts18 WT


title: MN2-WT-4L_S4_R1_001


title: t11_t13_bS

description:
liquid culture
Processed_data_rpkm_t111.txt
Processed_data_rpkm_t111.txt

value: spa type t111

value: S. aureus t111 + S. aureus t13595 co-culture, stationary phase

value: clinical isolate


title: WAT-M-CR

description: Single-Cell RNA


title: Brain-F-CR

description: Single-Nucleus RNA

value: Brain


title: MN1-WT-4L_S2_R1_001


title: t11_t13_bM

value: S. aureus t111 + S. aureus t13595 co-culture, exponential phase


title: t11_t13_aS


title: t11_t13_aM


title: WAT-M-Y

description: Single-Cell RNA

value: Y-AL


title: t11_Klox_bS

value: S. aureus t111 + K. oxytoca co-culture, stationary phase


title: Skin-F-CR

description: Single-Cell RNA

source_name: Skin

value: O-CR

value: Skin


title: t11_Klox_aS


title: MN1-KO-4R_S1_R1_001


title: t11_Klox_bM

value: S. aureus t111 + K. oxytoca co-culture, exponential phase


title: Skin-F-O

description: Single-Cell RNA

value: O-AL


title: t11_Klox_aM


title: spz_3

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

country: USA

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were initially trimmed using Trim_Galore
Reads were mapped to a custom genome and transcriptome that consisted of human (GRCh37v75) and Plasmodium berghei ANKA (PbANKAv3) chromosomes using the STAR aligner
The number of reads mapping to each gene was compiled using HTSeq
The count table was filtered to just the Plasmodium berghei genes (thus filtering out all human genes)
DESeq2 was used to normalize the expression value across all samples
Genome_build: GRCh37v75 and PbANKAv3
Supplementary_files_format_and_content: The DESeq2 normalized gene expression data

organism: Plasmodium berghei

source_name: Plasmodium berghei

growth_protocol: Hepatoma cells (HuH7/HepG2) were seeded day before in DMEM+10%FBS+1%anti-anti. Mosquito salivary glands were dissected and infected. Cells were then sorted for GFP- containing P.berghei_ANKA GFP parasites at appropriate time point.

extract_protocol:
SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clonetech)
and libraries were prepared at the Duke Next Generation Sequencing Core Facility and sequenced on the Illumina HiSeq 4000 as 50 base pair single-end reads

value: Plasmodium berghei ANKA

tag: time point

value: sporozoite

tag: sample type

value: Plasmodium berghei ANKA sporozoites


title: spz_2


title: spz_4


title: spz_1


title: t11_Bathu_bS

value: S. aureus t111 + B. thuringiensis co-culture, stationary phase


title: Skin-M-CR

description: Single-Cell RNA


title: 4hpi_4

organism:
Plasmodium berghei
Homo sapiens

value: Homo sapiens Host


title: t11_Bathu_aS

value: S. aureus t111 monoculture, stationary phase


title: Skin-F-Y

description: Single-Cell RNA


title: 4hpi_3


title: Skin-M-O

description: Single-Cell RNA


title: t11_aS

value: spa type t111


title: t11_aM

value: S. aureus t111 monoculture, exponential phase


title: t11_bM

value: S. aureus t111 + B. thuringiensis co-culture, exponential phase

value: clinical isolate


title: WAT-M-O

description: Single-Cell RNA

value: White adipose tissue


title: t11_bS


title: t13

description:
agar
Processed_data_rpkm_Biofilm_t13595.txt
Processed_data_rpkm_Biofilm_t13595.txt

value: spa type t13595

value: S. aureus t13595 monoculture in biofilm


title: 4hpi_2


title: t11

description:
agar
Processed_data_rpkm_Biofilm_t111.txt
Processed_data_rpkm_Biofilm_t111.txt

value: S. aureus t111 monoculture in biofilm


title: Liver-F-CR

description: Single-Cell RNA

source_name: Liver

value: O-CR

value: Liver


title: 2hpi_5


title: mix_t13

value: S. aureus t13595 co-culture in biofilm


title: Liver-F-O

description: Single-Cell RNA

value: O-AL


title: L-library-lncRNA

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

description: Column S in all-lncRNA-expression.txt

data_processing:
After discarding the reads containing adapters, trimming the reads with a poly(N) substrates (≥ 10%) and removing the low quality reads with a quality score less than 20, the remaining reads (clean reads) were used for downstream analyses.
All the clean reads were mapped to the Capra hircus genome (v1.01, https://www.ncbi.nlm.nih.gov/genome/?term=GOAT) using TopHat v2.0.9, and then were assembled by Cufflinks v2.1.1 (Trapnell et al., 2012). These transcripts were also removed as following: with a length less than 200 bp, only one exon, less than three. After the remaining transcripts of each sample were constructed, and then a set of transcripts were merged using Cuffmerge software to generate the corresponding transcriptome. The mRNAs, even though the rRNA, tRNA, snRNA (small nuclear RNA), snoRNA (small nucleolar RNA), premiRNA (precursor miRNA) and pseudogenes, were all recognized using bowtie2 and removed.
Finally, the expression abundance of all transcripts in each library were test using Cufflinks based on the FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Capra hircus v1.01
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for exons of transcripts from each sample

organism: Capra hircus

source_name: Late lactation stage Laoshan dairy goat mammary gland tissue

growth_protocol: All goats had free food and water access, and were housed with natural lighting prior to experiments.

extract_protocol:
Total RNA was individually extracted from the above fifteen samples using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s references, their integrity and quality were tested by 2100 Bioanalyzer (Agilent, USA) and the samples (RIN≥ 7.7) were used for library construction.
Each total RNA sample from five dairy goat mammary gland tissues in the same period was equal mixed, homogenized, and used further for three libraries construction using the Illumina TruSeq Stranded RNA Kit (Illumina, USA) according to the manufacturer’s recommendations and named the E library (early lactation), P library (high lactation) and L library (late lactation).

treatment_protocol: The mammary gland samples were collected surgically after general anaesthesia using Xylazine Hydrochloride injection solution (Huamu Animal Health Products Co., Ltd. China) at corresponding lactation stage, including early, peak and late lactations.

tag: breed

value: Laoshan

value: mammary gland

tag: tag

value: late lactation, 210th day after parturition


title: 2hpi_4

value: Plasmodium berghei ANKA

value: Homo sapiens Host


title: E-library-lncRNA

description: Column C in all-lncRNA-expression.txt

source_name: Early lactation stage Laoshan dairy goat mammary gland tissue

value: early lactation, 10th day after parturition


title: 2hpi_3


title: Liver-M-CR

description: Single-Cell RNA


title: 24hpi_5


title: Liver-M-O

description: Single-Cell RNA


title: WAT-F-Y

description: Single-Cell RNA

value: Y-AL


title: 24hpi_4


title: t11_Bathu_aM

value: spa type t111

value: S. aureus t111 monoculture, exponential phase


title: Liver-M-Y

description: Single-Cell RNA


title: 24hpi_3


title: P-library-lncRNA

description: Column H in all-lncRNA-expression.txt

source_name: Peak lactation stage Laoshan dairy goat mammary gland tissue

value: peak lactation, 90th day after parturition


title: 48hpi_4


title: Kidney-F-CR

description: Single-Cell RNA

source_name: Kidney

value: Kidney


title: 24hpi_8


title: 36hpi_4


title: EOS-reset

city: Kyoto

first: Hirofumi

last: Suemori

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

country: Japan

institute: Kyoto University

data_processing: All RNA-seq datasets including in this study were aligned using STAR (version 2.5.3) to the human genome (UCSC hg19) with 50 bp single-end mode and command options for 2-pass and unique mapping. The count data were obtained using htseq-count in HTSeq (version 0.9.1) with annotation from UCSC hg19. Reads per kilobase of exon per million mapped fragments (RPKM) were calculated by the R project (version 3.3.1). Genome build: hg19.  A text file including RPKM values for each sample is provided.

molecule: polyA RNA

source_name: tt2iLGöX-treated EOS-reset cells

extract_protocol:
Total RNA was extracted using TRIzol-LS Reagent. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with an Agilent 6000 RNA Pico Kit.
Libraries for Miseq sequencing were prepared using a TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. After adapter ligation, purified cDNA was amplified by 15 cycles of PCR. The libraries were evaluated using the Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit. The validated libraries were loaded into Miseq Reagent Kit v3 (150 cycles) at a final concentration of 10 pM, and sequencing was performed in a Miseq sequencer (Illumina) using the paired end mode.

value: Human embryonic stem cells (H9)

tag: culture condition

value: tt2iLGöX condition

value: Naive


title: t13_t11_bS

value: spa type t13595

value: S. aureus t13595 + S. aureus t111 co-culture, stationary phase

value: clinical isolate


title: Kidney-M-CR

description: Single-Cell RNA

value: O-CR


title: 18hpi_3


title: t11_Bathu_bM

value: S. aureus t111 + B. thuringiensis co-culture, exponential phase


title: EOS(N1)-tt2iLGöX_RNA-seq_rep2

source_name: tt2iLGöX-treated NR5A1-EOS-DOX (-) cells


title: Kidney-M-O

description: Single-Cell RNA

value: O-AL


title: Normal_fibrobalst_5_rep2

type: RNA

city: boston

first: Hensin

last: Tsao

state: Massachusetts

address: 50 Blossom Street

institute: massachusette general hospital

description: Gene expression data from Korean normal primary fibroblast cells

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45°C for 16hr at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 per the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

data_processing: Images were extracted with Affymetrix GeneChip Command Console (AGCC) and analyzed using GeneChip Expression Console. A Primeview CDF (provided by Affymetrix) that included probe information for the ERCC controls (GPL16043) was used to generate the CEL files.

label: Biotin

source_name: Human primary fibroblast cells_cultured

label_protocol: 100 ng of total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228)

growth_protocol: Fibroblast cultivation was performed using the dermal portion of keloid tissues obtained from 5 keloid patients. The specimens were cut into 2mm3 size and placed in 60mm culture dishes and were cultured in mixture of Dulbecco’s modified Eagle’s medium (DMEM; Gibco BRL) and Ham’s nutrient mixture F12 (Gibco BRL) medium, by a 3:1 ratio. The supplements included 10% fetal bovine serum (Hyclone), 100 U/ml of penicillin, 100 mg/ml streptomycin, 1×10-10 M cholera toxin, 0.4 μg/ml hydrocortisone, 5 μg/ml insulin, 5 μg/ml transferrin, and 2×10-11 M triiodothyronine. The outgrown cells were harvested and the identities of cells were verified by vimentin and alpha-smooth muscle actin (α-SMA) expression. All primary cells used in this study were at passage-3. Cells were maintained in incubators at 37°C and exposed to normoxia (20% O2, 5% CO2) or hypoxia (1% O2, 5% CO2).

extract_protocol: Briefly, 10 cell lines (5 NFs and 5 KFs) were grown in replicate cultures and subjected to RNA extraction using the Qiagen RNeasy Mini Kit (Qiagen).

value: Korean primary fibroblasts


title: Normal_fibrobalst_4_rep1

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC)

treatment_protocol: Cells were maintained in incubators at 37°C and exposed to normoxia (20% O2, 5% CO2)


title: Normal_fibrobalst_4_rep2


title: Kidney-F-O

description: Single-Cell RNA


title: 12hpi_3

value: Plasmodium berghei ANKA

value: Homo sapiens Host


title: Normal_fibrobalst_2_rep2


title: MN3-KO-4R_S5_R1_001

value: Adamts18 KO

value: mammary gland

value: FACS-sorted GFP+ MECs


title: Normal_fibrobalst_3_rep1


title: Normal_fibrobalst_1_rep2


title: Normal_fibrobalst_1_rep1


title: Normal_fibrobalst_5_rep1


title: Keloid_fibrobalst_6_rep2

description: Gene expression data from Korean keloid primary fibroblast cells


title: Normal_fibrobalst_3_rep2


title: Normal_fibrobalst_2_rep1


title: Skin-M-Y

description: Single-Cell RNA

value: Y-AL

value: Skin


title: Kidney-F-Y

description: Single-Cell RNA

value: Kidney


title: mix_t11

value: spa type t111

value: S. aureus t111 co-culture in biofilm


title: Liver-F-Y

description: Single-Cell RNA

value: Liver


title: Keloid_fibrobalst_5_rep2


title: EOS(N1)-tt2iLGöX_RNA-seq_rep1

value: Human embryonic stem cells (H9)

value: tt2iLGöX condition

value: Naive


title: Keloid_fibrobalst_6_rep1


title: 18hpi_2


title: EOSN1-CHIR_RNA-seq

source_name: CHIR-treated NR5A1-EOS-DOX (+) cells

value: CHIR condition

value: NR5A1 overexpression


title: BM-F-CR

description: Single-Cell RNA

source_name: BM

value: O-CR

value: Bone marrow


title: 12hpi_2

value: Plasmodium berghei ANKA

value: Homo sapiens Host


title: BM-F-O

description: Single-Cell RNA

value: O-AL


title: 4hpi_1


title: Keloid_fibrobalst_5_rep1

value: Korean primary fibroblasts


title: EOS-TF_RNA-seq

source_name: Parental-EOS-DOX (+) cells

value: TF condition

value: Parental


title: NR5A1-DOX (+)_CHIR_RNA-seq_rep3

source_name: CHIR-treated NR5A1-DOX (+) cells

growth_protocol: Parental-DOX (+) cells were cultured in mTeSR1 with doxycycline (DOX) on Matrigel-coated dishes. CHIR-treated NR5A1-DOX (+) cells were cultured in custom mTeSR1 lacking FGF2 and TGF-β with DOX and 3 µM CHIR99021 on Matrigel-coated dishes.


title: BM-F-Y

description: Single-Cell RNA

value: Y-AL


title: 2hpi_2


title: BM-M-CR

description: Single-Cell RNA


title: NR5A1-DOX (+)_CHIR_RNA-seq_rep2


title: 48hpi_3


title: 24hpi_7


title: 48hpi_2


title: BM-M-Y

description: Single-Cell RNA


title: NR5A1-DOX (+)_CHIR_RNA-seq_rep1


title: Parental-DOX (+)_RNA-seq_rep3

source_name: Parental-DOX (+) cells


title: BM-M-O

description: Single-Cell RNA


title: BAT-F-CR

description: Single-Cell RNA

source_name: BAT

value: Brown adipose tissue


title: Keloid_fibrobalst_4_rep1


title: Parental-DOX (+)_RNA-seq_rep2


title: Keloid_fibrobalst_4_rep2


title: Parental-DOX (+)_RNA-seq_rep1


title: BAT-F-O

description: Single-Cell RNA


title: 36hpi_3


title: Keloid_fibrobalst_3_rep1


title: 36hpi_2


title: Keloid_fibrobalst_1_rep2


title: Keloid_fibrobalst_1_rep1


title: Input for FLAG ChIP-seq CHIR_N1-DOX (+)

data_processing:
All ChIP-seq data were aligned using Bowtie2 (version 2.2.8) to the human genome UCSC hg19 with up to a single mismatch.
Peaks were called by using MACS2 (version 2.1.1) to identify regions of ChIP-seq enrichment over the background.
Log10 likelihood ratio (logLR) was calculated by using MACS2 bdgcmp to generate the data subtracting noise from treatment sample.
Libraries for Miseq sequencing were prepared using a TruSeq DNA Sample Preparation Kit (Illumina) according to a manufacturer’s instructions. After adapter ligation, DNA fragments of 300–400 bp were excised from 2% agarose gels. The purified DNA was amplified by 15–18 cycles of PCR. The libraries were evaluated using the Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit. The validated libraries were loaded into Miseq Reagent Kit v3 (150 cycles) at a final concentration of 10 pM. Sequencing was performed in a Miseq sequencer (Illumina) using the paired end mode.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated by MACS2 are provided. Values represent log10 likelihood ratio (logLR).

source_name: CHIR-treated 3xFLAG-NR5A1-DOX (+) cells

extract_protocol:
Chromatin was prepared from 10 million crosslinked cells for immunoprecipitation. The samples were sheared in a Covaris S220 Focused-ultrasonicator and then reacted with 10 µg rabbit anti-H3K4me3 (ab8580; Abcam) and rabbit anti-H3K27me3 (07-449; Merck Millipore) antibodies, and Normal Rabbit IgG (CST) for Histone-ChIP, and with 10 µg mouse anti-DDDDK-tag (FLA-1, MBL) and Normal Mouse IgG (Santa Cruz Biotechnology for NR5A1-ChIP. Total inputs and ChIPed samples were evaluated using an Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit for library preparation.
Libraries for Miseq sequencing were prepared using a TruSeq DNA Sample Preparation Kit (Illumina) according to a manufacturer’s instructions. After adopter ligation, DNA fragments of 300–400 bp were excised from 2% agarose gels. The purified DNA was amplified by 15–18 cycles of PCR. The libraries were evaluated using an Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit. The validated libraries were loaded into Miseq Reagent Kit v3 (150 cycles) at a final concentration of 10 pM. Sequencing was performed in a Miseq sequencer (Illumina) using the paired end mode.


title: BAT-F-Y

description: Single-Cell RNA


title: 24hpi_6


title: BAT-M-CR

description: Single-Cell RNA


title: FLAG ChIP-seq CHIR_N1-DOX (+)


title: 12hpi_1


title: Input for Histone ChIP-seq CHIR_N1DOX (+)


title: EOS(N1)-tt2iLGöX_RNA-seq_rep3


title: BAT-M-Y

description: Single-Cell RNA


title: 48hpi_1


title: BAT-M-O

description: Single-Cell RNA


title: Input for Histone ChIP-seq P-DOX (+)


title: 24hpi_1


title: 2hpi_1


title: Kidney-M-Y

description: Single-Cell RNA

value: Kidney


title: 36hpi_1


title: H3K27me3 ChIP-seq P-DOX (+)


title: NR5A1-DOX (+)_CHIR_rep3

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Parental-DOX (+) cells were cultured in mTeSR1 with doxycycline (DOX) on Matrigel-coated dishes. CHIR-treated NR5A1-DOX (+) cells were cultured in custom mTeSR1 lacking FGF2 and TGF-ß with DOX and 3 µM CHIR99021 on Matrigel-coated dishes.

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (Invitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: passage number


title: Aorta-F-O

description: Single-Cell RNA

source_name: Aorta

value: Aorta


title: H3K27me3 ChIP-seq CHIR_N1-DOX (+)

value: Human embryonic stem cells (H9)


title: H3K4me3 ChIP-seq CHIR_N1-DOX (+)


title: Aorta-F-Y

description: Single-Cell RNA


title: 24hpi_2

source_name: Plasmodium berghei

tag: strain


title: NR5A1-DOX (+)_CHIR_rep2


title: NR5A1-DOX (+)_CHIR_rep1


title: NR5A1-DOX (+)_rep3

source_name: NR5A1-DOX (+) cells


title: NR5A1-DOX (+)_rep2


title: 18hpi_1


title: H3K4me3 ChIP-seq P-DOX (+)


title: Aorta-F-CR

description: Single-Cell RNA


title: NR5A1-DOX (+)_rep1


title: Aorta-M-O

description: Single-Cell RNA


title: Klox_t13_bs

description:
liquid culture
Processed_data_rpkm_Klox.txt
Processed_data_rpkm_Klox.txt

organism: Klebsiella oxytoca

source_name: chronic wound

value: K. oxytoca + S. aureus t13595 co-culture, stationary phase

tag: origin

value: clinical isolate


title: Aorta-M-Y

description: Single-Cell RNA


title: NS580_2T1_TyRPB9_HAT2KD_48h_Input_2

city: Planegg-Martinsried

first: T.

middle: Nicolai

last: Siegel

address: Großhaderner Str. 9

department: Department of Physiological Chemistry

country: Germany

institute: Ludwig-Maximilians-Universität

description:
CpB_ws1_ss1_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

data_processing:
Reads were mapped using Bowtie 2 local
BAM files were sorted and indexed using SAMtools version 1.8
The number of reads was normalised per billion mapped reads and coverage files were generated in the wiggle format using COVERnant version 0.3.0 with the subcommand ratio
Genome_build: HGAP3_Tb427v9; from Zenodo https://doi.org/10.5281/zenodo.823671
Supplementary_files_format_and_content: wiggle format containing coverage tracks

organism: Trypanosoma brucei brucei

source_name: T. brucei 2T1_HAT2KD_TyRPB9 bloodstream form

growth_protocol: Cells were grown in HMI-11 medium to a density of 0.9 mio cells per ml. For depletion of HAT1 or HAT2, cells were treated with 1 µg/ml Doxycylcin for 48 h.

extract_protocol:
In brief, 3 x 10e8 cells were harvested, crosslinked in 1% formaldehyde and lysed using 200 µM digitonin (final concentration). After centrifugation, the pellet was resuspended in 1000 µl NP-S buffer and sonicated using Covaris S220 focused-ultrasonication (Peak Intensity: 150, intensity: 5, Duty Factor: 10, Counts Per Burst: 200, Time: 10 min). After centrifugation, 60 µl of the supernatant was separated as input control. Immunoprecipitation of fragmented RPB9-bound DNA was performed using Dynabeads Protein G (Invitrogen), coupled to 10 µg monoclonal, purified BB2 mouse antibody, overnight (~14 h) at 4 °C in presence of 300 mM NaCl (final concentration). Bound material was washed and eluted, and cross-links were reversed at 65 °C for ~11 h in the presence of 300 mM NaCl (final concentration).
ChIP-seq libraries were constructed using ~5 ng of immunoprecipitated or 35 ng input DNA for sequencing on an Illumina platform. Following blunt-ending and poly(A)-tailing, Y-shaped adapters (Ford et al., 2014) containing the Illumina Truseq-Adapter-sequences are ligated to each end of a DNA molecule. The libraries were size-selected (150 bp – 350 bp) on native PAGE and the library concentrations were determined in duplicates using Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. Q32854) for Qubit 2.0 Fluorometer (Invitrogen, cat. no. Q32866). ChIP-seq libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, cat. no. KK4824) according to the manufacturer’s instruction and sequenced in paired-end mode with 2 x 76 cycles using an Illumina NextSeq 500 platform.

tag: genotype/variation

tag: time

tag: chip antibody


title: sSKOV3-3_input

first: Xiao

last: Huo

address: No.1 ShuaiFuYuan,Dongcheng District

department: Department of Obstetrics and Gynecology

country: France

institute: Peking Union Medical College Hospital

data_processing:
RNA-Seq：Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20. The clean reads were then aligned to hg38_UCSC_2013 genome using the star program.
Htseq-count was used to calculate gene expression
The RNA-seq differential gene expression analysis was performed using DESeq2 algorithm
ChIP-seq raw reads were aligned to hg38 using bwa program (version 0.7.2).
The resulted sam files are converted to bam with samtools (version 0.1.18). MACS2 (version 2.0.10.20131216) was used to call peak with cutoff p value < 0.00001.
The HOMER's (version 4.10) findMotifsGenome.pl tool was used for Motif analysis.
ChIP-seq reads distributions (from bigwig) across gene body are presented as an average plot (average of reads signals across all genes) and the analysis of plotFingerprint were both used the deeptools (version 2.0).
Genome_build: hg38
Supplementary_files_format_and_content: Htseq-count; bigwig

source_name: SKOV3_wild type_input

growth_protocol: The SKOV3 cells were cultured in McCOY’5A medium supplemented with 10% fetal bovine serum (FBS, USA), 100μg/ml streptomycin and 100 U/ml penicillin. All cells were incubated in a 75 humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
For RNA-Seq，SKOV3 and SKOV3/sgEZH2 cells were harvested for RNA extraction using RNeasy mini kits (Qiagen).  For ChIP-seq, SKOV3 and SKOV3/sgEZH2 cells were fixed and then lysed, and the chromatin  was sheared to 200-500 bp in size using the Bioruptor sonicator (Diagenode). The chromatin was incubated with H3K27me3 antibody (Millipore 07-622) bound to protein G beads (Thermo Fisher) for overnight. After immunoprecipitation, samples were reversely crosslinked in 65°C water bath, and DNA was extracted with QIAquick PCR purification kit (Qiagen).
RNA-Seq library preparation with KAPA Stranded mRNA-Seq Kit (Illumina® platform) and then sequenced using Illumina HiSeq 4000. The ChIP-Seq libraries were prepared using NEBNext® UltraTMII DNA (NEB E7645S) and then sequenced using Illumina HiSeq 2500.

treatment_protocol: CRISPR/Cas9 system was used to establish the knock-out EZH2 SKOV3 cells

value: Human epithelial ovarian cancer cell

value: wild type


title: Klox_t13_bm

tag: condition

value: K. oxytoca + S. aureus t13595 co-culture, exponential phase

tag: collection date

tag: reference genome name

tag: eference genome


title: sSKOV3-3_ChIP-Seq

source_name: SKOV3_wild type_ChIP-seq

tag: cell line

value: H3K27me3 antibody (Millipore 07-622)


title: Klox_t13_as


title: Klox_t13_am


title: Parental-DOX (+)_CHIR_rep2

source_name: CHIR-treated Parental-DOX (+) cells

tag: cell type

value: CHIR condition


title: Aorta-M-CR

description: Single-Cell RNA

tag: Stage

value: O-CR

tag: tissue


title: NS578_2T1_TyRPB9_HAT2KD_0h_Input_2

description:
CpB_ws1_ss1_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Parental-DOX (+)_rep3


title: NS579_2T1_TyRPB9_HAT2KD_24h_Input_2

description:
CpB_ws1_ss1_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Parental-DOX (+)_CHIR_rep3


title: NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS580_2T1_TyRPB9_HAT2KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS575_2T1_TyRPB9_HAT2KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: monoclonal, purified BB2 mouse antibody; purified from hybridoma cells (Bastin et al. 1996)


title: Parental-DOX (+)_CHIR_rep1


title: sSKOV3-2_input


title: Klox_t11_bs

value: K. oxytoca + S. aureus t111 co-culture, stationary phase


title: NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS579_2T1_TyRPB9_HAT2KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS574_2T1_TyRPB9_HAT2KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Parental-DOX (+)_rep2

value: TF condition


title: Klox_t11_bm

value: K. oxytoca + S. aureus t111 co-culture, exponential phase


title: sSKOV3-2_ChIP-Seq


title: Parental-DOX (+)_rep1


title: sSKOV3-1_input


title: Klox_t11_as


title: NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS578_2T1_TyRPB9_HAT2KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS573_2T1_TyRPB9_HAT2KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS572_2T1_TyRPB9_HAT1KD_48h_Input_2

description:
CpB_ws1_ss1_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

source_name: T. brucei 2T1_HAT1KD_TyRPB9 bloodstream form


title: sSKOV3-1_ChIP-Seq


title: Klox_t11_am


title: NS571_2T1_TyRPB9_HAT1KD_24h_Input_2

description:
CpB_ws1_ss1_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: ID3_DP

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Tsuzuki-ku

institute: Shiseido

description: Gene expression of DP isolated from ID3

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100-Jul 11 and Grid: 028004_D_F_20150330) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature 'Non-uniform outliers', 'Population outliers' and 'Not positive and significant' were excluded. Normalized signal intensities were lcalculated by Gene spring 13.0.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Isogen (Nippon Gene, Toyama) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The dermal sheath cup, dermal papilla and upper dermal sheath were isolated from 3 individuals.

value: hair follicle


title: ID2_DP

description: Gene expression of DP isolated from ID2


title: ID3_DSC

description: Gene expression of DSC isolated from ID3


title: s1B11H-3_input


title: NS570_2T1_TyRPB9_HAT1KD_0h_Input_2

description:
CpB_ws1_ss1_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: ID1_DP

description: Gene expression of DP isolated from ID1


title: ID2_DSC

description: Gene expression of DSC isolated from ID2


title: s1B11H-2_input


title: Klox_bM

value: K. oxytoca monoculture, exponential phase


title: NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS572_2T1_TyRPB9_HAT1KD_48h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS569_2T1_TyRPB9_HAT1KD_48h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: s1B11H-2_ChIP-Seq


title: ID2_UDS

description: Gene expression of UDS isolated from ID2


title: Klox_aS

value: K. oxytoca monoculture, stationary phase


title: ID1_UDS

description: Gene expression of UDS isolated from ID1


title: s1B11H-1_input


title: ID1_DSC

description: Gene expression of DSC isolated from ID1


title: mix_Ko

description:
agar
Processed_data_rpkm_Biofilm_Klox.txt
Processed_data_rpkm_Biofilm_Klox.txt

value: K. oxytoca co-culture in biofilm


title: Klox_aM

description:
liquid culture
Processed_data_rpkm_Klox.txt
Processed_data_rpkm_Klox.txt


title: NS523_HAT2_KD_TyRPB9_48h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Klox_bS


title: s1B11H-1_ChIP-Seq


title: Ko

value: K. oxytoca monoculture in biofilm


title: s1B11H-3_ChIP-Seq


title: NS521_HAT2_KD_TyRPB9_0h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS571_2T1_TyRPB9_HAT1KD_24h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS568_2T1_TyRPB9_HAT1KD_24h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Bathu_t13_bS

description:
liquid culture
Processed_data_rpkm_Bathu.txt
Processed_data_rpkm_Bathu.txt

organism: Bacillus thuringiensis

value: B. thuringiensis + S. aureus t13595 co-culture, stationary phase


title: NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2

description:
CpB_ws1_ss1_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS570_2T1_TyRPB9_HAT1KD_0h_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS567_2T1_TyRPB9_HAT1KD_0h_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS520_HAT1_KD_TyRPB9_48h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: no treat (PDS, in vitro)

city: Wuhan

first: Xiaocheng

last: Weng

address: Bayi Road

department: School of Pharmaceutical Sciences

institute: Wuhan University

description:
no treat (PDS, in vitro)
HeLa_kethoxal_vs_no-treat.invitro.PDS.shape.out.txt

data_processing:
collapsed duplicated reads as in icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
trimmed 3' adaptor from reads using cutadapt
trimmed low quality bases using trimmomatic
mapping reads to transcriptome (mm10, hg38) by bowtie2 as in icSHAPE pipeline
calculate RPKM as icshape pipeline
calulate reactivity score for each base as in icshape pipeline
Genome_build: mm10,hg38
Supplementary_files_format_and_content: tab-delimited text files for shape reactivity files. Column 1-3 are: Refseq ID, transcript length, RPKM, followed by shape reactivity score of each nucleotide. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. Column 1-5: Refseq ID,  transcript length, unique mapped reads count, mulitple mapped reads count, RPKM.

source_name: HeLa

growth_protocol: mES cells (E14) were grown on gelatinized dishes in serum and LIF

extract_protocol:
Total RNA was isolated by Qiagen RNeasy plus mini kit, then use Dynabeads® mRNA Purification Kit to isolate mRNA from total RNA samples.
The library was prepared following icSHAPE protocol with slight changes (Nature2015, 519, 486)

treatment_protocol: N3-kethoxal was added into the medium of mES cells directly

value: HeLa

tag: agent

value: no treat (PDS, in vitro)


title: NS522_HAT2_KD_TyRPB9_24h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Bathu_t13_bM

value: B. thuringiensis + S. aureus t13595 co-culture, exponential phase

value: clinical isolate


title: kethxoal (in vitro)

description:
kethxoal (in vitro)
HeLa_kethoxal_vs_no-treat.invitro.shape.out.txt

value: kethxoal (in vitro)


title: Bathu_t13_aS


title: NS519_HAT1_KD_TyRPB9_24h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Bathu_t13_aM


title: Bathu_t11_bS

value: B. thuringiensis + S. aureus t111 co-culture, stationary phase


title: kethxoal (PDS, in vitro)

description:
kethxoal (PDS, in vitro)
HeLa_kethoxal_vs_no-treat.invitro.PDS.shape.out.txt

value: kethxoal (PDS, in vitro)


title: ID3_UDS

description: Gene expression of UDS isolated from ID3


title: HeLa_no-treat

data_processing:
Library strategy: N3-Kethoxal-seq
trimmed 3' adaptor from reads using cutadapt
trimmed low quality bases using trimmomatic
collapsed duplicated reads as in icSHAPE pipeline (https://github.com/qczhang/icSHAPE)
mapping reads to transcriptome (mm10, hg38) by bowtie2 as in icSHAPE pipeline
calculate RPKM as icshape pipeline
calulate reactivity score for each base as in icshape pipeline
Genome_build: mm10,hg38
Supplementary_files_format_and_content: tab-delimited text files for shape reactivity files. Column 1-3 are: Refseq ID, transcript length, RPKM, followed by shape reactivity score of each nucleotide. NULL means no confident score. Tab-delimited text files for read counts and rpkm files. Column 1-5: Refseq ID,  transcript length, unique mapped reads count, mulitple mapped reads count, RPKM.

tag: treatment

value: no treat


title: no treat (in vitro)

description:
no treat (in vitro)
HeLa_kethoxal_vs_no-treat.invitro.shape.out.txt

value: no treat (in vitro)


title: Bathu_t11_bM

value: B. thuringiensis + S. aureus t111 co-culture, exponential phase


title: HeLa_kethoxal

value: kethxoal


title: NS518_HAT1_KD_TyRPB9_0h_ChIP_1

description:
CpB_ws1_ss1_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: monoclonal, purified BB2 mouse antibody; purified from hybridoma cells (Bastin et al. 1996)


title: NS517_HAT2_KD_TyRPB9_48h_Input_1

description:
CpB_ws1_ss1_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS517_HAT2_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS523_HAT2_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS516_HAT2_KD_TyRPB9_24h_Input_1

description:
CpB_ws1_ss1_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS516_HAT2_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS522_HAT2_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: fit-1_Shoot_-Fe

city: Kunming

first: Gang

last: Liang

address: Xuefu Road 88, Wuhua district

institute: Xishuangbanna Tropical Botanical Garden,CAS

description: Gene expression after 5 days of -Fe

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2505C)

data_processing: Agilent Feature Extraction

organism: Oryza sativa

source_name: Shoot, -Fe

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Plants were grown in a growth chamber at 28°C/20°C (day/night) and 60 % to 70 % humidity, bulb type light with a photon density of ~300 μmol m-2 s-1 and a photoperiod of 14 h.

extract_protocol: RNA was prepared using the RNasey Mini Kit (Qiagen p/n 74104) following the manufacturer's recommendations.

treatment_protocol: Four-day-old seedlings germinated in wet paper were transferred to solution culture with 0.1 mM Fe(III)-EDTA for five days. Then seedlings were transferred to solution culture without Fe or with 0.1 mM Fe(III)-EDTA for five days. Roots and shoots were separated and used for RNA extraction.

tag: cultivar

value: Nipponbare

value: fit-1 mutant

value: Shoot

value: -Fe

tag: age


title: WT_Shoot_-Fe

description: Gene expression after 5 days of -Fe

value: WT


title: WT_Root_+Fe

description: Gene expression after 5 days of +Fe

source_name: Root, +Fe

value: Root

value: +Fe


title: WT_Root_-Fe

description: Gene expression after 5 days of -Fe

source_name: Root, -Fe


title: fit-1_Root_+Fe

description: Gene expression after 5 days of +Fe


title: WT_Shoot_+Fe

description: Gene expression after 5 days of +Fe

source_name: Shoot, +Fe


title: fit-1_Shoot_+Fe

description: Gene expression after 5 days of +Fe


title: fit-1_Root_-Fe

description: Gene expression after 5 days of -Fe


title: HeLa_kethoxal.PDS

value: HeLa

value: kethxoal (PDS)


title: HeLa_no-treat.PDS

value: no treat (PDS)


title: Bathu_t11_aS

value: B. thuringiensis + S. aureus t111 co-culture, stationary phase

value: clinical isolate


title: Bathu_t11_aM


title: Bathu_bM

value: B.thuringiensis monoculture, exponential phase


title: NS513_HAT1_KD_TyRPB9_24h_Input_1

description:
CpB_ws1_ss1_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS513_HAT1_KD_TyRPB9_24h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS519_HAT1_KD_TyRPB9_24h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: NS514_HAT1_KD_TyRPB9_48h_Input_1

description:
CpB_ws1_ss1_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS514_HAT1_KD_TyRPB9_48h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS520_HAT1_KD_TyRPB9_48h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Bathu_aS

value: B. thuringiensis monoculture, stationary phase


title: NS475_BF_2T1_TyRPB9_Input_2

description:
CpB_ws1_ss1_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

source_name: T. brucei 2T1_TyRPB9 bloodstream form


title: hCM_Sarrah gapmeR transfected_2

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

institute: Amsterdam UMC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-core
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: hCM_Sarrah gapmeR transfected

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: hCMs were transfected at a confluency of 70% and harvested 48h after transfection.

extract_protocol: All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment. cDNA synthesis and amplification was performed using the Ambion WT Expression Kit (Affymetrix).

value: hCM human cardiomyocytes (promocell)

tag: transfection

value: Sarrah gapmeR


title: hCM_Sarrah gapmeR transfected_3


title: Bathu_aM

data_processing:
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: 1280.1984_Staphylococcus_aureus GenBank: JAAFYP000000000.1             42 rc    DNA     linear   BCT 09-FEB-2020
Genome_build: 1428.155_Bacillus_thuringiensis Genbank: JAAFYT000000000.1
Genome_build: 571.31_Klebsiella_oxytoca GenBank: JAAFYN000000000.1             59 rc    DNA     linear   BCT 09-FEB-2020
Genome_build: 1280.1985_Staphylococcus_aureus GenBank: JAAFYO000000000.1             37 rc    DNA     linear   BCT 09-FEB-2020
Supplementary_files_format_and_content: Tab delimited text file

tag: origin


title: NS515_HAT2_KD_TyRPB9_0h_Input_1

description:
CpB_ws1_ss1_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS515_HAT2_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS521_HAT2_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

tag: genotype/variation


title: NS474_BF_2T1_TyRPB9_ChIP_2

description:
CpB_ws1_ss1_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS475_BF_2T1_TyRPB9_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS474_BF_2T1_TyRPB9_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: monoclonal, purified BB2 mouse antibody; purified from hybridoma cells (Bastin et al. 1996)


title: NS471_BF_2T1_TyRPB9_Input_1

description:
CpB_ws1_ss1_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: mix_Bt

description:
agar
Processed_data_rpkm_Biofilm_Bathu.txt
Processed_data_rpkm_Biofilm_Bathu.txt

value: B. thuringiensis co-culture in biofilm


title: hCM_Control gapmeR transfected_3

source_name: hCM_Control gapmeR transfected

value: Control gapmeR


title: hCM_Sarrah gapmeR transfected_1


title: Bt

value: B. thuringiensis monoculture in biofilm


title: Mycobacteriophage LadyBird lysogen

city: Pittsburgh

first: Katherine

middle: S

last: Wetzel

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.17 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.3.4.2
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.9
BAM format was converted to BED format using bedtools version 2.27.1
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.27.1
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: KT588442 (LadyBird)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycobacterium phage LadyBird

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

value: Mycobacterium smegmatis mc2155

tag: phage

value: Mycobacteriophage LadyBird


title: NS512_HAT1_KD_TyRPB9_0h_Input_1

description:
CpB_ws1_ss1_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS512_HAT1_KD_TyRPB9_0h_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS518_HAT1_KD_TyRPB9_0h_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

tag: time

tag: chip antibody


title: Bathu_bS

description:
liquid culture
Processed_data_rpkm_Bathu.txt
Processed_data_rpkm_Bathu.txt

extract_protocol:
Immediately after obtaining the cell pellet, 100 µl of killing buffer was added. Mechanical cell disruption was carried out with a Teflon vessel and a disruption ball filled with liquid N2 and pre-cooled in liquid N2 . The resulting cell powder was resuspended in 4 ml of lysis solution by repeated pipetting and transfer into 1 ml aliquots. Subsequently, one volume of acid phenol solution was added to cell lysate, and mixed on a tube shaker. Centrifugation and supernatant transfer into a new tube were followed by the addition of one volume acid phenol solution. This procedure was repeated twice; first by the addition of one volume chloroform/IAA and then by the addition of  Na-Acetate and isopropanol for overnight precipitation. RNA extraction was carried out by centrifugation at 4°C, where the pellet was washed twice with 80% ethanol, dry at room temperature, and dissolved in nuclease-free water. DNase Digestion and RNA clean-up (Qiagen, Hilden, Germany) were performed following manufacturer’s protocol. RNA concentration was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and RNA quality assessment was carried out by Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA) and the manufacturer’s recommended protocol.

tag: condition

tag: collection date

tag: reference genome name


title: hCM_Control gapmeR transfected_2

tag: cell type


title: hCM_Control gapmeR transfected_1


title: GFP_microglia_4

status: Public on Feb 21 2020

city: Stanford

first: Sean

middle: K

last: Wang

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
Smart-Seq2 libraries were constructed and sequenced by the Broad Institute Genomics Platform on an Illumina NextSeq 500
Reads were aligned using STAR and quantified using featureCounts
Analysis of differential gene expression was performed using DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: normalized abundance measurements

source_name: Retinal microglia

extract_protocol:
Retinas were dissected, dissociated with papain, and subjected to cell sorting. Microglia and non-microglia cells were isolated in Buffer TCL by antibody staining.
Libraries were constructed by the Broad Institute Genomics Platform using a modified Smart-Seq2 protocol

treatment_protocol: Mice were subretinally injected with either AAV8-GFP or AAV8-GFP + AAV8-TGFB1.

value: Retinal microglia

tag: strain

value: rd1 (FVB)

value: postnatal day 30


title: TGFB1_microglia_6

value: AAV8-GFP + AAV8-TGFB1


title: TGFB1_microglia_5


title: GFP_microglia_5


title: NS470_BF_2T1_TyRPB9_ChIP_1

description:
CpB_ws1_ss1_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws1_ss1_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS471_BF_2T1_TyRPB9_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS470_BF_2T1_TyRPB9_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: WT


title: GFP_microglia_6


title: GFP_microglia_8


title: TGFB1_microglia_8


title: GFP_Nonmicroglia_1

source_name: Retinal non-microglia cells

value: Retinal non-microglia cells


title: TGFB1_Nonmicroglia_2


title: GFP_microglia_7


title: TGFB1_microglia_7


title: GFP_Nonmicroglia_2


title: TGFB1_Nonmicroglia_1


title: CTR_7d_scATAC-seq

city: Utrecht

first: Cristian

last: Ruiz-Moreno

state: Utrecht

address: 25 Heidelberglaan

institute: Prinses Máxima Centrum

data_processing:
library strategy: scATAC-seq
CellRanger v1.1.0 was used to demultiplex NextSeq500 data.
CellRanger v1.1.0 was used for aligment and generation of filtered peaks.
Genome_build: mm10
Supplementary_files_format_and_content: scATAC-seq profiles are in bigWig format.

growth_protocol: LSK cells were purified from bone marrow of mice treated with 2 mg/kg Heme or equivalent vehicle dose (NaOH pH 7.4). Purification was done negative selection with MACS columns and subsequent sorting. Cells were frozen in 90% FCS and 10% DMSO until Nuclei preperation

extract_protocol:
Nuclei were isolated with a mix of detergents (Digitonin, Tween and NP40). Up-front tagmentation and single-nuclei partition into GEMs were performed using the Chromium Controller and 10x Genomics reagents.
Libraries were generated using the scATAC-seq reagent kit from 10x Genomics

value: NaOH (pH 7.4) i.p.

tag: tissue

value: Bone Marrow (BM)

tag: bm sampling/sorting time point

value: one week later

value: LSK cells


title: TGFB1_microglia_4

tag: treatment


title: GFP_microglia_2