title: Salmonella_YdcI_pH55_2

status: Public on Aug 15 2021

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: the reference genome ( Salmonella enterica Typhimurium LT2 = NC_003197.2 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: bacteria cells

growth_protocol: glycerol stocks of bacterial myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked bacterial cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.
ChIP-exo

treatment_protocol: For acidic stress (pH5.5), the overnight cultures were inoculated into the fresh 70 ml of M9 minimal medium at pH 5.5 (adjusted with HCl) in 500 ml flask and continued to culture at 37 degree with 250 r.p.m. to OD600=0.3±0.02. At the sampling point, the pH was measured to be 5.28±0.03. For acid stress with MES buffer, the culture medium was supplemented with 150 mM MES buffer to maintain the pH around 5.5 during the cell culture. The overnight cultures were inoculated into the fresh 70 ml of M9 minimal medium with MES buffer at pH 5.5 (adjusted with HCl) in 500 ml flask and continued to culture at 37 degree with 250 r.p.m. to OD600=0.3±0.02.

tag: myc-tagging

value: YdcI myc-tagging cells

value: ph55  (M9 medium was not supplemented with MES buffer to maintain the pH around 5.5 during cell culture)

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: CBL-RUNX1mut1Ly6G

status: Public on Aug 16 2021

type: SRA

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

library_source: transcriptomic

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.0)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

molecule: total RNA

organism: Mus musculus

extract_protocol:
Bone marrow cells were harvested from individual mice. HSCPs were purified using EasySep Mice CD117 positive selection kit and mutant clone was FACS sorted. Ly6G+ mutant myeloid BM cells were FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: CBL/RUNX1 mutant

tag: cell type

value: BM Ly6G+ myeloid cells


title: WT2Ly6G

value: wild type


title: E811, Embryo

city: Berlin

first: Vera

last: van der Weijden

address: Ihnestraße 63-73

department: Department of Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Trim Galore! for adaptor clipping, removal of sequences shorter than 50 bp and low-quality end score of 30
FastUniq tool for removal of duplicates
Read mapping with Salmon against the roe deer transcriptome
Count table filtering with CPM cut-off of 3.0 and sample cut-off of 5
Differential gene expression with ImpulseDE2
Genome_build: De novo assembled roe deer transcriptome
Supplementary_files_format_and_content: TPM_Embryos.xlsx

organism: Capreolus capreolus

source_name: Embryo

extract_protocol:
Qiagen AllPrep DNA/RNA Micro Kit
Clonetech pico-input mammalian total RNA kit

tag: number of embryonic cells

tag: developmental stage

value: Pre-elongation


title: E801, Embryo

value: Elongation


title: E98, Embryo

value: Early blastocyst


title: siTRPS1_1_APC1_ChIPSeq

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

library_source: genomic

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%.
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage.

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF-7 cells

extract_protocol:
For ChIP-seq, the crosslinked protein-DNA complex was extracted from the sonicated nuclei and isolated with antibody. For Repli-seq, EdU incorporated nascent DNA was sonicated and enriched with streptavidin magnetic beads. For extrachromosomal DNA sequencing, extrachromosomal DNA was purified from the nuclei treated with ATP-dependent exonuclease to remove linear genomic DNA.
Enriched DNA for ChIP-seq, Repli-seq or extrachromosomal DNA sequencing was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Sequencing adaptors were ligated to the DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by Qubit 2.0 and subjected to HiSeq X Ten or HiSeq 2500 sequencing according to the manufacturer’s instructions.

tag: cell line

value: Breast cancer cells

tag: antibodies

value: APC1 (ProteinTech, 21748-1-AP)


title: E991, Embryo

value: Early diapause


title: Salmonella_YdcI_MES5_2

country: USA

institute: UCSD

tag: treatment

value: MES5 (M9 medium was supplemented with MES buffer to maintain the pH around 5.5 during cell culture)


title: siNS_CDC16_ChIPSeq

value: siNS


title: WT_S1

city: Caen

first: Francois

last: Gravey

state: Normandy

address: Esplanade de la paix

department: Microbiology

country: France

institute: Normandy Université

data_processing:
fastqc
STAR alingment
Htseq
EdgeR package
Genome_build: S. lugdunensis reference genome: N920143 NC_017353.1
Supplementary_files_format_and_content: Count tables

organism: Staphylococcus lugdunensis

source_name: Bacteria

growth_protocol: 37°C - Aerobic - Brain Heart Infusion agar

extract_protocol: Direct-zol RNA miniprep kit

treatment_protocol: Wild type strain versus complete deltion of agrA gene in S. lugdunensis

value: Wild Type


title: BM1S1

type: RNA

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Serum sample of patient with oropharyngeal cancer treated with radiochemotherapy.

data_processing: The reference miRNA for normalization was selected using the NormiRazor. Based on the assumption that no single miRNA is suitable as a reference in serum miRNA qPCR profiling experiments30, we found that the most stable reference was the average expression level of two miRNAs (miR-142-5p and miR-23b-3p). Differentially expressed miRNAs were shortlisted on the basis of univariate, Benjamini-Hochberg adjusted, p values. Then, the expression levels of selected miRNAs were validated using the miRCURY LNA miRNA Custom PCR Panels (QIAGEN, Hilden, Germany). Selection of miRNAs for this part of the study was based on three criteria: expression in at least two thirds of samples, fold change greater than 1.5 or smaller than 0.67 and Benjamini-Hochberg adjusted p values <0.25. The normalization was performed using the formula ∆Ct = Ct(reference) - Ct(miRNA of interest), which provides a higher value for higher miRNA expression, facilitating its use and interpretation as a biomarker. Quantitative Real-Time PCR (qPCR) was performed in duplicates using the miRCURY LNA SYBR Green system (QIAGEN, Hilden, Germany) in a 96-well format. Undetectable expression (negative result) was reported if expression was not detected >37 PCR cycles. UniSp2, UniSp4, and UniSp5 were used as RNA isolation spike-in controls and UniSp6 was used as cDNA synthesis spike-in control.

label: miRCURY LNA SYBR Green

source_name: serum

label_protocol: cDNA synthesis was performed using miRCURY LNA RT Kit (QIAGEN, Hilden, Germany). We used real-time PCR arrays with locked nucleic acid-containing primers (miRCURY LNA miRNA miRNome PCR Panels; QIAGEN, Hilden, Germany) for serum profiling

extract_protocol: total RNA was isolated from 200 μL serum samples using miRCURY RNA Isolation kit (QIAGEN, Hilden, Germany)

tag: cohort

value: Discovery

tag: xerostomia

value: No

tag: time point

value: Prior to RT


title: E782, Embryo


title: Salmonella_YdcI_MES5_4

value: YdcI myc-tagging cells


title: Salmonella_YdcI_MES5_3

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: LG1S1


title: Salmonella_YdcI_MES5_1


title: E881, Embryo


title: E781, Embryo


title: E721, Embryo


title: E741, Embryo


title: Salmonella_YdcI_pH55_1

value: ph55  (M9 medium was not supplemented with MES buffer to maintain the pH around 5.5 during cell culture)


title: E722, Embryo

value: Late diapause


title: E591, Embryo


title: E691, Embryo


title: E631, Embryo


title: E501, Embryo


title: E382, Embryo


title: E381, Embryo


title: E301, Embryo

value: Early


title: E472, Embryo


title: E291, Embryo

value: Mid diapause


title: E511, Embryo


title: E231, Embryo


title: E491, Embryo


title: E2221, Embryo

value: Pre-elongation


title: E2222, Embryo


title: E212, Embryo


title: E2091, Embryo


title: E2181, Embryo

value: Elongation


title: E2011, Embryo


title: E2191, Embryo


title: E321, Embryo


title: E2251, Embryo


title: E2031, Embryo


title: E2092, Embryo


title: E2182, Embryo


title: E281, Embryo


title: E2032, Embryo


title: E632, Embryo


title: E1931, Embryo


title: E2012, Embryo


title: E2131, Embryo


title: E1932, Embryo


title: E1922, Embryo


title: E1912, Embryo


title: E1901, Embryo


title: E1921, Embryo


title: E1832, Embryo


title: E1822, Embryo


title: E1902, Embryo


title: E1861, Embryo


title: E1821, Embryo


title: E1871, Embryo


title: E1872, Embryo


title: E1721, Embryo


title: E1591, Embryo


title: E1722, Embryo


title: E1681, Embryo


title: E1911, Embryo


title: E1941, Embryo


title: E1421, Embryo


title: E1321, Embryo


title: E1322, Embryo


title: E1371, Embryo


title: E131, Embryo

value: Early blastocyst


title: E1402, Embryo


title: E1831, Embryo


title: E128, Embryo


title: E1401, Embryo


title: E181, Embryo


title: E1281, Embryo


title: E1422, Embryo


title: E1182, Embryo


title: E1192, Embryo


title: E1191, Embryo


title: E1141, Embryo


title: E1311, Embryo


title: E1041, Embryo


title: E1082, Embryo


title: E102, Embryo


title: E1181, Embryo


title: E1142, Embryo


title: E106, Embryo


title: RJ17_386, LE

data_processing:
Trim Galore! for adaptor clipping, removal of sequences shorter than 50 bp and low-quality end score of 30
FastUniq tool for removal of duplicates
Read mapping with Salmon against the roe deer transcriptome
Count table filtering with CPM cut-off of 3.0 and sample cut-off of 5
Differential gene expression with ImpulseDE2
Genome_build: De novo assembled roe deer transcriptome
Supplementary_files_format_and_content: TPM_LE.xlsx file containing TPM averages

source_name: Endometrial luminal epithelium

extract_protocol:
Qiagen AllPrep DNA/RNA Micro Kit
Smart-seq2 library preparation protocol


title: RJ17_392, LE


title: RJ17_385, LE


title: E1081, Embryo


title: E1091, Embryo


title: LT2_Fur_1

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build:  Reference genomes (E.coli EDL933 =  AE005174.2 / Klebsiella pneumoniae MGH78578 = CP000647.1 / Salmonella enterica Typhimurium LT2 = NC_003197.2 / E.coli SMS-3-5 = NC_010498.1 / Shigella flexneri 2a. 2457T = AE014073.1 / E.coli  UMN026 = CU928163.2 / Yersina pseudotuberculos IP32953 = NZ_CP009712.1 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Salmonella enterica

treatment_protocol: For iron-replete condition, M9 minimal media was supplemented with 0.1 mM FeCl2 ; for iron-depleted condition, M9 minimal media was supplemented with 0.2 mM 2,2’-dipyridyl at early-log phase and continue to culture at 37 oC for additional 2h with vigorous agitation; for regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

tag: strain

value: Typhimurium LT2

value: Fur myc-tagging cells


title: LT2_Fur_2


title: RJ17_397, LE


title: RJ17_383, LE


title: RJ17_382, LE


title: E1231, Embryo

value: Early diapause


title: E1101, Embryo


title: CD4_A2V_aPD1_4 [159_39]

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Reads were aligned to mouse genome build mm10 using HISAT2 (2.1.0) aligner and summarized to gene level with htseq (0.9.1).
Raw counts per gene were calculated with featureCounts, v1.4.4.
Sample counts were normalized with TMM method (edgeR package 3.28.1) and log2 transformed with voom (limma package 3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID.

source_name: CD4 from A2V+ aPD1 treated KPM tumor

growth_protocol: Cell isolation and growth protocol: KPM tumors were isolated from lungs, dissociated with the Tumor dissociation kit (130-096-730, Miltenyi), filtered through a 70um filter and stained with fluorochrome labelled antibodies for subset sorting by FACS. Sorted cells were harvested in Qiazol.

extract_protocol:
RNA was isolated using RNeasy plus mini (Qiagen) following manufacturer’s instructions. Isolated RNA sample quality was assessed by HS Total RNA 15nt on Fragment Analyzer (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
Library construction is performed based on manufacturer’s recommendation for SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input (Takara Bio USA Inc., California, USA). Final library size was about 300bp with an insert size of about 180bp
Sequencing protocol: Illumina® 8-nt unique dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq 6000(Illumina, California, USA) with a read length configuration of 150 Paired-End targeting150 M PE sequences per sample (75M in each direction).

treatment_protocol: KPM NSCLC tumor bearing mice were treated from week 15 post-tumor induction weekly for 4 weeks with 10mg/kg anti-PD1 (RMP1-14, Rat IgG2a, Bioxcell), 20mg/kg anti-VEGFA/ANGPT2 bispecific antibody (Roche) or 10mg/kg 2A3 (Rat IgG2a, Bioxcell) and 20mg/kg MOPC21 (mouse IgG1, Roche) isotype control antibodies diluted in PBS. Treatments were administered intraperitoneally.

value: KrasLSL-G12D/+; p53fl/fl;Msh2-/-

tag: Sex

value: f

tag: facs sort

tag: transgene

tag: group

tag: replicate


title: total_A2V_aPD1_4 [159_40]

source_name: Total viable cells from A2V + aPD1 treated KPM tumor

value: Single cells, DAPI-

value: total


title: E103, Embryo


title: AM_A2V_aPD1_4 [159_38]

source_name: T-AMs from A2V + aPD1 treated KPM tumor

value: AM


title: RJ17_381, LE


title: BMDM_A2V_aPD1_4 [159_37]

source_name: BM-TAMs from A2V + aPD1 treated KPM tumor

value: BMDM


title: total_A2V_aPD1_3 [159_36]

value: m


title: RJ17_374, LE


title: RJ17_378, LE


title: AM_A2V_aPD1_3 [159_34]


title: RJ17_359, LE


title: RJ17_356, LE


title: CD4_A2V_aPD1_3 [159_35]


title: RJ17_375, LE


title: CD4_A2V_aPD1_2 [159_31]


title: total_A2V_aPD1_2 [159_32]


title: RJ17_354, LE


title: AM_A2V_aPD1_2 [159_30]


title: BMDM_A2V_aPD1_3 [159_33]


title: RJ17_353, LE


title: RJ17_384, LE


title: BMDM_A2V_aPD1_2 [159_29]


title: RJ17_358, LE


title: RJ17_373, LE


title: CD4_A2V_aPD1_1 [159_27]


title: RJ17_346, LE


title: total_A2V_3 [159_24]

source_name: Total viable cells from A2V treated KPM tumor


title: BMDM_A2V_aPD1_1 [159_25]


title: RJ17_341, LE


title: RJ17_340, LE


title: AM_A2V_aPD1_1 [159_26]


title: BMDM_A2V_3 [159_21]

source_name: BM-TAMs from A2V treated KPM tumor


title: E401, Embryo


title: total_A2V_2 [159_20]


title: RJ17_345, LE


title: RJ17_337, LE


title: CD4_A2V_2 [159_19]

source_name: CD4 from A2V treated KPM tumor


title: RJ17_351, LE


title: AM_A2V_3 [159_22]

source_name: T-AMs from A2V treated KPM tumor


title: AM_A2V_1 [159_14]


title: SA.no1

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

description: mRNA-seq

data_processing:
Transcript quantification using Salmon.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: SA.vs.WT.salmon.GeneTPM.combined.txt: Tab-delimited text file includes transcript per million values.

source_name: Treg

growth_protocol: Spleen naïve CD4 T cells were isolated and induced to differentiate to Treg cells.

extract_protocol:
RNA was extracted using miRNeasy mini kit from Qiagen.
mRNA-seq library preparation protocol.

tag: genotype

value: Treg


title: CD4_A2V_3 [159_23]


title: RJ17_333, LE


title: WT.no3

description: mRNA-seq

value: WT


title: total_A2V_1 [159_16]


title: RJ17_338, LE

value: Late diapause


title: SA.no3

description: mRNA-seq


title: RJ17_328, LE


title: AM_A2V_2 [159_18]


title: RJ17_339, LE


title: CD4_IgG_3 [159_11]

source_name: CD4 from IgG treated KPM tumor

value: IgG


title: AM_IgG_3 [159_10]

source_name: T-AMs from IgG treated KPM tumor


title: SA.no2

description: mRNA-seq


title: WT.no2

description: mRNA-seq


title: RJ17_327, LE

value: Mid diapause


title: BMDM_A2V_1 [159_13]


title: CD4_IgG_2 [159_07]


title: total_IgG_3 [159_12]

source_name: Total viable cells from IgG treated KPM tumor


title: BMDM_A2V_2 [159_17]


title: BMDM_IgG_3 [159_09]

source_name: BM-TAMs from IgG treated KPM tumor


title: RJ17_330, LE

value: Pre-elongation


title: P10A-P10B_R393_L7

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Demultiplex each lane of sequencing using internal barcodes (nucleotides 1-6) & extract nuclotides 31-53 as the shRNA within the backone vector
Please see README.txt file for sample-barcode associations
Collapse reads to unique "tags" along with count of ocurrences of each tag in full file -- in-house software
Align tags to shRNA library using bwa 0.5.9, -n 4, -l 90, -k 4
Summarise number of reads mapping to each target, weighted by ocurrences of each tag - in-house code
Discard off-target reads (wrong pool or unmapped) and scale counts to maximum total reads aligned across all samples for that pool
Genome_build: MISSION Lentiplex Human Pooled shRNA library sequences (Sigma-Aldrich Cat. SHPH01)
Supplementary_files_format_and_content: _rawcounts.txt: tab delimited text file containing un-normalised counts of reads aligning to each feature

source_name: H23 cells

extract_protocol:
Genomic DNA was extracted and shRNA inserts were retrieved by PCR amplification
PCR primers contained Indexes and adaptors for deep sequencing: P5_Illuseq, P7 and barcodes.

treatment_protocol:
H23 cells were infected the whole-genome shRNA library, MISSION Lentiplex Pooled shRNA library from Sigma (SHPH01). The library was divided in 10 pools (treated individually) and the infection was done in triplicate.
Selected cells were treated with vehicle control, MEK inhibitor (Trametinib 1.5nM), IGF1R inhibitor (1mM Linsitinib) or the combination of both for 6 days. One fraction of cells was frozen at time 0 (before drug treatment).

tag: library pool

value: mixed  (non-demultiplexed)


title: P9A-P9B_R393_L6


title: total_IgG_1 [159_04]

tag: cell type


title: WT.no1

description: mRNA-seq


title: RJ17_319, LE

tag: number of embryonic cells


title: RJ17_323, LE

tag: developmental stage


title: AM_IgG_1 [159_02]


title: P8A-P8B_R393_L4


title: RJ17_325, LE


title: BMDM_IgG_2 [159_05]


title: RJ17_324, LE


title: BMDM_IgG_1 [159_01]


title: RJ17_314, LE


title: AM_IgG_2 [159_06]


title: P6C-P7C_R393_L2


title: total_IgG_2 [159_08]


title: P7A-P7B_R393_L3


title: CD4_IgG_1 [159_03]


title: RJ17_317, LE


title: P8C-P9C_R393_L5


title: RJ17_313, LE


title: Yersina_Fur_1

organism: Yersinia pseudotuberculosis

source_name: bacteria cells

tag: myc-tagging

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: P5A-P5B_R388_L7

tag: treatment


title: RJ17_311, LE


title: P6A-P6B_R393_L1


title: HCGWI_T2_rep17

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. We used the Bioconductor/R package DEXSeq to count individual exons and compare expression of exons. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 10 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Genome_build: GRCh38, release 86
Supplementary_files_format_and_content: tab delimited text files containing genes raw count
Supplementary_files_format_and_content: HISAT2_forDS.csv: raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 10 in all samples in at least one group
Supplementary_files_format_and_content: norm_counts_HISAT2.csv:normalized counts; HISAT2_forDS.csv: raw counts, genes selected for differential expression analysis

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: condition

value: Healthy Control

value: Peripheral blood mononuclear cell (PBMC)


title: HCGWI_T2_rep20


title: HCGWI_T2_rep18


title: HCGWI_T2_rep19


title: HCGWI_T2_rep16


title: P4C-P5C_R388_L6


title: P4A-P4B_R388_L5


title: RJ17_308, LE


title: Yersina_Fur_2

value: Fur myc-tagging cells


title: HCGWI_T2_rep15


title: HCGWI_T2_rep12


title: RJ17_300, LE


title: HCGWI_T2_rep13


title: RJ17_307, LE


title: HCGWI_T2_rep7


title: P2A-P2B_R398_L1


title: HCGWI_T2_rep9


title: HCGWI_T2_rep14


title: HCGWI_T2_rep5


title: P2C-P3C_R398_L2


title: P1B-P1C_R395_L8


title: HCGWI_T2_rep3


title: HCGWI_T2_rep6


title: P3A-P3B_R398_L3


title: HCGWI_T2_rep2


title: RJ17_264, LE


title: HCGWI_T2_rep11


title: RJ17_295, LE

value: Early diapause


title: HCGWI_T2_rep8


title: VraR_1

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( NC_010079 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Staphylococcus aureus

growth_protocol: glycerol stocks of bacterial myc-tagged strains were inoculated into RPMI1640 + 10% LB. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with custom monoclonal antibodies.
The experiment was performed following the procedures:  to identify each TF binding maps in vivo, we isolated the DNA bound to each TF from formaldehyde cross-linked bacterial cells by chromatin immunoprecipitation (ChIP) with the custom monoclonal antibodies (GenScript, NJ, USA) that specifically recognizes TFs of the interest, and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.

value: strain

value: custom anti-VraR monoclonal antibody (GenScript, NJ, USA)


title: VraR_2


title: HCGWI_T2_rep1


title: P1A_R369_L1


title: HCGWI_T1_rep20


title: HCGWI_T1_rep19


title: HCGWI_T2_rep4


title: RJ17_285, LE


title: HCGWI_T2_rep10


title: RJ17_267, LE


title: RJ17_263, LE


title: HCGWI_T1_rep15


title: SigS_M4_2

value: custom anti-SigS monoclonal antibody (GenScript, NJ, USA)


title: HCGWI_T1_rep16


title: RJ17_282, LE


title: HCGWI_T1_rep14


title: RJ17_261, LE


title: HCGWI_T1_rep18


title: SigS_M4_1


title: HCGWI_T1_rep13


title: SigS_M3_2


title: HCGWI_T1_rep17


title: HCGWI_T1_rep12


title: HCGWI_T1_rep11


title: HCGWI_T1_rep10


title: RJ17_253, LE


title: SigS_M3_1


title: HCGWI_T1_rep7


title: HCGWI_T1_rep9


title: HCGWI_T1_rep8


title: RB16_9w, LE

value: Early blastocyst


title: SigS_M2_1


title: SigS_M1_2


title: RJ17_243, LE


title: HCGWI_T1_rep6


title: HCGWI_T1_rep4


title: RJ17_242, LE


title: RJ17_259, LE


title: HCGWI_T1_rep5


title: HCGWI_T1_rep2


title: SigS_M1_1


title: HCGWI_T1_rep3


title: RB16_61g, LE


title: HCGWI_T1_rep1


title: RB16_238or, LE


title: RB16_211w, LE


title: HCGWI_T0_rep19


title: HCGWI_T0_rep18


title: SigS_M2_2


title: HCGWI_T0_rep16


title: RB16_10w, LE


title: HCGWI_T0_rep15


title: HCGWI_T0_rep14


title: HCGWI_T0_rep13


title: kidney, poly(I:C) 48h rep2

city: nanjing

first: ruixia

last: wang

address: xikang road

institute: hohai university

data_processing:
Illumina through the vendor-supported protocol
Agilent Bioanalyzer 2100 (Agilent) and RNA NanoDrop ND-2000 (Agilent, Palo Alto, CA, USA) with an RNA Integrity Number (RIN) value > 7.0 were used to evaluate the integrity, concentration, and quality of total RNA samples. Three replicate samples were selected at each time point for a total of nine samples (To0a, To0b, To0c, To12a, To12b, To12c, To48a, To48b, and To48c). Equal quantities of total RNA from the nine tissues were pooled to generate a sample for library preparation. The cleaved RNA fragments were then reverse transcribed to create the final cDNA library. Following the protocol of the mRNA Seq sample preparation kit (Illumina, San Diego, CA, USA) , the paired-end library inserts averaged 300 bp (±50 bp). Finally, paired-end sequencing was performed on Illumina through the vendor-supported protocol.
De novo transcriptome assembly was carried out with Trinity 2.4.0 (https://github.com/trinityrnaseq/trinityrnaseq/releases) (Grabherr et al. 2011). Based on the sequence content obtained from all individuals, adaptor sequences were filtered out, low-quality and poorly informative readings were trimmed, and clean readings were assembled from the beginning up to the final contigs
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Takifugu obscurus

source_name: kidney

extract_protocol:
Total RNA was extracted from kidney samples by using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

tag: tissue

value: kidney

tag: age

value: three months old


title: HCGWI_T0_rep12

tag: time point


title: HCGWI_T0_rep10


title: kidney, poly(I:C) 48h rep3


title: kidney, poly(I:C) 48h rep1


title: kidney, poly(I:C) 12h rep3


title: HCGWI_T0_rep8


title: HCGWI_T0_rep6


title: HCGWI_T0_rep17


title: kidney, poly(I:C) 12h rep2


title: HCGWI_T0_rep4


title: HCGWI_T0_rep7


title: HCGWI_T0_rep5


title: HCGWI_T0_rep3


title: GWI_T2_rep20

value: GWI


title: kidney, poly(I:C) 0h rep1

value: control


title: GWI_T2_rep19


title: HCGWI_T0_rep11


title: GWI_T2_rep18


title: HCGWI_T0_rep1


title: GWI_T2_rep14


title: GWI_T2_rep17


title: kidney, poly(I:C) 0h rep3


title: kidney, poly(I:C) 12h rep1


title: GWI_T2_rep10


title: GWI_T2_rep16


title: HCGWI_T0_rep9


title: GWI_T2_rep15


title: GWI_T2_rep13


title: GWI_T2_rep11


title: P3F-3_FOXO1_CUT&Tag

city: Paris

first: Vanessa

last: Ribes

address: 15 rue Helene Brion

institute: Institut Jacques Monod

description:
CUT&Tag FOXO1 on human foreskin fibroblasts expressing P3F-Line3
201230_X591_FCHF2YLCCX2_L4_CF2-FOXO1_q10_b1_s0_CPM

data_processing:
hg19
CUT&Tag: Trimmomatic (v0.39), BBmap clumpify (v38.87), Bowtie2 (v2.4.1) on hg19 reference genome
CUT&Tag: Peaks were called using SEACR (v1.3) with the parameters: relaxed (threshold 0,000001)
RNAseq: 3' adapter trimming with Trimmomatic: 0.32 (Bolger et al 2014), mapping with bowtie 2.0.5 and Tophat 2.0.6 on NCBI hg38 or hg19 (specified in the SAMPLES section above)
RNAseq: Pairwise differential analysis of RNAseq data was performed using Cufflinks (Fasteris). Genes with a q-value <0.05 after Bengamini-Hochberg correction for multiple-testing were considered to be significant
Genome_build: hg19 or hg38 (specified in the SAMPLES section above)
Supplementary_files_format_and_content: For CUT&Tag, processed files are in bigWig format; for RNAseq, there is two matrix with RPKM for all samples and genes

source_name: human foreskin fibroblasts

growth_protocol: DMEM, 10% serum, non essential amino acids, penicillin/streptomycin

extract_protocol:
Extraction was performed as in Kaya-Okur et al, following the procedure described in “Bench top CUT&Tag V.2” available on protocols.io (Henikoff lab)
Libraries were prepared as in Kaya-Okur et al, following the procedure described in “Bench top CUT&Tag V.2” available on protocols.io (Henikoff lab)
CUT&Tag

tag: antibody

value: FOXO1 Cell Signaling #2880

value: Doxycycline for 48 hours


title: GWI_T2_rep9


title: P7F-3_FOXO1_CUT&Tag

description:
CUT&Tag FOXO1 on human foreskin fibroblasts expressing P7F-Line3
201230_X591_FCHF2YLCCX2_L4_CF7-FOXO1_q10_b1_s0_CPM


title: GWI_T2_rep8


title: P7F-2_FLAG_CUT&Tag

description:
CUT&Tag FLAG on human foreskin fibroblasts expressing P7F-Line2
201230_X591_FCHF2YLCCX2_L4_CF6-FLAG_q10_b1_s0_CPM

value: FLAG Merck F3165


title: HCGWI_T0_rep2


title: GWI_T2_rep12


title: HFF_FLAG_CUT&Tag

description:
CUT&Tag FLAG on human foreskin fibroblasts
201230_X591_FCHF2YLCCX2_L4_HFF-FLAG_q10_b1_s0_CPM


title: P7F-1_FLAG_CUT&Tag

description:
CUT&Tag FLAG on human foreskin fibroblasts expressing P7F-Line1
201230_X591_FCHF2YLCCX2_L4_CF5-FLAG_q10_b1_s0_CPM


title: kidney, poly(I:C) 0h rep2


title: GWI_T2_rep7


title: GWI_T2_rep4


title: P3F-2_FLAG_CUT&Tag

description:
CUT&Tag FLAG on human foreskin fibroblasts expressing P3F-Line2
201230_X591_FCHF2YLCCX2_L4_CF3-FLAG_q10_b1_s0_CPM


title: GWI_T2_rep2


title: GWI_T2_rep1


title: GWI_T2_rep3


title: GWI_T1_rep18


title: P7F-3_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P7F-Line3
210104_X578_FCHF35KCCX2_L1_CF7-H3K27ac_q10_b1_s0_CPM

value: H3K27ac Diagenode C15410196


title: GWI_T1_rep15


title: P7F-2_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P7F-Line2
210104_X578_FCHF35KCCX2_L1_CF6-H3K27ac_q10_b1_s0_CPM


title: GWI_T1_rep17


title: P7F-1_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P7F-Line1
210104_X578_FCHF35KCCX2_L1_CF5-H3K27ac_q10_b1_s0_CPM


title: GWI_T1_rep10


title: P3F-1_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P3F-Line1
210104_X578_FCHF35KCCX2_L1_CF1-H3K27ac_q10_b1_s0_CPM


title: GWI_T1_rep7


title: P3F-2_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P3F-Line2
210104_X578_FCHF35KCCX2_L1_CF3-H3K27ac_q10_b1_s0_CPM


title: P3F-3_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts expressing P3F-Line3
210104_X578_FCHF35KCCX2_L1_CF2-H3K27ac_q10_b1_s0_CPM


title: GWI_T1_rep8


title: GWI_T2_rep5


title: GWI_T2_rep6


title: GWI_T1_rep5


title: GWI_T1_rep6


title: HFF-3_FOXO1_CUT&Tag

description:
CUT&Tag FOXO1 on human foreskin fibroblasts
201230_X591_FCHF2YLCCX2_L4_HFF-FOXO1_q10_b1_s0_CPM


title: GWI_T1_rep13


title: GWI_T1_rep3


title: GWI_T1_rep1


title: GWI_T0_rep20


title: P3F-1_FLAG_CUT&Tag

description:
CUT&Tag FLAG on human foreskin fibroblasts expressing P3F-Line1
201230_X591_FCHF2YLCCX2_L4_CF1-FLAG_q10_b1_s0_CPM


title: M45526 PDX707 MLL/AF4 KD

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Differential expression analysis using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file including raw counts for every gene and every sample, normalized values for each group, log2 fold change and p-value of differential expression

source_name: Patient derived xenograft acute leukemia cells

growth_protocol: PDX cells were injected into NSG mice

extract_protocol:
Qiagen-RNA Purification with DNAse I treatment
Three prime End sequencing using GenXPro-MACE-Seq technique (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-duplicate removal.
Massive Analysis of cDNA ends (MACE-Seq)

treatment_protocol: Mice were treated with 100 mg/kg tamoxifen 7 and 8 days after injection to induce recombination and shRNA expression

tag: translocation

value: MLL-AF4 KD


title: GWI_T1_rep16


title: GWI_T0_rep16


title: rcsA_2

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build:  the reference genome ( MG1655 =  NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli K-12

growth_protocol: glycerol stocks of E. coli myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.
ChIP-exo

treatment_protocol: To create oxidative stress, the overnight cultures were inoculated to an optical density 600 (OD600) = 0.01 into the fresh 70 ml of M9 minimal medium in a 500-ml flask supplemented with 250 μM paraquat (PQ) at OD600 = 0.3 ± 0.03 and incubated for 20 min with stirring.

tag: strain

value: RcsA myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: ZraR_1

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: glycerol stocks of bacterial myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with myc antibody.
The experiment was performed following the procedures:  to identify each TF binding maps in vivo, we isolated the DNA bound to each TF from formaldehyde cross-linked bacterial cells by chromatin immunoprecipitation (ChIP) with the myc monoclonal antibody (9E10, Santa Cruz Biotechnology) that specifically recognizes myc tag, and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.

value: ZraR myc-tagging cells


title: rcsA_1


title: GWI_T1_rep12

value: Peripheral blood mononuclear cell (PBMC)


title: GWI_T1_rep14


title: GWI_T0_rep18


title: M45528 PDX707 MLL/AF4 KD

value: Patient derived xenograft acute leukemia cells


title: HFF_H3K27ac_CUT&Tag

description:
CUT&Tag H3K27ac on human foreskin fibroblasts
210104_X578_FCHF35KCCX2_L1_HFF-H3K27ac_q10_b1_s0_CPM


title: GWI_T1_rep11


title: ZraR_2


title: puuR_1

value: PuuR myc-tagging cells


title: GWI_T0_rep13


title: M45410 PDX707 ctrl

value: Renilla KD


title: M45527 PDX707 MLL/AF4 KD


title: GWI_T0_rep19


title: narL_2

value: NarL myc-tagging cells


title: GWI_T1_rep4


title: M45409 PDX707 ctrl


title: GWI_T1_rep9


title: GWI_T0_rep17


title: M45411 PDX707 ctrl


title: GWI_T0_rep11


title: GWI_T1_rep2


title: Shigella_Fur_1

organism: Shigella flexneri

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked bacterial cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.
ChIP-exo

value: Fur myc-tagging cells


title: Klebsiella_Fur_1

organism: Klebsiella pneumoniae


title: GWI_T0_rep15


title: narL_1


title: MGH99_041914_bam

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

description: MGH Patient 99

data_processing:
summary read counts by featureCounts v1.5.1
Genome_build: hg19
Supplementary_files_format_and_content: csv of the read counts matrix generated by featureCounts

source_name: frozen or formalin-fixed tumor

extract_protocol:
RNA was purified from patients' frozen or formalin-fixed tumor specimens using the TRIzol protocol.  Illumina TruSeq RNA Sample PRE Immune Checkpoint Blockade Therapyp Kit (Cat#FC-122-1001) was used with 250 ng of total RNA for the construction of sequencing libraries.
RNA libraries were PRE Immune Checkpoint Blockade Therapypared for sequencing using standard Illumina protocols

tag: treatment state

value: ON

tag: timepoint (days)

tag: response immune checkpoint blockade therapy

value: NR

tag: age at the baseline

tag: batch

tag: tumor type

value: metastatic melanoma


title: MGH253_070616_bam

description: MGH Patient 253


title: puuR_2

tag: myc-tagging


title: MGH253_111214_bam

description: MGH Patient 253

value: PRE


title: Shigella_Fur_2

tag: chip-exo antibody


title: Klebsiella_Fur_2


title: Tus_2

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: E.coli genome (NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

value: Tus myc-tagging cells


title: MGH409_113015_bam

description: MGH Patient 409

value: R


title: GWI_T0_rep12

value: GWI

tag: cell type


title: GWI_T0_rep14

tag: condition


title: GWI_T0_rep10


title: MGH35_091015_bam

description: MGH Patient 35


title: ZCF8-MYC_IP_Rep3

city: Würzburg

first: Philipp

last: Reuter-Weissenberger

state: Bavaria

address: Josef-Schneider-Str.

institute: Institute of Molecular Infection Biology

data_processing:
Sequenced reads were aligned to the Candida albicans genome using Bowtie2 v2.3.5 with default parameters.
Duplicated and non-uniquely aligned reads were filtered out using Samtools v1.8.
BAM files were converted to BED files using BEDTools v2.29.2
Peak calling was performed using bPeaks v1.2 with parameters: T1: 2, T2: 1, T3, 1.8, T4: 0.9
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: *.txt are bed files generated from BAM files using BEDTools v2.29.2 with default parameters and contain a resolution of 1bp

organism: Candida albicans

source_name: yeast cells

growth_protocol: C. albicans cells were grown in standard YPD broth overnight at 30°C

extract_protocol:
Cell lysates were clarified from sonicated cells and Zcf8p-myc-DNA complexes were isolated with MYC antibody and Sepharose beads.
DNA libraries were prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® following the manufacturer's protocol.

tag: genotype/variation

value: wild-type reference strain

tag: chip tag

value: myc-tagged

value: Ms mAb Anti-Human c-myc (clone 9E10.3, Thermo Fisher Scientific)


title: GWI_T0_rep9


title: Tus_1

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: ZCF8-MYC-IP_Rep4


title: MGH27_070213_bam

description: MGH Patient 27


title: TopA_2

value: TopA myc-tagging cells


title: ZCF8-MYC_IP_Rep1


title: MGH27_032812_bam

description: MGH Patient 27


title: TopA_1


title: MGHIPIPD1001_070715_3_bam

description: MGH Patient IPIPD1001


title: MGHIPIPD1001_070715_2_bam

description: MGH Patient IPIPD1001


title: ZCF8-MYC_INPUT_Rep3


title: MGHIPIPD1001_070715_1_bam

description: MGH Patient IPIPD1001


title: GWI_T0_rep6

value: Peripheral blood mononuclear cell (PBMC)


title: ZCF8-MYC_INPUT_Rep4


title: StpA_2

value: StpA myc-tagging cells


title: Rob_2

value: Rob myc-tagging cells


title: StpA_1


title: ZCF8-MYC_INPUT_Rep1


title: Untagged_Control_IP_Rep2

value: untagged


title: GWI_T0_rep4


title: GWI_T0_rep5


title: Rob_1


title: ZCF8-MYC_INPUT_Rep2


title: ZCF8-MYC_IP_Rep2


title: MGHIPIPD1001_070215_1_bam

description: MGH Patient IPIPD1001


title: GWI_T0_rep3


title: GWI_T0_rep8


title: RdgC_2

value: RdgC myc-tagging cells


title: MGHIPIPD1001_092414_bam

description: MGH Patient IPIPD1001

value: ON


title: Untagged_Control_IP_Rep1


title: GWI_T0_rep1


title: GWI_T0_rep7


title: MGHIPIPD1001_041814_bam

description: MGH Patient IPIPD1001

value: NR


title: Untagged_Control_INPUT_Rep2


title: MGHIPIPD1001_070215_2_bam

description: MGH Patient IPIPD1001

value: metastatic melanoma


title: RdgC_1


title: KOA5

city: Peking

first: Zhengqin

last: Rong

address: Beiqing Road

institute: Basepedia

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: abdominal aorta

extract_protocol:
The abdominal aortas of 4 groups of mice were harvested and placed in liquid nitrogen immediately. Total RNA was extracted using TRIzol (Invitrogen, Life Technologies), labeled by a Quick Amp Labeling Kit, One-Color and purified by an RNasey Mini Kit (Qiagen). An Agilent Gene Expression Hybridization Kit (Agilent) was used for the hybridization of purified RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 6 months old

tag: genotype

value: Lysyl hydroxylase 1 knock out

tag: treatment group

value: AngII


title: AM14_CTRL_2

data_processing:
Library strategy: exome-seq
Reads were mapped against the mouse reference genome mm10 using BWA-MEM (GATK 4.1.4.1).
Duplicate reads were marked and base quality scores were recalibrated prior to variant calling.
Somatic SNVs and indels were subsequently identified using MuTect2 variant caller, with two control samples (ID: AM13 and AM14) treated as shared matching normals.
The identified variants were further annotated using Ensembl Variant Effect Predictor (VEP) and mutational load was computed with CallableLoci (GATK 4.1.4.1) to identify callable regions in each of the tumor-normal BAM files.
Genome_build: mm10
Supplementary_files_format_and_content: vcf file with output from MuTect2, vcf file with indels, vcf files with SNPs, vcf files annotated by VEP.

source_name: lung tumor

extract_protocol:
DNA extract protocol: Genomic DNA of KP and KPM tumors with DNeasy Blood & Tissue kit (69504, Qiagen) following manufacturer’s instructions and eluted it in 10mM Tris-Cl, 0.5mM EDTA, pH 9.0 (Buffer AE, Qiagen).
Exon capture was performed by Genewiz (Genewiz Germany GmbH, Leipzig) using Agilent SureSelect Mouse All Exon V1 Kit.
Sequencing protocol: Sequencing was was performed by Genewiz (Genewiz Germany GmbH, Leipzig) with Illummina HiSeq instrument, 2x150bp sequencing (~10 Gb per sample).

treatment_protocol: Cell isolation: Lung tumors were individually harvested, snap frozen on liquid nitrogen and stored at -80°C.

tag: strain background

tag: cre delivery

value: No

tag: transgene

value: KrasLSL-G12D/+; p53fl/fl; Msh2-/-

tag: group

value: CTRL

tag: mouse id

tag: tissue

value: lung tumor

tag: replicate


title: MGH530_FFPE_032417

description: MGH Patient 530

tag: treatment state

tag: timepoint (days)

tag: antibody

tag: response immune checkpoint blockade therapy

value: R

tag: age at the baseline

tag: batch

tag: tumor type


title: KOA3

tag: strain

tag: age


title: KOA2

tag: genotype

tag: treatment group


title: MGH530_FFPE_082916

description: MGH Patient 530

value: PRE


title: Untagged_Control_INPUT_Rep1

tag: genotype/variation

value: wild-type reference strain

tag: chip tag


title: MukB_1

tag: myc-tagging

value: MukB myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: GWI_T0_rep2

tag: condition

value: GWI

tag: time point

tag: cell type

value: Peripheral blood mononuclear cell (PBMC)


title: InfA_2

value: InfA myc-tagging cells


title: AM08_KPM_4

tag: strain background

tag: cre delivery

value: Yes

tag: transgene

tag: group

value: KPM

tag: mouse id

tag: tissue

tag: replicate


title: AM13_CTRL_1


title: MGHBI1_101415_bam

description: MGH Patient BI1

tag: treatment state

tag: timepoint (days)

tag: antibody

tag: response immune checkpoint blockade therapy

value: NR

tag: age at the baseline

tag: batch

tag: tumor type

value: metastatic melanoma


title: KOA1

tag: strain

tag: age

value: 6 months old

tag: genotype

value: Lysyl hydroxylase 1 knock out

tag: treatment group

value: AngII


title: AM07_KPM_3

tag: strain background

tag: cre delivery

value: KrasLSL-G12D/+; p53fl/fl; Msh2-/-


title: InfA_1

tag: myc-tagging

tag: chip-exo antibody


title: KO5

value: Saline


title: MGH200_FFPE_072716

description: MGH Patient 200

value: ON

value: R


title: AM06_KPM_2

tag: transgene

tag: group

tag: mouse id

tag: tissue

value: lung tumor


title: AM05_KPM_1

tag: replicate


title: HupB_1

value: HupB myc-tagging cells


title: MukB_2

value: MukB myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: HupA_2

value: HupA myc-tagging cells


title: MGH530_FFPE_091916

description: MGH Patient 530

tag: treatment state

tag: timepoint (days)

tag: antibody

tag: response immune checkpoint blockade therapy


title: KO2

tag: strain


title: KO4

tag: age


title: HFF-PCIG_6_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate6
Transient transfected cells_genes-fpkmsMatrix

data_processing:
hg38
CUT&Tag: Trimmomatic (v0.39), BBmap clumpify (v38.87), Bowtie2 (v2.4.1) on hg19 reference genome
CUT&Tag: Peaks were called using SEACR (v1.3) with the parameters: relaxed (threshold 0,000001)
RNAseq: 3' adapter trimming with Trimmomatic: 0.32 (Bolger et al 2014), mapping with bowtie 2.0.5 and Tophat 2.0.6 on NCBI hg38 or hg19 (specified in the SAMPLES section above)
RNAseq: Pairwise differential analysis of RNAseq data was performed using Cufflinks (Fasteris). Genes with a q-value <0.05 after Bengamini-Hochberg correction for multiple-testing were considered to be significant
Genome_build: hg19 or hg38 (specified in the SAMPLES section above)
Supplementary_files_format_and_content: For CUT&Tag, processed files are in bigWig format; for RNAseq, there is two matrix with RPKM for all samples and genes

extract_protocol:
RNAs were extracted using the NucleoSpin RNA kit (Macherey-Nagel) following manufacturer’s instructions
Libraries were prepared using Illumina TruSeq stranded mRNA kit
RNA-seq

tag: sample type


title: HupA_1


title: HupB_2


title: KO3

tag: genotype

tag: treatment group


title: AM03_KP_3

tag: strain background

tag: cre delivery

value: KrasLSL-G12D/+; p53f-/-

value: KP


title: HFF-PCIG_5_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate5
Transient transfected cells_genes-fpkmsMatrix


title: WTA5

value: Wild type


title: HFF-PCIG_3_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate3
Transient transfected cells_genes-fpkmsMatrix


title: AM04_KP_4

value: Yes


title: KO1


title: KOA4


title: HFF-PCIG_4_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate4
Transient transfected cells_genes-fpkmsMatrix


title: HFF-PCIG_2_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate2
Transient transfected cells_genes-fpkmsMatrix


title: H-NS_2

tag: myc-tagging

value: H-NS myc-tagging cells

tag: chip-exo antibody


title: GyrB_1

value: GyrB myc-tagging cells


title: MGH200_FFPE_031116

description: MGH Patient 200

value: PRE

tag: age at the baseline

tag: batch

tag: tumor type

value: metastatic melanoma


title: AM01_KP_1

tag: transgene

tag: group

tag: mouse id

tag: tissue

tag: replicate


title: WTA4

tag: strain

value: 6 months old

value: AngII


title: H-NS_1


title: HFF-Pax7_3_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax7-replicate3
Transient transfected cells_genes-fpkmsMatrix


title: WTA2

tag: age


title: HFF-Pax7_2_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax7-replicate2
Transient transfected cells_genes-fpkmsMatrix

tag: sample type


title: Neurofibroma_809 [Nf809]

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Paired-end fastq files were aligned to mm10 (mouse) genomes using HISAT2 v2.0.5
Raw counts were calculated using featureCounts v1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Nf1KO mouse tumor

growth_protocol: Mice raised in animal facility under standard conditions until a specific timepoint or tumor size limit reached.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the Illumina protocol (Nextera 817 XT DNA Sample Preparation Kit).

treatment_protocol: No drugs were administered to mice during these experiments.

tag: genotype/variation

tag: tumor stage

value: Neurofibroma tumor

value: Nf1fl/fl; DhhCre Neurofibroma


title: GyrB_2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.


title: AM02_KP_2

tag: strain background

value: lung tumor


title: GyrA_1

value: GyrA myc-tagging cells


title: Fis_2

value: Fis myc-tagging cells


title: Mir-155_KO_670 [MiRNC670]

source_name: miRR-155KONf1KO mouse tumor

value: Mir-155 KO


title: WTA1

tag: genotype

tag: treatment group


title: GyrA_2

tag: myc-tagging

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: WTA3


title: HFF-PCIG_1_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing PCIG-replicate1
Transient transfected cells_genes-fpkmsMatrix


title: Dps_1

value: Dps myc-tagging cells


title: HFF-Pax3_2_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax3-replicate2
Transient transfected cells_genes-fpkmsMatrix


title: Neurofibroma_827 [Nf827]


title: Neurofibroma_803 [Nf803]


title: HFF-Pax7_1_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax7-replicate1
Transient transfected cells_genes-fpkmsMatrix


title: Fis_1


title: HFF-Pax3_1_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax3-replicate1
Transient transfected cells_genes-fpkmsMatrix


title: putida_SigmaD_1

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( P. putida = NC_002947 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Pseudomonas putida

treatment_protocol: For iron-replete condition, M9 minimal media was supplemented with 0.1 mM FeCl2

value: SigmaD myc-tagging cells


title: Mir-155_KO_640 [MiRNC640]


title: WT4

value: Wild type

value: Saline


title: putida_Fur_1

value: Fur myc-tagging cells


title: Mir-155_KO_149 [MiRNC149]


title: Dps_2


title: HFF-Pax3_3_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing Pax3-replicate3
Transient transfected cells_genes-fpkmsMatrix


title: Wild-type_nigericin_Rep1

description: Total RNA with poly(A)+ selection.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.7.3a with parameters --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.11.2.
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.28.1.
Genome_build: Candida albicans build 21
Supplementary_files_format_and_content: *.counts.txt.txt: Tab-delimited text files include raw read counts for each sample. Each processed data file on the sample record represents the two read files (e.g., a104-1.fq.gz and a104-2.fq.gz) produced by paired-end sequencing.
Supplementary_files_format_and_content: *diff_genes.txt: Tab-delimited text files contain the mean of normalized counts, log2 fold change, log2 fold change standard error, p-value and adjusted p-value.

growth_protocol: C. albicans cells were starved for six hours at 30°C in minimal medium (YNB + glucose) lacking nitrogen source.

extract_protocol:
Total RNA was extracted using RiboPure™ RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by Novogene (Cambridge, UK) following standard operating procedures.

treatment_protocol: Prior to RNA preparation, nitrogen-starved cultures were treated with either 15 µg/ml nigericin or a mock control (Ethanol:DMSO) and incubated an additional 30 minutes at 30°C

value: Wild-type reference strain

tag: treatment

value: nigericin


title: HFF-P7F_1_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P7F-replicate1
Transient transfected cells_genes-fpkmsMatrix


title: Wild-type_control_Rep2

description: Total RNA with poly(A)+ selection.

value: no drug


title: WT3

value: 6 months old


title: WT2


title: BM sample, AA patient2

city: Hangzhou/Zhejiang Province

first: Liming

last: Yin

state: Zhejiang Province

address: 548 Binwen Road

department: Institute of hematology

institute: Zhejiang Chinese Medical University

data_processing:
The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: BM sample, AA patient2

extract_protocol:
BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation Ki according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics.
The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells

tag: disease state

value: aplastic anemia

value: bone marrow

tag: cell type

value: mixed sample (MNCs were mixed with CD34+ cells in a ratio of 4:1)

value: untreated


title: DeltaTat1

city: Wuhan

first: Qi

last: Huang

state: Hubei Province

address: No.1 Shizishan Street, Hongshan District, Wuhan 430007, China

institute: Huazhong Agricultural University

data_processing:
The raw RNA-seq data of fastq format were processed by Trimmomatic v.0.36 to remove adaptor sequences.
Clean reads were mapped to the reference genome by Hisat2 (v2.1.0) .
HTSeq-count (v0.9.1) was used to obtain the read count and function information of each gene according to the result of the mapping.
Genome_build: CP006632
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

organism: Escherichia coli

source_name: Bacteria

growth_protocol: The bacteria were grown in LB medium at 37 ℃ with shaking for 2 hours

extract_protocol:
Bacteria were harvested and mRNA extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DeltaTat


title: WT5


title: HFF-P7F_2_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P7F-replicate2
Transient transfected cells_genes-fpkmsMatrix


title: WT1


title: BM sample, healthy donor2

source_name: BM sample, healthy donor2

value: control


title: HFF-P7F_3_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P7F-replicate3
Transient transfected cells_genes-fpkmsMatrix


title: WT3

value: WT


title: HFF-P3F_1_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P3F-replicate1
Transient transfected cells_genes-fpkmsMatrix


title: BM sample, healthy donor1

source_name: BM sample, healthy donor1


title: 148-12-13-14_S10

description: MGH Patient 148

tag: treatment state

value: ON

tag: timepoint (days)

tag: antibody

tag: response immune checkpoint blockade therapy

value: NR

tag: age at the baseline

tag: batch

tag: tumor type

value: metastatic melanoma


title: Wild-type_nigericin_Rep2

description: Total RNA with poly(A)+ selection.

tag: genotype/variation

tag: strain


title: DeltaTat2


title: WT1


title: Deletion_control_Rep1

description: Total RNA with poly(A)+ selection.


title: HFF-P3F_3_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P3F-replicate3
Transient transfected cells_genes-fpkmsMatrix

tag: sample type


title: Wild-type_control_Rep1

description: Total RNA with poly(A)+ selection.


title: Deletion_nigericin_Rep2

description: Total RNA with poly(A)+ selection.


title: BM sample, AA patient1

source_name: BM sample, AA patient1

tag: tissue


title: HFF-P3F_2_RNAseq

description:
RNAseq on human foreskin fibroblasts transiently expressing P3F-replicate2
Transient transfected cells_genes-fpkmsMatrix


title: HFF-3_RNAseq

description:
RNAseq on human foreskin fibroblasts-replicate3
Stable lines_genes-fpkmsMatrix

value: Doxycycline for 48 hours

value: human foreskin fibroblasts-replicate3


title: MGH98_051514

description: MGH Patient 98

value: R


title: P7F-2_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P7F-Line2
Stable lines_genes-fpkmsMatrix


title: UMN_Fur_1

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build:  Reference genomes (E.coli EDL933 =  AE005174.2 / Klebsiella pneumoniae MGH78578 = CP000647.1 / Salmonella enterica Typhimurium LT2 = NC_003197.2 / E.coli SMS-3-5 = NC_010498.1 / Shigella flexneri 2a. 2457T = AE014073.1 / E.coli  UMN026 = CU928163.2 / Yersina pseudotuberculos IP32953 = NZ_CP009712.1 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

value: Fur myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: DeltaTat3

tag: genotype


title: P7F-1_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P7F-Line1
Stable lines_genes-fpkmsMatrix


title: Deletion_nigericin_Rep1

description: Total RNA with poly(A)+ selection.

value: nigericin


title: SMS_Fur_1

tag: myc-tagging


title: WT2


title: MGH51_041814

description: MGH Patient 51


title: Deletion_control_Rep2

description: Total RNA with poly(A)+ selection.

value: no drug


title: P3F-3_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P3F-Line3
Stable lines_genes-fpkmsMatrix


title: HFF-1_RNAseq

description:
RNAseq on human foreskin fibroblasts-replicate1
Stable lines_genes-fpkmsMatrix

value: human foreskin fibroblasts-replicate1


title: Deletion_CTL_Rep2

description: Total RNA with poly(A)+ selection.


title: HFF-2_RNAseq

description:
RNAseq on human foreskin fibroblasts-replicate2
Stable lines_genes-fpkmsMatrix

value: human foreskin fibroblasts-replicate2


title: MGHPDL002_080112

description: MGH Patient PDL002


title: UMN_Fur_2

tag: chip-exo antibody


title: P3F-2_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P3F-Line2
Stable lines_genes-fpkmsMatrix

tag: treatment


title: Wild-type_CTL_Rep2

description: Total RNA with poly(A)+ selection.

value: Wild-type reference strain


title: MGH51_081413

description: MGH Patient 51


title: P7F-3_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P7F-Line3
Stable lines_genes-fpkmsMatrix


title: EDL933_Fur_1


title: Deletion_CTL_Rep1

description: Total RNA with poly(A)+ selection.


title: Scale_E16_Control_Chuong236

status: Public on Aug 14 2021

city: Los Angeles

first: Gee-Way

last: Lin

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

data_processing:
Quality score: Phred+33
Low quality of sequencing bases were trimmed based on the Phred quality score (< 20) from both of the 5’- and 3’-ends of reads. After trimming, reads are discarded, if they are shorter than 30 bp for 50 bp single-end reads produced by the HiSeq 2000, or shorter than 50 bp for 75 bp single-end reads produced by the NextSeq 500.
The chicken galGal6 assembly including un-placed and un-localized scaffolds was downloaded from the UCSC Genome Browser. The RefSeq Release 104 annotation was downloaded from the NCBI. Keratin (KRT) gene annotation was added into the RefSeq annotation manually.
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.7.3a through Partek Flow (Partek Inc.), featureCounts in Rsubread 2.0.1, TMM, and edgeR 3.28.1, respectively.
Genes with count-per-mil-lion (CPM) values above 1 in at least two samples were retained, and genes with no or low expression levels were discarded.
Genome_build: UCSC galGal6
Supplementary_files_format_and_content: The tab-delimited text file: 1 file with count-per-million (CPM) values of 15242 genes produced by edgeR

molecule: polyA RNA

organism: Gallus gallus

source_name: skin appendage: scale

growth_protocol: In vivo

extract_protocol:
TRIzol
Illumina TruSeq RNA sample Prep kit v2

treatment_protocol: SATB2 RCAS-virus

tag: skin appendage

value: Scale

tag: embryonic developmental stage

tag: rcas virus

value: Control

tag: sample label


title: Scale_E16_Control_Chuong235


title: MGHPDL002_061812

description: MGH Patient PDL002

tag: treatment state

value: PRE

tag: timepoint (days)

tag: antibody


title: Wild-type_CTL_Rep1

description: Total RNA with poly(A)+ selection.


title: SMS_Fur_2

institute: UCSD


title: MGH98_030314

description: MGH Patient 98

tag: response immune checkpoint blockade therapy

tag: age at the baseline

tag: batch


title: EctopicZCF8_CTL_Rep1

description: Total RNA with poly(A)+ selection.

tag: genotype/variation

tag: strain


title: EDL933_Fur_2


title: Beak_E14_Control_Chuong243

source_name: skin appendage: beak

value: Beak


title: P3F-1_RNAseq

description:
RNAseq on human foreskin fibroblasts expressing P3F-Line1
Stable lines_genes-fpkmsMatrix

data_processing:
hg19
CUT&Tag: Trimmomatic (v0.39), BBmap clumpify (v38.87), Bowtie2 (v2.4.1) on hg19 reference genome
CUT&Tag: Peaks were called using SEACR (v1.3) with the parameters: relaxed (threshold 0,000001)
RNAseq: 3' adapter trimming with Trimmomatic: 0.32 (Bolger et al 2014), mapping with bowtie 2.0.5 and Tophat 2.0.6 on NCBI hg38 or hg19 (specified in the SAMPLES section above)
RNAseq: Pairwise differential analysis of RNAseq data was performed using Cufflinks (Fasteris). Genes with a q-value <0.05 after Bengamini-Hochberg correction for multiple-testing were considered to be significant
Genome_build: hg19 or hg38 (specified in the SAMPLES section above)
Supplementary_files_format_and_content: For CUT&Tag, processed files are in bigWig format; for RNAseq, there is two matrix with RPKM for all samples and genes

tag: sample type


title: Beak_E14_Control_Chuong242


title: EctopicZCF8_CTL_Rep2

description: Total RNA with poly(A)+ selection.


title: 259 microCurie_day14_rep3

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression in blood, 259 microCurie irradiated day 14

hyb_protocol: Agilent recommended protocols were used for hybridizations

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 259 microCurie_day14_rep3

label_protocol: We processed 152 samples from each of the following groups: 0 (control), 158, 191, 215 and 259 uCi at days 2, 3, 5, 7  and day 14 RNA for microarray hybridization.

growth_protocol: We obtained whole blood samples from injected mice (days 2, 3, 5, 7 and 14) from 6 replicates mice exposed to an internal emitter (cesium) in amounts of 0, 158, 191, 215 and 259 microCurie.

extract_protocol: We isolated RNA from the blood using the PAXgene Blood RNA method (PreAnalytix GmBH, catalog#762165), and then depleted Globin transcripts using the Ambion GLOBINclear-Mouse kit (Life Technologies, Grand Island, NY, catalog#AM1980). We evaluated the samples for RNA integrity using the Agilent 2100 bioanalyzer and samples with RINs >8.0 were used for further analysis.

treatment_protocol: Mice were injected with of 0, 158, 191, 215 and 259 microCurie of 137 CsCl solution.

tag: tissue

value: whole blood

tag: injected uci

tag: day


title: 259 microCurie_day7_rep6

description: Gene expression in blood, 259 microCurie irradiated day 7

source_name: 259 microCurie_day2_rep6


title: 259 microCurie_day7_rep1

source_name: 259 microCurie_day2_rep1


title: 259 microCurie_day14_rep6

source_name: 259 microCurie_day14_rep6


title: 259 microCurie_day7_rep5

source_name: 259 microCurie_day2_rep5


title: 259 microCurie_day5_rep4

description: Gene expression in blood, 259 microCurie irradiated day 5

source_name: 259 microCurie_day5_rep4


title: 259 microCurie_day14_rep1

source_name: 259 microCurie_day14_rep1


title: 259 microCurie_day5_rep3

source_name: 259 microCurie_day5_rep3


title: 259 microCurie_day7_rep3

source_name: 259 microCurie_day2_rep3


title: 259 microCurie_day14_rep2

source_name: 259 microCurie_day14_rep2


title: 259 microCurie_day7_rep4

source_name: 259 microCurie_day2_rep4


title: 259 microCurie_day5_rep1

source_name: 259 microCurie_day5_rep1


title: 259 microCurie_day14_rep4

source_name: 259 microCurie_day14_rep4


title: 259 microCurie_day7_rep2

source_name: 259 microCurie_day2_rep2


title: 259 microCurie_day3_rep6

description: Gene expression in blood, 259 microCurie irradiated day 3

source_name: 259 microCurie_day3_rep6


title: 259 microCurie_day14_rep5

source_name: 259 microCurie_day14_rep5


title: 259 microCurie_day5_rep2

source_name: 259 microCurie_day5_rep2


title: 259 microCurie_day5_rep5

source_name: 259 microCurie_day5_rep5


title: 259 microCurie_day3_rep5

source_name: 259 microCurie_day3_rep5


title: 259 microCurie_day3_rep1

source_name: 259 microCurie_day3_rep1


title: 259 microCurie_day3_rep2

source_name: 259 microCurie_day3_rep2


title: 259 microCurie_day3_rep3

source_name: 259 microCurie_day3_rep3


title: 259 microCurie_day2_rep6

description: Gene expression in blood, 259 microCurie irradiated day 2

source_name: 259 microCurie_day2_rep6


title: 259 microCurie_day2_rep5

source_name: 259 microCurie_day2_rep5


title: 259 microCurie_day5_rep6

source_name: 259 microCurie_day5_rep6


title: 259 microCurie_day3_rep4

source_name: 259 microCurie_day3_rep4


title: 259 microCurie_day2_rep4


title: 259 microCurie_day2_rep3

source_name: 259 microCurie_day2_rep3


title: 259 microCurie_day2_rep1

source_name: 259 microCurie_day2_rep1


title: 259 microCurie_day2_rep2


title: 215 microCurie_day14_rep6

description: Gene expression in blood, 215 microCurie irradiated day 14

source_name: 215 microCurie_day14_rep6


title: 215 microCurie_day14_rep4

source_name: 215 microCurie_day14_rep4


title: 215 microCurie_day14_rep3

source_name: 215 microCurie_day14_rep3


title: 215 microCurie_day5_rep6

description: Gene expression in blood, 215 microCurie irradiated day 5

source_name: 215 microCurie_day5_rep6


title: 215 microCurie_day14_rep5

source_name: 215 microCurie_day14_rep5


title: 215 microCurie_day14_rep1

source_name: 215 microCurie_day14_rep1


title: 215 microCurie_day7_rep3

description: Gene expression in blood, 215 microCurie irradiated day 7

source_name: 215 microCurie_day2_rep3


title: 215 microCurie_day14_rep2

source_name: 215 microCurie_day14_rep2


title: 215 microCurie_day7_rep4

source_name: 215 microCurie_day2_rep4


title: 215 microCurie_day7_rep1

source_name: 215 microCurie_day2_rep1


title: 215 microCurie_day7_rep2

source_name: 215 microCurie_day2_rep2


title: 215 microCurie_day7_rep5

source_name: 215 microCurie_day2_rep5


title: 215 microCurie_day7_rep6

source_name: 215 microCurie_day2_rep6


title: 215 microCurie_day5_rep4

source_name: 215 microCurie_day5_rep4


title: 215 microCurie_day5_rep3

source_name: 215 microCurie_day5_rep3


title: 215 microCurie_day5_rep1

source_name: 215 microCurie_day5_rep1


title: 215 microCurie_day3_rep6

description: Gene expression in blood, 215 microCurie irradiated day 3

source_name: 215 microCurie_day3_rep6


title: 215 microCurie_day5_rep5

source_name: 215 microCurie_day5_rep5


title: 215 microCurie_day7_rep7

source_name: 215 microCurie_day2_rep7


title: 215 microCurie_day3_rep3

source_name: 215 microCurie_day3_rep3


title: 215 microCurie_day3_rep4

source_name: 215 microCurie_day3_rep4


title: 215 microCurie_day3_rep2

source_name: 215 microCurie_day3_rep2


title: 215 microCurie_day2_rep5

description: Gene expression in blood, 215 microCurie irradiated day 2


title: 215 microCurie_day2_rep3


title: 215 microCurie_day3_rep5

source_name: 215 microCurie_day3_rep5


title: 215 microCurie_day5_rep2

source_name: 215 microCurie_day5_rep2


title: 215 microCurie_day2_rep6


title: 215 microCurie_day3_rep1

source_name: 215 microCurie_day3_rep1


title: 215 microCurie_day2_rep4

source_name: 215 microCurie_day2_rep4


title: 215 microCurie_day2_rep2


title: 191 microCurie_day14_rep2

description: Gene expression in blood, 191 microCurie irradiated day 14

source_name: 191 microCurie_day14_rep2


title: 191 microCurie_day14_rep4

source_name: 191 microCurie_day14_rep4


title: 191 microCurie_day14_rep5

source_name: 191 microCurie_day14_rep5


title: 191 microCurie_day14_rep1

source_name: 191 microCurie_day14_rep1


title: 191 microCurie_day14_rep3

source_name: 191 microCurie_day14_rep3


title: 191 microCurie_day7_rep5

description: Gene expression in blood, 191 microCurie irradiated day 7

source_name: 191 microCurie_day2_rep5


title: 191 microCurie_day7_rep4

source_name: 191 microCurie_day2_rep4


title: 215 microCurie_day2_rep1

source_name: 215 microCurie_day2_rep1


title: 191 microCurie_day14_rep6

source_name: 191 microCurie_day14_rep6


title: 191 microCurie_day5_rep3

description: Gene expression in blood, 191 microCurie irradiated day 5

source_name: 191 microCurie_day5_rep3


title: 191 microCurie_day5_rep4

source_name: 191 microCurie_day5_rep4


title: 191 microCurie_day7_rep3

source_name: 191 microCurie_day2_rep3


title: 191 microCurie_day7_rep2

source_name: 191 microCurie_day2_rep2


title: 191 microCurie_day5_rep5

source_name: 191 microCurie_day5_rep5


title: 191 microCurie_day7_rep6

source_name: 191 microCurie_day2_rep6


title: 191 microCurie_day5_rep6

source_name: 191 microCurie_day5_rep6


title: 191 microCurie_day5_rep2

source_name: 191 microCurie_day5_rep2


title: 191 microCurie_day3_rep4

description: Gene expression in blood, 191 microCurie irradiated day 3

source_name: 191 microCurie_day3_rep4


title: 191 microCurie_day5_rep1

source_name: 191 microCurie_day5_rep1


title: 191 microCurie_day3_rep5

source_name: 191 microCurie_day3_rep5


title: 191 microCurie_day3_rep3

source_name: 191 microCurie_day3_rep3


title: 191 microCurie_day2_rep7

description: Gene expression in blood, 191 microCurie irradiated day 2

source_name: 191 microCurie_day2_rep7


title: 191 microCurie_day7_rep1

source_name: 191 microCurie_day2_rep1


title: 191 microCurie_day2_rep5

source_name: 191 microCurie_day2_rep5


title: 191 microCurie_day2_rep4

source_name: 191 microCurie_day2_rep4


title: 191 microCurie_day2_rep6


title: 191 microCurie_day3_rep1

source_name: 191 microCurie_day3_rep1


title: 191 microCurie_day3_rep6

source_name: 191 microCurie_day3_rep6


title: 191 microCurie_day3_rep2

source_name: 191 microCurie_day3_rep2


title: 191 microCurie_day2_rep1


title: 191 microCurie_day2_rep2


title: 191 microCurie_day2_rep3

source_name: 191 microCurie_day2_rep3


title: 158 microCurie_day14_rep4

description: Gene expression in blood, 158 microCurie irradiated day 14

source_name: 158 microCurie_day14_rep4


title: 158 microCurie_day14_rep5

source_name: 158 microCurie_day14_rep5


title: 158 microCurie_day14_rep3

source_name: 158 microCurie_day14_rep3


title: Scale_E16_SATB2_Chuong608

source_name: skin appendage: scale


title: Feather_E16_Control_Chuong389

source_name: skin appendage: feather

value: Feather


title: Feather_E16_SATB2_Chuong603


title: Feather_E16_SATB2_Chuong604


title: 158 microCurie_day14_rep1

source_name: 158 microCurie_day14_rep1


title: Feather_E16_Control_Chuong388


title: Feather_E14_SATB2_Chuong658


title: 158 microCurie_day14_rep2

source_name: 158 microCurie_day14_rep2


title: 158 microCurie_day14_rep6

source_name: 158 microCurie_day14_rep6


title: 158 microCurie_day7_rep6

description: Gene expression in blood, 158 microCurie irradiated day 7

source_name: 158 microCurie_day2_rep6


title: 158 microCurie_day7_rep1

source_name: 158 microCurie_day2_rep1


title: 158 microCurie_day7_rep4

source_name: 158 microCurie_day2_rep4


title: 158 microCurie_day5_rep6

description: Gene expression in blood, 158 microCurie irradiated day 5

source_name: 158 microCurie_day5_rep6


title: P15-A

city: Beijing

first: Wei

last: Liu

address: 20 Dong-Da Street, Fengtai District

institute: Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity

data_processing:
FASTQ files of each sample were processed by using Cell Ranger (v.3.0.2) count pipeline coupled with human reference version GRCh38 to generate feature-barcode matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: tar file of gene expression matrix generated by Cell Ranger (v.3.0.2)

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from human peripheral blood samples. Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (16 rxns PN-1000075) was used with PBMCs  for the construction of 10x ScRNA sequencing libraries according to protocol provided by 10x Genomics.
10x ScRNA libraries were prepared for sequencing using standard Illumina and 10x Genomics protocols

tag: disease state

value: Severe fever with thrombocytopenia syndrome (SFTS)

tag: illness phase

value: Acute

tag: cell type

value: Peripheral blood mononuclear cells

tag: age

tag: Sex

value: female


title: 158 microCurie_day5_rep5

source_name: 158 microCurie_day5_rep5


title: Scale_E16_SATB2_Chuong607

tag: skin appendage

tag: embryonic developmental stage

tag: rcas virus

tag: sample label


title: 158 microCurie_day7_rep5

source_name: 158 microCurie_day2_rep5


title: 158 microCurie_day5_rep3

source_name: 158 microCurie_day5_rep3


title: 158 microCurie_day5_rep1

source_name: 158 microCurie_day5_rep1


title: 158 microCurie_day3_rep5

description: Gene expression in blood, 158 microCurie irradiated day 3

source_name: 158 microCurie_day3_rep5


title: 158 microCurie_day3_rep4

source_name: 158 microCurie_day3_rep4


title: 158 microCurie_day3_rep6

source_name: 158 microCurie_day3_rep6


title: 158 microCurie_day7_rep2

source_name: 158 microCurie_day2_rep2


title: 158 microCurie_day3_rep3

source_name: 158 microCurie_day3_rep3


title: Feather_E14_SATB2_Chuong657

source_name: skin appendage: feather


title: 158 microCurie_day3_rep2

source_name: 158 microCurie_day3_rep2


title: 158 microCurie_day5_rep4

source_name: 158 microCurie_day5_rep4


title: 158 microCurie_day7_rep3

source_name: 158 microCurie_day2_rep3


title: 158 microCurie_day5_rep2

source_name: 158 microCurie_day5_rep2


title: 158 microCurie_day3_rep1

source_name: 158 microCurie_day3_rep1


title: P12-A


title: P13-A

value: male


title: P14-A


title: 158 microCurie_day2_rep5

description: Gene expression in blood, 158 microCurie irradiated day 2


title: 158 microCurie_day2_rep6

source_name: 158 microCurie_day2_rep6


title: Beak_E14_SATB2_Chuong660

source_name: skin appendage: beak


title: Feather_E14_Control_Chuong387


title: 158 microCurie_day2_rep4

source_name: 158 microCurie_day2_rep4


title: 158 microCurie_day2_rep2


title: Feather_E14_Control_Chuong386


title: Beak_E14_SATB2_Chuong659


title: 158 microCurie_day2_rep3


title: P8-R

source_name: Peripheral blood mononuclear cells

value: Convalescent


title: Sarm1-/-BMDM 3h CL075 Rep3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description:
rRNA-depleted RNA
SKO CL075 3
SKO_CLO75_3

data_processing:
Base calling was carried out through an integrated primary analysis software called RTA (Real TimeAnalysis).
Reads were mapped against mm10 using kallisto 0.46.1.
Raw read counts and transcripts per million were extracted from abundance files and combined into a count matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_counts.txt: Matrix table with raw gene counts.
Supplementary_files_format_and_content: tpm_values.txt: TPM values for every gene and every sample.

source_name: Primary bone marrow-derived macrophages

growth_protocol: Bone marrow was flushed from the femurs and tibiae of 8-week-old female mice. pBMDM were generated from the bone marrow using L929-conditioned media as a source of M-CSF.

extract_protocol:
Supernatants were removed and total RNA was isolated using Roche High Pure RNA Isolation kit.
Library was prepared by Macrogen Inc. using Illumina TruSeq Stranded Total RNA with ribo-zero.

treatment_protocol: BMDM from each mouse were either left untreated of stimulated with CL075 for 3h.

value: B6.129X1-Sarm1tm1Aidi /J

tag: genotype

value: Female

value: pBMDM

tag: treatment

value: Treated for 3h with 5 ug/ml CL075


title: P9-A


title: Sarm1-/-BMDM 3h CL075 Rep2

description:
rRNA-depleted RNA
SKO CL075 2
SKO_CLO75_2


title: Sarm1-/-BMDM 3h CL075 Rep5

description:
rRNA-depleted RNA
SKO CL075 5
SKO_CLO75_5


title: P8-A


title: P11-A


title: 158 microCurie_day2_rep1

source_name: 158 microCurie_day2_rep1


title: control_day14_rep1

description: Gene expression in blood, un-irradiated control


title: control_day14_rep2


title: control_day7_rep6


title: control_day7_rep5


title: control_day14_rep5


title: control_day14_rep6


title: Sarm1-/-BMDM 3h CL075 Rep1

description:
rRNA-depleted RNA
SKO CL075 1
SKO_CLO75_1


title: control_day14_rep3


title: P10-A


title: control_day7_rep4


title: control_day7_rep3