title: LM_138


title: LM_50

status: Public on Aug 07 2020

type: SRA

city: Murcia

first: Ana

middle: María

last: Hurtado López

state: Murcia

address: Libertad, n

department: Hematology and Medical Oncology Department

country: Spain

institute: Hospital Morales Meseguer, Instituto Murciano de Investigación Biosanitaria (IMIB)

library_source: transcriptomic

data_processing:
Artifacts (low quality reads, adaptor sequence,  contaminant DNA, or PCR duplicates) were removed
Trimmed reads were mapped to reference genome with TopHat, splice-aware aligner.
Transcript was assembled by Cufflinks with aligned reads that contain paired-end information.
After the read mapping, Cufflinks was used for transcript assembly. Expression profile was calculated  for each sample and transcript/gene as FPKM (Fragment per Kilobase of transcript per Million mapped  reads).for each sample and transcript/gene as FPKM (Fragment per Kilobase of transcript per Million mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: cvs format. FPKM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Bone marrow samples were colected from CMML patients and healthy donors. RNA was then isolated from buffy coat using Qiagen Rneasy Mini kits as per manufacturer's recommendations.   RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Chronic Myelomonocytic Leukemia

tag: gender

value: female


title: EB14_loxp_RNA_d9_eb4

city: Boston

first: Bradley

middle: E

last: Bernstein

state: MA

address: 185 Cambridge Street

department: Pathology

country: USA

institute: Massachusetts General Hospital

description:
EB_day14_loxp_RNA_d9_eb4
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt

data_processing:
Sequencing RNA libraries, passed through general quality filter such as cluster density, total yield, and per-cycle base quality, were then split by library barcodes using bcl2fastq.
R2 reads were demultiplexed into separate files based on the cell barcode from R1 and mapped to a mouse reference genome (mm9) by Bowtie2. After eliminating reads sharing the same UMI by htseq-count, an accurate molecule count for each gene was generated and converted to the number of UMIs into transcript counts through binomial statistics (CEL-seq2).
Nanopore sequencing reads were converted to fastq files by Guppy (v2.3.5) and then demultiplexed to the each cell based on its matched cell barcode sequence with the highest mapping score by minimap2 with default parameters.
To detect tandem-loxP, different loxP flanking sequences were mapped to the demultiplexed nanopore sequence (minimap2) then assembled into a full tandem-loxP sequence based on their position in the nanopore sequence. Due to the sequencing error, we selected the top 1 combination with additional filter: 1) over 30 reads, 2) outlier from others, 3) full length with upstream and downstream sequence.
To detect the UCI, we first mapped the upstream and downstream of the UCI sequence to nanopore reads by minimap2 then extracted the sequence between M13F and WPRE_M13R_HSV. Due to the sequencing error, we selected the top 1 sequence with additional filter: 1) over 30 reads, 2) outlier from others, 3) represented by the sequence from UCI plasmid.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include UMI count values for each Sample.

molecule: polyA RNA

organism: Mus musculus

source_name: mESC (Mouse embryoid body at day 0)

growth_protocol:
Mouse v6.5 ESCs were cultured with feeder cells (mouse embryonic fibroblasts (MEF)) in knockout DMEM media supplemented with 15% FBS, and 0.01% Leukemia inhibitory factor (LIF). The media was replenished every day and cells were split every two days.
For differentiation, we detached and dissociated ESCs to single cells. MEFs were further removed by incubating single cell suspensions on a 100mm tissue culture dish for 40 minutes at 37°C. We seeded 1000 cells per well micro-well plate (STEMCELL Technologies) in EB media (mESC media without LIF). For inducible barcoding experiments, we seeded FACS sorted RFP+/GFP-/BFPmid cells. After 4 days of EB differentiation in the micro-well plate, we collected EBs and transferred them to 100mm petri dishes and pursued spontaneous differentiation for another 10 days. EB media was changed every day (micro-well plate) or every other day (petri dish) during EB differentiation.

extract_protocol:
mESC and EBs were dissociated by trypsin to single cells and sorted into 384 well plates. After freeze and thaw for twice, we performed a reverse transcription and second strand synthesis, then pooled samples and ran IVT. For DNA extraction (30%), before pooling, we added unique primers (DNA adapter) involving identical cell barcode with RNA-adapter, targeting dual-barcode region of genomic DNA to each well, and then amplified the region by PCR. For RNA extraction (70%), after 2nd reverse transcription, we amplified RNA fragments by Illumina adapter.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To perturb DNA methylation, we treated EBs with 5-azacytidine or DMSO (100 nM) and replenished them with every media change throughout all days of differentiation.

tag: cell type

value: Embryoid body

tag: media

value: Serum-LIF

tag: differentiation day

value: Day 14

tag: treatment


title: LM_27


title: EB14_loxp_RNA_d9_eb2

description:
EB_day14_loxp_RNA_d9_eb2
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: EB14_loxp_RNA_d8_eb4

description:
EB_day14_loxp_RNA_d8_eb4
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: EB14_loxp_RNA_d9_eb1

description:
EB_day14_loxp_RNA_d9_eb1
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: EB14_loxp_RNA_d8_eb3

description:
EB_day14_loxp_RNA_d8_eb3
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: LM_18

value: male


title: LM_19


title: EB14_loxp_RNA_d8_eb1

description:
EB_day14_loxp_RNA_d8_eb1
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: LM_13


title: LM_14


title: EB14_loxp_RNA_es_eb3

description:
EB_day14_loxp_RNA_es_eb3
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: EB14_loxp_RNA_es_eb1

description:
EB_day14_loxp_RNA_es_eb1
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: EB14_loxp_RNA_d9_eb3

description:
EB_day14_loxp_RNA_d9_eb3
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: LM_2


title: EB00_dmso

description:
EB_day0_dmso
scRNA-Seq
96 cells
processed data file: EB_dmso_5aza_rel_RNA.txt

value: Serum+LIF

value: Day 0

value: DMSO


title: LM_11


title: sgp53(1)_Line3

city: Stanford

first: Liz

middle: J

last: Valente

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Basecalls performed using CASAVA 1.8
STAR aligner was used for alignment to mouse genome version mm10
DESeq2 was used for statistical analysis and to generate a variance stabilized table of counts used for subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: Valente_Counts.txt: file containing the number of reads in each library that mapped to each gene in the Ensembl database

source_name: E1A;HrasG12V mouse embryonic fibroblasts

growth_protocol: 1E6 cells were plated into 10 cM plates in high glucose DMEM, 10% FCS, Pen/Step, and allowed to recover at 37˚C, 5% 02, 5% CO2 for 24 h prior to harvest

extract_protocol:
Cells were harvested by trypsinization before cell pellets were lyzed in TRIzol (ThermoFisher) and RNA extracted Qiagen's RNAeasy Micro Kit. RNA quality was assessed using a Bioanalyzer, and only samples with an RNA integrity number (RIN) greater than 8.0 were used for library preparation. RNA-Seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Each library was prepared from 1ug of RNA
Illumina TruSeq Stranded RNA LT Kit (Cat#15032612) was used and 1 µg of total RNA was entered for the construction of sequencing libraries. The libraries were prepared using the manufacturer's standard protocol.

tag: strain

value: mixed 129/Sv-C57BL/6

tag: genotype

value: sgp53(1), p53 null


title: EB14_loxp_RNA_es_eb2

description:
EB_day14_loxp_RNA_es_eb2
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt


title: LM_1


title: EB14_5aza

description:
EB_day14_5aza
scRNA-Seq
96 cells
processed data file: EB_dmso_5aza_rel_RNA.txt


title: EB14_rep2

description:
EB_day14_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: EB10_rep2

description:
EB_day10_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 10


title: sgNTC_Line2

value: sgNTC, p53 wild-type


title: sgp53(1)_Line2

value: sgp53(1), functionally inactive


title: EB08_rep2

description:
EB_day8_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 8


title: EB06_rep2

description:
EB_day6_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 6


title: sgp53(1)_Line1


title: EB12_rep2

description:
EB_day12_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 12


title: sgNTC_Line3


title: CX3CR1- CCCR2- MI-3

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

description:
CCR2_MI_4
processed_data_file_MI_gene_expression.xls

data_processing:
The RNA-Seq analysis is done in several steps using CLC Genomics Workbench: First, all genes are extracted from the reference genome (using annotations of type gene). Other annotations on the gene sequences are preserved (e.g. CDS information about coding sequences etc). Next, all annotated transcripts (using annotations of type mRNA) are extracted. If there are several annotated splice variants, they are all extracted. Note that the mRNA annotation type is used for extracting the exon-exon boundaries.
Next, the reads are mapped against all the transcripts plus the entire gene.
From this mapping, the reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated. After that, putative exons are identified.
Genome_build: mm10
Supplementary_files_format_and_content: The excel file includes RPKM values for each Sample.

source_name: visceral adipose tissue

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: visceral adipose tissue

value: CX3CR1- CCCR2-

value: Myocardial infarction


title: sgNTC_Line1


title: CX3CR1- CCCR2- MI-1

description:
CCR2_MI_1
processed_data_file_MI_gene_expression.xls


title: CX3CR1- CCCR2- No MI-3

description:
CCR2_Sham_1
processed_data_file_MI_gene_expression.xls

value: No myocardial infarction


title: EB14_loxp_RNA_d8_eb2

description:
EB_day14_loxp_RNA_d8_eb2
scRNA-Seq
384 cells
processed data file: EB_recording_RNA.txt

value: Embryoid body

value: Serum-LIF

value: Day 14


title: EB00_rep2

description:
EB_day0_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Serum+LIF

value: Day 0


title: EB04_rep2

description:
EB_day4_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 4


title: EB02_rep2

description:
EB_day2_rep2
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 2


title: CX3CR1- CCCR2- MI-2

description:
CCR2_MI_3
processed_data_file_MI_gene_expression.xls


title: EB14_rep1

description:
EB_day14_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: CX3CR1- CCCR2- No MI-1

description:
CCR2_Sham_3
processed_data_file_MI_gene_expression.xls


title: Monocytes3

description:
MonoC TPM
processed_data_file_gene_expression.xlsx

data_processing:
The RNA-Seq analysis is done in several steps using CLC Genomics Workbench: First, all genes are extracted from the reference genome (using annotations of type gene). Other annotations on the gene sequences are preserved (e.g. CDS information about coding sequences etc). Next, all annotated transcripts (using annotations of type mRNA) are extracted. If there are several annotated splice variants, they are all extracted. Note that the mRNA annotation type is used for extracting the exon-exon boundaries.
Next, the reads are mapped against all the transcripts plus the entire gene
From this mapping, the reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated. After that, putative exons are identified.
Genome_build: mm10
Supplementary_files_format_and_content: The excel file includes RPKM values for each Sample.

source_name: blood monocytes

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

value: Monocytes


title: Monocytes2

description:
MonoB TPM
processed_data_file_gene_expression.xlsx


title: CX3CR1- CCCR2- No MI-2

description:
CCR2_Sham_4
processed_data_file_MI_gene_expression.xls


title: EB08_rep1

description:
EB_day8_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: EB10_rep1

description:
EB_day10_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 10


title: EB06_rep1

description:
EB_day6_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: EB04_rep1

description:
EB_day4_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: CX3CR1- CCCR2-3

description:
CCR2-C TPM
processed_data_file_gene_expression.xlsx

source_name: CX3CR1-low and CCR2-low macrophages


title: CX3CR1- CCCR2-2

description:
CCR2-B TPM
processed_data_file_gene_expression.xlsx


title: EB00_rep1

description:
EB_day0_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: CX3CR1- CCCR2-1

description:
CCR2-A TPM
processed_data_file_gene_expression.xlsx


title: EB02_rep1

description:
EB_day2_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt


title: Teff_Dex [S12]

city: Cleveland

first: BOOKI

last: MIN

state: Ohio

address: 9500 Euclid Avenue

department: INFLAMMATION AND IMMUNITY

institute: Lerner Research Institute, Cleveland Clinic Foundation

description:
CWRU001541A3_S12
processed data file: raw_counts.txt

data_processing:
bcl2Fastq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCm38 whole genome using Hisat2 v2.0.5.
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the EdgeR Library in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.txt: Tab-delimited text file includes raw summarized reads.

source_name: Lung

extract_protocol:
RNA was isolated using the RNeasy Micro kit (Qiagen cat#74004). All subsequent sample quality assessment was performed on a Fragment Analyzer electrophoresis system (Agilent). Total RNA was normalized prior to oligo-dT capture and cDNA synthesis with SMART-Seq v4 (Takara cat#634892). The resulting cDNA was quantified using a Qubit 3.0 fluorometer (Life Technologies).
Libraries were generated using the Nextera XT DNA Library Prep kit (Illumina cat#FC-131-1096). flow cell using a 100 base pairs, Paired End run.
Medium depth sequencing (25 million reads per sample) was performed with a HiSeq 2500 (Illumina) on a Rapid Run.

treatment_protocol: Foxp3GFP mice were injected i.p. with CA in alum adjuvant on days 0 and 7. Starting at day 14, mice were intranasally challenged for 4 consecutive days with CA. Vehicle or Dex was intraperitoneally injected on the first and third days of CA challenge (days 14 and 16). Mice were sacrificed 24 hours after the last challenge. Foxp3+ Treg and effector CD4 T cells were FACS sorted from the lung tissues.

value: Lung

value: CD4+Foxp3- T cells

value: Dexamethasone


title: Treg_Dex [S11]

description:
CWRU001540A3_S11
processed data file: raw_counts.txt

value: CD4+Foxp3+ T cells


title: CX3CR1+ CCCR2+3

description:
CCR2+C TPM
processed_data_file_gene_expression.xlsx

source_name: CX3CR1-high CCR2-high macrophages

value: visceral adipose tissue

value: CX3CR1+ CCCR2+


title: Teff_Dex [S10]

description:
CWRU001539A3_S10
processed data file: raw_counts.txt


title: Treg_Dex [S9]

description:
CWRU001538A3_S9
processed data file: raw_counts.txt


title: CX3CR1+ CCCR2+1

description:
CCR2+A TPM
processed_data_file_gene_expression.xlsx


title: EB12_rep1

description:
EB_day12_rep1
scRNA-Seq
96 cells
processed data file: EB_replicates.txt

value: Day 12


title: Teff_Dex [S8]

description:
CWRU001537A3_S8
processed data file: raw_counts.txt


title: Treg_Dex [S7]

description:
CWRU001536A3_S7
processed data file: raw_counts.txt


title: K562-mIL21 rep1

city: Newark

first: Dongfang

last: Liu

state: New Jersey

address: 205 S Orange Ave

department: Department of Pathology, Immunology and Laboratory Medicine

institute: Rutgers-The State University of New Jersey

data_processing:
RNA sequencing (RNA-seq) was performed on a BGISEQ-500 platform by BGI Group (Shenzhen, Guangdong, China).
Clean reads in FASTQ format were obtained after filtering low quality reads (reads where more than 50% of the base’s qualities are lower than 15), reads with adaptors, and reads with more than 10% unknown bases (N).
FASTQ files were aligned to the hg38 human reference genome using STAR 2.6.1d. The aligned files were processed using the GenomicAlignments package (v.1.20.0) to get count matrices.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cell line

growth_protocol: K562, 221, K562-mIL21, 221-mIL21 cells were cultured in RPMI-1640 (Corning) supplemented with 10% (v/v) fetal bovine serum (FBS) and 100 U/mL Penicillin-Streptomycin (Corning) at 37 ℃ under 5% (v/v) CO2

extract_protocol:
Cells were directly lysed in Trizol reagent (Thermo Fisher Scientific) for RNA extraction using the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: To establish K562-mIL21 and 221-mIL21 cells, K562 and 221 cells were transduced with IL-21 retrovirus, respectively, and then membrane IL-21 positive cells were sorted using FACS Aria II cell sorter (BD Biosciences) using AF647 mouse IgG1 anti-human IL-21 (clone 3A3-N2).

tag: modification


title: Sample_13_MB_3432

first: Jihye

last: Kim

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

data_processing:
alignment: TopHat v2.1.0 using default settings
expression levels: Cufflinks v2.2.1 and cuffdiff using default settings
significant genes are with FDR < 0.05
Genome_build: hg19 (Ucsc)
Supplementary_files_format_and_content: text file with FPKM values

source_name: Melanoma tumor

extract_protocol:
Total RNA was extracted with the RNAeasymini  Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSEQ RNA Sample Prep v2 using standard Illumina protocols.

tag: sample type

value: Patient tumor specimen

tag: age at diagnosis

value: M

tag: stage at diagnosis

value: IIIC


title: K562 WT rep2

value: Wild type


title: K562-mIL21 rep2


title: K562 WT rep1


title: Monocytes1

description:
MonoA TPM
processed_data_file_gene_expression.xlsx


title: Sample_14_MB_4117

value: IIIA


title: Teff_Veh [S6]

description:
CWRU001535A3_S6
processed data file: raw_counts.txt

value: Vehicle


title: Sample_12_MB_3316

value: F

value: IIB


title: 221 WT rep2


title: 221-mIL21 rep1


title: 221 WT rep1


title: 221-mIL21 rep2


title: Teff_Veh [S4]

description:
CWRU001533A3_S4
processed data file: raw_counts.txt


title: Sample_11_MB_2855

value: IV


title: K562-mIL21 NK Day14 rep2

source_name: NK cells

growth_protocol: PBMCs were isolated from buffy coats using Lymphocyte Separation Medium (Corning). For NK cell expansion, 5 × 10^6 PBMCs were cultured with 1 × 10^7 10,000 Rad-irradiated feeder cells in 35 ml RPMI-1640 media with 10% Fetal Bovine Serum (Corning), 2mM L-Glutamine (Corning), 100 U/ml Penicillin-Streptomycin (Corning), 200 U/ml IL-2 (PeproTech), and 5 ng/ml IL-15 (PeproTech) in G-Rex 6 Multi-well cell culture plates (Wilson Wolf). Media were changed every 3-4 days and 2 × 10^7 cells were kept in each well for continued culture at each time.

extract_protocol:
Purified NK cells were directly lysed in Trizol reagent (Thermo Fisher Scientific) for RNA extraction using the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: On day 7 and day 14 of expansion, cells were collected and stained with PE-anti-CD3 and PE/Cy7-anti-CD56 antibodies on ice for 30 minutes. After washing with FACS staining buffer (PBS with 2% FBS) twice, cells were resuspended in FACS staining buffer and then CD3- CD56+ cells were sorted to a purity of > 98% for each replicate using FACS Aria II cell sorter (BD Biosciences).

tag: expansion system

tag: time

value: Day 14

value: NK cells


title: K562-mIL21 NK Day14 rep1


title: Sample_10_MB_2786


title: K562-mIL21 NK Day7 rep2

value: Day 7


title: CX3CR1+ CCCR2+2

description:
CCR2+B TPM
processed_data_file_gene_expression.xlsx


title: Treg_Veh [S3]

description:
CWRU001532A3_S3
processed data file: raw_counts.txt

value: Lung


title: 221-mIL21 NK Day14 rep2


title: K562-mIL21 NK Day7 rep1


title: 221-mIL21 NK Day14 rep1


title: Sample_08_MB_3178


title: 221-mIL21 NK Day7 rep2


title: Treg_Veh [S1]

description:
CWRU001530A3_S1
processed data file: raw_counts.txt

value: CD4+Foxp3+ T cells


title: Sample_07_MB_3025


title: Treg_Veh [S5]

description:
CWRU001534A3_S5
processed data file: raw_counts.txt


title: Sample_06_MB_1882


title: 221-mIL21 NK Day7 rep1


title: MF_p5_rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
wild-type
passage 5

data_processing:
Reads were mapped to the mm10 genome using Hisat2 (v2.0.0.0-beta) with default parameters. Only uniquely mapped reads were kept.
Coverage signal tracks (bigWigs) of primary alignments generated using Samtools (v1.1) and DeepTools2 (v2.4.1)
Primary alignments were counted using featureCounts (v1.4.6-p2)
Differential experesssion analysis was performed using DESeq2 (1.8.2). Only genes with FDR<0.05 were considered differentially expressed.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: featureCounts count table output

source_name: mouse embryonic stem cells

growth_protocol: Cells were cultured in 2i media: KnockOutTM DMEM (10829018, Gibco) supplemented with 15% KnockOutTM Serum Replacement (Gibco, A3181502), 0.1 mM MEAA (Gibco, non essential aminoacid), 1 nM Na-Pyruvate (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 4 mM GlutaMAX, 5 μg/mL Insulin (Sigma I0516), 50 U/mL Pen-Strep, 200 U/mL LIF (ESGRO #ESG1106), 1 μM PD0325901 (StemGent 04-0006), 3 μM CHIR99021 (StemGent 04-0003).

extract_protocol:
Samples were homogenized in TRIzol™ Reagent (Thermo Fisher 15596026) followed by RNA purification using a Direct-zol™ RNA MiniPrep kit (Zymo Research, R2050) according to the manufacturer's instruction.
TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: The medium was aspirated completely before addition of TriZol reagent directly on the culture plate

value: male

value: parental mESC line, wild-type


title: MF_p5_rep1

description:
wild-type
passage 5


title: Sample_04_MB_2750


title: Sample_05_MB_2781


title: GeCKO-B plasmid library

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

library_source: genomic

data_processing:
Library strategy: CRISPR Screen
50 bp single reads were trimmed using cutadapt (version 1.16) by removing the adapter sequence (-g GGACGAAACACCG) and setting the read length to 20 bp (-l 20).
Trimmed reads were separately aligned to Human GeCKOv2 Library A or B using bowtie2 (version 2.3.4.1) with parameter --norc.
Aligned reads were filtered by samtools (version 1.7) using the parameter -q 2.
Reads were subsampled to 5 million reads with replacement and counted for each sgRNA, annotated with gene information and library A and B from the same sample were merged into a table.
Genome_build: Human_GeCKOv2
Supplementary_files_format_and_content: Text file with annotated read counts subsampled to 5 million reads.

molecule: genomic DNA

organism: synthetic construct

source_name: plasmid library

extract_protocol:
HeLa cells were collected and gDNA was extracted from samples using NucleoSpin® Blood XL from MACHEREY-NAGEL GmbH & Co. according to the manufactures instructions. The sgRNA casette was initially amplified according to Shalem et al 2014 DOI: 10.1126/science.1247005 . Illumina primers were added through a second PCR as described. The amplicon was purified using AMPure XP beads and DNA was quantified using a Qubit dsDNA HS Assay Kit.
The library was constructed as in Sanjana et al 2014 doi: 10.1038/nmeth.3047

treatment_protocol: Knockout populations were treated with 3 μM olaparib or DMSO for 14 days

tag: cell line

value: plasmid library

tag: library

value: B


title: MF_p4_rep1

description:
wild-type
passage 4


title: Sample_09_MB_3838

value: Patient tumor specimen

value: M


title: Sample_03_MB_4103

value: IIIB


title: Teff_Veh [S2]

description:
CWRU001531A3_S2
processed data file: raw_counts.txt

value: CD4+Foxp3- T cells


title: M3

city: Belém

first: RAFAEL

middle: BORGES

last: VALADARES

address: Travessa Dom PEDRO 1, 575 Apto1303

country: Brazil

institute: Instituto Tecnologico Vale

description:
RNAseqfulltable1.xls
M3_ACAGTG_L001

data_processing:
quality check with Fastqc
merged according to CLCbio default parameters to yieal reads of 150bp
Trimming was performed in order to remove ambiguous nucleotides (maximum of 2 nucleotides allowed), terminal nucleotides (1 from the 5' end and 1 from the 3' end), adapter sequences, reads with less than 15 and more than 1000 nucleotides and low quality reads (limit =0.02).
Blast against Swissprot plant protein database with expect value=10
RNAseq mappings for all reads using the following parameters: minimum read length fraction of 0.9, minimum similarity of 0.95, allow up to 10 unspecific matches, and select RPKM as expression value.
Genome_build: de-novo assembly

organism: Oeceoclades maculata

source_name: mycorrhizal roots sections

growth_protocol: Plants were collected in nature growing in its natural conidtion (terrestrial orchids)

extract_protocol:
TRIzol
TRUSeq SBS Kit v3-HS

treatment_protocol: Colonized or uncolonized roots were separated for RNAseq analysis

value: myc


title: Control Mouse 3

type: RNA

city: Waco

first: Sudhiranjan

last: Gupta

state: TX

address: One Bear Place

department: Biology

institute: Baylor University

description: S03 WT3-cy3

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

growth_protocol: We perfomed a microRNA microarray on to assess differentially expressed miRNAs in bleomycin-induced lung fibrosis in C57 BL6 mice.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

treatment_protocol: To induce pulmonary fibrosis, belomycine (Sigma-Aldrich, St Louis, MO) was dissolved and administred intratracheally at a dose of 1.5U/kg body weight. Control animals received saline only.  21 days post bleomycin treatment, mice were sacrificed and lung tissue were collected for RNA extraction and microRNA microarray.

value: saline

value: lung


title: Bleomycin Mouse 2

description: S05 WT Bleo2-cy3

value: 1.5U/kg bw bleomycin


title: M1

description:
RNAseqfulltable1.xls
M1_CGATGT_L001


title: Control Mouse 1

description: S01 WT1-cy3


title: Bleomycin Mouse 3

description: S06 WT Bleo3-cy3


title: M2

description:
RNAseqfulltable1.xls
M2_TGACCA_L001


title: G2_p4_rep2

description:
3xFlag-His-Avi tag
passage 4

value: Msl2 CXC-CTD of Drosophila


title: Sample_02_MB_2674

value: F


title: Control Mouse 2

description: S02 WT2-cy3


title: S3

description:
RNAseqfulltable1.xls
S3_CTTGTA_L001

source_name: non-mycorrhizal roots sections

value: non-myc


title: G2_p5_rep1

description:
3xFlag-His-Avi tag
passage 5


title: Sample_01_MB_1692

value: IB


title: G2_p4_rep1

description:
3xFlag-His-Avi tag
passage 4


title: MF_p4_rep2

description:
wild-type
passage 4


title: S2

description:
RNAseqfulltable1.xls
S2_CAGATC_L001


title: Bleomycin Mouse 1

description: S04 WT-Bleo1-cy3


title: S1

description:
RNAseqfulltable1.xls
S1_GCCAAT_L001


title: F4_p5_rep2

description:
3xFlag-His-Avi tag
passage 5

value: Msl2 C-terminal domain (CTD) of Drosophila


title: GeCKO-A plasmid library

value: A


title: F4_p5_rep1

description:
3xFlag-His-Avi tag
passage 5

value: male


title: F4_p4_rep1

description:
3xFlag-His-Avi tag
passage 4


title: A3shNT_DMSO_24h_A

city: Stockholm

first: Daniel

middle: Wesley

last: Hagey

address: Nobels vag 3

country: Sweden

institute: Karolinska Institutet

data_processing:
Adapter trimming using Cutadapt 2.8
Alignment to GRCh37 transcriptome using Tophat 2.1.1
Genome_build: GRCh37
Supplementary_files_format_and_content: ENSEMBL raw count file .txt

source_name: A3shNT cells

extract_protocol:
Trizol extraction and Isopropanol precipitation
Smart-seq2

value: A3shNT cells

value: DMSO


title: A3shNT_5487_24h_C


title: A3shNT_DMSO_24h_C


title: A3shNT_5487_24h_B


title: A3shNT_DMSO_24h_B


title: F4_p4_rep2

description:
3xFlag-His-Avi tag
passage 4


title: D12_p5_rep2

description:
untagged, exon1-2 deleted
passage 5

value: Msl2 knock-out


title: D12_p5_rep1

description:
untagged, exon1-2 deleted
passage 5


title: 96-Bx2

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC 0.11.8
Reads aligned using STAR 2.7.1a
Count table generated using featureCounts 2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file containing a matrix of counts

source_name: Liver

extract_protocol:
Protocol Tru-Cut needle biopsies were taken from the left lobe intraoperatively after complete revascularization of the allograft (2 hours after reperfusion) prior to surgical closing of the abdomen.
Total RNA was first enriched for mRNA with the NEB NEBNext Poly(A) mRNA Magnetic isolation kit. The mRNA sam- ples were then put on a IntegenX Apollo 324 system for automated library preparation using the IntegenX PrepX RNA-Seq Library reagent kit for Illumina. Library products were next enriched through PCR, and multiplexing barcodes were also added.

tag: timepoint

value: Post-transplant

tag: iri

value: IRI+


title: 95-Bx1

value: Pre-transplant

value: IRI-


title: LD 7-Days Cultured cFHHs-rep1

city: Higashi-Hiroshima

first: Chise

last: Tateno

state: HIROSHIMA

address: 3-4-1, Kagamiyama

department: Dept of Reseach & Development

country: Japan

institute: PhoenixBio Co., Ltd

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, followed by Robust Multichip Averaging (RMA) normalization using Avadis (Strand Genomics, Inc.). Values for probe sets that were judged to be Absent in all 25 Chips by the MAS5.0 analysis were left blank in the Sample data tables. The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).

label: biotin

source_name: Cultured cFHHs at low density (0.53x10^5 cells/cm2)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For microarray analysis, cFHHs were plated at HD (2.13x10^5 cells/cm2) or LD (0.53x10^5 cells/cm2) on wells of type I collagen-coated 24-well plates and cultured for 7 days with dHCGM (Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 2% dimethylsulfoxide, 20 mM HEPES, 44 mM NaHCO3, 15 µg/mL L-proline, 0.25 µg/mL insulin, 5x10-8 M dexamethasone, 5 ng/mL epidermal growth factor, 0.1 mM L-ascorbic acid 2-phosphate, 100 IU/mL penicillin G, and 100 µg/mL streptomycin). The medium was replaced every 3 to 4 days.

extract_protocol: Total RNA was isolated from pooled cFHHs and three wells of cultured cFHH at high density or low density at day 7 using TRIzol (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: host strain

value: cDNA-uPA/SCID

tag: donor phh

value: BD195 (2-year-old Hispanic girl) (BD Biosicence)

tag: mouse model

value: Chimeric mice with human hepatocytes (BD195)

tag: cell type

value: Cultured cFHHs at low density for 7 days


title: HD 7-Days Cultured cFHHs-rep3

source_name: Cultured cFHHs at high density (2.13x10^5 cells/cm2)

value: Cultured cFHHs at high density for 7 days


title: 96-Bx1


title: 95-Bx2


title: 98-Bx1


title: LD 7-Days Cultured cFHHs-rep3


title: 98-Bx2


title: LD 7-Days Cultured cFHHs-rep2


title: HD 7-Days Cultured cFHHs-rep1


title: A3shNT_5487_24h_A

tag: treatment


title: D12_p4_rep1

description:
untagged, exon1-2 deleted
passage 4

tag: gender

tag: genotype


title: D11_p5_rep2

description:
3xFlag-His-Avi tag
passage 5

value: wild-type Msl2, 3xFlag-His-Avi tag


title: 93-Bx1


title: 94-Bx1


title: 93-Bx2


title: 92-Bx2


title: B12Dmel_WD_male_msl1_CyOGFP_R3

data_processing:
The mapping was performed to dm6 using STAR (2.6.1b) with default parameters, indexed using samtools (1.9) and QC done using deepTools (3.1.2), fastqc (0.11.7) and multiQC (1.6)
The bigwig file was prepared using deepTools bamCoverage (3.1.2), RPKM with bin size 25.
featureCounts (subread v1.6.1) using params: -p -B -C -Q 10 --primary.
For differential expression analysis we used DESeq2  (v1.18.1).
Genome_build: BDGP6
Supplementary_files_format_and_content: featureCounts count table output

organism: Drosophila melanogaster

source_name: Wing imaginal disc from third instar larva

growth_protocol: Drosophila melanogaster were reared on a cornflour-molasses fruit fly medium [1l water, 12g agar-agar threads, 18g bakery yeast, 10g soya flour, 80g corn flour, 22g molasses, 80g malt extract, 2.4g 4-hydroxibenzoic acid methylester (Nipagin), 6.25ml propionic acid] at 25¡C, 70% relative humidity and 12 hr dark/12 hr light cycle.

treatment_protocol: 3rd instar larval were collected, the gender separated by visual inspection of the genitals; then wing imaginal discs were dissected and transferred to TriZol reagent.

tag: strain

tag: genotype/variation

value: msl-1 heterozygous


title: D11_p4_rep2

description:
3xFlag-His-Avi tag
passage 4


title: 97-Bx2


title: 97-Bx1


title: D12_p4_rep2

description:
untagged, exon1-2 deleted
passage 4


title: 92-Bx1


title: B11Dmel_WD_male_msl1_CyOGFP_R2


title: HD 7-Days Cultured cFHHs-rep2


title: cFHH-Not cultured-Day0-rep2

source_name: human Hepatocytes (cFHHs) isolated from chimeric mice

value: Pooled cFHHs isolated from 3-4 chimeric mice of 14-17 weeks


title: 94-Bx2


title: 91-Bx1


title: 89-Bx1


title: cFHH-Not cultured-Day0-rep3


title: 91-Bx2


title: B10Dmel_WD_male_msl1_CyOGFP_R1


title: B9Dmel_WD_male_msl1_R3

value: msl-1 null mutant


title: D11_p4_rep1

description:
3xFlag-His-Avi tag
passage 4

value: male


title: 88-Bx2


title: Replicate 1

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

data_processing:
Base calling and trimming of adapter and index sequences was performed using bcl2fastq version 2.17.1.14.
For replicate 1, feature-barcode matrices were generated from FASTQ files using Cell Ranger v2.2.0 with default options.
For replicate 2, feature-barcode matrices were generated from FASTQ files using Cell Ranger v3.0.1 specifying the utilized chemistry with the command flag "--chemistry=SC3Pv3".
Genome_build: mm10

source_name: Foxd1Cre;Rosa-Tomato mouse kidneys

extract_protocol:
Dissected kidneys stored in RNA later solution (Invitrogen, Cat. AM7020). RNA was extracted with the QIAGEN's RNeasy Micro Kit (QIAGEN Cat. 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: mixed

tag: tissue

value: kidney


title: Replicate 2


title: 89-Bx2


title: 87-Bx2


title: B8Dmel_WD_male_msl1_R2


title: 87-Bx1


title: B6Dmel_WD_male_roX12_R4

value: roX1.SMC17A, roX2delta, Kindly provided by Victoria Meller

value: roX1 roX2 double null mutant


title: 85-Bx2

value: Post-transplant


title: cFHH-Not cultured-Day0-rep1


title: HCD34C-d16-control

city: Seattle

first: hongjie

last: wang

state: WA

address: 1959 NE Pacific Street

institute: University of washington

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build hg19 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq R library.
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library.
Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro, NCBI, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: gene counts

source_name: CD34+ cell

growth_protocol: Human CD34+ cells were obtained from G-CSF-mobilized healthy donors (Fred Hutchinson Cancer Research Center)

extract_protocol:
Total RNA was isolated with E.Z.N.A.® Total RNA Kit (Omega Bio-tek, Norcross, GA) according to the manufacturer`s protocol. The RNA concentration was measured with Nanodrop 2000c spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA) and integrity was assessed using Agilent 2200 Tapestation instrument (Agilent Technologies, Santa Clara, CA, USA).
Libraries were prepared according to Illumina's instructions. One microgram of total RNA was used to prepare Ribo-Zero RNA-Sequencing (RNA-Seq) libraries.   Briefly, Ribosomal RNA (rRNA) is removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads following Illumina Reference Guide (Illumina, San Diego, CA). After purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. First strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexamers and ProtoScript II Reverse Transcriptase (NEW ENGLAND BioLabs Inc.). In a second strand cDNA synthesis the RNA templates were removed, and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. The blunt-ended cDNA was cleaned up from the second strand reaction mix with beads. The 3`ends of the cDNA were then adenylated and followed by the ligation of indexing adaptors. PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.   The libraries were quantified and qualified using the High Sensitivity D1000 Screen Tape on an Agilent 2200 TapeStation instrument. The libraries were normalized, pooled and subjected to cluster and pair read sequencing was performed for 150 cycles on a HiSeq instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions.

treatment_protocol: CD34+ cells were transduced and expanded in erythroid differentiation medium for 16 days.

value: Hematopoietic stem cell

value: Cells transduced with HDAd5/35++-GFP/mgmt vector only


title: HCD34C-GFP

value: Cells transduced with HDAd5/35++-GFP/mgmt and HDAd5/35++-SB vectors


title: 85-Bx1

value: Pre-transplant

value: IRI-


title: B5Dmel_WD_male_roX12_R3


title: 82-Bx2

value: IRI+


title: 88-Bx1


title: 86-Bx1


title: BS-50-3wk-Juv-Unop-2

city: Albany

first: Ben

middle: Gregory

last: Szaro

state: NY

address: 1400 Washington Avenue

department: Biological Sciences

institute: University at Albany, State University of New York

description: 6 unoperated frog eyes, 3 weeks after contralateral orbital optic nerve crush

data_processing:
Read alignments were performed against Xenopus laevis gemome (Xenbase v9.1) using Bowtie2 (V2.2.9) and TopHat (v2.1.1), and annotated using the Mayball gene model.
Differential expression and associated analysis were carried out using Cufflinks/Cuffdiff2 (v2.2.1; per condition dispersion with a min. count of 10) and CummRbund (v2.16.0).
Genome_build: Xenopus laevis Xenbase v9.1
Supplementary_files_format_and_content: text files; FPKM read counts for each transcript

organism: Xenopus laevis

source_name: Whole eye

growth_protocol: All animals used in this study were purchased from Xenopus Express, Inc (Brooksville, FL). Prior to surgery, they were acclimated to the lab for at least one week, under a 12L:12D photoperiod, in tanks of condition water at 22C, and fed every other day.

extract_protocol:
Eyes for optic nerve crush studies were rapidly dissected and then homogenized immediately, pooling six eyes for each biological replicate. Because dissections of hindbrain required more time, each hindbrain was placed in 1 mL of RNAlater at room temperature over-night. RNAlater was then aspirated and five pooled hindbrains homogenized for each biological replicate. Total RNA was isolated using the RNA/DNA/Protein Purification kit from Norgen Biotek Corp. with DNase I treatment, following manufactuer's protocols.
Total RNA was enriched for mRNA by ribosomal RNA depletion, which was then used to prepare cDNA libraries using Illumina's TruSeq Stranded Total RNA LT Sample Prep Kit (A&B), with Ribo-Zero Gold.

treatment_protocol: Unilateral orbital optic nerve crushes (Zhao and Szaro 1994, doi: 10.1002/cne.903430112) and complete spinal cord transections (Gibbs and Szaro 2018, doi: 10.1101/pdb.prot101030) were performed on fully anesthetized animals (MS222).

value: albino, Xenopus Express

tag: age

value: 1-3 mos. postmetamorphic juvenile

tag: Sex

value: not determined


title: BS-51-3wk-Juv-Unop-3


title: 82-Bx1


title: 129-Bx2


title: 128-Bx2


title: B4Dmel_WD_male_roX12_R2


title: 129-Bx1


title: A7Dmel_WD_male_mle9_R3

value: Bloomington Drosophila Stock Center BDSC #5873

value: mle null mutant


title: BS-49-3wk-Juv-Unop-1


title: A6Dmel_WD_male_mle9_R2

value: male


title: 128-Bx1


title: B7Dmel_WD_male_msl1_R1

value: msl-1 null mutant


title: BS-48-3wk-Juv-OpticNerveCrushed-3

description: 6 operated frog eyes, 3 weeks after orbital optic nerve crush


title: BS-47-3wk-Juv-OpticNerveCrushed-2


title: 86-Bx2


title: 127-Bx1


title: BS-46-3wk-Juv-OpticNerveCrushed-1


title: 126-Bx1


title: A5Dmel_WD_male_mle9_R1


title: BS-44B-11d-Juv-Unop-2

description: 6 unoperated frog eyes, 11 days after contralateral orbital optic nerve crush


title: BS-45B-11d-Juv-Unop-3


title: A3Dmel_WD_male_msl2_227_R3

value: Bloomington Drosophila Stock Center BDSC #5871

value: msl-2 null mutant


title: A4Dmel_WD_male_msl2_227_R4


title: 126-Bx2


title: A2Dmel_WD_male_msl2_227_R2


title: BS-43B-11d-Juv-Unop-1


title: 125-Bx2


title: A1Dmel_WD_male_msl2_227_R1


title: PPF WT 2

city: Salt Lake City

first: Gabrielle

last: Kardon

state: Utah

department: Human Genetics

institute: University of Utah

data_processing:
Fastq files were aligned with STAR and samtools using command ~/STAR-2.4.0a/STAR --genomeDir $genomeDB --readFilesCommand zcat --seedSearchStartLmax 50 --runThreadN 4 --outSAMunmapped Within  --outFilterIntronMotifs RemoveNoncanonical  --readFilesIn $file --outStd SAM --outSAMmode Full --outSJfilterReads Unique --sjdbGTFfile $gtf | ~/samtools-1.3/samtools view -bS -> ${file}.bam
Samtools was then used to sort and index the aligned bam file and featurecounts was used to count reads per feature: path_to_/featureCounts  -s 0 -O -t exon -g gene_name -a $gtf -o ./featureCountsResult/$bam_base.counts.txt.temp $bam tail -n +3 $bam_base.counts.txt.temp | awk '{print $1 "\t" $7}' > $bam_base.counts.txt.temp.body  echo -e "gene\t$bam_base" > $bam_base.counts.txt  cat $bam_base.counts.txt.temp.body >> $bam_base.counts.txt
Transcript counts were then normalized to transcript per million based on total reads and gene lengths in R, these normalized expression values were then used to determine expression of CDH and diaphragm related genes
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are gene coordinates, gene names, gene lenghts in base pairs, the number of gene feature counts and the TPM

source_name: Pleuroperitneal fold

extract_protocol:
Pleuroperitoneal folds (PPFs) were isolated from wild-type E12.5 mouse embryos by cutting embryos just above the hindlimbs and below the forelimbs and removing the heart and lungs cranially, leaving the trunk with attached nascent diaphragm. The PPFs were manually dissected and stored in RNAlater (Thermo Fisher, #AM7020) at -80°c. RNA was isolated using a RNeasy Micro Kit (Qiagen, #74004), RNA quality confirmed with RNA TapeStation ScreenTape Assay (Agilent, # 5067-5576), and sequenced using TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed, 129s/SvlmJ-C57/BL6J

value: Pleuroperitneal fold

value: Embryonic day 12.5

value: wild type


title: 127-Bx2

value: Post-transplant


title: BS-42B-11d-Juv-OpticNerveCrushed-3

description: 6 operated frog eyes, 11 days after orbital optic nerve crush


title: PPF WT 1


title: B1Dmel_WD_male_mle9_CyOGFP_R2

value: mle heterozygous


title: RP 48hpi Rep. 2

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg

description: ribosome footprint RNA

data_processing:
Library strategy: Ribosome profiling
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 1.0 was used to align all reads to the mouse genome, Ensembl transcripts (v87), ribosomal rRNA, the MCMV genome (NC_004065) and the MCMV transcripts. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
At each alignment position a greedy algorithm successively discarded alignments such that no read sequence remained that has hamming distance 1 to any other read. The total number of unique sequences was taken as the conservative fragment count.
PRICE 1.0.1 was used to call ORFs.
Genome_build: mm10, NC_004065
Supplementary_files_format_and_content: The output table of PRICE contains all called ORFs with associated scores (start codon prediction score, p value) and total estimated codon activity per condition as described.

source_name: MCMV infected cells 48hpi

growth_protocol: NIH-3T3 cells were grown in DMEM supplemented with 10% NCS and P/S. Cells were split 24h prior to infection.

extract_protocol:
Ribosome profiling was performed as described in Rutkowski et al. Nature Communications 2015.
50bp SE sequencing (including barcode)

treatment_protocol: NIH-3T3 cells were split 24h prior to infection and seeded on a full six-well plate per condition at 5x10e05 cells / well. 24h later, cells were infected with wildtype MCMV (BAC-derived Smith strain, m129-repair) at a multiplicity of infection (MOI) of 10 using centrifugal enhancement (30min 800g) calculating with 1x10e06 cells per well. Inoccullum was replaced with fresh media after 1h. End of centrifugation was considered begin of infection. Ribosome profiling was performed at the indicated times of infection as described in Rutkowski et al., Nature Communications 2015.

tag: cell line

tag: infected with

value: wildtype MCMV


title: RP 48hpi Rep. 1

description: ribosome footprint RNA


title: A12Dmel_WD_male_mle9_CyOGFP_R1


title: BS-40B-11d-Juv-OpticNerveCrushed-1


title: A11Dmel_WD_male_msl2_227_CyOGFP_R4

value: msl-2 heterozygous


title: 125-Bx1

tag: timepoint

value: Pre-transplant

value: IRI-


title: 124-Bx1

tag: iri

value: IRI+


title: 124-Bx2


title: 123-Bx2


title: 123-Bx1


title: RP Mock Rep. 2

description: ribosome footprint RNA

source_name: uninfected cells

value: nothing (mock)


title: RP Mock Rep. 1

description: ribosome footprint RNA


title: BS-38-3d-Juv-Unop-2

description: 6 unoperated frog eyes, 3 days after contralateral orbital optic nerve crush

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile

value: not determined


title: BS-39B-3d-Juv-Unop-3


title: A9Dmel_WD_male_msl2_227_CyOGFP_R2

value: male

value: Bloomington Drosophila Stock Center BDSC #5871


title: A8Dmel_WD_male_msl2_227_CyOGFP_R1


title: 122-Bx2


title: A549 cell treating with siRNA #1 for EPEL

city: Goyang

first: Seong-min

last: Park

address: Ilsan-ro

country: South Korea

institute: NCC

description:
replicate 1
siEPEL #1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio

source_name: A549_siRNA for EPEL

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: A549 cells (ATCC) were maintained in complete RPMI 1640 medium (Hyclone) at 37°C in a humidified 5% CO2 incubator. The complete media was supplemented with 10% fetal bovine serum (Hyclone), 100 U/ml penicillin/streptomycin (WelGENE), and 2 mM L-glutamine (Hyclone).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For siRNA transfection, 150000 ~ 200000 lung cancer cells were plated in each of a 6-well plate and incubated overnight. The siRNAs or non-targeting controls at a concentration of 50 nM were transfected into lung cancer cells using Lipofectamin 2000 in Opti-MEM media. After 4 hours of incubation, the media were changed to complete media, and 48 hours after transfection, gene knockdown was confirmed by RT-qPCR.

value: lung cancer cells

tag: treated with

value: siRNA #1 for EPEL


title: Dmel_male_H4K16ac_roX12_Input

description: roX1 roX2 double null mutant

data_processing:
Paired-end 75 bp reads with a minimal overlap of 10 bp were merged and Illumina adapters were trimmed using bbmerge (v7.3). Only merged reads were kept and mapped to dm6 with bowtie2 (v2.2.3) using parameters: --sensitive, --end-to-end for histones and --sensitive --local for all other profiles.
Coverage files were generated with deepTools3 (v3.0.1) bamCompare with a binsize of 2. Duplicate reads and reads with a mapping quality < 10 were removed, the X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H4K16ac; Input subtraction for Drosophila MSL2-Flag.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files of uniquely mapped reads

source_name: Third instar larvae

extract_protocol:
Larvae were dissected and the front part fixed at RT for 15 min with 1% or 0.2% Formaldehyde. Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using Phenol-Chloroform Extraction and Ethanol precipitation.
NEB Next Ultra II

treatment_protocol: Third instar larvae were collected, the heterozygous (CyO-GFP+) larvae were discarded. Males / Females (non-fluorescent larvae) were separated by visual inspection of the genitals.

value: roX1.SMC17A, roX2{delta}, Kindly provided by Victoria Meller

tag: chip antibody

value: none, input


title: BS-37-3d-Juv-Unop-1


title: Ctrl IgG

city: Lund

first: Christopher

last: Douse

address: Sölvegatan 17

institute: Lund University

data_processing:
Library strategy: CUT&RUN
Read alignment with bowtie2 (v2.3.4.3) --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
For CUT&RUN, conversion to bedgraph format and normalization was done with bedtools genomecov (v2.27.1; -bg -scale), where the scale factor was 1e4 divided by the number of reads mapping to the yeast spike-in genome (R64-1-1).
See also GSE155693
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with normalized coverage plots
Supplementary_files_format_and_content: bed file listing 393 TASOR-regulated H3K9me3 loci

source_name: HeLa cells

growth_protocol: HeLa and HEK293T cells (ECACC) were grown in RPMI plus 10% fetal calf serum (FCS) and penicillin/streptomycin (100 U/mL). Cell lines were routinely tested for mycoplasma contamination using the MycoAlert detection kit (Lonza). Exogenous expression of TASOR variants was done with lentiviral vectors pHRSIN-pSFFV-V5-PPHLN-WPRE-pPGK-Hygro. Lentivirus was generated through the triple transfection of HEK 293T cells with the lentiviral transfer vector plus the two packaging plasmids pCMVΔR8.91 and pMD.G using TransIT-293 transfection reagent (Mirus) as recommended by the manufacturer. Viral supernatant was typically harvested 48 h post-transfection, cell debris removed using a 0.45 µm filter, and PPHLN KO HeLa cells transduced by spin infection at 1,000 g for 90 min.

extract_protocol:
DNA was cleaved by antibody-directed MNase (CUT&RUN) treatment of digitonin-permeabilised cells and purified from the cell supernatant
KAPA Hyperprep kit was used as per instructions. Final cleanup was done with 1.1x KAPA SPRI beads

value: HeLa

value: Clone bearing HUSH-repressed GFP transgene reporter

tag: antibody

value: guinea pig α-rabbit IgG CSB-PA00150E1Gp


title: 122-Bx1


title: BS-36B-3d-Juv-OpticNerveCrushed-3

description: 6 operated frog eyes, 3 days after orbital optic nerve crush


title: A549 cell treating with siRNA #3 for EPEL

description:
replicate 3
siEPEL #3

tag: cell type

value: siRNA #3 for EPEL


title: BS-41-11d-Juv-OpticNerveCrushed-2


title: A549 cell treating with siRNA #2 for EPEL

description:
replicate 2
siEPEL #2

value: siRNA #2 for EPEL


title: A549 cell treating with a non-targeting control siRNA

description:
control
siControl

source_name: A549_non-targeting control siRNA

value: non-targeting control siRNA


title: Dmel_male_H4K16ac_roX12_ChIP

description: roX1 roX2 double null mutant

value: Anti-acetyl-Histone H4 (Lys16) Antibody (Merck Milipore 07-329)


title: Ctrl H3K9me3 rep2

value: rabbit anti-H3K9me3 abcam ab8898


title: 121-Bx2

value: Post-transplant

value: IRI-


title: 121-Bx1

value: Pre-transplant


title: 1d127 PPHLN comp H3K9me3 rep2

value: PPHLN KO with expression of 1d127 V5-PPHLN


title: BS-35-3d-Juv-OpticNerveCrushed-2

value: albino, Xenopus Express

value: 1-3 mos. postmetamorphic juvenile

value: not determined


title: 1d127 PPHLN comp H3K9me3 rep1


title: 120-Bx2

value: IRI+


title: BS-34B-3d-Juv-OpticNerveCrushed-1


title: Dmel_male_H4K16ac_msl1_Input

description: msl-1 null mutant

value: none, input

value: male


title: Dmel_male_H4K16ac_msl1_ChIP

description: msl-1 null mutant


title: Dmel_male_H4K16ac_mle9_Input

description: mle null mutant

value: Bloomington Drosophila Stock Center BDSC #5873


title: BS-33-NA-Juv-Naive-3

description: 6 surgically naive frog eyes


title: Dmel_male_H4K16ac_mle9_ChIP

description: mle null mutant


title: L356R PPHLN comp H3K9me3 rep2

value: HeLa

value: PPHLN KO with expression of L356R V5-PPHLN


title: BS-32-NA-Juv-Naive-2

description: 6 surgically naive frog eyes


title: 118-Bx2


title: BS-31-NA-Juv-Naive-1

description: 6 surgically naive frog eyes


title: Dmel_male_H4K16ac_Input

description: wild-type

value: White-eyed (w1118) Oregon-R


title: BS-30-3wk-Juv-Transected-3

description: 5 frogs, 3 weeks after spinal cord transection

source_name: Hindbrain


title: WT PPHLN comp H3K9me3 rep1

value: PPHLN KO with expression of WT V5-PPHLN


title: 120-Bx1


title: 117-Bx2


title: 118-Bx1


title: 117-Bx1


title: BS-28-3wk-Juv-Transected-1


title: Dmel_male_31_MSL2Flag_hsRING_Input

description: hs = human RING domain swap hybrid

value: msl-2.227 / msl-2.km ; tub-Gal4/UAS-msl-2(hsRING)::3xFlag


title: PPHLN KO H3K9me3 rep1

value: Reporter clone with PPHLN KO

value: rabbit anti-H3K9me3 abcam ab8898


title: BS-29-3wk-Juv-Transected-2


title: PPHLN KO H3K9me3 rep2


title: Dmel_male_31_MSL2Flag_hsRING_ChIP

description: hs = human RING domain swap hybrid

value: Monoclonal ANTI-FLAG® M2 antibody (Sigma F1804)


title: 116-Bx2

value: Post-transplant

value: IRI-


title: BS-27-1wk-Juv-Transected-3

description: 5 frogs, 1 week after spinal cord transection

value: albino, Xenopus Express


title: Dmel_male_H4K16ac_ChIP Sample

description: wild-type

value: Anti-acetyl-Histone H4 (Lys16) Antibody (Merck Milipore 07-329)


title: Dmel_male_23_MSL2Flag_Input

description: wild-type Drosophila melanogaster msl-2 transgene

value: msl-2.227 / msl-2.km ; tub-Gal4/UAS-msl-2::3xFlag


title: 116-Bx1

value: Pre-transplant


title: DAs-3

city: Beijing

first: Fangfei

last: Nie

address: 49 North Garden Rd.,Haidian District

department: Department of Plastic Surgery

country: China

institute: Peking university third hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
EdgeR package(Version 3.3.3) was used for the differential expression analysis.P-value of 0.05 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Dedifferentiated adipose Cells

growth_protocol: Cells were cultured in complete culture medium for adult ADSCs ( Cyagen,CHN)

extract_protocol:
Cultured cells were harvested with trypsin digestion.The total RNA was extracted and tested to be qualified.mRNA were enriched using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and 150 bp paired-end reads were generated.

tag: passages

tag: donor's age

tag: biopsy site

value: thigh


title: BS-26-1wk-Juv-Transected-2

tag: strain

value: 1-3 mos. postmetamorphic juvenile

value: not determined


title: L356R PPHLN comp H3K9me3 rep1

value: HeLa

tag: genotype


title: DAs-2


title: Dmel_male_23_MSL2Flag_ChIP

tag: gender

value: male


title: 115-Bx2

source_name: Liver


title: WT PPHLN comp H3K9me3 rep2


title: DAs-1

value: Abdomen


title: Dmel_male_19_MSL2Flag_hsCTD_Input_Rep1

description: hs = human CTD domain swap hybrid

value: msl-2.227 / msl-2.km ; tub-Gal4/UAS-msl-2(hsCTD)::3xFlag

value: none, input


title: BS-25-1wk-Juv-Transected-1


title: 114-Bx2


title: ADSCs-3

source_name: Adipose-derived stem cells


title: Dmel_male_19_MSL2Flag_hsCTD_ChIP

description: hs = human CTD domain swap hybrid


title: BS-23-3d-Juv-Transected-2

description: 5 frogs, 3 days after spinal cord transection


title: Dmel_male_18_MSL2Flag_hsCXC_CTD_Input

description: hs = human CXC-CTD domain swap hybrid

value: msl-2.227 / msl-2.km ; tub-Gal4/UAS-msl-2(hsCXC-CTD)::3xFlag


title: 114-Bx1


title: Dmel_male_18_MSL2Flag_hsCXC_CTD_ChIP

description: hs = human CXC-CTD domain swap hybrid


title: 113-Bx2

value: IRI+


title: BS-22-3d-Juv-Transected-1


title: BS-21R-NA-Juv-Unop-3

description: 5 unoperated frogs


title: Dmel_female_H4K16ac_Input

description: wild-type

value: White-eyed (w1118) Oregon-R

value: female


title: ADSCs-1


title: BS-20R-NA-Juv-Unop-2

description: 5 unoperated frogs


title: Dmel_female_H4K16ac_ChIP Sample

description: wild-type


title: 113-Bx1


title: BS-19R-NA-Juv-Unop-1

description: 5 unoperated frogs


title: 115-Bx1

value: IRI-


title: BS-24-3d-Juv-Transected-3

value: albino, Xenopus Express


title: Dmel_female_18_MSL2Flag_hsCXC_CTD_Input

description: hs = human CXC-CTD domain swap hybrid


title: BS-18-3wk-Tadpole-Control-3

description: 5 unoperated tadpoles, age-matched with 3 week, spinal cord transected tadpoles

value: stage 53 tadpole


title: BS-17-3wk-Tadpole-Control-2


title: 112-Bx1


title: 111-Bx2

value: Post-transplant


title: ADSCs-2


title: BS-16-3wk-Tadpole-Control-1


title: BilIN of Patient 15 [B15]

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

institute: Heidelberg University Hospital

description: nCounter® Technology

hyb_protocol: miRNAs were  hybridized for 16h at 65°C to a capture/reporter probe pair equipped with a fluorescent barcode

scan_protocol: nCounter Digital Analyzer

data_processing:
nSolver version 3.0
Raw data was normalised according to Nanostring standart procedures. The geometric mean of included negative controls (background subtraction) and positive controls (computing normalisation factor) was calculated in order to diminish differences in hybridization. The expression of every miRNA was then normalised by geometric mean of the top 100 most expressed miRNAs.

label: barcode

source_name: BilIN of Patient 15

label_protocol: 100ng total RNA were used as input

growth_protocol: FFPE tissue

extract_protocol: AllPrep DNA/RNA FFPE Kit Qiagen

treatment_protocol: Laser Capture Microdissection

tag: subject id

value: patient 15

tag: subject status

value: patient with distal cholangiocarcinoma

tag: tissue

value: BilIN


title: invasive dCCA of Patient 15 [T15]

description: nCounter® Technology

source_name: invasive dCCA of Patient 15

value: invasive dCCA


title: invasive dCCA of Patient 13 [T13]

description: nCounter® Technology

source_name: invasive dCCA of Patient 13

value: patient 13


title: 111-Bx1

value: Pre-transplant


title: non-neoplastic biliary epithelia of Patient 15 [N15]

description: nCounter® Technology

value: non-neoplastic biliary epithelia


title: MDA-MB-231 nanoNOMe

city: Baltimore

first: Isac

last: Lee

state: MD

address: 3400 N. Charles St.

institute: Johns Hopkins University

data_processing:
Library strategy: Oxford Nanopore Sequencing (NOMe-seq)
Raw current signals were converted to DNA sequences using Guppy version 3.0.3 (ONT), using the “high-accuracy” basecalling model.
DNA sequences were aligned to hg38 human reference genome without alternative contigs using NGMLR version 0.2.8 with default settings for aligning Oxford nanopore reads (-x ont)
CpG and GpC methylation were called using nanopolish version 0.11.1.
Nanopolish outputs were converted to methylation bed files (one line per read) as specified by https://github.com/isaclee/nanopore-methylation-utilities using mtsv2bedGraph.py
Methylation bed files were subsequently converted to bismark-style methylation counts (one line per locus)  using parseMethylbed.py frequency in https://github.com/isaclee/nanopore-methylation-utilities
Single-read anallysis was performed on select genomic contexts (CTCF binding sites and gene promoter regions), and the resulting data was deposited into Zenodo (https://zenodo.org/record/3969567)
Genome_build: hg38
Supplementary_files_format_and_content: Methylation Counts files contain the counts of methylation states for each observed genomic locus in the same format as bismark cytosine reports : <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context> (https://rawgit.com/FelixKrueger/Bismark/master/Docs/Bismark_User_Guide.html)

source_name: nanoNOMe on MDA-MB-231 Cell line

growth_protocol: Cell lines were grown according to manufacturer's specifications

extract_protocol:
Samples were treated with proteinase K (NEB) at 55 °C for > 2 hours, and DNA was extracted via phenol:chloroform extraction and ethanol precipitation. After proteinase K treatment, and in all following steps, samples were handled with care using large orifice pipette tips to avoid excessive fragmentation of DNA.
Purified gDNA was prepared for nanopore sequencing following the protocol in the genomic sequencing by ligation kit LSK-SQK108 (ONT). Samples were first sheared to ~10 kb using G-tubes (Covaris): by centrifuging 2-3 μg of unfragmented gDNA at 5,000x g for 1 minute, then inverting the tube and centrifuging again. We sheared the DNA to 10 kb because it produces long fragments of DNA while maximizing the yield of nanopore sequencing. Shearing to larger sizes or unsheared DNA may be used to maximize the length of sequenced reads, with the caveat that sequencing yield will drop. In two samples (GM12878 samples 8 and 9), we targeted 20kb fragments, with an additional step of removing short fragments using the Short Read Eliminator module by Circulomics, following the manufacturer’s specifications. The sheared samples were end-repaired and dA-tailed using NEBnext Ultra II end-repair module (NEB), followed by clean-up using 1x v/v AMPure XP beads (Beckman Coulter). Sequencing adaptors, comprised of leader adaptor DNA and motor proteins, were ligated to the end-prepared DNA fragments using Blunt/TA Ligase Master Mix (NEB), followed by clean-up using 0.4x v/v AMPure XP beads and sequencing kit reagents. >400 ng of adaptor ligated samples per flow cell were loaded onto FLO-MIN106 or PRO-002 flowcells and run on MinION Mk1b, GridION, or PromethION sequencers for up to 72 hours.

treatment_protocol: NOMe-seq was performed on the cells with adjustments for nanopore sequencing. Cells were collected by trypsinization, then nuclei were extracted by incubating in resuspension buffer (100 mM Tris-Cl, pH 7.4, 100 mM NaCl, 30 mM MgCl2) with 0.25 % NP-40 for 5 minutes on ice. Intact nuclei were collected by centrifugation for 5 minutes at 500xg at 4 °C. Nuclei were subjected to a methylation labeling reaction using a solution of 1x M. CviPI Reaction Buffer (NEB), 300 mM sucrose, 96 μM S-adenosylmethionine (SAM; New England Biolabs, NEB), and 200 U M. CviPI (NEB) in 500 μL volume per 500,000 nuclei. The reaction mixture was incubated at 37 °C with shaking on a thermomixer at 1,000 rpm for 15 minutes. SAM was replenished at 96 μM at 7.5 minutes into the reaction. The reaction was stopped by the addition of an equal volume of stop solution (20 mM Tris-Cl, pH 7.9, 600 mM NaCl, 1% SDS, 10 mM disodium EDTA).

tag: cell line

value: Basal breast carcinoma cell line


title: 109-Bx2


title: non-neoplastic biliary epithelia of Patient 13 [N13]

description: nCounter® Technology


title: BilIN of Patient 13 [B13]

description: nCounter® Technology

source_name: BilIN of Patient 13


title: MCF-7 nanoNOMe

source_name: nanoNOMe on MCF-7 Cell line

value: Luminal breast carcinoma cell line


title: 109-Bx1


title: BS-15-1wk-Tadpole-Control-3

description: 5 unoperated tadpoles, age-matched with 1 week, spinal cord transected tadpoles

tag: age

tag: Sex

value: not determined


title: 112-Bx2

tag: timepoint

tag: iri

value: IRI+


title: MCF-10A nanoNOMe

source_name: nanoNOMe on MCF-10A Cell line

value: Mammary epithelial cell line


title: BS-14-1wk-Tadpole-Control-2


title: 108-Bx2


title: Dmel_female_18_MSL2Flag_hsCXC_CTD_ChIP

city: Freiburg

first: Asifa

last: Akhtar

institute: Max Planck Institute of Immunobiology and Epigenetics

description: hs = human CXC-CTD domain swap hybrid

value: msl-2.227 / msl-2.km ; tub-Gal4/UAS-msl-2(hsCXC-CTD)::3xFlag

tag: chip antibody

value: Monoclonal ANTI-FLAG® M2 antibody (Sigma F1804)

value: female


title: invasive dCCA of Patient  [T7]

description: nCounter® Technology

source_name: invasive dCCA of Patient

value: patient 7


title: BS-13-1wk-Tadpole-Control-1

value: albino, Xenopus Express

value: stage 53 tadpole


title: Mcm4_Input_G0_105_combined

city: Albuquerque

first: Po-Hsuen

state: NM

address: MSC 08 4660, 1 University of New Mexico

department: Molecular Genetics & Microbiology

institute: University of New Mexico Health Science Center

data_processing:
All DNA sequencing reads were trimmed of barcode sequences using fastq-multx, with 5 bp removed to account for the barcode.
For BrdU IP-seq analysis, the trimmed data were aligned to the Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2) using Bowtie2 and then sorted using Samtools. BrdU IP-seq data analysis was performed as described previously with the following modifications.  For each labeling period, aligned sequences were filtered and sorted into 50-bp nonoverlapping bins using bamCompare from the deepTools package.  Each IP bin was normalized after dividing by its corresponding Input bin to generate the IP/In ratio, which was median-smoothed over a 2000 bp window across all time course experiments.  Two biological replicates were averaged, and to facilitate comparisons between G1 and G0 experiments, the data were scaled to the maximum average G1 signal among the time course points, which was arbitrarily set as “1”. In parallel, BrdU enriched peaks were called using MACS2 (P < 0.01), and origin peaks were identified by their overlap with at least one ARS (autonomously replicating sequence; replication origin) across the samples during the time course experiment in both replicates.  ARS co-ordinates were obtained from the oriDB database.
For Mcm4-Myc ChIP-seq analysis, the trimmed data were aligned to the Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2) using BWA.  Aligned sequences from Mcm4 ChIP-seq samples from G1 arrested cells and from G0 cells released into YPD + HU for 90 and 105 min were filtered and binned into 50-bp nonoverlapping bins, and the IP/In ratio was median-smoothed over a 2000 bp window as described above.  Two biological replicates were averaged, and both the G1 and G0 data were scaled to the maximum average G1 signal, set as “1”.  Mcm4-Myc enriched peaks were called using MACS2 (P < 0.01), and origin peaks were identified by their overlap with at least one identified ARS.
Genome_build: Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2)
Supplementary_files_format_and_content: bedGraph

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD medium (1% yeast extract, 2% peptone, 2% dextrose) at 30°C to a density of OD600 = 0.4 and arrested in G1 phase by the addition of alpha-factor (5 μg/mL; United Biochemical Research) at 0, 45, and 90 min for a total incubation time of 135 min. G0 quiescent (Q) cells were isolated by Percoll gradient centrifugation 7 days after culture inoculation. G1 cells were released into YPD + 60 μg/ml pronase + 5 mM CaCl2 + 0.2 M HU, and G0 cells were released into YPD + 0.2 M HU before collected for sequencing.

extract_protocol:
For BrdU IP-seq, genomic DNA was isolated from each pulse-labelled sample by the “smash and grab” protocol (Hoffman, 1987), and 0.2 mg/ml RNase A was added for 30 min at 37C, followed by addition of 0.1 mg/ml of Proteinase K for 30 min at 50C.  DNA was purified with a Qiagen QIAquick PCR purification kit and its concentration was measured by an Invitrogen Qubit 2.0 Fluorometer.  DNA was transferred to a 50 l Covaris microTUBE and sheared to 200 – 250 bp using a Covaris M220 Focused-ultrasonicator (peak power: 75W; duty factor: 10%; cycles per burst: 200; treatment time: 400 sec). For Mcm4 ChIP-seq, twenty-four OD600 units of cells were collected and fixed with 1% formaldehyde for 15 min at room temperature.  Fixation was stopped by the addition of glycine to a final concentration of 125 mM for 5 min and the cells were washed with 50 mM Tris, pH 7.4, followed by centrifugation. Cell pellets were resuspended in 0.6 ml of ice-cold FA lysis buffer (1% Triton X-100, 0.1% sodium deoxycholate, 50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0) supplemented with 1x protease inhibitor cocktail (Millipore-Sigma) and 1 mM of phenylmethylsulfonyl fluoride (PMSF), and then vortexed at highest speed with an equal volume of acid-washed glass beads (Millipore-Sigma) for 25 min at 4°C.  Cell lysates were sonicated using a Branson 250 Sonifier to generate DNA fragments of 200-500 bp.  After centrifugation for 15 min at 17,900 x g, soluble chromatin was collected from the supernatant fraction and protein concentration was determined by a Bradford assay.  Between 1-1.5 mg of chromatin was diluted in 1 ml of FA lysis buffer, and 20 µl was set aside as Input.  Anti-Myc (Millipore-Sigma) or anti-HA (Biolegend) antibodies were added to the remaining chromatin solution and incubation was continued overnight at 4°C  Protein G agarose beads (Invitrogen) were added for 2 h at 4°C, and the beads were then sequentially washed with FA lysis buffer, wash buffer I (1% Triton X-100, 0.1% sodium deoxycholate, 50 mM HEPES-KOH, pH 7.5, 500 mM NaCl, 1 mM EDTA, pH 8.0), wash buffer II (0.5% sodium deoxycholate, 0.5% NP-40, 10 mM Tris, pH 8.0, 250 mM LiCl), and TE, pH 8.0. Immunocomplexes were eluted from beads by incubation with 0.2 ml of elution buffer (1% SDS in TE) for 20 min at 65°C. Immunoprecipitated and Input samples were incubated with pronase solution (2 mg/ml pronase and 10 mM CaCl2) for 2 h at 42°C, followed by reverse crosslinking for 14-16 h at 65°C. DNA was purified with a Qiagen QIAquick PCR purification kit.
For BrdU IP-seq, extracted genomic DNA was transferred to a 50 ml Covaris microTUBE and sheared to 200 – 250 bp using a Covaris M220 Focused-ultrasonicator (peak power: 75W; duty factor: 10%; cycles per burst: 200; treatment time: 400 sec).  One microgram of sheared DNA was end-repaired and ligated to Ion Torrent-compatible barcode adapters (Ion XpressTM Barcode Adapters, Invitrogen) using an Ion Xpress Plus Fragment Library kit (Invitrogen). The adapter-ligated DNA was purified by Agencourt AMPure XP Reagent and DNA concentration was measured by Qubit.  An equal concentration of each pulse-labeled G1 or G0 released DNA sample was pooled for immunoprecipitation (IP) and 20 ng of the mixture was set aside as input (IN) DNA. The pooled DNA was heated for 10 min at 95°C, followed by a snap cooling on ice.  Immunoprecipitation was performed with a 1:250 dilution of anti-BrdU antibody (GE Healthcare, RPN202) for 2h at 4°C, followed by the chromatin immunoprecipitation procedure described above. For Mcm4 ChIP-seq, multiple immunoprecipitation reactions were carried out in order to obtain a total of ~5 mg of immunoprecipitated DNA per sample.  For each sample, 5 mg of DNA was extracted from lysates and processed in parallel as input DNA.  IP and Input DNAs were processed for library preparation, including DNA end-repairing, barcoded adapter ligation, and PCR amplification using Ion Xpress Plus Fragment Library kit (Invitrogen).

tag: cell cycle stage

tag: time point

value: G0 105 min post release into HU

tag: antibody

value: Anti-Myc (Millipore-Sigma, 05-419)


title: 108-Bx1


title: BilIN of Patient 7 [B7]

description: nCounter® Technology

source_name: BilIN of Patient 7

value: patient with distal cholangiocarcinoma

value: BilIN


title: Mcm4_Input_G0_90_combined

value: G0 90 min post release into HU


title: 107-Bx2

value: Post-transplant

value: IRI-


title: non-neoplastic biliary epithelia of Patient 7 [N7]

description: nCounter® Technology

value: non-neoplastic biliary epithelia


title: BS-11-3wk-Tadpole-Transected-2

description: 5 tadpoles, 3 weeks after spinal cord transection

value: not determined


title: Mcm4_Input_G0_0_combined

value: G0 0 min post release into HU


title: invasive dCCA of Patient 6 [T6]

description: nCounter® Technology

source_name: invasive dCCA of Patient 6

value: patient 6

value: invasive dCCA


title: 107-Bx1

value: Pre-transplant


title: 106-Bx2

value: IRI+


title: BS-10-3wk-Tadpole-Transected-1


title: Mcm4_ChIP_G0_105_combined


title: non-neoplastic biliary epithelia of Patient 6 [N6]

description: nCounter® Technology


title: BilIN of Patient 6 [B6]

description: nCounter® Technology

source_name: BilIN of Patient 6


title: 106-Bx1


title: Mcm4_ChIP_G0_90_combined


title: BS-08-1wk-Tadpole-Transected-2

description: 5 tadpoles, 1 week after spinal cord transection


title: Mcm4_ChIP_G0_0_combined


title: 105-Bx2


title: invasive dCCA of Patient 12 [T12]

description: nCounter® Technology

source_name: invasive dCCA of Patient 12

value: patient 12


title: BS-07-1wk-Tadpole-Transected-1

value: albino, Xenopus Express


title: BS-12-3wk-Tadpole-Transected-3

value: stage 53 tadpole


title: Mcm4_ChIP_G1_combined

value: G1 0 min post release into HU


title: BilIN of Patient 12 [B12]

description: nCounter® Technology

source_name: BilIN of Patient 12


title: non-neoplastic biliary epithelia of Patient 12 [N12]

description: nCounter® Technology


title: BS-06-3d-Tadpole-Transected-3

description: 5 tadpoles, 3 days after spinal cord transection

source_name: Hindbrain


title: 105-Bx1


title: 103-Bx2


title: BS-05-3d-Tadpole-Transected-2


title: 103-Bx1


title: BS-04-3d-Tadpole-Transected-1


title: BrdU_Input_G0_165_combined

value: BrdU pulse-labeling 140-160 min post release into HU

value: Anti-BrdU (GE Healthcare, RPN202)


title: BrdU_Input_G0_145_combined

value: BrdU pulse-labeling 125-145 min post release into HU


title: invasive dCCA of Patient 11 [T11]

description: nCounter® Technology

source_name: invasive dCCA of Patient 11

value: patient 11

value: patient with distal cholangiocarcinoma


title: Mcm4_Input_G1_combined

value: Anti-Myc (Millipore-Sigma, 05-419)


title: BilIN of Patient 11 [B11]

description: nCounter® Technology

source_name: BilIN of Patient 11

value: BilIN


title: BS-09-1wk-Tadpole-Transected-3

value: not determined


title: 102-Bx2

source_name: Liver

value: Post-transplant


title: BS-03-NA-Tadpole-Unop-3

description: 5 unoperated tadpoles, age-matched with 3 day, spinal cord transected tadpoles


title: BrdU_Input_G0_130_combined

value: BrdU pulse-labeling 110-130 min post release into HU


title: BrdU_Input_G0_115_combined

value: BrdU pulse-labeling 95-115 min post release into HU


title: 102-Bx1

value: Pre-transplant


title: BS-02-NA-Tadpole-Unop-2


title: 100-Bx2

value: IRI-


title: BrdU_Input_G0_100_combined

value: BrdU pulse-labeling 80-100 min post release into HU


title: BS-01-NA-Tadpole-Unop-1

value: albino, Xenopus Express


title: BrdU_Input_G0_85_combined

value: BrdU pulse-labeling 65-85 min post release into HU


title: invasive dCCA of Patient 10 [T10]

description: nCounter® Technology

source_name: invasive dCCA of Patient 10

value: patient 10

value: invasive dCCA


title: 100-Bx1


title: EB14_loxp_gDNA_d9_eb10

city: Boston

first: Bradley

last: Bernstein

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description:
EB_day14_loxp_gDNA_d9_eb10
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

data_processing:
Sequencing RNA libraries, passed through general quality filter such as cluster density, total yield, and per-cycle base quality, were then split by library barcodes using bcl2fastq.
R2 reads were demultiplexed into separate files based on the cell barcode from R1 and mapped to a mouse reference genome (mm9) by Bowtie2. After eliminating reads sharing the same UMI by htseq-count, an accurate molecule count for each gene was generated and converted to the number of UMIs into transcript counts through binomial statistics (CEL-seq2).
Nanopore sequencing reads were converted to fastq files by Guppy (v2.3.5) and then demultiplexed to the each cell based on its matched cell barcode sequence with the highest mapping score by minimap2 with default parameters.
To detect tandem-loxP, different loxP flanking sequences were mapped to the demultiplexed nanopore sequence (minimap2) then assembled into a full tandem-loxP sequence based on their position in the nanopore sequence. Due to the sequencing error, we selected the top 1 combination with additional filter: 1) over 30 reads, 2) outlier from others, 3) full length with upstream and downstream sequence.
To detect the UCI, we first mapped the upstream and downstream of the UCI sequence to nanopore reads by minimap2 then extracted the sequence between M13F and WPRE_M13R_HSV. Due to the sequencing error, we selected the top 1 sequence with additional filter: 1) over 30 reads, 2) outlier from others, 3) represented by the sequence from UCI plasmid.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include UMI count values for each Sample.

source_name: mESC (Mouse embryoid body at day 0)

growth_protocol:
Mouse v6.5 ESCs were cultured with feeder cells (mouse embryonic fibroblasts (MEF)) in knockout DMEM media supplemented with 15% FBS, and 0.01% Leukemia inhibitory factor (LIF). The media was replenished every day and cells were split every two days.
For differentiation, we detached and dissociated ESCs to single cells. MEFs were further removed by incubating single cell suspensions on a 100mm tissue culture dish for 40 minutes at 37°C. We seeded 1000 cells per well micro-well plate (STEMCELL Technologies) in EB media (mESC media without LIF). For inducible barcoding experiments, we seeded FACS sorted RFP+/GFP-/BFPmid cells. After 4 days of EB differentiation in the micro-well plate, we collected EBs and transferred them to 100mm petri dishes and pursued spontaneous differentiation for another 10 days. EB media was changed every day (micro-well plate) or every other day (petri dish) during EB differentiation.

extract_protocol:
mESC and EBs were dissociated by trypsin to single cells and sorted into 384 well plates. After freeze and thaw for twice, we performed a reverse transcription and second strand synthesis, then pooled samples and ran IVT. For DNA extraction (30%), before pooling, we added unique primers (DNA adapter) involving identical cell barcode with RNA-adapter, targeting dual-barcode region of genomic DNA to each well, and then amplified the region by PCR. For RNA extraction (70%), after 2nd reverse transcription, we amplified RNA fragments by Illumina adapter.
DNA libraries were prepared for sequencing using standard Nanopore protocols.

treatment_protocol: To perturb DNA methylation, we treated EBs with 5-azacytidine or DMSO (100 nM) and replenished them with every media change throughout all days of differentiation.

tag: cell type

value: Embryoid body

tag: media

value: Serum-LIF

tag: differentiation day

value: Day 14

tag: treatment


title: BilIN of Patient 10 [B10]

description: nCounter® Technology

source_name: BilIN of Patient 10

value: patient with distal cholangiocarcinoma


title: non-neoplastic biliary epithelia of Patient 10 [N10]

description: nCounter® Technology

value: non-neoplastic biliary epithelia


title: BrdU_Input_G1_70_combined

value: BrdU pulse-labeling 50-70 min post release into HU

value: Anti-BrdU (GE Healthcare, RPN202)


title: EB14_loxp_gDNA_d9_eb9

description:
EB_day14_loxp_gDNA_d9_eb9
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt


title: NLX-4 Control, replicate 3

city: Jiangsu

first: Jinchi

last: Zhang

state: Nanjing,

address: Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China

department: Co-innovation Center for Sustainable Forestry in Southern China

institute: Nanjing Forestry University

data_processing:
Raw data produced by Illumina Hiseq 2000 were initially processed to obtain clean data by discarding dirty reads containing adapter, ploy-N, or low-quality bases.
Clean reads were mapped to reference genome (fully assembled genome of strain NLX-4) using SOAP2
Reads per kb per million reads (RPKM) method was used to calculate individual gene expression
The RPKM level data of control and treatment samples were also analyzed using edgeR, limma and Glimma statistical analysis packages to obtain statistically significant differentially expressed genes.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Pseudomonas protegens

source_name: bacteria

growth_protocol: The isolated bacteria were cultured on Alexander Rove agar plates which is composed of 5.0g sucrose, 2.0g Na2HPO4, 0.5g MgSO4·7H2O, 0.005g FeCl3, 0.l g CaCO3, l.0g rock sample, 15.0g agar, 1000mL deionized water). Around 200μL of each dilution (10-4, 10-5, 10-6) was spread onto the surface of Alexander Rove agar plate. The inoculated plates were incubated at 28℃ for 24-72h to isolate individual colonies based on their size, color and morphology. Selected colonies were further purified using standard re-culturing techniques.

extract_protocol:
The total RNA of NLX-4 was separately extracted from control group and treated group cultures by using the Trizol method. RNA quality was analyzed on a bioanalyzer (Agilent 2100, Agilent Technologies, USA). Ribosomal RNAs (rRNA) were removed with kit after total RNA was collected from prokaryote. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primers were used to synthesize the first-strand cDNA.
The second-strand cDNA was synthesized using buffer, dATPs, dGTPs, dCTPs, dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick® PCR extraction kit and resolved with elution buffer for repairing the end of the strands and adding poly (A). After that, the short fragments were connected with sequencing adapters. Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute® PCR Purification Kit before PCR amplification. The library obtained was sequenced using Illumina HiSeq2000 platform.

treatment_protocol: The culture medium supplemented with 5.0 g L-1 silicate rock sample (sole K+ source) was inoculated with NLX-4 strain and incubated at 30℃ with 180 rpm for time periods ranging from 0, 2, 5, 9, 12, 15, 22, and 30 days respectively. The culture medium was regularly monitored (the above mentioned time periods) for determining the concentration of K+ and Al3+ ions, using inductively coupled plasma-atomic emission spectrometry (ICP-AES, Vista MPX, Varian, USA) as per the protocol reported by Wu, Zhang and Kanicky and Mermet.The NLX-4 cultured in fermentation medium added with 0.3 g L-1 KCl was set as control.

tag: strain


title: non-neoplastic biliary epithelia of Patient 11 [N11]

description: nCounter® Technology

tag: subject id

value: patient 11


title: BrdU_Input_G1_55_combined

value: BrdU pulse-labeling 35-55 min post release into HU


title: invasive dCCA of Patient 9 [T9]

description: nCounter® Technology

source_name: invasive dCCA of Patient 9

value: patient 9

tag: subject status


title: EB14_loxp_gDNA_d9_eb8

department: Pathology

description:
EB_day14_loxp_gDNA_d9_eb8
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt


title: NLX-4 Control, replicate 2

value: fermentation medium added with 0.3 g L-1 KCl


title: BrdU_Input_G1_40_combined

value: BrdU pulse-labeling 20-40 min post release into HU


title: BilIN of Patient 9 [B9]

description: nCounter® Technology

source_name: BilIN of Patient 9

tag: tissue

value: BilIN


title: NLX-4 Control, replicate 1


title: EB14_loxp_gDNA_d9_eb7

description:
EB_day14_loxp_gDNA_d9_eb7
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt


title: BrdU_Input_G1_25_combined

value: BrdU pulse-labeling 5-25 min post release into HU


title: EB14_loxp_gDNA_d8_eb10

description:
EB_day14_loxp_gDNA_d8_eb10
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt


title: invasive dCCA of Patient 14 [T14]

description: nCounter® Technology

source_name: invasive dCCA of Patient 14

value: patient 14


title: BrdU_ChIP_G0_160_combined

value: BrdU pulse-labeling 140-160 min post release into HU


title: EB14_loxp_gDNA_d8_eb9

description:
EB_day14_loxp_gDNA_d8_eb9
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt


title: NLX-4 Treatment, replicate 2

value: cultured with rock sample 5.0 g L-1 using fermentation medium at 30℃ with 180 rpm for 15 days


title: BilIN of Patient 14 [B14]

description: nCounter® Technology

source_name: BilIN of Patient 14


title: NLX-4 Treatment, replicate 1


title: BrdU_ChIP_G0_145_combined

value: BrdU pulse-labeling 125-145 min post release into HU


title: non-neoplastic biliary epithelia of Patient 14 [N14]

description: nCounter® Technology


title: EB14_loxp_gDNA_d8_eb8

description:
EB_day14_loxp_gDNA_d8_eb8
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

value: Embryoid body

value: Serum-LIF


title: DAP-R Sample_3-B (SI)

city: Catania

first: Viviana

last: Cafiso

state: Italy

address: Via Santa Sofia,97

department: Biometec

country: Italy

institute: University of Catania

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads quality has been checked using FastQC v0.11.2
Sequences were trimmed using Trimmomatic 0.32. For Tru-Seq library a minimum base quality 15 over a 4 bases sliding window were required. Only sequences longer than 36 nucleotide were considered. For Short-Insert library a minimum base quality of 15 (Phred scale) and a minimum read lenght of 15 nucleotides were required.
Sequence mapping and quantification was performed using Rockhopper v2.0.2
Genome_build: Staphylococcus aureus NCTC8325 (ASM1342v1)
Supplementary_files_format_and_content: Excel files derived from Rockhopper include for both the DAP-R/DAP-S isogenic couple mRNAs and smallRNAs: Trancription Start, Translation Start, Translation Stop, Transcription Stop, Strand, Name, Synonym, Product, Raw Counts, Normalized Count, RPKM, Expression, pValue and qValue.

organism: Staphylococcus aureus

source_name: DAP-R Staphylococcus aureus_3-B

growth_protocol: The 4 samples were grown in BHI solid culture and incubated over night at 37 °C.

extract_protocol:
A single colony was used to inoculate 7 ml of BHI liquid culture and incubated at 37 °C  for 12h. Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Sequencing libraries were prepared using the Illumina mRNA-seq sample preparation kit following  the supplier's instructions except that total RNA was not fragmented and double-stranded cDNA was size-selected (100 to 400 bp) to maximize the recovery of small size RNAs. The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified in triplicates with the ABI7900 qPCR instrument using the KAPA Library Quantification Kit, according to the manufacturer’s protocol (KapaBiosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 4 nM were used for sequencing using Illumina Miseq with a A single end stranded library with reads of 50bp. After sequence data generation, raw reads were processed using FastQC v0.11.2 to assess data quality. Reads were then trimmed using Trimmomatic v.0.33.2 to remove sequencing adapters for Single End reads, requiring a minimum base quality of 15 (Phred scale) and a minimum read length of 15 nucleotides. Only trimmed reads were included into downstream analysis.

tag: phenotype

value: Daptomycin resistant S.aureus

tag: infection

value: bloodstream infection

tag: library

value: Short-Insert (SI) Library


title: BrdU_ChIP_G0_130_combined

value: BrdU pulse-labeling 110-130 min post release into HU

value: Anti-BrdU (GE Healthcare, RPN202)


title: invasive dCCA of Patient 8 [T8]

description: nCounter® Technology

source_name: invasive dCCA of Patient 8

value: patient 8

value: patient with distal cholangiocarcinoma

value: invasive dCCA


title: DAP-S Sample_3-A (SI)

source_name: DAP-S Staphylococcus aureus_3-A

value: Daptomycin sensitive S.aureus