title: 23R-2, sort 2

city: Seattle

first: David

last: Baker

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

data_processing:
Read aligned (software developed in-house)
Counts determined for unmutated sequence and all single-position mutants (scripts developed in-house)
Enrichment ratios calculated based on counts in naïve library and sorted population
Assembly: 23R-1: MESEKYLRELVKKYYEGKLSVQEAVEEVRKYARKKGLEAWMLTWMFMELVKRYI
Assembly: 23R-2: NLWQIFYQLSTILKRTGDPTAKKLLKALAEALKKGDEKALKELAKKATKYIRS
Assembly: 17-1: TWHIDVLAPPEVVKTAASQAGAEVHKAPGDWWRITTDDETAVDIVELILFIAGYQFHISSS
Assembly: 17-2: EPREEEAEKYIKRANGDYDLAELLAFLDGNAEIASAIVEYKER
Assembly: 17-3: TWHIDVKADPSIVKAAASAAGAEVHKLPGDKWRITVDDETAVDIVELILFIWGVEFHISSS
Assembly: 23R-49: NLWQIFYQLSTILKRTGDPTAKKLLKALAEALKKGDEKALKELAKKATKYIRS
Assembly: 23R-64: MEPEKYLRELCKKYYEGKLSQQEAVEEIRKYARKKGLEAWKLVWYFMQCVKRDI
Assembly: 23R-95: CKVKCGPVEFQAQMNWMCFYWRWRYC
Assembly: 23R-96: CKVKCGPVEFQATARWMCFYWWWKYC
Assembly: 23R-97: CRVCMNNFCVDAQMCWMAFYLLNKYN
Supplementary files format and content: The processed data file in Excel format (.xlsx) contains enrichment ratios per variant per selection pool normalized to the enrichment ratio of the unmutated sequence.

organism: Saccharomyces cerevisiae

growth_protocol: Please see our corresponding publication for the yeast protocols for growth and induction of protein expression.

extract_protocol:
Yeast were lysed with 125 U/ml Zymolase at 37 ºC for 5 h, and DNA was harvested (Zymoprep kit from Zymo Research). Genomic DNA was digested with 2 U/µl Exonuclease I and 0.25 U/µl Lambda exonuclease (New England Biolabs) for 90 min at 30 ºC, and plasmid DNA purified with a QIAquick kit (Qiagen).
In some instances, gene sequences were diversified by overlapping PCR for site-directed mutagenesis libaries as described in Procko et al. J Mol Bio 2013. In other instances, gene sequences were commercially synthesized. Genes were prepared with 5’ and 3’ overhangs >20 bp to enable homologous recombination with the plasmid backbone (pETCON) for yeast expression and surface display via fusion to Aga2p.
DNA amplicon sequencing

treatment_protocol: Please see our corresponding publication for library treatments prior to FACS selection


title: hiPSC-CMs, hsa-miR548v, rep1

status: Public on Jun 26 2024

type: SRA

city: PARIS

first: Jean-Sebastien

last: Hulot

address: 56 Rue Leblanc

department: PARCC

country: France

institute: Universite Paris Cite

library_source: transcriptomic

data_processing:
STAR was used to obtain the number of reads associated to each gene in the Gencode v31 annotation
Raw counts for each sample were imported into R statistical software. Extracted count matrix was normalized for library size and coding length of genes to compute FPKM expression levels.
The Bioconductor edgeR package was used to import raw counts into R statistical software, and compute normalized log2 CPM (counts per millions of mapped reads) using the TMM (weighted trimmed mean of M-values) as normalization procedure.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: iCell cardiomyocytes

growth_protocol: iCell cardiomyocytes were thawed according to the manufacturer’s recommendations on a 10 μg/mL fibronectin coating, and were maintained for 6 days of culture using the maintainance medium.

extract_protocol:
RNA was harvested using Nucleospin RNA kit (Macherey Nagel). 400ng total RNA was used for the construction of sequencing librairies.
RNA-seq libraries were prepared with NEBNext® Ultra™ II mRNA-Seq kit following manufacturer's protocols.

treatment_protocol: After 6 days of culture, iCell cardiomyocytes were transfected with has-miR-548v or miR negative control ( 25 nM of microRNA in OptiMEM using Lipofectine RNAimax). Medium was changed 24 hours after transfection and total RNA was extracted 3 days after transfection.

tag: cell line

value: iCell cardiomyocytes

tag: cell type

value: human induced pluripotent stem cells derived cardiomyocytes

tag: genotype

value: WT

tag: treatment


title: 4SD_ref_TL

city: New Haven

first: Jackson

last: Gordon

state: CT

address: 333 Cedar St

department: MB&B

country: USA

institute: Yale University

data_processing:
PacBio: Reads were trimmed with cutadapt (settings: --cores=14 --discard-untrimmed --no-indels --revcomp -e 0.2)
PacBio: Deduplication was carried out with PrinSeq-lite (settings: settings -derep 2 -out_format 3), then again (settings: -trim_left 5 -out_format 3)
PacBio: Reads were mapped with minimap2 to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: -x splice:hq –secondary no -t 12 -a -u f).
PacBio: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence. Bedtools bamtobed (setting -bed12) was used to generate bed12 files from .bam files.
PacBio: The flair software suite (https://flair.readthedocs.io/en/latest/) was used to assign reads to splice isoforms, quantify isoform usage between samples, and mark isoforms with retained introns.
PacBio: Poly(A) tail lengths were counted using a custom script that counts soft-clipped bases on 3′ ends of reads.
RNA-seq: Illumina adapters were trimmed using fastp.
RNA-seq: Reads were mapped with STAR to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
RNA-seq: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence.
RNA-seq: Read coverage for each sample was quantified using salmon (settings: -l A --validateMappings –gcBias).
RNA-seq: Differential expression between conditions was quantified using DESeq2.
TimeLapse-seq: Reads were filtered for unique sequences using FastUniq v.1.1
TimeLapse-seq: Reads were trimmed trimmed of adaptor sequences with Cutadapt v3.2
TimeLapse-seq: Reads were aligned to GRCh38/hg38 genome with HISAT-3N
TimeLapse-seq: Reads aligning to annotated transcripts were quantified with HTSeq htseq-count
TimeLapse-seq: SAMtools v.1.539 was used to collect only uniquely mapped read pairs (SAM flag = 83/163 or 99/147).
TimeLapse-seq: Mutation calling and cB file generation was carried out with bam2bakR (https://github.com/simonlabcode/bam2bakR)
TimeLapse-seq: RNA synthsis and degradation kinetics were assessed using the BakR software suite (https://github.com/simonlabcode/bakR).
TimeLapse-seq: Differential expression between conditions was quantified using DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: For long-read sequencing: Tab-delimited files containing poly(A) tail lengths for each read, mapped to either genome or transcriptome.
Supplementary files format and content: For Illumina sequencing: Tab-delimited files include transcripts per million (TPM) values for each sample.
Supplementary files format and content: For TimeLapse-seq: Tab-delimited file includes T to C mutation counts for each sample.
Library strategy: TimeLapse_seq

growth_protocol: HEK293T cells capable of expressing PABPN1 mutants (Empty Vector, Wild-Type, S19/S150/S197/S304 to A, S19/S150/S197/S304 to A) were maintained at 37°C and 5% CO2 in DMEM + Glutamax medium (GIBCO) containing 100 U/ml penicillin, 100 μg/ml streptomycin (GIBCO), and 10% tetracycline-free fetal bovine serum (GIBCO).

extract_protocol:
Cells were harvested by scraping or rinsing in ice cold PBS followed by centrifugation at 270 x g for 10 minutes. Cell pellets were washed twice in ice cold PBS and either used immediately or flash frozen in liquid nitrogen and stored at -80°C. RNA was extracted using TRIzol (Invitrogen)
For long read sequencing: RNA was then reverse transcribed with TGIRT-III reverse transcriptase (InGex). Following reverse transcription, RNA was digested with RNase H (New England Biolabs) to remove any bound TGIRT-III and cDNA purified with the Qiagen MinElute kit. To prepare the 5′ adapter, single stranded DNA adapter oligo was treated with Mnth ligase (New England Biolabs). The prepared adapter was then ligated to the cDNA pool using Thermostable 5´ App DNA/RNA Ligase (New England Biolabs) and again purified with the Qiagen MinElute kit. PCR amplification of cDNA library was carried out with Advantage PCR kit with primers that anneal to the 5 and 3′ adapter sequences. Samples were barcoded with overhanging reverse primers and amplified to PCR 18 cycles. DNA purification was carried out using AMPure beads (Beckman Coulter) and pooled at equimolar ratios. The PacBio SMRTbell prep kit was used for final library preparation according to the manufacturer (Pacific Biosciences) and sequenced on a PacBio Sequel II Long-Read Sequencer. Replicates 1 and 2 were sequenced on separate flow cells (1 flow cell each).
For RNA seq: Extracted RNA was used to prepare RNA-seq libraries using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq 6000 platform generating ~25 million paired-end reads per sample.
For TimeLapse-seq: RNA was precipitated in isopropanol supplemented with 1 mM DTT and 20 μg glycogen and washed with freshly prepared 75% ethanol. Dried pellets were resuspended in nuclease-free water. Turbo DNase was used to deplete any remaining genomic DNA. RNAclean beads were used to isolate the RNA, which was then subjected to TimeLapse chemistry (2,2,2-trifluoroethylamine and mCPBA) and further purified with RNAclean beads. This recoded RNA was prepared for sequencing using the mammalian pico-input SMARTer stranded Total RNA-Seq kit v2 according to the manufacturer. The RNA-seq library was sequenced on the Illumina Novaseq 6000 platform generating ~30 million paired-end reads per sample.

treatment_protocol: For induction of PABPN1 mutant expression, cells were treated with 1 µg/mL Doxycycline Hyclate (ThermoFisher) for 3 days. For TimeLapse-seq experiments: During the last two hours of Doxycycline induction, 100 μM s4U was added to all samples (200 μM s4U for empty vector samples). A single replicate of each cell line received DMSO (no s4U).

tag: group

value: Human embryonic Kidney

value: WT + 4SD PABPN1

value: Doxycycline induction, 3 days


title: mouse mammary tumor mid120

type: RNA

city: Berkeley

first: Jian-Hua

last: Mao

state: CA

address: One Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with by Robust Multi-array Analysis (RMA).
MoEx-2_0-st-v1.r2.pgf
MoEx-2_0-st-v1.r2.dt1.mm8.mps

label: biotin

organism: Mus musculus

source_name: biospy of mammary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2016, Affymetrix).

growth_protocol: spontaneous mammary tumors from genetically diverse MMTV-ErbB2 mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Biopsy before docetaxel treatment

tag: strain

tag: tissue

value: biospy of mammary tumor


title: VMCUB_DMSO_R3

city: Cambridge

first: Patrick

last: Trojer

state: Massachusetts

address: 215 First Street, Suite 200

institute: Constellation Pharmaceuticals

data_processing:
Sequencing reads were mapped to the genome using STAR v2.7.3a with default settings
The transcript and gene read count quantification were performed using RSEM v1.3.1 with default settings
Genome_build: hg38
Supplementary_files_format_and_content: txt file: raw counts

source_name: VMCUB

growth_protocol: Cells were grown in the individual growth medium for each cell line (varies by line). HT1197, HT1376, TCCSUP--MEM(Earl's Salts) + 10% FBS, 1% Non-essential AA, 1 mM NaPyruvate, 1% Pen/Strep; SW780, VMCUB1--DMEM +10% FBS, 1% Pen/Strep; KU1919--RPMI1640 +10% FBS, 1% Pen/Strep; 639V--DMEM + 10% FBS, 1% Pen/Strep; T24--McCoy's 5A + 10% FBS, 1% Pen/Strep.

extract_protocol:
Total RNA was extracted with Trizol, in accordance with the manufacturer’s protocol.
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit (v2). The resulting libraries were sequenced on an Illumina HiSeq 4000, with 9 samples multiplexed per lane.  2x150 base pair paired-end reads using the Illumina TruSeq strand specific protocol, for an expected 40 million reads per sample.

treatment_protocol: Cells were treated with 250 nM of CPI-0209 for 4 days.

value: VMCUB

value: DMSO


title: mouse mammary tumor mid79

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female


title: NR1_replicate 1

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

country: China

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Assembly: Nannochloropsis oceanica IMET1
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

growth_protocol: Nannochloropsis oceanica IMET1 was cultured in modified f/2 liquid medium，which was prepared with 35 g L-1 sea salt (Realocean, USA), 3.65 mg L-1 FeCl3*6H2O, 4.37 mg L-1 Na2EDTA*2H2O, 67 mg L-1 NaH2PO4*H2O, 1 g L-1 NaNO3, trace metal mix (0.01 mg L-1 CoCl2, 0.0126 mg L-1 NaMoO4*2H2O, 0.0196 mg L-1 CuSO4*5H2O, 0.044 mg L-1 ZnSO4*7H2O, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (0.5 µg L-1 thiamine HCl, 2.5 µg L-1 VB12, and 2.5 µg L-1 biotin). The cells were initially cultivated in this medium in a 1 L column reactor with an internal diameter of 5 cm at 25 °C with continuous light (∼50 µmol photons m-2 s-1). 1.5% CO2  was used to bubble the cells.

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were collected by centrifugation once they had reached the logarithmic phase of growth (OD750 = 2.5). Following three rounds of washing with axenic seawater, cell pellets were equally inoculated into f/2 medium (800 mL) and nitrogen-free f/2 medium (800 mL) in triplicate. Starting from an initial cell concentration of OD750 = 2.5, all cultures were continuously illuminated at a rate of 50 μmol m-2 s-1. After being transferred to the designated environment for 72 hours, cell samples were collected for subsequent experiments. Algal cultures were established in three replicates under the ND and NR conditions described above.

value: nitrogen repletion


title: mouse mammary tumor mid105


title: mouse mammary tumor mid36


title: mouse mammary tumor mid147


title: mouse mammary tumor mid11


title: 4SD_R3_TL

value: Doxycycline induction, 3 days, 100 µM s4U, 2 hours


title: mouse mammary tumor mid135


title: VMCUB_DMSO_R2


title: mouse mammary tumor mid2


title: 23R-2, sort 1

state: WA

library_source: genomic

molecule: genomic DNA


title: 23R-2, naïve


title: 4SD_R2_TL


title: 4SD_R1_TL


title: 23R-1, sort 1


title: TCCSUP_CPI-0209_R3

source_name: TCCSUP

value: TCCSUP


title: 4SA_ref_TL

value: WT + 4SA PABPN1


title: 4SA_R3_TL


title: TCCSUP_CPI-0209_R2


title: TCCSUP_CPI-0209_R1


title: 23R-1, naïve


title: mouse mammary tumor mid38


title: mouse mammary tumor mid115


title: TCCSUP_DMSO_R3


title: 4SA_R2_TL


title: 23R-1, sort 2


title: VMCUB_DMSO_R1


title: 4SA_R1_TL


title: mouse mammary tumor mid131


title: TCCSUP_DMSO_R2


title: WT_ref_TL

value: WT + wild-type PABPN1


title: mouse mammary tumor mid142


title: mouse mammary tumor mid75


title: mouse mammary tumor mid117


title: mouse mammary tumor mid65


title: TCCSUP_DMSO_R1


title: WT_R3_TL


title: MSC2

city: 豊明市

first: Sumie

last: Fujii

state: 愛知県

address: 沓掛町田楽ケ窪1番地98

country: Japan

institute: 藤田医科大学　医学部輸血細胞治療科

hyb_protocol: 600ng Cy3-Labeled cRNA was fragmented using Gene Expression Hybridization Kit (Agilent) according to the manufacturer’s protocol and hybridized to SurePrint G3 Human GE Microarray 8 x 60K Ver2.0 (G4858A) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 and Buffer 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing on the Microarray Scanner G2565BA (Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Healthy donor, bone marrow

label_protocol: 150ng total RNA was labeled with Cyanine-3 (Cy3) using Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer’s protocol, followed by RNAeasy column purification (QIAGEN). Dye incorporation was checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using RNA easy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using the NanoDrop-1000 spectrophotometer. Quality of total RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: disease state

value: healthy donor

value: mesenchymal stromal/stem cells


title: MSC3

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: mouse mammary tumor mid54


title: 639V_CPI-0209_R3


title: MSC1

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: mouse mammary tumor mid127


title: 639V_CPI-0209_R2


title: WT_R1_TL


title: WT_R2_TL


title: 639V_DMSO_R3


title: EV_ref_TL

value: WT + Empty Vector


title: mouse mammary tumor mid47


title: EV_R2_TL


title: KDP1_replicat3

data_processing:
In brief, reads were trimmed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), then aligned against the N. oceanica reference genome using BWA (Li, Durbin, 2009). The mapped reads were with duplication marked using Picard and analyzed by DeepTools (Ramirez, Dundar, Diehl, Gruning, Manke, 2014) and MACS2 (Liu, 2014; Zhang, Liu, Meyer, Eeckhoute, Johnson, Bernstein, Nusbaum, Myers, Brown, Li, Liu, 2008). The “--broad” flag was on for peak calling, with reads from the input samples used as controls. Besides, differential analysis was performed using diffReps (Shen, Shao, Liu, Maze, Feng, Nestler, 2013), the resulting differential peaks were annotated using ChIPpeakAnno package (Zhu, Gazin, Lawson, Pages, Lin, Lapointe, Green, 2010).
Assembly: Nannochloropsis oceanica IMET1 genome
Supplementary files format and content: bedgraph for each Sample
Supplementary files format and content: differential peak text files

extract_protocol:
N. oceanica cells (1-2 million cells · mL-1) from 800 mL culture were fixed under vacuum for 30 min with 1% formaldehyde (Sigma)at room temperature. After fixation, cells were incubated at room temperature for ten min under vacuum with 0.15 M glycine. Nuclei were isolated as described (Wei, Xu, 2018).
All subsequent end repairing, A-tailing, adaptor ligation, and library amplification steps were done following a standard protocol (Illumina). The final library was sequenced on an Illumina HiSeq 2500 instrument with 1×150-bp reads.

tag: chip antibody

value: nitrgen deprivation


title: 639V_CPI-0209_R1


title: EV_R3_TL


title: F5

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科

source_name: Lymphoma

value: follicular lymphoma

value: Lymph node mesenchymal stromal cells


title: mouse mammary tumor mid37


title: 639V_DMSO_R2


title: F3

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: KDP1_replicat2


title: 639V_DMSO_R1


title: EV_R1_TL

value: Human embryonic Kidney


title: mouse mammary tumor mid100


title: T24_CPI-0209_R3


title: KDP1_replicat1


title: F1

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: mouse mammary tumor mid42


title: mouse mammary tumor mid29


title: F4

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: F2

address: 沓掛町田楽ケ窪1番地98

institute: 藤田医科大学　医学部輸血細胞治療科


title: mouse mammary tumor mid16


title: T24_CPI-0209_R2


title: mouse mammary tumor mid9


title: 4SD_R3_Illumina

data_processing:
PacBio: Reads were trimmed with cutadapt (settings: --cores=14 --discard-untrimmed --no-indels --revcomp -e 0.2)
PacBio: Deduplication was carried out with PrinSeq-lite (settings: settings -derep 2 -out_format 3), then again (settings: -trim_left 5 -out_format 3)
PacBio: Reads were mapped with minimap2 to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: -x splice:hq –secondary no -t 12 -a -u f).
PacBio: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence. Bedtools bamtobed (setting -bed12) was used to generate bed12 files from .bam files.
PacBio: The flair software suite (https://flair.readthedocs.io/en/latest/) was used to assign reads to splice isoforms, quantify isoform usage between samples, and mark isoforms with retained introns.
PacBio: Poly(A) tail lengths were counted using a custom script that counts soft-clipped bases on 3′ ends of reads.
RNA-seq: Illumina adapters were trimmed using fastp.
RNA-seq: Reads were mapped with STAR to GRCh38/hg38 genome (ammended to also contain exogenous WT PABPN1 sequence) (settings: --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
RNA-seq: Samtools sort was used to sort reads by genomic position. Samtools view (settings -S -b) was used to convert .sam files to .bam files. Samtools index was used to generate index files corresponding to each .bam file. Samtools view was also used to separate reads mapping to hg38 from those mapping to the plasmid sequence.
RNA-seq: Read coverage for each sample was quantified using salmon (settings: -l A --validateMappings –gcBias).
RNA-seq: Differential expression between conditions was quantified using DESeq2.
TimeLapse-seq: Reads were filtered for unique sequences using FastUniq v.1.1
TimeLapse-seq: Reads were trimmed trimmed of adaptor sequences with Cutadapt v3.2
TimeLapse-seq: Reads were aligned to GRCh38/hg38 genome with HISAT-3N
TimeLapse-seq: Reads aligning to annotated transcripts were quantified with HTSeq htseq-count
TimeLapse-seq: SAMtools v.1.539 was used to collect only uniquely mapped read pairs (SAM flag = 83/163 or 99/147).
TimeLapse-seq: Mutation calling and cB file generation was carried out with bam2bakR (https://github.com/simonlabcode/bam2bakR)
TimeLapse-seq: RNA synthsis and degradation kinetics were assessed using the BakR software suite (https://github.com/simonlabcode/bakR).
TimeLapse-seq: Differential expression between conditions was quantified using DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: For long-read sequencing: Tab-delimited files containing poly(A) tail lengths for each read, mapped to either genome or transcriptome.
Supplementary files format and content: For Illumina sequencing: Tab-delimited files include transcripts per million (TPM) values for each sample.
Supplementary files format and content: For TimeLapse-seq: Tab-delimited file includes T to C mutation counts for each sample.

value: WT + 4SD PABPN1

value: Doxycycline induction, 3 days


title: KRP1_replicat3


title: KRP1_replicat2


title: 4SD_R1_Illumina


title: KRP1_replicat1


title: mouse mammary tumor mid60

value: biospy of mammary tumor


title: mouse mammary tumor mid30


title: 4SD_R2_Illumina


title: KD1_replicat3


title: T24_CPI-0209_R1


title: T24_DMSO_R2

value: DMSO


title: mouse mammary tumor mid82

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female


title: 4SA_R2_Illumina


title: T24_DMSO_R1


title: KD1_replicat2


title: SW780_CPI-0209_R3


title: KD1_replicat1


title: 4SA_R1_Illumina


title: WT_R3_Illumina


title: KR1_replicat3

value: nitrogen repletion


title: T24_DMSO_R3


title: SW780_CPI-0209_R2


title: KR1_replicat2


title: mouse mammary tumor mid85


title: WT_R2_Illumina


title: SW780_CPI-0209_R1


title: 4SA_R3_Illumina


title: WT_R1_Illumina


title: mouse mammary tumor mid114


title: mouse mammary tumor mid145


title: KR1_replicat1


title: SW780_DMSO_R3


title: EV_R3_Illumina


title: mouse mammary tumor mid177


title: SW780_DMSO_R1


title: E33_D1_3

city: Newark

first: Mark

middle: A.

last: Blenner

state: Delaware

department: Chemical and Biomolecular Engineering

institute: University of Delaware

data_processing:
Data processing was performed using the Palmetto Cluster, R, and Python
Trimmomatic (0.36) for adapter removal
FastQC (0.11.8) for quality control analysis of raw reads
STAR (2.6.0a) for alignment of the raw reads to the CHO CriGri-PICR reference genome assembly (GCF_003668045.1_CriGri-PICR)
HTSeq (0.10.0) for generation of the read count tables
To generate read counts for the three product mRNAs, the CriGri-PICR genome file was amended to include three additional gene sequence files for the products: IgG1 light chain (IgG1 LC), IgG1 heavy chain (IgG1 HC), and EPO-Fc.
Temporal expression profile groups were generated through hierarchical clustering using the DEGreport (1.30.0) package after performing the likelihood ratio test (LRT) on a reduced DESeq2 (1.34.0) model. The full model included variables denoting cell line, time, and the interaction between cell line and time. The interaction variable was removed in the reduced model to test for variance due to cell line over time. We analyzed 2500 genes with the lowest adjusted p-values, with 0.01 as the upper cutoff limit.
The clusterProfiler package (4.2.2) was used to conduct Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway and Gene Ontology (GO) enrichment on the obtained temporal expression cluster profiles. The organism identifier “cge” was used to denote Chinese hamster KEGG pathway enrichment. The Chinese hamster annotation AH96228, available through Annotation Hub, was used for GO enrichment categories. Enrichment analyses were calculated using an adjusted p-value cutoff of 0.05.
Principal component analysis (PCA) and differential expression testing based on the Wald statistical pairwise test was conducted using DESeq2 (1.34.0). Fragments per kilobase pair million (FPKM) were calculated using the built-in DESeq2 function based on the known lengths of target genes. For all pairwise differential gene expression analysis (DGEA), the absolute value of the log2 fold change (log2FC) cutoff was set to 0.5 and an adjusted p-value cutoff of 0.01 was used, as identified by an elbow of all DEGs versus various adjusted p-value cutoffs.
Assembly: CHO CriGri-PICR reference genome assembly (GCF_003668045.1_CriGri-PICR)
Supplementary files format and content: Text file of read counts generated for each geneID (RefSeq format) for a specific sample (e.g. ZN_D0_1)

organism: Cricetulus griseus

source_name: CHOZN GS-/- clone 2

growth_protocol: Cell cultures were maintained according to the CHOZN® Platform Technical Bulletin (Sigma-Aldrich) with some modifications. Both passage and fed-batch cultures were grown in Erlenmeyer shake flasks (VWR®, Cat. No. 89095-262) at 100 rpm, 37˚C, and 5% CO2. Each cell line was passaged at least three times post-thaw to ensure similarly aged, healthy cultures for subsequent transcriptomic analysis of fed-batch samples. For passages, the culture volume corresponding to 0.5 million cells/mL was spun for 5 min at 500 rpm, aspirated, washed with 1X phosphate buffered saline (PBS), spun for 5 min at 500 rpm, aspirated, and resuspended in 25 mL of fresh EX-CELL® CD CHO Fusion media (Sigma-Aldrich, Cat. No. 14365C). Fed-batch cultures were run in biological triplicate. Fed-batch cultures were passaged in the same way, but resuspended in 30 mL of fresh EX-CELL® Advanced™ CHO Fed-batch media (Sigma-Aldrich, Cat. No. 14366C). Both passage and fed-batch medium for the host cell line were supplemented with L-glutamine (Corning, Cat. No. MT25005CI) to a final concentration of 5 mM. Feedings always took place after sampling and were carried out according to the CHOZN® Platform Technical Bulletin. Briefly, the host cell line was fed L-glutamine to a final concentration of 5 mM starting on day 3 and on all remaining odd days. All cell lines were fed an EX-CELL® AdvancedTM CHO Feed 1 (Sigma-Aldrich, Cat. No. 24368C-1L) at 5% of the culture volume on day 3 and on all remaining odd days. Finally, all cell lines were fed D-(+)-Glucose solution (Sigma-Aldrich, Cat. No. G8769-100 mL) to a final concentration of approximately 4g/L daily, once the glucose concentration dropped below 2g/L.

extract_protocol:
Extractions of RNA were carried out using the Qiagen RNeasy Plus Mini Kit (Qiagen, Cat. No. 74136). Extractions were performed according to the manufacturer’s protocol for “Purification of Total RNA from Animal Cells” with the following changes: samples were prepared per treatment protocol above, option 3c was followed for Step 3, molecular grade ethanol was used for Step 5, optional Step 10 was used, and Dnase/Rnase-free water was heated to 37 ˚C and allowed to incubate on the column for 5 min for elution. Quantification of RNA was performed by measuring absorbance at 260 and 280 nm using a nanospectrophotometer.  Multiple aliquots of 100 ng/µL were prepared and stored at -80 ˚C until ready for analysis. Concentrations of RNA and RNA Integrity Numbers (RIN) were determined by Qubit fluorometer (Invitrogen) and 2100 Bioanalyzer (Agilent), respectively.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries,  rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using  mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the  second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and  PCR enrichment.
The quality control of library consists of three steps:
(1) Qubit 2.0: tests the library concentration preliminarily.
(2) Agilent 2100: tests the insert size.
(3) Q-PCR: quantifies the library effective concentration precisely.

treatment_protocol: A cell culture volume not exceeding 5 million cells/mL was collected, spun down at 500 rpm for 5 min, aspirated, washed with 1X PBS, spun down at 500 rpm for 5 min, and aspirated. Cell pellets for RNA isolation were resuspended in 100 µL of RNALaterTM Stabilization Solution (Thermo Fisher Scientific, Cat. No. AM7021) and stored at -80˚C until ready for extraction.

tag: time

value: Day 1

value: CHOZN GS-/- clone 2

value: Chinese hamster ovary (CHO)

value: selected clone 2

tag: phenotype

value: EPO-Fc producer

tag: replicate

value: rep 3


title: KU1919_CPI-0209_R3


title: ZN_D3_1

source_name: CHOZN GS-/-

value: Day 3

value: CHOZN GS-/-

value: WT

value: control, host cell line

value: rep 1


title: mouse mammary tumor mid111


title: SW780_DMSO_R2


title: E33_D1_2

value: rep 2


title: EV_R2_Illumina

value: Human embryonic Kidney

value: WT + Empty Vector

value: Doxycycline induction, 3 days


title: KU1919_CPI-0209_R2


title: E33_D1_1


title: A549, Co-culture, rep3

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description:
CC3
counts.txt

data_processing:
We firstly retained the qualified reads which passed the quality control step by Trim Galore (v0.6.7).
By taking advantage of HISAT2 (v2.2.1), clean reads of each sample were then aligned to the GRCh38 human reference genome retrieved from GENECODE.
Gene and transcript expression were estimated with featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
the RNA of LUAD and pleural mesothelial cells of control group and co-culture group was respectively extracted with RNAsimple Total RNA Kit (TIANGEN, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cancer cell

value: Co-culture


title: EV_R1_Illumina


title: A549, Co-culture, rep2

description:
CC2
counts.txt


title: KU1919_CPI-0209_R1


title: I23_D1_3

source_name: CHOZN GS-/- clone 1

value: Day 1

value: CHOZN GS-/- clone 1

value: selected clone 1

value: IgG1 producer


title: mouse mammary tumor mid33

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female

value: biospy of mammary tumor


title: KU1919_DMSO_R3

value: DMSO


title: A549, Co-culture, rep1

description:
CC1
counts.txt


title: I23_D1_2

value: Chinese hamster ovary (CHO)


title: mouse mammary tumor mid26


title: mouse mammary tumor mid91


title: A549, Control, rep3

description:
CS3
counts.txt

value: Control


title: mouse mammary tumor mid23


title: I23_D1_1


title: mouse mammary tumor mid186


title: A549, Control, rep2

description:
CS2
counts.txt


title: ZN_D1_3

description: no count file generated

value: CHOZN GS-/-

value: WT

value: control, host cell line

value: rep 3


title: A549, Control, rep1

description:
CS1
counts.txt


title: HT1376_CPI-0209_R3


title: mouse mammary tumor mid128


title: ZN_D1_2

value: rep 2


title: MET-5A, Co-culture, rep3

description:
MC3
counts.txt

value: mesothelial cell


title: mouse mammary tumor mid102


title: ZN_D1_1

value: rep 1


title: mouse mammary tumor mid99


title: mouse mammary tumor mid25


title: HT1376_CPI-0209_R2


title: MET-5A, Co-culture, rep2

description:
MC2
counts.txt

value: Co-culture


title: HT1376_CPI-0209_R1


title: KU1919_DMSO_R2


title: mouse mammary tumor mid101


title: E33_D0_3

value: Day 0

value: CHOZN GS-/- clone 2

value: selected clone 2

value: EPO-Fc producer


title: E33_D0_2


title: MET-5A, Control, rep3

description:
MS3
counts.txt


title: MET-5A, Co-culture, rep1

description:
MC1
counts.txt


title: HT1376_DMSO_R2


title: HT1376_DMSO_R3


title: E33_D0_1


title: mouse mammary tumor mid71

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female


title: KU1919_DMSO_R1


title: MET-5A, Control, rep2

description:
MS2
counts.txt


title: mouse mammary tumor mid182

value: biospy of mammary tumor


title: I23_D0_3

value: CHOZN GS-/- clone 1

value: selected clone 1

value: IgG1 producer


title: MET-5A, Control, rep1

description:
MS1
counts.txt

value: Control


title: HT1376_DMSO_R1

value: DMSO


title: HT1197_CPI-0209_R3


title: I23_D0_2

value: Chinese hamster ovary (CHO)


title: mouse mammary tumor mid7


title: HT1197_CPI-0209_R2


title: SEM-CD9 Dexa

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Partek Flow version 10
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using STAR - 2.7.8a.
Count per million + 0.001 were calculated.
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

source_name: cell line

growth_protocol: BCP-ALL cell line SEM were transduced with control GFP-only or CD9-GFP lentiviral particles and cultured in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin (P/S), stable cell lines were generated by selection with puromycin (1μg/mL).

extract_protocol:
RNA was isolated using Trizol reagent and Qiagen RNAeasy kit. NEBNext Ultra Directional RNA Library Prep Kit for Illumina(Cat No. 7420) was used with 1 ug RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells (3 × 106) were treated with control DMSO or Dexamethasone (1μM) for 8 hours.

tag: tumor

value: tumor cell line

value: Childhood B acute lymphoblastic leukemia


title: mouse mammary tumor mid43


title: SEM-GFP Dexa


title: HT1197_CPI-0209_R1


title: mouse mammary tumor mid130


title: mouse mammary tumor mid125


title: ZN_D0_3

value: CHOZN GS-/-

value: WT

value: control, host cell line

value: rep 3


title: mouse mammary tumor mid122


title: HT1197_DMSO_R2


title: Gill of L47_3 from the Vibrio susceptible family

city: Qingdao

first: Quanchao

last: Chen

state: Shandong

address: Yushan Campus, No. 5 Yushan Road,Qingdao

institute: Ocean university of china

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke v1.5.2(parameters- -l 15 -q 0.2 -n 0.05)
Trimmed sequence reads were mapped to Cse_v1.0 using HISAT2 v2.0.4(parameters- -p 20 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000)
Read count extraction and normalization were performed using Bowtie2 v2.2.5(parameters- -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 10 -k 200) and RSEM v1.2.12(parameters- default)
Assembly: Cse_v1.0
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each sample
Supplementary files format and content: tab-delimited text files include differentially expressed genes for each tissue between the H16 and L47 groups

organism: Cynoglossus semilaevis

source_name: Gill

extract_protocol:
Total RNA was extracted from three biological replicates of each group with TRIzol (Invitrogen, USA).
RNA libraries for RNA-seq were prepared using Truseq mRNA stranded RNA-Seq Library Prep Kit (Illumina, USA) following manufacturer's protocols.

value: Gill


title: Spleen of L47_3 from the Vibrio susceptible family

source_name: Spleen

value: Spleen


title: SEM-CD9 DMSO


title: ZN_D0_2

value: Day 0

value: rep 2


title: SEM-GFP DMSO


title: mouse mammary tumor mid87

value: F1Bx((C57BL/6J x FVB/NJ) x FVB/NJ MMTV-Erbb2) Female

value: biospy of mammary tumor


title: ZN_D0_1

value: rep 1


title: I23_D0_1

value: CHOZN GS-/- clone 1

value: selected clone 1

value: IgG1 producer


title: 24_A1A_DX_0209_C

growth_protocol: Cells were grown in MEM(Earl's Salts) + 10% FBS, 1% Non-essential AA, 1 mM NaPyruvate, 1% Pen/Strep

treatment_protocol: T1376-TetON control cells and a clonal HT1376-TetON-ARID1A cell line were induced with 50 ng/ml doxycycline for 24 hours and then treated for 4 days with DMSO or 250 nM CPI-0209.

value: with Dox


title: Liver of L47_3 from the Vibrio susceptible family

source_name: Liver

value: Liver


title: PS24FL8-LATE

city: Bordeaux

first: Victor

last: Appay

address: 2 Rue Dr Hoffmann Martinot

institute: Immunoconcept

description: SMARTseq v4

library_source: transcriptomic single cell

data_processing:
Raw sequences were processed with Trimmomatic for adapter removal and quality trimming, ensuring that only high-quality data is retained for further analysis. After processing, the sequences were aligned to the hg38 genome build using STAR version 2.7.0. Gene expression quantification was performed using featureCounts, and the resulting data was imported into R for further analysis. The output cn be find in the "AllCells_sceobject_Processed.rds" file.
Quality control was performed using scater version 1.20.1 with the following metrics: library size, number of expressed features, and proportion of reads mapped to the mitochondrial genome. Outlier cells were identified for each metric based on the median absolute deviation (MAD) from the median value of each metric across all cells, with the cutoff for exclusion set at >3 MADs. Fixed thresholds were also used to exclude cells expressing <500 or >5,000 genes. Retained cells were normalized using scran version 1.20.1, which implements the deconvolution strategy for scaling normalization. The ouput can be find in the "FilteredCells_Normalized_sceobject_Processed.rds" file.
Assembly: hg38
Supplementary files format and content: SingleCellExperiment object as .rds files.

source_name: PBMC

extract_protocol:
HIV-1 and HIV-2 specific CD8 T cells were detetced by tetramer staining and sorted into 96-well microtiter plates containing lysis buffer (Takara Bio) using a BD FACSAria II and frozen immediately at −80 °C.
Extracted mRNA was converted into cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) and subsequently amplified by PCR. The cDNA was then isolated with the Agencourt AMPure XP Kit (Beckman Coulter) and quantified using the Agilent High Sensitivity DNA Kit on an Agilent 2100 Bioanalyser (Agilent Technologies). Finally, the cDNA was indexed with the Nextera XT DNA Library Preparation Kit (Illumina).

value: PBMC

value: HIV-1-specific CD8 T cell


title: 23_A1A_DX_0209_B


title: HT1197_DMSO_R1

value: DMSO


title: 21_A1A_0209_C

value: without Dox


title: PS24FL8-INT

description: SMARTseq v4


title: PS24EI8-INT

description: SMARTseq v4


title: HT1197_DMSO_R3


title: Skin of L47_3 from the Vibrio susceptible family

source_name: Skin

value: Skin


title: PS24FL8-EARLY

description: SMARTseq v4


title: PS24EI8-EARLY

description: SMARTseq v4


title: Gill of L47_1 from the Vibrio susceptible family

value: Gill


title: PS212-LATE

description: SMARTseq v4


title: PS212-INT

description: SMARTseq v4


title: Spleen of L47_2 from the Vibrio susceptible family

value: Spleen


title: 17_A1A_DX_DMSO_B


title: Gill of L47_2 from the Vibrio susceptible family


title: 20_A1A_0209_B


title: PS24EI8-LATE

description: SMARTseq v4


title: Liver of L47_2 from the Vibrio susceptible family


title: 22_A1A_DX_0209_A


title: Skin of L47_2 from the Vibrio susceptible family


title: 19_A1A_0209_A


title: 18_A1A_DX_DMSO_C


title: Spleen of L47_1 from the Vibrio susceptible family


title: Intestine of L47_3 from the Vibrio susceptible family

source_name: Intestine

value: Intestine


title: PS14-LATE

description: SMARTseq v4


title: Intestine of L47_2 from the Vibrio susceptible family


title: PS14-INT

description: SMARTseq v4


title: PS212-EARLY

description: SMARTseq v4


title: Liver of L47_1 from the Vibrio susceptible family


title: Skin of L47_1 from the Vibrio susceptible family


title: 16_A1A_DX_DMSO_A


title: PS14-EARLY

description: SMARTseq v4


title: sA0626NC

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. Fastp was used to trim adaptor sequences from fastq data and remove 15 bp from the two ends of the reads based on Swift protocol. MCALL module in MOABS software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig; DNA methylation ratio in single CpG resolution

source_name: pediatric cerebrum from autopsy

extract_protocol:
For autopsy tissues, up to 20 mg of tumor tissues was snap frozen with liquid nitrogen and grinded. DNA was then isolated using an AllPrep DNA/RNA mini kit according to the manufacturers protocol. The isolated DNA concentration was measured by a Qubit 4 Fluorometer with the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific).
The whole genome bisulfite sequencing (WGBS) analysis was used to measure the genome-wide DNA methylation status. The ctDNA WGBS libraries were generated using SWIFT Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences). Briefly, adaptase was applied to the bisulfite-converted DNA, with adaptors as well as a low-complexity tail simultaneously ligated to the 3′ end of the DNA fragments. Following a primer extension, the bottom strand DNA was synthesized and the 3′ end was ligated with adaptor sequences. ctDNA was mixed with 0.1% unmethylated λ-bacteriophage DNA (NEB) .  Constructed libraries were run on 2% agarose gel to assess the size distribution and library concentration was measured by a Qubit 4 Fluorometer with a Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific). Normalized libraries were then pooled in an equimolar ratio and sequenced on NovaSeq 6000  S4 (pair-end reads, 150 bp) following the manufacturer’s protocols.   Enriched DNA fragments were purified using the conventional phenol/chloroform/isomyl-alcohol method, and amplified with random primers, followed by adaptor ligation and final amplification with Methyl-Seq Combinatorial Dual Indexing Kit (Swift Biosciences). DNA library sizes and concentrations were verified by Bioanalyzer. The DNA libraries were then sequenced in Novaseq S4 (pair-end reads, 150 Cycles) following the manufacturer’s protocols.

tag: age

tag: Sex

value: M

value: cerebrum


title: 15_A1A_DMSO_C


title: Intestine of L47_1 from the Vibrio susceptible family


title: Gill of H16_3 from the Vibrio resistant family


title: s8080NC

value: F

value: cerebellum


title: 13_A1A_DMSO_A


title: 14_A1A_DMSO_B


title: Liver of H16_3 from the Vibrio resistant family


title: PS03-EARLY

description: SMARTseq v4


title: s1129NC


title: r0315NCb

source_name: pediatric cerebellum from autopsy


title: PS03-LATE

description: SMARTseq v4


title: 10_EV_DX_0209_A


title: HIV2-Donor2

description: SMARTseq v4

value: HIV-2-specific CD8 T cell


title: nC10206


title: Skin of H16_3 from the Vibrio resistant family


title: 12_EV_DX_0209_C


title: PS03-INT

description: SMARTseq v4


title: s1129NCb


title: c1220NC


title: 8_EV_0209_B


title: 9_EV_0209_C


title: C1029NC


title: HIV2-Donor1

description: SMARTseq v4


title: Intestine of H16_3 from the Vibrio resistant family


title: E33_D5_2

value: Day 5

value: CHOZN GS-/- clone 2

value: Chinese hamster ovary (CHO)

value: selected clone 2

value: EPO-Fc producer

value: rep 2


title: 7_EV_0209_A


title: Gill of H16_2 from the Vibrio resistant family


title: E33_D5_3

value: rep 3


title: Spleen of H16_3 from the Vibrio resistant family


title: 11_EV_DX_0209_B

value: with Dox


title: Liver of H16_2 from the Vibrio resistant family

value: Liver


title: A1429NC


title: Spleen of H16_2 from the Vibrio resistant family


title: I23_D5_3

value: CHOZN GS-/- clone 1

value: selected clone 1

value: IgG1 producer


title: pinonNcb

description: pinonNcb

value: M


title: Skin of H16_2 from the Vibrio resistant family

value: Skin


title: 4_EV_DX_DMSO_A

value: DMSO


title: A1429NCb

value: cerebellum


title: I23_D5_2


title: Intestine of H16_2 from the Vibrio resistant family

value: Intestine


title: 3_EV_DMSO_C

value: without Dox


title: I23_D5_1

value: Day 5

value: rep 1


title: A1123NC

value: cerebrum


title: A1123NCb


title: 2_EV_DMSO_B


title: 6_EV_DX_DMSO_C


title: C1029NCb


title: ZN_D5_3

value: CHOZN GS-/-

value: Chinese hamster ovary (CHO)

value: WT

value: control, host cell line


title: 1_EV_DMSO_A


title: A0518NC

value: F


title: Spleen of H16_1 from the Vibrio resistant family

value: Spleen


title: Liver of H16_1 from the Vibrio resistant family

value: Liver


title: A0518NCb


title: 5_EV_DX_DMSO_B

value: with Dox


title: Skin of H16_1 from the Vibrio resistant family


title: ZN_D5_1


title: E33_D5_1

value: CHOZN GS-/- clone 2

value: selected clone 2

value: EPO-Fc producer


title: iKrasG12D; Trp53R172H/+ OT 2 weeks ON + 3 days OFF

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

description: 5 x 104  A9993 cells were implanted into syngeneic FVB/N mice. Mice were provided doxycycline chow for 2 weeks to maintain KrasG12D expression, and then randomly selected to return to regular diet for an additional 3 days (KrasG12D “OFF”) before tumor harvest. 1 female and 2 male mice were pooled in this submission.

data_processing:
The University of Michigan Advanced Genomics Core performed processing and alignment of the raw data using Cell Ranger (versions 2.2.0-6.1.2 depending on date of sequencing) with default settings and an initial expected cell count of 10,000.
Assembly: mm10, mm10-2020-A, mm10-2020-A_EGFP, mm10-3.0.0, mm10-GFP-3.0.0
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: Orthotopic pancreas tumor

extract_protocol:
To prepare tissues for sequencing, samples were disrupted to single cell suspension by mechanically mincing the tissue, followed by enzymatic digestion with Collagenase V (1 mg/mL in RPMI, #C9263, Sigma-Aldrich) at 37°C for 30 min under constant shaking. After digestion, suspensions underwent serial filtration through 500 µm, 100 µm, and 40 µm mesh cell strainers. We then enriched for live cells using the MACS Dead Cell Removal Kit (#130-090-101, Miltenyi Biotec). The resulting single cell suspensions were brought to the University of Michigan Advanced Genomics Core for cDNA library preparation and sequencing.
Samples were run using 50-cycle paired-end reads on the HiSeq 4000 (Illumina) or NovaSeq 6000 (Illumina) to a depth of 100,000 reads.

value: Orthotopic pancreas tumor

tag: number of_mice_pooled

value: WT FVB/N

tag: cell ranger_version

tag: genome

tag: run date


title: Cattle, Illumina, sRNA-seq, rep2

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 147, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
short RNAs (20-65nt)
sRNA_Bos_taurus-Blood_Illumina.reps.merged.tss.txt

data_processing:
Reads were trimmed of their adapter sequences using HOMER (homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20).
Reads were subsampled using SeqKit's sample v2.5.1 to acheieve equal read depth.
Reads were aligned to the the appropriate reference genome using STAR v2.7.10a for humans and Hisat2 v2.2.1 for the livestock.
Alignment files were converted to tag directories using HOMER2 batchMakeTagDirectory.pl.
BedGraph files were generated from the tag directories using makeUCSCfile.
Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSR.pl and findPeaks, respectively. A minimum read count of 10 per 10 million was required for regions to be considered.
Assembly: hg38, GCF_002263795.2, modified_GCA_018282365.1
Supplementary files format and content: BedGraph files (.bedGraph.gz) containing the locations that denote TSS positions.
Supplementary files format and content: Text files (.tss.txt) containing tab-delimited data on identified transcription start site clusters (TSRs).
Supplementary files format and content: Modified gtf file that underwent an ID update to achieve consistency with the fasta genome.

organism: Bos taurus

source_name: Blood

growth_protocol: A375 and BT474 cells were grown at 37°C with 5% CO2 in DMEM (Cellgro) supplemented with 10% FBS (Gibco), and 50 U Penicillin and 50 μg Streptomycin per mL (Gibco). Cattle and bison samples were obtained from experimental animals housed at Washington State University, Pullman, WA and University of Wyoming, Laramie WY, respectively. 2.8 ml blood was collected from healthy animals using PAXgene Blood RNA tubes (BD Bioscience) by venipuncture (jugular) and transported on ice to the laboratory for processing.

extract_protocol:
Cells were washed once with ice cold DPBS (Gibco), rested on ice for 5 minutes, washed one more time with ice cold DPBS and then lysed in 1 ml TROZOL. RNA isolated as described by the manufacturer.
csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5'-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5'-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5'dephosphorylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.

value: Blood


title: cell infiltrate ascites_ID8_def29_vegf

city: New York City

first: Tito Alejandro

middle: A

last: Sandoval Medina

email: tas2037@med.cornell.edu, tito@wustl.edu

state: New York

address: 1300 York Avenue E907

department: OBGyN

institute: Weill Cornell Medine

description: 10x genomics

data_processing: none provided

source_name: ascites

extract_protocol: none provided

value: ascites

tag: cell line

value: cell infiltrate from ascites

tag: genotype


title: E33_D3_3

value: Day 3

tag: cell type

value: rep 3


title: Gill of H16_1 from the Vibrio resistant family

value: Gill


title: Cattle, Illumina, sRNA-seq, rep1


title: E33_D3_2

value: Chinese hamster ovary (CHO)

value: rep 2


title: Cattle, AVITI, sRNA-seq, rep2

description:
short RNAs (20-65nt)
Cloudbreak_FreeStyle
sRNA_Bos_taurus-Blood_AVITI.reps.merged.tss.txt


title: Cattle, AVITI, sRNA-seq, rep1


title: Cattle, Illumina, csRNA-seq, rep2

description:
short RNAs (20-65nt)
Bos_taurus-Blood_Illumina.reps.merged.tss.txt

data_processing:
Reads were trimmed of their adapter sequences using HOMER (homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20).
Reads were subsampled using SeqKit's sample v2.5.1 to acheieve equal read depth.
Reads were aligned to the the appropriate reference genome using STAR v2.7.10a for humans and Hisat2 v2.2.1 for the livestock.
Alignment files were converted to tag directories using HOMER2 batchMakeTagDirectory.pl.
BedGraph files were generated from the tag directories using makeUCSCfile.
Peaks representing Transcription Start Regions (TSRs) for csRNA-seq and expressed small RNAs for sRNA-seq, were defined using HOMER’s findcsRNATSR.pl and findPeaks, respectively. A minimum read count of 10 per 10 million was required for regions to be considered.
Assembly: hg38, GCF_002263795.2, modified_GCA_018282365.1
Supplementary files format and content: BedGraph files (.bedGraph.gz) containing the locations that denote TSS positions.
Supplementary files format and content: Text files (.tss.txt) containing tab-delimited data on identified transcription start site clusters (TSRs).
Supplementary files format and content: Modified gtf file that underwent an ID update to achieve consistency with the fasta genome.
Library strategy: csRNA-seq


title: T7b-biolrep3

city: college station

first: Brendan

last: MORMILE

address: 211 redmond drive

institute: University of Michigan

data_processing:
Trimmomatic tool was used to preprocess raw RNA-seq reads by performing quality filtering and trimming of low-quality bases from sequencing reads to ensure that only high-quality reads were used for alignment and assembly.
The alignment of RNA-seq reads to the G. hirsutum (AD1) TM-1 genome was executed using HISAT2, employing an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini index.
Transcriptional assembly was conducted using StringTie, which reconstructed full-length transcripts from aligned reads while estimating their abundance and quantifying gene expression levels.
Differential gene expression was analyzed using Cuffdiff, a component of the Cufflinks suite, which facilitated the comparison of transcript abundances between different treatments.
Genes were considered differentially expressed if they demonstrated a log2 fold expression change >1 and an adjusted p-value < 0.05.
Assembly: G. hirsutum (AD1) TM-1 genome was used for the RNA-seq read alignment
Supplementary files format and content: Excel file includes transcript abundances, log2 fold expression changes, p-values, and gene annotations

organism: Gossypium hirsutum

source_name: Mesophyll

extract_protocol:
Total RNA was extracted using a Spectrum Plant Total RNA Kit (Sigma-Aldrich) and 1 μg of purified RNA was used for construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kit following the manufacturer’s protocol

value: Mesophyll


title: T7b-biolrep2


title: Cattle, Illumina, csRNA-seq, rep1


title: Cattle, AVITI, csRNA-seq, rep2

description:
short RNAs (20-65nt)
Cloudbreak_FreeStyle
Bos_taurus-Blood_AVITI.reps.merged.tss.txt


title: I23_D3_3

value: CHOZN GS-/- clone 1

value: selected clone 1

value: IgG1 producer


title: HM-biolrep3


title: T7b-biolrep1


title: I23_D3_1

value: rep 1


title: ZN_D5_2

value: Day 5

value: CHOZN GS-/-

value: WT

value: control, host cell line


title: I23_D3_2


title: Intestine of H16_1 from the Vibrio resistant family

value: Intestine


title: HM-biolrep2


title: ZN_D3_3


title: ZN_D3_2


title: HM-biolrep1


title: Donor 3 and 4, scRNAseq

city: New York

first: Kacie

middle: Lee

last: McCarty

address: 550 E First Ave

institute: New York University Grossman School of Medicine

data_processing:
A combined reference genome containing both the human genome (GRch38) and E. intestinalis genome (ATCC 50506) was generated using Cell Ranger software 5.0.1 with a Cell Ranger mkref function (10X Genomics, USA). Raw sequencing reads were mapped to the combined reference genome and the gene expression matrices were generated using Cell Ranger count function with default parameters.
Assembly: human genome (GRch38) and E. intestinalis genome (ATCC 50506)
Supplementary files format and content: tab separated value files and matrix files

molecule: polyA RNA

organism:
Homo sapiens
Encephalitozoon intestinalis

source_name: Macrophages

extract_protocol: The library preparation was carried out using a Chromium Single-Cell 3′ Reagent Kits v2 Chemistry (10x Genomics, USA) according to the manufacturer’s protocol.

value: Macrophages

tag: treatment

value: infected with the human infecting species of microsporidia, Encephalitozoon intestinalis


title: Donor 2, scRNAseq


title: Donor 1, scRNAseq


title: SKNAS cells CMLD12824 replicate 3 RNAseq

status: Public on Jun 25 2024

city: Boston

last: Volegova

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw Illumina reads from ribosome profiling and matched total RNA sequencing libraries were collapsed and adapters were trimmed using fastx_collapser from the FASTX Toolkit. Bowtie2 was used to remove rRNA reads, TopHat2 to align reads to the human genome (GRCh38), Cufflinks v2.2.1 and Cuffdiff v2.2.1 to extract and merge raw read counts of the biological replicates (N = 3).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited values files, cufflinks output

source_name: SK-N-AS

extract_protocol:
Total RNA was extracted from matched samples using miRNeasy RNA Extraction kit (QIAGEN) according to manufacturer’s instructions.
RNA sequencing libraries prepared with the Illumina TruSeq stranded mRNA kit (Illumina) following the manufacturers’ instructions.

value: SK-N-AS

value: Neuroblastoma

value: Non-amplified


title: SKNAS cells CMLD12824 replicate 2 RNAseq


title: E33_D3_1

source_name: CHOZN GS-/- clone 2

value: Day 3

value: CHOZN GS-/- clone 2

value: Chinese hamster ovary (CHO)

value: selected clone 2

value: EPO-Fc producer


title: SKNAS cells solvent replicate 3 RNAseq

value: Solvent


title: SKNAS cells solvent replicate 1 RNAseq


title: SKNAS cells solvent replicate 2 RNAseq


title: Kelly cells CMLD12824 replicate 1 RNAseq

source_name: Kelly

value: Kelly

value: MYCN-amplified


title: Kelly cells solvent replicate 3 RNAseq


title: Cattle, AVITI, csRNA-seq, rep1

tag: tissue

value: Blood


title: Kelly cells solvent replicate 2 RNAseq


title: Kelly cells solvent replicate 1 RNAseq


title: SKNAS cells CMLD12824 replicate 1 ribosome profiling

library_source: other

data_processing:
*library strategy: Ribo-Seq
Raw Illumina reads from ribosome profiling and matched total RNA sequencing libraries were collapsed and adapters were trimmed using fastx_collapser from the FASTX Toolkit. Bowtie2 was used to remove rRNA reads, TopHat2 to align reads to the human genome (GRCh38), Cufflinks v2.2.1 and Cuffdiff v2.2.1 to extract and merge raw read counts of the biological replicates (N = 3).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited values files, cufflinks output

molecule: other


title: SKNAS cells solvent replicate 3 ribosome profiling


title: SKNAS cells solvent replicate 2 ribosome profiling


title: SKNAS cells CMLD12824 replicate 2 ribosome profiling


title: SKNAS cells CMLD12824 replicate 3 ribosome profiling


title: SKNAS cells solvent replicate 1 ribosome profiling


title: SKNAS cells CMLD12824 replicate 1 RNAseq


title: Kelly cells CMLD12824 replicate 3 ribosome profiling


title: Kelly cells CMLD12824 replicate 3 RNAseq


title: Kelly cells CMLD12824 replicate 2 ribosome profiling


title: Kelly cells solvent replicate 1 ribosome profiling


title: Kelly cells solvent replicate 3 ribosome profiling


title: Kelly cells solvent replicate 2 ribosome profiling


title: BCBM cells, T347-RET+, rep3

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

data_processing:
Quality control to remove reads mapped to rRNAs, adapter sequences, reads with more than 0.1% unknown bases and low-quality reads (more than 20% of the bases qualities are lower than 10) was performed by BGI Genomics (Hong Kong) using internal software SOAPnuke and FASTQC.
Salmon (v1.4.0) workflow was then used for allignment and quantification of RNA-seq data (parameters: --libType A --seqBias --gcBias --biasSpeedSamp 5 --threads 18 --validateMappings) and GRCH38 genome build (v36) was used as the reference.
DESeq2 package (v1.26.0) was used to calculate differential gene expression between T347-RET+ and T347-Ctrl control using log2FC=0.5 and FDR=0.05 as cut-offs.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text files for each sample include relative abundance of transcripts in units of transcripts per million (TPM), as output by Salmon.

source_name: breast cancer brain metastasis

extract_protocol:
BCBM T347-Ctrl and T347-RET+ cells (n =3) were collected, RNA was extracted using Qiagen RNeasy Kit (Qiagen; #74104), following manufacturer instructions.
Poly-A containing mRNA molecules were purified using poly-T oligoattached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. PCR yield was quantified by Qubit and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.  DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform. The DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

value: breast cancer brain metastasis

value: Luc-GFP-RET overexpression vector


title: BCBM cells, T347-RET+, rep2


title: BCBM cells, T347-Ctrl, rep2

value: Luc-GFP as a control (Ctrl)


title: Kelly cells CMLD12824 replicate 2 RNAseq


title: BCBM cells, T347-RET+, rep1


title: BCBM cells, T347-Ctrl, rep3


title: hNSC_cNSC_scRNAseq_multiplex_lane1

city: New Haven

first: Atreyo

last: Pal

department: Genetics

institute: Yale University

description: 2 sets of fastq files generated (GEX - gene expression with I1, R1 and R2 files, MUX - species multiplexing with I1, R1 and R2 files). Processed files are the demultiplexed cNSC scRNA-Seq data counts

data_processing:
library strategy: single cell RNA-Seq (with Cellplex multiplexing)
CHi-C: Ligated reads were truncated, mapped and filtered to DpnII digested reference genomes (generated from the GRCh38 and panTro6 reference assemblies for human and chimpanzee respectively) using the HiCUP pipeline (truncating RE site flag = ^GATC,DpnII; mapping flags for Bowtie2: --very-sensitive, --no_unal, --reorder; ditag pairing criteria: MAPQ score >= 30, XS – AS tag ID score >= 10; filtering ditag range = 50 to 800bp). Valid ditags were deduplicated using the adapter UMIs through the umitools package. All DpnII fragments containing HARs and HGEs were then merged into a single bait file and significant interactions were called using CHiCAGO after combining 3 replicates from the HiCUP pipeline. Briefly, we weighted the 4-parameter Delaporte model in CHiCAGO using parameters: weight(alpha) = 24.5, weight(beta) = -2.16, weight(gamma) = -21.2 and weight(delta) = -9.2, and this was used to compute weighted P-values for every interaction. We then set a threshold for the CHiCAGO scores as >4.5 for human and >4.4 for chimpanzee samples. CUT&RUN: Reads were trimmed for adapters using Trimmomatic and aligned to either the GRCh38 (human) or panTro6 (chimpanzee) genomes using Bowtie2 (flags: --very-sensitive, -X 2000). Aligned reads were filtered based on quality and PCR duplicates were marked using the MarkDuplicates function in Picard (courtesy the Broad Institute bioinformatic toolkit). Reads with the following flags – “reads unmapped”, “not primary alignment reads” and “failing platform duplicates” were removed and the remaining properly mapped reads were used for peak calling using the program SEACR (with the --stringent flag), which was used to call enriched regions in target data by selecting the top 0.5-1% of regions by AUC depending on the mark assayed. RNA-Seq: For the hNSC versus cNSC comparison, paired-end reads were mapped to the XSAnno whole transcriptome annotation modified to compare GRCh38 to panTro6 genomes on the GENCODEv43 annotation. Briefly, this annotation subsets out genes with exons that reciprocally liftover between both species (>98% sequence similarity), then filters out those with ambiguous annotations using BLAT [blat parameters: % ID between species = 95%, % len between species = 95%, % ID within species (paralogs) = 97%, % len within species = 97%] and finally simulates reads and filters exons that are differentially expressed in the simulation using DESeq2. Mapping was performed using the STAR aligner (flags: --outSAMunMapped Within, --twopassMode Basic, --outFilterMultimapNmax 1, --quantMode TranscriptomeSAM). Using the package RSEM we generated a counts matrix for each species’ replicate and then used DESeq2 for differential gene expression analysis. Genes with FDR-adjusted P-value < 0.01 and |log2FC| > 1 were considered differentially expressed between human and chimpanzee. For the hNSC- human neuron comparison, reads were mapped to native GRCh38 RefSeq coordinates and TPM counts from RSEM in each cell type were compared for specific gene targets.  scRNA-Seq: Reads were aligned to GRCh38 using the multi function of CellRanger 6.0.1. For quality control, cells with nFeature_RNA (number of genes) and/or nCount_RNA (number of molecules) values 2 standard deviations away from the mean were removed, alongside cells with mitochondrial reads greater than 10% of total reads. Counts were normalized using Seurat v4.3.0, via the NormalizeData function with default parameters. Human and Chimpanzee count matrices were then integrated using  the SelectIntegrationFeautres, FindIntegrationAnchors, and IntegrateData functions with default parameters. Dimensionality reduction was performed using RunPCA(params: npcs = 30) and RunUMAP on the integrated data, and Louvain clustering was performed using FindNeighbors(params: dims = 1:15) and FindClusters(params: resolution = 0.3). Cluster identities were assigned by identifying cell-type markers using FindAllMarkers(params: min.pct = 025).
Assembly: Human: GRCh38, chimpanzee: panTro6
Supplementary files format and content: C-HiC: Output txt files from HiCUP pipeline based on aligned and deduplicated Capture HiC reads linked to HARs and HGEs (one per replicate), which can be input for CHiCAGO to call significant interactions;  CUT& RUN: bigwig and bed files with signal and peak calls for each chromatin mark
Supplementary files format and content: RNA-Seq: Output txt files post transcript quantification by RSEM containing raw counts, FPKM and TPM values per replicate. hNSC and cNSC processed files are in XSAnno human-chimpanzee consensus coordinates based on GENCODEv43, human neuron processed files are in native GRCh38 RefSeq coordinates;  scRNA-Seq: txt files with feature, barcodes, matrix information for each species separately (demultiplexed)

organism:
Pan troglodytes
Homo sapiens

growth_protocol: Detailed information on growth and differentiation protocols is provided in the manuscript

extract_protocol:
Nuclei isolation performed using Celplex recommended 10x Genomics protocol CG000124
Libraries were prepared and sequenced (2×150 bp) using CellPlex 10xGenomics compliant Illumina protocols on an Illumina NovaSeq 6000.

value: Neural Stem Cells derived from IPSCs

tag: cut &_run_antibody


title: hNSC_cNSC_scRNAseq_multiplex_lane2

description: 2 sets of fastq files generated (GEX - gene expression with I1, R1 and R2 files, MUX - species multiplexing with I1, R1 and R2 files). Processed files are the demultiplexed hNSC scRNA-Seq data counts

extract_protocol:
Nuclei isolation performed using Celplex recommended 10x Genomics protocol CG000125
Libraries were prepared and sequenced (2×150 bp) using CellPlex 10xGenomics compliant Illumina protocols on an Illumina NovaSeq 6000.


title: MOLM13_FKBP-SETD1A_dTAG13_24h_RPA2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

treatment_protocol: Doxycycline were treated for 4 days. DMSO or 500 nM dTAG-13 were treated for 1 h or 24 h before fixation.

value: leukemia

value: 500nM dTAG-13 1h

tag: chip antibody

value: RPA32/RPA2 (abcam, ab10359)


title: MOLM13_FKBP-SETD1A_DMSO_24h_RPA2

value: DMSO 1h


title: Kelly cells CMLD12824 replicate 1 ribosome profiling

value: Neuroblastoma


title: BCBM cells, T347-Ctrl, rep1


title: L4_mut-16_mRNA-25C_rep_2

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

description: mRNA from total RNA

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2(Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts.
Assembly: WS258
Supplementary files format and content: tab-delimited text files including total reads mapping to each gene

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1s of wild-type and mut-16(pk710) worms were plated on enriched peptone plates and cultured at 20°C and 25°C until they reached the L4 developmental stage.

extract_protocol:
10,000 animals per sample were harvested as L4s8,000 animals per sample were harvested as L4s (~56hrs at 20°C and ~39hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
mRNA-seq library preparation. Nuclease-free H2O was added to 7.5μg of each RNA sample, extracted from whole animals, to a final volume of 100μL. Samples were incubated at 65°C for 2 minutes then incubated on ice. The Dynabeads mRNA Purification Kit (ThermoFisher 61006) was used according to the manufacturer’s protocol. 20μL of Dynabeads was used for each sample. 100ng of each mRNA sample was used to prepare libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) according to the manual, using NEBNext multiplex oligos for Illumina (NEB E7335S). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q33231). Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Two biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

value: whole animal

tag: developmental stage

tag: strain

tag: temperature


title: L4_mut-16_mRNA-20C_rep_1

description: mRNA from total RNA


title: L4_mut-16_mRNA-25C_rep_1

description: mRNA from total RNA


title: L4_WT_mRNA-20C_rep_2

description: mRNA from total RNA

value: N2- wild type


title: S. pombe, fkbp39del_sRNA

city: Memphis

first: Mario

last: Halic

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichment was calculated with our house Perl scripts
Normalization to reads per million
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: tdf can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

source_name: 3XFLAG-ago1, fkbp39Δ

growth_protocol: cells were grown in liquid, rich YES medium or low adenine YEA

extract_protocol:
ChIP libraries: IP of crosslinked (1% formaldehyde, 15 min) sonycated lysate, followed by decrosslinking and protein and RNA degradation. DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). Nascent RNA: RNA was labeled with 4 Thiouracil (Sigma), extracted, after removal of DNA was treated EZ-Link HPDP-Biotin (Thermo Scientific). Labeled RNA was recovered using streptavidin beads (Roche). RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Total RNA was isolated applying the hot phenol method. The extracted nucleic acids were treated with DNAse I, which was removed by a second phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Small RNA libraries: endogenous 3xFLAG-tagged Ago1-bound siRNA were purified by protein affinity purification and subsequent size selection on an 18% acrylamide gel. 2 pmol of a preadenylated 3' adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, 5'-App CTG TAG GCA CCA TCA AT/ddC/-3') were ligated in a 10 µl reaction with 5 U T4 RNA ligase (TaKaRa), ligation buffer without ATP and 5 U RNasin (Promega) at 20°C for 2 hours. The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor ligation was performed in a 10 µl reaction with 2 pmol 5' adaptor oligonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), 5 U RNasin (Promega), 0.06 µg BSA, 5 U T4 RNA ligase (Thermo Scientific) and 1x ligation buffer with ATP (Thermo Scientific) for 2 h at 20°C. The ligated products were gel purified and reverse transcribed with 10 pmol primer (RT primer: 5'- GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC GAT TGA TGG TGC CTA CAG-3') and the SuperScript III First Strand Synthesis System (Thermo Scientific). The cDNA was PCR-amplified with Q5 High-Fidelity 2x Master Mix (NEB) for 14-20 cycles using the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') and the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3').
DNA and RNA libraries were prepared using NEBnext Ultra Directional RNA or DNA Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer instruction. siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.

tag: strain number

value: 3XFLAG-ago1, fkbp39{delta}

tag: ip antibody

value: anti FLAG M2 affinity gel Sigma, n° A 2220

tag: target molecule

value: small RNA


title: L4_mut-16_mRNA-20C_rep_2

description: mRNA from total RNA


title: L4_WT_mRNA-25C_rep_2

description: mRNA from total RNA


title: L4_WT_mRNA-20C_rep_1

description: mRNA from total RNA


title: L4_WT_mRNA-25C_rep_1

description: mRNA from total RNA


title: S. pombe, swi6del_nascentRNA_2min_4

value: nascent RNA


title: S. pombe, chp1del_nascentRNA_2min_4


title: S. pombe, clr4del_nascentRNA_10min_4


title: S. pombe, wildtype_sRNA


title: S. pombe, chp1del_nascentRNA_10min_4


title: S. pombe, swi6del_nascentRNA_10min_3


title: S. pombe, clr4del_nascentRNA_2min_4


title: S. pombe, wildtype_nascentRNA_2min_4

source_name: wild type

value: wild type


title: S. pombe, swi6del_nascentRNA_2min_3


title: S. pombe, chp1del_nascentRNA_2min_3


title: S. pombe, chp1del_nascentRNA_10min_3


title: S. pombe, wildtype_nascentRNA_10min_4


title: S. pombe, clr4del_nascentRNA_10min_3


title: S. pombe, wildtype_nascentRNA_10min_3


title: S. pombe, swi6del_nascentRNA_10min_4


title: S. pombe, ago1del_nascentRNA_2min_2


title: S. pombe, ago1del_nascentRNA_10min_1


title: S. pombe, ago1del_nascentRNA_10min_2


title: S. pombe, fkbp39del_ago1del_totalRNA_2

value: total RNA


title: S. pombe, fkbp39del_totalRNA_2


title: S. pombe, wildtype_nascentRNA_2min_3


title: S. pombe, wildtype_totalRNA_2


title: S. pombe, fkbp39del_ago1del_totalRNA_1


title: S. pombe, clr4del_nascentRNA_2min_3


title: S. pombe, ago1del_nascentRNA_2min_1


title: S. pombe, ago1del_totalRNA_1


title: S. pombe, wildtype_PolII_ChIP2

value: antiRNA Polymerase II CTD repeat phospho S2, abcam n° 5095

value: Pol II bound DNA


title: S. pombe, wildtype_PolII_ChIP1


title: S. pombe, wildtype_totalRNA_1


title: S. pombe, ago1del_totalRNA_2


title: S. pombe, wildtype_H3_ChIP2

value: anti H3 active motif, n° 61475

value: H3 bound DNA


title: S. pombe, ago1del_PolII_ChIP2


title: S. pombe, fkbp39del_PolII_ChIP2


title: S. pombe, fkbp39del_totalRNA_1


title: S. pombe, fkbp39del_H3K9me_ChIP4

value: anti H3K9me2, abcam n° 1220

value: H3K92me bound DNA


title: S. pombe, ago1del_PolII_ChIP1


title: S. pombe, fkbp39del_H3_ChIP2


title: S. pombe, fkbp39del_PolII_ChIP1


title: S. pombe, wildtype_H3K9me_ChIP4


title: S. pombe, wildtype_H3_ChIP1


title: S. pombe, fkbp39del_H3K9me_ChIP2


title: S. pombe, fkbp39del_H3K9me_ChIP1


title: S. pombe, wildtype_H3K9me_ChIP3


title: S. pombe, fkbp39del_H3K9me_ChIP3


title: S_6_R6_1

city: Hannover

first: Matthias

middle: M

last: Wehr

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer ITEM

data_processing: Data analysis of exported and normalized “Cycle Threshold” (CT) values was performed based on the comparative ∆∆CT method described by Schmittgen and Livak.

label: not provided

growth_protocol: The A549 cell line was purchased from a commercial supplier (ATCC; LGC Promochem). Cells were routinely taken from a stock pool and grown in 75cm2 flasks by use of Dulbecco´s MEM medium (Seromed, Berlin) supplemented with 10% FCS and antibiotics. Cells were passaged every 3 to 4 days. During each passage beside continuous microscopic observation, cell quality and quantity were checked by use of an electronic cell counter (CASY® Cell Counter + Analyser System; Schärfe System, Reutlingen, Germany).

extract_protocol: RNA was isolated and purified using the RNeasy MiniKit (Qiagen) and treated with DNase (Qiagen). RNA concentration (A260) and purity (A260/A280 ratio) were measured by spectrophotometry (NanoDrop™ 2000 Spectrophotometer, software version 1.6.198, ThermoFisher Scientific). RNA integrity number (RIN) was evaluated using an Agilent 2100 Bioanalyzer® (Agilent Technologies). All RNA samples showed very good quality as indicated by high RIN values between 9.0 and 10.0.

treatment_protocol: To mimic the exposure situation of the epithelium in the in vivo lung the most common approach used is the air-liquid-interface (ALI) technique based on cell cultures on microporous membranes. Therefore, cells were initially cultivated under their cell type specific conditions in 75cm² culture flasks using submerged conditions. Culture medium was changed every to 2-3 days. Before reaching 80% confluence, cells were subcultivated. During a cell passage an aliquot of the cells was then seeded on microporous membranes (Inserts, BD Falcon; 0.4µm pore size; growth area ~1cm²). Cells were further cultivated on the membranes for approximately 72hrs until they reached a confluent monolayer as inspected by light microscopy. Serum was removed from the culture during a medium change 18hrs before exposure. Previous to the exposure with the model substances, residual liquid from the apical side of each cell monolayer was gently removed. During the treatment, cells were nutrified by culture media from beneath the membrane solely while being exposed to the test substances from the top.

value: clean air

tag: concentration

value: 0 ppm

tag: replicate

tag: exposure plate

tag: group

value: CA


title: S. pombe, wildtype_H3K9me_ChIP2


title: S. pombe, fkbp39del_H3_ChIP1


title: S_6_R5_1

tag: cell line


title: S. pombe, fkbp39del_ago1del_H3K9me_ChIP1

tag: genotype


title: S_6_R1_1


title: S. pombe, wildtype_H3K9me_ChIP1


title: S_6_NEC1_1

value: non exposed control

value: NEC


title: S_6_B6_3

value: Dimethylamine

value: HD


title: S_6_NEC6_1


title: S_6_B6_2


title: S_6_B6_1


title: S_6_B5_3

value: MD


title: S_6_B5_1


title: S_6_B5_2


title: S_6_B1_2

value: LD


title: S_6_B1_3


title: T5_DOWN_R3

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

data_processing:
reads quality-check using FastQC
alignments were performed with Hisat2
read counts with HTSeq
Differential expression analysis usignDESeq2 (v1.30)
Assembly: Prunus persica genome V2
Supplementary files format and content: raw_counts.txt

organism: Prunus persica

source_name: buds

extract_protocol:
Spectrum™ Plant Total RNA Kit
Illumina TruSeq Stranded mRNA Library

value: buds

value: Platinet 1

value: 79 DAFB


title: S_6_B1_1


title: T5_DOWN_R2


title: S_6_NEC5_1


title: T5_DOWN_R1


title: T5_UP_R2


title: T3_DOWN_R3

value: 58 DAFB


title: T5_UP_R3


title: T5_UP_R1


title: T3_UP_R3


title: Twins No1 with TB

type: genomic

city: Tongliao

first: Batudeligen

last: Batudeligen

address: 536 West Hollin River Street

institute: Affiliated Hospital of Inner Mongolia University for the Nationalities

description: SAMPLE 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K Bead Chip using standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: BeadStudio software v3.2; Average Beta

label: Biotin and DNP

source_name: blood from Twins No1 with TB

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Blood using  EDTA DNA Blood Mini Kit (Qiagen) according to standard instructions

tag: subject id

value: Twins No1

tag: subject status

value: with TB

tag: blood

value: Blood


title: T3_UP_R2

tag: tissue

tag: treatment


title: T3_UP_R1


title: T3_DOWN_R1


title: T3_DOWN_R2


title: Twins No2 without TB

description: SAMPLE 4

source_name: bloodf rom Twins No2 without TB

value: Twins No2

value: without TB


title: Twins No1 without TB

description: SAMPLE 2

source_name: blood from Twins No1 without TB


title: T1_DOWN_R3

value: 45 DAFB


title: T1_DOWN_R2


title: Twins No2 with TB

description: SAMPLE 3

source_name: blood from Twins No2 with TB


title: T1_DOWN_R1


title: T1_UP_R3


title: T1_UP_R1


title: T1_UP_R2


title: Z2H12

city: Edmonton

first: Patrick

middle: E

last: MacDonald

state: Alberta

address: 6-126 Li Ka Shing Centre

country: Canada

institute: University of Alberta

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Assembly: GRCh38
Supplementary files format and content: Combined csv count table of all cells

source_name: Human Donor Islet Cell

extract_protocol: SmartSeq2 (21X-23X PCR cycles)

tag: cell type

value: Human Donor Islet Cell

tag: Sex

value: Female

tag: disease state

tag: patched

value: Yes


title: Z2G4

value: Male


title: Z2H2


title: Z2G7


title: Z2H6


title: Z2H8


title: Z2H9


title: Z2G6


title: Z2H5


title: Z2G5


title: Z2H11


title: Z2H7


title: Z2H4


title: Z2G3


title: Z2H3


title: Z2G9


title: Z2H10


title: Z2G12


title: Z2G11


title: Z2G2


title: Z2G1


title: Z2F9


title: Z2F8


title: Z2G10


title: Z2F7


title: Z2F6


title: Z2F5


title: Z2F4


title: Z2H1


title: Z2G8


title: Z2F3


title: Z2F11


title: Z2F12


title: Z2F2


title: Z2F1


title: Z2E5


title: Z2D7


title: Z2E3


title: Z2E11


title: Z2D9


title: Z2E1


title: Z2D5


title: Z2E4


title: Z2E10


title: Z2E9


title: Z2D8


title: Z2E8


title: Z2E12


title: Z2D4


title: Z2D2


title: Z2D6


title: Z2D12


title: Z2D10


title: Z2D1


title: Z2F10


title: Z2E7


title: Z2E6


title: Z2E2


title: Z2C9


title: Z2C8


title: Z2C7


title: Z2C6


title: Z2C12


title: Z2C5


title: Z2C2


title: Z2B9


title: Z2D3


title: Z2B8


title: Z2C3


title: Z2C11


title: Z2C1


title: Z2B5


title: Z2B6


title: Z2C4


title: Z2B3


title: Z2B12


title: Z2B4


title: Z2D11


title: Z2B10


title: Z2B2


title: Z2B11


title: Z2B1


title: Z2A9


title: Z2C10


title: Z2A8


title: Z2A4


title: Z2A5


title: Z2A3


title: Z2B7


title: Z2A6


title: Z2A2


title: Z2A12


title: Z2A10


title: Z2A1


title: Y2H8


title: Y2H4


title: Y2H7


title: Y2H3


title: Z2A11


title: Y2H6


title: Y2H9


title: Y2H11


title: Y2H12


title: Y2H5


title: Y2H1

value: ND


title: Y2G8


title: Z2A7


title: Y2H10


title: Y2G6


title: Y2G7


title: Y2G9


title: Y2G5


title: Y2G4


title: Y2G3


title: Y2G2


title: Y2G12


title: Y2G1


title: Y2G11


title: Y2G10


title: Y2F9


title: Y2F8


title: Y2F7


title: Y2F5


title: Y2F4


title: Y2F12


title: Y2F11


title: Y2F10


title: Y2E5


title: Y2E7


title: Y2E9


title: Y2E2


title: Y2E4


title: Y2E3


title: Y2E8


title: Y2E6


title: Y2F1


title: Y2E12


title: Y2D8


title: Y2E11


title: Y2D4


title: Y2H2


title: Y2D7


title: Y2E1


title: Y2F2


title: Y2F3


title: Y2F6


title: Y2D11


title: Y2D12


title: Y2C9


title: Y2D10


title: Y2D1


title: Y2D2


title: Y2E10


title: Y2C8


title: Y2C6


title: Y2D9


title: Y2C7


title: Y2D6


title: Y2C4


title: Y2D5


title: Y2C3


title: Y2C5


title: Y2C2


title: Y2D3


title: Y2C10


title: Y2C11


title: Y2C1


title: Y2B8


title: Y2B7


title: Y2B5


title: Y2B9


title: Y2B3


title: Y2B6


title: Y2B4


title: Y2B2


title: Y2B12


title: Y2B10


title: Y2A7


title: Y2A9


title: Y2A8


title: Y2B1


title: Y2C12


title: Y2A4


title: Y2A5


title: Y2A6


title: Y2A10


title: Y2A2


title: Y2A3


title: Y2A11


title: Y2A1


title: Y2A12


title: X2H4


title: X2H5


title: X2H2


title: X2H10


title: X2H12


title: X2H8


title: Y2B11


title: X2G9


title: X2H7


title: X2H3


title: X2H11


title: X2G6


title: X2G7


title: X2G8


title: X2H1


title: X2G2


title: X2G10


title: X2G12


title: X2H9


title: X2H6


title: X2G5


title: X2G1


title: X2F8


title: X2F9


title: X2G11


title: X2F6


title: X2F7


title: X2F11


title: X2F10


title: X2F12


title: X2E8


title: X2G4


title: X2F2


title: X2G3


title: X2E7


title: X2F1


title: X2E5


title: X2E9


title: X2E4


title: X2E3


title: X2E12


title: X2E2


title: X2E11


title: X2E6


title: X2F5


title: X2F3


title: X2E1


title: X2D2


title: X2D9


title: X2D12


title: X2D6


title: X2D7


title: X2D5


title: X2E10


title: X2D10


title: X2D11


title: X2F4


title: X2D8


title: X2C9


title: X2C8


title: X2D1


title: X2C6


title: X2C7


title: X2C4


title: X2C5


title: X2C1


title: X2C3


title: X2C2


title: X2C10


title: X2C11


title: X2B9


title: X2D4


title: X2D3


title: X2B8


title: X2B4


title: X2B3


title: X2B2


title: X2B5


title: X2B7


title: X2A8


title: X2B10


title: X2B11


title: X2C12


title: X2A9


title: X2B6


title: X2A6


title: X2A5


title: X2A2


title: X2B12


title: X2A11


title: X2A12


title: X2A3


title: X2A4


title: X2A10


title: X2B1


title: X2A1


title: W2H5


title: W2H9


title: W2H8


title: W2H6


title: W2H7


title: W2H4


title: W2H3


title: W2H2


title: W2H10


title: W2H11


title: X2A7


title: W2H12


title: W2G9


title: W2G8


title: W2H1


title: W2G5


title: W2G2


title: W2G3


title: W2G12


title: W2F9


title: W2F8


title: W2G7


title: W2G4


title: W2G6


title: W2G1


title: W2F6


title: W2F7


title: W2G11


title: W2F5


title: W2G10


title: W2F4


title: W2F3


title: W2F12


title: W2F2


title: W2F11


title: W2F10


title: W2F1


title: W2E7


title: W2E9


title: W2E8


title: W2E5


title: W2E4


title: W2E6


title: W2E3


title: W2E2


title: W2E11


title: W2E12


title: W2E10


title: W2E1


title: W2D6


title: W2D7


title: W2D3


title: W2D4


title: W2D5


title: W2D10


title: W2D2


title: W2D1


title: W2C9


title: W2D11


title: W2C7


title: W2C8


title: W2C6


title: W2C5


title: W2C4


title: W2C3


title: W2C12


title: W2C2


title: W2C10


title: W2C1


title: W2B9


title: W2D8


title: W2B8


title: W2B5


title: W2B6


title: W2D9


title: W2B4


title: W2D12


title: W2B3


title: W2B10


title: W2B2


title: W2B11


title: W2B1


title: W2A8


title: W2A9


title: W2A6


title: W2A5


title: W2A3


title: W2A4


title: W2A2


title: W2C11


title: W2A12


title: W2A10


title: V2H9


title: W2A1


title: W2B7


title: V2H8


title: V2H7


title: V2H6


title: V2H5


title: V2H2


title: V2H3


title: W2B12


title: V2H12


title: V2H11


title: V2H4


title: V2H10


title: W2A7


title: V2G9


title: V2G8


title: V2G7


title: V2G4


title: V2G6


title: V2G3


title: V2G2


title: V2H1


title: W2A11


title: V2G12


title: V2G1


title: V2G11


title: V2F9


title: V2F8


title: V2F7


title: V2F4


title: V2F6


title: V2G10


title: V2F5


title: V2F3


title: V2F11


title: V2F10


title: V2F2


title: V2F12


title: V2E8


title: V2E7


title: V2F1


title: V2E6


title: V2E9


title: V2E4


title: V2G5


title: V2E2


title: V2E3


title: V2E5


title: V2E11


title: V2E1


title: V2E12


title: V2D9


title: V2E10


title: V2D8


title: V2D7


title: V2D4


title: V2D6


title: V2D5


title: V2D2


title: V2D12


title: V2D11


title: V2D3


title: V2D1


title: V2D10


title: V2C7


title: V2C8


title: V2C3


title: V2C9


title: V2C5


title: V2C6


title: V2C4


title: V2C12


title: V2C2


title: V2B8


title: V2B9


title: V2C10


title: V2B6


title: V2B4


title: V2B5


title: V2B3


title: V2B12


title: V2B10


title: V2B11


title: V2A8


title: V2A5


title: V2A7


title: V2A6


title: V2A3


title: V2A4


title: V2C11


title: V2A12


title: V2A2


title: U2H9


title: U2H8


title: V2A1


title: V2C1


title: U2H7


title: U2H4


title: V2B7


title: U2H3


title: U2H6


title: U2H2


title: U2H12


title: U2H11


title: V2A9


title: V2B1


title: U2H1


title: U2G9


title: U2G8


title: V2B2


title: U2G7


title: U2G4


title: U2G6


title: V2A10


title: U2G3


title: U2G2


title: U2G11


title: U2G12


title: U2G1


title: U2G5


title: U2F9


title: U2H5


title: U2F8


title: U2G10


title: U2F4


title: U2F3


title: U2F2


title: U2F12


title: U2F11


title: U2F10


title: U2F7


title: U2E9


title: U2F6


title: U2H10


title: U2E8


title: U2F1


title: U2E7


title: U2E6


title: U2E5


title: U2E4


title: U2E11


title: U2E2


title: U2E12


title: U2E10


title: U2D9


title: U2D7


title: U2D8


title: U2D5


title: U2F5


title: U2D3


title: U2D2


title: U2D12


title: U2D11


title: U2D1


title: U2C9


title: U2D10


title: U2C6


title: U2C7


title: U2C3


title: U2C5


title: U2C8


title: U2E3


title: U2C2


title: U2C11


title: U2E1


title: U2C10


title: U2D6


title: U2B9


title: U2B6


title: U2D4


title: U2B7


title: U2B8


title: U2B4


title: U2B5


title: U2B2


title: U2B12


title: U2B11


title: U2B10


title: U2B3


title: U2B1


title: U2A9


title: U2C4


title: U2A6


title: U2C12


title: U2A5


title: U2A7


title: U2A4


title: U2A2


title: U2C1


title: U2A3


title: U2A12


title: U2A10


title: T2H9


title: U2A1


title: T2H7


title: T2H8


title: T2H3


title: T2H5


title: T2H6


title: T2H2


title: T2H12


title: T2H4


title: T2H11


title: U2A8


title: T2H1


title: T2G8


title: T2G7


title: T2G9


title: T2H10


title: T2G6


title: T2G5


title: T2G4


title: T2G3


title: U2A11


title: T2G11


title: T2G2


title: T2F8


title: T2G1


title: T2G10


title: T2F9


title: T2F7


title: T2F6


title: T2F5


title: T2F4


title: T2F12


title: T2F3


title: T2F10


title: T2F11


title: T2F2


title: T2F1


title: T2E7


title: T2E5


title: T2E3


title: T2E8


title: T2E4


title: T2E2


title: T2G12


title: T2E6


title: T2E11


title: T2E10


title: T2E12


title: T2D9


title: T2E1


title: T2D6


title: T2D7


title: T2D4


title: T2D5


title: T2D3


title: T2D8


title: T2D12


title: T2D11


title: T2D1


title: T2D10


title: T2C9


title: T2E9


title: T2C5


title: T2C7


title: T2D2


title: T2C8


title: T2C6


title: T2C4


title: T2C12


title: T2C2


title: T2C11


title: T2C3


title: T2C10


title: T2B9


title: T2C1


title: T2B8


title: T2B6


title: T2B7


title: T2B5


title: T2B4


title: T2B2


title: T2B12


title: T2B3


title: T2B10


title: T2B11


title: T2B1


title: T2A9


title: T2A8


title: T2A7


title: T2A4


title: T2A5


title: T2A3


title: T2A1


title: T2A10


title: T2A12


title: T2A2


title: S2H6


title: S2H7


title: S2H9


title: S2H4


title: S2H2


title: S2H3


title: S2H8


title: S2H5


title: S2H12


title: S2G9


title: S2G7


title: S2H10