title: Clinical isolate 608

status: Public on Sep 30 2024

type: SRA

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 20 –max-intronlen 3000 --rna-strandness RF
Properly oridented reads and mapped to maximum three locations were extracted using samtools (version: 1.11)
Transcriptome assembly on these aligned reads were performed using StringTie version 2.1.4 with parameters --fr -m 150 -j 3 -g 20.  Each assembled transcripts were quantified by same version of Stringtie with e options.
Assembly: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary files format and content: Comma-delimited text file includes TPM values assembled transcripts for each samples

molecule: total RNA

organism: Plasmodium falciparum

source_name: packed red blood cells

growth_protocol: Material has been obtained from in vivo clinical samples.

extract_protocol:
8 volumes of TRIzol reagent (Invitrogen) (v/v) were added to 0.5 ml infected packed red blood cells. Samples were vortexed at 7000 RPM for 1 min. Chlorophorm was added in 1:5 volumetric ratio, vortexed and samples were centrifuged for 15 min to separate phases as previously described (2,3). Supernatant was aspirated and transferred to the new tubes. Equal volume of 100% ethanol was added to the supernatant and RNA was extracted using ZYMO DirectZol-96 RNA kit (ZYMO) following manufacturer instructions. RNA was eluted in 17 ul of RNAse/DNAse free water, and its purity was assessed by spectrometry on Nanodrop (Thermo Scientific). RNA concentration was estimated using RNA-specific Qubit fluorometric assay (Invitrogen). RNA integrity was assessed on Bioanalyzer RNA Nano Chip (Agilent).
RNA sequencing libraries have been prepared from 100 ng of purified total RNA using ZYMO-Seq RiboFree Total RNA Library Kit (ZYMO) following manufacturer’s instructions with some modifications to the protocol described below. This protocol allows for generation of stranded, rRNA and human globin depleted libraries. Whole protocol has been scaled down to use half of the recommended volume of each reagent. Depletion step of rRNA (both human and the parasite) and globin has been adjusted to 4 hours at 68oC. 14 cycles of PCR have been used for final index incorporation. Resulted libraries have been eluted in 15ul of the elution buffer and verified by real-time PCR, fluorometric DNA concentration assay (Invitrogen) and Bioanalyzer DNA High-Sensitivity chip (Agilent Technologies) by Novogene Singapore. 96 libraries (total RNA) have been equimolarly pooled and sequenced per one lane of Novaseq S4 sequencing technology (Illumina) generating approximately 750GB data per lane (Novogene, Singapore). Technical replicates of 3D7 lab strain gDNA/RNA were also included on each sequencing lane to control for library preparation and sequencing efficiency.

treatment_protocol: Patients were randomly assigned (1:1) to one of two treatments using block randomisation, depending on their location: in Thailand, Cambodia, Vietnam, and Myanmar patients were assigned to either dihydroartemisinin-piperaquine or dihydroartemisinin-piperaquine plus mefloquine; at three sites in Cambodia they were assigned to either artesunate-mefloquine or dihydroartemisinin-piperaquine plus mefloquine; and in Laos, Myanmar, Bangladesh, India, and the Democratic Republic of the Congo they were assigned to either artemether-lumefantrine or artemether-lumefantrine plus amodiaquine. All drugs were administered orally and doses varied by drug combination and site.

tag: time point

tag: cell type

value: packed red blood cells

tag: treatment

value: Prior to ACT/TACT treatment


title: Clinical isolate 606


title: Clinical isolate 605


title: Clinical isolate 607


title: Clinical isolate 610


title: Clinical isolate 603


title: Clinical isolate 609


title: Clinical isolate 599


title: Clinical isolate 598


title: Clinical isolate 600


title: Clinical isolate 596


title: Clinical isolate 595


title: Clinical isolate 591


title: Clinical isolate 590


title: Clinical isolate 593


title: Clinical isolate 592


title: Clinical isolate 589


title: Clinical isolate 597


title: Clinical isolate 587


title: Clinical isolate 588


title: Clinical isolate 586


title: Clinical isolate 594


title: Clinical isolate 583


title: Clinical isolate 585


title: Clinical isolate 570


title: Clinical isolate 582


title: Clinical isolate 578


title: Clinical isolate 577


title: Clinical isolate 566


title: Clinical isolate 580


title: Clinical isolate 573


title: Clinical isolate 581


title: Clinical isolate 576


title: Clinical isolate 579


title: Clinical isolate 564


title: Clinical isolate 604


title: Clinical isolate 602


title: Clinical isolate 572


title: Clinical isolate 565


title: Clinical isolate 584


title: Clinical isolate 562


title: Clinical isolate 563


title: Clinical isolate 561


title: Clinical isolate 568


title: Clinical isolate 560


title: Clinical isolate 601


title: Clinical isolate 567


title: Clinical isolate 575


title: Clinical isolate 574


title: Clinical isolate 571


title: Clinical isolate 569


title: Clinical isolate 559


title: Clinical isolate 557


title: Clinical isolate 554


title: Clinical isolate 558


title: Clinical isolate 556


title: Clinical isolate 551


title: Clinical isolate 547


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title: Clinical isolate 552


title: Clinical isolate 549


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title: Clinical isolate 535


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title: Clinical isolate 537


title: Clinical isolate 532


title: Clinical isolate 531


title: Clinical isolate 553


title: Clinical isolate 527


title: Clinical isolate 528


title: Clinical isolate 540


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title: Clinical isolate 529


title: Clinical isolate 525


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title: Clinical isolate 521


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title: Clinical isolate 515


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title: Clinical isolate 516


title: Clinical isolate 517


title: Clinical isolate 519


title: Clinical isolate 514


title: Clinical isolate 513


title: Clinical isolate 509


title: Clinical isolate 511


title: Clinical isolate 512


title: Clinical isolate 510


title: Clinical isolate 507


title: Clinical isolate 508


title: Clinical isolate 506


title: Clinical isolate 504


title: Clinical isolate 530


title: Clinical isolate 505


title: Clinical isolate 503


title: Clinical isolate 502


title: Clinical isolate 500


title: Clinical isolate 555


title: Clinical isolate 498


title: Clinical isolate 501


title: Clinical isolate 495


title: Clinical isolate 496


title: Clinical isolate 499


title: Clinical isolate 497


title: Clinical isolate 492


title: Clinical isolate 493


title: Clinical isolate 491


title: Clinical isolate 487


title: Clinical isolate 488


title: Clinical isolate 486


title: Clinical isolate 490


title: Clinical isolate 489


title: Clinical isolate 485


title: Clinical isolate 479


title: Clinical isolate 494


title: Clinical isolate 480


title: Clinical isolate 481


title: Clinical isolate 478


title: Clinical isolate 477


title: Clinical isolate 476


title: Clinical isolate 482


title: Clinical isolate 472


title: Clinical isolate 471


title: Clinical isolate 469


title: Clinical isolate 473


title: Clinical isolate 470


title: Clinical isolate 474


title: Clinical isolate 466


title: Clinical isolate 467


title: Clinical isolate 483


title: Clinical isolate 465


title: Clinical isolate 475


title: Clinical isolate 463


title: Clinical isolate 461


title: Clinical isolate 464


title: Clinical isolate 459


title: Clinical isolate 457


title: Clinical isolate 458


title: Clinical isolate 456


title: Clinical isolate 455


title: Clinical isolate 484


title: Clinical isolate 453


title: Clinical isolate 454


title: Clinical isolate 451


title: Clinical isolate 450


title: Clinical isolate 452


title: Clinical isolate 468


title: Clinical isolate 460


title: Clinical isolate 449


title: Clinical isolate 444


title: Clinical isolate 447


title: Clinical isolate 446


title: Clinical isolate 448


title: Clinical isolate 443


title: Clinical isolate 442


title: Clinical isolate 462


title: Clinical isolate 440


title: Clinical isolate 439


title: Clinical isolate 437


title: Clinical isolate 436


title: Clinical isolate 435


title: Clinical isolate 432


title: Clinical isolate 433


title: Clinical isolate 434


title: Clinical isolate 431


title: Clinical isolate 430


title: Clinical isolate 429


title: Clinical isolate 428


title: Clinical isolate 425


title: Clinical isolate 445


title: Clinical isolate 427


title: Clinical isolate 424


title: Clinical isolate 422


title: Clinical isolate 423


title: Clinical isolate 421


title: Clinical isolate 420


title: Clinical isolate 417


title: Clinical isolate 419


title: Clinical isolate 418


title: Clinical isolate 415


title: Clinical isolate 416


title: Clinical isolate 426


title: Clinical isolate 441


title: Clinical isolate 438


title: Clinical isolate 412


title: Clinical isolate 413


title: Clinical isolate 414


title: Clinical isolate 411


title: Clinical isolate 409


title: Clinical isolate 406


title: Clinical isolate 407


title: Clinical isolate 408


title: Clinical isolate 405


title: Clinical isolate 403


title: Clinical isolate 404


title: Clinical isolate 402


title: Clinical isolate 401


title: Clinical isolate 400


title: Clinical isolate 399


title: Clinical isolate 397


title: Clinical isolate 396


title: Clinical isolate 398


title: Clinical isolate 395


title: Clinical isolate 394


title: Clinical isolate 391


title: Clinical isolate 392


title: Clinical isolate 388


title: Clinical isolate 387


title: Clinical isolate 393


title: Clinical isolate 386


title: Clinical isolate 382


title: Clinical isolate 410


title: Clinical isolate 383


title: Clinical isolate 384


title: Clinical isolate 379


title: Clinical isolate 380


title: Clinical isolate 375


title: Clinical isolate 374


title: Clinical isolate 373


title: Clinical isolate 372


title: Clinical isolate 371


title: Clinical isolate 390


title: Clinical isolate 389


title: Clinical isolate 369


title: Clinical isolate 368


title: Clinical isolate 370


title: Clinical isolate 377


title: Clinical isolate 367


title: Clinical isolate 366


title: Clinical isolate 365


title: Clinical isolate 385


title: Clinical isolate 381


title: Clinical isolate 360


title: Clinical isolate 363


title: Clinical isolate 362


title: Clinical isolate 378


title: Clinical isolate 359


title: Clinical isolate 357


title: HepG2-miR27a-KO rep2

city: Birmingham

first: Lizhong

last: Wang

address: 720 20th St S

country: USA

institute: University of Alabama at Birmingham

data_processing:
In our project, we sequenced 6 samples on BGISEQ-500 Platform in total
After reads filtering, we map clean reads to reference genome using HISAT
IGV(Integrative Genomics Viewer) tool can be used to review the mapping result.
we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks ) and predict the coding ability of those new transcripts using CPC
After genome mapping, we use GATK to call  SNP  and  INDEL  variant for each sample.
Assembly: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: liver cancer cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: triple-negative liver cancer cells

tag: genotype


title: Clinical isolate 376


title: Clinical isolate 361


title: Clinical isolate 358


title: Clinical isolate 355


title: HepG2-miR23a-KO rep1


title: HepG2-Scr rep2

value: WT


title: Clinical isolate 354


title: Clinical isolate 364


title: Clinical isolate 352


title: HepG2-Scr rep1


title: Clinical isolate 353


title: Clinical isolate 351


title: Clinical isolate 350


title: Clinical isolate 349


title: Clinical isolate 348


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_Tr_B1

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.36
Mapping was performed using BWA
and reverse transcripts were counted using python script HTSeq .
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation .
Assembly: A_nidulans_FGSC_A4_version_s10-m03-r07
Supplementary files format and content: Transcript_NCBI.txt
Supplementary files format and content: AMM_24h_A1 rawcounts  AMM_24h_A2 rawcounts  AMM_24h_B1 rawcounts  AMM_24h_B2 rawcounts  AMM_20h_Salt_4h_A1 rawcounts  AMM_20h_Salt_4h_A2 rawcounts  AMM_20h_Salt_4h_B1 rawcounts  AMM_20h_Salt_4h_B2 rawcounts  AMM_24h_AMM_2h_Old_1h_A1 rawcounts  AMM_24h_AMM_2h_Old_1h_A2 rawcounts  AMM_24h_AMM_2h_Old_1h_B1 rawcounts  AMM_24h_AMM_2h_Old_1h_B2 rawcounts  AMM_20h_Salt_4h_AMM_2h_Old_1h_A1 rawcounts  AMM_20h_Salt_4h_AMM_2h_Old_1h_A2 rawcounts  AMM_20h_Salt_4h_AMM_2h_Old_1h_B1 rawcounts  AMM_20h_Salt_4h_AMM_2h_Old_1h_B2 rawcounts  AMM_24h_AMM_2h_A1 rawcounts  AMM_24h_AMM_2h_A2 rawcounts  AMM_24h_AMM_2h_B1 rawcounts  AMM_24h_AMM_2h_B2 rawcounts  AMM_20h_Salt_4h_AMM_2h_A1 rawcounts  AMM_20h_Salt_4h_AMM_2h_A2 rawcounts  AMM_20h_Salt_4h_AMM_2h_B1 rawcounts  AMM_20h_Salt_4h_AMM_2h_B2 rawcounts  AMM_24h_AMM_2h_Salt_1h_A1 rawcounts  AMM_24h_AMM_2h_Salt_1h_A2 rawcounts  AMM_24h_AMM_2h_Salt_1h_B1 rawcounts  AMM_24h_AMM_2h_Salt_1h_B2 rawcounts  AMM_20h_Salt_4h_AMM_2h_Salt_1h_A1 rawcounts  AMM_20h_Salt_4h_AMM_2h_Salt_1h_A2 rawcounts  AMM_20h_Salt_4h_AMM_2h_Salt_1h_B1 rawcounts  AMM_20h_Salt_4h_AMM_2h_Salt_1h_B2 rawcounts  AMM_24h_FPKM FPKM AMM_20h_Salt_4h_FPKM FPKM  AMM_24h_AMM_2h_Old_1h_FPKM FPKM  AMM_20h_Salt_4h_AMM_2h_Old_1h_FPKM FPKM  AMM_24h_AMM_2h_FPKM FPKM  AMM_20h_Salt_4h_AMM_2h_FPKM FPKM  AMM_24h_AMM_2h_Salt_1h_FPKM FPKM  AMM_20h_Salt_4h_AMM_2h_Salt_1h_FPKM FPKM

molecule: polyA RNA

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Aspergillus nidulans WT FGSC#4 (Pontecorvo et al., 1953) and alcA(p)-sGFP-aflR named RKIS42.17 (Shimizu et al., 2003) were used in this study. Media preparation of Aspergillus minimal medium (AMM) was done as described earlier (Todd et al., 2007). AMM was prepared containing Aspergillus salt stock solution and modified Hutner’s TE (Hill and Kafer, 2001), 50mM glucose and 10mM nitrate as sole nitrogen source. Salt solution composition was identical to AMM but missing both carbon and nitrogen sources. For cultures grown in liquid AMM, conidiospores suspended in sterile deionized water with 0.1 % Tween-20 were inoculated to reach a final spore density of 4*106 conidia/mL medium. Cultures were inoculated in 200mL of liquid AMM in 1000mL Erlenmeyer flasks and the cultures grown at 37°C and shaking at 180rpm. The following auxotrophic markers and working concentrations were used: p-aminobenzoic acid (pabaA1/pabaB22, 2µg/mL), biotin (biA1, 1.4µg/mL). The cultures were harvested by filtering the mycelia through sterile Miracloth (Merck, 475855-1R). Cells were immediately frozen in liquid nitrogen and freeze-dried for 1–2days for expression analysis.

extract_protocol:
RNA was extracted from freeze-dried mycelium using TRIzol Reagent (Thermo Fisher Scientific, 15596018). 2 µg total RNA were then subjected to DNase I digestion (Thermo Fisher Scientific, EN0521) and checked by PCR for absence of residual DNA.
Illumina sequencing libraries were made from RNA samples according to TruSeq RNA Sample prep kit v2 (Illumina) following the manufacturers protocol with 1µg total RNA input. 50 bp single end sequencing was performed using a HiSeq Illumina sequencer. Obtained sequences were de-multiplexed, quality controlled and mapped on the Aspergillus nidulans genome assembly (A_nidulans_FGSC_A4_version_s10-m03-r07).

treatment_protocol: A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) and then shifted on Salt medium (no C or N source) for 4 hours --> AMM_20h_Salt_4h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) --> AMM_24h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h --> AMM_20h_Salt_4h_AMM_2h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h --> AMM_24h_AMM_2h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h, shifted on Salt medium (no C or N source) for 1 hour  --> AMM_20h_Salt_4h_AMM_2h_Salt_1h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h, shifted on Salt medium (no C or N source) for 1 hour --> AMM_24h_AMM_2h_Salt_1h A. nidulans was growth for 20h on Aspergillus minimal medium (AMM) , shifted on Salt medium (no C or N source) for 4 hours , shifted on AMM for 2 h, shifted on used medium (C or N source used up by A. nidulans growth for 48h) for 1 hour  --> AMM_20h_Salt_4h_AMM_2h_Old_1h A. nidulans was growth for 24h on Aspergillus minimal medium (AMM) , shifted on AMM for 2 h, shifted on used medium (C or N source used up by A. nidulans growth for 48h) for 1 hour --> AMM_24h_AMM_2h_Old_1h A nd B denote biological replicates, 1 and 2 technical replicates

tag: tissue

value: mycelium


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_Tr_A1


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_Tr_B2


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_Tr_B2


title: Clinical isolate 347


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_Tr_B1


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_Tr_A2


title: HepG2-miR27a-KO rep1


title: Clinical isolate 345


title: HepG2-miR23a-KO rep2


title: Clinical isolate 356


title: Clinical isolate 344


title: Clinical isolate 342


title: Clinical isolate 343


title: Clinical isolate 346


title: AMM_24h_AMM_2h_Salt_1h_Tr_B2


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_Tr_A1


title: AMM_24h_AMM_2h_Salt_1h_Tr_B1


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_Tr_A2


title: Clinical isolate 340


title: AMM_24h_AMM_2h_Salt_1h_Tr_A2


title: Clinical isolate 341


title: AMM_24h_AMM_2h_Salt_1h_Tr_A1


title: Horse sperm 3

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

country: Spain

institute: INIA

data_processing:
Raw reads were processed and mapped using CLC Genomics Workbench
Bowtie2 was used to asses the presence of rRNA and filter the reads
Unmapped reads were aligned to the RefsSeq bacterial genome library using Kraken2 and Bracken was used to improve abundance estimation
Assembly: Bos Taurus ARS-UCD1.3 and Equus Caballus EquCab3.0
Supplementary files format and content: Excel files include bacterial abundance for each sample

organism: Equus caballus

source_name: Spermatozoa

extract_protocol:
Total RNA was isolated from sperm using TRIzol reagent, treated with Dnase for 15 min and purified by phenol:chloroform extraction
RNA libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit

value: Spermatozoa

value: Fertile


title: Clinical isolate 339


title: Horse sperm 2


title: Horse sperm 4


title: AMM_20h_Salt_4h_AMM_2h_Tr_B2


title: Horse sperm 1


title: Clinical isolate 338


title: Clinical isolate 337


title: AMM_20h_Salt_4h_AMM_2h_Tr_A2


title: Clinical isolate 336


title: Clinical isolate 335


title: AMM_20h_Salt_4h_AMM_2h_Tr_B1


title: AMM_20h_Salt_4h_AMM_2h_Tr_A1


title: AMM_24h_AMM_2h_Old_1h_Tr_B2


title: AMM_24h_AMM_2h_Old_1h_Tr_B1


title: ATAC-seq-duodenum-high4

city: 武汉

first: jahui

last: sun

state: 湖北

address: 湖北省武汉市

country: China

institute: 华中农业大学

library_source: genomic

data_processing:
In this study, we utilized six Large White pigs, three with extremely high FCR values and three with extremely low FCR values. These pigs were raised on the same commercial farm under similar conditions and fed the same diet. All pigs were euthanized at 180 days of age after an overnight fasting period. Muscle and duodenal samples were collected and stored at -80°C for subsequent experiments. The sampling procedures received approval from the Ethics Committee of Huazhong Agricultural University. RNA-seq analysis was conducted on samples from three pigs with the highest FCR levels and three with the lowest FCR levels. In addition, ATAC-seq analysis was performed on samples from two pigs with extremely high FCR levels and two with extremely low FCR levels.
Assembly: Sscrofa11.1
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Sus scrofa

source_name: duodenum

extract_protocol:
TRIzol solution (1 ml) was added to a centrifuge tube containing either muscle or duodenal tissue for tissue lysis. RNA extraction was then performed following the protocol provided by the manufacturer (Thermo Fisher Scientific, 15596026).
The extracted RNA was quantified using a Qubit fluorometer. RNA enrichment was performed using VAHTS mRNA Capture Beads (Vazyme, CN).
library construction for RNA-seq was carried out following the protocol provided by the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, CN).

value: duodenum

tag: fcr value

value: high


title: ATAC-seq-duodenum-low3

value: low


title: Clinical isolate 334


title: ATAC-seq-duodenum-low6


title: Clinical isolate 333


title: RNA-seq-duodenum-high1


title: AMM_24h_AMM_2h_Old_1h_Tr_A2


title: Clinical isolate 332


title: RNA-seq-duodenum-low5


title: RNA-seq-duodenum-high4


title: RNA-seq-duodenum-high5


title: AMM_24h_AMM_2h_Old_1h_Tr_A1


title: Clinical isolate 331


title: AMM_20h_Salt_4h_Tr_B2


title: RNA-seq-duodenum-low3


title: Clinical isolate 330


title: AMM_20h_Salt_4h_Tr_B1


title: ATAC-seq-muscle-high4

source_name: muscle

value: muscle


title: RNA-seq-duodenum- low6


title: Clinical isolate 329


title: AMM_20h_Salt_4h_Tr_A2


title: ATAC-seq-muscle-low-3


title: ATAC-seq-muscle-high5


title: ATAC-seq-duodenum-high5


title: Clinical isolate 328


title: ATAC-seq-muscle-low-6


title: RNA-seq-muscle-low6


title: RNA-seq-muscle-low5-FCR


title: RNA-seq-muscle-high-FCR


title: Clinical isolate 327


title: AMM_24h_AMM_2h_Tr_B2


title: Clinical isolate 326


title: RNA-seq-muscle-high5-FCR


title: AMM_24h_AMM_2h_Tr_B1


title: RNA-seq-muscle-high4-FCR


title: Clinical isolate 325


title: AMM_24h_AMM_2h_Tr_A2


title: MDAMB231_long_siSRSF1_10Gy_bio_rep3

city: Oxford

first: Majd

last: Abdulghani

state: oxfordshire

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Collected 48 hours after irradiation or mock irradiation

data_processing:
Quality control with Pychopper: pychopper -k PCS111 -r ${report_output} -u ${unclassified_output} -w ${rescued_output} ${input_file} ${full_length_output}
Long-read error correction with short reads (short-read data accession GSE242550) using FMLRC: FM-index Long Read Corrector (FMLRC) v0.1.8 (Mak et al. 2023; Wang et al. 2018b). First, I build a Burrows-Wheeler Transform file from the short reads, as required by FMLRC, using msbwt2-build, then used that to correct the long reads as follows: fmlrc2 "$BWT_PATH" "$input_file" "$output_file". This generated a list of corrected gzipped fasta files for each sample.
aligned those reads to the transcriptome of T2T-CHM13v2.0 with the following command: minimap2 -ax splice rna.fna $file -uf --secondary=no -t 24 > $out_sam_file
Salmon was run in alignment-based mode, with the following command: salmon quant -l SF --ont -t rna.fna -a ${sample}_mapped.sam -o ${sample}_salmon_output
Assembly: human NCBI genome build T2T-CHM13v2.0
Supplementary files format and content: salmon output files (with quant.sf)

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Thermo Fisher Scientific, #41966029) supplemented with 10% FBS (Sigma-Aldrich, #F9665-500ML)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN)
The library was constructed according to Nanopore protocol, with cDNA and PCR amplification steps. The kit used was PCS111, and the 12 samples were barcoded and ran 5 times (5 flow cells, 12 samples per flow cell) on PromethION.

treatment_protocol: 4.5 million cells were transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific, #13778030) with siRNA against SRSF1 (Dharmacon, #A-018672-13-0005) or a non-targeting siRNA pool (Dharmacon, #D-001910-10-50). One-and-a-half days later, the cells were irradiated in a 137Cesium irradiator at 10 Gy, or mock-irrdiated (0 Gy). Forty-eight hours later, the cells were collected by scraping.

value: SRSF1 knockdown, 10 Gy radiation


title: Clinical isolate 324


title: MDAMB231_long_siControl_10Gy_bio_rep3

value: no knockdown, 10 Gy radiation


title: MDAMB231_long_siSRSF1_10Gy_bio_rep1


title: Clinical isolate 323


title: MDAMB231_long_siControl_10Gy_bio_rep2


title: AMM_20h_Salt_4h_Tr_A1


title: RNA-seq-muscle-low3-FCR


title: MDAMB231_long_siSRSF1_0Gy_bio_rep3

value: SRSF1 knockdown, no radiation


title: Clinical isolate 322


title: AMM_24h_Tr_A2


title: Clinical isolate 321


title: MDAMB231_long_siSRSF1_0Gy_bio_rep1


title: MDAMB231_long_siSRSF1_0Gy_bio_rep2


title: MDAMB231_long_siControl_0Gy_bio_rep3

value: no knockdown, no radiation


title: MDAMB231_long_siControl_0Gy_bio_rep2


title: Clinical isolate 320


title: AMM_24h_Tr_A1


title: H3K4me3 eSPAN- HXK2Δ

city: Minneapolis

first: Quinn

last: Dickinson

state: MN

address: 100 Church Street SE

institute: University of Minnesota

data_processing:
Reads were trimmed with trimmomatic 0.39, forward and reverse reads were merged with ngmerge, and reads were size selected to be between 120 and 170 base pairs. the middle 74 base pairs were selected for each read
Trimmed reads were aligned to the genome using bowtie2, samtools was used to sort and index each bam, and total coverage was calculated with bamcoverage
for each bam, forward and reverse reads were separated. Coverage was calculated for forward and reverse read bams. For reverse bigwigs, a script multiplied each coverage by -1 to generate the flipped bigwig files
Assembly: GCA_000146045.2_R64_genomic (SacCer3)
Supplementary files format and content: bigwig files containing coverage at each nucleotide for all reads
Supplementary files format and content: bigwig files containing coverage at each nucleotide for forward reads
Supplementary files format and content: bigwig files containing coverage at each nucleotide for reverse reads
Supplementary files format and content: bigwig files containing coverage at each nucleotide for reverse reads flipped for view in igv

organism: Saccharomyces cerevisiae

extract_protocol:
Soluble chromatin (eSPAN samples) was immunoprecipitated with anti-H3K4me3 antibody (ab8580 Abcam). Prewashed Protein G Sepharose beads (17-0618-02, GE Healthcare) was used to recover the immunoprecipitated chromatin. After washing the beads extensively, DNA from ChIP was recovered using the Chelex-100 protocol. ChIP DNA was denatured by incubating it at 100°C for 5 mins and then snapping chill on ice for 5 min. DNA was diluted with BrdU IP buffer (1X PBS, 0.0625% Triton X-100 (v/v)). BrdU antibody (0.17 μg/ml; 555627, BD Biosciences) was added and samples were incubated at 4°C for 2 hours. Next, 20 µl prewashed Protein G beads (17-0618-02, GE Healthcare) were added to each sample and incubated for an additional hour at 4°C. The beads were extensively washed, DNA was eluted with 100 ul 1X TE buffer containing 1% SDS and purified using a QIAGEN MinElute PCR Purification kit.
ssDNA libraries were prepared using an Accel-NGS 1S Plus DNA library kit (10096, Swift Biosciences).

tag: antibody

tag: strain

value: MATA ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 hk2delta::KanMX+ LEU2::BrdU-Inc+PSF-TEFI-URA3

value: eSPAN


title: MDAMB231_long_siSRSF1_10Gy_bio_rep2


title: H3K4me3 eSPAN- HXK2Δ + PSF-HXK2

value: MATA ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 hk2delta::KanMX+ LEU2::BrdU-Inc +PSF-TEFI- yHK2-URA3


title: Clinical isolate 318

value: packed red blood cells

value: Prior to ACT/TACT treatment


title: AMM_24h_Tr_B2


title: AMM_24h_AMM_2h_Old_1h_H3K4me3_B

data_processing:
Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.39
Mapping was performed using BWA
bw (bigwig) files were prozessed and normalized using samtools, bedtools and wigToBigwig.
Assembly: A_nidulans_FGSC_A4_version_s10-m03-r07
Supplementary files format and content: bigwig files

source_name: mycelia

growth_protocol: Aspergillus nidulans WT FGSC#4 (Pontecorvo et al., 1953) and alcA(p)-sGFP-aflR named RKIS42.17 (Shimizu et al., 2003) were used in this study. Media preparation of Aspergillus minimal medium (AMM) was done as described earlier (Todd et al., 2007). AMM was prepared containing Aspergillus salt stock solution and modified Hutner’s TE (Hill and Kafer, 2001), 50mM glucose and 10mM nitrate as sole nitrogen source. Salt solution composition was identical to AMM but missing both carbon and nitrogen sources. For cultures grown in liquid AMM, conidiospores suspended in sterile deionized water with 0.1 % Tween-20 were inoculated to reach a final spore density of 4*106 conidia/mL medium. Cultures were inoculated in 200mL of liquid AMM in 1000mL Erlenmeyer flasks and the cultures grown at 37°C and shaking at 180rpm. The following auxotrophic markers and working concentrations were used: p-aminobenzoic acid (pabaA1/pabaB22, 2µg/mL), biotin (biA1, 1.4µg/mL). The cultures were harvested by filtering the mycelia through sterile Miracloth (Merck, 475855-1R). Cells were immediately frozen in liquid nitrogen and freeze-dried for 1–2days for expression analysis. For ChIP, the cells were crosslinked for 10 min in 1 % formaldehyde followed by quenching in 125 mM glycine for 5 min prior freezing in liquid nitrogen.

extract_protocol:
Chromatin immunoprecipitation was performed according to (Gacek-Matthews et al., 2015). The chromatin pulldown was done using antibodies against H3K4me2 (Active Motif, 39141), and H3K4me3 (Abcam, 8580) in combination with Dynabeads Protein A (Invitrogen, 10002D). The ChIP was performed in biological duplicates using two technical replicates. After cleanup (New England Biolabs, T1030L), the DNA was quantified by qPCR using the same protocol as described in 2.2.
Library preparation was don at the Vienna BioCenter Core facilities (Vienna, Austria) using NEB and Nextera Library prep kit.

value: mycelia

tag: chip antibody


title: MDAMB231_long_siControl_0Gy_bio_rep1


title: H3K4me3 eSPAN- WT

value: MATA ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100+ LEU2::BrdU-Inc+PSF-TEFI-URA3


title: Clinical isolate 319


title: AMM_24h_AMM_2h_Old_1h_H3K4me3_A


title: AMM_24h_Tr_B1

value: mycelium


title: H3K4me3 eSPAN- WT+PSF-HXK2

value: MATA ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100+ LEU2::BrdU-Inc+PSF-TEFI- yHK2-URA3


title: AMM_24h_AMM_2h_Tr_A1


title: MDAMB231_long_siControl_10Gy_bio_rep1


title: H3K4me3 ChIP-ssSeq- HXK2Δ


title: H3K4me3 ChIP-ssSeq- HXK2Δ + PSF-HXK2


title: Clinical isolate 316


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_H3K4me3_A


title: H3K4me3 ChIP-ssSeq- WT


title: Clinical isolate 315


title: AMM_24h_AMM_2h_Salt_1h_H3K4me3_B


title: Input- HXK2Δ


title: H3K4me3 ChIP-ssSeq- WT+PSF-HXK2


title: Clinical isolate 314


title: Input- HXK2Δ + PSF-HXK2


title: Input- WT


title: Input- WT+PSF-HXK2


title: Clinical isolate 313


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_H3K4me3_B


title: Clinical isolate 317


title: Brdu-IP-ssSeq- HXK2Δ + PSF-HXK2

value: Brdu


title: Clinical isolate 312


title: AMM_24h_AMM_2h_Salt_1h_H3K4me3_A


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_H3K4me3_B


title: Clinical isolate 311


title: Brdu-IP-ssSeq- WT


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_H3K4me3_A


title: Clinical isolate 291


title: AMM_20h_Salt_4h_AMM_2h_H3K4me3_B


title: AMM_20h_Salt_4h_AMM_2h_H3K4me3_A


title: Brdu-IP-ssSeq- WT+PSF-HXK2


title: YLL032C_1

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq and adapter removal(internal barcode)
adapter removal with cutadapt
U-string extraction and counting from R2 using custom made script
alignment with bowtie2
gene coverage for different U-counts with bedtools
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.txt.gz file contains zipped U-count table for 6629 yeast ORFs (indicated) first row correpsonds to U-string length of 0, second to 1, aso.

source_name: cells

growth_protocol: Yeast cells were grown to saturation overnight in SD+glucose. They were then diluted in fresh,pre-warmed SC+glucose and incubated for at least 6 hours to reach exponential phase at which cells were pellet and frozen at -80C.

extract_protocol:
RNA Extraction with NucleoSpin 96 RNA(MN)
RNAtagging (mRNA); Libraries were constructed as described in Zigdon (2023) to measure RNA tagging.

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: YLL032C_2


title: YHC1_2

value: BY4741 YHC1::Yhc1-Pup2


title: Clinical isolate 290


title: YHC1_1


title: AMM_20h_Salt_4h_H3K4me3_B


title: Clinical isolate 289


title: TIS11_1


title: SRO9_1_new

value: BY4741 SRO9::Sro9-Pup2


title: AMM_20h_Salt_4h_H3K4me3_A


title: SRO9_2_new


title: Brdu-IP-ssSeq- HXK2Δ


title: Clinical isolate 288


title: SLF1_3

value: BY4741 SLF1::Slf1-Pup2


title: AMM_24h_AMM_2h_Old_1h_H3K4me2_B


title: SLF1_2


title: Clinical isolate 287


title: Clinical isolate 286


title: SLF1_1


title: SCP160_ThirdDel_C2_1_NR

value: BY4741 SCP160::Scp160_{delta}IDR_2-Pup2


title: AMM_24h_AMM_2h_Old_1h_H3K4me2_A


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_H3K4me2_B


title: SCP160_ThirdDel_C1_1_NR


title: Clinical isolate 285


title: SCP160_SixthDel_C2_1_NR


title: AMM_20h_Salt_4h_AMM_2h_Old_1h_H3K4me2_A


title: TIS11_2


title: AMM_24h_AMM_2h_Salt_1h_H3K4me2_B


title: SCP160_FourthDel_2_4R


title: SCP160_FirstDel_C2_1_NR

value: BY4741 SCP160::Scp160_{delta}IDR_1-Pup2


title: SCP160_FourthDel_1_4R


title: SCP160_SixthDel_C1_1_NR


title: Clinical isolate 283


title: SCP160_FirstDel_C1_1_NR


title: Clinical isolate 284


title: SCP160_FifthDel_2_NR

value: BY4741 SCP160::Scp160_{delta}IDR_3-Pup2


title: SCP160_4


title: Clinical isolate 281


title: AMM_24h_AMM_2h_Salt_1h_H3K4me2_A


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_H3K4me2_B


title: SCP160_FifthDel_1_NR


title: SCP160_1


title: AMM_20h_Salt_4h_AMM_2h_Salt_1h_H3K4me2_A


title: RMD9_3

value: BY4741 RMD9::Rmd9-Pup2


title: RMD9_2


title: AMM_24h_AMM_2h_H3K4me2_A


title: RMD9_1


title: Clinical isolate 279


title: RIE1_ThirdDel_C2_1_NR

value: BY4741 RIE1::Rie1_{delta}IDR_2-Pup2


title: RIE1_ThirdDel_C1_1_NR


title: Clinical isolate 278


title: RIE1_SecondDel_2_R

value: BY4741 RIE1::Rie1_{delta}2-Pup2


title: AMM_20h_Salt_4h_AMM_2h_H3K4me2_A


title: Clinical isolate 277


title: RIE1_SecondDel_1_R


title: RIE1_FourthDel_2_2R

value: BY4741 RIE1::Rie1_{delta}4-Pup2


title: AMM_24h_H3K4me2_A


title: Clinical isolate 280

value: packed red blood cells


title: RIE1_FourthDel_1_2R


title: Clinical isolate 282

value: Prior to ACT/TACT treatment


title: AMM_20h_Salt_4h_H3K4me2_B

value: mycelia


title: RIE1_FirstDel_1_NR

value: BY4741 RIE1::Rie1_{delta}IDR_1-Pup2


title: RIE1_FifthDel_C2_1_NR

value: BY4741 RIE1::Rie1_{delta}IDR_3-Pup2


title: RIE1_FifthDel_C1_1_NR


title: RIE1_4

value: BY4741 RIE1::Rie1-Pup2


title: AMM_20h_Salt_4h_AMM_2h_H3K4me2_B


title: un_t1_WT_3

city: Princeton

first: Rebecca

middle: Ann

last: Jones

state: New Jersey

address: Lewis Thomas Laboratory

department: Molecular Biology

institute: Princeton University

data_processing:
Cutadapt  1.9.1
rsem 1.3.0
star 2.5.2a
Assembly: GRCz11 assembly
Supplementary files format and content: *.genes.results are rsem count files

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos after collection were maintained at 28.5C in E2 medium at a density ⋜  50 embryos

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN)
rRNA depletion (Rio-Zero Plus rRNA Depletion Kit (Ilumina), then library prep using KAPA mRNA HyperPrep Kit for Ilumina Platforms

treatment_protocol: Embryos were exposed to gamma-IR of 20 Gy at 24 hpf

value: whole embryo

tag: timepoint

value: WT

value: un


title: Clinical isolate 274


title: RIE1_1


title: Clinical isolate 272


title: RIE1_3


title: Clinical isolate 276


title: RAT1_3

value: BY4741 RAT1::Rat1-Pup2


title: RAT1_1


title: RAT1_2


title: Clinical isolate 271


title: Puf6_C2_2

value: BY4741 PUF6::Puf6-Pup2


title: un_t1_K2_3


title: Clinical isolate 270


title: Puf6_C1_C2


title: un_t1_K2_2


title: Puf5_dead_3

value: BY4741 PUF5::Puf5-deadPup2


title: un_t1_WT_2


title: Clinical isolate 269


title: AMM_20h_Salt_4h_H3K4me2_A


title: RIE1_FirstDel_2_NR


title: Puf5_dead_2


title: un_t1_K2_1


title: Puf5_Trc6_C1_3

value: BY4741 PUF5::Puf5_T6-Pup2


title: Clinical isolate 268


title: Puf5_Trc6_C1_2


title: un_t1_K1_3


title: Puf5_Trc6_C1_1


title: Clinical isolate 267


title: Puf5_Trc5_C1_2

value: BY4741 PUF5::Puf5_T5-Pup2


title: un_t1_K1_2


title: un_t1_WT_1


title: Puf6_C2_1


title: un_t1_K1_1


title: Clinical isolate 265


title: Puf5_Trc4_C1_4

value: BY4741 PUF5::Puf5_T3-Pup2


title: Clinical isolate 266


title: Clinical isolate 264


title: Puf5_Trc5_C1_1


title: Puf5_Trc4_C1_3


title: unDMSO_t1_WT_2

value: unDMSO


title: Clinical isolate 263


title: Puf5_Trc2_C2_1

value: BY4741 PUF5::Puf5_T2-Pup2


title: unDMSO_t1_WT_3


title: Puf5_Trc4_3


title: Puf5_Trc4_C1_2


title: Puf5_Trc2_C1_3


title: unDMSO_t1_WT_1


title: Clinical isolate 262

value: packed red blood cells


title: Puf5_Trc2_C1_2


title: Puf5_Trc2_C1_1


title: Puf5_Trc1_C2_2

value: BY4741 PUF5::Puf5_T1-Pup2


title: unDMSO_t1_K2_3


title: Clinical isolate 261

value: Prior to ACT/TACT treatment


title: Puf5_Trc5_C2_1


title: Puf5_Trc1_C1_2


title: unDMSO_t1_K2_2


title: Clinical isolate 260


title: Puf5_Trc1_C1_1


title: Puf5_CSWAT_ctrl_3

value: BY4741 PUF5::Puf5_C-SWAT


title: Clinical isolate 275


title: Clinical isolate 259


title: unDMSO_t1_K2_1


title: Puf5_C1_7

value: BY4741 PUF5::Puf5-Pup2


title: Puf5_C2_1


title: Puf5_C1_6


title: unDMSO_t1_K1_2


title: Puf5_C1_3


title: Clinical isolate 257


title: unDMSO_t1_K1_1


title: Puf5_C1_2


title: Puf5_C1_1


title: Clinical isolate 256


title: Clinical isolate 310


title: IR_t2_WT_3

value: IR


title: IR_t2_WT_2

value: whole embryo


title: Clinical isolate 255


title: Puf4_Trc4_C1_1

value: BY4741 PUF4::Puf4_T4-Pup2


title: Puf4_Trc4_C1_2


title: Puf4_Trc3_3

value: BY4741 PUF4::Puf4_T3-Pup2


title: IR_t2_WT_1

value: WT


title: Clinical isolate 254


title: Puf5_CSWAT_ctrl_1


title: unDMSO_t1_K1_3


title: Clinical isolate 258


title: IR_t2_K2_3


title: Puf4_Trc2_C2_1

value: BY4741 PUF4::Puf4_T2-Pup2


title: Clinical isolate 253


title: Puf4_Trc2_C1_3


title: IR_t2_K2_2


title: Puf4_Trc2_C1_1


title: Puf4_Trc1_C2_1

value: BY4741 PUF4::Puf4_T1-Pup2


title: Clinical isolate 252


title: Puf4_dead_2

value: BY4741 PUF4::Puf4-deadPup2


title: Puf4_dead_1


title: Puf4_Trc1_C1_3


title: IR_t2_K2_1


title: Puf4_Trc1_C1_2


title: IR_t2_K1_3


title: Puf4_CSWAT_ctrl_1

value: BY4741 PUF4::Puf4_C-SWAT


title: Puf4_CSWAT_ctrl_2


title: Puf4_Trc3_2


title: Clinical isolate 249


title: IR_t2_K1_2


title: Puf4_C1_C2_1

value: BY4741 PUF4::Puf4-Pup2


title: IR_t2_K1_1


title: Puf4_C1_5


title: Clinical isolate 309


title: Puf4_C1_2


title: Puf4_Trc3_1


title: Puf4_C1_1


title: Clinical isolate 248


title: Puf3_dead_C2_3

value: BY4741 PUF3::Puf3-deadPup2


title: Puf3_dead_C1_8


title: Clinical isolate 247


title: Puf4_Trc1_C1_1


title: IR_t1_WT_3


title: IR_t1_K2_3


title: IR_t1_WT_1


title: Puf3_dead_C1_6


title: Clinical isolate 246


title: Clinical isolate 250


title: Clinical isolate 251


title: Puf3_dead_C1_4


title: Clinical isolate 245


title: IR_t1_K2_2


title: Puf3_dead_C1_2


title: Puf3_Trc6_2

value: BY4741 PUF3::Puf3_T6-Pup2


title: Puf3_dead_C1_5


title: Clinical isolate 244

value: packed red blood cells


title: Clinical isolate 243


title: Puf3_Trc5_4

value: BY4741 PUF3::Puf3_T5-Pup2


title: IR_t1_K2_1


title: Puf3_Trc6_1


title: Puf3_Trc5_2


title: IR_t1_K1_3


title: Puf3_dead_C2_6


title: Puf3_Trc5_1


title: IR_t1_WT_2


title: Clinical isolate 242

value: Prior to ACT/TACT treatment


title: Puf3_Trc4_4

value: BY4741 PUF3::Puf3_T4-Pup2


title: IR_t1_K1_2


title: Puf3_Trc4_3


title: Clinical isolate 241


title: Puf3_Trc4_2


title: Clinical isolate 240


title: Puf3_Trc3_C2_3

value: BY4741 PUF3::Puf3_T3-Pup2


title: Puf3_Trc4_1


title: AD_t2_WT_3

value: AD


title: Puf3_Trc3_C1_2


title: Clinical isolate 239


title: Puf3_Trc2_6

value: BY4741 PUF3::Puf3_T2-Pup2


title: AD_t2_WT_2

value: whole embryo


title: Puf3_Trc2_3


title: Puf3_Trc2_5


title: AD_t2_WT_1


title: Clinical isolate 308


title: Puf3_Trc2_1


title: Puf3_Trc1_C2_3

value: BY4741 PUF3::Puf3_T1-Pup2


title: Clinical isolate 238


title: AD_t2_K2_3


title: Puf3_Trc1_C2_2


title: Puf3_Trc1_C1_2


title: AD_t2_K2_2


title: LF82 RpoD V445D mutant 3

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

state: MD

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with bbduk.sh tool from bbtools software (v37.62).
Trimmed reads were mapped to the Escherichia coli LF82 genome with STAR (v2.7.10a)
Quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1). Multimapper reads were counted as a fraction.
BigWig files were generated with bamCoverage tool from DeepTools (v3.5.1).
Genes with less than 20 reads per gene across samples were discarded
Differential expression analysis was carried out with the R package DESeq2 (v1.42.0)
Assembly: NC_011993.1
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: comma-separated values text file that includes based normalized gene expression across samples, RpoD V445D mutant vs WT differential gene expression expressed as log2FoldChange and their corresponding p-value and p-adjusted value for each gene as estimated by DESeq2.

organism: Escherichia coli LF82

source_name: bacteria

growth_protocol: Isogenic E. coli LF82 and rpoD V445D mutant were grown to a cell density of OD600 ~0.4-0.5 in LB broth at 37o C.

extract_protocol:
RNA was isolated using method II of (Hinton 1989; https://doi.org/10.1016/S0021-9258(18)71697-9).
Library for RNA-seq was prepared using a modified version of the methods published by  Alexander Shishkin et al. (doi:10.1038/nmeth.3313). rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions. cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).

value: RpoD V445D mutant

value: bacteria


title: IR_t1_K1_1

value: IR


title: Puf3_Trc1_C1_1


title: LF82 RpoD V445D mutant 1


title: AD_t2_K2_1


title: LF82 RpoD V445D mutant 2


title: AD_t2_K1_3


title: Clinical isolate 234


title: Puf3_CSWAT_ctrl_7

value: BY4741 PUF3::Puf3_C-SWAT


title: AD_t2_K1_2


title: LF82 WT 3

value: WT


title: Clinical isolate 233


title: LF82 WT 2


title: Clinical isolate 232


title: Clinical isolate 273


title: Clinical isolate 235


title: Puf3_CSWAT_ctrl_4


title: AD_t1_WT_2


title: AD_t2_K1_1


title: AD_t1_WT_3


title: AD_t1_K2_3


title: Puf3_C2_8

value: BY4741 PUF3::Puf3-Pup2


title: Clinical isolate 237


title: Clinical isolate 231


title: Clinical isolate 236


title: non tumor 16

city: Chicago

first: Shejuan

last: An

state: IL

address: 303 East Superior Street

institute: Northwestern University

library_source: other

data_processing:
Sequencing read adapters were removed by cutadapt (version 4.8), and low-quality trim was performed by trimmomatic (version 0.39) with paired-end trimming mode. Sequencing reads were aligned with the human reference genome hg38 using Bowtie2(version 2.5.3) in paired mode. Reads were sorted and indexed using SAMtools (version 1.19). Data was reduced to 300 bp genomic windows with the MEDIPS (1.54.0) package .
Sequences mapping to chromosomes X, Y or the mitochondrial genome were excluded.
Count per million (CPM) values were calculated for these windows (edgeR, version 4.0.16), with windows < 1 CPM filtered out across all samples.
CPM was normalized with log2(1000*CPM + 2) (R4.3.3) transformation
Assembly: hg38
Supplementary files format and content: comma delimited .csv

molecule: other

source_name: Non-neoplastic rep 16

extract_protocol:
Cell-free DNA (cfDNA) was extracted from 1-4 ml of plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, 55114). All of the cfDNA were performed Right Side Size Selection (0.95X) by using SPRIselect beads (Beckman Coulter, B23317) immediately after the DNA extraction to eliminate genomic DNA contamination.
cfDNA libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems, CN: KK8502).
End-repair, A-tailing, and adaptor ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit (index primer set I), E7335L) were performed.

value: Non-neoplastic rep 16


title: non tumor 15

source_name: Non-neoplastic rep 15

value: Non-neoplastic rep 15


title: Clinical isolate 229

value: packed red blood cells


title: Puf3_C2_6


title: non tumor 13

source_name: Non-neoplastic rep 13

value: Non-neoplastic rep 13


title: Clinical isolate 228

value: Prior to ACT/TACT treatment


title: Puf3_CSWAT_ctrl_5


title: LF82 WT 1


title: Puf3_CSWAT_ctrl_6


title: AD_t1_K2_1


title: Clinical isolate 227


title: AD_t1_K2_2


title: Puf3_C2_5


title: Puf3_C2_2


title: non tumor 12

source_name: Non-neoplastic rep 12

value: Non-neoplastic rep 12


title: tumor 77

source_name: Glioneuronal tumor rep 16

value: Glioneuronal tumor rep 16


title: Clinical isolate 230


title: AD_t1_WT_1

value: AD


title: Clinical isolate 226


title: AD_t1_K1_3


title: Puf3_C1_9


title: non tumor 14

source_name: Non-neoplastic rep 14

value: Non-neoplastic rep 14


title: Puf3_C2_7


title: Clinical isolate 225


title: tumor 76

source_name: Pediatric type diffuse low grade glioma rep 1


title: tumor 75

source_name: Glioneuronal tumor rep 15

value: Glioneuronal tumor rep 15


title: Clinical isolate 224

source_name: packed red blood cells


title: Puf3_C1_8


title: AD_t1_K1_2

value: whole embryo


title: Puf3_C1_2


title: tumor 73

source_name: Circumscribed astrocytic glioma rep 23

value: Circumscribed astrocytic glioma rep 23


title: tumor 74

source_name: Ependymal tumor rep 7

value: Ependymal tumor rep 7


title: Puf3_C1_7


title: AD_t1_K1_1


title: Clinical isolate 221


title: Clinical isolate 222


title: Puf3_C1_15


title: Puf3_C1_11


title: tumor 72

source_name: Circumscribed astrocytic glioma rep 22

value: Circumscribed astrocytic glioma rep 22


title: Clinical isolate 223


title: tumor 70

source_name: Embryonal tumor rep 3

value: Embryonal tumor rep 3


title: tumor 71

source_name: Embryonal tumor rep 4

value: Embryonal tumor rep 4


title: Clinical isolate 220


title: Puf3_C1_10

source_name: cells

value: BY4741 PUF3::Puf3-Pup2


title: Clinical isolate 219


title: Puf2_2

value: BY4741 PUF2::Puf2-Pup2


title: Clinical isolate 307


title: tumor 69

source_name: Embryonal tumor rep 2

value: Embryonal tumor rep 2


title: Puf2_1


title: Clinical isolate 218

value: packed red blood cells


title: tumor 68

source_name: Embryonal tumor rep 1

value: Embryonal tumor rep 1


title: M1 BMDMs_EVs_rep1

type: RNA

city: shanghai

first: shu

middle: I

last: zhao

address: Road siping 1239

institute: Tongji University

description: Gene expression in EVs derived from M1 BMDMs in OA rats

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat Gene Expression（8*15K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k 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 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: EVs derived from M1 BMDMs in OA rats, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Male wild-type (WT) Sprague-Dawley (SD) rats, six-week-old, were obtained from SLAC Laboratory Animal Co. Ltd. (Shanghai, China). Rats were housed at Tongji University Animal Unit under normal conditions (22±2°C ambient temperature, 50±5% humidity and 12-h light cycle). When the rats were eight weeks old, they were subjected to destabilization of the medial meniscus (DMM) and anterior cruciate ligament transection (ACLT) operations in the right knee joints to produce mechanical instability-related OA. The sham operation was conducted by incision of the muscular planes and cutaneous at baseline. After 8 weeks of surgery,  the femurs and tibias were isolated.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: The cervical dislocation was used to euthanize SD rats, and the tibia and femur were both removed. The bone marrow was washed out with a 1 mL syringe and cold phosphate-buffered saline (PBS) with 1% penicillin-streptomycin (P/S). After filtering through a 70-μm strainer, 1 mL of red blood cell lysis solution was added to eliminate red blood cells (RBC) (Solarbio, China, R1010). After waiting 10 min, cells were centrifugated for 10min at 450g, 4°C, and the supernatant was discarded; 10mL PBS was put into the tube and mixed. Following centrifugation, cells were rinsed two time and then were blocked with in PBS with rat Fc Block (BD, 550271) at 4°C for 20 min. After rinsing with PBS, cells were reconstituted in the FACS buffer containing the following antibodies: CD45-PerCP/Cy5.5 (1:500, Biolegend, 201818), CD11b-PE/Cy7 (1:500, Biolegend, 202220), for 30 min at at 4°C, and then sorted with BD FACS Flow cytometry. The sorted BMDMs were resuspended in Iscove’s modified Dulbecco’s medium (IMDM) (Gibco, USA) comprising 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (P/S), and 20 ng/mL M-CSF (R&D System, USA). Non-adherent macrophage precursors were cultivated after one day, and the medium was substituted every three days. On the 7th day, the mature BMDMs were defined as M0 BMDMs. To promote M1 polarization, M0 BMDMs were incubated with Lipopolysaccharide (LPS, 100 ng/mL, serotype O55:B5, Enzo), IFN-γ (20 ng/mL) for 48 hours before being stimulated with 5mM ATP for further 60 minutes to activate the inflammasome. Flow cytometry was utilized to determine polarization. Moreover, BMDMs-derived EVs were isolated from the supernatant for additional studies.

value: monocytes isolated from  femurs and tibias

tag: Sex

value: male


title: M1 BMDMs_EVs_rep2

source_name: EVs derived from M1 BMDMs in OA rats, replicate 2


title: M0 BMDMs_EVs_rep1

description: Gene expression in EVs derived from M0 BMDMs in sham rats

source_name: EVs derived from M0 BMDMs in sham rats, replicate 1


title: Puf1_5

value: BY4741 PUF1::Puf1-Pup2


title: T3

city: Tianjin

first: Jianwen

last: Song

address: Jinnan District

institute: Nankai Unversity

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: tumor

extract_protocol:
Tumor was removed, flash frozen on dry ice, and total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor

value: BALB/C

value: therapy


title: T4


title: M0 BMDMs_EVs_rep2

source_name: EVs derived from M0 BMDMs in sham rats, replicate 2


title: non tumor 11

source_name: Non-neoplastic rep 11

value: Non-neoplastic rep 11


title: Clinical isolate 306

value: Prior to ACT/TACT treatment


title: T2


title: T5


title: tumor 67

source_name: Pediatric type diffuse low grade glioma rep 2


title: T1


title: Puf1_4


title: Clinical isolate 217


title: Clinical isolate 305


title: Clinical isolate 216


title: Puf1_3


title: PUB1_Trc9_C2_2

value: BY4741 PUB1::Pub1_T2-Pup2


title: C4

value: control


title: C5


title: tumor 65

source_name: Glioneuronal tumor rep 14

value: Glioneuronal tumor rep 14


title: PUB1_Trc9_C2_1


title: Clinical isolate 215

source_name: packed red blood cells


title: tumor 64

source_name: Circumscribed astrocytic glioma rep 21

value: Circumscribed astrocytic glioma rep 21


title: C3


title: PUB1_Trc6_2


title: tumor 63

source_name: Circumscribed astrocytic glioma rep 20

value: Circumscribed astrocytic glioma rep 20


title: Clinical isolate 214


title: C2


title: PUB1_Trc6_1


title: C1


title: Clinical isolate 304


title: PUB1_Trc1_C2_1

value: BY4741 PUB1::Pub1_{delta}T1-Pup2


title: Clinical isolate 213


title: tumor 66

source_name: Ependymal tumor rep 6

value: Ependymal tumor rep 6


title: tumor 62

source_name: Circumscribed astrocytic glioma rep 19

value: Circumscribed astrocytic glioma rep 19


title: tumor 60

source_name: Circumscribed astrocytic glioma rep 17

value: Circumscribed astrocytic glioma rep 17


title: PUB1_Trc1_C1_1

source_name: cells


title: Clinical isolate 212

value: packed red blood cells


title: tumor 61

source_name: Circumscribed astrocytic glioma rep 18

value: Circumscribed astrocytic glioma rep 18


title: non tumor 10

source_name: Non-neoplastic rep 10

value: Non-neoplastic rep 10


title: tumor 50

source_name: Circumscribed astrocytic glioma rep 16

value: Circumscribed astrocytic glioma rep 16


title: norrnal PSCs, GFP, scRNAseq

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S Moody Ave

department: Department of Biology Medical Engineering

institute: Oregon Health Science University

description: 10X Genomics 3'

library_source: transcriptomic single cell

data_processing:
We aligned the sequenced reads to the mm10 mouse reference genome, and the unique molecule identifier (UMIs) for each gene in each cell were counted using the Cell Ranger 3.1.0(10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix file

source_name: Pancreas

extract_protocol:
To isolate healthy PSCs, pancreata were harvested from Rosa26mTmG/+;Fabp4-Cre mice at 6-9 weeks of age, trimmed to remove any associated adipose tissue, minced with scissors, digested with 0.02% Pronase (Sigma-Aldrich), 0.05% Collagenase P (Sigma-Aldrich), and 0.1% DNase I (Sigma-Aldrich) in Gey's balanced salt solution (GBSS; Sigma-Aldrich) at 37°C for 10 minutes. Pancreata were further mechanically dissociated via serological pipette before returning to chemical dissociation at 37°C for 5 minutes. The resulting cell suspension was filtered through a 100 μm cell strainer nylon mesh. Cells were washed with GBSS, pelleted, and subject to red blood cell lysis via ACK lysis buffer (Thermo Fisher Scientific) for 3 minutes at room temperature. Then, cells were washed in cold FACS buffer (PBS containing 2% FBS), pelleted, and resuspended in FACS buffer. Cells were kept on ice as a single-cell suspension, then GFP-positive cells were isolated by FACS using a BD FACSAria III or BD FACSymphony S6. To isolate CAFs, 8-week-old Rosa26mTmG/+;Fabp4-Cre mice were orthotopically implanted with FC1245 PDAC cells as described above. At 21 days post-implantation, pancreata were harvested, and any apparent normal pancreas tissue was trimmed away from the PDAC specimen. Tumors were briefly minced, placed in digestion media (DMEM with 1 mg/ml Collagenase IV, 0.1% soybean trypsin inhibitor, 50 U/ml DNase, and 0.125 mg/ml Dispase), and incubated at 37°C for 1 h. Whole tissue digests were centrifuged at 450 g for 5 min, then resuspended in 10 ml pre-warmed 0.25% Trypsin and incubated at 37°C for 10 min. Cold DMEM (10 ml) was added to the suspension, which was then passed through a 100 μm cell strainer. Cells were centrifuged as above, washed with DMEM containing 10% FBS and centrifuged again, then centrifuged as above and resuspended in 1 ml ACK red cell lysis buffer. Cells were incubated at room temperature for 3 minutes, then 9 ml FACS buffer added and cells centrifuged as above. Pelleted cells were counted and resuspended at 1 x 10^7 cells/ml in FACS buffer, CD16/CD32 Fc block (BD 553141) added 1:20 and incubated at room temperature for 2 min, then biotinylated PDPN antibody (BioLegend 127404) was added 1:200. Cell suspensions were incubated on ice for 30 min. Cold FACS buffer was added, cells centrifuged at 300 g for 5 min at 4°C, and cell pellets were resuspended in 500 ml cold FACS buffer containing 1:1000 APC-streptavidin (BD 554067) and incubated for 30 min on ice protected from light. Cold FACS buffer (2 ml) was added, cells were pelleted as above and resuspended in cold FACS buffer containing SYTOX Blue Dead Cell Stain (Invitrogen S34857). Cells were incubated for 30 min on ice, washed with FACS buffer, pelleted, and resuspended in cold FACS buffer. GFP-positive PDPN-positive cells were isolated by FACS using a BD FACSAria III or BD FACSymphony S6.
Single cell capture and cDNA library generation were performed using the 10x Genomics Chromium single-cell 3’ library construction kit v3.1 according to the manufacturer’s instructions. Libraries were pooled prior to sequencing based on estimated cell number in each library per flow cytometry cell counts.

value: Pancreas

value: PSC (normal)


title: tumor CAFs, GFP, scRNAseq

description: 10X Genomics 3'

value: CAF (tumor)


title: Clinical isolate 210

value: Prior to ACT/TACT treatment


title: PUB1_ThirdDel_C1_2_NR

value: BY4741 PUB1::Pub1_{delta}IDR_2-Pup2


title: PUB1_ThirdDel_C1_1_NR


title: Clinical isolate 209


title: non tumor 7

source_name: Non-neoplastic rep 9

value: Non-neoplastic rep 9


title: Clinical isolate 211


title: PUB1_SecondDel_2_2R

value: BY4741 PUB1::Pub1_{delta}2-Pup2


title: Lung cultured ILC2, Yoda1 (5µM), rep2

city: Seoul

first: MinYeong

last: Lim

address: 103, Daehak-ro, Jongno-gu

department: Department of biomedical scicence

country: South Korea

institute: Seoul National University, College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: Lung


title: Lung cultured ILC2, Yoda1 (5µM), rep4


title: Lung cultured ILC2, Yoda1 (5µM), rep3


title: Clinical isolate 208


title: tumor 43

source_name: Ependymal tumor rep 5

value: Ependymal tumor rep 5


title: PUB1_ThirdDel_C2_1_NR


title: tumor 40

source_name: High grade glioma NOS rep 2

value: High grade glioma NOS rep 2


title: Lung cultured ILC2, DMSO (0.1%), rep4

value: DMSO


title: PUB1_SecondDel_1_2R


title: tumor 42

source_name: Tumors of the sellar region

value: Tumors of the sellar region


title: Clinical isolate 303


title: PUB1_FourthDel_C2_1_R

value: BY4741 PUB1::Pub1_{delta}4-Pup2


title: non tumor 6

source_name: Non-neoplastic rep 8

value: Non-neoplastic rep 8


title: Clinical isolate 206

source_name: packed red blood cells

value: packed red blood cells


title: PUB1_FourthDel_C1_1_R


title: PUB1_FirstDel_2_NR

value: BY4741 PUB1::Pub1_{delta}IDR_1-Pup2


title: tumor 37

source_name: Ependymal tumor rep 4

value: Ependymal tumor rep 4


title: Lung cultured ILC2, DMSO (0.1%), rep3


title: Lung cultured ILC2, DMSO (0.1%), rep2


title: Clinical isolate 205


title: Lung cultured ILC2, DMSO (0.1%), rep1


title: Clinical isolate 204


title: tumor 28

source_name: Meningioma rep 2

value: Meningioma rep 2


title: Lung cultured ILC2, Yoda1 (5µM), rep1


title: Clinical isolate 207


title: PUB1_FifthDel_C2_1_NR

value: BY4741 PUB1::Pub1_{delta}IDR_3-Pup2


title: Clinical isolate 203


title: non tumor 4

source_name: Non-neoplastic rep 7

value: Non-neoplastic rep 7


title: PUB1_FifthDel_C1_1_NR


title: LPS-induced RAW264.7 cells coculture with BMSCs biol rep 3

city: Suzhou

first: Yichao

last: Ni

state: --- Select One ---

address: No.1055 Sanxiang Road, Gusu District, Soochow , Jiangsu, China.

institute: Second affiliated hospital of Soochow university

data_processing:
HISAT2 v2.0.5
Assembly: mm10
Supplementary files format and content: Excel files with counts and FPKM values

extract_protocol:
Total RNA was extracted using the Trizol Reagent. The concentration and purity of the RNA samples were assessed using the Nanodrop 2000 microspectrophotometer, and the RNA integrity was evaluated using the LabChip GX Touch microfluidic capillary system.
Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads;  Add Fragmentation Buffer for mRNA fragmentation; One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification;  Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp;  PCR enrichment was performed to obtain cDNA libraries.


title: Clinical isolate 302

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 20 –max-intronlen 3000 --rna-strandness RF
Properly oridented reads and mapped to maximum three locations were extracted using samtools (version: 1.11)
Transcriptome assembly on these aligned reads were performed using StringTie version 2.1.4 with parameters --fr -m 150 -j 3 -g 20.  Each assembled transcripts were quantified by same version of Stringtie with e options.
Assembly: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary files format and content: Comma-delimited text file includes TPM values assembled transcripts for each samples

extract_protocol:
8 volumes of TRIzol reagent (Invitrogen) (v/v) were added to 0.5 ml infected packed red blood cells. Samples were vortexed at 7000 RPM for 1 min. Chlorophorm was added in 1:5 volumetric ratio, vortexed and samples were centrifuged for 15 min to separate phases as previously described (2,3). Supernatant was aspirated and transferred to the new tubes. Equal volume of 100% ethanol was added to the supernatant and RNA was extracted using ZYMO DirectZol-96 RNA kit (ZYMO) following manufacturer instructions. RNA was eluted in 17 ul of RNAse/DNAse free water, and its purity was assessed by spectrometry on Nanodrop (Thermo Scientific). RNA concentration was estimated using RNA-specific Qubit fluorometric assay (Invitrogen). RNA integrity was assessed on Bioanalyzer RNA Nano Chip (Agilent).
RNA sequencing libraries have been prepared from 100 ng of purified total RNA using ZYMO-Seq RiboFree Total RNA Library Kit (ZYMO) following manufacturer’s instructions with some modifications to the protocol described below. This protocol allows for generation of stranded, rRNA and human globin depleted libraries. Whole protocol has been scaled down to use half of the recommended volume of each reagent. Depletion step of rRNA (both human and the parasite) and globin has been adjusted to 4 hours at 68oC. 14 cycles of PCR have been used for final index incorporation. Resulted libraries have been eluted in 15ul of the elution buffer and verified by real-time PCR, fluorometric DNA concentration assay (Invitrogen) and Bioanalyzer DNA High-Sensitivity chip (Agilent Technologies) by Novogene Singapore. 96 libraries (total RNA) have been equimolarly pooled and sequenced per one lane of Novaseq S4 sequencing technology (Illumina) generating approximately 750GB data per lane (Novogene, Singapore). Technical replicates of 3D7 lab strain gDNA/RNA were also included on each sequencing lane to control for library preparation and sequencing efficiency.

value: Prior to ACT/TACT treatment


title: LPS-induced RAW264.7 cells coculture with BMSCs biol rep 2


title: non tumor 2

source_name: Non-neoplastic rep 6

value: Non-neoplastic rep 6


title: LPS-induced RAW264.7 cells coculture with BMSCs biol rep 1


title: PUB1_FirstDel_1_NR


title: PUB1_4

value: BY4741 PUB1::Pub1-Pup2


title: Clinical isolate 202


title: PUB1_3


title: PUB1_2


title: tumor 13

source_name: Circumscribed astrocytic glioma rep 15

value: Circumscribed astrocytic glioma rep 15


title: Clinical isolate 201


title: LPS-induced RAW264.9 cells biol rep 3


title: MsOc3HBC Replicate 3

city: Innsbruck

first: Kamila

last: Nykiel

address: Innrain 52

institute: Medical University of Innsbruck

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.   BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: hit-counts: hit count for all the genes, log2 fold change and (adjusted) p-value table: Differential_expression_analysis_table_DMSO_530.csv, Differential_expression_analysis_table_DMSO_C3Ms.csv

growth_protocol: HEK293T cells were maintained in DMEM/F-12 supplemented with 10% FBS and GlutaMAX (1x) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted with innuPREP RNA Mini Kit 2.0 (analytikjena) followed by DNA digestion (NEB), phenol chloroform extraction and isopropanol precipitation.
NEBNext Ultra II  RNA Library Preparation Kit

treatment_protocol: Cells were treated with 10 µM ligand/DMSO for 5h.

tag: group


title: MsOc3HBC Replicate 2


title: MsOc3HBC Replicate 1


title: Clinical isolate 301

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

institute: Nanyang Technological University


title: PUB1_1

source_name: cells


title: PSP2_2

value: BY4741 PSP2::Psp2-Pup2


title: LPS-induced RAW264.7 cells biol rep 2


title: Clinical isolate 300


title: HBC530 Replicate 3


title: Clinical isolate 198


title: PIN4_3

value: BY4741 PIN4::Pin4-Pup2


title: Clinical isolate 199


title: MNs.female.post-exp. # 3

city: Chongqing

first: Bin

last: Wu

address: 136 Zhongshan Er Road

department: Pediatric Research Institute

institute: Children's Hospital of Chongqing Medical University

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is  generated. Sequencing data contains a number of connectors, low-quality Reads, so we use  Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis. The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Meningeal neutrophils

extract_protocol:
RNA was extracted from the samples using the Trizol Reagent (Invitrogen Life Technologies) followed by RNA isolation according to the manufacturer's protocol.
Three micrograms of RNA were used as input material for the RNA sample  preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA  was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was  carried out using divalent cations under elevated temperature in an Illumina proprietary  fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and  Super Script II. Second strand cDNA synthesis was subsequently performed using DNA  Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via  exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′  ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for  hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library  fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).  DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP  system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100  system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform  (Illumina).

value: Meningeal neutrophils

value: female

value: Neutrophils

value: WT


title: MNs.female.post-exp. # 2


title: MNs.female.post-exp. # 1


title: PSP2_1


title: HBC530 Replicate 2


title: MNs.male.post-exp. # 3

value: male


title: Clinical isolate 299

value: packed red blood cells


title: HBC530 Replicate 1


title: LPS-induced RAW264.7 cells biol rep 1


title: Clinical isolate 200


title: DMSO Replicate 3

value: DMSO


title: PIN4_2


title: PIN4_1


title: MNs.male.post-exp. # 2


title: DMSO Replicate 1


title: Clinical isolate 197


title: PBP2_2

value: BY4741 PBP2::Pbp2-Pup2


title: Clinical isolate 195


title: PBP2_1


title: DMSO Replicate 2


title: mpkCCDc11 cells, TAZ-siRNA, dDAVP, rep2

city: Daegu

first: HongSeok

last: Choi

address: 680, Gukchaebosang-ro, Jung-gu

department: School of medicine

institute: Kyungpook national university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each samples
Supplementary files format and content: tab-delimited text file includes FPKM and TPM values for each samples

source_name: Kidney; cortical collecting duct

growth_protocol: mpkCCDc11 cells (murine kidney cortical collecting duct cells) were cultured in a 1:1 mixture of DMEM and Ham’s F-12 medium (11330032, Thermo Fisher Scientific), containing 60 nM sodium selenite (S9133, Sigma), 5 g/mL transferrin (T8158, Sigma), 50 nM dexamethasone (D8893, Sigma), 1 nM triiodothyronine (T5516, Sigma), 10 ng/mL epidermal growth factor (E4127, Sigma), 5 g/mL insulin (I5500, Sigma), 1% antibiotic and antimycotic (15240062, Thermo Fisher Scientific), and 2% decomplemented fetal bovine serum (FBS, SV30207.02, HycloneTM, Cytiva, Marlborough, MA) at 37℃ with 5% CO2.

extract_protocol:
mpkCCDc11 cells were detached using trypsin/EDTA, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer’s protocols

treatment_protocol: To induce a response by treating with dDAVP (1-deamino-8-D-arginine vasopressin, 10-9 M, V1005, Sigma) on the basolateral membrane, cells were grown on semipermeable filters of the Transwell system (0.4 m pore size, Transwell Permeable Supports, 3450, Corning, NY) in a culture medium for 3 days and in a serum- and hormone-free medium for an additional 24 h. After the starvation step, cells were treated with dDAVP, which was applied to the basolateral side of the cells for 15 min, 30 min or 24 h. The passage numbers of the mpkCCDc11 cells used were 11 - 16.  DharmaFECT4 (T-2004-03, Dharmacon; Horizon Discovery, Cambridge, UK).

value: Kidney; cortical collecting duct

value: mpkCCDc11 cells

value: epithelial cell

value: TAZ knockdown

value: Desmopressindiacetateargininevasopressin (DDAVP), 10-9 M


title: MNs.male.post-exp. # 1


title: Clinical isolate 196

value: Prior to ACT/TACT treatment


title: Clinical isolate 194


title: PBP1_3

value: BY4741 PBP1::Pbp1-Pup2


title: mpkCCDc11 cells, TAZ-siRNA, dDAVP, rep1


title: Clinical isolate 298


title: PBP1_2


title: mpkCCDc11 cells, TAZ-siRNA, vehicle, rep3

value: vehicle


title: mpkCCDc11 cells, TAZ-siRNA, vehicle, rep2


title: P5_Trc1WInt_C2_1

value: BY4741 PUF5::Puf5_T1{delta}intron-Pup2


title: Clinical isolate 192


title: mpkCCDc11 cells, TAZ-siRNA, vehicle, rep1


title: mpkCCDc11 cells, TAZ-siRNA, dDAVP, rep3


title: E26NEW_sg13_1_D5_AAFJGKVM5

city: Rochester

first: Fergus

last: Couch

address: 200 1st St SW

institute: MAYO CLINIC ROCHESTER

description: targeted DNA

data_processing:
FASTQ files of sequenced samples from Illumina MiSeq or NextSeq were trimmed for adapter sequences using cutadapt (v3.5).
SeqPrep (v1.2) converted the paired-end reads into single reads.
The single reads were aligned to the human reference genome (GRCh38) utilizing bwa-mem (v0.7.17).
Following alignment, a custom-developed tool `CountReads` was used for the analysis of DNA sequencing data, with a particular focus on mutation identification and characterization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited files for each variant from the library, day 5 and d14 for each replicate
Library strategy: amplicon based sequencing (AMPLN)

source_name: HAP1 cell

growth_protocol: HAP1 cell (Horizon discovery) were maintained in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Harvested cell pellets were thawed and genomic DNA were extracted by using Monarch Genomic DNA purification kit (NEB). Target region specific primer were used for PCR using Q5 High-Fidelity 2X Master Mix (NEB). Addaptor and index were added for each target region PCR product and samples were purified using AMPure XP beads and sent for sequencing.
Homologous arms (HA) that are 600-1000bp upstream and downstream flanking each target region were amplied from HAP1 cells and cloned into TOPO vector; site-directed mutagenesis PCR were performed in the HA arm vector to introduce target region saturation mutations with the PAM or sgRNA recognition site -destroying to avoind re-cutting by Cas9. Pooled mutagenesis PCR product was phosphorylated and transformed into MaxEfficient DH5a competent cells, grow overnight at 37 degree and library plasmids were extracted by ZymoPUREII MaxiPrep kit.

treatment_protocol: day -1: 2 million HAP1 cells seeded; day 0: transfection with library and sgRNA/Cas9 counstruct; day 1: 1ug/ml puromycin treatment; day 4: change back to regular medium; day 5: half of the cells were harvested for genomic DNA extraction, remaining cells continue culturing and passaged at 3-day interval; day 14: 5 million cells were harvested.

value: HAP1 cell

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: A>G

tag: fixd mut_aa_pos


title: P5_Trc1WInt_C1_2

tag: genotype


title: E26NEW_sg13_1_D14_AAFJGKVM5

description: targeted DNA

tag: cell line


title: E18C_NEW_sg4_1_pUCSSMmu_lib_AAFG7MNM5

description: targeted DNA

value: C>G


title: mpkCCDc11 cells, control-siRNA, dDAVP, rep3

tag: tissue

tag: cell type

value: WT

tag: treatment


title: E26NEW_sg13_1_pUCSSMmu_lib_AAFJGKVM5

description: targeted DNA


title: Clinical isolate 297

tag: time point


title: Clinical isolate 191


title: mpkCCDc11 cells, control-siRNA, dDAVP, rep2


title: E18C_NEW_sg4_1_D5_AAFG7MNM5

description: targeted DNA


title: P5_Trc1WInt_C1_1

tag: strain

tag: strainname

tag: protein of interest


title: E18C_NEW_sg4_1_D14_AAFG7MNM5

description: targeted DNA


title: P5_RBDdel_W_trc3_C1_2

value: BY4741 PUF5::Puf5_{delta}RBD-Pup2

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 190

value: packed red blood cells


title: PBP1_1


title: Clinical isolate 193


title: E22NEW_sg7_2_pUCSSMmu_lib_AAFG7CLM5

description: targeted DNA


title: Clinical isolate 295


title: P5_CterCompIDR_del_2

value: BY4741 PUF5::Puf5_T4-Pup2


title: E22NEW_sg7_2_D5_AAFG7CLM5

description: targeted DNA


title: mpkCCDc11 cells, control-siRNA, vehicle, rep2


title: P5_CterCompIDR_del_1


title: mpkCCDc11 cells, control-siRNA, vehicle, rep1


title: E22NEW_sg7_2_D14_AAFG7CLM5

description: targeted DNA


title: P4_Trc4ToRBD_del_2

value: BY4741 PUF4::Puf4_T4&{delta}IDR-Pup2


title: Clinical isolate 188


title: E22NEW_sg7_3_pUCSSMmu_lib_AAFG75JM5

description: targeted DNA


title: P4_Trc4ToRBD_del_1


title: Clinical isolate 189


title: LPS_CBD_24h_3

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

description:
DESeq2_results_CBD_vs_EtOH_t24h_W_basal
DESeq2_results_CBD_vs_DMF_t24h_W_basal
DESeq2_results_CBD_vs_LPS_t24h_W_basal
DESeq2_results_CBD_vs_MMF_t24h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_CBD_W_basal

data_processing:
FastQC v0.12.1 and Cutadapt v4.4 were used for quality control of the raw reads and removal of the adapter sequences, respectively. Trimmomatic v0.39 was employed to further select trimmed reads larger than 20 nucleotides and with a mapping quality greater than 30. Reads were aligned with HISAT2 v2.2.1 to the mouse genome assembly GRCm39. Mapped reads were annotated using the Ensembl gene annotation v110 for the mouse genome and were quantified using HTSeq v2.0.3. Gene counts were analysed using principal components with custom R scripts (R version 4.3.1). DESeq2 v1.40.2 was used for differential expression analysis
Assembly: GRCm39
Supplementary files format and content: Raw counts of sequencing read in TSV format

source_name: Cell

growth_protocol: For microglial cells we used the BV-2 immortalized murine cell line. Microglial cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 4.5 g/l D-glucose, 2 mM L-glutamine, 100 U/ml of penicillin-streptomycin and 10% heat-inactivated fetal bovine serum. Cells were maintained at 37 ºC in a humidified incubator with 5% CO2. All culture media were purchased from Thermo Fisher Scientific (Waltham, MA, USA).

extract_protocol:
RNA was extracted using the Maxwell® 16 LEV simply RNA Cells kit and the robotic platform Maxwell® 16 (both from Promega Biotech Ibérica), following the manufacturer’s instructions.
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies)

treatment_protocol: DMF and MMF (both from Sigma-Aldrich, Saint Louis, MO, USA) were prepared as stock solutions in dimethyl sulfoxide (DMSO); CBD (Cayman chemical, Ann Arbor, MI, USA) was prepared in ethanol (EtOH). All the compounds were titrated in their respective vehicle and diluted into the culture media for cell treatments. Lipopolysaccharide (LPS) from Escherichia coli 026:B6  in aqueous solution (Thermo Fisher Scientific) was used as a proinflammatory stimuli in microglia at a final concentration of 600 ng/ml. For LPS experiments, the concentration of fetal bovine serum in the microglia culture medium was reduced to 0.1% immediately before drug treatment.The final concentration of vehicle (DMSO, EtOH or H2O) was consistent for all treated cells (0.2%). For RNA-seq experiments, microglia were activated with LPS and treated with  30 µM DMF, 30 µM MMF or 6 µM CBD and their respective vehicles for 4 and 24 hours. Each experiment was repeated 3 times.

value: Cell

value: Microglia

value: Wild-type


title: Clinical isolate 186


title: P4_RBD_del_C2_1

value: BY4741 PUF4::Puf4_{delta}RBD-Pup2


title: E22NEW_sg7_3_D5_AAFG75JM5

description: targeted DNA


title: Clinical isolate 187


title: P5_RBDdel_W_trc3_C2_2


title: Clinical isolate 296


title: mpkCCDc11 cells, control-siRNA, dDAVP, rep1

value: Kidney; cortical collecting duct

value: mpkCCDc11 cells

value: epithelial cell

value: Desmopressindiacetateargininevasopressin (DDAVP), 10-9 M


title: E18C_NEW_sg3_1_pUCSSMmu_lib_AAFG75HM5

description: targeted DNA

value: G>A


title: P4_RBD_del_C1_2


title: Clinical isolate 184

value: Prior to ACT/TACT treatment


title: LPS_DMF_24h_3

description:
DESeq2_results_CBD_vs_DMF_t24h_W_basal
DESeq2_results_DMF_vs_DMSO_t24h_W_basal
DESeq2_results_DMF_vs_LPS_t24h_W_basal
DESeq2_results_DMF_vs_MMF_t24h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_DMF_W_basal


title: P4_RBD_del_C1_3


title: Clinical isolate 185


title: mpkCCDc11 cells, control-siRNA, vehicle, rep3

value: vehicle


title: LPS_24h_3

description:
DESeq2_results_CBD_vs_LPS_t24h_W_basal
DESeq2_results_DMF_vs_LPS_t24h_W_basal
DESeq2_results_DMSO_vs_LPS_t24h_W_basal
DESeq2_results_EtOH_vs_LPS_t24h_W_basal
DESeq2_results_MMF_vs_LPS_t24h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_W_basal


title: E18C_NEW_sg3_1_D5_AAFG75HM5

description: targeted DNA

value: HAP1 cell


title: LPS_MMF_24h_3

description:
DESeq2_results_CBD_vs_MMF_t24h_W_basal
DESeq2_results_DMF_vs_MMF_t24h_W_basal
DESeq2_results_MMF_vs_DMSO_t24h_W_basal
DESeq2_results_MMF_vs_LPS_t24h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_MMF_W_basal


title: P4_RBD_del_C1_1


title: E18C_NEW_sg3_1_D14_AAFG75HM5

description: targeted DNA


title: E22NEW_sg7_3_D14_AAFG75JM5

description: targeted DNA

value: C>G


title: P4_IDRMost_del_2

value: BY4741 PUF4::Puf4_{delta}IDR-Pup2


title: DMSO_24h_6

description:
DESeq2_results_DMF_vs_DMSO_t24h_W_basal
DESeq2_results_DMSO_vs_EtOH_t24h_W_basal
DESeq2_results_DMSO_vs_LPS_t24h_W_basal
DESeq2_results_MMF_vs_DMSO_t24h_W_basal
DESeq2_results_t24h_vs_t4h_DMSO_W_basal


title: LPS_CBD_4h_3

description:
DESeq2_results_CBD_vs_DMF_t4h_W_basal
DESeq2_results_CBD_vs_EtOH_t4h_W_basal
DESeq2_results_CBD_vs_LPS_t4h_W_basal
DESeq2_results_CBD_vs_MMF_t4h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_CBD_W_basal


title: E23NEW_sg7_3_pUCSSMmu_lib_AAFG757M5

description: targeted DNA

value: C>T G


title: P4_IDRMost_del_1


title: E23NEW_sg7_3_D5_AAFG757M5

description: targeted DNA


title: P3_RBD_del535_4

value: BY4741 PUF3::Puf3_{delta}RBD-Pup2


title: Clinical isolate 180

value: packed red blood cells


title: E23NEW_sg7_3_D14_AAFG757M5

description: targeted DNA


title: Clinical isolate 181


title: LPS_MMF_4h_3

description:
DESeq2_results_CBD_vs_MMF_t4h_W_basal
DESeq2_results_DMF_vs_MMF_t4h_W_basal
DESeq2_results_MMF_vs_DMSO_t4h_W_basal
DESeq2_results_MMF_vs_LPS_t4h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_MMF_W_basal

value: Cell


title: LPS_DMF_4h_3

description:
DESeq2_results_CBD_vs_DMF_t4h_W_basal
DESeq2_results_DMF_vs_DMSO_t4h_W_basal
DESeq2_results_DMF_vs_LPS_t4h_W_basal
DESeq2_results_DMF_vs_MMF_t4h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_DMF_W_basal

value: Microglia


title: Clinical isolate 179


title: P3_RBD_del535_3


title: E18N_NEW_5_pUCSSMmu_lib_AAFG73YM5

description: targeted DNA

value: G>C


title: LPS_4h_3

description:
DESeq2_results_CBD_vs_LPS_t4h_W_basal
DESeq2_results_DMF_vs_LPS_t4h_W_basal
DESeq2_results_DMSO_vs_LPS_t4h_W_basal
DESeq2_results_EtOH_vs_LPS_t4h_W_basal
DESeq2_results_MMF_vs_LPS_t4h_W_basal
DESeq2_results_t24h_vs_t4h_LPS_W_basal

value: Wild-type


title: ETOH_24h_6

description:
DESeq2_results_CBD_vs_EtOH_t24h_W_basal
DESeq2_results_DMSO_vs_EtOH_t24h_W_basal
DESeq2_results_EtOH_vs_LPS_t24h_W_basal
DESeq2_results_t24h_vs_t4h_EtOH_W_basal


title: P3_RBD_del535_1


title: E18N_NEW_5_D5_AAFG73YM5

description: targeted DNA


title: ETOH_4h_6

description:
DESeq2_results_CBD_vs_EtOH_t4h_W_basal
DESeq2_results_DMSO_vs_EtOH_t4h_W_basal
DESeq2_results_EtOH_vs_LPS_t4h_W_basal
DESeq2_results_t24h_vs_t4h_EtOH_W_basal


title: Clinical isolate 182


title: Clinical isolate 177


title: DMSO_4h_6

description:
DESeq2_results_DMF_vs_DMSO_t4h_W_basal
DESeq2_results_DMSO_vs_EtOH_t4h_W_basal
DESeq2_results_DMSO_vs_LPS_t4h_W_basal
DESeq2_results_MMF_vs_DMSO_t4h_W_basal
DESeq2_results_t24h_vs_t4h_DMSO_W_basal


title: E18N_NEW_5_D14_AAFG73YM5

description: targeted DNA


title: Clinical isolate 183


title: P3_IDR_del535_C1_1

value: BY4741 PUF3::Puf3_{delta}non-RBD-Pup2


title: P3_IDR_del535_C2_1


title: LPS_CBD_24h_2


title: E21NEW_sg5_2_pUCSSMmu_lib_AAF7LGMM5

description: targeted DNA

value: C>T


title: Clinical isolate 176


title: Clinical isolate 175


title: E21NEW_sg5_2_D5_AAF7LGMM5

description: targeted DNA


title: P3_IDR_del535_2


title: LPS_DMF_24h_2


title: P3_IDR_del513_4

value: BY4741 PUF3::Puf3_T7-Pup2


title: Clinical isolate 173


title: Clinical isolate 178


title: Clinical isolate 174


title: LPS_24h_2


title: P3_IDR_del513_3


title: Clinical isolate 172


title: E22NEW_sg7_1_D5_AAF7LG3M5

description: targeted DNA


title: ETOH_24h_5


title: E21NEW_sg5_2_D14_AAF7LGMM5

description: targeted DNA


title: E22NEW_sg7_1_pUCSSMmu_lib_AAF7LG3M5

description: targeted DNA


title: LPS_MMF_24h_2


title: P3_IDR_del465_8


title: P3_IDR_del513_2


title: Clinical isolate 171


title: Clinical isolate 170


title: P3_IDR_del465_7


title: E23NEW_sg7_2_pUCSSMmu_lib_AAF7K5VM5

description: targeted DNA


title: E22NEW_sg7_1_D14_AAF7LG3M5

description: targeted DNA


title: P3_IDR_del465_4


title: LPS_CBD_4h_2


title: Clinical isolate 169


title: LPS_MMF_4h_2


title: P3_IDR_del465_3


title: E23NEW_sg7_2_D14_AAF7K5VM5

description: targeted DNA


title: LPS_DMF_4h_2


title: P3_IDRMost_del_2

value: BY4741 PUF3::Puf3_{delta}IDR-Pup2


title: Clinical isolate 167


title: E23NEW_sg7_1_pUCSSMmu_lib_AAF7FYVM5

description: targeted DNA


title: LPS_4h_2


title: P3_IDRMost_del_1


title: ETOH_4h_5


title: DMSO_24h_5


title: E23NEW_sg7_1_D14_AAF7FYVM5

description: targeted DNA


title: Clinical isolate 165


title: Clinical isolate 164


title: NSR1_3

value: BY4741 NSR1::Nsr1-Pup2


title: E21NEW_sg5_1_pUCSSMmu_lib_AAF7CVJM5

description: targeted DNA


title: LPS_CBD_24h_1


title: NSR1_2


title: Clinical isolate 163

value: Prior to ACT/TACT treatment


title: E21NEW_sg5_1_D5_AAF7CVJM5

description: targeted DNA


title: E23NEW_sg7_2_D5_AAF7K5VM5

description: targeted DNA


title: Clinical isolate 162


title: Clinical isolate 168


title: NSR1_1


title: LPS_MMF_24h_1


title: E21NEW_sg5_1_D14_AAF7CVJM5

description: targeted DNA


title: LPS_DMF_24h_1


title: NRD1_4

value: BY4741 NRD1::Nrd1-Pup2


title: Clinical isolate 166


title: Clinical isolate 161


title: E21NEW_sg5_3_pUCSSMmu_lib_AAF77MNM5

description: targeted DNA

value: HAP1 cell


title: DMSO_4h_5


title: E21NEW_sg5_3_D5_AAF77MNM5

description: targeted DNA


title: NSR1_4


title: E23NEW_sg7_1_D5_AAF7FYVM5

description: targeted DNA


title: LPS_24h_1


title: NRD1_3


title: E21NEW_sg5_3_D14_AAF77MNM5

description: targeted DNA


title: NRD1_1


title: Clinical isolate 159


title: LPS_DMF_4h_1


title: E26NEW_Cas9_sg4_pUCSSMmu_lib_AAF3553M5

description: targeted DNA

value: C>G


title: Clinical isolate 155


title: Clinical isolate 156


title: LPS_CBD_4h_1


title: ETOH_24h_4


title: NPL3_1

value: BY4741 NPL3::Npl3-Pup2


title: NPL3_3


title: Clinical isolate 158


title: NPL3_4


title: Clinical isolate 157


title: Clinical isolate 154


title: ETOH_4h_4


title: NGR1_2

value: BY4741 NGR1::Ngr1-Pup2


title: NRD1_2


title: NPL3_2


title: E18N_NEW_4_D14_AAF5YWGM5

description: targeted DNA


title: Clinical isolate 153


title: E26NEW_Cas9_sg4_D14_AAF3553M5

description: targeted DNA


title: E18N_NEW_4_pUCSSMmu_lib_AAF5YWGM5

description: targeted DNA


title: DMSO_24h_4


title: DMSO_4h_4


title: LPS_MMF_4h_1


title: Clinical isolate 152


title: E26NEW_Cas9_sg4_D5_AAF3553M5

description: targeted DNA


title: LPS_4h_1


title: NGR1_1


title: E21NEW_sg4_3_pUCSSMmu_lib_AAF352VM5

description: targeted DNA

value: T>A


title: Clinical isolate 160

value: packed red blood cells


title: E21NEW_sg4_3_D5_AAF352VM5

description: targeted DNA


title: Clinical isolate 151


title: NAM8_2

value: BY4741 NAM8::Nam8-Pup2


title: Vehicle3

city: Cambridge

first: Tetsuo

last: Hasegawa

address: Francis Crick Ave

department: Medicine

institute: University of Cambridge

data_processing:
Fastq files from sequencing libraries were trimmed of the first 3 nucleotides of the R1 strand. Contaminating adaptor sequences and poor-quality bases were removed using Trim Galore (Babraham bioinformatics). Libraries were only trimmed for quality.
Quality of resulting files were assessed by FastQC and aligned to the mm10 genome using HISAT2, followed by gene-level quantification using the Featurecount function from the Rsubread package in R.
Assembly: mm10
Supplementary files format and content: Raw counts matrix (txt) - individual libraries
Supplementary files format and content: Raw counts matrix (txt) - combined

source_name: Synovium

extract_protocol:
RNA extraction was performed using RNeasy plus mico kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA contamination was removed using Optimal DNA depletion columns (Qiagen).
Libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit according to the manufacturer’s instructions.
Total RNA-seq, 2 x 150bp paired-end sequencing performed on Novaseq6000 (Illumina)

value: Synovium

value: fibroblasts

value: Control


title: Clinical isolate 294


title: Vehicle2

description: Illumina Stranded Total RNA Prep with Ribo-Zero Plus


title: E21NEW_sg4_3_D14_AAF352VM5

description: targeted DNA


title: Vehicle1


title: NAM8_1


title: Clinical isolate 150


title: NAM7_3

value: BY4741 NAM7::Nam7-Pup2


title: Clinical isolate 149


title: IC2

value: IC


title: IC3


title: E21NEW_sg4_2_D5_AAF352NM5

description: targeted DNA


title: E21NEW_sg4_2_D14_AAF352NM5

description: targeted DNA


title: IC1


title: Clinical isolate 293


title: NAM7_1


title: NAM7_2


title: E19_Cas9_2778_1_lib_AAF33YYM5

description: targeted DNA

value: G>C


title: input, Female, Control, Z-input

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

data_processing:
Fastq files were assembled from the base call files using bcl2f.
The fastq files were trimmed with Trimmomatic.
Sequence files were aligned with STAR aligner. The reference genome was Mus musculus GRCm38, downloaded with annotations from Ensembl.
SAM files were converted to BAM format using samtools.
Assembly: GRCm38/mm10
Supplementary files format and content: Comma-separated file, read-counts per gene.

source_name: Hippocampus

extract_protocol:
TRAP was carried out on dissected hippocampal tissue as previously described (Heiman et al., 2014) with modifications (Sanz et al., 2009). Briefly, homogenization buffer (HB) was used as described in Sanz et al., with heparin omitted. Lysed tissue in HB were centrifuged at 10,000 g for 10 min. at 4° C to remove insoluble debris and the supernatant used for all subsequent steps. Input samples were saved from the supernatant equivalent to 5% of the initial HB volume. 50 mg of two GFP antibodies (bioreactor supernatant, clones 19C8 & 19F7 from the Memorial Sloan-Kettering Institute Monoclonal Antibody Facility) were added to each sample for 4h at 4° C under gentle end-over-end rotation. Samples were transferred to tubes containing 200 mL Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific; 88803; lot VF298063) and incubated overnight at 4° C with end-over-end rotation. The following day, beads were washed in high-salt buffer as described in Sanz et al., and RNA was isolated from the beads and input samples using TRIzol (Thermo Fisher Scientific, 15596018) and the Direct-zol RNA Microprep Kit (Zymo Research, R2062).
RNA libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit according to the manufacturer's protocol.

treatment_protocol: Litters were exposed to ethanol vapor or control air for 4 hours per day from postnatal day (PD) 2 to 7.

value: Hippocampus

tag: vapor study

tag: trap study

tag: Sex

value: Female

tag: litter

tag: age

value: Postnatal day 7

tag: antibody