title: NAB6_SecondDel_2_R

first: Naama

last: Barkai

address: Herzl St 234

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.

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

value: BY4741 NAB6::Nab6_{delta}2-Pup2


title: Clinical isolate 147

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: NAM8_3

city: Rehovot

state: --- Select a state ---

department: Molecular Genetics

country: Israel

organism: Saccharomyces cerevisiae

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.

tag: strain

tag: genotype

value: BY4741 NAM8::Nam8-Pup2

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: E21NEW_sg4_2_pUCSSMmu_lib_AAF352NM5

city: Rochester

first: Fergus

last: Couch

address: 200 1st St SW

country: USA

institute: MAYO CLINIC ROCHESTER

description: targeted DNA

library_source: genomic

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)

molecule: genomic DNA

organism: Homo sapiens

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.

tag: cell line

value: HAP1 cell

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: T>A

tag: fixd mut_aa_pos


title: E19_Cas9_2778_1_D5_AAF33YYM5

description: targeted DNA

value: G>C


title: Clinical isolate 148


title: Clinical isolate 146


title: NAB6_SecondDel_1_R


title: input, Male, Control, W-input

city: Portland

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.

organism: Mus musculus

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.

tag: tissue

value: Hippocampus

tag: vapor study

tag: trap study

tag: Sex

value: Male

tag: litter

tag: age

value: Postnatal day 7

value: Control

tag: antibody


title: NAB6_FourthDel_C2_1

tag: strain

tag: genotype

value: BY4741 NAB6::Nab6_{delta}4-Pup2

tag: strainname


title: E19_Cas9_2778_1_D14_AAF33YYM5

description: targeted DNA

tag: cell line


title: input, Male, EtOH, T-input

tag: treatment

value: EtOH


title: E25C_NEW_sg5_3_pUC_SSM_lib_AAF33MTM5

description: targeted DNA

tag: gene

tag: exon

value: C>G


title: Clinical isolate 145

tag: time point

tag: cell type


title: input, Male, EtOH, S-input


title: E25C_NEW_sg5_3_D5_AAF33MTM5

description: targeted DNA

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: NAB6_FourthDel_C1_1

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 144


title: NAB6_FirstDel_C2_1_NR

value: BY4741 NAB6::Nab6_{delta}IDR_1-Pup2


title: E25C_NEW_sg5_3_D14_AAF33MTM5

description: targeted DNA


title: Clinical isolate 143


title: input, Female, EtOH, R-input

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

value: Female

tag: litter

tag: age


title: NAB6_FirstDel_C1_1_NR

tag: strain

tag: genotype

tag: strainname


title: E15_Cas9_sg2_1_lib_AAF33MLM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

value: G>A


title: input, Male, Control, Q-input

tag: treatment

tag: antibody


title: NAB6_FifthDel_C2_1_NR

value: BY4741 NAB6::Nab6_{delta}IDR_2-Pup2


title: Clinical isolate 142

tag: time point

tag: cell type

value: packed red blood cells


title: E15_Cas9_sg2_1_D5_AAF33MLM5

description: targeted DNA

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: input, Female, EtOH, X-input

tag: tissue

tag: vapor study

tag: trap study

tag: Sex


title: input, Male, Control, P-input

tag: litter

tag: genotype

tag: age


title: NAB6_FifthDel_C1_1_NR

tag: strain

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 140

tag: time point

tag: treatment

value: Prior to ACT/TACT treatment


title: E15_Cas9_sg2_1_D14_AAF33MLM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: Clinical isolate 139

tag: cell type


title: NAB6_4

value: BY4741 NAB6::Nab6-Pup2


title: input, Female, EtOH, M-input

tag: tissue

tag: vapor study

tag: antibody


title: E21NEW_sg4_pUCSSMmu_lib_AACYVFCM5

description: targeted DNA

value: HAP1 cell

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: E21NEW_sg4_D5_AACYVFCM5

description: targeted DNA

value: T>A


title: NAB6_2

tag: strain

tag: genotype


title: Clinical isolate 138


title: input, Female, Control, L-input

tag: trap study

tag: Sex

tag: litter

tag: age


title: input, Male, EtOH, K-input

tag: treatment


title: E21NEW_sg4_D14_AACYVFCM5

description: targeted DNA

tag: cell line

tag: gene


title: Clinical isolate 136

tag: time point


title: Clinical isolate 137

tag: cell type


title: NAB6_1

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 135


title: Clinical isolate 141


title: E25C_NEW_sg5_2_pUCSSM_lib_AACYVCKM5

description: targeted DNA

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position


title: E25C_NEW_sg5_2_D5_AACYVCKM5

description: targeted DNA

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: input, Male, EtOH, I-input

tag: tissue

tag: vapor study

tag: trap study

tag: genotype

tag: antibody


title: input, Male, EtOH, J-input

tag: Sex

tag: litter

tag: age

tag: treatment


title: MSS116_1

tag: strain

tag: strainname


title: Clinical isolate 134

tag: time point

tag: cell type


title: input, Male, EtOH, N-input


title: E25C_NEW_sg5_2_D14_AACYVCKM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: input, Female, EtOH, H-input

tag: tissue


title: MRN1_RBD_del_C2_1

value: BY4741 MRN1::Mrn1_{delta}RBD-Pup2

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: input, Female, EtOH, G-input

value: Hippocampus

tag: vapor study

tag: trap study

tag: genotype


title: MSS116_3


title: Clinical isolate 133


title: input, Female, EtOH, F-input

tag: Sex

tag: litter

tag: antibody


title: E20NEW_sg1_2_D14_AACYV7YM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: E20NEW_sg1_2_pUCSSMmu_lib_AACYV7YM5

description: targeted DNA


title: input, Male, Control, E-input

value: Male

tag: age

tag: treatment


title: Clinical isolate 130

tag: time point

tag: cell type


title: MRN1_IDR_del_C1_1

tag: strain

value: BY4741 MRN1::Mrn1_{delta}IDR-Pup2

tag: strainname


title: E20NEW_sg1_3_D5_AACYV75M5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: MRN1_RBD_del_C1_1

tag: genotype

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 132


title: input, Female, Control, B-input

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

tag: litter

value: Postnatal day 7

value: Control

tag: antibody


title: MRN1_IDR_del_C2_1


title: input, Male, Control, D-input

tag: age

tag: treatment


title: E20NEW_sg1_2_D5_AACYV7YM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: Clinical isolate 131

tag: time point

tag: cell type


title: Clinical isolate 129


title: MRN1_3

tag: strain

value: BY4741 MRN1::Mrn1-Pup2

tag: strainname


title: MRN1_2

tag: genotype

tag: protein of interest


title: E25N_NEW_sg3_3_pUCSSM_lib_AACYV5TM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid

value: C>T


title: Clinical isolate 128


title: E20NEW_sg1_3_D14_AACYV75M5

description: targeted DNA


title: MRN1_1

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 127


title: E25N_NEW_sg3_3_D5_AACYV5TM5

description: targeted DNA


title: input, Male, EtOH, 2-input

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

tag: litter

value: EtOH

tag: antibody


title: GBP2_1

value: BY4741 GBP2::Gbp2-Pup2


title: E20NEW_sg1_3_pUCSSMmu_lib_AACYV75M5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: G>A

tag: fixd mut_aa_pos


title: Clinical isolate 126

tag: time point

tag: cell type

tag: treatment


title: input, Female, Control, C-input

value: Female

tag: genotype

tag: age


title: Clinical isolate 125

value: packed red blood cells


title: GBP2_2

tag: strain

tag: strainname

tag: protein of interest


title: E25N_NEW_sg3_3_D14_AACYV5TM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: Clinical isolate 124

value: Prior to ACT/TACT treatment


title: ECM32_3

tag: tag (none/pup2/dead_pup2)


title: input, Female, Control, 1-input

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

tag: litter

tag: antibody


title: E25N_NEW_sg3_2_pUCSSM_lib_AACYTHHM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: input, Female, Control, A-input

tag: genotype

tag: age

tag: treatment


title: IP, Female, EtOH, X-IP

description:
RNA200923MG_X-IP
translating RNA

value: GFP


title: ECM32_1

tag: strain

tag: strainname

tag: protein of interest


title: ECM32_2


title: Clinical isolate 122

tag: time point

tag: cell type


title: E25N_NEW_sg3_2_D5_AACYTHHM5

description: targeted DNA

tag: cell line

value: HAP1 cell

tag: gene

tag: exon

tag: flowcellid


title: IP, Male, Control, W-IP

description:
RNA200923MG_W-IP
translating RNA

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

tag: litter


title: DHH1_4

tag: genotype

value: BY4741 DHH1::Dhh1-Pup2

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 121

tag: treatment


title: IP, Male, EtOH, Y-IP

description:
RNA200923MG_Y-IP
translating RNA

tag: age

tag: antibody


title: IP, Male, Control, V-IP

description:
RNA200923MG_V-IP
translating RNA


title: E18N_NEW_4_D5_AAF5YWGM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: G>C

tag: fixd mut_aa_pos


title: Clinical isolate 120

tag: time point

tag: cell type


title: Clinical isolate 123


title: DHH1_3

tag: strain

tag: strainname

tag: protein of interest


title: E25N_NEW_sg3_D5_AACYFC3M5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: E25N_NEW_sg3_D14_AACYFC3M5

description: targeted DNA


title: IP, Male, EtOH, T-IP

description:
RNA200923MG_T-IP
translating RNA

tag: tissue

value: Hippocampus

tag: vapor study

tag: trap study

tag: Sex

tag: litter

tag: genotype


title: Clinical isolate 119

tag: treatment


title: E25N_NEW_pUCSSM_lib_AACYFC3M5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: IP, Female, Control, U-IP

description:
RNA200923MG_U-IP
translating RNA

tag: age

tag: antibody


title: Clinical isolate 118

tag: time point

tag: cell type


title: E26NEW_sg5_pUCSSM_lib_AACYCJYM5

description: targeted DNA

tag: cell line

tag: gene

value: C>A


title: E25N_NEW_sg3_2_D14_AACYTHHM5

description: targeted DNA

tag: exon

tag: flowcellid


title: DHH1_1

tag: strain

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: DBP1_3

tag: genotype

value: BY4741 DBP1::Dbp1-Pup2


title: Clinical isolate 117

tag: treatment


title: IP, Male, Control, P-IP

description:
RNA200923MG_P-IP
translating RNA

tag: tissue

tag: vapor study

tag: trap study

tag: Sex

value: Male

tag: litter

value: Postnatal day 7


title: MSS116_2


title: E26NEW_sg5_D14_AACYCJYM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: DBP1_2


title: Clinical isolate 116

tag: time point

tag: cell type


title: Clinical isolate 115


title: E20NEW_sg1_pUCSSMmu_lib_AACWNNMM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid


title: DHH1_2

tag: strain

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: IP, Female, Control, O-IP

description:
RNA200923MG_O-IP
translating RNA

tag: tissue

tag: vapor study

tag: genotype

tag: age

tag: treatment

value: Control

tag: antibody


title: IP, Male, EtOH, N-IP

description:
RNA200923MG_N-IP
translating RNA

tag: trap study

tag: Sex

tag: litter


title: Clinical isolate 114

tag: time point

tag: cell type


title: BFR1_2

value: BY4741 BFR1::Bfr1-Pup2


title: Clinical isolate 113


title: E20NEW_sg1_D14_AACWNNMM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: BFR1_1

tag: strain

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: IP, Female, EtOH, M-IP

description:
RNA200923MG_M-IP
translating RNA

tag: tissue

tag: vapor study

tag: genotype

tag: age

tag: treatment

value: EtOH


title: IP, Male, Control, Q-IP

description:
RNA200923MG_Q-IP
translating RNA

tag: trap study

tag: Sex

tag: litter

tag: antibody


title: Clinical isolate 112

tag: time point

tag: cell type


title: Clinical isolate 111


title: WT-gut2

city: Toronto

first: Aleixo

last: Muise

state: ON

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
The raw RNAseq reads were aligned to the zebrafish genome (GRCz11) using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2
Assembly: zebrafish (GRCz11)
Supplementary files format and content: tab-delimited text files include the count values for each Sample. Rows = genes; Columns = samples.

organism: Danio rerio

source_name: gut

growth_protocol: For wt and itgav KO mutants at 8dpf ,embryos were obtained via natural mating and cultured in embryo E3 buffer, raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf,,embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26-28.5°C and the lighting conditions are 14:10 hr (light: dark).

extract_protocol:
RNA were extracted using RNAeasy mini kit(Qiagen). 600ng of total RNA were used for the construction of sequencing libraries.
RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus protocol to generate polyA-enriched, rRNA-depleted libraries.

treatment_protocol: Wt and itgav KO mutants at 8dpf underwent tailfin-clipping genotyping.The wildtype and itgav (-/-) mutants were pooled (n=15), repectively. Wt and itgav KO mutants at 50dpf underwent tailfin-clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut,brain and heart tissues were collected for RNA extration.

value: gut

value: wildtype

tag: time


title: E26NEW_sg5_D5_AACYCJYM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

tag: fixd mut_aa_pos


title: E25C_NEW_sg5_1_D5_AACTYYHM5

description: targeted DNA

value: C>G


title: IP, Female, Control, L-IP

description:
RNA200923MG_L-IP
translating RNA

tag: tissue

tag: vapor study

value: Female

tag: genotype


title: IP, Male, EtOH, K-IP

description:
RNA200923MG_K-IP
translating RNA

tag: trap study

tag: age

tag: treatment


title: E25C_NEW_sg5_1_pUCSSM_lib_AACTYYHM5

description: targeted DNA


title: IP, Male, EtOH, J-IP

description:
RNA200923MG_J-IP
translating RNA

tag: Sex

tag: litter

tag: antibody


title: Clinical isolate 110

tag: time point

tag: cell type

value: packed red blood cells

value: Prior to ACT/TACT treatment


title: WT-gut1

tag: time


title: itgavKO-gut3

value: itgavKO mutant


title: IP, Female, EtOH, R-IP

description:
RNA200923MG_R-IP
translating RNA

value: GFP


title: WT-gut3


title: DBP1_1

tag: strain

tag: strainname

tag: protein of interest

tag: tag (none/pup2/dead_pup2)


title: Clinical isolate 109


title: E20NEW_sg1_D5_AACWNNMM5

description: targeted DNA

tag: cell line

value: HAP1 cell

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: G>A

tag: fixd mut_aa_pos


title: IP, Male, EtOH, I-IP

description:
RNA200923MG_I-IP
translating RNA

tag: tissue

value: Hippocampus

tag: vapor study

tag: trap study

tag: Sex

tag: genotype

tag: age

tag: treatment


title: itgavKO-gut2

tag: time


title: E24NEW_sg3_3_pUCSSM_lib_AACTYNGM5

description: targeted DNA

value: G>C


title: E24NEW_sg3_3_D5_AACTYNGM5

description: targeted DNA


title: IP, Female, EtOH, H-IP

description:
RNA200923MG_H-IP
translating RNA

tag: litter

tag: antibody


title: itagvKO-gut1


title: Clinical isolate 107

tag: time point

tag: cell type


title: E24NEW_sg3_3_D14_AACTYNGM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon


title: IP, Female, EtOH, G-IP

description:
RNA200923MG_G-IP
translating RNA


title: WT-brain-3

source_name: brain

value: brain


title: Clinical isolate 106


title: E25C_NEW_sg5_1_D14_AACTYYHM5

description: targeted DNA

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut


title: WT-brain-2

tag: tissue


title: IP, Male, Control, E-IP

description:
RNA200923MG_E-IP
translating RNA

tag: vapor study

tag: trap study

value: Male

value: Postnatal day 7


title: E24NEW_sg3_2_D5_AACTYNCM5

description: targeted DNA

tag: fixd mut_aa_pos


title: WT-brain-1

tag: genotype


title: E24NEW_sg3_2_pUCSSM_lib_AACTYNCM5

description: targeted DNA


title: IP, Female, EtOH, F-IP

description:
RNA200923MG_F-IP
translating RNA

tag: Sex

tag: age

tag: treatment


title: E24NEW_sg3_2_D14_AACTYNCM5

description: targeted DNA


title: itgavKO-brain-3

tag: time


title: IP, Female, Control, C-IP

description:
RNA200923MG_C-IP
translating RNA

tag: litter

value: Control

tag: antibody


title: E16NEW_2542_3_pUCSSMmu_lib_AACTJMKM5

description: targeted DNA

tag: cell line

value: T>C


title: IP, Male, Control, D-IP

description:
RNA200923MG_D-IP
translating RNA


title: Clinical isolate 103

tag: time point

tag: cell type


title: itgavKO-brain-2


title: Clinical isolate 108


title: E16NEW_2542_3_D5_AACTJMKM5

description: targeted DNA

tag: gene

tag: exon

tag: flowcellid


title: Clinical isolate 102


title: IP, Female, Control, B-IP

description:
RNA200923MG_B-IP
translating RNA

tag: tissue


title: Clinical isolate 101


title: E16NEW_2542_3_D14_AACTJMKM5

description: targeted DNA

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut


title: IP, Female, Control, A-IP

description:
RNA200923MG_A-IP
translating RNA

tag: vapor study

tag: trap study


title: Clinical isolate 100


title: zebrafish-itgavko-tc-8d-3

source_name: whole fish (with tailfin cut)

value: whole fish (with tailfin cut)

tag: genotype


title: E16NEW_2542_2_pUCSSMmu_lib_AACTJ7GM5

description: targeted DNA

tag: fixd mut_aa_pos


title: Clinical isolate 105

tag: treatment


title: hippocampus 5-weeks replicate 3 (084)

city: Stockholm

first: Klas

last: Blomgren

address: Solnavägen 9, 171 65 Solna

country: Sweden

institute: Karolinska institutet

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultplexing, barcoded processing, gene counting, aggregateion were made using Cell Ranger software (v5.0.1).
https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse brain hippocampal tissue

extract_protocol:
Freshly collected brain cortical and hippocampal tissues from female WT C57Bl/6J were washed with 1ml of 1× Hanks’s balanced salt solution without phenol red, Ca2+ and Mg2+ (HBSS). White matter was removed to the possible maximum, before the tissue was chopped into small pieces using scalpel and transferred into conical tubes containing 1 ml of an enzymatic mixture of dispase II (0.1%), papain (0.01%) and DNase I (0.05%) made in 1× HBSS containing 12.4 mM magnesium sulfate (Si6). Tubes were incubated at 37ºC for 10 min without agitation. The enzymic activity was stopped by adding 4 ml of 20% ice-cold FBS solution made in 1× HBSS. The cell suspension was centrifuged at 500× g at 4 ºC for 5 min. For myelin removal, the cell pellet was resuspended in 1 ml of 20% Percoll® solution made using 10× phenol red HBSS and 1× HBSS. After complete resuspension of the cell pellet, an additional 4 ml of the 20% Percoll® solution was added, bringing the volume up to 5 ml. The suspension was then gently overlaid with 5 ml of 1× HBSS. Tubes were spun at 500× g at 4ºC for 10 min with no break. The supernatant containing the myelin debris was carefully discarded, and the cell pellet was resuspended in 1 ml flow cytometry buffer. At this step, samples from the three animals were pooled into one 15 ml conical tube and centrifuged at 500× g at 4ºC for 5 min.  The supernatant was carefully discarded, and the cell pellet was resuspended in 500 μl flow cytometry buffer. The cell suspension was transferred into a 1.5 ml microtube. Cell viability was accessed using the trypan blue exclusion method and processed for single-cell RNA sequencing.
Isolated cells were processed for single-cell RNA sequencing at the eukaryotic single-cell genomics facility (ESCG) at Karolinska Institutet, Sweden using the 10x Genomics Chromium method (version 3.0.1) and sequenced using Illumina NovaSeq 600 with an S2 flow cell.

value: mouse brain hippocampal tissue

value: brain hippocampal cell types

tag: strain


title: E16NEW_2542_2_D5_AACTJ7GM5

description: targeted DNA


title: Clinical isolate 104


title: zebrafish-itgavko-tc-8d-2

tag: time


title: hippocampus 5-weeks replicate 2 (083)

description: 10X Genomics


title: Clinical isolate 99


title: E16NEW_2542_2_D14_AACTJ7GM5

description: targeted DNA


title: zebrafish-itgavko-tc-8d-1


title: itgavKO-brain-1


title: zebrafish-wt-tc-8d-3

value: wildtype


title: Clinical isolate 98

value: packed red blood cells


title: E24NEW_sg3_pUCSSM_lib_AACTFCHM5

description: targeted DNA


title: zebrafish-wt-tc-8d-2


title: Clinical isolate 97

value: Prior to ACT/TACT treatment


title: hippocampus 5-weeks replicate 1 (082)

description: 10X Genomics


title: cortex 3-weeks replicate 3 (028)

description: 10X Genomics

source_name: mouse brain cortical tissue

value: mouse brain cortical tissue

value: brain cortical cell types


title: cortex 3-weeks replicate 2 (027)

description: 10X Genomics


title: Clinical isolate 96


title: zebrafish-wt-tc-8d-1


title: Clinical isolate 95


title: E24NEW_sg3_D5_AACTFCHM5

description: targeted DNA

value: HAP1 cell


title: E24NEW_sg3_D14_AACTFCHM5

description: targeted DNA


title: Azin1_uneditable_IRI_72h_3

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

data_processing:
STAR v2.7.11a
Assembly: mm10
Supplementary files format and content: featureCounts

source_name: kidney

extract_protocol:
Kidneys were snap frozen and RNA was extracted using Zymo Direct-zol RNA kit.
Library preparation was done following the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Document # 1000000124514 v02 (total RNA-seq).

value: kidney

value: IRI


title: E18N_NEW_pUCSSMmu_lib_AACMF75M5

description: targeted DNA

value: G>C


title: E18N_NEW_D5_AACMF75M5

description: targeted DNA


title: Azin1_uneditable_IRI_72h_2


title: Clinical isolate 92


title: Clinical isolate 93


title: E18N_NEW_D14_AACMF75M5

description: targeted DNA


title: Azin1_uneditable_IRI_72h_1


title: Azin1_locked_IRI_72h_3


title: Clinical isolate 91


title: Clinical isolate 90


title: Azin1_locked_IRI_72h_2


title: E19NEW_pUCSSMmu_lib_AACMF5YM5

description: targeted DNA


title: Clinical isolate 88


title: Azin1_locked_IRI_72h_1


title: E19NEW_D14_AACMF5YM5

description: targeted DNA


title: cortex 3-weeks replicate 1 (026)

description: 10X Genomics


title: E16NEW_2542_pUCSSMmu_lib_AACMCKWM5

description: targeted DNA


title: E19NEW_D5_AACMF5YM5

description: targeted DNA


title: Clinical isolate 94


title: Clinical isolate 87


title: HeLa_siKIF23-430_5U>FA

type: RNA

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

country: Japan

institute: The University of Tokyo

hyb_protocol: Cy3-labeled RNAs were fragmented using the Gene Expression Hybridization Kit (Agilent Technologies) and hybridized to a SurePrint G3 Human GE Microarray (version 3, 8 x 60 K) (Agilent Technologies) at 65℃ for 16 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing: Signals were quantified by Feature Extraction version 12.1.1.1 (Agilent Techinologies).

label_protocol: cDNA and Cy3-labeled RNA were synthesized using the Quick Amp Labeling kit for One Color (Agilent Technologies).

growth_protocol: A HeLa cell suspension (0.5 x 10^5 cells/mL) was inoculated into a well of 24-well culture plate 1 day before transfection.

extract_protocol: Total RNA was purified using FastGene RNA Premium Kit (NIPPON Genetics) and the quality of the total RNA was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were transfected with 50 nM of each siRNA using 2 µL of Lipofectamine 2000 (Thermo Fisher Scientific). At 24 h post-transfection, cells were harvested from two wells per one sample.

value: HeLa

value: cervical cancer cells


title: HeLa_siKIF23-430_6U>FA


title: HeLa_siKIF23-430_4U>FA


title: HeLa_siVIM-270


title: HeLa_siVIM-270_3G>FA


title: Azin1_uneditable_IRI_48h_4


title: Azin1_uneditable_IRI_48h_3


title: E16NEW_2542_D5_AACMCKWM5

description: targeted DNA


title: E16NEW_2542_D14_AACMCKWM5

description: targeted DNA


title: HeLa_Mock

value: Mock


title: Clinical isolate 86


title: Clinical isolate 89


title: Clinical isolate 85


title: Azin1_uneditable_IRI_48h_1


title: Azin1_uneditable_IRI_48h_5


title: Azin1_locked_IRI_48h_5


title: HeLa_siVIM-270_8C>FA


title: HeLa_siKIF23-430


title: Clinical isolate 84


title: E18C_NEW_2758_3_D5_AACM5JVM5

description: targeted DNA


title: Clinical isolate 83


title: Clinical isolate 82


title: E18C_NEW_2758_3_D14_AACM5JVM5

description: targeted DNA


title: E18C_NEW_2758_2_pUCSSMmu_lib_AACM5GNM5

description: targeted DNA


title: Clinical isolate 81


title: Azin1_locked_IRI_48h_3


title: E18C_NEW_2758_3_pUCSSMmu_lib_AACM5JVM5

description: targeted DNA


title: Azin1_locked_IRI_48h_2


title: E18C_NEW_2758_pUCSSMmu_lib_AACLFYTM5

description: targeted DNA


title: Clinical isolate 79


title: Clinical isolate 78


title: E18C_NEW_2758_2_D5_AACM5GNM5

description: targeted DNA


title: E18C_NEW_2758_D14_AACLFYTM5

description: targeted DNA


title: Clinical isolate 80


title: E18C_NEW_2758_2_D14_AACM5GNM5

description: targeted DNA


title: Azin1_uneditable_IRI_48h_2


title: Azin1_locked_IRI_48h_4


title: Azin1_locked_IRI_48h_1


title: Clinical isolate 75


title: WT_IRI_72h_6

value: WT


title: Sample 12 - NSI-2 | 011 | Full ROI

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road E

department: Medicine, Respirology

institute: Western University

library_source: other

data_processing:
Probe count and sample metadata files were obtained from GeoMx DSP control center/v3.0.0.113. standR package was used to perform data exploration and normalization (Liu et al 2023 NAR).
Raw or log2 normalized count output from 'assay' function of standR package
Assembly: hg38
Supplementary files format and content: DCC: output from GeoMX NGS pipeline (Nanostring)

molecule: other

source_name: Lung

growth_protocol: not applicable

extract_protocol:
FFPE sections underwent immunofluorescence with morphology markers (DNA SYTO 13, pan-cytokeratin Alexa Fluor 532, alpha-smooth muscle actin PE-Cy5, and CD45 Alexa Fluor 593) to locate lung microenvironments of interest
in situ RNA probes conjugated to barcodes by a photocleavable linker were hybridized to the sections
Regions of interest were exposed to UV light to decouple the barcoding oligo from RNA probes. Decoupled oligos were collected, indexed by ROI location, and sequenced on Nextseq 1000/2000. GeoMx NGS pipeline (Illumina) was used to produce DCC files from FASTQ files on the GeoMX DSP software.

treatment_protocol: not applicable

value: Lung

tag: patient id

tag: annotation

value: airway

tag: condition

value: NSIP

tag: roi replicate

tag: anno

tag: patid

tag: disease

value: Y

tag: batch

value: second

tag: type

tag: anno type

tag: outcome

value: Good


title: E18C_NEW_2758_D5_AACLFYTM5

description: targeted DNA

tag: cell line

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut


title: Clinical isolate 74

tag: time point

tag: cell type

value: packed red blood cells

tag: treatment

value: Prior to ACT/TACT treatment


title: Clinical isolate 77


title: WT_IRI_72h_1

tag: tissue

tag: genotype

tag: time


title: Sample 12 - NSI-2 | 009 | Full ROI

tag: patient id

tag: annotation

value: inflammatory

tag: condition

tag: roi replicate

tag: anno

tag: patid

tag: disease


title: Clinical isolate 76


title: Sample 12 - NSI-2 | 012 | Full ROI

tag: batch

tag: type

tag: anno type

tag: outcome


title: WT_IRI_72h_4


title: Sample 12 - NSI-2 | 008 | Full ROI


title: Sample 12 - NSI-2 | 010 | Full ROI


title: WT_IRI_72h_2


title: WT_IRI_72h_5


title: WT_IRI_48h_5


title: Sample 12 - NSI-2 | 006 | Full ROI

value: central


title: WT_IRI_48h_3

value: kidney


title: WT_IRI_72h_3

value: IRI


title: Clinical isolate 73

tag: time point


title: Clinical isolate 72

tag: cell type


title: Clinical isolate 69

tag: treatment


title: Clinical isolate 68


title: WT_IRI_48h_1

tag: tissue


title: WT_IRI_36h_5

tag: genotype


title: Sample 12 - NSI-2 | 003 | Full ROI

value: peripheral


title: Clinical isolate 71


title: Clinical isolate 67


title: WT_IRI_48h_4

tag: time


title: Clinical isolate 66


title: Sample 12 - NSI-2 | 005 | Full ROI

tag: patient id


title: WT_IRI_48h_2


title: Sample 12 - NSI-2 | 004 | Full ROI

tag: annotation


title: Sample 12 - NSI-2 | 002 | Full ROI

tag: condition


title: WT_IRI_36h_3


title: K562ci_ZNF800_KD_1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

data_processing:
Reads were aligned with STAR, deduplicated with UMI-tools dedup, and then the resulting bam was turned into a deduplicated FASTQ using SAMTOOLS.  This was then re-processesd with Salmon v 0.14 to get transcript counts.
All reads were aligned to hg38_gencode.v28
Differential gene expression matricies were made with DESeq2, version 1.24, and stability was calulated as relative expression.
Assembly: hg38, gencode 28
Supplementary files format and content: The processed data contains the differential gene expression of each KO relative to the control

molecule: polyA RNA

growth_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. The K562 cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). All cell lines were routinely screened for mycoplasma with a PCR-based assay.

extract_protocol:
Total RNA for RNA-seq and RT-qPCR was isolated using the Zymo QuickRNA isolation kit with in-column DNase treatment per the manufacturer’s protocol.
RNA-seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara), and sequenced on Illumina NovaSeq 6000 instrument, in a PE150 (paired end 150 cycles) setting, at Novogene Corporation.

treatment_protocol: K562 cells expressing dCas9-KRAB fusion protein were constructed by lentiviral delivery of pMH0006 (Addgene #135448) and FACS isolation of BFP-positive cells. The lentiviral constructs were co-transfected with pCMV-dR8.91 and pMD2.D plasmids using TransIT-Lenti (Mirus) into 293T cells, following the manufacturer’s protocol. The virus was harvested 48 hours post-transfection and passed through a 0.45 µm filter. Target cells were then transduced overnight with the filtered virus in the presence of 8 µg/mL polybrene (Millipore). Guide RNA sequences for CRISPRi-mediated gene knockdown were cloned into pCRISPRia-v2 (Addgene #84832) via BstXI-BlpI sites. After transduction with sgRNA lentivirus, K562 cells were selected with 2 µg/mL puromycin (Gibco). Knockdown of target genes was assessed by RT-qPCR using PerfeCTa SYBR Green SuperMix (QuantaBio) per the manufacturer’s instructions. HPRT1 was used as endogenous control.

tag: cell line

value: Lymphocyte

value: ZNF800 KO


title: Sample 12 - NSI-2 | 007 | Full ROI

tag: roi replicate

tag: anno


title: Sample 12 - NSI-2 | 001 | Full ROI

tag: patid

tag: disease


title: Sample 11 - NSI-1 | 012 | Full ROI

tag: batch

tag: type


title: K562ci_ZNF800_KD_2


title: Clinical isolate 65


title: Clinical isolate 63


title: WT_IRI_36h_2


title: Clinical isolate 70


title: Sample 11 - NSI-1 | 010 | Full ROI

tag: anno type

tag: outcome


title: Clinical isolate 64

tag: time point

tag: cell type


title: K562ci_QKI_KD_2

value: QKI KO


title: Sample 11 - NSI-1 | 011 | Full ROI

tag: tissue


title: Sample 11 - NSI-1 | 009 | Full ROI


title: K562ci_QKI_KD_1

tag: genotype


title: K562ci_control_1

value: Control


title: WT_IRI_36h_1

value: WT

tag: treatment

tag: time


title: WT_IRI_24h_3


title: WT_IRI_36h_4


title: Clinical isolate 62


title: MS_9_Tconv_Exvivo

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

data_processing:
The official pipeline of the Encyclopedia of DNA Elements consortium (https://github.com/kundajelab/atac_dnase_pipelines) was adopted to preprocess the ATAC-seq raw data. The preprocessing started with the paired-end ATAC-seq fastq files for each individual. More specifically, reads were trimmed for adapters using cutadapt (97) and mapped to the human reference genome (hg19) using bowtie2. The output raw bam files were filtered, deduped, and converted to single-ended Tn5-shifted tagalign files, which were then used as the input for peak calling. The deduped bam files were used in the downstream motif and footprint analyses described in a later section.  Details are described in the Supplementary Methods.
Assembly: hg19
Supplementary files format and content: txt

source_name: Tconv

extract_protocol:
na
Cells were pelleted by centrifugation at 500 x g for 7 min at 4°C, then resuspended with 50 μl of transposase mixture (25 μL of 2x TD buffer (Illumina), 2.5 μL of TDE1 (Illumina), 0.5 μL of 1% digitonin (Thermo Fisher), 22 μL of nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in a thermal shaker with agitation at 300 RPM. Transposed DNA was purified using a MinElute Reaction Cleanup kit (QIAgen) and purified DNA was eluted in 20 μL elution buffer. Transposed fragments were amplified and purified as described previously with modified primers. Libraries were quantified using qPCR (KAPA Library Quantification Kit) prior to sequencing. All Fast-ATAC libraries were sequenced using a 2x100 bp paired-end protocol on the HiSeq 4000 Sequencing System (Illumina).

value: Tconv

tag: group

value: MS

value: primary T cells


title: WT_IRI_24h_5


title: WT_IRI_24h_4


title: Clinical isolate 61


title: Sample 11 - NSI-1 | 006 | Full ROI

value: Lung

tag: patient id

tag: annotation

tag: condition

value: NSIP

value: Y

value: second


title: Sample 11 - NSI-1 | 008 | Full ROI

value: inflammatory

tag: roi replicate

tag: anno

value: Good


title: Clinical isolate 59

value: packed red blood cells

value: Prior to ACT/TACT treatment


title: Sample 11 - NSI-1 | 007 | Full ROI

tag: patid

tag: disease


title: MS_8_Tconv_Exvivo

tag: cell line


title: MS_7_Treg_Exvivo

source_name: Treg

value: Treg


title: WT_IRI_16h_5

value: kidney

value: IRI


title: Sample 11 - NSI-1 | 004 | Full ROI

value: central

tag: batch

tag: type

tag: anno type


title: WT_IRI_16h_4


title: MS_7_Tconv_Exvivo


title: MS_8_Treg_Exvivo


title: Clinical isolate 55

tag: time point

tag: cell type


title: Sample 11 - NSI-1 | 003 | Full ROI

tag: tissue

value: peripheral

tag: outcome


title: Clinical isolate 57

tag: treatment


title: Clinical isolate 58


title: Sample 11 - NSI-1 | 005 | Full ROI


title: Clinical isolate 56


title: K562ci_control_2

value: Lymphocyte

tag: genotype

value: Control


title: WT_IRI_24h_2

value: WT

tag: time


title: WT_IRI_16h_3


title: Sample 11 - NSI-1 | 002 | Full ROI

tag: patient id

tag: annotation


title: Clinical isolate 54


title: MS_6_Treg_Exvivo

tag: group

value: MS

value: primary T cells


title: WT_IRI_16h_2


title: WT_IRI_24h_1


title: WT_IRI_4h_4


title: Sample 11 - NSI-1 | 001 | Full ROI

value: Lung

tag: condition

value: NSIP

tag: roi replicate

tag: anno


title: Sample 10 - CHP-2 | 010 | Full ROI

value: neutral

value: CHP

tag: patid

tag: disease

value: Y

value: second


title: MS_4_Tconv_Exvivo

tag: cell line

value: Tconv


title: MS_5_Treg_Exvivo

value: Treg


title: WT_IRI_4h_3

value: kidney


title: WT_IRI_16h_1

value: IRI


title: Clinical isolate 48

value: packed red blood cells

value: Prior to ACT/TACT treatment


title: WT_IRI_4h_2


title: Clinical isolate 52


title: WT_IRI_4h_5


title: WT_IRI_4h_1


title: Sample 10 - CHP-2 | 012 | Full ROI

tag: batch

tag: type

tag: anno type

value: Good


title: Clinical isolate 49

tag: time point

tag: cell type


title: Clinical isolate 53

tag: treatment


title: MS_4_Treg_Exvivo

tag: genotype


title: Clinical isolate 51


title: Clinical isolate 47


title: Clinical isolate 50


title: Sample 10 - CHP-2 | 009 | Full ROI

tag: tissue

value: fibrosis

tag: outcome


title: WT_Ischemia_20min_without_reperfusion_5

value: WT

tag: time


title: Sample 10 - CHP-2 | 008 | Full ROI

tag: patient id

tag: annotation


title: MS_6_Tconv_Exvivo

tag: group

value: MS


title: MS_3_Tconv_Exvivo

value: primary T cells


title: Sample 10 - CHP-2 | 011 | Full ROI

value: Lung

tag: condition

tag: roi replicate

tag: anno


title: Clinical isolate 46


title: Sample 10 - CHP-2 | 006 | Full ROI

value: inflammatory

tag: patid

tag: disease


title: Sample 10 - CHP-2 | 005 | Full ROI

tag: batch

tag: type


title: MS_20_Treg_Exvivo

tag: cell line


title: Sample 10 - CHP-2 | 004 | Full ROI

tag: anno type


title: MS_5_Tconv_Exvivo


title: WT_Ischemia_20min_without_reperfusion_2

tag: treatment


title: MS_20_Tconv_Exvivo

tag: genotype


title: MS_2_Treg_Exvivo


title: MS_2_Tconv_Exvivo


title: Sample 10 - CHP-2 | 002 | Full ROI

tag: tissue

value: granuloma


title: Sample 10 - CHP-2 | 007 | Full ROI

value: CHP

tag: outcome


title: Clinical isolate 40

tag: time point

tag: cell type


title: MS_19_Treg_Exvivo


title: MS_21_Treg_Exvivo


title: MS_3_Treg_Exvivo


title: WT_Ctl-No-IRI_3

tag: time


title: WT_Ischemia_20min_without_reperfusion_4


title: WT_Ischemia_20min_without_reperfusion_3


title: Clinical isolate 45


title: MS_18_Treg_Exvivo

tag: group


title: Sample 9 - CHP-1 | 010 | Full ROI

tag: patient id

tag: annotation

value: neutral

tag: condition

value: Y


title: Sample 10 - CHP-2 | 003 | Full ROI

tag: roi replicate

tag: anno

tag: patid

value: second


title: Clinical isolate 43


title: WT_Ischemia_20min_without_reperfusion_1


title: Clinical isolate 42


title: Clinical isolate 37


title: MS_21_Tconv_Exvivo

value: Tconv


title: WT_Ctl-No-IRI_5

value: kidney


title: Clinical isolate 44


title: Clinical isolate 41


title: C32

city: Tucson

first: Marissa

middle: Anne

last: Lopez-Pier

state: AZ

address: 1656 E. Mabel St.

department: Physiology

institute: The University of Arizona

data_processing:
Raw reads were aligned to the Mus musculus genome (GRCm38.p6) using the Spliced Transcripts Alignment to a Reference (STAR) R package (version 2.1.3) (Dobin 2013)(26). STAR alignment outperforms most in terms of speed, sensitivity, and precision, yet it is memory intensive. For each transcript reads per kilobase of transcripts per million mapped reads (RPKMs) were quantified with DeSeq (version 1.38.0) R/Bioconductor pack-age in the pre-menopausal (control), peri-menopausal, and menopause groups
The RPKMs of each treatment group were fed into bioinformatic platforms for enrichment analysis of GO terms and KEGG pathways, in order to obtain a high level of gene function within each group. Either Ensemble IDs, UNIPROT IDs (from aim 1 analysis of this chapter), or both were inputted into Metascape and DAVID platforms (Huang 2009, Xie 2011, Zhou 2019)(21, 28, 29). Data was then fed into statistical software R (v3.3.3) to produce principle component analysis (PCA) plots, heat maps, and volcano plots to generally quantify gene expression across pre-, peri, and menopausal groups. These tables and figures contained p-value (p<0.05) enrichment significance and relative values of fold enrichment.
A network correlation was also conducted with statistical software R (v3.3.3) and compares results from RNA-Seq (EN-SEMBL_IDs) and proteome (UNIPROT_IDs) utilizing pairwise comparisons across groups (peri- vs. pre-; meno vs. pre-; peri- vs. meno). Each point corresponds to a single gene/protein expression (log2 RPKM and log2 Abundance). Points were colored red to indicate upregulation in the gene from both RNA-Seq and proteome experiments. Points were colored green to indicate downregulation in the gene from both RNA-Seq and proteome experiments. Finally, points annotated with a yellow outline represented significant differentiated expression in both RNA-Seq and proteome experiments.
Assembly: Mus musculus genome (GRCm38.p6)

source_name: Cardiac-Left ventricle

extract_protocol:
RNA was extracted from flash frozen heart tissue with Qiagen RNeasy plus mini kit (74134, Germantown, MD). The integrity of RNA was analyzed at the University of Arizona Sequencing Core with the 2100 Bioanalyzer (Agilent Technologies INC. (serial no.DE24802066; Assay Eukaryote Total RNA Nano Series II.xsy; Chip lot no. WH29BK20) and samples with RINs scores at 8.7-9.5 were sent to Novogene for subsequent sequencing (Sacramento, CA). then converted to library using NEBNext Ultra II RNA Library Prep by Illumina
Novogene sequenced each sample according to standard protocol, which entailed 1 ug of RNA for the cDNA library construction using an NEBNext Ultra II RNA Library Prep by Illumina according to the manufacturer’s protocol (E7775, New England Biolabs, Ipswich, MA). In brief, mRNA was isolated with the Ribo-Zero Kit (20037135; Illumina, San Diego, CA) then fragmented randomly with a fragmentation buffer. Double-stranded cDNA was synthesized using Il-lumina (RS-122-2001, TrueSeq RNA Sample Preparation, San Diego, CA) and random hexamer primers. The cDNA was then terminally repaired using (AMPure XP system (SPRI bead cleanup); A63881, Beckman Coulter, Indianapolis, IN), ‘A’ ligated, and added sequencing adaptors. The quality of the enriched 250-350 bp cDNA libraries were assessed with a Qubit 2.0 fluorometer (Thermo Scientific, Waltham, MA, USA), quantitative PCR, and analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Cardiac-Left ventricle

tag: developmental stage

value: Menopause

value: VCD


title: MS_19_Tconv_Exvivo

tag: cell line


title: WT_Ctl-No-IRI_4


title: Sample 9 - CHP-1 | 012 | Full ROI

tag: disease

tag: batch

tag: type

tag: anno type

value: Good


title: Sample 10 - CHP-2 | 001 | Full ROI

tag: tissue

tag: outcome


title: Clinical isolate 38

tag: time point

tag: cell type

value: packed red blood cells

tag: treatment

value: Prior to ACT/TACT treatment


title: Sample 9 - CHP-1 | 007 | Full ROI

tag: patient id

value: fibrosis


title: Clinical isolate 39


title: Sample 9 - CHP-1 | 008 | Full ROI

tag: annotation


title: MS_17_Tconv_Exvivo

tag: group

value: MS

tag: genotype

value: primary T cells


title: WT_Ctl-No-IRI_2

value: WT

tag: time


title: Sample 9 - CHP-1 | 009 | Full ROI

value: Lung

tag: condition

tag: roi replicate

tag: anno

tag: patid


title: WT_Ctl-No-IRI_1


title: MS_18_Tconv_Exvivo

tag: cell line


title: Clinical isolate 33


title: B29

tag: developmental stage

value: Perimenopause


title: Clinical isolate 32


title: MS_17_Treg_Exvivo

value: Treg


title: Sample 9 - CHP-1 | 011 | Full ROI

value: neutral

value: CHP

tag: disease

value: Y

tag: batch

tag: type

tag: anno type


title: Clinical isolate 36

tag: time point

tag: cell type


title: Sample 9 - CHP-1 | 003 | Full ROI

tag: tissue

tag: patient id

value: granuloma

value: second

tag: outcome


title: Clinical isolate 30

tag: treatment


title: Clinical isolate 35


title: C31

value: Cardiac-Left ventricle

value: Menopause

tag: genotype


title: B22

value: VCD


title: MS_16_Treg_Exvivo

tag: group


title: C30


title: Clinical isolate 34

value: packed red blood cells


title: Sample 9 - CHP-1 | 006 | Full ROI

tag: annotation

value: inflammatory

tag: condition

tag: roi replicate

value: Good


title: C25


title: MS_16_Tconv_Exvivo

tag: cell line

value: Tconv

value: MS


title: MS_12_Tconv_Exvivo

value: primary T cells


title: A34

tag: developmental stage

value: Premenopause

value: Sesame Oil


title: MS_11_Treg_Exvivo

value: Treg


title: Sample 9 - CHP-1 | 005 | Full ROI

value: Lung

tag: anno

tag: patid

tag: disease


title: Clinical isolate 27

value: Prior to ACT/TACT treatment


title: B28

value: Perimenopause


title: Sample 9 - CHP-1 | 004 | Full ROI

value: CHP

value: Y

tag: batch

tag: type

tag: anno type


title: MS_15_Tconv_Exvivo


title: MS_14_Tconv_Exvivo


title: A26

tag: tissue

value: Cardiac-Left ventricle


title: Clinical isolate 31

tag: time point

tag: cell type


title: Clinical isolate 292

tag: treatment


title: MS_13_Tconv_Exvivo

tag: genotype


title: B27


title: Sample 8 - IPF-2 | 009 | Full ROI

tag: patient id

value: lymphoid

value: IPF

value: second

tag: outcome


title: MS_10_Tconv_Exvivo

tag: group


title: Sample 9 - CHP-1 | 002 | Full ROI

tag: annotation

value: granuloma

tag: condition

tag: roi replicate


title: Sample 8 - IPF-2 | 008 | Full ROI

tag: anno

value: Good


title: Clinical isolate 25

value: packed red blood cells


title: MS_11_Tconv_Exvivo

tag: cell line

value: Tconv

value: MS


title: MS_12_Treg_Exvivo

value: primary T cells


title: Clinical isolate 29


title: Sample 9 - CHP-1 | 001 | Full ROI

tag: patid

tag: disease


title: Sample 8 - IPF-2 | 007 | Full ROI

tag: batch

tag: type


title: non-diabetic retinal neuronal cells 3

first: Subrata

last: Chakrabarti

address: Richmond St

department: Pathology

data_processing:
GeoMx® DSP counts from each AOI were scaled to the 75th percentile of expression
Assembly: mm10
Supplementary files format and content: .dcc.gz: Digital count conversion files for each AOI
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc: the PKC file used to align the probes to the genome build.
Library strategy: Spatial Transcriptomics

source_name: retina

extract_protocol:
Mouse FFPE tissues were processed in accordance with the GeoMx® DSP Slide Preparation user manual (MAN-10150-01). Slides were baked for 3 hours at 60°C prior to deparaffinization. Proteinase K was used to digest the proteins. Slides were hybridized overnight with UV cleavable oligonucleotide probes then stained with morphology markers. Oligos from CD31+ and/or NeuN+ regions of interest were UV-cleaved and collected into a PCR plate for library prep. PCR products were purified and sequenced using a NovaSeq 6000 instrument.
FASTQ sequences of barcode oligonucleotides were processed into digital count conversion (DCC) files using NanoString’s GeoMX NGS Pipeline. Sequences that uniquely identify each probe are found in the PKC.

treatment_protocol: 8 week old C57BL/6 mice were given consecutive intraperitoneal injections of streptozotocin (50 mg/kg in citrate buffer, pH = 4.5) over 5 days to induce diabetes. non-diabetic mice were given mock injections with citrate buffer. mice were sacrificed 2 months after injections

tag: tissue

value: retina

tag: Sex

value: Male

tag: strain

value: non-diabetic


title: A35

tag: developmental stage

value: Premenopause

tag: treatment

value: Sesame Oil


title: Clinical isolate 22

tag: time point

tag: cell type

value: Prior to ACT/TACT treatment


title: non-diabetic retinal neuronal cells 2

tag: group


title: HC_8_Tconv_Exvivo

value: HC

tag: genotype


title: Sample 8 - IPF-2 | 012 | Full ROI

value: Lung

tag: patient id

tag: annotation

value: neutral

tag: condition

value: Y

tag: anno type

tag: outcome


title: HC_7_Treg_Exvivo

tag: cell line

value: Treg


title: Clinical isolate 20


title: Clinical isolate 28


title: diabetic mouse heart 3

source_name: heart

value: heart

value: diabetic


title: Sample 8 - IPF-2 | 011 | Full ROI

value: IPF

tag: roi replicate

tag: anno

tag: patid

tag: disease

tag: batch

value: second

value: Good


title: A33

tag: tissue

value: Cardiac-Left ventricle

tag: developmental stage


title: Clinical isolate 26

tag: time point

value: packed red blood cells

tag: treatment


title: HC_7_Tconv_Exvivo

value: Tconv

tag: group

value: primary T cells


title: MS_10_Treg_Exvivo

value: MS

tag: genotype


title: Sample 8 - IPF-2 | 010 | Full ROI

tag: patient id

tag: type


title: diabetic mouse heart 2

tag: Sex

value: Male

tag: strain


title: MS_1_Treg_Exvivo


title: Clinical isolate 23

tag: cell type

value: Prior to ACT/TACT treatment


title: Clinical isolate 24


title: diabetic retinal neuronal cells 3

value: retina


title: Sample 8 - IPF-2 | 006 | Full ROI

value: Lung

tag: annotation

value: fibrosis

tag: condition

tag: anno type

tag: outcome


title: Sample 8 - IPF-2 | 001 | Full ROI

value: fibroblast

tag: roi replicate

tag: anno

tag: patid

tag: disease

value: Y


title: HC_9_Tconv_Exvivo

tag: cell line

value: HC


title: Clinical isolate 17

tag: time point

tag: treatment


title: HC_9_Treg_Exvivo

value: Treg

tag: group

tag: genotype


title: Sample 8 - IPF-2 | 005 | Full ROI

tag: tissue

tag: patient id

value: IPF

tag: batch

tag: type


title: diabetic retinal neuronal cells 1

tag: Sex

tag: strain

value: diabetic


title: Clinical isolate 21

tag: cell type


title: diabetic retinal neuronal cells 2


title: Sample 8 - IPF-2 | 004 | Full ROI

tag: annotation

tag: condition

value: second

tag: anno type

tag: outcome

value: Good


title: non-diabetic retinal neuronal cells 1

value: non-diabetic


title: Sample 8 - IPF-2 | 003 | Full ROI

tag: roi replicate

tag: anno

tag: patid

tag: disease


title: Clinical isolate 19

tag: time point

value: packed red blood cells

tag: treatment


title: HC_5_Tconv_Exvivo

tag: cell line

value: Tconv

tag: group

tag: genotype

value: primary T cells


title: Clinical isolate 18


title: HC_4_Treg_Exvivo


title: diabetic cardiac MEC 1

tag: tissue

value: heart

value: Male


title: HC_4_Tconv_Exvivo


title: HC_6_Tconv_Exvivo


title: Sample 7 - IPF-1 | 009 | Full ROI

tag: patient id

value: lymphoid

tag: batch

tag: type

value: Bad


title: non-diabetic cardiac MEC 3

tag: Sex

tag: strain


title: Sample 7 - IPF-1 | 012 | Full ROI

value: Lung

tag: annotation

value: neutral

tag: condition

tag: anno type


title: Sample 7 - IPF-1 | 011 | Full ROI

tag: roi replicate

tag: anno

value: Y

tag: outcome


title: Clinical isolate 16

tag: time point

tag: cell type

value: Prior to ACT/TACT treatment


title: HC_6_Treg_Exvivo

tag: cell line

value: Treg

value: HC


title: Sample 8 - IPF-2 | 002 | Full ROI

value: fibroblast

value: IPF

tag: patid

tag: disease


title: non-diabetic cardiac MEC 2

tag: tissue

tag: group


title: HC_5_Treg_Exvivo

tag: genotype


title: Clinical isolate 15

tag: treatment


title: non-diabetic cardiac MEC 1

tag: Sex


title: HC_3_Tconv_Exvivo


title: Sample 7 - IPF-1 | 006 | Full ROI

tag: patient id

value: fibrosis

tag: batch

value: second

tag: type


title: Clinical isolate 14

value: packed red blood cells


title: diabetic renal MEC 3

value: kidney

tag: strain

value: diabetic


title: Clinical isolate 13


title: Sample 7 - IPF-1 | 008 | Full ROI

tag: annotation

tag: condition

tag: roi replicate

tag: anno type


title: non-diabetic renal MEC 3

value: non-diabetic


title: diabetic renal MEC 2

value: Male


title: Sample 7 - IPF-1 | 007 | Full ROI

value: lymphoid

tag: anno

tag: outcome


title: HC_21_Treg_Exvivo

tag: cell line

value: primary T cells


title: non-diabetic renal MEC 2


title: Clinical isolate 11

tag: time point

tag: cell type


title: Clinical isolate 12


title: Sample 7 - IPF-1 | 010 | Full ROI

tag: tissue

value: Lung

tag: patid

tag: disease

value: Bad


title: diabetic renal MEC 1

tag: Sex

tag: group


title: HC_20_Treg_Exvivo

tag: genotype


title: non-diabetic renal MEC 1


title: Clinical isolate 10

tag: treatment


title: Sample 7 - IPF-1 | 005 | Full ROI

tag: patient id

value: Y

tag: batch

tag: type


title: HC_21_Tconv_Exvivo

value: Tconv


title: Clinical isolate 8

value: Prior to ACT/TACT treatment


title: Clinical isolate 9


title: diabetic retinal MEC 3

value: retina

tag: strain


title: Clinical isolate 7


title: Sample 7 - IPF-1 | 003 | Full ROI

tag: annotation

value: fibroblast

tag: condition

tag: roi replicate

tag: anno type


title: HC_20_Tconv_Exvivo

tag: cell line

value: HC


title: HC_2_Tconv_Exvivo


title: HC_3_Treg_Exvivo

value: Treg


title: diabetic retinal MEC 2


title: Sample 7 - IPF-1 | 002 | Full ROI

value: IPF

tag: anno

value: second

tag: outcome


title: HC_2_Treg_Exvivo


title: Clinical isolate 6

tag: time point

tag: cell type

value: packed red blood cells


title: Clinical isolate 4


title: Sample 7 - IPF-1 | 001 | Full ROI

tag: tissue

tag: patid

tag: disease


title: Clinical isolate 5

tag: treatment


title: HC_19_Treg_Exvivo

tag: group

tag: genotype


title: Sample 6 - UNC-2 | 011 | Full ROI

tag: patient id

value: neutral

value: UNC

tag: batch

tag: type


title: Clinical isolate 2


title: Sample 7 - IPF-1 | 004 | Full ROI

tag: annotation

value: fibrosis

tag: condition


title: Sample 6 - UNC-2 | 009 | Full ROI

tag: roi replicate

tag: anno type


title: non-diabetic retinal MEC 2

tag: Sex

value: Male

tag: strain

value: non-diabetic


title: HC_19_Tconv_Exvivo

tag: cell line

value: primary T cells


title: non-diabetic retinal MEC 3


title: HC_18_Tconv_Exvivo


title: Sample 6 - UNC-2 | 010 | Full ROI

value: Lung

tag: anno

tag: outcome

value: Bad


title: Clinical isolate 3

tag: time point

tag: cell type


title: diabetic retinal MEC 1

tag: tissue

value: diabetic


title: Sample 6 - UNC-2 | 012 | Full ROI

tag: patid

tag: disease

value: Y


title: HC_18_Treg_Exvivo

tag: group

tag: genotype


title: SCC, DUSP1KO, DMBATPA treated_rep2

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: IdiPAZ

description:
s12_RNAKOSC3
DUSP1mice_RNAseq_Counts.txt

data_processing:
Mapping was done using HISAT2
StringTie was used for transcriptome assembly
Deseq was used to identify differentially expressed genes
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Skin

growth_protocol:
A431 control or knock-out cells were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C. 100,000 cells were injected intradermically, and tumors grew for 3 weeks. Tumors were disected and cancer epithelial cells isolated using the Mouse cell Depletion kit (130-104-694, Miltenyi).
Full sections OCT from WT skin, WT SCC, Dusp1KO papilloma, Dusp1KO SCC were used to extract RNA

extract_protocol:
total RNA was extracted using Trizol and the microprep RNA extraction kit, Zymo
RNA libraries for RNA-seq were prepared using  the llumina® Stranded mRNA Prep and following the manufacture's instructions

value: Skin

value: Keratinocytes

value: DUSP1 KO

value: SCC


title: non-diabetic retinal MEC 1

value: retina


title: Clinical isolate 1

source_name: packed red blood cells

tag: treatment

value: Prior to ACT/TACT treatment


title: SCC, DUSP1KO, DMBATPA treated_rep1

description:
s11_RNAKOSC2
DUSP1mice_RNAseq_Counts.txt


title: HC_17_Treg_Exvivo

value: Treg

value: HC


title: Sample 6 - UNC-2 | 008 | Full ROI

tag: patient id

tag: annotation

value: UNC

tag: batch

value: second

tag: type


title: Sample 6 - UNC-2 | 006 | Full ROI

value: lymphoid

tag: condition

tag: roi replicate

tag: anno type


title: 52 hours post invasion IDC

source_name: infected erythorcytes in vitro

value: 52 hours post invasion IDC

value: infected erythorcytes in vitro

value: No treatment


title: HC_16_Treg_Exvivo

tag: cell line

value: primary T cells


title: 56 hours post invasion IDC

value: 56 hours post invasion IDC


title: Sample 6 - UNC-2 | 005 | Full ROI

value: Lung

tag: anno

value: Y

tag: outcome

value: Bad


title: HC_16_Tconv_Exvivo

value: Tconv


title: 54 hours post invasion IDC

tag: time point

value: 54 hours post invasion IDC

tag: cell type


title: Papilloma, DUSP1KO, DMBATPA treated_rep2

description:
s8_RNAKOpap2
DUSP1mice_RNAseq_Counts.txt

tag: tissue

value: Skin

tag: strain

value: Keratinocytes

value: DUSP1 KO

value: Papilloma


title: HC_17_Tconv_Exvivo

tag: group

value: HC


title: Sample 6 - UNC-2 | 004 | Full ROI

value: UNC

tag: patid

tag: disease

value: second


title: Sample 6 - UNC-2 | 007 | Full ROI

tag: patient id

value: fibrosis


title: 48 hours post invasion IDC

value: 48 hours post invasion IDC

value: infected erythorcytes in vitro

tag: treatment


title: HC_15_Treg_Exvivo

value: Treg

tag: genotype

value: primary T cells


title: Papilloma, DUSP1KO, DMBATPA treated_rep1

description:
s7_RNAKOpap1
DUSP1mice_RNAseq_Counts.txt


title: 50 hours post invasion IDC

value: 50 hours post invasion IDC

value: No treatment


title: Papilloma, DUSP1KO, DMBATPA treated_rep3

description:
s9_RNAKOpap3
DUSP1mice_RNAseq_Counts.txt


title: SCC, WT, DMBATPA treated_rep3

description:
s6_RNAWTSCC3
DUSP1mice_RNAseq_Counts.txt

value: WT

value: SCC


title: Sample 6 - UNC-2 | 003 | Full ROI

value: Lung

tag: annotation

value: fibroblast

value: Y

tag: batch

tag: type

value: Bad


title: HC_15_Tconv_Exvivo

value: Tconv


title: SCC, WT, DMBATPA treated_rep2

description:
s5_RNAWTSCC2
DUSP1mice_RNAseq_Counts.txt

value: Skin

value: Keratinocytes


title: 46 hours post invasion IDC

value: 46 hours post invasion IDC


title: Skin, WT, DMBATPA treated_rep2

description:
s2_RNAWTsk45
DUSP1mice_RNAseq_Counts.txt


title: HC_14_Tconv_Exvivo

value: HC


title: Skin, WT, DMBATPA treated_rep3

description:
s3_RNAWTsk46
DUSP1mice_RNAseq_Counts.txt


title: SCC, WT, DMBATPA treated_rep1

description:
s4_RNAWTSCC1
DUSP1mice_RNAseq_Counts.txt


title: 40 hours post invasion IDC

value: 40 hours post invasion IDC


title: Sample 6 - UNC-2 | 002 | Full ROI

tag: condition

value: UNC

tag: roi replicate

value: second

tag: anno type


title: Skin, WT, DMBATPA treated_rep1

description:
s1_RNAWTsk43
DUSP1mice_RNAseq_Counts.txt


title: 44 hours post invasion IDC

value: 44 hours post invasion IDC

value: infected erythorcytes in vitro


title: HC_14_Treg_Exvivo

tag: cell line

value: Treg

value: primary T cells


title: 36 hours post invasion IDC

tag: time point

value: 36 hours post invasion IDC

value: No treatment


title: 42 hours post invasion IDC

value: 42 hours post invasion IDC

tag: cell type


title: Sample 5 - UNC-1 | 012 | Full ROI

tag: tissue

value: Lung

value: neutral

tag: anno

value: Y

tag: outcome


title: Sample 5 - UNC-1 | 010 | Full ROI

tag: patid

value: Bad


title: Sample 5 - UNC-1 | 009 | Full ROI

value: fibrosis

tag: disease


title: HC_13_Treg_Exvivo

tag: group


title: Efferent ductules of adult cKO mice 4 of 4 months old

city: Québec

first: Charles

last: Joly Beauparlant

state: QC

address: 2705 Bd Laurier

institute: Université Laval

data_processing:
Reads were trimmed using fastp v0.20.0. Quality control was performed on raw and trimmed data to ensure the quality of the reads using FastQC v0.11.8 and MultiQC v1.8. The quantification was performed with Kallisto v0.46.2 against the Mus musculus transcriptome (downloaded from Ensembl release 101).
Assembly: Mus musculus transcriptome (downloaded from Ensembl release 101)
Supplementary files format and content: Comma-delimited file that contains the raw count values
Supplementary files format and content: Comma-delimited file that contains the TPM values

source_name: Efferent ductules

extract_protocol:
Total RNA was extracted from total efferent ductules of 5 cKO and 5 Ctl mice at 4 months old using Qiagen RNeasy Mini Kit. A minimum of 488ng of RNA  was used for the construct of the library.
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare total RNA sequencing libraries according to manufacturer’s instruction using 1 ug of total RNA

value: Efferent ductules

value: VillinCre; Arl13bflox/flox


title: HC_12_Tconv_Exvivo

value: Tconv

value: HC


title: Sample 5 - UNC-1 | 011 | Full ROI

tag: patient id

value: UNC

value: second


title: HC_13_Tconv_Exvivo

tag: genotype


title: Efferent ductules of adult cKO mice 5 of 4 months old


title: HC_12_Treg_Exvivo


title: HC_11_Treg_Exvivo


title: 38 hours post invasion IDC

value: 38 hours post invasion IDC

value: infected erythorcytes in vitro

tag: treatment


title: HC_11_Tconv_Exvivo

value: primary T cells


title: Efferent ductules of adult cKO mice 2 of 4 months old


title: 30 hours post invasion IDC

value: 30 hours post invasion IDC


title: Sample 6 - UNC-2 | 001 | Full ROI

tag: annotation

value: fibroblast

tag: batch


title: 34 hours post invasion IDC

value: 34 hours post invasion IDC

value: No treatment


title: Sample 5 - UNC-1 | 008 | Full ROI

value: Lung

tag: condition

tag: type


title: Efferent ductules of adult cKO mice 3 of 4 months old


title: 28 hours post invasion IDC

value: 28 hours post invasion IDC


title: Efferent ductules of adult control mice 5 of 4 months old

value: VillinCre; Arl13bflox/+


title: HC_10_Treg_Exvivo

value: Treg


title: 32 hours post invasion IDC

value: 32 hours post invasion IDC


title: HC_10_Tconv_Exvivo


title: Sample 5 - UNC-1 | 004 | Full ROI

value: lymphoid

tag: roi replicate

value: Y

tag: anno type

value: Bad


title: 26 hours post invasion IDC

tag: time point

value: 26 hours post invasion IDC


title: HC_1_Treg_Exvivo

tag: cell line

value: HC


title: Sample 5 - UNC-1 | 003 | Full ROI

tag: tissue

value: UNC

value: second


title: Sample 5 - UNC-1 | 002 | Full ROI

tag: anno


title: Sample 5 - UNC-1 | 007 | Full ROI

value: fibrosis

tag: outcome


title: 22 hours post invasion IDC

value: 22 hours post invasion IDC

tag: cell type

value: infected erythorcytes in vitro


title: Efferent ductules of adult control mice 3 of 4 months old

value: Efferent ductules


title: GC135808_Cl7_Ctrl

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Quality control of the generated raw fastq sequence files was performed with FastQC v0.11.7 and adapters were filtered with ea-utils fastq-mcf v1.05
Splice-aware alignment was performed with HiSat2 against the human reference genome hg38 using default parameters
Reads mapping to multiple loci in the reference genome were discarded. Resulting BAM alignment files were handled with Samtools v1.5.
Reads per gene were calculated with HT-seq Count v2.7.14 and count-based differential expression analysis was done with R-based Bioconductor package DESeq2
Assembly: human reference genome hg38
Supplementary files format and content: raw counts in .csv or .count

source_name: human iPSC-derived oligodendrocyte-like cells

growth_protocol: SOX10 overexpression based OPC differentiation protocol (Garcia et al 2018. doi: 10.1016/j.stemcr.2017.12.014. )

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit
Libraries were prepared from 500 ng using the QuantSeq 3’ mRNA-seq library prep kit (Lexogen)
Libraries were pooled equimolar to 2 nM for single-read sequencing on the HiSeq4000 (Illumina) with settings 51-8-8

value: Isogenic control


title: Sample 5 - UNC-1 | 006 | Full ROI

value: Lung

tag: patid

tag: disease


title: Efferent ductules of adult control mice 2 of 4 months old


title: Efferent ductules of adult cKO mice 1 of 4 months old

value: VillinCre; Arl13bflox/flox


title: GC135807_Cl7_Ctrl

value: human iPSC-derived oligodendrocyte-like cells


title: GC135806_Cl7_Ctrl


title: 18 hours post invasion IDC

value: 18 hours post invasion IDC

value: No treatment


title: GC135805_Cl7_Ctrl


title: Efferent ductules of adult control mice 4 of 4 months old

value: VillinCre; Arl13bflox/+


title: Sample 5 - UNC-1 | 001 | Full ROI

tag: patient id

value: fibroblast

value: Y


title: Efferent ductules of adult control mice 1 of 4 months old

tag: genotype


title: Ntg-PLX-487

city: Bethesda

first: Changyoun

last: Kim

state: Maryland

address: 35 Convent Dr. Rm 1A-1002

department: Molecular Neuropathology Unit

institute: National Institute on Aging, National Institutes of Health

data_processing:
Quality of sequence reads was assessed using FastQC tool (v0.11.9)
Trim Galore (v0.6.4_dev) was employed to remove adapters from paired-end sequencing reads
Alignment of trimmed reads and transcript quantification was performed with mouse reference genome (mm10) using STAR aligner (v2.7.5c) and RSEM (v1.3.1) software.
Assembly: mm10
Supplementary files format and content: Read counts were generated by RSEM

source_name: Brain

growth_protocol: meninge-removed mouse cortices were incubated with papain solution (HBSS containing 10 U/ml papain, 0.2 mg/ml cysteine, 0.5 mM EDTA, 1 mM CaCl2, and 0.003N NaOH), followed by incubation with a trypsin inhibitor solution (MEM with Earl's salts containing 5% fetal bovine serum, 2.5 mg/ml bovine serum albumin, and 2.5 mg/ml trypsin inhibitor). Tissues were dissociated by pipetting and centrifuged for 1 minute at 200g to pellet the cells. The pellet was resuspended with complete neurobasal media (2% B-27, 0.5 mM Glutamax-1) and anti-mitotic media (2 mg/ml 5-Fluoro-2’deoxyuridine and 9.6 mg/ml Uridine) and seeded onto PDL/laminin-coated culture plates and incubated for 5 days.

extract_protocol:
Following treatment, mouse microglia were isolated from the brain utilizing Adult Brain Dissociation Kit (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instruction. Briefly, enzyme-mixed chopped brains were dissociated by gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) for 30 minutes. The brain homogenates were filtered with 70 mm strainer, and incubated with CD11b magnetic beads (Miltenyi Biotec) at 4°C. After a 15-minute incubation, the beads were rinsed with MACS buffer (Miltenyi Biotec) and microglia were eluted from the brain by the pressure
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

treatment_protocol: Age-matched non-transgenic (non-tg) and synucleinopathy transgenic mice (a-syn-tg, Line 61, mThy1 promoter) were given controls AIN-76A or AIN-76A with 290 mg of the PLX3397/kg diet for 3 weeks and injected intraperitoneally with either a control vehicle (DMSO) or CSFR1 inhibitor (PLX3397, 40 mg/kg) twice per week for 3 weeks.

value: Brain

value: Isolated microglia from mouse brain

value: Microglia

tag: treatment

value: CSFR1 inhibitor (PLX3397, 40 mg/kg)

tag: Sex

value: female

tag: age


title: Sample 4 - Nor 3 | 010 | Full ROI

tag: annotation

value: pleura

tag: condition

value: NOR

value: N

tag: batch

value: second


title: 20 hours post invasion IDC

value: 20 hours post invasion IDC

value: infected erythorcytes in vitro


title: 16 hours post invasion IDC

value: 16 hours post invasion IDC


title: Sample 4 - Nor 3 | 012 | Full ROI

value: Lung

tag: roi replicate

tag: type

tag: anno type


title: Sample 4 - Nor 3 | 011 | Full ROI

tag: tissue


title: 10 hours post invasion IDC

tag: time point

value: 10 hours post invasion IDC

value: No treatment


title: Ntg-PLX-466

tag: cell line

value: male


title: Sample 4 - Nor 3 | 009 | Full ROI

value: airway

tag: anno

tag: outcome


title: Ntg-con-485

value: Brain

tag: cell type

value: vehicle


title: Ntg-PLX-490

value: Isolated microglia from mouse brain

value: Microglia


title: 14 hours post invasion IDC

value: 14 hours post invasion IDC


title: Pooled IDC stages 7

value: Pooled IDC stages


title: 12 hours post invasion IDC

value: 12 hours post invasion IDC


title: Ntg-PLX-467

value: CSFR1 inhibitor (PLX3397, 40 mg/kg)


title: Sample 5 - UNC-1 | 005 | Full ROI

tag: patient id

value: lymphoid

value: UNC

tag: patid

tag: disease

value: Y

value: second

value: Bad


title: GC135803_Cl7_Ctrl

value: human iPSC-derived oligodendrocyte-like cells

tag: genotype

tag: treatment

value: Isogenic control


title: Ntg-con-482

tag: Sex

value: male

tag: age


title: GC135800_c2002_Mutant

value: Genome-edited mutant


title: Pooled IDC stages 6

value: infected erythorcytes in vitro

value: No treatment


title: 8 hours post invasion IDC

value: 8 hours post invasion IDC


title: Sample 4 - Nor 3 | 008 | Full ROI

value: Lung

tag: annotation

value: airway

tag: condition

value: NOR

value: N

tag: batch


title: Pooled IDC stages 5

value: Pooled IDC stages


title: GC135802_c2002_Mutant


title: Ntg-con-474

value: Brain

value: Isolated microglia from mouse brain

value: Microglia

value: vehicle

value: female


title: Sample 4 - Nor 3 | 007 | Full ROI

tag: roi replicate

value: second

tag: type

tag: anno type


title: GC135801_c2002_Mutant

value: human iPSC-derived oligodendrocyte-like cells


title: GC135804_Cl7_Ctrl

value: Isogenic control


title: a-syn-tg-PLX-489

tag: tissue

tag: cell line

value: CSFR1 inhibitor (PLX3397, 40 mg/kg)


title: Sample 4 - Nor 3 | 006 | Full ROI

value: central

tag: anno

tag: outcome


title: Ntg-con-476

tag: cell type


title: GC135798_c2002_Mutant

value: Genome-edited mutant


title: Sample 4 - Nor 3 | 003 | Full ROI

tag: patient id

value: peripheral

tag: patid


title: Pooled IDC stages 4

tag: time point

value: infected erythorcytes in vitro

value: No treatment


title: Pooled IDC stages 2

tag: treatment


title: Sample 4 - Nor 3 | 004 | Full ROI

value: Lung

value: NOR

tag: disease


title: Sample 4 - Nor 3 | 001 | Full ROI

value: N


title: GC135797_c2002_Mutant

tag: genotype


title: a-syn-tg-PLX-488

value: Brain

tag: Sex

tag: age


title: a-syn-tg-PLX-468

value: Isolated microglia from mouse brain

value: male


title: GC135796_2g6_Ctrl


title: Sample 3 - Nor 2-1 | 012 | Full ROI

tag: annotation

value: pleura

tag: condition

tag: batch


title: Sample 4 - Nor 3 | 002 | Full ROI

tag: roi replicate

tag: type

tag: anno type


title: a-syn-tg-PLX-481

tag: tissue

tag: cell line

value: Microglia

value: female


title: GC135795_2g6_Ctrl

tag: cell type

value: human iPSC-derived oligodendrocyte-like cells


title: Pooled IDC stages 3

value: Pooled IDC stages


title: GC135799_c2002_Mutant


title: Pooled IDC stages 1


title: Sample 4 - Nor 3 | 005 | Full ROI

tag: patient id

tag: anno

value: second

tag: outcome


title: Pisatin 24 hour-set 3

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

institute: Tulane University

description: Pisatin-Processed.txt

data_processing:
The sequencing reads which contained low-quality, adaptor-polluted and high content of unknown base (N) reads, were removed prior to further downstream  analyses
After reads filtering,  clean reads were mapped to reference human genome using HISAT. On average 88.91% reads are mapped, and the uniformity of the mapping result for each sample suggests that the samples are comparable.
Assembly: not provided
Supplementary files format and content: Data files represent differentially expressed genes as detected by RSEM, gene expression values are identiifed by TPM. Gene change is Log2 fold change with phytocompound as numerator and vehicle control as denominator

source_name: cell line

extract_protocol:
Extracted RNA was quantified and assessed for integrity using a Bioanalyzer (Agilent Technologies, Santa Clara, CA). The total RNA was extracted using a Direct-zol RNA purification kit (Zymo research, Irvine, CA).
The mRNA was then purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces. The fragmented mRNA was synthesized into first-strand cDNA using random primers. The second strand of cDNA was synthesized with dUTP instead of dTTP. The cDNA thus synthesized was subjected to end-repair and 3′ adenylation. Subsequently, adaptors were ligated to the ends of this 3 ′ adenylated cDNA fragments. U-labeled second-strand template was digested with Uracil-DNA-Glycosylase (UDG) and PCR amplification was performed and sequencing on the DNBSEQ (DNBSEQ Technology) platform was performed

value: cell line

value: Breast cancer

value: WT

tag: treatment

value: Pisatin 24 hour


title: GC135794_2g6_Ctrl

value: Isogenic control


title: a-syn-tg-con-486

value: vehicle


title: DMSO 24 hour-set 3

value: DMSO 24 hour


title: Pisatin 24 hour-set 2

description: Pisatin-Processed.txt


title: GC119666_2g6_Ctrl


title: Sample 3 - Nor 2-1 | 011 | Full ROI

value: Lung

value: NOR

tag: patid

tag: disease

value: N


title: a-syn-tg-con-484

value: Brain

value: Isolated microglia from mouse brain

tag: genotype

tag: Sex

value: male


title: a-syn-tg-con-477

value: Microglia

value: female

tag: age


title: GC119665_2g6_Ctrl

value: human iPSC-derived oligodendrocyte-like cells


title: DMSO 24 hour-set 2


title: GC135792_2010_Mutant

value: Genome-edited mutant


title: Sample 3 - Nor 2-1 | 008 | Full ROI

tag: annotation

value: airway

tag: condition

value: second


title: D5_rpt5 RNA

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

country: Australia

institute: University of Technology Sydney

description:
mmu_lncRNA_rawcount_matrix.txt
mmu_mRNA_rawcount_matrix.txt

data_processing:
Single end reads were sequenced, each samples was run in two lanes resulting in two Fastq files (L001 and L002), which were merged before processing. The quality of the miRNA seq and total RNA seq raw Fastq files was assessed using FastQC v0.11.9, and adapters were removed using Cutadapt v1.12. For miRSeq fastq files, reads with lengths <18bp and >26bp were discarded also using Cutadapt. The mature miRNA sequences of Mus musculus were retrieved from miRbase (Release 22.2) and were used to build the index for alignment using Bowtie2 and miRSeq reads were aligned to the mature M. musculus miRNAs. MiRNA seq reads that did not align against the M. musculus miRNAs were then aligned against all published miRNA sequences for F. hepatica derived from miRBase version 21 repositorry [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021 using Bowtie version 1.3.0. Counts for M. musculus and F. hepatica miRNAs were extracted from the resultant Sam files using SamTools. For Total RNA sequencing the Mus musculus genome sequences (GRCm39.genome.ensembl release 108) were retrieved from Gencode (Release M31) and was used to build the index for alignment using Bowtie2. Counts for Mus musculus mRNA and lncRNAs were extracted using Gencode (Release M31) annotation files and HT-Seq count.
Assembly: mm10
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu miRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu mRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu lncRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for fhe miRNAs for each sample

source_name: peritoneal macrophage

extract_protocol:
Total RNA was harvested from five replicates for each timepoint using RNAzol (Molecular Research Centre) according to manufactureres instructions. For construction of sequencing libraries, 2ug of totoal RNA was use for miRNA-seq and 1.5ug total RNA for RNA seq.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA prep with RiboZero Plus kit (35M reads/sample) and for miRSeq using Qiaseq miRNA prep kit (75M reads/sample)  following manufacturers insctructions.

value: peritoneal macrophage

value: Day 5


title: Sample 3 - Nor 2-1 | 010 | Full ROI

value: pleura

tag: roi replicate

tag: batch


title: GC119664_2g6_Ctrl

value: Isogenic control


title: Pisatin 24 hour-set 1

description: Pisatin-Processed.txt

value: cell line

value: Breast cancer

value: WT

value: Pisatin 24 hour


title: Sample 3 - Nor 2-1 | 009 | Full ROI

value: Lung

value: NOR

value: N

tag: type

tag: anno type


title: GC135793_2010_Mutant


title: Sample 3 - Nor 2-1 | 005 | Full ROI

tag: tissue

value: central


title: a-syn-tg-con-483

value: Brain

tag: cell line

value: Isolated microglia from mouse brain

tag: cell type

value: Microglia

value: vehicle

value: male


title: Sample 3 - Nor 2-1 | 007 | Full ROI

tag: patient id

value: airway

tag: anno

value: second


title: D5_rpt3 RNA

value: peritoneal macrophage

tag: treatment

value: Day 5


title: Tuberosin 24 hour-set 3

description: Tuberosin-Processed.txt

value: cell line

value: Tuberosin 24 hour


title: Sample 3 - Nor 2-1 | 006 | Full ROI

tag: patid

tag: outcome


title: DMSO 24 hour-Set 1

value: Breast cancer

tag: genotype

value: WT

value: DMSO 24 hour


title: Tuberosin 24 hour-set 2

description: Tuberosin-Processed.txt


title: GC119661_2010_Mutant

value: human iPSC-derived oligodendrocyte-like cells

value: Genome-edited mutant


title: GC119663_2010_Mutant


title: Sample 3 - Nor 2-1 | 003 | Full ROI

value: Lung

value: peripheral

value: NOR

tag: disease

value: N


title: Sample 3 - Nor 2-1 | 004 | Full ROI

value: central


title: D5_rpt2 RNA


title: GC119662_2010_Mutant


title: GC135791_2010_Mutant


title: 18hr_rpt5 RNA


title: OCI-AML3 cells, dTAG, Ribo-seq, replicate 2

city: Perugia

first: Brunangelo

last: Falini

address: Piazza Università, 1

country: Italy

institute: University of Perugia

description: Supplementary Table 1_OCI-AML3 Translation sheet

data_processing:
For RNA-seq reads, the adapters were trimmed by cutadapt program, while for Ribo-seq reads, the adapters were trimmed, and the random barcodes were extracted by custom script. PotentialrRNAcontamination was removed with bowtie program, and those remaining reads were then mapped to thehuman genomewith gene annotation by using STAR program. Using BAM tools, the alignments were extracted from mapping human genome for further downstream analysis.
Assembly: hg19
Supplementary files format and content: Excel file include Z-score for each sample
Library strategy: Ribo-seq

growth_protocol: OCI-AML3 and IMS-M2 cells were maintained in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine (Glu) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Kit (Zymo Research)
Libraries for RNA-seq were prepared using TruSeqRNA Sample Prep Kit (Illumina) following manufacturer's protocols. Libraries for Ribo-seq were prepared using NEBNext Multiple Small RNA Library Prep Set for Illumina (New England Biolabs) following manufacturer's protocols.

treatment_protocol: Cells were treated with 500nM dTAG-13 (Tocris Bioscience) or 0.3% DMSO (control) for 6h.

value: NPM1-mutated acute myeloid leukemia cells

value: NPM1 gene mutation (type A)


title: 18hr_rpt4 RNA


title: Tuberosin 24 hour-set 1

description: Tuberosin-Processed.txt


title: D5_rpt4 RNA


title: D5_rpt1 RNA


title: OCI-AML3 cells, dTAG, RNA-seq, replicate 2

description: Supplementary Table 1_OCI-AML3 RNA-seq sheet

data_processing:
For RNA-seq reads, the adapters were trimmed by cutadapt program, while for Ribo-seq reads, the adapters were trimmed, and the random barcodes were extracted by custom script. PotentialrRNAcontamination was removed with bowtie program, and those remaining reads were then mapped to thehuman genomewith gene annotation by using STAR program. Using BAM tools, the alignments were extracted from mapping human genome for further downstream analysis.
Assembly: hg19
Supplementary files format and content: Excel file include Z-score for each sample


title: Sample 3 - Nor 2-1 | 001 | Full ROI

value: second


title: 18hr_rpt2 RNA

value: peritoneal macrophage


title: Sample 2 - Nor 1 | 012 | Full ROI

value: pleura


title: Sakur 24 hour-set 3

value: cell line

value: Sakur 24 hour


title: Sakur 24 hour-set 2

value: Breast cancer


title: Sample 3 - Nor 2-1 | 002 | Full ROI


title: 18hr_rpt3 RNA


title: OCI-AML3 cells, DMSO, Ribo-seq, replicate 2


title: Sakur 24 hour-set 1

value: WT


title: IMS-M2 cells, dTAG, Ribo-seq, replicate 1

description: Supplementary Table 1_IMS-M2 Translation sheet


title: Sample 2 - Nor 1 | 010 | Full ROI


title: Medicar 24 hour-set 3

value: Medicar 24 hour


title: 6hr_rpt5 RNA


title: 6hr_rpt4 RNA


title: Naringe 24 hour-set 2

value: Naringe 24 hour


title: OCI-AML3 cells, DMSO, RNA-seq, replicate 2


title: Sample 2 - Nor 1 | 011 | Full ROI


title: Naringe 24 hour-set 3


title: 6hr_rpt3 RNA


title: 18hr_rpt1 RNA


title: 6hr_rpt2 RNA


title: Naringe 24 hour-set 1


title: Medicar 24 hour-set 1


title: IMS-M2 cells, dTAG, Ribo-seq, replicate 2


title: Sample 2 - Nor 1 | 009 | Full ROI

value: airway


title: IMS-M2 cells, dTAG, RNA-seq, replicate 2

description: Supplementary Table 1_IMS-M2 RNA-seq sheet


title: Sample 2 - Nor 1 | 008 | Full ROI

value: Lung


title: IMS-M2 cells, DMSO, Ribo-seq, replicate 1


title: 6hr_rpt1 RNA


title: Sample 2 - Nor 1 | 006 | Full ROI


title: D0_rpt5 RNA

value: Uninfected


title: Maaikain 24 hour-set 2

value: Maaikain 24 hour


title: IMS-M2 cells, DMSO, RNA-seq, replicate 2


title: Maaikain 24 hour-set 3


title: IMS-M2 cells, dTAG, RNA-seq, replicate 1


title: Maaikain 24 hour-set 1


title: D0_rpt4 RNA


title: IMS-M2 cells, DMSO, RNA-seq, replicate 1


title: Sample 2 - Nor 1 | 003 | Full ROI

value: peripheral

value: NOR

value: N


title: Sample 2 - Nor 1 | 004 | Full ROI

value: central


title: Medicar 24 hour-set 2


title: Sample 2 - Nor 1 | 005 | Full ROI

value: second


title: D0_rpt3 RNA

value: peritoneal macrophage


title: GWB5 24 hour-set 3

value: GWB5 24 hour


title: Sample 2 - Nor 1 | 007 | Full ROI


title: IMS-M2 cells, DMSO, Ribo-seq, replicate 2

value: NPM1-mutated acute myeloid leukemia cells

value: NPM1 gene mutation (type A)


title: PMA Treated, Day 11, Clone C

city: Santa Cruz

first: Susan

last: Carpenter

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

description:
yesPMA_D11_C
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

data_processing:
for i in *fastq.gz; do name=$(basename $i); cutadapt -j 24 -a GTTTAAGAGCTAAGCTGGAAACAGCATAGCA -o "${name%%_S*}"_trimmed.fastq.gz  "$i" ;done
mageck count -l lib7_Mageck_format.txt -n LPS_HiLo --sample-label hi_A,hi_B,hi_C,lo_A,lo_B,lo_C,LPS_A,LPS_B,LPS_C --fastq GFPhi_A_trimmed.fastq.gz GFPhi_B_trimmed.fastq.gz GFPhi_C_trimmed.fastq.gz GFPlo_A_trimmed.fastq.gz GFPlo_B_trimmed.fastq.gz GFPlo_C_trimmed.fastq.gz yesLPS_A_trimmed.fastq.gz yesLPS_B_trimmed.fastq.gz yesLPS_C_trimmed.fastq.gz
Bin <- c('lo','hi') binStartQ <- c(0.001, 0.799); binEndQ <- c(0.20, 0.999);  binStats <- data.frame(Bin,binStartQ,binEndQ); binStats$fraction = binStats$binEndQ - binStats$binStartQ; binStats$binStartZ = qnorm(binStats$binStartQ); binStats$binEndZ = qnorm(binStats$binEndQ)
guideLevelStats = findGuideHitsAllScreens(experiments = unique(binReadMat["expt"]),                                             countDataFrame = binReadMat, binStats = binStats,                                             sortBins = c("lo", "hi"), unsortedBin = "LPS",                                            negativeControl = "isNontargeting")
PMA analysis: DESeq2 log2fold change was determined for each guide between noPMA and PMA_day_11. PMA_day_11 was removed from analysis due to low coverage. Sets of guides that target a specific gene were compared via Mann Whitney U with log2fold change as the input.
Assembly: Hg19
Supplementary files format and content: lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.
Supplementary files format and content: LPS_HiLo.count.txt; raw counts of guide RNAs from mageck count function for LPS Screen.
Supplementary files format and content: PMA.count.tsv
Supplementary files format and content: All_genes_UnsortedBackground.tsv; MAUDE significance testing output by sample from LPS experiment.
Supplementary files format and content: 5kb_hicFindTADs_domains.bed; TAD calls from HiCExplorer hicFindTads function against Hg38.
Supplementary files format and content: chr_THP1.Ctrl_5kb.cool; Cool file for canonical chromosomes generated with cooler cload pairs function against Hg38.

growth_protocol: All THP1 cell lines were cultured in RPMI 1640 supplemented with 10% low-endotoxin fetal bovine serum (ThermoFisher), 1X penicillin/streptomycin, and incubated at 37°C in 5% CO2.

extract_protocol:
Flow cytometry and PCR amplification of genomic sgRNA sequences were conducted as previously described in detail in https://doi.org/10.1016/j.celrep.2020.108541.
10 sgRNAs were designed for each TSS of hg19 annotated lncRNAs expressed in THP1s at baseline and upon stimulation. The sgRNA library also included 700 non-targeting control sgRNAs, and sgRNAs targeting 50 protein coding genes as positive controls. The sgRNA library was designed and cloned as previously described in DOI: 10.1126/science.aah7111
Guide-Seq

treatment_protocol: Library infected and selected THP1-NFkB-EGFP-CRISPRi-sgRNA cells were expanded to 2000X coverage. Cells were stimulated with LPS (200 ng/mL) for 24 h to induce expression of NFkB-EGFP.

value: human leukemia monocytic cells

tag: clonal line

value: clone C

value: 11 days PMA


title: Sample 2 - Nor 1 | 001 | Full ROI

tag: annotation


title: PMA Treated, Day 11, Clone A

description:
yesPMA_D11_A
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: clone A


title: GWB5 24 hour-set 2

value: cell line

value: Breast cancer

value: WT


title: Sample 2 - Nor 1 | 002 | Full ROI

value: Lung

tag: condition


title: D0_rpt2 RNA

value: Uninfected


title: GLY III 24 hour-set 3

value: GLY III 24 hour


title: NSIP-B1 | 012 | Full ROI

value: airway

value: NSIP

tag: roi replicate

value: Y

value: first

value: Bad


title: GWB5 24 hour-set 1

value: GWB5 24 hour


title: D5_rpt5 miRNA

description:
fhe_miRNA_rawcount_matrix.txt
mmu_miRNA_rawcount_matrix.txt

value: peritoneal macrophage

value: Day 5


title: GLY III 24 hour-set 2


title: D0_rpt1 RNA


title: NSIP-B1 | 011 | Full ROI

tag: batch


title: GLY III 24 hour-set 1


title: Untreated, Day 3, Clone C

description:
noPMA_D3_C
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: human leukemia monocytic cells

value: clone C

value: 3 days No PMA


title: NSIP-B1 | 010 | Full ROI

tag: type


title: D5_rpt4 miRNA


title: GLY II 24 hour-set 3

value: cell line

value: GLY II 24 hour


title: Untreated, Day 3, Clone A

description:
noPMA_D3_A
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: clone A


title: Untreated, Day 3, Clone B

description:
noPMA_D3_B
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: clone B


title: D5_rpt3 miRNA


title: GLY II 24 hour-set 1

value: Breast cancer

value: WT


title: PMA Treated, Day 11, Clone B

description:
yesPMA_D11_B
PMA.count.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: 11 days PMA


title: Unsorted, clone C

description:
LPS_C
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: 24h LPS

tag: sorted population

value: Unsorted


title: GLY II 24 hour-set 2

tag: tissue


title: D5_rpt1 miRNA


title: NSIP-B1 | 008 | Full ROI

value: Lung

value: inflammatory

value: NSIP

value: Y

value: first

tag: anno type


title: Unsorted, clone B

description:
LPS_B
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

tag: cell line

tag: cell type

value: human leukemia monocytic cells


title: Glycinol 24 hour-set 3

value: Glycinol 24 hour


title: 18hr_rpt5 miRNA

value: peritoneal macrophage


title: Unsorted, clone A

description:
LPS_A
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.


title: NSIP-B1 | 007 | Full ROI

tag: patient id

tag: anno

value: Bad


title: NSIP-B1 | 005 | Full ROI

value: central

tag: patid


title: NSIP-B1 | 006 | Full ROI

tag: outcome


title: Glycinol 24 hour-set 2

value: cell line

tag: genotype

tag: treatment


title: 18hr_rpt3 miRNA


title: NSIP-B1 | 009 | Full ROI

tag: disease


title: D5_rpt2 miRNA

value: Day 5


title: Glycinol 24 hour-set 1

value: Breast cancer


title: GFP Low, clone C

description:
GFPlo_C
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

tag: clonal line

value: clone C

value: GFP Low


title: NSIP-B1 | 004 | Full ROI

tag: annotation

tag: condition