title: MEFB12input [0072_2022]


title: rpoB R200P M9 glucose with methionine R2

status: Public on Aug 07 2023

type: SRA

city: La Jolla

first: Christopher

last: Dalldorf

state: CA

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: UCSD

description:
same as sample name
RPO_HRS_R200P_rpoB_M9_Methionine_R2
24

library_source: transcriptomic

data_processing:
Processed according to https://github.com/avsastry/modulome-workflow
Assembly: GCA_000005845.2
Supplementary files format and content: counts.csv
Supplementary files format and content: log_tpm.csv

molecule: total RNA

organism: Escherichia coli K-12

source_name: rpoB00P M9 glucose with methionine

growth_protocol: M9 4 g/L glucose

extract_protocol:
3 ml of culture was added to 6 ml of Qiagen RNA-protect Bacteria Reagent after sample collection
Sequencing libraries were created using a Kapa Biosystems RNA HyperPrep per vendor protocol.

tag: strain

value: MG1655 substrain BOP27

tag: cell type

value: bacterial cell

tag: genotype

value: rpoB R200P

tag: treatment

value: rpoB R200P M9 glucose with methionine


title: snf2del R3

city: Berkeley

first: Elçin

last: Ünal

address: 628 Barker Hall

institute: UC Berkeley

data_processing:
reads aligned to genome using Hisat2 and quantification of RNA transcripts per million with StringTie.
fold change quantification performed with DESeq2 with default settings
Assembly: sacCer3 (R64)
Supplementary files format and content: SWI3_SNF2strains.xlsx contains TPM values for all samples. Genes are labeled in the first column and rows are labeled with sample name
Supplementary files format and content: DESeq2 output comparing each mutant to wild type expression (e.g. snf2W935_v_SNF2.xlsx) are provided and labeled in column 1 with gene names

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells grown in YPD to mid-log phase. Biological replicates were collected on separate days.

extract_protocol:
Cells were collected by vacuum filtration and then flash frozen in liquid nitrogen. RNA was extracted by acid phenol chloroform exctration and precipitated in isopropanol.
PolyA selection and library generation was performed on 10ug of total RNA using NEXTflexTM Rapid Directional mRNA-Seq Kit

value: snf2[delta]; LEU2

value: Cells grown in YPD to mid-log phase and collected by vacuum filtration


title: P30.Dataset, 206535570103_R06C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to the the Beadchip HorvathMammalMethylChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Mus musculus

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted

tag: age

tag: confidenceinageestimate

tag: tissue

value: Spleen

tag: female

tag: tissuedetailed

tag: specieslatinname

value: Mus musculus


title: P30.Dataset, 206535570103_R03C01

value: Kidney


title: snf2del R2


title: rpoB R200P M9 glucose with methionine R1

description:
same as sample name
RPO_HRS_R200P_rpoB_M9_Methionine_R1
23


title: MEFnoB12input [0071_2022]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

library_source: genomic

data_processing:
Reads were aligned to the mm10 reference genome using bowtie (v.0.12.9) with parameters -n 2 and -m 1. Read deduplication was performed using the markdup function from the sambamba package.
Peaks were called using MACS2 (v.2.2.6) with the --broad option considering the corresponding INPUT files as controls (-c option)
Assembly: mm10
Supplementary files format and content: Peak files from MACS2 in excel format

source_name: Mouse Embryo E13.5

growth_protocol: Cells were seeded in 6-well plates (300 000 cells per well) in DMEM (10% FBS, pen/strep). The following day, media was replaced with iPSC media and cells were treated as described. DNA was harvested 72h after transfer to iPSC media.

extract_protocol:
Cells were fixed with 1% (v/v) PFA for 2 minutes and then quenched with 750 mM Tris for 5 minutes. Cells were washed twice with PBS, scraped, and spun down at 1200 x g for 5 minutes. Pellets were lysed with 100 uL (per well) lysis buffer on ice for 10 minutes, the sonicated using a Diagenode BioRuptor Pico for 10 cycles (30’ on, 30’ off) at 4°C. Lysates were clarified for 10 minutes at 8000 x g, 1% input samples were reserved, and supernatant was used for immunoprecipitation with Diagenode Magnetic beads and H3K3me3 mAb (Cell Signaling Technologies #4909). The following day, cells were washed 3 times and eluted. Cross-links were reversed with RNaseA, proteinase K and NaCl, and chromatin fragments were purified using Qiagen PCR cleanup kit .
ChIP libraries were prepared for sequencing using the kit NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat#E7645), following manufacturer´s instructions and 11 cycles of amplification.

treatment_protocol: MEFs were grow in iPSC media. Doxy-OSKM were grown in iPSC media treated continuously with 1μg/mL doxycycline. Samples treated with vitamin B12 had 2 µM supplemented continuously throughout the 72h of growth (starting at the time of transfer to iPSC media)

tag: clone

value: Clone 1

tag: condition

value: MEF

tag: ip

value: INPUT

value: Mouse Embryo E13.5


title: snf2del R1


title: wt M9 glucose with methionine R2

description:
same as sample name
RPO_HRS_BOP27_M9_Methionine_R2
22

source_name: wt M9 glucose with methionine

value: wt

value: wt M9 glucose with methionine


title: snf2-Q928K R1

value: snf2[delta]; snf2-Q928K::LEU2


title: snf2-Q928K R3


title: snf2-W935R R3

value: snf2[delta]; snf2-W935R::LEU2


title: snf2-W935R R2


title: P30.Dataset, 206535570103_R04C01


title: rpoB R200P M9 R2

description:
same as sample name
RPO_HRS_R200P_rpoB_M9_R2
20

source_name: rpoB00P M9

value: MG1655 substrain BOP27

value: rpoB R200P M9


title: wt M9 glucose with methionine R1

description:
same as sample name
RPO_HRS_BOP27_M9_Methionine_R1
21

value: bacterial cell


title: snf2-W935R R1


title: SNF2 R3

value: snf2[delta]; SNF2::LEU2


title: P30.Dataset, 206535570103_R02C01


title: rpoB R200P M9 R1

description:
same as sample name
RPO_HRS_R200P_rpoB_M9_R1
19

value: rpoB R200P


title: SNF2 R2

value: Cells grown in YPD to mid-log phase and collected by vacuum filtration


title: HCC78_Criz3

city: Aurora

first: Robert

last: Doebele

state: CO

address: 12801 E. 17th Ave, Building RC1-S, Rm L18-8401A

department: Devision of Medical Oncology

institute: University of Colorado Anschutz Medical Campus

description: HCC78 crizotinib IC50 is 790 nM (measured by 3-day MTS assay).

data_processing:
Low quality reads were trimmed following three steps: 1) remove reads with adaptor contamination; 2) remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); 3) remove reads with Qscores of over 50% bases below 5.
Trimmed reads were mapped to the reference genome hg19 using STAR (v2.6.1) and quantified by HTseq (v0.6.1).
Raw counts were further normalized and differential expression analyses were performed by DESeq2 (v1.6.3).
Assembly: hg19
Supplementary files format and content: Each processed file (xls) contains (from left to right column header): gene id, DESeq2 median of ratio-normalized counts, differential expression analysis performed by DESeq2 (log2foldchange, pvalue and padj), gene name, chromosome location, strand orientation, start and end positions of the gene at the chromosome, gene length, gene type, gene description, raw read counts, FPKM counts.

organism: Homo sapiens

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with fetal bovine serum at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
RNA was extracted using RNeasy Plus Kit (Qiagen).
The Ultra II RNA Library Prep Kit for Illumina was used for library construction.

treatment_protocol: Cells were treated with DMSO or 250 nM crizotinib in biological triplicates for 24 hours before the harvest.

tag: cell line

value: Lung adenocarcinoma

value: 250 nM crizotinib


title: P30.Dataset, 206535570093_R06C02

value: Kidney

value: Mus musculus


title: P30.Dataset, 206535570093_R03C02


title: P30.Dataset, 206535570103_R01C01


title: HCC78_Criz2


title: P30.Dataset, 206535570093_R04C02


title: SNF2 R1


title: wt M9 R2

description:
same as sample name
RPO_HRS_BOP27_M9_R2
18

source_name: wt M9

value: wt M9


title: swi3del R3

value: swi3[delta]; LEU2


title: HCC78_Criz1


title: swi3del R2


title: wt M9 R1

description:
same as sample name
RPO_HRS_BOP27_M9_R1
17


title: swi3del R1


title: swi3-E815X R3

value: swi3[delta]; swi3-E815X::LEU2


title: HCC78_Ctl3

value: DMSO


title: P30.Dataset, 206535570093_R06C01


title: P30.Dataset, 206535570093_R05C02


title: P30.Dataset, 206535570093_R02C02


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, S-starvation, replicate 2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

institute: University of California, San Diego

description: Total RNA with depleted ribosomal RNA

data_processing:
Raw read files were processed with the reference genome of E. coli K-12 MG1655 (NC_000913.3) by running an in-lab pipeline (https://github.com/avsastry/modulome-workflow) developed for analyzing microbial gene expression profiles (Sastry et al, 2021) to obtain transcripts per million values for each gene. Differentially expressed gene analysis was conducted by using DEseq (Love et al, 2014).
Assembly: NC_000913.3
Supplementary files format and content: csv and log tpm

growth_protocol: E. coli K-12 MG1655 on an LB agar plate was inoculated into 10 mL of the M9 medium and grown overnight. Next day, the cultures were re-inoculated into 100 mL of the same medium at optical density at 600 nm (OD600) of 0.1. When OD600 reached ~1.0, cells were centrifuged and washed with a 75 mM potassium phosphate buffer. Washed cells were inoculated to 500 mL of the M9 medium containing 2 L flasks and OD600 was regularly monitored.

extract_protocol:
Cells were treated using the Qiagen RNA-protect bacterial reagent (Hilden, Germany) according to the instruction from the manufacturer. Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater. Subsequently, the total RNA was extracted using a Qiagen RNA purification kit. After total RNA extraction, ribosomal RNA was removed.
Paired-end RNA sequencing libraries were prepared by using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA)

value: MG1655 Wildtype

tag: carbon sources

value: Glucose

tag: supplements

tag: growth

value: minimal medium at 24 h, S-starvation


title: swi3-E815X R2


title: swi3-E815X R1


title: HCC78_Ctl2


title: SWI3 R3

value: swi3[delta]; SWI3::LEU2


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01090


title: HCC78_Ctl1


title: SWI3 R2


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, S-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01089

value: minimal medium at 12 h, S-starvation


title: CUTO38_Criz3

description: CUTO38 crizotinib IC50 is 143 nM (measured by 3-day MTS assay).


title: snf2-Q928K R2

value: snf2[delta]; snf2-Q928K::LEU2


title: P30.Dataset, 206535570093_R04C01


title: SWI3 R1


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01088


title: SWI3_noclip_DTT

description: no Cap-Clip control

data_processing:
3' and 5' adapters were trimmed with cutadapt
reads that had a 5' adapter were carried forward for alignment to the sacCer3 reference genome with Hisat2
BAM files were input into CAGEr for TPM normalization, consensus clustering, gene annotation, and export of normalized reads in bedGraph format (see Morse et al., 2023 for details)
Differential expression analysis was performed using DEseq2
Assembly: sacCer3 (R64)
Supplementary files format and content: bedGraph files, split into plus and minus strands for visualization in IGV. Minus strand values have been inverted.
Supplementary files format and content: DESeq2 output comparing each mutant to wild type expression from each condition (e.g. snf2W935vsSNF2_DTT.xlsx), or wild type untreated compared with DTT treatment (WT_DTTvsUntreated.xlsx), are provided in Excel format. The CAGEr consensus cluster ID is provided in column 12 and gene name in column 13.

growth_protocol: Cells were grown in YPD to late-log phase and split into two flasks. One flask was untreated and the other treated with 5 mM DTT. Two biological replicates were collected 1 hour post-treatment. Replicates were collected on separate days.

extract_protocol:
Cells were collected by vacuum filtration and then flash frozen in liquid nitrogen. RNA was extracted by acid phenol chloroform exctration and precipitated in isopropanol.
Libraries were generated following a protocol from Tresenrider et al., 2022. Illumina adapter ligation and PCR amplification of libraries were performed using a NEXTflex Rapid DNA-Seq Kit 2.0 bundle.

tag: strain

value: Cells were grown in YPD, treated with 5 mM DTT in log phase, and collected after 1 hour with vacuum filtration


title: SWI3_noclip_untreated

description: no Cap-Clip control

value: Cells were grown in YPD and collected  in log phase by vacuum filtration


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, S-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01087

value: minimal medium at 8 h, S-starvation


title: snf2Q928K_DTT_R2

description:
5' end sequencing
snf2Q928KvsWT_DTT.xlsx


title: P30.Dataset, 206535570093_R03C01


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01086


title: P30.Dataset, 206535570093_R02C01


title: P30.Dataset, 206535570093_R01C01


title: P30.Dataset, 206535570103_R05C02

value: Spleen


title: snf2W935R_DTT_R2

description:
5' end sequencing
snf2W935RvsWT_DTT.xlsx

value: snf2[delta]; snf2-W935R::LEU2


title: snf2W935R_DTT_R1


title: CUTO38_Ctl3

tag: cell type

value: Lung adenocarcinoma


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, S-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01085

tag: genotype

value: minimal medium at 6 h, S-starvation


title: swi3E815X_DTT_R2

description:
5' end sequencing
swi3E815XvsWT_DTT.xlsx

tag: treatment


title: P30.Dataset, 206535570093_R05C01

tag: age

value: Kidney

value: Mus musculus


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01084


title: SNF2_DTT_R1

description:
5' end sequencing
WT_DTTvsUntreated.xlsx

value: snf2[delta]; SNF2::LEU2


title: CUTO38_Ctl2

value: DMSO


title: SWI3_DTT_R2


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, S-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01083

value: MG1655 Wildtype

value: minimal medium at 4 h, S-starvation


title: CUTO37_Criz3

description: CUTO37 crizotinib IC50 is 154 nM (measured by 3-day MTS assay).

value: 250 nM crizotinib


title: CUTO38_Criz2


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01082

value: Glucose


title: SNF2_DTT_R2


title: CUTO38_Criz1


title: SWI3_DTT_R1

value: swi3[delta]; SWI3::LEU2


title: snf2Q928K_untreated_R1

description:
5' end sequencing
snf2Q928KvsWT_untreated.xlsx

value: snf2[delta]; snf2-Q928K::LEU2


title: CUTO38_Ctl1


title: snf2W935R_untreated_R2

description:
5' end sequencing
snf2W935RvsWT_untreated.xlsx


title: P30.Dataset, 206535570093_R01C02

tag: confidenceinageestimate


title: snf2Q928K_untreated_R2


title: snf2Q928K_DTT_R1

value: Cells were grown in YPD, treated with 5 mM DTT in log phase, and collected after 1 hour with vacuum filtration


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, S-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01081

value: minimal medium at 3 h, S-starvation


title: snf2W935R_untreated_R1

value: Cells were grown in YPD and collected  in log phase by vacuum filtration


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, S-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01080


title: CUTO37_Criz2


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01079

value: minimal medium at 24 h, N-starvation


title: swi3E815X_untreated_R1

description:
5' end sequencing
swi3E815XvsWT_untreated.xlsx

value: swi3[delta]; swi3-E815X::LEU2


title: CUTO37_Ctl3

value: Lung adenocarcinoma


title: SWI3_untreated_R2


title: CUTO37_Ctl2


title: SNF2_untreated_R1


title: SNF2_untreated_R2


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01078


title: SWI3_untreated_R1

value: Cells were grown in YPD and collected in log phase by vacuum filtration


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01077

value: minimal medium at 12 h, N-starvation


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01076


title: snf2Q928K_DTT_R2_MNase

data_processing:
Spike in normalization was performed according to SNP-ChIP pipeline from Vale-Silva et al., 2019
reads were aligned to the sacCer3 reference genome using Bowtie and filtered for mononucleosome-sized fragments using deeptools
deeptools was used to generate bedGraph files from filtered BAM files
bedGraph files were adjusted by multiplying read depth at each position with the calculated SNP-MNase normalization factor for each sample
Spike-in adjusted, normalized bedGraph files were converted to BigWig files using deeptools
Assembly: sacCer3 (R64)
Supplementary files format and content: BigWig (.bw) files scaled using SNP-MNase spike-in normalization for visualization in IGV

extract_protocol:
Cells were fixed in 1% formaldehyde, spheroplasted, MNase samples were digested with varying concentrations of MNase enzyme. An undigested gDNA control was sequenced  for each sample to calculate spike-in normalization factors. DNA was extracted by phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation (see Morse et al., 2023 materials and methods for further details).
DNA libraries were prepared using a NEXTflex Rapid DNA-Seq Kit 2.0 bundle

treatment_protocol: Spike-in cells from an SK1 strain were added at a ratio of 1:5 to each sample prior to MNase digestion. MNase samples were digested with 10, 20, or 40 units of MNase and optimal digests were carried forward  for library preparation (see Morse et al., 2023 materials and methods for details).

value: snf2[delta]; snf2-Q928K-3V5::LEU2

value: MNase. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01075

value: minimal medium at 8 h, N-starvation


title: Cauris8978_dsbiofilm_rep1

city: Glasgow

first: Alicia

middle: Ann

last: Ware

address: Cowcaddens Rd

department: Biological & Biomedical Sciences

country: United Kingdom

institute: Glasgow Caledonian University

description: Column 11

data_processing:
fastq files were pseudoaligned to the Candida auris B8441 reference genome (version s01-m01-r31), using the quant fuction from the Kallisto package (v0.48.0)
tsv files resulting from the pseudoalignments were summarised to genes using the tximport function from the TxImport package (v1.28.0)
Expression count data were converted to a DGEList, log2-cpm calculated, and data were normalised and filtered using EdgeR (v3.42.4)
Assembly: Candida auris B8441 reference genome (version s01-m01-r31 from Candida Genome Database)
Supplementary files format and content: Tab-delimited text file containing raw count data for each sample
Supplementary files format and content: Tab-delimited text file containing normalised, log-2 transformed counts per million for all samples.

organism: Candidozyma auris

growth_protocol: Cells were standardised to 1x106 cells/mL in RPMI-1640 (5% foetal calf serum), seeded into wells of a 24-well plate and incubated at RT for 48 hr. Biofilms were grown by alternating cycles of media on for 48 hr, then media off for 48 hr, for 12 days total.

extract_protocol:
RNA was isolated from cells and biofilm samples using the RiboPure Yeast Kit (Invitrogen), as per manufacturer's instructions
Libraries were prepared using the Novogene PT042 NGS RNA Library Prep Set (Novogene Ltd) and processed as per Novogene standard protocols

value: Dry-surface biofilm

value: WT

value: Untreated


title: Cauris8978_dsbiofilm_rep2

description: Column 12


title: snf2Q928K_DTT_R1_gDNA

value: undigested gDNA. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: Cauris8978_dsbiofilm_rep3

description: Column 13


title: swi3E815X_DTT_R1


title: snf2Q928K_DTT_R2_gDNA


title: CUTO33_Criz1

description: CUTO33 crizotinib IC50 is 4662 nM (measured by 3-day MTS assay).

value: 250 nM crizotinib


title: CUTO37_Criz1


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01074

value: MG1655 Wildtype

value: Glucose


title: snf2Q928K_DTT_R1_MNase


title: CUTO33_Criz2


title: CUTO33_Ctl3

value: DMSO


title: CUTO37_Ctl1


title: CUTO33_Criz3


title: Cauris8973_dsbiofilm_rep3

description: Column 10


title: snf2W935R_DTT_R2_gDNA

value: snf2[delta]; snf2-W935R-3V5::LEU2


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01073

value: minimal medium at 6 h, N-starvation


title: CUTO33_Ctl2


title: Cauris8973_dsbiofilm_rep2

description: Column 9


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01072


title: Cauris8973_dsbiofilm_rep1

description: Column 8


title: snf2W935R_DTT_R1_gDNA


title: snf2W935R_DTT_R2_MNase


title: CUTO33_Ctl1


title: swi3E815X_untreated_R2

value: swi3[delta]; swi3-E815X::LEU2

value: Cells were grown in YPD and collected  in log phase by vacuum filtration


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01071

value: minimal medium at 4 h, N-starvation


title: Cauris8978_plank_rep3

description: Column 7

growth_protocol: Broths were grown in YPD broth at 37℃ with 150 rpm shaking. 2x108 cells were harvested from washed broths.

value: Planktonic cells


title: CUTO28_Criz3

description: CUTO28 crizotinib IC50 is 28 nM (measured by 3-day MTS assay).

value: Lung adenocarcinoma


title: CUTO28_Criz2


title: Cauris8978_plank_rep1

description: Column 5


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01070


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, N-starvation, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01068

value: minimal medium at 3 h, N-starvation


title: snf2W935R_DTT_R1_MNase

value: MNase. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: swi3E815X_DTT_R1_gDNA


title: swi3E815X_DTT_R2_gDNA


title: CUTO28_Criz1


title: Cauris8973_plank_rep3

description: Column 4


title: swi3E815X_DTT_R2_MNase


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01067

value: minimal medium at 24 h


title: Cauris8973_plank_rep2

description: Column 3

value: WT


title: swi3E815X_DTT_R1_MNase


title: CUTO28_Ctl2


title: E. coli K-12 MG1655 grown in a minimal medium at 24 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01066


title: Cauris8973_plank_rep1

description: Column 2

value: Untreated


title: SWI3_DTT_R2_gDNA

value: undigested gDNA. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: Cauris8978_plank_rep2

description: Column 6


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01065

value: minimal medium at 12 h


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, N-starvation, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01069

value: MG1655 Wildtype


title: CUTO28_Ctl3


title: E. coli K-12 MG1655 grown in a minimal medium at 12 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01064

value: Glucose


title: CUTO27_Criz3

description: CUTO27 crizotinib IC50 is 281 nM (measured by 3-day MTS assay).

value: 250 nM crizotinib


title: ILK_Rx_BMP_4

city: Edinburgh

first: Alexander

last: Loftus

address: Crewe Road

institute: The University of Edinburgh

data_processing:
Data were processed using the DESeq2 pipeline integrated on the BlueBee genomics analysis platform.
Assembly: mm9
Supplementary files format and content: ENSEMBL gene IDs and associated read counts for each sample.

source_name: Brain

growth_protocol: Cells were grown in defined stem cell medium as detailed in Gangoso et al. 2021 (PMID _33857425)

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit according to the manufacturer's instructions.
Libraries were prepared from 110 ng RNA using the QuantSeq 3' mRNA Library Prep Kit for Illumina according to the manufacturer's protocol.

treatment_protocol: Cells were untreated or treated with 10 ng/µL recombinant murine BMP-4 (Peprotech) for 24 h.

tag: tissue

value: Brain

value: NPE

value: Glioblastoma stem cell

value: NF1-/- Pten-/- Egfrviii+

value: BMP-4 10ng/mL 24 h


title: ILK_Rx_BMP_3


title: SWI3_DTT_R2_MNase


title: SWI3_DTT_R1_MNase


title: SNF2_DTT_R2_gDNA

value: snf2[delta]; SNF2-3V5::LEU2


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01063

value: minimal medium at 8 h


title: E. coli K-12 MG1655 grown in a minimal medium at 8 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01062


title: CUTO27_Criz1

value: Lung adenocarcinoma


title: SWI3_DTT_R1_gDNA


title: ILK_Rx_BMP_1


title: CUTO27_Ctl2

value: DMSO


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01061

value: minimal medium at 6 h


title: ILK_KO_BMP_4

value: ILK-/- NF1-/- Pten-/- Egfrviii+


title: CUTO28_Ctl1


title: E. coli K-12 MG1655 grown in a minimal medium at 6 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01060


title: ILK_KO_BMP_3


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01059

value: minimal medium at 4 h


title: CUTO27_Ctl1


title: SNF2_DTT_R1_gDNA

value: undigested gDNA. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: SNF2_DTT_R2_MNase

value: MNase. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: CUTO23_Criz3

description: CUTO23 crizotinib IC50 is 88 nM (measured by 3-day MTS assay).


title: CUTO27_Criz2


title: SNF2_DTT_R1_MNase


title: ILK_KO_BMP_1


title: ILK_Rx_BMP_2


title: E. coli K-12 MG1655 grown in a minimal medium at 4 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01058

value: MG1655 Wildtype


title: CUTO27_Ctl3


title: snf2Q928K_untreated_R2_gDNA

value: snf2[delta]; snf2-Q928K-3V5::LEU2

value: undigested gDNA. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: CUTO23_Criz2

value: 250 nM crizotinib


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, replicate 2

description:
Total RNA with depleted ribosomal RNA
p1k_01057

value: Glucose

value: minimal medium at 3 h


title: CUTO23_Ctl3


title: snf2Q928K_untreated_R1_gDNA


title: E. coli K-12 MG1655 grown in a minimal medium at 3 h, replicate 1

description:
Total RNA with depleted ribosomal RNA
p1k_01056


title: CUTO23_Ctl2


title: NPE_BMP_3

value: Brain

value: NPE

value: Glioblastoma stem cell

value: NF1-/- Pten-/- Egfrviii+


title: snf2Q928K_untreated_R2_MNase

value: MNase. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: snf2Q928K_untreated_R1_MNase


title: NPE_BMP_2

value: BMP-4 10ng/mL 24 h


title: snf2W935R_untreated_R2_gDNA

value: snf2[delta]; snf2-W935R-3V5::LEU2


title: Tetraploid L4 worms, Doxorubicin-treated, Rep 2

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
Novogene performed data analysis in the Novogene platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignments were performed with HISAT2 v2.0.5 by Novogene
Differentially expressed genes were determined with the R package DESeq2
Assembly: wbcel235

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: C. elegans were cultured at 15C on K-agar plates with OP50 E. coli bacteria seeded for a food source.

extract_protocol:
C elegans lysates were prepared by homogenization in the bullet blender and RNA was isolated using the RNeasy Qiagen kit with the optional DNaseI step
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Drugs were added to the seeded plate and allowed to dry at 30C for 1 hr before cooling to 15C and adding worms.

value: Whole Animal

value: Tetraploid N2 strain

value: L4 larval stage

value: Wild-Type (N2)

value: Doxorubicin 5 uM


title: NPE_BMP_1


title: Tetraploid L4 worms, Doxorubicin-treated, Rep 3


title: ILK_Rx_4

value: Ctl


title: ILK_KO_BMP_2

value: ILK-/- NF1-/- Pten-/- Egfrviii+


title: CUTO23_Ctl1

value: Lung adenocarcinoma

value: DMSO


title: Tetraploid L4 worms, Doxorubicin-treated, Rep 1


title: snf2W935R_untreated_R2_MNase


title: CNV_C1

city: Iowa City

first: Andrew

middle: P

last: Voigt

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build GRCh38 with CellRanger (v7.0.0) using the CellRanger human GTF
Assembly: GRCh38
Supplementary files format and content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.csv) and processed/normalized (*_normalized.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

extract_protocol:
From the right eyes of both donors, a 4 mm diameter macular punch was collected centered on the fovea centralis, as was a 4 mm peripheral punch approximately 12 mm superotemporal from the macula. Both central and peripheral punches (spanning retina, choroid and sclera) were placed in optimal cutting temperature compound (OCT) and were rapidly snap frozen in liquid nitrogen and stored at -80C
Sequencing was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Spatial RNA-Seq

tag: disease

value: MNV


title: snf2W935R_untreated_R1_gDNA

value: undigested gDNA. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: Tetraploid L4 worms, Cisplatin-treated, Rep 3

value: Cisplatin 5 uM


title: ILK_Rx_3

value: Brain

value: NPE

value: Glioblastoma stem cell


title: Tetraploid L4 worms, Cisplatin-treated, Rep 2


title: NPE_BMP_4

value: NF1-/- Pten-/- Egfrviii+

value: BMP-4 10ng/mL 24 h


title: ILK_Rx_2


title: CUTO23_Criz1

value: 250 nM crizotinib


title: snf2W935R_untreated_R1_MNase

value: snf2[delta]; snf2-W935R-3V5::LEU2

value: MNase. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: CNV_B1


title: CNV_A1


title: ILK_Rx_1


title: Control_D1

value: control


title: swi3E815X_untreated_R2_gDNA


title: Tetraploid L4 worms, Vehicle-treated, Rep 3

value: Whole Animal

value: Tetraploid N2 strain

value: L4 larval stage

value: Wild-Type (N2)

value: Vehicle (9 mg/ml NaCl, pH 3.6)


title: swi3E815X_untreated_R2_MNase


title: Tetraploid L4 worms, Vehicle-treated, Rep 2


title: Tetraploid L4 worms, Vehicle-treated, Rep 1


title: ILK_KO_3

value: ILK-/- NF1-/- Pten-/- Egfrviii+

value: Ctl


title: ILK_KO_2


title: Patient 14 HSPCs, mRNA-derived cDNA

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Fluent PIPseq
matrix_patient14.mtx
barcodes_patient14.tsv

library_source: transcriptomic single cell

data_processing:
FASTQ files from single-cell CITEseq were processed via the Fluent Cloud Platform. This analysis platform trims adapter sequences, demultiplexes sequencing data into single cells matched against a list of known barcodes, maps reads against the GRCh38.p13 reference transcriptome, and separates putative cells from background.
Genes were filtered if detected in <3 cells and cells were filtered based on having low-complexity libraries (feature count < 200) or high mitochondrial content (>15%).
Downstream bioinformatics analysis, including scaling and log-normalization of single-cell transcriptional data and centered-log ratio normalization of single-cell protein expression data, was performed using Seurat 4.3.0. Across all samples, data integration was performed using reciprocal principal component analysis (RPCA).
Supplementary files format and content: matrix files (.mtx)
Supplementary files format and content: tab-separated values files (.tsv)

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
We performed SC CITEseq sequencing on unsorted mononuclear cells from 12 patients using a pre-templated instant partitions (PIPs) sequencing platform.
Briefly, cryopreserved cells were thawed, normalized combined in a 1:10 ratio with barcoded PIPs, which were then vortexed and centrifuged into emulsifications. Emulsions were thermocycled, broken, mixed, washed, and pelleted. Reverse transcription was performed, and cDNA synthesis completed. After whole transcriptome amplification, PIPs were column filtered and purified with Ampure XP. Libraries were generated from WTA amplified material using the Nextera XT DNA Library Preparation Kit with a custom primer (PIPs_P5library) and standard Nextera P7 indexing primers (N70x). Libraries were pooled and sequenced using an Illumina NextSeq 2000.

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: Patient 14 HSPCs, ADT-derived cDNA

library_source: other

molecule: protein


title: swi3E815X_untreated_R1_MNase


title: SWI3_untreated_R2_gDNA

value: undigested gDNA. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: Diploid L4 worms, Doxorubicin-treated, Rep 2

value: Diploid N2 strain

value: Doxorubicin 5 uM


title: Tetraploid L4 worms, Cispatin-treated, Rep 1

value: Cisplatin 5 uM


title: SWI3_untreated_R2_MNase


title: swi3E815X_untreated_R1_gDNA


title: Patient 11 HSPCs, mRNA-derived cDNA

description:
Fluent PIPseq
matrix_patient11.mtx
barcodes_patient11.tsv


title: NPE_2

value: Brain

value: NPE

value: Glioblastoma stem cell

value: NF1-/- Pten-/- Egfrviii+


title: Diploid L4 worms, Doxorubicin-treated, Rep 3

value: Whole Animal


title: Diploid L4 worms, Cisplatin-treated, Rep 3


title: Patient 11 HSPCs, ADT-derived cDNA


title: NPE_3


title: Patient 8 HSPCs, mRNA-derived cDNA

description:
Fluent PIPseq
matrix_patient8.mtx
barcodes_patient8.tsv


title: NPE_4


title: Patient 8 HSPCs, ADT-derived cDNA


title: SWI3_untreated_R1_gDNA


title: ILK_KO_4


title: Control_A1

value: control


title: Diploid L4 worms, Doxorubicin-treated, Rep 1

value: L4 larval stage


title: SWI3_untreated_R1_MNase

value: MNase. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: ILK_KO_1


title: NPE_1


title: Patient 4 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient4.mtx
barcodes_patient4.tsv


title: SNF2_untreated_R2_gDNA

value: snf2[delta]; SNF2-3V5::LEU2


title: SNF2_untreated_R2_MNase


title: Patient 4 HSPCs, mRNA-derived cDNA


title: Diploid L4 worms, Cispatin-treated, Rep 1

value: Wild-Type (N2)


title: Patient 1 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient1.mtx
barcodes_patient1.tsv


title: SNF2_untreated_R1_gDNA


title: Diploid L4 worms, Vehicle-treated, Rep 2

value: Vehicle (9 mg/ml NaCl, pH 3.6)


title: Diploid L4 worms, Vehicle-treated, Rep 1


title: BALB/cJ primary, ENPP1-T238A-OE 4T1, biol rep 2

city: Palo Alto

first: FEIQIAO

middle: Brian

last: YU

address: 3181 Porter Dr.

department: Multi-Omics

institute: Arc Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Ensembl release 93 GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary tumor

extract_protocol:
Mammary fat pad primary tumors and lungs containing metastases were harvested from two ENPP1WT-OE or ENPP1T238A-OE tumor bearing mice when primary tumors reached 1000 mm^3. Cryopreserved single cell suspensions were thawed into warm RPMI media with 10% HI-FBS. Cells were washed with PBS and 0.04% w/v BSA, passed through 40 m Flowmi cell strainer (Bel-Art, 974-25244), and assessed for concentration and viability with an automated cell counter. Viability varied between 72-87% for tumor samples and 91-96% for lung samples. Cells were resuspended in PBS and 0.04% w/v BSA to 1000 cells/uL.
Library was performed according to the manufacter’s instructions (single cell 3’ HT reagent kits v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: BALB/cJ

tag: Sex

value: Female

value: 6 weeks

value: Mammary tumor

value: 4T1 Enpp1-KO ENPP1-T238A-OE

value: Murine breast cancer

value: WT


title: BALB/cJ metastasis, ENPP1-T238A-OE 4T1, biol rep 2

source_name: Lung

value: Lung


title: Diploid L4 worms, Cisplatin-treated, Rep 2

value: Diploid N2 strain

value: Cisplatin 5 uM


title: BALB/cJ metastasis, ENPP1-WT-OE 4T1, biol rep 2

value: 4T1 Enpp1-KO ENPP1-WT-OE


title: Patient 1 HSPCs, mRNA-derived cDNA

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: BALB/cJ primary, ENPP1-WT-OE 4T1, biol rep 2


title: LS_183_HAM_2h +Mtb

city: San Antonio

first: Larry

middle: S

last: Schlesinger

state: TX

address: 8715 W. Military Dr

department: Host-Pathogen Interaction Program

institute: Texas Biomedical Research Institute

data_processing:
CLC Genomics Workbench v 20.0
Low-quality sequences and adapters were trimmed.
Trimmed reads were mapped to the human hg38 reference genome.
The reads were assigned to the transcripts using the EM algorithm.
The TMM normalization  in EdgeR and multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM) were carried out for differential expression analysis.
Assembly: hg38
Supplementary files format and content: Ch2+vsCh2-RawCounts.xlsx
Supplementary files format and content: Ch72+VsCh72-RawCounts.xlsx
Supplementary files format and content: Ch24+VsCh24-RawCounts.xlsx

source_name: Bronchoalveolar lavage fluid

growth_protocol: Human alveolar macrophges (HAMs) were isolated from bronchoalveolar lavage fluid, and plated in 96-well Falcon tissue culture plates in 20% autologous plasma in humidified atmosphere with 5% CO2 at 37C  for 2hrs to allow HAMs to adhere. Non-adhering cells were removed by washing with RMPI-HEPES (Sigma).

extract_protocol:
Cells were retrieved from plates using 5mM EDTA (Sigma) and incubating the cells on ice for 30mins. Cells were stored in RNALater (Invitrogen) at -80C. Prior to shipment the cells were spun down and RNALater replaced with Trizol. RNA was isolated using Quick-RNA Microprep Kit (R1050; Zymo Research) as per the manufacturer’s instructions. Isolated RNA was quantified using the Qubit RNA High Sensitivity Assay Kit (Q32852) and Qubit 4 Fluorometer (both from ThermoFisher Scientific).
RNA sequencing libraries were prepared from 25-500ng of Total RNA using the NEB Next directional RNA library preparation Kit with poly (A) enrichment module (Ipswich, MA).
stranded RNA-seq

treatment_protocol: HAMs were infected with H37Rv Mtb (MOI 1:1) for 2hrs and unbound Mtb washed away with RPMI-HEPES. Cells were then maintanained in RMPI supplemented with 2mM glutamine and 20% human AB serum (Celtic Molecular Diagnostics).

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Mtb infected

tag: time

value: 2h post infection


title: Patient 7 HSPCs, mRNA-derived cDNA

description:
Fluent PIPseq
matrix_patient7.mtx
barcodes_patient7.tsv


title: Patient 7 HSPCs, ADT-derived cDNA


title: SNF2_untreated_R1_MNase

value: snf2[delta]; SNF2-3V5::LEU2

value: MNase. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: BALB/cJ primary, ENPP1-T238A-OE 4T1, biol rep 1

value: BALB/cJ

value: Female

value: 6 weeks


title: Patient 2 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient2.mtx
barcodes_patient2.tsv


title: snf2Q928K_DTT_R2_input

data_processing:
Spike in normalization was performed according to SNP-ChIP pipeline from Vale-Silva et al., 2019
reads were aligned to the sacCer3 reference genome using Bowtie
MACS2 was used to generate bedGraph files for ChIP samples normalized to input
bedGraph files were adjusted by multiplying read depth at each position with the calculated SNP-ChIP normalization factor for each sample
Spike-in adjusted, normalized bedGraph files were converted to BigWig files using deeptools
Assembly: sacCer3 (R64)
Supplementary files format and content: BigWig (.bw) files scaled using SNP-ChIP spike-in normalization for visualization in IGV

extract_protocol:
Cells were fixed in 1% formaldehyde, lysed in FA lysis buffer with beadbeating, chromatin was extracted by fractionation and sheared using a Bioruptor Pico (see Morse et al., 2023 materials and methods for further details).
DNA libraries were prepared using a NEXTflex Rapid DNA-Seq Kit 2.0 bundle.

treatment_protocol: Spike-in cells from an SK1 strain harboring a SNF2-3V5 allele were added at a ratio of 1:5 to each sample prior to immunoprecipitation. IP samples were immunoprecipitated using anti-V5 agarose beads (see Morse et al., 2023 materials and methods for details).

tag: antibody

value: snf2[delta]; snf2-Q928K-3V5::LEU2

value: input. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: snf2Q928K_DTT_R1_input


title: snf2Q928K_DTT_R2_ChIP

value: IP. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: snf2Q928K_DTT_R1_ChIP


title: LS_181_HAM_72h +Mtb

value: 72h post infection


title: BALB/cJ metastasis, ENPP1-WT-OE 4T1, biol rep 1

value: Lung

value: Murine breast cancer

value: WT


title: BALB/cJ metastasis, ENPP1-T238A-OE 4T1, biol rep 1

value: 4T1 Enpp1-KO ENPP1-T238A-OE


title: LS_178_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Uninfected

value: 2h post culture


title: Patient 2 HSPCs, mRNA-derived cDNA

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: Diploid L4 worms, Vehicle-treated, Rep 3

value: Whole Animal

value: Diploid N2 strain

value: L4 larval stage

value: Wild-Type (N2)

value: Vehicle (9 mg/ml NaCl, pH 3.6)


title: snf2W935R_DTT_R2_input

value: snf2[delta]; snf2-W935R-3V5::LEU2

value: input. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: Patient 12 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient12.mtx
barcodes_patient12.tsv


title: BALB/cJ primary, ENPP1-WT-OE 4T1, biol rep 1

value: BALB/cJ

value: Female

value: 6 weeks

value: Mammary tumor

value: 4T1 Enpp1-KO ENPP1-WT-OE


title: LS_177_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Mtb infected

value: 2h post infection


title: LS_182_HAM_72h -Mtb

value: Uninfected

value: 72h post culture


title: Patient 12 HSPCs, mRNA-derived cDNA

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: snf2W935R_DTT_R2_ChIP

value: IP. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: snf2W935R_DTT_R1_input


title: LS_170_HAM_2h -Mtb

value: 2h post culture


title: LS_164_HAM_24h -Mtb

value: 24h post culture


title: Patient 5 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient5.mtx
barcodes_patient5.tsv


title: snf2W935R_DTT_R1_ChIP

value: snf2[delta]; snf2-W935R-3V5::LEU2


title: LS_163_HAM_24h +Mtb

value: 24h post infection


title: Patient 5 HSPCs, mRNA-derived cDNA


title: swi3E815X_DTT_R2_input

value: input. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: Patient 3 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient3.mtx
barcodes_patient3.tsv


title: LS_161_HAM_2h +Mtb


title: Patient 3 HSPCs, mRNA-derived cDNA


title: IL-10 + Fedratinib, 2 H, biol rep 1

city: Pittsburgh

first: Rachel

middle: A.

last: Gottschalk

state: Pennsylvania

address: 200 Lothrop St., W1047 BST

department: Immunology

institute: University of Pittsburgh

data_processing:
Rsubread was used for the file alignment and read counting
DESeq2 was used for normalization
Assembly: mm10
Supplementary files format and content: JAK2i_DESeq2_normalizedCounts.csv

source_name: primary macrophages

growth_protocol: Cells were cultured for six days in DMEM with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 U/ml), 2 mM l-glutamine, and 20 mM Hepes supplemented with recombinant mouse M-CSF (60 ng/ml) at 37C.

extract_protocol:
RNA was extracted with the Direct-zol RNA MicroPrep Kit (Zymo Research).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep protocol.
Final libraries were sequenced on the NextSeq2000 (Illumina)

treatment_protocol: On day 7, BMDM were stimulated with the appropriate dose of IL-6 or IL-10 at the specified time and lysed with TRIzol Reagent (Ambion) for RNA isolation.Fedratinib-treated samples were pre-treated with 1 nM of inhibitor 20 minutes prior to cytokine stimulation.

value: Female

value: 8-12 weeks

value: BMDM

value: primary macrophages

value: WT

value: IL-10 + Fedra

value: 2 H


title: IL-10 + Fedratinib, 1 H, biol rep 1

value: 1 H


title: IL-10, 1 H, biol rep 2


title: IL-10, 2 H, biol rep 2


title: Patient 6 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient6.mtx
barcodes_patient6.tsv


title: IL-10 + Fedratinib, 2 H, biol rep 2


title: IL-10, 2 H, biol rep 1


title: Patient 6 HSPCs, mRNA-derived cDNA


title: LS_152_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Uninfected


title: LS_151_HAM_24h +Mtb

value: Mtb infected


title: IL-10, 1 H, biol rep 1


title: IL-10 + Fedratinib, 1 H, biol rep 2


title: Patient 9 HSPCs, ADT-derived cDNA

description:
Fluent PIPseq
matrix_patient9.mtx
barcodes_patient9.tsv

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: LS_169_HAM_2h +Mtb

value: 2h post infection


title: SWI3_DTT_R2_input


title: LS_149_HAM_2h +Mtb


title: Patient 9 HSPCs, mRNA-derived cDNA


title: IL-6 + Fedratinib, 2 H, biol rep 2

value: IL-6 + Fedra


title: LS_146_HAM_72h -Mtb

value: 72h post culture


title: swi3E815X_DTT_R2_ChIP

value: IP. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: M6 HSPCSs, ADT-derived cDNA

description: Mission Bio Tapestri

data_processing:
FASTQ files from single-cell DAbseq samples were processed via an open-source pipeline. This analysis pipeline trims adaptor sequences, demultiplexes DNA panel amplicons and antibody tags into single cells, and aligns panel reads to the hg19 reference genome. Valid cell barcodes were called using the inflection point of the cell-rank plot in addition to the requirement that 60% of DNA intervals were covered by at least eight reads. Variants were called using GATK (v 4.1.3.0) according to GATK best practices. ITDseek was used to detect FLT3 internal tandem duplication (ITD) from amplicon sequencing reads. For each valid cell barcode, variants were filtered according to quality and sequence depth reported by GATK, with low quality variants and cells excluded based on the cutoffs of quality score < 30, read depth < 10, and alternate allele frequency < 20%. Cell-surface protein reads were normalized using centered log ratio transformation.
To de-multiplex individual patients combined into a single sample, we used a novel computational approach incorporating both patient-specific anti-CD45 oligo-conjugated “hash” antibody tags as well as single nucleotide polymorphisms (SNPs) covered by the SC DNA panel. Individual samples were multiplexed together into groups of 3 and all SNPs were treated as binary (mutated or wildtype). For each multiplexed run, to identify SNPs that maximally differ between samples we filtered all SNPs mutated in <10% or >80% of cells. We performed a series of hierarchical clustering steps to further refine antibody hash data.
Assembly: hg19
Supplementary files format and content: hdf5 files
Supplementary files format and content: h5ad files
Library strategy: DAbseq

extract_protocol:
We performed DAbseq on unsorted mononuclear cells from 14 patients using a microfluidic approach with molecular barcode technology using the Tapestri platform (MissionBio) as previously described .
Briefly, cryopreserved cells were blocked and stained with a pool of 22 oligo-conjugated antibodies. Individual samples were also incubated with unique anti-CD45 oligo-conjugated antibodies to provide sample-level identifiers, and groups of 2-3 individual patients were pooled together for multiplexed runs. Pooled samples were run through Mission Bio Tapestri platform as previously described. DNA from barcoded cells was amplified via PCR using a targeted panel that included 127 amplicons across 20 genes associated with acute leukemia. DNA PCR products were isolated and purified with standard library preparation protocol. Protein PCR products were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD), and purified using Streptavidin C1 beads.


title: SWI3_DTT_R2_ChIP


title: IL-6 + Fedratinib, 1 H, biol rep 2

value: Female

value: 8-12 weeks


title: LS_145_HAM_72h +Mtb

value: 72h post infection


title: Control for Fedratinib 2, biol rep 2

value: BMDM

value: primary macrophages

value: WT

value: Control

value: 0 H


title: M4 HSPCSs, ADT-derived cDNA

description: Mission Bio Tapestri


title: LS_144_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: 24h post culture


title: M5 HSPCs, barcode-derived cDNA

description: Mission Bio Tapestri

value: Bone Marrow/Peripheral Blood


title: IL-6, 2 H, biol rep 2

value: 2 H


title: swi3E815X_DTT_R1_input

value: input. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: IL-6, 1 H, biol rep 2

value: 1 H


title: swi3E815X_DTT_R1_ChIP


title: SWI3_DTT_R1_input


title: SNF2_DTT_R2_input

value: snf2[delta]; SNF2-3V5::LEU2


title: SWI3_DTT_R1_ChIP

value: IP. Cells grown in YPD to late-log phase, treated with 5 mM DTT for 1 hour, and fixed in 1% formaldehyde.


title: M3 HSPCs, barcode-derived cDNA

description: Mission Bio Tapestri

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: LS_142_HAM_2h -Mtb

value: Uninfected

value: 2h post culture


title: SNF2_DTT_R2_ChIP


title: Control for Fedratinib 1, biol rep 2

value: Female

value: 8-12 weeks

value: BMDM


title: SNF2_DTT_R1_input


title: M2 HSPCSs, ADT-derived cDNA

description: Mission Bio Tapestri


title: LS_141_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: IL-6 + Fedratinib, 2 H, biol rep 1

value: primary macrophages

value: WT

value: IL-6 + Fedra


title: M1 HSPCs, barcode-derived cDNA

description: Mission Bio Tapestri

value: Bone Marrow/Peripheral Blood


title: IL-6 + Fedratinib, 1 H, biol rep 1


title: J3

city: Houston

first: Mary

last: Estes

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description: transwell monolayer

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: feature count comma separated file

source_name: Human jejunal enteroid

growth_protocol: Enteroids were generated from intestinal tissue samples using standard protocols. Enteroids were then grown in enteroid growth media during proliferation. Growth factors were withdrawn for differentiation.

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro kit according to the manufacturer's protocol.
Sequencing and library preparation was performed by Novogene

treatment_protocol: No specific treatments were performed on infant and adult enteroids

tag: segment

value: jejunum

tag: developmental stage

value: adult


title: SNF2_DTT_R1_ChIP


title: LS_126_HAM_72h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: 72h post culture


title: LS_143_HAM_24h +Mtb

value: 24h post infection


title: J2

description: transwell monolayer

tag: cell line


title: snf2Q928K_untreated_R2_input

value: snf2[delta]; snf2-Q928K-3V5::LEU2

value: Input. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: snf2Q928K_untreated_R2_ChIP

value: IP. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: J11

description: transwell monolayer


title: LS_124_HAM_24h -Mtb

value: Uninfected

value: 24h post culture


title: snf2Q928K_untreated_R1_input


title: LS_123_HAM_24h +Mtb

value: Mtb infected


title: IL-6, 1 H, biol rep 1

value: Female

value: 8-12 weeks

value: BMDM

value: 1 H


title: snf2Q928K_untreated_R1_ChIP


title: J1009

description: transwell monolayer

value: infant


title: IL-6, 2 H, biol rep 1

value: primary macrophages

value: WT

value: 2 H


title: J1006

description: transwell monolayer

value: jejunum


title: Control for Fedratinib 1, biol rep 1

value: Control

value: 0 H


title: LS_121_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: 2h post infection


title: Combo 10 ng/ml, 4 H, biol rep 2

data_processing:
Rsubread was used for the file alignment and read counting
DESeq2 was used for normalization
Assembly: mm10
Supplementary files format and content: STAT_final_DESeq2_normalizedCounts.csv

treatment_protocol: On day 7, BMDM were stimulated with the appropriate dose of IL-6 or IL-10 at the specified time and lysed with TRIzol Reagent (Ambion) for RNA isolation.

value: 4 H


title: snf2W935R_untreated_R2_input

value: snf2[delta]; snf2-W935R-3V5::LEU2

value: Input. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: J1005

description: transwell monolayer


title: LS_122_HAM_2h -Mtb

value: Uninfected

value: 2h post culture


title: snf2W935R_untreated_R2_ChIP

value: IP. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: LS_114_HAM_72h -Mtb

value: 72h post culture


title: snf2W935R_untreated_R1_input


title: LS_125_HAM_72h +Mtb

value: Mtb infected

value: 72h post infection


title: Control for Fedratinib 2, biol rep 1

value: Female

value: 8-12 weeks

value: BMDM

value: primary macrophages

value: WT


title: Combo 10 ng/ml, 2 H, biol rep 2

value: 2 H


title: LS_113_HAM_72h +Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage


title: Combo 10 ng/ml, 1 H, biol rep 2

value: 1 H


title: snf2W935R_untreated_R1_ChIP

value: snf2[delta]; snf2-W935R-3V5::LEU2


title: LS_112_HAM_24h -Mtb

value: 24h post culture


title: Combo 1 ng/ml, 4 H, biol rep 2

value: IL-6 + IL-10 1 ng/ml

value: 4 H


title: Donor4_PBMC+BTP2

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

data_processing:
Raw data from RNA sequencing experiments was aligned to the human genome (Assembly: GRCh37/hg19) using STAR short read aligner software (v-2.6)[51] for individual samples.
The gene expression counts for individual samples were estimated by setting the --quantMode argument to GeneCounts. The gene expression values for individual samples were compiled into a single table for downstream analysis.
Assembly: GRCh37/hg19
Supplementary files format and content: CSV file with gene expression count matrix

source_name: PBMC

growth_protocol: Peripheral venous whole blood was obtained from healthy volunteers after obtaining informed written consent. PBMC were isolated by density gradient centrifugation using Ficoll-PaqueTM centrifugation and suspended in complete medium composed of RPMI 1640 + L-Glutamine + HEPES (25mM), Penicillin (100 units/ml), and Streptomycin (0.1 mg/ml) and 5 % FBS (complete medium). PBMC were washed twice with PBS and the final wash performed with complete medium.

extract_protocol:
PBMCs were washed with PBS (1000µl) and centrifuged at 13,400g for 2 minutes in room temperature. The supernatant was discarded, and RNAlater (50µl) and Buffer RLT with β-mercaptoethanol (350µl) were added to the cell pellet. The pellet was mechanically lysed with a 1ml 25G 5/8 syringe. The lysate was transferred to a QIAshredder spin column and centrifuged at maximum speed for 2 minutes in room temperature. Total RNA was isolated from the lysate using RNeasy mini kit, according to the manufacturer’s protocol (Qiagen). The quantity (absorbance at 260nm) and purity (ratio of the absorbance at 260 and 280nm) of the total RNA isolated from the lysate were measured using the NanoDrop® ND-1000 UV-Vis spectrophotometer (Thermo Scientific).
The total RNA samples were treated with DNase using RNase-Free DNase kit (Qiagen) according to the manufacturer’s protocol to remove DNA prior to RNA sample library preparation and sequencing. The RNA libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina) and sequenced using NovaSeq 6000 System (Illumina) as 100 x 2 paired-end reads.

treatment_protocol: PBMC at 1x10^6/ml were incubated without PHA or BTP2 (control), with BTP2 (1000 nM), with PHA (2µg/ml), or with PHA (2µg/ml) + BTP2 (1000 nM) for 16 hours at 370C in 95% air and 5% CO2 atmosphere. Because DMSO was used to dissolve BTP2, DMSO was added to control PBMC and to PBMC stimulated with PHA.

tag: individual

value: PBMC


title: Donor4_PBMC+PHA+BTP2


title: Donor4_PBMC+PHA

value: PHA


title: LS_111_HAM_24h +Mtb

value: Mtb infected

value: 24h post infection


title: swi3E815X_untreated_R2_ChIP

value: IP. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: swi3E815X_untreated_R2_input

value: Input. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: LS_109_HAM_2h +Mtb

value: 2h post infection


title: Donor4_PBMC(Control)

value: DMSO


title: Combo 1 ng/ml, 2 H, biol rep 2

value: Female

value: 8-12 weeks

value: BMDM

value: primary macrophages

value: WT


title: Donor3_PBMC+PHA+BTP2


title: IL-10 10 ng/ml, 2 H, biol rep 2

value: IL-10 10 ng/ml

value: 2 H


title: H1N1-3

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

country: China

institute: Zijingang Campus of Zhejiang University

description: infected at MOI=10 and harvested at 18 hour post infection

data_processing:
The adaptors, low-quality reads and poly-N were removed by the Trim Galore_v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/). Quality control analysis was performed by Fast QC_v0.11.5 software
Clean reads were mapped to the human reference genome (version: Homo_sapiens. GRCh38) by STAR_v2.5.2b software suite.
CIRCexplorer2 was used to identify circRNAs
The transcripts were assembled with the mapped reads using Stringtie_v1.3.1
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited excel files include  normalized  values for each Sample

source_name: human lung epithelial cells

extract_protocol:
Total RNA was isolated by trizol reagent (Vazyme, China) according to the manufacturer’s instruction
Ribosomal RNAs were further removed by using ribo-zero-magnetic-kit (Epicentre, USA). RNAs were incubated with RNase R (Epicentre, USA), then purified by using AmpureBeads (Beckman, USA). RNA-seq libraries were prepared by using TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA) and were sequenced on Illumina Hiseq 3000 platform

treatment_protocol: A549 cells were infected with H1N1 at a multiplicity of infection (MOI) of 10 and harvested at 18 hour post infection or without, respectively.

tag: agent

value: infected with H1N1

value: A/Puerto Rico/8/34 (H1N1)


title: H1N1-2


title: Combo 1 ng/ml, 1 H, biol rep 2

value: IL-6 + IL-10 1 ng/ml

value: 1 H


title: swi3E815X_untreated_R1_input


title: swi3E815X_untreated_R1_ChIP


title: SWI3_untreated_R2_input


title: IL-10 10 ng/ml, 4 H, biol rep 2

value: 4 H


title: IL-10 10 ng/ml, 1 H, biol rep 2


title: SWI3_untreated_R2_ChIP


title: Donor3_PBMC+PHA

value: PBMC

value: PHA


title: IL-10 1 ng/ml, 4 H, biol rep 3

value: IL-10 1 ng/ml


title: A549-3

description: control

value: uninfected


title: SWI3_untreated_R1_input

value: Input. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde


title: A549-2

description: control


title: IL-10 1 ng/ml, 2 H, biol rep 2

value: Female


title: Donor2_PBMC+BTP2


title: Donor2_PBMC+PHA+BTP2


title: Donor3_PBMC(Control)

value: DMSO


title: A549-1

description: control


title: SWI3_untreated_R1_ChIP

value: IP. Cells grown in YPD to late-log phase and fixed in 1% formaldehyde.


title: IL-10 1 ng/ml, 1 H, biol rep 2

value: 8-12 weeks

value: BMDM

value: primary macrophages


title: Donor3_PBMC+BTP2


title: SNF2_untreated_R2_input

value: snf2[delta]; SNF2-3V5::LEU2


title: CM-P2-4h-3

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Calculated manually based on the method in the following paper. (Lee, J., Jang, H., Kang, W. H., & Yeom, S. I. (2023). Transcriptome analysis of pepper-phytophthora infestans interaction based on a pipeline of a simplified and effective RNA-seq analysis (PoRAS).)
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of FPKM/RPKM for each sample

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

value: WT

tag: timepoint


title: Donor2_PBMC(Control)


title: Donor2_PBMC+PHA


title: SNF2_untreated_R2_ChIP

city: Berkeley

first: Elçin

last: Ünal

institute: UC Berkeley

tag: strain


title: CM-P2-4h-1


title: SNF2_untreated_R1_input


title: H1N1-1

value: infected with H1N1

value: A/Puerto Rico/8/34 (H1N1)


title: IL-6 10 ng/ml, 2 H, biol rep 2

tag: cell type

value: IL-6 10 ng/ml

value: 2 H


title: Donor1_PBMC+BTP2

value: PBMC


title: Donor1_PBMC+PHA+BTP2


title: SNF2_untreated_R1_ChIP

tag: genotype


title: IL-6 10 ng/ml, 4 H, biol rep 2

tag: treatment

value: 4 H


title: CM-P2-3D-3


title: Donor1_PBMC+PHA

value: PHA


title: CM-P2-3D-2


title: DNRAR3: MD41

city: Nashville

first: Mark

last: de Caestecker

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

data_processing:
Aligned reads with STAR 2.5.0a, controlling for unannotated, non-canonical and rare junctions.
Read counting with HTSeq 0.6.1 in the intersection, non-empty mode
Differential expression analysis was performed using edgeR and limma
Gene set enrichment analysis wad done using clusterProfiler
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file, Raw counts output from HTSeq-count function

source_name: Kidney CD11B+ MACS sorted cells

growth_protocol: 10–12-week-old male PTEC DN RAR and CRE- control mice

extract_protocol:
Whole kidneys were harvested after cardiac perfusion with 0.9% saline, kidneys were finely minced in DMEM with 0.3mg/ml Liberase DL (Sigma/Roche) and homogenized at 37°C in MACS C-tubes using the gentle MACS dissociator (Miltenyi Biotec), digestion neutralized with PEB buffer (2 mM EDTA, 1% BSA in PBS), and cell suspension passed through 40μm cell strainer. Cells were then incubated with anti-mouse CD11b MACS beads (Miltenyi Biotech, 130-126-725) for 15 minutes, and CD11b+ cells separated by loading cells into MACS separator. The cell pellet was re-suspended in 350μl of buffer RLT (Qiagen), and RNA extracted with RNeasy Plus Mini Kits (Qiagen, 74134). RNA quality control was confirmed with RIN scores >7.9.
cDNA library preparation was performed using a polyA-selected library preparation kit by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility

treatment_protocol: Mice underwent bilateral renal pedicle clamping for 28 minutes, and were euthanized Day 3 after surgery

value: Kidney CD11B+ MACS sorted cells

value: PEPCK CRE+; Rosa26-LSL-RARaT403X

value: Day 3 after IRI-AKI


title: IL-6 10 ng/ml, 1 H, biol rep 2

value: Female

tag: age

value: 1 H


title: IL-6 1 ng/ml, 4 H, biol rep 2

value: 8-12 weeks

value: BMDM

value: IL-6 1 ng/ml


title: DNRAR2: MD40


title: CM-P2-3D-1

value: Leaves


title: Donor1_PBMC(Control)

value: DMSO


title: IL-6 1 ng/ml, 2 H, biol rep 2

value: primary macrophages

value: WT


title: Control 2, biol rep 2

value: Control

value: 0 H


title: CBLM-Evs

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

data_processing:
Original BAM files were converted into FASTQ format using Picard tools (SamToFastq command).
Reads shorter than 15 nt were removed from the raw FASTQ data using cutadapt software v1.18.
The reads were aligned to the custom curated human reference transcriptomes in a sequential manner using bowtie allowing 1 mismatch tolerance:  trimmed and size-selected reads were mapped to RNA species with low sequence complexity and/or high number of repeats: rRNA, tRNA, RN7S, snRNA, snoRNA/scaRNA, vault RNA, RNY as well as mitochondrial chromosome (mtRNA). All reads that did not map to the above RNAs were aligned sequentially to mature miRNA, pre-miRNA, protein-coding mRNA transcripts (mRNA), and long non-coding RNAs (lncRNAs). The numbers of reads mapped to each RNA type were extracted using eXpress software.
Assembly: Hg38
Supplementary files format and content: Excel file contains all mapped reads

extract_protocol:
RNA was extracted from bdEVs of eight brain regions by miRNeasy Mini Kit reagents (Qiagen 217004) and Zymo-Spin I Columns (Zymo Research C1003-50) according to the manufacturer’s instructions.
RNA was resuspended in 40 μL Rnase-free water, and 8 µl was used for small RNA libraries construction by the D-Plex Small RNA-seq Kit (Diagenode C05030001). Indexes were attached using the D-Plex Single Indexes for Illumina - Set A (Diagenode C05030010) according to the manufacturer’s protocol.

value: Brain

tag: region

value: cerebellum


title: DNRAR1: MD39

tag: tissue


title: IL-6 1 ng/ml, 1 H, biol rep 2


title: CM-P2-30m-3


title: CORP-Evs

value: corpus callosum


title: DN Cont3: MD38

value: Kidney CD11B+ MACS sorted cells

value: PEPCK CRE-; Rosa26-LSL-RARaT403X


title: CM-P2-4h-2


title: CM-P2-30m-2


title: Control 1, biol rep 2


title: DN Cont2: MD37

value: Day 3 after IRI-AKI


title: CM-P2-30m-1


title: DN Cont1: MD36


title: OCC-Evs

value: occipital gyrus


title: MED-Evs

value: medulla


title: Combo 10 ng/ml, 4 H, biol rep 1

value: Female

value: 8-12 weeks

value: 4 H


title: CM-P2-2D-3

value: Leaves


title: Combo 10 ng/ml, 2 H, biol rep 1

value: BMDM

value: 2 H


title: 3T3 cells, Input, Pus1 WT, Replicate B

city: Cambridge

first: Tony

last: Kouzarides

address: Wellcome/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
Raw RNA-Seq data were processed using the SeqImp pipeline (Davis et al, PMID: 23816787).
The SeqImp pipeline was configured with the mm10 assembly of the Mus musculus genome, the transcriptome annotation from Ensembl (v89) and the miRbase annotation of microRNAs (v21). The pipeline was executed with the default mouse miRNA configuration and default parameters, specifying the sequence of the 3' adapter used for library preparation (AGATCGGAAGAGCACACGTC).
Assembly: mm10
Supplementary files format and content: Raw count matrix in standard SeqImp tab-delimited output format. Rows represent miRNAs and columns represent different samples. The first row contains column names. For each sample, the table reports two count columns, one ending in “_Mapped_Reads” and the other ending in “_Unique_Reads”. The former reports the total number of reads mapping to the given miRNA. The latter instead reports the number of unique reads that map to the given miRNAs. The row labelled as “Mapped_library_depth” reports the total number of reads for each sample.

growth_protocol: NIH3T3 were cultured in DMEM (Invitrogen), supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSQ). Cell lines were obtained from the ATCC and tested negative for mycoplasma contamination.

extract_protocol:
Total RNA was purified from 3T3 cells using the miRNEasy mini kit (QIAGEN) according to the manufacturer’s instructions. Small RNAs were (< 200nt) size-fractionated using RNA Clean & Concentrator 5 column kits (Zymo), as per the manufacturer’s instructions.
NEBNext small RNA sequencing kit according to manufacturer’s protocol

value: fibroblast

value: WildType

value: Input


title: CM-P2-2D-2

value: WT


title: Combo 10 ng/ml, 1 H, biol rep 1

value: primary macrophages

value: 1 H


title: CM-P2-2D-1


title: 3T3 cells, Input, Pus1 WT, Replicate A


title: HIPPO-EVs

value: Brain

value: hippocampus


title: CM-P2-1D-3


title: Combo 1 ng/ml, 4 H, biol rep 1

value: IL-6 + IL-10 1 ng/ml


title: 3T3 cells, psi-IP, Pus1 WT, Replicate B

value: Pseudouridine Immunoprecipitation


title: Combo 1 ng/ml, 2 H, biol rep 1


title: ORB-EVs

value: orbitofrontal gyrus


title: CM-P2-1D-2


title: Combo 1 ng/ml, 1 H, biol rep 1

value: Female


title: CM-P2-1D-1


title: 3T3 cells, psi-IP, Pus1 WT, Replicate C


title: IL-10 10 ng/ml, 4 H, biol rep 1

value: 8-12 weeks

value: IL-10 10 ng/ml


title: IW0077_P

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

data_processing:
Data was demultiplexed and counted using Cell Ranger version 6.0.0
Cell Ranger output was analyzed using Seurat version 4.1.1

extract_protocol:
Biopsies were briefly washed with DMEM/15%FBS, minced, digested with dispase (5000 caseinolytic Units) followed by trypsin (0.25%). Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Esophageal mucosal biopsy

tag: esophagus region

value: Proximal

tag: disease state

value: Gastroesophageal Reflux Disease

tag: subject id


title: 3T3 cells, Input, Pus1 WT, Replicate C

value: fibroblast


title: IW0077_D

value: Distal


title: 3T3 cells, psi-IP, Pus1 WT, Replicate A

value: WildType


title: THAL-Evs

value: thalamus


title: CM-PC-1D-2

value: Leaves

value: WT


title: 3T3 cells, Input, Pus1 KD day3, Replicate C

value: Pus1 KnockDown 3 days

value: Input


title: IL-10 10 ng/ml, 2 H, biol rep 1

tag: Sex

value: BMDM

value: primary macrophages

tag: time

value: 2 H


title: IL-10 10 ng/ml, 1 H, biol rep 1

value: Female

value: 1 H


title: IW0076_P


title: 3T3 cells, psi-IP, Pus1 KD day3, Replicate A

value: Pseudouridine Immunoprecipitation


title: CM-PC-1D-1


title: POSTCENTRAL-Evs

value: Brain

value: postcentral gyrus


title: IL-10 1 ng/ml, 4 H, biol rep 1

value: 8-12 weeks

value: IL-10 1 ng/ml

value: 4 H


title: 3T3 cells, Input, Pus1 KD day3, Replicate A

value: fibroblast


title: 3T3 cells, Input, Pus1 KD day3, Replicate B


title: IW0071_P

value: Esophageal mucosal biopsy

value: Proximal

value: Gastroesophageal Reflux Disease


title: IL-10 1 ng/ml, 2 H, biol rep 1

value: WT


title: IL-10 1 ng/ml, 1 H, biol rep 1


title: IW0065_D

value: Distal


title: 3T3 cells, Input, Pus1 KD day6, Replicate A

value: Pus1 KnockDown 6 days

value: Input


title: CM-PC-12h-1

value: Leaves


title: Control 2, biol rep 1

value: Female

value: BMDM

value: primary macrophages

value: Control

value: 0 H


title: IW0065_P


title: CM-PC-1D-3


title: 3T3 cells, Input, Pus1 KD day6, Replicate B


title: HEK SCZ MPRA Rep 7

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

description: Barcoded RNA

data_processing:
The variant and barcode region of the AAV-variant-barcode library was PCR amplified using NEBNext 2X Q5 Hifi HS Mastermix with primers that contain Illumina P5 and P7 adapters (Bcmap_P5_AAV_R and Bcmap_P7_AAV_F). The PCR product was cleaned up using Zymo PCR clean and concentrator-5. The resulting library was sequenced using custom sequencing primers (BCmap_R1Seq_AAV_R and BCmap_R2Seq_AAV_F) via Novaseq 6000 SP (2x250bp) by the UNC High-Throughput Sequencing Facility (HTSF). Barcodes were assigned to each variant using the custom code available in the github repository (https://github.com/kiminsigne-ucla/bc_map).
Using the barcode-variant relationship decoded from the barcode mapping step, RNA and DNA barcodes from RNA- and DNA-sequencing were mapped back to their corresponding variants. We counted the number of barcodes mapped to each variant and found that each variant was mapped to ~1000 barcodes on average. Next, we aggregated the RNA and DNA barcode counts for each variant. Because different combinations of barcodes could be introduced to different biological replicates, using the same DNA counts measured from the AAV-MPRA library for all biological replicates could lead to incorrect normalization. To mitigate this, if a given RNA barcode was missing in one biological replicate, that barcode was not counted in aggregating DNA counts for that replicate. This way, even when the DNA from the AAV-MPRA library was used, each biological replicate could have different DNA barcode counts guided by RNA barcodes. For example, if barcodes 1, 2, and 3 were mapped to the variant1, and barcode 2 was missing from the RNA barcode count, we would simply sum up the counts for barcodes 1 and 3 for both DNA and RNA. In contrast, if none of the barcodes were measured, that corresponding variant will have NA count. After merging both DNA and RNA counts by those criteria, we discarded any variants that had more than eight NAs across ten replicates.
Assembly: hg19
Supplementary files format and content: Aggregated RNA and DNA counts

molecule: other

source_name: Human embryonic kidney

growth_protocol: Donor number 54 was used for all experiments. 6-well plates were coated with PBS with Poly-L-Ornithine (10 μg/ml; Sigma-Aldrich, cat#P3655-100MG) and PBS with fibronectin (5 μg/ml; Sigma-Aldrich, cat#F1141-5MG). HEKs were plated at 400K cells/well. The cells were plated in Neurobasal A media (Thermo Fisher, cat#10888022) supplemented with primocin (100 μg/ml; Invitrogen, cat#ant-pm-2), BIT 9500 (10%; STEMCELL, cat#09500), glutamax 100X (1%; Fisher Scientific, cat#5112367), Heparin (1 μg/ml; Sigma-Aldrich, cat#H3393-100KU), and growth factors: EGF (20 μg/ml; PeproTech, cat#AF-100-15), FGF (20 μg/ml; PeproTech, cat#AF-100-15), PDGF (20 ng/ml; PeproTech, cat#100-00AB), and LIF (2 ng/ml; PeproTech, cat# 300-05).

extract_protocol:
RNA was extracted from each well using Qiagen RNeasy kit (Qiagen, cat#74004), using 10 uL of -Mercaptoethanol (Sigma-Aldrich, cat#60-24-2) per 1 mL of Qiagen RLT buffer. The columns were treated with DNase (Qiagen, cat#79256). To acquire an initial input of DNA put into the cells, DNA was extracted from the AAV2 virus which contained the AAV-MPRA library using a NucleoSpin virus kit (Macherey-Nagel, cat#740983.50).
The AAV-variant-minP-GFP-barcode library was grown in 2 L of LB with ampicillin, and maxi prepped using Qiagen Maxi prep kit.  The UNC vector core packaged the AAV-variant-minP-GFP-barcode library into AAV serotype 2 (AAV2). The resulting virus had the titer of 7x1012 viral particles/uL. After cellular transfection and RNA extraction, cDNA was generated from the extracted RNA by SuperScript IV Reverse Transcriptase (Invitrogen, cat#18090050) using a primer that targets downstream of the barcodes. DNA extracted from the AAV-MPRA library and cDNA from each transduced well were amplified via PCR using NEBNext 2X Q5 Hifi HS Mastermix. The samples were cleaned up using Zymo clean and concentrator-5. This was followed by the second amplification step to add on sequencing adaptors and unique Illumina indices. Again, NEBNext 2X Q5 Hifi HS Mastermix was used for amplification. The resulting libraries were cleaned up using 0.75X ampure beads (Beckman Coulter, cat#A63881) and sequenced by UNC HTSF via Novaseq 6000 SP (1x35bp), with custom primers that capture the barcode sequence and sequencing index.

treatment_protocol: each well was transduced with the AAV-MPRA library at 7,000 multiplicity of infection (MOI). One well per plate was a no-virus control to monitor general cell health. After the AAV-MPRA library was added to the cells, the plates were spun in a centrifuge for 5 minutes at 37°C at 1000 rcf. Cells were half-fed with 2X growth factors every other day for two weeks after transduction.

value: Human embryonic kidney


title: 3T3 cells, psi-IP, Pus1 KD day3, Replicate B

value: Pus1 KnockDown 3 days

value: Pseudouridine Immunoprecipitation


title: IW0076_D


title: IL-6 10 ng/ml, 2 H, biol rep 1

value: 8-12 weeks

value: IL-6 10 ng/ml

value: 2 H


title: CM-PC-6h-3


title: IL-6 10 ng/ml, 1 H, biol rep 1

value: 1 H


title: CM-PC-6h-2

value: WT


title: IL-6 10 ng/ml, 4 H, biol rep 1

value: 4 H


title: HEK SCZ MPRA Rep 5

description: Barcoded RNA


title: IW0071_D

value: Esophageal mucosal biopsy

value: Distal

value: Gastroesophageal Reflux Disease


title: 3T3 cells, Input, Pus1 KD day6, Replicate C

value: fibroblast

value: Pus1 KnockDown 6 days

value: Input


title: HEK SCZ MPRA Rep 6

description: Barcoded RNA


title: CM-PC-12h-3

value: Leaves


title: CM-PC-4h-3


title: CM-PC-6h-1


title: CM-PC-12h-2


title: IL-6 1 ng/ml, 4 H, biol rep 1

value: Female

value: BMDM

value: primary macrophages

value: IL-6 1 ng/ml


title: 3T3 cells, psi-IP, Pus1 KD day6, Replicate B

value: Pseudouridine Immunoprecipitation


title: CM-PC-4h-1


title: HEK SCZ MPRA Rep 3

description: Barcoded RNA

value: Human embryonic kidney


title: HEK SCZ MPRA Rep 4

description: Barcoded RNA


title: CM-PC-4h-2


title: IL-6 1 ng/ml, 2 H, biol rep 1

value: 8-12 weeks

value: 2 H


title: Control 1, biol rep 1

value: WT

value: Control

value: 0 H


title: 3T3 cells, psi-IP, Pus1 KD day6, Replicate C


title: CM-PC-2h-3


title: 3T3 cells, psi-IP, Pus1 KD day3, Replicate C

value: Pus1 KnockDown 3 days


title: HEK SCZ MPRA Rep 1

description: Barcoded RNA


title: HEK SCZ MPRA Rep 2

description: Barcoded RNA


title: CM-PC-2h-2


title: sample.sss2

city: West Lafayette

first: Kyle

middle: A

last: Cottrell

state: IN

address: 201 S University Street

institute: Purdue University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Gene counts, including transposable elements, were determined using the TEcount function from Tetranscripts using a GTF containing transposable elements from RepeatMasker, GRCh38_Ensembl_rmsk_TE.gtf, Jin Y., Tam O.H., Paniagua E. and Hammell M. (2015). TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 31: 3593-3599. Pubmed ID: 26206304
Assembly: GRCh38.101
Supplementary files format and content: gene level count data, Tab-separated values
Supplementary files format and content: gene level count data including transposable elements from repeatmasker, Tab-separated values

source_name: SK-BR-3, shSCR + shSCR

growth_protocol: All cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone) with 10% fetal bovine serum (Invitrogen), 2 mM glutamine (Hyclone), 0.1 mM nonessential amino acids (Hyclone), and 1 mM sodium pyruvate (Hyclone).

extract_protocol:
RNA was isolated using the NucleoSpin RNA, Mini kit for RNA purification from Macherey-Nagel per manufacturers instructions
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were transduced with lentivirus for 16 hours in the presence of 10 µg/mL protamine sulfate. The cells were selected with puromycin at 2 µg/mL and 150 μg/mL hygromycin (Invitrogen). Transductions were done sequentially, shSCR or shADAR1, followed by shSCR or shDHX9

value: cell line, breast cancer

value: control knockdown

value: transduced with scramble control shRNA


title: sample.sss1


title: snRNA-seq of 23hpf S. purpuratus embryos

city: PITTSBURGH

first: Hinman

last: Veronica

state: PA

address: 587 S Negley Ave, Apt 17

department: Biological Sciences

institute: Carnegie Mellon University

description: 10X Genomics

data_processing:
Cell Ranger V4.0.0 (Zheng et al., 2017) was used to create  aligned to a pre- mRNA indexes for P. miniatagenome V3.0 (GenBank assembly accession: GCA_015706575.1) andS. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4). The pre-mRNA indices were constructed using gene annotation files modified by an in-house script to remove intron annotations. Read were aligned using the cellranger count command. The raw, unfiltered count files are presented in this GEO entry. In the P. miniata entries, note that when applicable, the gene names are consistant with the names of their 1:1 othologs in S. purpuratus, as is consistant with the gene page naming system of echinobase.org
A Standard Seurat processing pipeline (V4.2.0 ) was used to prepare the final .RDS atlases provided in this entry.
Assembly: P miniatagenome V3.0 (GenBank assembly accession: GCA_015706575.1); S. purpuratusgenome V5.0 (GenBank assembly accession: GCA_000002235.4)
Supplementary files format and content: annotated and processed S. purpuratus developmental atlas in .RDS format

organism: Strongylocentrotus purpuratus

source_name: whole embryo nuclar extract

extract_protocol:
Nuclear isolation protocol adapted from Omni-ATAC-seq protocol (Corces et al., 2017). Full protocol in Meyer et al 2021, biorxiv
Single nuclei libraries were created using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 RevD (10X Genomics) and the Chromium X instrument (10X Genomics) using manufacturer protocols

value: whole embryo nuclear extract

tag: developmental stage


title: snRNA-seq of 15hpf S. purpuratus embryos

description: 10X Genomics


title: CM-PC-2h-1

value: Leaves


title: sample.ssd2

source_name: SK-BR-3, shSCR + shDHX9

tag: cell line

value: DHX9 knockdown

value: transduced with shRNA for DHX9 and a scramble control


title: 3T3 cells, psi-IP, Pus1 KD day6, Replicate A

value: fibroblast

value: Pus1 KnockDown 6 days


title: snRNA-seq of 33hpf S. purpuratus embryos

description: 10X Genomics