title: infection in the presence of CPSF6 lacking MCD domain replicate 4


title: Prrx1-Cre Pdgfra GOF E14.5 biol rep 2

status: Public on Apr 01 2025

type: SRA

city: Oklahoma city

first: Lorin

middle: E

last: Olson

state: OK

department: CVB

country: USA

institute: OMRF

description:
Library name: I2043.6
NanoString GeoMX

library_source: transcriptomic

data_processing:
Data was transferred to the GeoMx DSP instrument for further processing and analysis.
Please note that the data columns in 'Nanostring_all_ROIs_genes_normalized_expression.xlsx' refer to different regions of interest among the 4 samples, which are notated within the document. Additionally, the .RDS object contains the relevant metadata assigned to its corresponding data.
Assembly: Mouse mm10
Supplementary files format and content: Nanostring_joint_e14.5.RDS: Seurat object made from nanostring data
Supplementary files format and content: Nanostring_all_ROIs_genes_normalized_expression.xlsx
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Knee

extract_protocol:
Tissues were fixed in 10% NBF, embedded in paraffin, and sectioned at 5 μm. For GeoMx WTA profiling, slides were deparaffinized and rehydrated, underwent antigen retrieval and Proteinase K digestion, then were hybridized overnight with UV-photocleavable, barcoded oligonucleotide probes from the Mouse Whole Transcriptome Atlas (WTA) RNA probe set. After stringent washing, slides were incubated with Sox9 (EMD-Millipore) and SYTOX13 (NanoString) to allow for visualization of tissue morphology for ROI selection. Slides were placed in the GeoMx Digital Spatial Profiler instrument and ROIs were selected. These selected areas then underwent barcode cleavage from the hybridized probes, with the barcodes collected into individual wells of the collection plate based on ROI of origination.
PCR was used to uniquely index each ROIs barcodes with specific Illumina i5/i7 dual indexing primers. These library products were then pooled, purified, and assessed for quality. Paired-end sequencing was performed on a NextSeq 2K P1 PE50 (Illumina), targeting the NanoString recommended read depth of 86 million read-pairs (based on ROI summed areas).

tag: tissue

value: Knee

tag: genotype

value: Prrx1-Cre Pdgfra GOF

tag: batch


title: Prrx1-Cre E14.5 biol rep 2

description:
Library name: I2043.10
NanoString GeoMX


title: Tet1/3-cDKO CD8 T cells, Naive, EM-seq Rep1

city: Iowa City

first: Priya

middle: D

last: Issuree

state: IA

address: 431 Newton Road

department: Internal Medicine

institute: University of Iowa

library_source: genomic

data_processing:
*library strategy: EM-seq
Sequencing data quality was assessed using FastQC v0.11.4. Adapters were trimmed from the sequencing reads using Trimmomatic v0.39. Alignment to the GRCm39/mm39 reference genome was performed using Bismark v0.23.1 with options. Deduplication was performed with deduplicate_bismark. Library quality was assessed on the basis of the percentage of reads that aligned to the genome. Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome. Enzymatic methyl conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context. Enzymatic methyl conversion was considered sufficient when this value was less than 3%. Genome coverage was assessed using the bedtools genomecov software v2.25.0. Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. For each library that met these quality metrics, methylation percentages at individual CpG positions in the reference genome were quantified using the Bismark Methylation Extractor.
Assembly: GRCm39/mm39 reference
Supplementary files format and content: .bismark.cov.gz for each file

molecule: genomic DNA

source_name: Lymph nodes and spleen

extract_protocol:
DNA was extracted using the Qiagen Genomic DNA extraction kit
EM-Seq libraries were prepared using the NEBNext Enzymatic Methyl-seq Kit following the manufacturer's instructions

value: Lymph nodes and spleen

tag: cell type

value: CD8 T cells

value: Tet1/3 cDKO

tag: treatment

value: No treatment


title: WT, Activated, Cut&Tag Rep2

data_processing:
*library strategy: Cut&Tag
Sequencing adapters were removed from paired‐end reads using Trimmomatic version 0.39. Trimmed reads were aligned to mouse reference genome GRCm38/mm10 using Bowtie 2 version 2.4.1. Following genome alignment, Picard was used to mark PCR duplicates, and samtools version 1.3.1 was used to remove PCR duplicates, discordant pairs, and alignments to the mitochondrial genome. Peak calling was performed using MACS2 version 2.2.7.1, and differential accessibility analyses of MACS2 peaks were performed using the R package DiffBind version 2.10.0. Differentially accessible peaks were annotated to genome regions of interest using the R package ChIPseeker version 1.18.0.
Assembly: mm10 reference genome
Supplementary files format and content: narrow peaks

extract_protocol:
Nuclei for tagmentation was prepared using the Cut and Tag Kit from Active Motif following the manufacturer's instructions
Cut&Tag libraries were prepared using the Cut&Tag Kit from Active Motif following the manufacturer's instructions

value: WT

value: TCR activation


title: infection in the presence of CPSF6 lacking MCD domain replicate 3

city: Boston

first: Parmit

middle: Kumar

last: Singh

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

library_source: other

data_processing:
Reads were trimmed for U5 LTR and linker sequences; aligned to human genome hg19 to obtained unique integration sites.
Assembly: hg19
Supplementary files format and content: bed formate containing genomic coordinates for integration sites.
Library strategy: Amplicon-seq

molecule: other

organism: Homo sapiens

source_name: Kidney

extract_protocol:
genomic DNA was isolated from infected cells.
Genomic DNA from infected cells were fragmented by MseI and BglII, ligated to linker to amplyfy virus-host junction by PCR. PCR products were used for Illumina sequencing.

value: Kidney

tag: cell line


title: Prrx1-Cre E14.5 biol rep 1

description:
Library name: I2043.7
NanoString GeoMX


title: WT CD8 T cells, Activated, EM-seq Rep2


title: Prrx1-Cre Pdgfra GOF E14.5 biol rep 1

description:
Library name: I2043.1
NanoString GeoMX


title: WT CD8 T cells, Activated, EM-seq Rep1


title: ALDIDOd0_29

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

description: Library name: ALDIDOd0_29

data_processing:
Raw sequencing reads were processed using nf-core RNAseq pipeline v3.14.0
Assembly: GRCm39.110
Supplementary files format and content: tsv files contains read counts for each sample

source_name: Right Ear Punch

extract_protocol:
Mouse ear punch samples were collected in RNAlater (Ambion, AM7020) and stored at -80⁰C until RNA extraction. Total RNA was extracted using TRI reagent (Ambion, AM9738) and BCP (MRC, BP151) using AM1839 kit following user manufactturer's instructions
1 µg of total RNA was used for library construction, RNA libraries for Bulk RNAseq were prepared using Universal Plus mRNA kit (Tecan Genomics 0520-A01)  following user manufacturer' sinstructions

treatment_protocol:
The disease was induced by a topical application of Imiquimod cream (5% imiquimod, Meda GmbH, batch number GRB095F) onto the ears of the mouse. Imiquimod cream was applied  once per day from day 0 (first application) until day 7 (last application), which is a total of  8 applications.
Animals received IDOR-1117-2520 in drinking water at least one day before Imiquimod application (day 0) and continued up to end of the study.

value: Right Ear Punch

tag: strain

value: C57BL/6J Rj

tag: gender

value: Female

tag: time of_treatment

value: Day 8

value: Imiquimod5%+IDOR-1117-2520C starting at D0


title: PD_M_81_Left_3_atac

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

institute: Van Andel Research Institute

description: Human prefrontal cortex tissue for this study was obtained NIH NeuroBioBank with approval from the ethics committee of the Van Andel Research Institute (IRB #15025)

data_processing:
ATAC-seq: Trimmed (trim_galore) fastq files were aligned to HG19 using BWA v7.15.
ATAC-seq: Alignments (bam files) were input to macs2 callpeak BAMPE -q 0.1 to determine peaks.
RNA-seq: Alignments (bam files) were converted to .tdf files using  igvtools (V2.3.60) count -z 5 -w 25 -e 250
Assembly: Hg19
Assembly: Illumina Nextera DNA UD Indexes Set C (cat 20027215) (version 1)
Supplementary files format and content: high sensitivity DNA assay

extract_protocol:
Neuronal nuclei were isolated from the human prefrontal cortex using flow cytometry and filtering for an anti-NeuN antibody.
DNA was isolated from the neurons using Zymo DNA concentrator Kit. Library generated using the Nextera XT DNA Library Kit with Tagment Enzyme (TDE1) on 30k nuclei, size selection to remove fragments >1kb
average size 400-500bp
bulk ATAC-seq on neuronal nuclei.

value: Frozen BA46,9 LT

tag: Sex

value: M

tag: age

tag: symptom onset

value: Left

tag: brain type

value: PD

tag: source

value: U. of Miami Brain Endowment Bank

tag: hemisphere

value: LT

tag: cod

value: Cancer

tag: race

value: W

tag: pmi

value: Liz

tag: nucleic acid(ng/ul)

tag: library prep

value: C

tag: sequencing run

tag: index id_(i7)


title: ALDIDOd0_30

description: Library name: ALDIDOd0_30

tag: tissue

tag: treatment


title: ALDIDOd0_27

description: Library name: ALDIDOd0_27

tag: strain

tag: gender


title: infection in the presence of CPSF6 lacking MCD domain replicate 2

tag: cell line

tag: genotype


title: ALDIDOd0_26

description: Library name: ALDIDOd0_26

tag: time of_treatment


title: infection in the presence of CPSF6 lacking MCD domain replicate 1


title: Tet1/3-cDKO CD8 T cells, Activated, EM-seq Rep2

value: Lymph nodes and spleen

tag: cell type

value: CD8 T cells

value: Tet1/3 cDKO

value: TCR activation


title: ALDIDOd0_25

description: Library name: ALDIDOd0_25

value: Right Ear Punch

value: C57BL/6J Rj

value: Female


title: infection in the presence of CPSF6 lacking binding site of CPSF5 replcate 3

value: Kidney


title: Tet1/3-cDKO CD8 T cells, Activated, EM-seq Rep1


title: Ex vivo, WT,Naïve, Rep2

data_processing:
Sequencing adapters were removed from paired‐end reads using Trimmomatic version 0.39. Trimmed reads were aligned to mouse reference genome GRCm38/mm10 using Bowtie 2 version 2.4.1. Following genome alignment, Picard was used to mark PCR duplicates, and samtools version 1.3.1 was used to remove PCR duplicates, discordant pairs, and alignments to the mitochondrial genome. Peak calling was performed using MACS2 version 2.2.7.1, and differential accessibility analyses of MACS2 peaks were performed using the R package DiffBind version 2.10.0. Differentially accessible peaks were annotated to genome regions of interest using the R package ChIPseeker version 1.18.0.
Assembly: mm10 reference genome
Supplementary files format and content: narrow peaks

extract_protocol:
Nuclei for tagmentation was prepared using the ATAC-Seq Kit from Active Motif following the manufacturer's instructions
ATAC-Seq libraries were prepared using the ATAC-Seq Kit from Active Motif following the manufacturer's instructions

value: WT

value: No treatment


title: ALDIDOd3_23

description: Library name: ALDIDOd3_23

value: Day 5

value: Imiquimod 5%+IDOR-1117-2520C starting at D3


title: ALDIDOd3_22

description: Library name: ALDIDOd3_22


title: Ex vivo, WT,Naïve, Rep1


title: infection in the presence of CPSF6 lacking binding site of CPSF5 replcate 2


title: ALDIDOd3_21

description: Library name: ALDIDOd3_21


title: Ex vivo, Tet1/3DKO,Naïve, Rep2

value: Tet1/3 DKO


title: ALDIDOd3_20

description: Library name: ALDIDOd3_20


title: infection in the presence of CPSF6 lacking binding site of CPSF5 replcate 1


title: infection in the presence of cMyc fused with CPSF6 lackign MCD replicate 4


title: ALDIDOd5_18

description: Library name: ALDIDOd5_18

value: Day 3

value: Imiquimod 5%+IDOR-1117-2520C starting at D5


title: ALDIDOd0_28

description: Library name: ALDIDOd0_28

value: Day 8

value: Imiquimod5%+IDOR-1117-2520C starting at D0


title: Ex vivo, Tet1/3DKO,Naïve, Rep1

value: Lymph nodes and spleen


title: infection in the presence of cMyc fused with CPSF6 lackign MCD replicate 3


title: ALDIDOd5_17

description: Library name: ALDIDOd5_17


title: ALDIDOd5_15

description: Library name: ALDIDOd5_15


title: infection in the presence of cMyc fused with CPSF6 lackign MCD replicate 2


title: ALDIDOd5_14

description: Library name: ALDIDOd5_14


title: ALDIDOd5_16

description: Library name: ALDIDOd5_16


title: ALDIDOd5_13

description: Library name: ALDIDOd5_13


title: infection in the presence of cMyc fused with CPSF6 lackign MCD replicate 1


title: ALDARA_12

description: Library name: ALDARA_12

value: Imiquimod 5%


title: infection in the presence of CPSF6 lacking RRM domain replicate 1


title: ALDIDOd3_24

description: Library name: ALDIDOd3_24


title: Ex vivo, WT, LCMV D5, Rep2

source_name: Spleen

value: Spleen

value: P14Tg CD8 T cells

value: LCMV D5


title: Ex vivo, Tet1/3DKO, LCMV D5, Rep2


title: ALDIDOd3_19

description: Library name: ALDIDOd3_19

value: Right Ear Punch

value: C57BL/6J Rj


title: ALDARA_11

description: Library name: ALDARA_11

value: Female


title: ALDARA_9

description: Library name: ALDARA_9


title: infection in the presence of cMyc fused with WT CPSF6 replicate 5

value: Kidney


title: Ex vivo, Tet1/3DKO, LCMV D5, Rep3


title: ALDARA_10

description: Library name: ALDARA_10


title: Ex vivo, Tet1/3DKO, LCMV D5, Rep1


title: infection in the presence of cMyc fused with WT CPSF6 replicate 3


title: infection in the presence of cMyc fused with WT CPSF6 replicate 4


title: ALDARA_7

description: Library name: ALDARA_7


title: Ex vivo, WT, LCMV D5, Rep3

value: WT


title: SHAM_6

description: Library name: SHAM_6

value: Vehicle


title: In vitro, WT, Activated, 18hrs, Rep2

value: CD8 T cells

value: TCR activation


title: ALDARA_8

description: Library name: ALDARA_8


title: SHAM_5

description: Library name: SHAM_5


title: infection in the presence of cMyc fused with WT CPSF6 replicate 2


title: SHAM_3

description: Library name: SHAM_3


title: SHAM_2

description: Library name: SHAM_2


title: In vitro, Tet1/3DKO, Activated, 18hrs, Rep2

value: Tet1/3 DKO


title: infection in the presence of cMyc fused with WT CPSF6 replicate 1


title: infection in the presence of cMyc fused with 50 RS replicate 2


title: SHAM_1

description: Library name: SHAM_1


title: SHAM_4

description: Library name: SHAM_4


title: In vitro, WT, Activated, 18hrs, Rep1


title: infection in the presence of cMyc fused with 50 RS replicate 3


title: ALDIDOd8_53

description: Library name: ALDIDOd8_53


title: ALDIDOd8_56

description: Library name: ALDIDOd8_56


title: ALDIDOd8_54

description: Library name: ALDIDOd8_54


title: infection in the presence of cMyc fused with 10 RS replicate 2


title: ALDARAd8_49

description: Library name: ALDARAd8_49


title: ALDARAd8_47

description: Library name: ALDARAd8_47


title: ALDARAd8_46

description: Library name: ALDARAd8_46


title: infection in the presence of cMyc fused with 10 RS replicate 1


title: ALDIDOd8_51

description: Library name: ALDIDOd8_51


title: ALDARAd8_48

description: Library name: ALDARAd8_48


title: infection in the presence of cMyc fused with 50 RS replicate 1


title: GAAco_mouse2(4519)_microglia_rep2

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

country: United Kingdom

institute: UCL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology).
For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina).

value: Microglia

value: Brain

value: Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice)

tag: age

value: 32 weeks

tag: Sex

value: F


title: GAAco_mouse2(4519)_microglia_rep1

description: 10x Genomics


title: In vitro, Tet1/3DKO, Activated, 18hrs, Rep1

value: Lymph nodes and spleen


title: infection in the presence of cMyc fused with 50 RD replicate 2


title: GAAco_mouse1(4517)_microglia_rep2

description: 10x Genomics

value: M


title: ALDARAd8_45

description: Library name: ALDARAd8_45

value: Day 8

value: Imiquimod 5%


title: GAAco_mouse1(4517)_microglia_rep1

description: 10x Genomics


title: ALDIDOd8_52

description: Library name: ALDIDOd8_52

value: Right Ear Punch

value: C57BL/6J Rj


title: ALDARAd8_44

description: Library name: ALDARAd8_44

value: Female


title: ALDIDOd8_55

description: Library name: ALDIDOd8_55


title: infection in the presence of cMyc fused with 10RD replicate 3

value: Kidney


title: SHAMd8_42

description: Library name: SHAMd8_42

value: Vehicle


title: infection in the presence of cMyc fused with 50 RD replicate 1


title: GILT_mouse1(3535)_microglia_rep1

description: 10x Genomics


title: GILT_mouse1(3535)_microglia_rep2

description: 10x Genomics


title: SHAMd8_41

description: Library name: SHAMd8_41


title: SHAMd8_40

description: Library name: SHAMd8_40


title: SHAMd8_39

description: Library name: SHAMd8_39


title: SHAMd8_38

description: Library name: SHAMd8_38


title: infection in the presence of cMyc fused with 10RD replicate 2


title: GILT_mouse2(3536)_microglia_rep2

description: 10x Genomics


title: GILT_mouse2(3536)_microglia_rep1

description: 10x Genomics


title: SHAMd8_37

description: Library name: SHAMd8_37


title: infection in the presence of cMyc fused with CypA replicate 2


title: ALDIDOd5_36

description: Library name: ALDIDOd5_36

value: Day 5


title: ALDIDOd5_34

description: Library name: ALDIDOd5_34


title: ALDIDOd5_33

description: Library name: ALDIDOd5_33


title: SV469_JE_WT_CT1

city: Freising

first: Marjolein

last: Heddes

address: Gregor mendel str 2

country: Germany

institute: TUM

description:
SV469_JE_WT_CT1
MUC28166

data_processing:
The quality of Next Generation Sequencing data was assessed with FastQC v0.11.5
Adapter content and low quality reads were removed using Trimmomatic v0.39 (Anthony et al., 2014)
Trimmed FASTQ files were then mapped against the mouse mm10 genome with the STAR v2.7.5c aligner
Format conversions were performed using samtools v1.3.1 (Li et al., 2009). The featureCounts program v1.4.6 (Liao et al., 2014) was used to count reads located within an exon, do not overlap multiple features, with a threshold of MAPQ > = 4 and are not chimeric.
DESeq2 version 1.22.0 (RRID:SCR_015687 (Love et al., 2014) was used to normalize the read count matrix and perform differential expression analysis.
Assembly: mm10
Supplementary files format and content: txt files include feature counts for all samples in one table

source_name: Jejunum

extract_protocol:
RNA was harvested using NucleoSpin® RNA kit (MACHEREY-NAGEL).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Jejunum

tag: time


title: SV477_JE_KO_CT5

description:
SV477_JE_KO_CT5
MUC28167


title: infection in the presence of cMyc fused with CypA replicate 1


title: SV481_JE_KO_CT17

description:
SV481_JE_KO_CT17
MUC28168


title: ALDIDOd5_32

description: Library name: ALDIDOd5_32


title: SV453_JE_WT_CT17

description:
SV453_JE_WT_CT17
MUC28165


title: ALDIDOd5_31

description: Library name: ALDIDOd5_31


title: infection in the presence of wild type CPSF6 replicate 9


title: infection in the presence of wild type CPSF6 replicate 8


title: ALDARAd5_30

description: Library name: ALDARAd5_30


title: SV447_JE_WT_CT5

description:
SV447_JE_WT_CT5
MUC28164


title: ALDARAd5_27

description: Library name: ALDARAd5_27


title: infection in the presence of wild type CPSF6 replicate 7


title: ALDARAd5_26

description: Library name: ALDARAd5_26


title: ALDARAd5_28

description: Library name: ALDARAd5_28


title: infection in the presence of wild type CPSF6 replicate 6


title: ALDARAd5_25

description: Library name: ALDARAd5_25


title: SV439_JE_KO_CT5

description:
SV439_JE_KO_CT5
MUC28162


title: infection in the presence of cMyc fused with 10RD replicate 1


title: infection in the presence of wild type CPSF6 replicate 5


title: SHAMd5_21

description: Library name: SHAMd5_21


title: ALDIDOd5_35

description: Library name: ALDIDOd5_35


title: SHAMd5_19

description: Library name: SHAMd5_19


title: infection in the presence of wild type CPSF6 replicate 4


title: SV433_JE_WT_CT21

description:
SV433_JE_WT_CT21
MUC28161


title: ALDIDOd2_16

description: Library name: ALDIDOd2_16

value: Day 2

value: Imiquimod 5%+IDOR-1117-2520C


title: ALDIDOd2_17

description: Library name: ALDIDOd2_17


title: ALDARAd5_29

description: Library name: ALDARAd5_29


title: infection in the presence of wild type CPSF6 replicate 3


title: ALDIDOd2_15

description: Library name: ALDIDOd2_15


title: infection in the presence of wild type CPSF6 replicate 2


title: SV476_JE_WT_CT21

description:
SV476_JE_WT_CT21
MUC28159


title: ALDIDOd2_13

description: Library name: ALDIDOd2_13


title: infection in the presence of wild type CPSF6 replicate 1


title: SV450_JE_KO_CT13

description:
SV450_JE_KO_CT13
MUC28157


title: ALDARAd2_12

description: Library name: ALDARAd2_12


title: SV468_JE_WT_CT1

description:
SV468_JE_WT_CT1
MUC28158


title: SHAMd5_22

description: Library name: SHAMd5_22


title: SV480_JE_KO_CT1

description:
SV480_JE_KO_CT1
MUC28160


title: ALDARAd2_11

description: Library name: ALDARAd2_11


title: SV446_JE_WT_CT5

description:
SV446_JE_WT_CT5
MUC28156


title: infection in the presence of SRSF2 replicate 2

value: infection in the presence of SRSF2


title: ALDARAd2_10

description: Library name: ALDARAd2_10


title: ALDARAd2_9

description: Library name: ALDARAd2_9


title: ALDARAd2_8

description: Library name: ALDARAd2_8


title: ALDIDOd2_18

description: Library name: ALDIDOd2_18


title: ALDIDOd2_14

description: Library name: ALDIDOd2_14


title: SHAMd2_6

description: Library name: SHAMd2_6


title: SV438_JE_WT_CT17

description:
SV438_JE_WT_CT17
MUC28154


title: infection in the presence of SRSF2 replicate 1


title: SHAMd2_5

description: Library name: SHAMd2_5


title: infection in the presence of SRSF1 replicate 3

value: infection in the presence of SRSF1


title: SHAMd2_4

description: Library name: SHAMd2_4


title: SV443_JE_WT_CT5

description:
SV443_JE_WT_CT5
MUC28163


title: SV424_JE_WT_CT13

description:
SV424_JE_WT_CT13
MUC28153


title: SHAMd2_2

description: Library name: SHAMd2_2


title: infection in the presence of SRSF1 replicate 2


title: infection in the presence of SRSF2 replicate 3


title: SV479_JE_KO_CT1

description:
SV479_JE_KO_CT1
MUC28152


title: infection in the presence of SRSF1 replicate 1


title: E6_Hypoxia_Th2_6_Crepos

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib96235

data_processing:
Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using NextSeq P3 sequencing kits (Illumina) with a target depth of 5 million reads per sample. Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the GRCm38.91  mouse reference genome, using STAR v.2.4.2a40 and gene counts were generated using htseq-count41. Quality control (QC) and metrics analysis was performed using the Picard family of tools (v1.134, http://broadinstitute.github.io/picard/).
Supplementary files format and content: Plain text file with Ensembl gene IDs (ENSMUSG) in the first column and counts in the second column. Each filename begins with the library ID.

source_name: T cells

growth_protocol: We cultured naïve CD4+ T cells from Control or HIF2a-ON mice under TH0 or Th2-skewing conditions, in normoxia (20% O2) or hypoxia (4% O2) for 4 days, prior to sorting viable cells for SmartSeq.

extract_protocol:
SmartSeq
NexteraXT

treatment_protocol: 3 technical replicates of 8 conditions, being Th0 normoxia ctrl, Th0 normoxia HIF2A-ON, Th0 hypoxia ctrl, Th0 hypoxia HIF2A-ON, Th2 normoxia ctrl, Th2 normoxia HIF2A-ON, Th2 hypoxia ctrl, Th2 hypoxia HIF2A-ON.

value: T cells

value: Th2 skewed

tag: study group

value: Hypoxia

tag: stimulation

value: soluble anti-CD3/CD28 and irradiated APCs


title: E5_Hypoxia_Th2_5_Crepos

description: Library name: lib96234


title: SHAMd2_3

description: Library name: SHAMd2_3


title: infection in the presence of SNRNP70 replicate 2

value: infection in the presence of SNRNP70


title: ALDARAd2_7

description: Library name: ALDARAd2_7

value: Imiquimod 5%


title: SV455_JE_WT_CT1

description:
SV455_JE_WT_CT1
MUC28150


title: SV442_JE_WT_CT5

description:
SV442_JE_WT_CT5
MUC28155


title: E4_Hypoxia_Th2_4_Crepos

description: Library name: lib96233


title: SHAMd5_20

description: Library name: SHAMd5_20

value: Right Ear Punch


title: E3_Hypoxia_Th2_3_Creneg

description: Library name: lib96232


title: SV471_JE_KO_CT21

description:
SV471_JE_KO_CT21
MUC28151


title: infection in the presence of SNRNP70 replicate 1


title: E2_Hypoxia_Th2_2_Creneg

description: Library name: lib96231


title: infection in the presence of 50 RS replicate 2

value: infection in the presence of 50 RS


title: E1_Hypoxia_Th2_1_Creneg

description: Library name: lib96230


title: D6_Hypoxia_Th0_6_Crepos

description: Library name: lib96229

value: Th0 skewed


title: SV445_JE_KO_CT21

description:
SV445_JE_KO_CT21
MUC28148


title: infection in the presence of 50 RS replicate 1

value: Kidney


title: SV449_JE_KO_CT13

description:
SV449_JE_KO_CT13
MUC28149


title: D3_Hypoxia_Th0_3_Creneg

description: Library name: lib96226


title: infection in the presence of 10RS replicate 5

value: infection in the presence of 10RS


title: SV441_JE_WT_CT21

description:
SV441_JE_WT_CT21
MUC28147


title: D2_Hypoxia_Th0_2_Creneg

description: Library name: lib96225


title: SV437_JE_KO_CT17

description:
SV437_JE_KO_CT17
MUC28146


title: infection in the presence of 10RS replicate 4


title: D1_Hypoxia_Th0_1_Creneg

description: Library name: lib96224


title: SV421_JE_WT_CT13

description:
SV421_JE_WT_CT13
MUC28145


title: infection in the presence of 10RS replicate 3


title: C5_Normoxia_Th2_5_Crepos

description: Library name: lib96222

value: Normoxia


title: C6_Normoxia_Th2_6_Crepos

description: Library name: lib96223


title: SV470_JE_KO_CT21

description:
SV470_JE_KO_CT21
MUC28143

value: Jejunum


title: SV478_JE_KO_CT5

description:
SV478_JE_KO_CT5
MUC28144


title: C3_Normoxia_Th2_3_Creneg

description: Library name: lib96220


title: infection in the presence of 10RS replicate 1


title: B6_Normoxia_Th0_6_Crepos

description: Library name: lib96217


title: C4_Normoxia_Th2_4_Crepos

description: Library name: lib96221


title: SV454_JE_WT_CT1

description:
SV454_JE_WT_CT1
MUC28142


title: infection in the presence of 10RS replicate 2


title: D4_Hypoxia_Th0_4_Crepos

description: Library name: lib96227


title: B5_Normoxia_Th0_5_Crepos

description: Library name: lib96216


title: C1_Normoxia_Th2_1_Creneg

description: Library name: lib96218


title: C2_Normoxia_Th2_2_Creneg

description: Library name: lib96219


title: D5_Hypoxia_Th0_5_Crepos

description: Library name: lib96228


title: infection in the presence of fused RRM, CypA and MCD replicate 2


title: B3_Normoxia_Th0_3_Creneg

description: Library name: lib96214


title: infection in the presence of fused RRM, CypA and MCD replicate 1


title: SV448_JE_KO_CT13

description:
SV448_JE_KO_CT13
MUC28141


title: B1_Normoxia_Th0_1_Creneg

description: Library name: lib96212


title: B2_Normoxia_Th0_2_Creneg

description: Library name: lib96213


title: infection in the presence of 50 RD replicate 4

value: infection in the presence of 50 RD


title: H. poly infected

description:
Library name: lib56389
10x Genomics 5' Gene Expression

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 3.7.17)
Libraries were demultiplexed using 10x Cell Ranger mkfastq (v 5.0.1); All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10x Cell Ranger count (v. 5.0.1).
Barcodes were called as cells or background using default settings in 10x Cell Ranger (v. 5.0.1).
Assembly: GRCm38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID for barcodes called as cells

source_name: small intestine lamina propria

growth_protocol: C57BL6/J (WT) mice were purchased from The Jackson Laboratory.

extract_protocol:
Small intestinal lamina propria leukocytes were isolated from naïve and H. polygyrus infected mice and live CD4+ T cells were FACS purified.
Cells were loaded onto a 10x Genomics Chromium Controller, and single cells captured and processed for gene expressionusing 10x Genomics 5’ GEX V2 Kit.

treatment_protocol: Mice were either infected with Heligmosomoides polygyrus (H. polygyrus) or left uninfected (naïve).

value: small intestine lamina propria

value: CD4 T cells


title: naïve uninfected

description:
Library name: lib56388
10x Genomics 5' Gene Expression


title: infection in the presence of 50 RD replicate 3


title: SV440_JE_KO_CT5

description:
SV440_JE_KO_CT5
MUC28139


title: P20_SL_3

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
Samples were aligned to mm10 using nfcore/rnaseq v3.12.0
Reads were mapped using STAR, removing multi-mappers
Count tables were generated using Salmon
Fold change values were determined using the DESeq2 package
Assembly: mm10
Supplementary files format and content: fastq.gz
Supplementary files format and content: raw_counts_RNA_20240705.tsv

source_name: Mouse Embryonic Stem Cells

growth_protocol: Cells were grown in standard ESC medium supplemented with LIF

extract_protocol:
RNA was extracted using the Rneasy Plus mini kit. 1ug RNA was used to construct the sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep kit, according to manufacturer's instructions.

treatment_protocol: Cells cultured in SL, EMM or 2iL for 10 or 20 passages before RNA was collected

value: Mouse Embryonic Stem Cells

value: Embryonic Stem Cells

value: SL


title: infection in the presence of 50 RD replicate 2


title: P20_SL_1


title: SV434_JE_WT_CT21

description:
SV434_JE_WT_CT21
MUC28138


title: P20_EMM_2

value: EMM


title: B4_Normoxia_Th0_4_Crepos

description: Library name: lib96215

value: T cells

value: soluble anti-CD3/CD28 and irradiated APCs


title: P20_EMM_3


title: P20_SL_2


title: P20_EMM_1


title: SV400_JE_KO_CT9

description:
SV400_JE_KO_CT9
MUC28135


title: infection in the presence of 10RD replicate 1

value: infection in the presence of 10RD


title: infection in the presence of 10RD replicate 2


title: P20_2iL_2


title: P20_2iL_3


title: SV444_JE_KO_CT21

description:
SV444_JE_KO_CT21
MUC28140


title: SV418_JE_KO_CT9

description:
SV418_JE_KO_CT9
MUC28136


title: SV399_JE_KO_CT17

description:
SV399_JE_KO_CT17
MUC28127


title: SV417_JE_WT_CT17

description:
SV417_JE_WT_CT17
MUC28128


title: P20_2iL_1


title: P10_SL_3


title: infection in the presence of CPSF6 MCD domain replicate 2


title: P10_EMM_3


title: SV420_JE_WT_CT9

description:
SV420_JE_WT_CT9
MUC28137


title: P10_SL_1


title: SV398_JE_WT_CT17

description:
SV398_JE_WT_CT17
MUC28119


title: P10_EMM_2


title: P10_2iL_2


title: P10_2iL_1


title: P10_EMM_1


title: infection in the presence of CPSF6 MCD domain  replicate 1


title: WT_F_3M_REP.4

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Raw FASTQ files were aligned using STAR v2.7.9a against a custom-built genome containing the human SNCA gene in the GCRm39 standard mouse genome. Raw read counts were loaded into DESeq2 and analyzed in R. Genes with fewer than 20 normalized mean reads across all samples were removed, leaving ~18.500 genes for differential expression.
Assembly: GRCm39 + SNCA locus from GRCh39, Ensembl v104
Supplementary files format and content: tab-separated text file with raw counts per gene and sample, including the human SNCA gene (hsSNCA)

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
RNA was extracted from frozen hippocampi with the RNeasy Plus Universal Mini kit (Qiagen) according to manufacturer’s instructions and as previously described (Garcia et al., 2022). RNA was kept on ice for immediate use or stored at -80°C. RNA quality and concentration were measured using a NanoDropTM 2000 (ThermoFischer Scientific) and an Agilent 2100 Bioanalyzer.
Using 1 µg of RNA, sequencing libraries were prepared using the Illumina Stranded mRNA Prep kit. Library quantification was performed using a QubitTM 4 Fluorometer (Invitrogen).

value: hippocampus

value: WT


title: HET_F_3M_REP.4

value: TG


title: infection in the presence of CPSF6 glu mutant replicate 3

value: Kidney


title: WT_F_6M_REP.4


title: SV412_JE_WT_CT9

description:
SV412_JE_WT_CT9
MUC28104


title: SV397_JE_WT_CT13

description:
SV397_JE_WT_CT13
MUC28111


title: P10_2iL_3


title: infection in the presence of CPSF6 MCD domain replicate 3


title: infection in the presence of CPSF6 F284A mutant replicate 2


title: P10_SL_2


title: WT_F_6M_REP.3


title: infection in the presence of CPSF6 glu mutant replicate 1


title: infection in the presence of CPSF6 glu mutant replicate 2


title: SV415_JE_WT_CT9

description:
SV415_JE_WT_CT9
MUC28112


title: SV416_JE_KO_CT17

description:
SV416_JE_KO_CT17
MUC28120


title: SV396_JE_WT_CT13

description:
SV396_JE_WT_CT13
MUC28103


title: infection in the presence of CPSF6 F284A mutant replicate 1


title: HET_F_6M_REP.4


title: WT_M_6M_REP.4


title: WT_M_3M_REP.4


title: SV395_JE_KO_CT13

description:
SV395_JE_KO_CT13
MUC28095


title: SV410_JE_KO_CT9

description:
SV410_JE_KO_CT9
MUC28096


title: infection in the presence of CPSF7 replicate 4

value: infection in the presence of CPSF7


title: HET_F_6M_REP.3


title: infection in the presence of CypA fused with MCD domain of CPSF6 replicate 2


title: WT_M_6M_REP.3


title: HET_F_6M_REP.2


title: infection in the presence of CypA fused with MCD domain of CPSF6 replicate 1


title: HET_M_6M_REP.4


title: WT_F_3M_REP.3


title: SV402_JE_KO_CT9

description:
SV402_JE_KO_CT9
MUC28088


title: infection in the presence of CPSF7 replicate 3


title: WT_F_6M_REP.1


title: SV401_JE_WT_CT9

description:
SV401_JE_WT_CT9
MUC28080


title: HET_M_3M_REP.4


title: WT_M_6M_REP.2


title: infection in the presence of CPSF7 replicate 1


title: HET_M_6M_REP.3


title: SV385_JE_KO_CT1

description:
SV385_JE_KO_CT1
MUC28087


title: HET_F_6M_REP.1


title: db/db, 35w, 06

city: Takatsuki

first: Mariko

last: MAEKAWA

state: Osaka

address: Murasaki-cho

country: Japan

institute: Japan Tobacco Inc.

data_processing:
DRAGEN Bio-IT Platform v 3.6.3
Trimmed sequence reads were mapped to GRCm38/mm10 using DRAGEN Bio-IT Platform
Read count extraction and normalization were performed using DRAGEN Bio-IT Platform
Assembly: mm10
Supplementary files format and content: Comma separated value files include CPM values for each Sample

source_name: kidney

extract_protocol:
RNA extraction was performed according to the TRIzol® Reagent (Life Technologies Corporation) protocol and RNeasy Kit (Qiagen) protocol.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: kidney

value: db/db

value: Unx

value: M


title: SV384_JE_KO_CT1

description:
SV384_JE_KO_CT1
MUC28079

value: Jejunum


title: WT_F_3M_REP.2


title: infection in the presence of CPSF7 fused with CPSF6 replicate 2


title: HET_M_3M_REP.3


title: WT_F_6M_REP.2


title: HET_M_6M_REP.1


title: infection in the presence of CPSF7 replicate 2


title: WT_M_3M_REP.3


title: HET_M_6M_REP.2


title: db/db, 35w, 03


title: WT_M_6M_REP.1


title: CKO infected replicate 8

value: CKO infected


title: CKO infected replicate 7


title: WT_M_8M_REP.4


title: CKO infected replicate 5


title: HET_F_8M_REP.4


title: CKO infected replicate 6


title: db/m, 35w, 06

value: db/m

value: intact


title: HET_M_8M_REP.4


title: db/m, 35w, 05


title: WT_M_8M_REP.3


title: WT_M_8M_REP.2


title: HET_M_8M_REP.3


title: db/db, 35w, 01


title: db/db, 35w, 05


title: WT_F_8M_REP.2


title: db/m, 35w, 04


title: CKO infected replicate 4


title: db/db, 35w, 02


title: CKO infected replicate 2


title: WT_F_8M_REP.4


title: HET_F_8M_REP.3


title: WT_F_8M_REP.3


title: HET_F_8M_REP.2


title: CKO infected replicate 3


title: infection in the presence of CPSF7 fused with CPSF6 replicate 1


title: WT_F_8M_REP.1


title: db/m, 35w, 03


title: infection in the presence of 50 RD replicate 1

value: infection in the presence of 50 RD


title: HET_F_8M_REP.1


title: db/m, 35w, 02


title: HET_M_8M_REP.2


title: HET_M_8M_REP.1


title: db/m, 35w, 01


title: WT_M_8M_REP.1


title: WT infected replicate 7

value: wildtype


title: WT_M_3M_REP.2


title: WT infected replicate 6


title: HET_F_3M_REP.3


title: WT infected  replicate 5


title: HET_F_3M_REP.2


title: HET_M_3M_REP.2


title: db/db, 26w, 12


title: db/db, 26w, 10


title: HET_M_3M_REP.1


title: CKO infected replicate 1


title: HET_F_3M_REP.1


title: WT infected replicate 3


title: WT_M_3M_REP.1


title: db/db, 26w, 09


title: WT infected replicate 4


title: WT_F_14M_REP.4


title: db/db, 26w, 08


title: WT infected replicate 2


title: db/db, 26w, 07


title: WT_F_14M_REP.3


title: HET_F_14M_REP.4


title: WT_M_14M_REP.4


title: infected cells depleted for SON and SRRM2 replicate 3

source_name: Bone

value: Bone


title: db/db, 26w, 11


title: HET_M_14M_REP.3


title: WT_M_14M_REP.3


title: WT infected replicate 1


title: db/db, 26w, 04


title: WT_F_14M_REP.2


title: HET_F_14M_REP.3


title: db/db, 26w, 06


title: db/db, 26w, 05


title: HET_M_14M_REP.4


title: infected cells depleted for SON and SRRM2 replicate 1


title: HET_M_14M_REP.2


title: HET_F_14M_REP.2


title: infected cells depleted for SRRM2 replicate 3


title: db/db, 26w, 03


title: infected cells depleted for SRRM2 replicate 2


title: db/db, 26w, 01


title: WT_F_14M_REP.1


title: infected cells depleted for SRRM2 replicate 1


title: infected cells depleted for SON and SRRM2 replicate 2


title: WT_F_3M_REP.1


title: IgG_EMM_GFPplus_c85

data_processing:
library strategy: CUT&Tag
Reads were trimmed using TrimGalore! with  option “--nextseq 20”
CUT&Tag reads were aligned to the UCSC mm10 genome using Bowtie2
Reads were quality filtered to keep only uniquely mapping reads with MAPQ > 10
Fragment bedgraphs wer produced using Deeptools bamCoverage with RPKM normalization, extend_reads, and binsize 1
Peak calling was performed using Seacr “stringent” for histone marks and Seacr “relaxed” for transcription factors, with “norm” mode.
Bigwig files were generated from fragment bedgraphs usiing UCSC bedGraphToBigWig
Assembly: mm10/GRCm38
Supplementary files format and content: bigwig, bed files of peaksets (except IgG samples)

growth_protocol: Cultured in DMEM+Fetal Bovine Serum (10%), with 2nM glutamine, minimal non-essential amino acids, B-mercaptoethanol and 1:1000 LIF. Cell cultured at 37°C at 20% O2

extract_protocol:
DNA extracted according to protocol as described in "Kaya-Okur, H.S.  Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc 15, 3264–3283 (2020)"
Libraries prepared according to protocol as described in "Kaya-Okur, H.S.  Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc 15, 3264–3283 (2020)"

treatment_protocol: Cells cultured in media condition described above, either with 4.5g/L D-glucose and 10mM pyurvate, or with 4.5g/L D-galactose, for 24h.

value: Mouse Embryonic Stem Cells

tag: antibody

value: IgG (Santa Cruz, sc2028)

value: Cells were pretreated with doxycycline for 48h prior to sorting for GFP by FACS, after which the cells were collected for CUT&Tag


title: infected cells depleted for SON replicate 3


title: db/m, 26w, 05


title: WT_M_14M_REP.2

value: hippocampus

value: WT


title: IgG_SL_GFPplus_c85


title: Sox2_EMM_dTag_c85_biolrep1

value: Cells were pretreated with dTag-13 for 24h prior to collection for CUT&Tag


title: infected cells depleted for SON replicate 2


title: db/m, 26w, 03

value: kidney


title: HET_M_14M_REP.1

value: TG


title: WT_M_14M_REP.1


title: infected cells depleted for SON replicate 1


title: Sox2_EMM_GFPplus_c85_biolrep3


title: db/m, 26w, 02


title: HET_F_14M_REP.1


title: Sox2_EMM_GFPplus_c85_biolrep1


title: infected cells depleted for CPSF6 replicate 4


title: Sox2_EMM_GFPplus_c85_biolrep2


title: Sox2_SL_GFPplus_c85_biolrep3


title: Sox2_SL_GFPplus_c85_biolrep2


title: Sox2_SL_GFPplus_c85_biolrep1


title: db/m, 26w, 01


title: SHAMd2_1

description: Library name: SHAMd2_1

value: Right Ear Punch

value: C57BL/6J Rj

value: Female

value: Day 2

value: Vehicle


title: db/m, 26w, 04

value: db/m

value: intact

value: M


title: WTP0_9

city: New York

first: Ryan

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

data_processing:
Raw paired-end reads were processed using an automated Salmon pipeline, Seq-N-Slide, on New York University’s Ultra Violet computing cluster.
Ensembl stable transcripts were then mapped to gene names using the gencode mouse M28 annotation release and parsed for protein coding genes.
The raw count matrices were further processed using DESeq2 for differential statistics and other custom analyses for visualization.
Assembly: mm10 reference genome

source_name: colon

growth_protocol: Homozygous Piebald male mice were crossed to Ret+/CFP heterozygous female mice and resulting progeny were collected at sample timepoints embryonic day post coital 14.5 (E14.5) or postnatal day 0 (P0).

extract_protocol:
Entire intestine from stomach to anal pore (E14.5) or colon to anal pore (P0) were collected from euthanized animals, rinsed in 1X PBS, and snap frozen in liquid N2. RNA was then extracted and purified.
cDNA and libraries were prepared using Illumina's Truseq kit on an automated Beckman Coulter Biomek SPRIworks platform.

value: colon

value: Ret+/+ Ednrb+/+

value: male


title: WTP0_6

value: female


title: db/db, 26w, 02

value: db/db

value: Unx


title: infected cells depleted for CPSF6 replicate 3

value: Bone


title: IgG_EMM_dTag_c85

value: Mouse Embryonic Stem Cells

value: IgG (Santa Cruz, sc2028)

value: Cells were pretreated with dTag-13 for 24h prior to collection for CUT&Tag


title: IgG_EMMplusNAM_E14

value: Wild Type


title: IgG_SL_E14


title: infected cells depleted for CPSF6 replicate 2


title: WTP0_5

value: WT


title: infected cells depleted for CPSF6 replicate 1


title: Sox2_EMM_E14_biolrep3


title: Sox2_SL_E14_biolrep3


title: Sox2_EMM_dTag_c85_biolrep2


title: non targeting infected cells replicate 7


title: Sox2_EMM_E14_biolrep2


title: Sox2_SL_E14_biolrep2


title: non targeting infected cells replicate 6


title: WTP0_10


title: Sox2_EMMplusNAM_E14_biolrep2


title: Sox2_EMM_E14_biolrep1


title: WTP0_2


title: WTP0_1


title: Sox2_EMMplusNAM_E14_biolrep1


title: non targeting infected cells replicate 4


title: Sox2_SL_E14_biolrep1


title: IgG_EMM_Jup27_H3K4me1

value: IgG (Abcam, ab171870)


title: non targeting infected cells replicate 5


title: IgG_SL_Jup27_H3K4me1


title: P0_9

value: Ret+/+ Ednrbs/s


title: non targeting infected cells replicate 3


title: IgG_EMMplusNAM_Jup27_H3K4me1


title: IgG_EMMplusNAM_Jup21_H3K4me1


title: non targeting infected cells replicate 2


title: IgG_EMM_GLCp25_H3K4me1


title: IgG_SL_Jup21_H3K4me1


title: IgG_SL_GLCp25_H3K4me1


title: H3K4me1_EMM_Jup27

value: H3K4me1(Abcam, ab8895)


title: IgG_EMM_E14


title: H3K4me1_SL_Jup27


title: P0_7

value: Ret+/CFP Ednrbs/s


title: P0_30


title: infected HeLa cells depleted for SON and SRRM2 replicate 1

source_name: Uterus

value: Uterus

value: HeLa


title: infected HeLa cells depleted for SRRM2 replicate 2


title: P0_8

value: colon


title: H3K4me1_EMM_Jup21


title: IgG_EMMplusNAM_GLCp25_H3K4me1


title: P0_28

value: male


title: infected HeLacells depleted for SRRM2 replicate 1


title: P0_27

value: female


title: H3K4me1_SL_Jup21


title: H3K4me1_EMMplusNAM_GLCp25


title: infected HeLa cells depleted for SON replicate 2


title: H3K4me1_EMM_GLCp25


title: non targeting infected cells replicate 1


title: IgG_EMMplusNAM_Jup20_H3K27ac


title: infected HeLa cells depleted for SON and SRRM2 replicate 2


title: infected HeLa cells depleted for SON replicate 1


title: P0_5


title: H3K4me1_SL_GLCp25


title: IgG_EMMplusNAM_Jup16_H3K27ac


title: P0_19

value: Ret+/CFP Ednrb+/s


title: P0_29


title: IgG_SL_Jup20_H3K27ac


title: IgG_EMM_Jup20_H3K27ac


title: IgG_EMMplusNAM_GLCp13_H3K27ac


title: IgG_SL_Jup16_H3K27ac


title: P0_16


title: H3K4me1_EMMplusNAM_Jup21


title: IgG_SL_GLCp13_H3K27ac


title: A427 cells, KRAS/MYC co-targeting siRNA, 24 hrs, Biol Rep 3

city: Chapel Hill

first: Alessandro

last: Porrello

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
RNA-seq quantification with STAR/Salmon workflow.
Reads were mapped to GRCh38 using STAR 2.7.6a (parameters: --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM).
Quantification of transcripts (gene-level) was performed using Salmon 1.4.0, based on the human transcriptome defined by GENCODE, Release 36
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes Salmon-quantification of transcripts (gene-level) for each sample

growth_protocol: A427 cells were grown in Modified Eagle’s Medium (MEM) media (Gibco) containing 10% FBS and 1% P-S antibiotic.

extract_protocol:
RNA was extracted using the Zymo RNA Micro-Prep Kit.
mRNAseq libraries were generated from 100-1000 ng of total RNA using an Illumina TruSeq Stranded mRNA library prep kit (cat 20020595) following the manufacturer's protocol (document 1000000040498).

treatment_protocol: A427 cells were transfected for 24 hours with either negative control, KRAS-targeting, MYC-targeting, or KRAS/MYC co-targeting siRNAs at 20nM.

value: epithelial lung carcinoma

value: KRAS/MYC knockdown

value: transfection, KRAS/MYC co-targeting siRNA

value: 24 hrs


title: non targeting infected HeLa cells replicate 2


title: H3K27ac_EMMplusNAM_Jup20

value: Mouse Embryonic Stem Cells

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_EMM_Jup20

value: Wild Type


title: A427 cells, KRAS/MYC co-targeting siRNA, 24 hrs, Biol Rep 1


title: H3K4me1_EMMplusNAM_Jup27


title: A427 cells, KRAS/MYC co-targeting siRNA, 24 hrs, Biol Rep 2


title: P0_17


title: A427 cells, KRAS siRNA, 24 hrs, Biol Rep 3

value: KRAS knockdown

value: transfection, KRAS siRNA


title: IgG_EMM_Jup21_H3K4me1

value: IgG (Abcam, ab171870)


title: H3K27ac_EMMplusNAM_Jup16


title: H3K27ac_SL_Jup20


title: P0_2


title: IgG_EMM_GLCp13_H3K27ac


title: P0_15

value: Ret+/+ Ednrbs/s


title: non targeting infected HeLa cells replicate 1

value: Uterus


title: P0_14


title: IgG_EMM_Jup16_H3K27ac


title: H3K27ac_EMM_Jup16


title: H3K27ac_SL_Jup16


title: A427 cells, KRAS siRNA, 24 hrs, Biol Rep 1


title: H3K27ac_EMMplusNAM_GLCp13


title: A427 cells, KRAS siRNA, 24 hrs, Biol Rep 2


title: P0_10


title: E145_8

source_name: GI tract, stomach to colon

value: GI tract, stomach to colon

value: Ret+/CFP Ednrbs/s


title: P0_1

value: colon


title: A427 cells, MYC siRNA, 24 hrs, Biol Rep 2

value: MYC knockdown

value: transfection, MYC siRNA


title: H3K27ac_SL_GLCp13


title: H3K27ac_EMM_GLCp13


title: IgG_EMMplusNAM_Jup27_Tead1


title: A427 cells, MYC siRNA, 24 hrs, Biol Rep 1

value: epithelial lung carcinoma


title: A427 cells, MYC siRNA, 24 hrs, Biol Rep 3


title: E145_7

value: male


title: E145_5

value: Ret+/+ Ednrb+/s


title: A427 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 3

value: WT

value: transfection, negative control siRNA

value: 24 hrs


title: P0_12

value: Ret+/CFP Ednrb+/s


title: IgG_SL_Jup27_Tead1

value: Mouse Embryonic Stem Cells

value: Wild Type


title: IgG_EMMplusNAM_Jup25_Tead1

value: IgG (Abcam, ab171870)


title: IgG_EMMplusNAM_Jup30_Tead1


title: IgG_EMM_Jup25_Tead1


title: E145_4


title: A427 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 2


title: IgG_SL_Jup25_Tead1


title: E145_2


title: Tead1_EMMplusNAM_Jup30

value: TEAD1 (CST, D9X2L)


title: IgG_EMM_Jup30_Tead1


title: A427 cells, Neg Ctrl siRNA, 24 hrs, Biol Rep 1


title: E145_17


title: Tead1_EMM_Jup30


title: IgG_SL_Jup30_Tead1


title: Tead1_SL_Jup30


title: PC2416-DEC PDX [105147-001-088]

city: Rotterdam

first: Stefan

last: Buck

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
The nf-core/RNA-seq pipeline (v3.8.1) implemented in Nextflow (version 22.04.5) with default human settings was utilized for data analysis. Steps listed below
Paired-end FASTQ files underwent quality control using FASTQC (v0.11.9) both before and after preprocessing with Trim Galore (v6.7), which removed adapter sequences and eliminated reads with low Phred scores (≤ 30)
Reads were mapped with the STAR read aligner (v2.7.3a)
AstraZeneca's disambiguation algorithm (Python variant, 2018) was applied to evaluate the best alignments and separate the resulting BAM files into human and mouse data
Gene-level count files were generated from the disambiguated BAM files using subread featureCounts (v2.0.1).
Assembly: UCSC genome builds GRCh38 (human) and GRCm38 (mouse, reference strain C57BL/6J), along with GENCODE annotation releases v34 (human) and M24 (mouse) were employed for the analysis and downstream disambiguation of human/mouse data.
Supplementary files format and content: Paired-end FASTQ files
Supplementary files format and content: Matrix table with raw gene counts for every gene (ensembl) and every sample

source_name: prostate cancer cells

extract_protocol:
Tumor tissue was lysed and homogenized in QIAzol (Qiagen, Hilden, Germany, cat. no. 79306) using an Ultra-Turrax T25 (Janke & Kunkel, Staufen, Germany). Total RNA was isolated using a miRNA-easy mini kit (Qiagen, cat. no. 217004) and an RNase-Free DNase Set (Qiagen, cat. no. 79254).
samples were processed with a NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA, cat. no. E7760S)

value: prostate cancer cells

value: Docetaxel + darolutamide


title: Tead1_EMMplusNAM_Jup27


title: IgG_EMM_Jup27_Tead1


title: Tead1_EMM_Jup27


title: E145_16

value: GI tract, stomach to colon


title: E145_14

value: Ret+/+ Ednrbs/s

value: female


title: PC2416-DEC PDX [105147-001-087]


title: Tead1_EMMplusNAM_Jup25


title: Tead1_EMM_Jup25


title: PC2416-DEC PDX [105147-001-086]


title: Tead1_SL_Jup27


title: Tead1_SL_Jup25


title: PC2416-DEC PDX [105147-001-085]


title: IgG_EMMplusNAM_Jup24_Sox2Klf4

value: IgG (Santa Cruz, sc2028)


title: E145_12

value: Ret+/CFP Ednrbs/s


title: IgG_EMM_Jup24_Sox2Klf4


title: E145_11

value: male


title: E145_10


title: PC2416-DEC PDX [105147-001-083]


title: IgG_EMMplusNAM_Jup20_Sox2Klf4


title: IgG_SL_Jup20_Sox2Klf4


title: PC2416-DEC PDX [105147-001-084]


title: IgG_EMM_GLCp18_Sox2Klf4


title: IgG_EMMplusNAM_GLCp18_Sox2Klf4


title: sham_6

city: Changsha

first: En

last: Hu

state: Hunan

address: Kaifu Street, Xiangya Road No.87

department: Xiangya Hospital

country: China

institute: Central South university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
the read counts were adjusted by edgeR program package through one scaling normalized factor
Assembly: mm10
Supplementary files format and content: Excel files  include RPKM values for all Sample

source_name: brain

extract_protocol:
The total RNA is extracted by standard Trizol RNA extraction
TruSeq Stranded Total RNA Library Prep Kit (Illumina, RS-122-2001, San Diego, CA, USA)
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, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. 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.

value: brain

value: Sham operation


title: sham_5

value: WT


title: PC2416-DEC PDX [105147-001-081]


title: IgG_SL_GLCp18_Sox2Klf4


title: PC2416-DEC PDX [105147-001-080]

value: Vehicle


title: Klf4_EMM_Jup24


title: Klf4_SL_Jup24


title: IgG_EMM_Jup20_Sox2Klf4


title: PC2416-DEC PDX [105147-001-078]


title: sham_3


title: Klf4_EMM_Jup20


title: Klf4_EMMplusNAM_Jup24


title: IgG_SL_Jup24_Sox2Klf4


title: Klf4_SL_Jup20


title: sham_2


title: PC2416-DEC PDX [105147-001-079]


title: Klf4_EMMplusNAM_GLCp18


title: sham_1


title: ICH_6

value: ICH


title: sham_4


title: PC2416-DEC PDX [105147-001-082]


title: PC2416-DEC PDX [105147-001-077]


title: Klf4_SL_GLCp18

value: Mouse Embryonic Stem Cells


title: Klf4_EMM_GLCp18

value: Wild Type


title: PC2416-DEC PDX [105147-001-076]


title: Sox2_EMMplusNAM_Jup24


title: ICH_5


title: Sox2_SL_Jup24


title: PC2416-DEC PDX [105147-001-075]


title: Sox2_EMMplusNAM_Jup20


title: PC2416-DEC PDX [105147-001-074]


title: Sox2_EMM_Jup20


title: Sox2_SL_Jup20


title: ICH_2


title: PC2416-DEC PDX [105147-001-073]


title: Sox2_SL_GLCp18


title: ICH_3


title: Sox2_EMMplusNAM_GLCp18


title: Sox2_EMM_Jup24


title: PC2416 PDX [105147-001-063]


title: E145_98

value: Ret+/+ Ednrb+/s


title: E145_99


title: B1a B miR-15 dKO 4

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R20

data_processing:
single end reads were trimmed using Trimmomatic
aligned using STAR aligner
counted with FeatureCounts
Assembly: GRCm39
Supplementary files format and content: Excel file including all samples

source_name: bone marrow

extract_protocol:
RNeasy Micro Kit (Qiagen; 74004)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: FACS sorted B1a B cells

value: miR-15a/bfl/fl Vav-Cre

value: 10-12 weeks


title: ICH_1


title: E145_96

value: GI tract, stomach to colon

value: Ret+/+ Ednrbs/s


title: PC2416 PDX [105147-001-062]

value: prostate cancer cells

value: Docetaxel + darolutamide


title: E145_51

value: female


title: B1a B miR-15 dKO 2

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R18


title: ICH_4

value: brain


title: E145_3

value: Ret+/CFP Ednrb+/s

value: male


title: PC2416 PDX [105147-001-060]


title: Klf4_EMMplusNAM_Jup20


title: Sox2_EMM_GLCp18


title: PC2416 PDX [105147-001-059]


title: E145_18


title: B1a B, control 4

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R16

value: miR-15a/b+/+ Vav-Cre


title: B1a B, control 3

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R15


title: PC2416 PDX [105147-001-064]


title: PC2416 PDX [105147-001-058]


title: E145_105


title: E145_93


title: PC2416 PDX [105147-001-057]


title: sgRAC1 CRIPSR CAS9 clone 3 biological rep 2

city: Manchester

first: Martin

middle: James

last: Baker

state: England

address: 555 Wilmslow Rd

department: Division of Cancer Sciences

institute: University of Manchester

description: Library name: DU145_RAC1_biol_KO3_rep2

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 with adapter trimming turned off.
Alignment was performed using STAR v.2.6.1d and GRCh38 as a reference
Uniquely mapped reads were quantified at the exon level and summarized to gene counts using Rsubread
Counts were converted to units of TPM.
Differential expression analysis was performed with DESeq2  in R
Assembly: GRCh38
Supplementary files format and content: csv file with DESeq2 output

source_name: Prostate Cancer

growth_protocol: Cells were grown in 10% FBS RPMI

extract_protocol:
RNA was extracted from cells using TRIzol, followed by a chloroform treatment and RNA purified using the RNA clean and concentrator kit (Zymo Research).
Library preparation was performed using SMARTScribe reverse transcriptase (Takara bio) with 160 ng of RNA following the manufacturer’s protocol. Library amplification was performed using Advantage 2 DNA polymerase (Takara Bio). After cDNA fragmentation, the library underwent tagmentation and purified with SPRI beads (Beckman Coulter).

treatment_protocol: Cells were transfected with sgRNA:CAS9 complexes and plated as single cells. Clones were then selected and expanded followed by validation of the KO.

value: Prostate Cancer

value: Prostate cancer

tag: batch


title: PC2416 PDX [105147-001-061]


title: PC2416 PDX [105147-001-056]

value: Vehicle


title: sgRAC1 CRIPSR CAS9 clone 1 biological rep 2

description: Library name: DU145_RAC1_biol_KO1_rep2


title: B1a B, control 2

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R14


title: E145_85

value: Ret+/CFP Ednrbs/s


title: B1a B miR-15 dKO 3

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R19

value: bone marrow


title: B1a B, control 1

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R13

value: FACS sorted B1a B cells


title: B1a B miR-15 dKO 1

description:
RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol
R17

value: miR-15a/bfl/fl Vav-Cre


title: E145_15


title: sgNTC CRIPSR CAS9 clone 1 biological rep 2

description: Library name: DU145_NTC1_biol_rep2

value: WT


title: Parental DU145 cells biological rep 2

description: Library name: DU145_Parental_biol_rep2

value: Parental


title: E145_100

value: GI tract, stomach to colon

value: Ret+/+ Ednrbs/s


title: model 1_3

city: Wenzhou

first: meihong

last: wang

state: Zhejiang

address: Central North Road

institute: Wenzhou Medical University

description: APAP 400 mg/kg  for  6h

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver APAP

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice of sample 5 and 6 are pretreated with cos (20mg/kg) 12h and 40min  before i.p. of APAP (400mg/kg), and APAP last for 6h.

value: liver

value: APAP 400 mg/kg  for  6h


title: sgNTC CRIPSR CAS9 clone 2 biological rep 2

description: Library name: DU145_NTC2_biol_rep2


title: sgRAC1 CRIPSR CAS9 clone 2 biological rep 2

description: Library name: DU145_RAC1_biol_KO2_rep2


title: PC2416 PDX [105147-001-054]

value: prostate cancer cells


title: PC2416 PDX [105147-001-053]


title: E145_1

value: Ret+/CFP Ednrb+/s


title: E145_106

value: female


title: sgRAC1 CRIPSR CAS9 clone 1 biological rep 1

description: Library name: DU145_RAC1_biol_KO1_rep1


title: sgRAC1 CRIPSR CAS9 clone 2 biological rep 1

description: Library name: DU145_RAC1_biol_KO2_rep1


title: drug 2_3

description: cos 20mg/kg  pretreatment twice before i.p. of APAP

source_name: liver COS+APAP


title: sgRAC1 CRIPSR CAS9 clone 3 biological rep 1

description: Library name: DU145_RAC1_biol_KO3_rep1


title: PC2416 PDX [105147-001-052]

value: male


title: model 1_1

description: APAP 400 mg/kg  for  6h


title: drug 2_2

value: cos 20mg/kg  pretreatment twice before i.p. of APAP


title: sgNTC CRIPSR CAS9 clone 2 biological rep 1

description: Library name: DU145_NTC2_biol_rep1

value: Prostate Cancer

value: Prostate cancer


title: control 1_3

description: normal

source_name: liver con

value: control


title: PC2416 PDX [105147-001-051]

value: Vehicle


title: iPSC>SMCdifferentiation #1, RNAseR, day12, pooled samples

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

description: The RNAseR-treated samples were used just for identification of novel isoforms, which were quantified in all other samples. Thus there are no processed data as counts for these samples (just alignment files as BAMs).

data_processing:
Fastq-files were generated using Illumina bcl2fastq and demultiplexed.
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using FastQC software.
Sequenced reads were mapped to the reference genome GRch37 using HISAT2 for quantification of genes and transcripts and segemehl for quantification of circular RNAs.
Aligned reads were quantified using StringTie for genes and transcripts and featureCounts for circular RNAs.
Assembly: GRCh37
Supplementary files format and content: Genes: Tab-delimited text files include raw counts for each sample.
Supplementary files format and content: Transcripts: Tab-delimited text files include raw counts for each sample.
Supplementary files format and content: Circular RNAs: Tab-delimited text files include raw counts for each sample.

growth_protocol: The human iPS cell line ISFi001-A was maintained on hESC-qualified Matrigel (BD Biosciences)-coated dishes in mTeSR1 medium (StemCell Technologies).

extract_protocol:
Isolation of RNA was performed using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using Ovation Universal RNA-Seq System Kit (Nugen) following manufacturer's protocols.

treatment_protocol: The human iPS cells were differentiated according to Patsch et al. 2015 (PMID: 26214132).

value: Differentiated human pluripotent stem cells

tag: differentiation

tag: biological replicate

value: pool


title: Parental DU145 cells biological rep 1

description: Library name: DU145_Parental_biol_rep1

tag: tissue

value: WT


title: iPSC>SMCdifferentiation #1, RNAseR, day11, pooled samples

tag: treatment


title: PC2416 PDX [105147-001-050]


title: control 1_1

description: normal

tag: strain


title: PC2416 PDX [105147-001-049]


title: iPSC>SMCdifferentiation #1, RNAseR, day08, pooled samples


title: PC2400 PDX [105147-001-039]

value: Docetaxel + darolutamide


title: iPSC>SMCdifferentiation #1, RNAseR, day09, pooled samples


title: iPSC>SMCdifferentiation #1, RNAseR, day07, pooled samples


title: PC2416 PDX [105147-001-055]


title: PC2400 PDX [105147-001-037]


title: iPSC>SMCdifferentiation #1, RNAseR, day03, pooled samples


title: iPSC>SMCdifferentiation #1, RNAseR, day04, pooled samples


title: P0_25

value: colon


title: iPSC>SMCdifferentiation #1, RNAseR, day02, pooled samples


title: PC2400 PDX [105147-001-038]


title: sgNTC CRIPSR CAS9 clone 1 biological rep 1

description: Library name: DU145_NTC1_biol_rep1


title: iPSC>SMCdifferentiation #1, RNAseR, day01, pooled samples


title: iPSC>SMCdifferentiation #1, RNAseR, day00, pooled samples


title: iPSC>SMCdifferentiation #1, RNAseR, day10, pooled samples


title: PC2400 PDX [105147-001-036]


title: iPSC>ECdifferentiation #1, RNAseR, day11, pooled samples


title: iPSC>ECdifferentiation #1, RNAseR, day12, pooled samples


title: PC2400 PDX [105147-001-034]


title: PC2400 PDX [105147-001-035]


title: iPSC>ECdifferentiation #1, RNAseR, day10, pooled samples


title: iPSC>ECdifferentiation #1, RNAseR, day09, pooled samples


title: FGM4_3

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk and FASTX-Toolkit.
mRNA-seq reads were aligned to the Fusarium graminearum genome sequence using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.4
Expression levels from different samples were normalized by the DESeq2.
Differential expression were analysed  using edgeR.
Genome_build: Fusarium graminearum genome sequence (ASM24013v3)
Supplementary_files_format_and_content: Text files include normalized counts for each Sample

organism: Fusarium graminearum

source_name: FgM4 knock out strain (Δfgm4) cultured in minimal medium with 5mM agmatine as nitrogen source for 72h

growth_protocol: F. graminearum spores were grown in liquid medium for 48h/72h at 25°C and shaken at 180 rpm.

extract_protocol:
Total RNA was isolated using EasyPure Plant RNA kit (Transgen biotech) according to the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrated number (RIN) value of 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We generated three independent transgenic knockout strains (Δkmt6, Δset1, Δkmt3,Δfgm4) using homologous recombination-mediated knockout technology to replace the target gene with hygromycin resistance gene.

tag: genotype/variation

value: FgM4 knock out

tag: medium

value: MM-N+agmatine

value: hyphae


title: PC2400 PDX [105147-001-033]

value: prostate cancer cells


title: FGM4_2

value: FGM4 knock out


title: iPSC>ECdifferentiation #1, RNAseR, day07, pooled samples

tag: cell line


title: iPSC>SMCdifferentiation #1, RNAseR, day05, pooled samples


title: iPSC>SMCdifferentiation #1, RNAseR, day06, pooled samples


title: PC2400 PDX [105147-001-032]


title: iPSC>ECdifferentiation #1, RNAseR, day04, pooled samples


title: FGM4_1

source_name: FGM4 knock out strain (Δfgm4) cultured in minimal medium with 5mM agmatine as nitrogen source for 72h


title: iPSC>ECdifferentiation #1, RNAseR, day05, pooled samples


title: iPSC>ECdifferentiation #1, RNAseR, day03, pooled samples


title: PC2400 PDX [105147-001-031]


title: PC2400 PDX [105147-001-030]


title: iPSC>ECdifferentiation #1, RNAseR, day02, pooled samples


title: iPSC>ECdifferentiation #1, RNAseR, day01, pooled samples


title: spore2

source_name: spores of wild type strain

value: wild type

value: MM

value: spores


title: iPSC>ECdifferentiation #1, RNAseR, day00, pooled samples


title: Control Heart Tissue Replicate 2

type: genomic

city: Fuzhou

first: Jingmin

last: Li

state: Fujian

address: 18 Daoshan Road, Gulou District

department: department of gynecology

institute: Fujian Maternal and Child Health Hospital

description: Biological replicate 2 of 3. Neonatal rats of control SD rats given the same volume of saline during pregnancy.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Raw excel data files obtained from tiling array experiments were analyzed using NimbleScan v2.5 software.

data_processing: A one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log2-ratios than those in the rest of the array. Each probe receives a -log10 p-value score from the windowed KS test around that probe.

organism: Rattus norvegicus

source_name: MeDIP DNA_Newborn - Control - Methylation

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours.

growth_protocol: Rats were housed under 12/12h -light/dark pathogen-free conditions for 1 week after acclimatization to start experimental manipulations, with relative temperature (25±2) °C and humidity (55±5) % in the animal room, allowing free access to food and water.

extract_protocol: The fetal hearts were rapidly isolated after euthanasia.

treatment_protocol: Rats were anesthetized by inhalation of ether until they became unconscious and their breathing slowed to an appropriate, steady rate.An epidural catheter cut to the appropriate length was tightly attached to the catheter tip,  Insert the catheter to a depth of approximately 1 cm above the tracheal bifurcation, take an amount of 30 μL of NS, or different concentrations of PM2.5 suspension with a pipette, align the pipette tip with the catheter connector, a moderate and steady drip of the reagent into the trachea within a few seconds of each breath.

value: day 1

value: SD

value: cardiac muscle

source_name: Input DNA_Newborn - Control - Methylation


title: iPSC>SMCdifferentiation #2, total RNA, day12, biological replicate #3

description:
counts_raw_genes_SMC.txt
counts_raw_transcripts_SMC.txt


title: PM2.5 Exposure Heart Tissue Replicate 1

description: Biological replicate 1 of 3. Neonatal rats of PM2.5 exposure SD rats given the same volume of PM2.5 during pregnancy.

source_name: MeDIP DNA_Newborn - PM2.5 - Methylation

source_name: Input DNA_Newborn - PM2.5 - Methylation


title: PC2400 PDX [105147-001-029]

value: Vehicle

value: male


title: iPSC>ECdifferentiation #1, RNAseR, day08, pooled samples

value: Differentiated human pluripotent stem cells

value: pool


title: PM2.5 Exposure Heart Tissue Replicate 2

description: Biological replicate 2 of 3. Neonatal rats of PM2.5 exposure SD rats given the same volume of PM2.5 during pregnancy.


title: Control Heart Tissue Replicate 3

description: Biological replicate 3 of 3. Neonatal rats of control SD rats given the same volume of saline during pregnancy.


title: iPSC>SMCdifferentiation #2, total RNA, day12, biological replicate #1


title: spore1


title: Control Heart Tissue Replicate 1

description: Biological replicate 1 of 3. Neonatal rats of control SD rats given the same volume of saline during pregnancy.


title: PM2.5 Exposure Heart Tissue Replicate 3

description: Biological replicate 3 of 3. Neonatal rats of PM2.5 exposure SD rats given the same volume of PM2.5 during pregnancy.


title: KMT3_3

source_name: kmt3 knock out strain (Δset1) cultured in minimal medium for 72h

value: kmt3 knock out


title: KMT3_1


title: iPSC>SMCdifferentiation #2, total RNA, day06, biological replicate #2


title: iPSC>SMCdifferentiation #2, total RNA, day12, biological replicate #2


title: KMT6_3

source_name: kmt6 knock out strain (Δset1) cultured in minimal medium for 72h

value: kmt6 knock out


title: PC2400 PDX [105147-001-028]


title: spore3


title: iPSC>ECdifferentiation #1, RNAseR, day06, pooled samples


title: iPSC>SMCdifferentiation #2, total RNA, day09, biological replicate #2


title: PC2400 PDX [105147-001-027]


title: iPSC>SMCdifferentiation #2, total RNA, day03, biological replicate #3


title: iPSC>SMCdifferentiation #2, total RNA, day09, biological replicate #3


title: PC2400 PDX [105147-001-025]


title: iPSC>SMCdifferentiation #2, total RNA, day06, biological replicate #3


title: KMT3_2


title: PC2400 PDX [105147-001-026]


title: iPSC>SMCdifferentiation #2, total RNA, day06, biological replicate #1


title: PC346C PDX [105147-001-016]

value: Docetaxel + darolutamide


title: iPSC>SMCdifferentiation #2, total RNA, day03, biological replicate #2


title: KMT6_2


title: iPSC>SMCdifferentiation #2, total RNA, day03, biological replicate #1


title: iPSC>SMCdifferentiation #2, total RNA, day09, biological replicate #1


title: PC346C PDX [105147-001-015]


title: iPSC>SMCdifferentiation #2, total RNA, day00, biological replicate #3

description:
counts_raw_genes_SMC.txt
counts_raw_transcripts_SMC.txt
counts_raw_circRNAs_SMC.txt


title: iPSC>SMCdifferentiation #2, total RNA, day00, biological replicate #2


title: iPSC>SMCdifferentiation #2, total RNA, day00, biological replicate #1


title: PC346C PDX [105147-001-014]


title: KMT6_1


title: SET1_3

source_name: set1 knock out strain (Δset1) cultured in minimal medium for 72h

value: set1 knock out


title: iPSC>ECdifferentiation #2, total RNA, day12, biological replicate #3

description:
counts_raw_genes_EC.txt
counts_raw_transcripts_EC.txt


title: PC346C PDX [105147-001-013]

source_name: prostate cancer cells


title: PC346C PDX [105147-001-012]


title: iPSC>ECdifferentiation #2, total RNA, day09, biological replicate #2


title: iPSC>ECdifferentiation #2, total RNA, day09, biological replicate #1


title: PC346C PDX [105147-001-011]


title: SET1_1

value: hyphae


title: iPSC>ECdifferentiation #2, total RNA, day06, biological replicate #3


title: iPSC>ECdifferentiation #2, total RNA, day06, biological replicate #2


title: iPSC>ECdifferentiation #2, total RNA, day03, biological replicate #3


title: PC346C PDX [105147-001-010]

value: prostate cancer cells


title: iPSC>ECdifferentiation #2, total RNA, day12, biological replicate #1


title: SET1_2


title: iPSC>ECdifferentiation #2, total RNA, day06, biological replicate #1


title: MA72_3

source_name: wild type strain cultured in minimal medium with 5mM agmatine as nitrogen source for 72h

value: MM-N+agmatine


title: MA72_2

value: wild type


title: MA72_1


title: iPSC>ECdifferentiation #2, total RNA, day03, biological replicate #2


title: PC346C PDX [105147-001-008]


title: iPSC>ECdifferentiation #2, total RNA, day03, biological replicate #1


title: MA48_3

source_name: wild type strain cultured in minimal medium with 5mM agmatine as nitrogen source for 48h


title: iPSC>ECdifferentiation #2, total RNA, day00, biological replicate #3

description:
counts_raw_genes_EC.txt
counts_raw_transcripts_EC.txt
counts_raw_circRNAs_EC.txt


title: iPSC>ECdifferentiation #2, total RNA, day12, biological replicate #2


title: MA48_2


title: PC346C PDX [105147-001-006]


title: iPSC>ECdifferentiation #2, total RNA, day00, biological replicate #2


title: iPSC>ECdifferentiation #2, total RNA, day09, biological replicate #3


title: hiPSC>SMC differentiation #1, total RNA, day12, biological replicate #4


title: iPSC>ECdifferentiation #2, total RNA, day00, biological replicate #1


title: PC346C PDX [105147-001-009]


title: MA48_1


title: hiPSC>SMC differentiation #1, total RNA, day12, biological replicate #2


title: PC346C PDX [105147-001-005]


title: hiPSC>SMC differentiation #1, total RNA, day12, biological replicate #1


title: M72_2

source_name: wild type strain cultured in minimal medium for 72h

value: MM


title: M72_3


title: PC346C PDX [105147-001-004]


title: hiPSC>SMC differentiation #1, total RNA, day11, biological replicate #3


title: hiPSC>SMC differentiation #1, total RNA, day10, biological replicate #4


title: M72_1


title: PC346C PDX [105147-001-003]


title: hiPSC>SMC differentiation #1, total RNA, day11, biological replicate #1


title: hiPSC>SMC differentiation #1, total RNA, day11, biological replicate #2


title: PC346C PDX [105147-001-002]


title: M48_3

source_name: wild type strain cultured in minimal medium for 48h


title: hiPSC>SMC differentiation #1, total RNA, day10, biological replicate #3


title: hiPSC>SMC differentiation #1, total RNA, day10, biological replicate #2


title: PC346C PDX [105147-001-007]


title: M48_2


title: hiPSC>SMC differentiation #1, total RNA, day10, biological replicate #1


title: hiPSC>SMC differentiation #1, total RNA, day12, biological replicate #3


title: M48_1


title: hiPSC>SMC differentiation #1, total RNA, day09, biological replicate #4


title: Healthy control 5 [25]

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

description:
25
10x Genomics

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on hg38 reference genome and quantification with gencode v42 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: skin

extract_protocol:
We included patients with skin lesions of VEXAS syndrome (n=6), myelodysplasia-cutis (n=4), idiopathic sweet syndrome (n=5) and leukemia cutis (n=5). Five healthy controls (HC) were recruited for skin biopsy from plastic breast surgery waste. The study was approved by the by our institutional ethic committee, and all patients were consented. Total RNA was automatically extracted from one lesional formaldehyde-fixed and paraffin-embedded skin biopsy for each patient and control using the Maxwell RSC RNA FFPE kit according to the manufacturer’s protocol.
SMARTer® Stranded Total RNA-Seq Kit v3-Pico Input Mammalian Kit from Takara

value: skin

value: female

tag: disease

value: Healthy control


title: hiPSC>SMC differentiation #1, total RNA, day09, biological replicate #2

tag: cell type


title: hiPSC>SMC differentiation #1, total RNA, day09, biological replicate #3


title: Healthy control 4 [24]

description:
24
10x Genomics


title: WGBS, round sperm, Daxx knockdown, biol rep2

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

description: Library name: Sample 40

data_processing:
Adapters and low qualities bases were trimmed with Trim Galore (0.6.10)，the clean reads were aligned to the UCSC mm39 genome carried out with Bismark (v0.24.2)with the following set of parameters: –score_min L,0,-0.4, which incorporates Bowtie2(2.5.4). CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor. Only CpGs covered by a minimum of three reads were retained for downstream analyses in each replicate.
Assembly: UCSC mm39
Supplementary files format and content: bed file includes Methylation information at CpG sites

source_name: testis

extract_protocol:
After samples DNA testing, positive control DNAs were added into the DNAs, and then they were fragmented into 200-400bp using Covaris S220 (Covaris, USA).
Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragments. The library kit is Accel-NGS Methyl-Seq DNA Library Kit (Swift, USA, Catalog #:30096). Subsequently, library quality was assessed on the Agilent 5

value: testis

value: round sperm

tag: genotype

value: DAXX knockdown


title: hiPSC>SMC differentiation #1, total RNA, day11, biological replicate #4

value: Differentiated human pluripotent stem cells


title: hiPSC>SMC differentiation #1, total RNA, day08, biological replicate #4


title: WGBS, round sperm, Daxx knockdown, biol rep1

description: Library name: Sample 39


title: Healthy control 2 [22]

description:
22
10x Genomics

tag: Sex


title: hiPSC>SMC differentiation #1, total RNA, day08, biological replicate #3

tag: time


title: hiPSC>SMC differentiation #1, total RNA, day08, biological replicate #2


title: hiPSC>SMC differentiation #1, total RNA, day09, biological replicate #1


title: WGBS, round sperm, Wild type, biol rep2

description: Library name: Sample 38

value: WT


title: Healthy control 3 [23]

description:
23
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day07, biological replicate #4


title: Healthy control 1 [21]

description:
21
10x Genomics


title: WGBS, round sperm, Wild type, biol rep1

description: Library name: Sample 37


title: PC346C PDX [105147-001-001]

value: Vehicle

value: male


title: WGBS, meiotic cells, Daxx knockdown, biol rep2

description: Library name: Sample 36

value: meiotic cells


title: hiPSC>SMC differentiation #1, total RNA, day07, biological replicate #2


title: hiPSC>SMC differentiation #1, total RNA, day07, biological replicate #1


title: MDS-cutis 4 [19]

description:
19
10x Genomics

value: MDS-cutis


title: hiPSC>SMC differentiation #1, total RNA, day06, biological replicate #4


title: WGBS, meiotic cells, Daxx knockdown, biol rep1

description: Library name: Sample 35


title: hiPSC>SMC differentiation #1, total RNA, day06, biological replicate #3


title: hiPSC>SMC differentiation #1, total RNA, day06, biological replicate #2


title: MDS-cutis 3 [18]

description:
18
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day06, biological replicate #1


title: hiPSC>SMC differentiation #1, total RNA, day05, biological replicate #4


title: WGBS, meiotic cells, Wild type, biol rep2

description: Library name: Sample 34


title: hiPSC>SMC differentiation #1, total RNA, day05, biological replicate #2


title: WGBS, meiotic cells, Wild type, biol rep1

description: Library name: Sample 33


title: hiPSC>SMC differentiation #1, total RNA, day08, biological replicate #1


title: Prrx1-Cre Pdgfra GOF E13.5 biol rep 2

city: Oklahoma city

first: Lorin

last: Olson

institute: OMRF

description:
Library name: F1123_2
10x Genomics

data_processing:
The 10X Genomics Cellranger software (version 6.0.2) pipeline was run for demultiplexing and sequence alignment to the murine mm10 genome reference.
Assembly: Mouse mm10
Supplementary files format and content: Cellranger output files: *barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz

source_name: Hindlimb

extract_protocol:
At E13.5, hindlimbs were harvested in ice cold PBS and the paws were removed. The samples were digested in 0.25% trypsin-EDTA for 1hr at 37 oC. For E15.5, knees were dissected in ice cold pbs and digested in 3 mg/ml collagenase D in DMEM for 45 minutes at 37 oC. They were then digested in 1 mg/ml collagenase D in DMEM for 3 hours at 37 oC. Following digestion, samples from both timepoints were gently dissociated by pipetting, filtered through a 40 μm strainer, and centrifuged for 10 minutes at 400 g. The cells resuspended in 0.4% FBS in PBS at a concentration of 1000/μL.
Samples (maximum 10,000 cells per sample) were loaded on the 10X Genomics Chromium platform, barcoded, and sequenced on the Illumina NovaSeq SP flowcell platform at a depth of 500 million reads per sample.

value: Hindlimb

value: Prrx1-Cre Pdgfra GOF


title: hiPSC>SMC differentiation #1, total RNA, day05, biological replicate #3


title: Leukemia-cutis 5 [15]

description:
15
10x Genomics

value: Leukemia-cutis


title: Prrx1-Cre E13.5 biol rep 2

description:
Library name: F1123_1
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day04, biological replicate #3


title: hiPSC>SMC differentiation #1, total RNA, day04, biological replicate #1


title: MDS-cutis 1 [16]

description:
16
10x Genomics


title: VEXAS syndrome 6 [20]

description:
20
10x Genomics

value: VEXAS syndrome


title: Prrx1-Cre Pdgfra GOF E13.5 biol rep 1

description:
Library name: E3140.2
10x Genomics


title: MDS-cutis 2 [17]

description:
17
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day04, biological replicate #2


title: Leukemia-cutis 3 [13]

description:
13
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day03, biological replicate #4


title: Prrx1-Cre E13.5 biol rep 1

description:
Library name: E3140.1
10x Genomics


title: WT_Microglia_mouse2

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

institute: UCL

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
After transcardial perfusion, the brains of four female mice, two from SFFV.GILT and two from the SFFV.GAAco experimental groups were processed by enzymatic digestion (Neural Tissue Dissociation Kit (P), Miltenyi Biotec). The resulting single cell suspensions were stained with viability dye and antibodies for microglia cells, neurons, astrocytes and endothelial cells (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher; CD45.1 clone A20 in BV421 (BD); CD45.2 clone 104 in BV421 (BD); CD11b clone M1/70 in APC-780 (ThermoFisher); CX3CR1 clone SA011F11 in BV605 (BioLegend); PECy7 Thy1.1 (also known as CD90.1) clone OX-7 in PE-Cy7 (BD); Thy1.2 (also known as CD90.2) clone 53-2.1 in PE-Cy7 (BD); ACSA-2 clone IH3-18A3 in PE (Miltenyi Biotec); CD31 clone 390 in PerCP/Cy5.5 (BioLegend). Microglia cells, defined as CD45+ CD11b+ Cx3cr1+, were FACSsorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology).
For the generation of single cell transcriptomes, a target cell number of 2.5E3 or 5E3 cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 (WT vs Pompe microglia datasets) or the NovaSeq 6000 (GILT vs GAAco datasets) Sequencing System (Illumina) using either the using NextSeq 500/550 High Output v2.5 (150 cycles) Kit or the NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles) Kit (Illumina).

value: Microglia

value: Brain

tag: age

value: 32 weeks


title: hiPSC>SMC differentiation #1, total RNA, day03, biological replicate #3


title: Leukemia-cutis 2 [12]

description:
12
10x Genomics

value: skin


title: hiPSC>SMC differentiation #1, total RNA, day03, biological replicate #2


title: hiPSC>SMC differentiation #1, total RNA, day05, biological replicate #1


title: Leukemia-cutis 1 [11]

description:
11
10x Genomics

value: female


title: Prrx1-Cre E15.5 biol rep 2

description:
Library name: B211_4
10x Genomics

source_name: Knee

value: Knee


title: Leukemia-cutis 4 [14]

description:
14
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day07, biological replicate #3


title: PompeKO_Microglia_mouse2

description: 10x Genomics

value: Gaatm1Rabn/J mice (Gaa-/- mice, Pompe mice)


title: Idiopathic sweet syndrome 5 [10]

description:
10
10x Genomics

value: Idiopathic sweet syndrome


title: PompeKO_Microglia_mouse1

description: 10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day02, biological replicate #4

value: Differentiated human pluripotent stem cells


title: Solid_WB_r3_RNA-seq

city: Koto-ku

first: Yutaka

last: Saito

state: Tokyo

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: RNA-seq for hyphae from solid culture with WB replicate 3

data_processing:
Base-calling and de-multiplexing were conducted by HCS version 2.2.58, RTA version 1.18.64, and bcl2fastq version 1.8.3. Reads were adapter-trimmed and quality-filtered by cutadapt version 1.1 and Trimmomatic version 0.32.
Read mapping was performed by TopHat2 version 2.1.1 where the gene annotation GFF file was used as the transcriptome reference.
Expression levels were measured as fragments per kbp per million mapped reads (FPKM) by Cufflinks version 2.2.1.
For differential expression analysis, the number of reads mapped to each gene was counted by HTSeq version 0.7.2, and differentially expressed genes (DEGs) were detected by edgeR version 3.20.9. DEGs were defined as genes with the false discovery rate (FDR) < 0.05 and the more than 2-fold expression change between CD-Glc and WB.
The read mapping statistics and the detail setting of program options were provided in Supplementary Material.
Genome_build: The reference genome sequence and the gene annotation of the A. oryzae RIB40 strain (revision s01-m09-r05) were downloaded from AspGD.
Supplementary_files_format_and_content: Tab-delimited text files that include the number of reads mapped for each gene.

organism: Aspergillus oryzae RIB40

source_name: Solid culture with WB replicate 3

growth_protocol: The Aspergillus oryzae wild-type strain RIB40 was distributed by the National Research Institute of Brewing (NRIB, Hiroshima, Japan). The strain was maintained at 30°C on Czapek–Dox (CD) agar containing 2% glucose for spore formation (Tamano et al. 2007). Liquid culture (CD-Glc) was performed by inoculating 2.5 × 107 spores of RIB40 to 50 mL of CD liquid medium in a 250-mL flask, followed by incubation at 30°C with shaking at 200 rpm for 48 h. Solid medium was prepared by mixing 2.8 g of wheat bran with Milli-Q water (2.2 mL) in a 150 mL flask, followed by autoclaving at 121°C for 30 min as previously described (Tamano et al. 2008). Solid culture (WB) was performed by inoculating 1 × 107 spores of RIB40 per flask, followed by stationary incubation at 30°C for 20 h. Then, the medium with hyphae was mixed by shaking the flask, and incubated similarly for another 28 h.

extract_protocol:
Hyphae were harvested and immediately ground based on the same protocol as the DNA extraction for bisulfite-seq. All frozen powders of ground hyphae were transferred to 10 mL of ISOGEN reagent (Nippongene, Toyama, Japan), and then total RNA was extracted using a spin column attached to ISOGEN according to the manufacturer’s protocol. Contaminating chromosomal DNA was removed from total RNA by the treatment with RNase-free DNase I (New England Biolabs, Ipswich, MA, USA). DNase I-treated total RNA was then applied to RNeasy® mini kit (QIAGEN, Hilden, Germany) for purification. RNA was finally eluted by 100 µL of nuclease-free water in a purified form, and stored at -80°C.
Sequencing experiments were conducted by the outsourcing company (Hokkaido System Science, Japan). Briefly, RNA quality was checked by NanoDrop (Thermo Fisher Scientific, USA) and BioAnalyzer 2100 (Agilent Technologies, USA). For each sample, 2 µg of RNA was used for library construction by TruSeq Stranded mRNA Sample Prep Kit following the manufacturer's protocol. Paired-end 101 bp reads were obtained by HiSeq 2500 (Illumina, USA).

value: Hyphae


title: hiPSC>SMC differentiation #1, total RNA, day03, biological replicate #1


title: Idiopathic sweet syndrome 4 [9]

description:
9
10x Genomics


title: Prrx1-Cre Pdgfra GOF E15.5 biol rep 1

description:
Library name: B211_1
10x Genomics


title: Prrx1-Cre Pdgfra GOF E15.5 biol rep 2

description:
Library name: B211_2
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day02, biological replicate #3


title: CAS_2_10h_G

first: Xiaowei

last: Chai

address: Siping Road

institute: Tongji University

description: Library name: Treated_10h_2 rep 3

data_processing:
Fastp (0.20.1), HISAT2(2.1.0), DESeq2(1.22.2)
Raw reads of fastq format were firstly processed using fastp software and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2
Differential expression analysis was performed using the DESeq2
Assembly: C_albicans_SC5314_A22_current_chromosomes
Supplementary files format and content: xls files includes FPKM values for each Sample

organism: Candida albicans SC5314

source_name: Candida albicans SC5314

growth_protocol: Candida albicans was cultured in RPMI1640 medium at a constant temperature of 30°C for 6 hours and 10 hours.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Candida albicans was cultured  in RPMI1640 medium at 30°C for 6 hours and 10 hours in the presence of the compound at concentrations of 0.5 μg/mL and 2 μg/mL.

value: Candida albicans SC5314

value: 2 μg/mL compound


title: hiPSC>SMC differentiation #1, total RNA, day02, biological replicate #2


title: Solid_WB_r2_RNA-seq

description: RNA-seq for hyphae from solid culture with WB replicate 2

source_name: Solid culture with WB replicate 2


title: Idiopathic sweet syndrome 3 [8]

description:
8
10x Genomics


title: Idiopathic sweet syndrome 2 [7]

description:
7
10x Genomics


title: CAS_2_10h_F

description: Library name: Treated_10h_2 rep 2


title: hiPSC>SMC differentiation #1, total RNA, day04, biological replicate #4


title: Idiopathic sweet syndrome 1 [6]

description:
6
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day02, biological replicate #1


title: WT_Microglia_mouse1

description: 10x Genomics


title: CAS_2_10h_E

description: Library name: Treated_10h_2 rep 1


title: Prrx1-Cre E15.5 biol rep 1

description:
Library name: B211_3
10x Genomics


title: Liquid_CD-Glc_r3_RNA-seq

description: RNA-seq for hyphae from liquid culture with CD-Glc replicate 3

source_name: Liquid culture with CD-Glc replicate 3


title: CAS_05_10h_G

description: Library name: Treated_10h_05 rep 3

value: 0.5 μg/mL compound


title: hiPSC>SMC differentiation #1, total RNA, day01, biological replicate #4


title: VEXAS syndrome 5 [5]

description:
5
10x Genomics

value: male


title: hiPSC>SMC differentiation #1, total RNA, day01, biological replicate #3


title: VEXAS syndrome 3 [3]

description:
3
10x Genomics


title: Liquid_CD-Glc_r2_RNA-seq

description: RNA-seq for hyphae from liquid culture with CD-Glc replicate 2

source_name: Liquid culture with CD-Glc replicate 2


title: VEXAS syndrome 4 [4]

description:
4
10x Genomics


title: hiPSC>SMC differentiation #1, total RNA, day01, biological replicate #1


title: CAS_05_10h_F

description: Library name: Treated_10h_05 rep 2


title: hiPSC>SMC differentiation #1, total RNA, day01, biological replicate #2


title: VEXAS syndrome 2 [2]

description:
2
10x Genomics


title: CAS_05_10h_E

description: Library name: Treated_10h_05 rep 1


title: Solid_WB_r1_RNA-seq

description: RNA-seq for hyphae from solid culture with WB replicate 1

source_name: Solid culture with WB replicate 1


title: Liquid_CD-Glc_r1_RNA-seq

description: RNA-seq for hyphae from liquid culture with CD-Glc replicate 1

source_name: Liquid culture with CD-Glc replicate 1


title: CON_10h_G

description: Library name: Untreated_10h rep 3

value: Control


title: CON_10h_F

description: Library name: Untreated_10h rep 2