title: wounded versus non wounded repl. 2

description: Biological replicate 2 of 2. Locally damaged and intact tissues

value: 4 weeks


title: Boscalid, uninfected biol rep 1

status: Public on Apr 22 2024

type: SRA

city: Winnipeg

first: Mark

last: Belmonte

state: MB

address: 50 Sifton Road

country: Canada

institute: University of Manitoba

description:
BoscU1
B.napus_RawCounts.txt

library_source: transcriptomic

data_processing:
Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: B.napus genome v5.0 - GenBank assembly accession: GCA_000751015.1 (Chalhoub et al. 2014)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: B.napus_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to B. napus
Supplementary files format and content: S.sclerotiorum_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum

molecule: total RNA

organism: Brassica napus

source_name: Leaf

growth_protocol: Canola (B. napus) cultivar Westar was grown to the 30% flowering stage in Sungrow mix #4 supplemented with Osmocote fertilizer (1.5-2g/pot) in pots sized 8.5cm x 8.5cm x 9cm. Plants were grown in greenhouse, long day conditions.

extract_protocol:
RNA was extracted using the Qiagen RNEasy Plant Mini Kit with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000)

treatment_protocol: Plants were treated with 4.5mL of foliar spray treatment per plant. Treatments consisted of distilled water, 40mM boric acid (as a boron source), and 10 ppm boscalid. Treatment remained on the plants for 24 hours prior to incoulation. As inoculant, 4.0mL of S. sclerotiorum ascospore suspension was sprayed onto plants (1x10^6 spores/mL in potato dextrose broth). Plants then went into a humidty chamber to maintain 90-100% humidity for four day sto allow for infection to progress. At this point, leaves were collected and flash frozen in liquid N  as samples for RNA extraction.

tag: tissue

value: Leaf

tag: cell line

value: Cultivar - Westar

tag: treatment

value: Boscalid, uninfected


title: Day7,naïve,replicate1

city: Cincinnati

first: Michael

last: Jankowski

state: OH

address: 3333 Burnet Ave

department: Anesthesia

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Datasets were processed and analyzed using an in-house automated pipeline ; the following steps describe briefly the characteristics of the NextGenAligner pipeline.
Basic quality control for raw sequencing reads was performed using FASTQC (version 0.11.2) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The quality controlled reads were aligned to the reference human genome (hg19; chromosomes 1-22, X, Y, M) using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012).
Adapter sequences were removed using Trim Galore (version 0.4.2) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper script that runs cutadapt (version 1.9.1) to remove the detected adapter sequence from the reads.
Aligned reads were then sorted using samtools (version 1.8)(Li et al., 2009) and duplicate reads were removed using picard (version 1.89) (https://broadinstitute.github.io/picard/).
Peaks were called using MACS2 (version 2.1.0) (https://github.com/taoliu/MACS)(Zhang et al., 2008).
ENCODE blacklist regions (Amemiya et al., 2019) were removed
Assembly: mm9
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format, peak text files in standard MACS2 output format for narrow peak mode (columns : chromosome,start,end,name,score,strand,signalValue,pValue,qValue,peak)
Supplementary files format and content: Normalized bigwig files are generated using a scaling factor proportional to the total number of reads in the BAM file

molecule: genomic DNA

organism: Mus musculus

source_name: Peritoneal isolated

extract_protocol:
Transposase Tn5 with adapter sequences was used to cut accessible DNA (Buenrostro et al. 2015).
Accessible DNA with adaptor sequences were isolated, then libraries were prepared from 17-50,000 cells using the OMNI protocol (Corces et al. 2017).

value: Peritoneal isolated

tag: cell type

value: Macrophage

tag: genotype

value: LysM;TdTomato

value: naive

tag: time

value: Day 7


title: Untreated control, uninfected biol rep 3

description:
UTCU3
B.napus_RawCounts.txt

value: Control, uninfected


title: senescent, METTL3, HiChIP

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
library strategy: HiChIP-seq
Raw fastq files were demultiplexed and HiC-Pro 3.1.0 was used to align the reads to the hg19 human genome.
Reads were assigned to MboI restriction site and duplicated reads were removed.
hichipper 0.7.7 were used for loop calling using a restriction fragment-aware approach based on pre-determined narrow peaks.
Loops that passed FDR < 0.05 was considered significant.
Assembly: hg19
Supplementary files format and content: interaction mango files

organism: Homo sapiens

source_name: IMR90 cells

growth_protocol: IMR90 primary human diploid lung embryonic fibroblasts were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), l-glutamine, sodium pyruvate, non-essential amino acids, sodium bicarbonate and 1% penicillin-streptomycin under low oxygen tension (2%).

extract_protocol:
IMR90 cells were fixed in freshly made 1% formaldehyde at room temperature for 10 min followed by quenching with 125 mM glycine. Samples was lysed in ice-cold Hi-C lysis (10 mM Tris, pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630 with protease inhibitors) buffer and digested with MboI for 2 h at 37°C.
IP samples were reversed-crossed, pulled down with streptavidin C1 beads and went through tagmentation by transposaseTn5. Samples were amplified with certain cycle numbers according to qPCR with 5-cycle pre-amplified library.

treatment_protocol: Senescence was induced in primary human lung fibroblasts (IMR90) cells through the inducible expression of a fusion protein (estrogen receptor and H-RASG12V, ER: RAS). METTL3 HiChIP-seq was performed to monitor three-dimensional (3D) chromatin organization in control and senescent IMR90 cells.

value: IMR90 cells

value: human fibroblast

value: WT

value: senescent


title: HC21-V2D0, PBMC

city: Chicago

first: Kai

last: Huang

state: IL

address: 909 S. Wolcott Ave COMRB Room 3060

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Sequence reads were trimmed for adaptor/low quality sequences using fastp with default settings.
Reads were mapped to hg38 and quantified using salmon v1.6.0 with default settings.
Reads were imported into a count matrix using the R package tximeta
Assembly: hg38
Supplementary files format and content: raw unormalized count matrix with all samples is supplied in csv format.

source_name: peripheral blood

extract_protocol:
PBMCs were extracted from heparinized blood using Ficoll-Paque PLUS (Cytiva) density gradient centrifugation. Extracted cells were preserved in -80 in RNAlater (Invitrogen). RNA was harvested using the PureLink RNA Mini kit (Invitrogen).
RNA libraries were prepared using 50ng of RNA with the NEBNext Ultra II Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer directions.

value: peripheral blood

value: PBMC

tag: disease

value: healthy control

tag: batch

tag: sars cov2_hx

value: Yes

tag: age

tag: gender

value: Male

tag: diabetes

value: No


title: Day35,naïve,replicate3

value: Day 35


title: HC26-V1D0, PBMC


title: Untreated control, uninfected biol rep 2

description:
UTCU2
B.napus_RawCounts.txt

value: Leaf

value: Cultivar - Westar


title: HC21-V1D7, PBMC


title: Untreated control, uninfected biol rep 1

description:
UTCU1
B.napus_RawCounts.txt


title: control, METTL3, HiChIP

value: control


title: HC21-V1D1, PBMC


title: Day35,naïve,replicate1

value: Peritoneal isolated

value: Macrophage

value: LysM;TdTomato

value: naive


title: HC21-V1D0, PBMC


title: senescent, METTL14 knockdown, H3K27Ac, HiChIP-seq

data_processing:
library strategy: HiChIP-seq
Raw fastq files were demultiplexed and HiC-Pro 3.1.0 was used to align the reads to the hg19 human genome.
Reads were assigned to MboI restriction site and duplicated reads were removed.
hipper 0.7.7 were used for loop calling using a restriction fragment-aware approach based on pre-determined narrow peaks.
Loops that passed FDR < 0.01 with at least 4 reads was considered significant.
Assembly: hg19
Supplementary files format and content: interaction mango files

treatment_protocol: Senescence was induced in primary human lung fibroblasts (IMR90) cells through the inducible expression of a fusion protein (estrogen receptor and H-RASG12V, ER: RAS). H3K27Ac HiChIP-seq was performed to monitor enhancer- and promoter-centered interactions in control and senescent IMR90 cell lines with vector, METTL3, or METTL4 knockdown.

value: IMR90 cells

value: human fibroblast


title: senescent, METTL3 knockdown, H3K27Ac, HiChIP-seq

value: senescent


title: Day35,Day7-incised,replicate3

value: incised


title: Day35,naïve,replicate2


title: senescent, control knockdown, H3K27Ac, HiChIP-seq

value: shcontrol


title: HC20-V2D1, PBMC

value: peripheral blood

value: PBMC

value: healthy control


title: Day35,Day7-incised,replicate2


title: control, H3K27Ac, HiChIP-seq

value: WT


title: HC20-V2D7, PBMC

value: No

value: Male


title: HC20-V1D7, PBMC


title: Day35,Day7-incised,replicate1

value: Day 35


title: senescent, shMETTL14, KAS-seq, input

data_processing:
library strategy: kethoxal-assisted single-stranded DNA sequencing (KAS-seq)
Reads were trimmed using trim-galore and low-quality reads or duplicates were removed.
Aligned reads were extended to 150 bp to fit the average length of DNA fragments from the KAS-seq libraries.
Bedtools were used to convert Bam files to bed files and bedGraph files.
Bigwig files were generated by using ucsc-bedgraphtobigwig tools.
Assembly: hg19

extract_protocol:
IMR90 cells were incubated in media with 5 mM N3-kethoxal for 10 min at 37°C. Cells were pelleted and labelled genomic DNA (gDNA) was extracted by using Quick gDNA mini plus kit. DNA was eluted with 25 mM K3BO3 (pH 7.0) and went through click reaction with 20 mM DBCO-PEG4-biotin in PBS solution.
Biotinylated gDNA was fragmented by Tn5 transposase at 37°C for 30 min. Fragmented DNA was purified and eluted by DNA Clean & Concentrator-5 kit and was pulled down by streptavidin C1 beads. DNA-conjugated beads and corresponding inputs were used for library construction by using index primers and purified by two-sided size selection with Ampure XP beads.

treatment_protocol: Senescence was induced in primary human lung fibroblasts (IMR90) cells through the inducible expression of a fusion protein (estrogen receptor and H-RASG12V, ER: RAS). KAS-seq was performed to monitor transcriptional activation in control and senescent IMR90 cells with vector, METTL3, and METTL14 knockdown.


title: senescent, shMETTL14, KAS-seq, IP


title: HC20-V2D0, PBMC


title: HC20-V1D1, PBMC


title: HC20-V1D0, PBMC


title: senescent, shMETTL3, KAS-seq, IP


title: HC19-V2D7, PBMC

value: Female

value: Yes


title: senescent, shMETTL3, KAS-seq, input


title: HC19-V2D1, PBMC


title: senescent, shcontrol, KAS-seq, IP


title: mpglr-7 systemic 3

city: Madrid

first: Enrique

last: Rojo

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

country: Spain

institute: CSIC

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter out the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. Clean reads were mapped to Genome build MpTak1v5.1r2 with HISAT2 and read counts per gene were measured using HTseq-count
Assembly: MpTak1v5.1r2
Supplementary files format and content: Tab-delimited text file includes FPKM data for each sample

organism: Marchantia polymorpha

source_name: Thallus

growth_protocol: Plants were grown for 26 days in vitro in half strength Gamborg's B5 media (Duchefa) with 1% bactoagar prior to the experiment.

extract_protocol:
Total RNA was extracted with Favorgen Total RNA Purification Mini Kit and treated with DNAse.
We used the following workflow for library preparation:
1.mRNA enrichment and purification. Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2.RNA fragment and reverse transcription.RNA fragmentation and first-strand cDNAs were generated using random N6-primed reverse transcription, followed by the second-strand cDNA synthesis. 3.End repair, add A and adaptor ligation.The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. 4.PCR amplification.Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. 5.Cyclization.Denature the PCR product by heat and the DNA is cyclized by splint oligo and DNA ligase. 6.DNA nanoball synthesis. 7.Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Thallus

value: systemic undamaged tissues of wounded plants


title: senescent, shcontrol, KAS-seq, input


title: control, KAS-seq, IP

value: control


title: HC19-V2D0, PBMC


title: HC19-V1D7, PBMC


title: mpglr-7 systemic 1


title: PDX201.2, vehicle, ChIP-H3K27Ac, repeat 2

city: Boston

first: Zifeng

last: Wang

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

institute: UMASS Boston

description: PDX201.2, H3K27Ac, abcam

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Mapped to hg19 with bowtie2 (default parameters), Filtered (minimum MAPQ score = 30) using samtools filter,Removed duplicates using samtools rmdup
Bigwig files Generated using deeptools bamCoverage (default parameters i.e. bin size 50, scaling/normalization 1x)
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were crosslinked with 1% formaldehyde and then sonicated. DNA were immunoprecipitatted with antibody and magnetic beads . After reverse crosslinking, the DNA was purified using Phenol/Chloroform.
Libraries were generated according to the Qiagen Qiaseq UltraLow Input Library Kit protocol and included 10 cycles of amplification.  amplification

value: Prostate cancer cells

tag: chip antibody

value: anti-H3K27Ac, abcam


title: mpglr-7 systemic 2


title: PDX201.2, vehicle, ChIP-H3K27Ac, repeat 1

description: PDX201.2, H3K27Ac, abcam


title: HC19-V1D0, PBMC


title: control, KAS-seq, input

value: IMR90 cells

value: human fibroblast


title: mpglr-7 wounded 2

value: damaged tissues of wounded plants


title: HC11-V2D1, PBMC

value: peripheral blood


title: PDX201.2, vehicle, ChIP-FOXA2, repeat 4

description: PDX201.2, FOXA2, abcam

value: anti-FOXA2, abcam


title: PDX201.2, vehicle, ChIP-FOXA2, repeat 2

description: PDX201.2, FOXA2, abcam


title: mpglr-7 control 3

value: Intact plants


title: mpglr-7 wounded 1


title: HC11-V2D0, PBMC

value: PBMC

value: healthy control


title: HC11-V2D7, PBMC

value: No


title: PDX201.2, vehicle, ChIP-FOXA2, repeat 1

description: PDX201.2, FOXA2, abcam


title: HC11-V1D7, PBMC


title: HC11-V1D1, PBMC


title: PDX201.1, vehicle, ChIP-H3K27Ac, repeat 3

description: PDX201.1, H3K27Ac, abcam


title: HC19-V1D1, PBMC


title: mpglr-7 wounded 3


title: PDX201.1, vehicle, ChIP-H3K27Ac, repeat 1

description: PDX201.1, H3K27Ac, abcam


title: mpglr-7 control 1


title: HC11-V1D0, PBMC


title: wild type systemic 1

value: WT


title: wild type systemic 3


title: PDX201.1, vehicle, ChIP-FOXA1, repeat 4

description: PDX201.1, FOXA1, abcam

value: anti-FOXA1, abcam


title: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 2

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

data_processing:
The data quality was assessed with FastQC (version 0.11.5), low-quality reads were removed, and remaining adapter sequences were hard clipped with cutadapt (version 1.12) whenever applicable. The quality filtered reads were aligned with STAR (version 2.6.90c) to human reference genome (hg38) with its respective RefSeq annotation, at last, the expression levels of genes were obtained with FeatureCounts (version 1.5.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for each Sample

growth_protocol: The cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in 5% CO2/95% air.

extract_protocol:
Total RNA was extracted from human esophageal squamous cell carcinoma cells (KYSE70) using RNeasy Kit (Qiagen; Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with 10 µM pyrimethamine or 20 nM mitoxantrone for 72 h.

value: 20 nM mitoxantrone for 72 h.


title: PDX201.1, vehicle, ChIP-FOXA1, repeat 3

description: PDX201.1, FOXA1, abcam


title: mpglr-7 control 2

value: Thallus


title: PDX201.1, vehicle, ChIP-H3K27Ac, repeat 2

description: PDX201.1, H3K27Ac, abcam


title: wild type wounded 2


title: PDX201.1, vehicle, ChIP-FOXA1, repeat 2

description: PDX201.1, FOXA1, abcam


title: wild type systemic 2

value: systemic undamaged tissues of wounded plants


title: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 1

value: 10 µM pyrimethamine for 72 h.


title: wild type wounded 1


title: PDX201.1, vehicle, ChIP-FOXA1, repeat 1

description: PDX201.1, FOXA1, abcam

value: Prostate cancer cells


title: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 3


title: PDX201.2, vehicle, ChIP-FOXA2, repeat 3

description: PDX201.2, FOXA2, abcam


title: wild type wounded 3


title: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 3

value: untreated


title: wild type control 3


title: PDX201.1, vehicle, ChIP-AR, repeat 2

description: PDX201.1, AR, abcam_Millipore

value: anti-AR, abcam_Millipore


title: wild type control 2


title: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 1


title: PDX201.1, vehicle, ChIP-AR, repeat 1

description: PDX201.1, AR, abcam_Millipore


title: PDX201.1_PDX201.2_PDX_pooled_input

description: PDX201.1 and PDX201.2, input

value: none (input)


title: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 1


title: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 2


title: wild type control 1


title: visceral_BPA_sheep984

status: Public on Apr 21 2024

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
raw fastq files from ncRNA sequencing were 5’ trimmed using cutadapt (v3.2) as per manufacturers recommendation using the adapter sequence ‘AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’
Using the built-in function for cutadapt, reads that were of low quality and <17bps were removed from the sequencing data
aligned to sheep reference genome (Oar_rambouillet_v1.0) using STAR (2.6.0c)
counting of reads for each class of ncRNA evaluated in this study was achieved by first subsetting the whole genome annotation files for the reference genome into files that contained only references for a particular ncRNA
aligned reads were then used in featureCounts (1.6.1) with genes as the identifier, with all multimapping reads included in the analysis, along with annotation files specific for each ncRNA to obtain counts
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: normalized counts of long non-coding RNA for prenatal T cohort
Supplementary files format and content: normalized counts of mircoRNA for prenatal T cohort
Supplementary files format and content: normalized counts of small nucleolar RNA for prenatal T cohort
Supplementary files format and content: normalized counts of small nuclear RNA for prenatal T cohort
Supplementary files format and content: normalized counts of long non-coding RNA for BPA cohort
Supplementary files format and content: normalized counts of mircoRNA for BPA cohort
Supplementary files format and content: normalized counts of small nucleolar RNA for BPA cohort
Supplementary files format and content: normalized counts of small nuclear RNA for BPA cohort

organism: Ovis aries

source_name: visceral

growth_protocol: Animals from both cohorts (control and prenatal Testosterone-treated; control and prenatal BPA-treated) were co-inhabited under similar conditions, fed a similar maintenance diet to prevent obesity, and potential phytoestrogen exposure via diet was similar across treatment groups.

extract_protocol:
Adipose tissue was homogenized with liquid nitrogen and dissolved in Trizol reagent (Life Technologies, Carlsbad, CA) and total RNA isolated as per manufacturer’s recommendations. Residual DNA was removed using the RNeasy binding column, treating with RNAse free DNAse (Qiagen, Germantown, MD) then eluting RNA in nuclease free water.
Libraries for ncRNA were prepared from total RNA using NEBNext smallRNA kit (New England BioLabs, Ipswich, MA) at the University of Michigan Advanced Genomics Core as per manufacturers recommendations

treatment_protocol: Between gestational days 30-90, 100mg T propionate (~1.2mg/kg; Millipore Sigma, St. Louis, MO) suspended in corn oil was administered intramuscularly twice a week to the prenatal T-treated group. In the BPA cohort, between days 30 and 90 of gestation, control animals received vehicle (corn oil) and the BPA-treated group received 0.5mg/kg/day BPA (purity ≥ 99%, catalog number 239658; Aldrich Chemical Co, Milwaukee, Wisconsin) solubilized in corn oil. Both injections of vehicle and BPA were administered daily, subcutaneously.

value: visceral

value: BPA

tag: cohort

tag: sheepid


title: visceral_BPA_sheep977


title: visceral_BPA_sheep910


title: visceral_BPA_sheep918


title: visceral_control_sheep924

value: control


title: visceral_control_sheep928


title: subcutaneous_BPA_sheep977

source_name: subcutaneous

value: subcutaneous


title: subcutaneous_BPA_sheep984


title: visceral_control_sheep908


title: visceral_control_sheep902


title: subcutaneous_BPA_sheep918


title: subcutaneous_BPA_sheep910


title: subcutaneous_control_sheep928


title: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 2


title: subcutaneous_control_sheep924


title: perirenal_prenatalT_sheep255

source_name: perirenal

value: perirenal

value: prenatalT


title: perirenal_prenatalT_sheep233


title: perirenal_prenatalT_sheep185


title: perirenal_prenatalT_sheep48


title: perirenal_control_sheep201


title: perirenal_control_sheep132


title: epicardial_prenatalT_sheep185

source_name: epicardial

value: epicardial


title: epicardial_control_sheep131


title: epicardial_prenatalT_sheep233


title: epicardial_prenatalT_sheep48


title: epicardial_control_sheep132


title: epicardial_control_sheep201


title: epicardial_control_sheep098


title: visceral_prenatalT_sheep255


title: subcutaneous_control_sheep902


title: visceral_prenatalT_sheep48


title: visceral_control_sheep201


title: visceral_prenatalT_sheep185


title: subcutaneous_control_sheep908


title: visceral_control_sheep132


title: visceral_control_sheep131


title: visceral_control_sheep098


title: subcutaneous_prenatalT_sheep233


title: genomic DNA from FFPE material of MB patient biopsie 38

type: genomic

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

country: Germany

institute: University Hospital Hamburg Eppendorf

description: SHH sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: raw .idat files were processed in Rstudio (Version 4.0.5). (minfi package, Version 1.36.0). Briefly, samples were read from EPIC and 450k arrays separately and combined using combinedarrays(). The samples were normalized using single sample noob normalization since we combined intensities from two different arrays and casted as a 450k array.

label: Cy5 and Cy3

source_name: FFPE material of MB patient biopsie 38

label_protocol: Standard Illumina Protocol

extract_protocol: Illumina FFPE Restore Kit for  was used to extract DNA from FFPE samples,100 - 250 ng DNA was hybridized. Concentrations of DNA was measured with Qubit High Sensitivity DNA Kit

value: Female

tag: proteome subtype

value: pSHHt


title: genomic DNA from FFPE material of MB patient biopsie 35

description: SHH sample

source_name: FFPE material of MB patient biopsie 35

value: Male


title: subcutaneous_prenatalT_sheep185


title: subcutaneous_control_sheep132


title: subcutaneous_control_sheep131


title: subcutaneous_control_sheep098


title: subcutaneous_prenatalT_sheep48


title: genomic DNA from FFPE material of MB patient biopsie 40

description: GR4 sample

source_name: FFPE material of MB patient biopsie 40


title: subcutaneous_control_sheep201


title: genomic DNA from FFPE material of MB patient biopsie 39

description: GR3 sample

source_name: FFPE material of MB patient biopsie 39


title: D11_NT_Rep2

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Data was processed using the nf-core rnaseq pipeline with the following options: --genome mm10 --aligner star_salmon --skip_biotype_qc --deseq2_vst -r 3.5
Assembly: mm10
Supplementary files format and content: DESeq2 differential expression results

source_name: neural progenitor

growth_protocol: 60-80,000 mouse ES cells were plated onto the pre-coated CellBIND dishes (Corning) in N2B27 medium (Advanced DMEM - F12 (Gibco, Cat. No. 21331-020) and Neurobasal medium (Gibco, Cat. No. A35829-01) (1:1), supplemented with 1xN2 (Gibco Cat no. 17502001), 1xB27 (Gibco Cat no. 17504001), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma-Aldrich, Cat No. A7979-50ML), and 0.1 mM 2-mercaptoethanol) supplemented with 10 ng/ml bFGF (R&D, Cat. No. 100-18B). On day 2, the media was changed to N2B27 supplemented with 5 μM CHIR99021 (GSK3β inhibitor; Axon, 1386). 20-21 h later, on day 3, the media was changed to N2B27 with 100 nM RA and 10 nM of Smoothened Agonist (SAG; Calbiochem, 566660). From day 5 onwards, cells were kept in N2B27 supplemented with 10 nM SAG. From day 3 onwards, media changes were performed daily.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit with DNAse digest (Qiagen, Cat. No. 74106) according to the manufacturer’s instructions and stored at -80°C.
Libraries were prepared using the NEBNext Ultra II Directional kit(NEB, Cat no E7760L) with ribodepletion (Qiagen QIAseq FastSelect -rRNA HMR Kit, Cat. No. 334386), following manufacturer’s instructions.

treatment_protocol:
One day before transfection with CRISPR guides, Cas9 was induced in R1-iCas9 ES cells by exposure to 1 µg/ml Doxycycline (Sigma-Aldrich, Cat. No. D9891), which was supplemented to the ES cell medium. On the next day, flat µClear polystyrene bottom 96-well plates (Greiner, PS, F-Bottom, 655090) were coated with 60-70 µl matrigel (Corning, 356231, diluted 1:50 in cold DMEM/F12) per well. Plates were briefly spun down for 1 min at 1000 rpm and incubated for 3 hr at room temperature. ES cells were prepared as described above. During the panning steps, CRISPR guide RNA (gRNA) complex and transfection reagents were prepared.
The Edit-R CRISPR-Cas9 platform (Horizon Discovery) was used. The platform includes two components required for gene editing: A chemically synthesized trans-activating CRISPR RNA (tracrRNA), and a chemically synthesized CRISPR RNA (crRNA) designed to the gene target site of interest. For transfection, 5 crRNAs (20 µM stock) were pooled and combined with tracrRNA (20 µM stock, U-002005) to form a guide RNA (gRNA) complex (crRNA:tracrRNA) (final concentration: 10 µM). gRNA was then diluted in 1x HBSS buffer (Gibco, 14170-088) to make up 200 nM. As an example: 10 µl crRNA (2 µl of each individual crRNA), 10 µl tracrRNA were combined (20 µl of gRNA). 20 µl of gRNA was diluted into 1 ml HBSS. In parallel, negative, and positive controls were prepared. Non-targeting control (Control #1, 5 nmol stock, Horizon Discovery, U-007501-01-05) was used as negative control.

value: neural progenitor

value: neural progenitor differentiation

value: NT KO

value: Day D11


title: subcutaneous_prenatalT_sheep255


title: D11_Ezh2_Rep3

value: Ezh2 KO


title: D11_Nr6a1_Rep1

value: Nr6a1 KO


title: D11_NT_Rep3


title: D11_NT_Rep1


title: D11_Ezh2_Rep1


title: D11_Nr6a1_Rep3


title: genomic DNA from FFPE material of MB patient biopsie 37

description: SHH sample

source_name: FFPE material of MB patient biopsie 37


title: D11_Eed_Rep3

value: Eed KO


title: D11_Eed_Rep2


title: D11_Ezh2_Rep2


title: D11_Eed_Rep1


title: D11_Brd8_Rep3

value: Brd8 KO


title: genomic DNA from FFPE material of MB patient biopsie 36

description: SHH sample

source_name: FFPE material of MB patient biopsie 36


title: D11_Brd8_Rep2


title: D11_Brd8_Rep1


title: D09_Nr6a1_Rep3

value: Day D09


title: D09_NT_Rep2


title: D09_Ezh2_Rep3


title: D09_NT_Rep3


title: D09_Nr6a1_Rep1


title: D09_Ezh2_Rep2


title: D09_NT_Rep1


title: D09_Eed_Rep3


title: D09_Eed_Rep1


title: D09_Brd8_Rep1


title: D07_Nr6a1_Rep2

value: Day D07


title: D07_NT_Rep1


title: D09_Eed_Rep2


title: D07_NT_Rep2


title: D09_Brd8_Rep2


title: D07_NT_Rep3


title: D07_Nr6a1_Rep3


title: D07_Ezh2_Rep3


title: D07_Ezh2_Rep2


title: senescent_fastGRO-seq_shMETTL14_knockdown_ replicate 1

data_processing:
library strategy: fastGRO-seq
Reads were aligned to the hg19 human genome by STAR and bam files were normalized based on the drosophila spike-in RNA among each group.
bigwig files were generated with deeptools 3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: nuclear RNA

extract_protocol:
Nascent RNA was extracted from nuclei and purified through RNA Clean and Purification kit.
Purified RNA was used to constructed RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: Senescence was induced in primary human lung fibroblasts (IMR90) cells through the inducible expression of a fusion protein (estrogen receptor and H-RASG12V, ER: RAS). fastGro-seq was performed to monitor nascent gene transcription in control and senescent IMR90 cell lines with vector, METTL3, or METTL14 knockdown.

value: IMR90 cells

value: human fibroblast

value: senescent


title: D07_Ezh2_Rep1


title: D07_Eed_Rep2


title: D07_Eed_Rep3


title: D07_Brd8_Rep3


title: D07_Eed_Rep1


title: D07_Brd8_Rep1


title: D09_Ezh2_Rep1


title: neural progenitors, Nr6a1OE, rep 2

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10  --skip_diff_analysis --min_reps_consensus 2 -r 1.2.1
Assembly: mm10
Supplementary files format and content: Counts in consensus peaks, columns are samples, rows are genomic intervals

source_name: neural progenitor differentiation

extract_protocol:
On day 9, cells were sorted for mScarlet3 fluorescence and 50,000 per sample were used for ATAC-seq library preparation. Samples were resuspended in 0.5 ml of RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% Igepal CA-630 (Sigma, Cat. No. I8896-100ML), 0.1% Tween-20 (Sigma, Cat. No. P2287-500ML), and 0.01% digitonin (Invitrogen, Cat No. BN2006), and incubated on ice for 3 min. 1 ml of RSB with 0.1% Tween-20 was then added and samples were spun for 10 min at 2000 g and 4ºC. The samples were then resuspended in 1 ml of ATAC mix (2X TDE buffer , 50 µl Tn5 enzyme, 0.01% digitonin, 0.1% Tween-20 and 330 µl of PBS). Transposition was carried out at 37ºC with 1000 rpm shaking for exactly 30 min. DNA was isolated using the DNA clean up & Concentrator kit (Zymo, Cat. No. D4013) as per manufacturer’s instructions. DNA was eluted in 21 µl of DNAse-free water. DNA was stored at -20ºC until ready to be processed.
Transposed DNA was first amplified with 2X PCR Master Mix NEB (Cat. No. M0541S), and 1 µl of constant forward primer and indexed reversed primer (Table S1) (both at 25 µM) in a total reaction volume of 50 ul. The program was as follows: 5 min at 72ºC, 30 s at 98ºC, followed by 7 cycles of 30 s at 98ºC, 30 s at 63 ºC and 60 s at 72 ºC, with a final extension of 5 min at 72 ºC. DNA was cleaned up with 1.8x volumes of AMPureXP beads (Beckman Coulter, Cat. No. A63882) and eluted in 18 µl of EB buffer. qPCR was carried out to determine the number of extra cycles using 2 µl of the amplified DNA in technical duplicates. Each 20 µl reaction contained 20 µl of 2X SYBR Green PCR assay, using PowerUP SYBR Green Master Mix (Thermo Fisher, Cat. No. A25742) and 2.5 µl of each primer (at 25 µM each). The qPCR program was as follows: initial activation for 2 min at 50ºC, 30 s at 98ºC, followed by 40 cycles of 10 s at 98ºC, 30 s at 63ºC and 60 s at 72ºC. The number of additional cycles was calculated as ¼ of the maximum amplification 86. The second amplification was done using 12.5 µl of amplified DNA, 2X PCR Master Mix NEB and 2.5 µl of each primer (at 25 uM) in a total volume of 50 ul. The program was the same as the first amplification without the initial extension and for the calculated number of cycles. Finally, re-amplified DNA was cleaned up using 1.8x volumes AMPureXP beads and eluted in 30 ul.

treatment_protocol: On day 5, differentiations were transduced with lenvirus overexpressing either control (mScarlet3, here called mScarlet) or Nr6a1-2A-mScarlet3 (here called Nr6a1).


title: neural progenitors, mScarlet, rep 3

value: Control


title: neural progenitors, Nr6a1OE, rep 1


title: neural progenitors, mScarlet, rep 1


title: Control-1,  TCR-seq

city: nan jing

first: shiliang

last: ji

address: No. 163，Xianlin Avenue

department: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences

country: China

institute: Nanjing University

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 v2.1.1 (https://support. 10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cel-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Tumor

extract_protocol:
MC38 tumors were harvested on day 21 post inoculation, then the dissociated tumor cells were subsequently filtered through a 70-μm cell strainer, centrifuged at 500 g for 10 minutes, and resuspended in MACS buffer (1x PBS with 2mM EDTA and 0.5% BSA) for counting. CD45+ cells were isolated by flow cytometry, washed and re-suspended in FACS buffer (1x PBS with 2% FBS).
Library was performed according to the manufacter's instructions (single cel 3' v2 protocol, 10x Genomics), Briefly, GCs were resuspended in the master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an IIumina R1 primer sequence, Unique Molecular Identifier(UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments and selected with SPRIselect reagent for subsequent library construction. During the library construction IIumina R2 primer seqence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor

value: Mouse colon adenocarcinoma cell line

value: WT

value: mTubulin-LNP


title: Vac-2,  TCR-seq

description: 10X Genomics

value: mTMG-LNP


title: Vac-2, scRNA-seq

description: 10X Genomics


title: Vac-1,  TCR-seq

description: 10X Genomics


title: Control-2, scRNA-seq

description: 10X Genomics


title: Control-1,  scRNA-seq

description: 10X Genomics


title: 7_PKCz_Standard

city: New Haven

first: Rieke-Marie

last: Hackbarth

state: CT

address: 300 Cedar St

department: Immunobiology

institute: Yale

data_processing:
We used CellRanger (version 7.1.0; 10x Genomics) to align the reads against the mouse mm10 reference genome provided by CellRanger with “include-introns” as an option.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral cortex

extract_protocol:
Nuclei were isolated from flash-frozen mouse cerebral cortices collected at indicated postnatal days from indicated genotypes (6mm punch biopsies from n=3-5 mice of each genotype were pooled per sample). 15 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.9), 25 mM KCl, 1 mM EDTA (pH 8.0), 10% glycerol, and freshly added Rnase inhibitors (80 U/ml)] were used to homogenize the tissues with Dounce tissue grinder (10 strokes with loose pestle and 10 strokes with tight pestle). Homogenates were transferred into an ultracentrifuge tube on top of 10 ml of fresh nuclei homogenization buffer and centrifuged at 24,000 rpm for 60 min at 4°C on a high-speed centrifuge. The nuclei pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes pH 7.4, 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and freshly added Rnase inhibitors (80 U/ml)] and counted using a hemocytometer. The nuclei were centrifuged at 800 g for 10 min at 4°C and resuspended at a concentration of 500 to 1000 nuclei/μl for 10x Genomics Chromium loading.
The single nucleus (sn)RNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer’s instructions (10x Genomics) and sequenced using Illumina NovaSeq 6000 S4 at the Yale Center for Genome Analysis (YCGA).

treatment_protocol: A 10-mg/ml tamoxifen stock suspension was prepared for the induction experiment by mixing 10 mg tamoxifen with 100µl of ethanol and 900 µl of sunflower oil, followed by 30 min sonication. Mice were injected at the indicated time points for 5 consecutive days intraperitoneally with 100 µl of suspension (1mg tamoxifen/day). Plp1-creERT+ Prkci f/f, Plp1-creERT+ Prkcz f/f mice and littermate controls were injected with 4-OH Tamoxifen (Sigma Aldrich, MO) for 5 days starting at postnatal day 35. Two weeks after tamoxifen delivery, cuprizone-mediated demyelination was induced by feeding mice pellets containing 0.3% cuprizone (Envigo, IN) for 6 weeks. Food was refreshed and mice were monitored daily. For remyelination studies (cuprizone washout group), food was switched to standard diet for 3 weeks prior to sample collection.

value: Cerebral cortex

tag: Sex

value: Male

tag: strain

value: Plp1-cre+ Prkcz f/f

value: Tamoxifen


title: Control-2,  TCR-seq

description: 10X Genomics

tag: tissue

tag: cell line


title: D07_Brd8_Rep2

tag: cell type

value: neural progenitor

tag: treatment

value: neural progenitor differentiation


title: 6_PKCi_Cup+washout

tag: genotype

value: Plp1-cre+ Prkci f/f

value: Tamoxifen+Cuprizone


title: 9_PKCz_Cup+Washout


title: neural progenitors, Nr6a1OE, rep 3


title: 5_PKCi_Cuprizone


title: 2_Control_Curprizone

value: wildtype


title: 3_Control_Cup+washout


title: neural progenitors, mScarlet, rep 2


title: 1_Control_Standard


title: 4_PKCi_Standard


title: Control_P60


title: Control_P0

value: Mixed


title: Vac-1, scRNA-seq

description: 10X Genomics


title: P30_Control

value: Pooled Prkci f/f and Prkcz f/f


title: 8_PKCz_Cuprizone


title: Prkcz3, P30

data_processing:
Raw reads were input into FastQC to perform initial quality control checks and TrimGalore was used to trim adapter sequences. We employed STAR for alignment of the trimmed reads to the annotated mouse genome GRCm38. Transcript abundance was quantified using RSEM.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values file containing with edger normalized counts for all samples.

extract_protocol:
For total mRNA isolation, mice were euthanized at the indicated postnatal timepoints by CO2 inhalation and brains were immediately dissected on ice. Equal amounts of tissue were obtained from cerebral cortices using a 4mm punch biopsy tool, flash frozen in liquid nitrogen and stored at -80°C until further processing. Total mRNA was extracted using RNAeasy Mini Kit, as per manufacturer’s instructions (QIAGEN).
Library preparation and sequencing of RNA from cerebral cortex samples (3-4 biological replicates for each genotype) was performed at the Yale Center for Genome Analysis using 100-base pair, paired-end reading on a NovaSeq instrument (Illumina) at a sequencing depth of 25 million reads per sample

value: Ng2-Cre+ Prkcz f/f


title: Prkci3, P30

value: Ng2 Cre+ Prkci f/f


title: Prkcz2, P30


title: Prkci4, P30


title: Prkci2, P30


title: Prkci1, P30


title: Control2, P30

value: Pkcz f/+


title: Control4, P30

value: Pkcz f/f


title: Control3, P30


title: Control1, P30


title: FMTCon_cecum-IP3

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The cecums were dissected from twelve-week-old germ-free mice

data_processing:
All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content,  and reads with more than half low quality (Q-value <20) bases were removed.
For MeRIP-Seq data, the sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) and transfer RNA(tRNA) database using  HISAT2(version 2.1.0) to remove rRNA and tRNA reads and get the clean sequencing data.
For MeRIP-Seq data, clean sequencing data were mapped to the mouse reference genome (mm39) using the default parameters of HISAT2 (version 2.1.0) after establishing the epitranscriptome index. And PCR duplicate sequences were removed by sambamba (version 0.8.2).
The m6A peak calling by using exomepeak2 (v1.6.1)
Sequence motifs on m6A peaks were identified by HOMER
Assembly: mm39
Supplementary files format and content: bed

source_name: germ-free mice

growth_protocol: SPF mice were fed with sterilized food and water with different antibiotics, while germ-free mice were fed with sterilized water and food in a sterile environment, both maintained at room temperature in a 12-hour light and dark cycle.

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted,the extracted total RNA was subjected to poly-A selection using Oligo d(T)25 Magnetic Beads (#S1419S, NEB). Purified poly-A RNA fragmentation to roughly 150-nt fragment size was performed according to the protocol with the Invitrogen RNA Fragmentation Reagents kit (Invitrogen). The purified poly-A RNA was fragmented and used for the construction of both m6A immunoprecipitation (IP) and untreated control (input) MeRIP-seq libraries. m6A IP was conducted using an EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, NEB) following the product manual. The resultant m6A-enriched and untreated poly-A RNA fragments were then used to construct strand-specific IP and input libraries for MeRIP-seq, respectively. All libraries were sequenced using Illumina NovaSeq 6000 by Berry Genomics.
MeRIP-Seq

treatment_protocol: Mice were fed with ampicillin, gentamicin, metronidazole, vancomycin, neomycin, and antibiotic cocktail. Germ-free mice were transplanted with the intestinal contents from ampicillin-treated mice or control mice.

tag: animal

value: germ-free mice

value: cecum

value: Gavage with the intestinal contents of normal mice


title: epicardial_prenatalT_sheep255

value: epicardial

value: prenatalT


title: FMTCon_cecum-IP2


title: FMTAmp_cecum-IP3

value: Gavage with ampicillin-treated intestinal contents of mice


title: Abx_intestine-IP3

description: The intestines were dissected from twelve-week-old mice

source_name: SPF mice

value: SPF mice

value: intestine

value: Water with multiple antibiotics


title: FMTAmp_cecum-IP2


title: P30_PKCi

value: Cerebral cortex

value: Male

value: Ng2 cre+ Prkci f/f


title: P30_PKCz

value: Ng2 cre+ Prkcz f/f


title: Abx_intestine-IP2


title: Abx_intestine-IP1


title: Amp_intestine-IP3

value: Water with ampicillin


title: Amp_intestine-IP2


title: Prkcz1, P30

value: Ng2-Cre+ Prkcz f/f


title: Amp_intestine-IP1


title: Con_intestine-IP3

value: Water


title: FMTCon_liver-IP2

description: The livers were dissected from twelve-week-old germ-free mice

value: liver


title: Con_intestine-IP2


title: Con_intestine-IP1


title: FMTCon_liver-IP3

value: germ-free mice


title: FMTCon_liver-IP1


title: FMTAmp_liver-IP3


title: FMTCon_cecum-IP1

value: cecum


title: Abx_liver-IP3

description: The livers were dissected from twelve-week-old mice


title: FMTAmp_cecum-IP1


title: FMTAmp_liver-IP1


title: FMTAmp_liver-IP2


title: Abx_liver-IP2


title: Amp_liver-IP2


title: Amp_liver-IP3


title: Amp_liver-IP1


title: Con_liver-IP3


title: Con_liver-IP1


title: Con_liver-IP2


title: FMTCon_brain-IP2

description: The brains were dissected from twelve-week-old germ-free mice

value: brain

value: Gavage with the intestinal contents of normal mice


title: FMTCon_brain-IP3


title: visceral_prenatalT_sheep233

value: visceral

value: prenatalT


title: FMTAmp_brain-IP3

value: Gavage with ampicillin-treated intestinal contents of mice


title: Abx_brain-IP3

description: The brains were dissected from twelve-week-old mice

value: SPF mice


title: FMTAmp_brain-IP1


title: FMTAmp_brain-IP2


title: Abx_brain-IP2

value: Water with multiple antibiotics


title: Van_brain-IP3

value: Water with vancomycin


title: Van_brain-IP1


title: Van_brain-IP2


title: Abx_brain-IP1


title: Neo_brain-IP2

value: Water with neomycin


title: Neo_brain-IP1


title: perirenal_control_sheep098

value: perirenal

value: control


title: Met_brain-IP3

value: Water with metronidazole


title: Met_brain-IP2


title: Gen_brain-IP3

value: Water with gentamicin


title: Met_brain-IP1


title: Gen_brain-IP2


title: Gen_brain-IP1


title: Amp_brain-IP3

value: Water with ampicillin


title: Amp_brain-IP1


title: FMTCon_brain-IP1


title: Con_brain-IP2

value: Water


title: Con_brain-IP1


title: Con_brain-IP3


title: FMTCon_liver-Input3

description: The liver were dissected from twelve-week-old germ-free mice

data_processing:
All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content,  and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data, the sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) and transfer RNA(tRNA) database using  HISAT2(version 2.1.0) to remove rRNA and tRNA reads and get the clean sequencing data.
For RNA-seq data, The clean sequencing data were mapped to the Mus musculus reference genome (mm39) using HISAT2 (version 2.1.0) with default parameters after index building of the transcriptome.
For RNA-seq data, The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
For RNA-seq data, RNA differential expression analyses among groups were performed by DESeq2 (version 1.36.0). The genes/transcripts with the a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files (.txt) include raw reads of RNA-seq data from all SPF mice and GF mice.

source_name: liver

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmenta-tion buffer and reverse transcripted into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Berry Genomics.

treatment_protocol: Mice were fed with ampicillin, gentamicin, metronidazole, vancomycin, and neomycin, and germ-free mice were transplanted with the intestinal contents of ampicillin and control mice.

value: twelve-week-old germ-free mice

tag: culture environment

value: Feeding with sterile food and water

tag: replicate


title: FMTCon_liver-Input1


title: FMTCon_cecum-Input2

description: The cecum were dissected from twelve-week-old germ-free mice

source_name: cecum


title: FMTCon_liver-Input2


title: Abx_liver-IP1

value: liver


title: FMTCon_cecum-Input1

value: Gavage with the intestinal contents of normal mice


title: FMTCon_brain-Input3

description: The brain were dissected from twelve-week-old germ-free mice

source_name: brain


title: FMTCon_brain-Input1


title: FMTCon_brain-Input2


title: Neo_brain-IP3

value: brain


title: FMTAmp_liver-Input3


title: FMTAmp_liver-Input2


title: perirenal_control_sheep131

source_name: perirenal

value: prenatalT


title: FMTAmp_liver-Input1

value: Gavage with ampicillin-treated intestinal contents of mice


title: FMTAmp_cecum-Input3


title: FMTAmp_cecum-Input1


title: FMTAmp_brain-Input2


title: FMTAmp_cecum-Input2


title: FMTAmp_brain-Input1


title: Van_brain-Input3

description: The brain were dissected from twelve-week-old mice

value: twelve-week-old mice

value: Feeding with sterilized food


title: FMTAmp_brain-Input3


title: Van_brain-Input2

value: Water with vancomycin


title: Amp_brain-IP2

value: SPF mice


title: FMTCon_cecum-Input3


title: Van_brain-Input1


title: Neo_brain-Input1

value: Water with neomycin


title: Neo_brain-Input2


title: H9 cells, 8d,replicate 2

city: Sydney

first: Carissa

state: NSW

address: 214 Hawkesbury Rd, Westmead

country: Australia

institute: Children's Medical Research Institute

data_processing:
image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Demultiplexing was performed by bcl2fastq 2.17. Raw data was filtered as follows: Pair-end reads with adapter,  pair-end reads when the content of N bases is more than 10% in either read and pair-end reads when the ratio of bases of low quality (Q<20) is more than 0.5 in either read, were discarded.
Paired-end 150bp reads were mapped to the human (GRCh38) genome using STAR (v2.7.9a) allowing up to three mismatches per pair
Assembly: hg38
Supplementary files format and content: RNA_gene_counts.txt

source_name: organoid

extract_protocol:
RNA extraction was performed using the Bioline Isolate II RNA Mini Kit (Bioline BIO-52071) according to the Bench-Top Protocol by the manufacturer.
RNA library preparations were constructed according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®)

value: organoid

tag: time

value: WT

value: neural differentiation


title: Met_brain-Input3

value: Water with metronidazole


title: H9 cells, 6d, replicate 2


title: H9 cells, 2d, replicate 2


title: H9 cells, 4d, replicate 2


title: H9 cells, 1d, replicate 2


title: Met_brain-Input2


title: H9 cells, 6h, replicate 2


title: Met_brain-Input1


title: H9 cells, 1h, replicate 2


title: H9 cells, 0h, replicate 2


title: Gen_brain-Input3

value: Water with gentamicin


title: H9 cells, 6d, replicate 1


title: Neo_brain-Input3


title: Gen_brain-Input2


title: H9 cells, 4d, replicate 1


title: H9 cells, 8d, replicate 1


title: 7_H3K4me3_ChIPseq_SWD2-9MYC&RAD6-FLAG_strain_rep2

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

description: 4_H3K4me3_ChIPseq_SWD2-9MYC_RAD6-FLAG_mean.bw

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombe spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: Yeast cell

growth_protocol: Cells were prepared from exponentially growing at OD600=1.0. Harvested cells were resuspended with 4ml of 1XTBS and evenly divided into 4 eppendorf tubes. Cell is harvested by Centrifuge 3000 rpm 5min and supernatant was removed. After one more wash step, samples were stored at -80℃.

extract_protocol:
Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. S.cerevisiae chromatin lysates, containing 10% S.pombe chromatin extract for control of sample-to-sample normalization, were incubated with antibody and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Before wash the cells with 1XTBS, cells were treated with 1% formaldehyde for 5mins and quenched with 2.5M Glycine for 20mins

value: Yeast cell

value: Anti-trimethyl-Histone H3 (Lys4) (Merck, 07-473)

value: SWD2-9MYC & RAD6-FLAG

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) SWD2::9MYC::TRP RAD6::FLAG::LEU2


title: H9 cells, 2d, replicate 1


title: H9 cells, 1d, replicate 1


title: Gen_brain-Input1


title: 6_H3K4me3_ChIPseq_SWD2-9MYC&RAD6-FLAG_strain_rep1


title: H9 cells, 6h, replicate 1


title: double-0-2

type: RNA

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

institute: Chinese Academy of Sciences

description: Gene expression in 24-d-old Arabidopsis thaliana rosette leaves

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis Oligo 44K DNA microarray (Version 4.0, Agilent Technology) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: d14 kai2, Rosette leaves, 24 d,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and d14 kai2 mutant plants were transferred from GM plates to soil and grown for 10 additional day.

extract_protocol: Total RNA was prepared using the RNAprep Pure Plant kit (DP432, TIANGEN) following the manufacturer's recommendations.

treatment_protocol: The rosette leaves of 24-d-old seedlings were harvested and frozen in liquid nitrogen immediately.

value: Rosette leaves

tag: age

value: d14 kai2


title: double-0-1

source_name: d14 kai2, Rosette leaves, 24 d,replicate 1


title: double-0-3

source_name: d14 kai2, Rosette leaves, 24 d,replicate 3


title: H9 cells, 1h, replicate 1


title: Col-0-3

source_name: WT, Rosette leaves, 24 d,replicate 3


title: Con_testis-3

description: The testis were dissected from twelve-week-old mice

source_name: testis

value: Water


title: 5_H3K4me3_ChIPseq_SWD2-9MYC&FLAG-RAD6_strain_rep2

description: 3_H3K4me3_ChIPseq_SWD2-9MYC_FLAG-RAD6_mean.bw

value: SWD2-9MYC and FLAG-RAD6

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) SWD2::9MYC::TRP FLAG::RAD6::LEU2


title: Col-0-2

source_name: WT, Rosette leaves, 24 d,replicate 2


title: Col-0-1

source_name: WT, Rosette leaves, 24 d,replicate 1


title: H9 cells, 0h, replicate 1


title: PBMC-T700

city: Florham Park

first: Kathy

last: Karasiewicz

state: New Jersey

address: 1700 Ave Park

institute: Celularity

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Trimmed reads  were mapped to the Homo sapiens reference genome GRCh38 using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
DESeq2 for comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.

source_name: peripheral blood

extract_protocol:
Total RNA was purified from individual CAR-T donor products using RNeasy Mini Kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: peripheral blood

value: T cell

value: CD19 CAR transducted and TRAC knockout


title: PBMC-T500


title: Con_testis-1

value: twelve-week-old mice

value: Feeding with sterilized food


title: 4_H3K4me3_ChIPseq_SWD2-9MYC&FLAG-RAD6_strain_rep1


title: 3_H3K4me3_ChIPseq_Δrad6_strain

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) rad6{delta} KanMX


title: PBMC-T200


title: PBMC-T400


title: Con_spleen-3

description: The spleen were dissected from twelve-week-old mice

source_name: spleen


title: 2_H3K4me3_ChIPseq_WT_strain_rep2

value: Wildtype

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere))


title: PBMC-T3000


title: PBMC-T100


title: 1_H3K4me3_ChIPseq_WT_strain_rep1

value: Yeast cell


title: Con_spleen-2


title: P-T30890

source_name: placenta

value: placenta


title: 16_a-Set1_551Δbre1_strain_rep2

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, C. albicans spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

source_name: ura3-52 his3Δ200 ade2-101(ochre) lys2-80(1m) trp-1Δ1 leu2-Δ1 TELadh4::URA3(VIIL Telomere) bre1Δ::KanMX

extract_protocol:
Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. S.cerevisiae chromatin lysates, containing 5% C.albicans Δset1 chromatin extract for control of sample-to-sample normalization, were incubated with antibody and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

value: ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TELadh4::URA3(VIIL Telomere) bre1{delta}::KanMX


title: Con_spleen-1


title: P-T28410


title: 15_a-Set1_551Δbre1_strain_rep1


title: Con_lung-3

description: The lung were dissected from twelve-week-old mice

source_name: lung


title: P-T23019


title: Con_testis-2


title: P-T21923


title: P-T20284


title: 13_a-Set1_551WT_strain_rep1

source_name: ura3-52 his3Δ200 ade2-101(ochre) lys2-80(1m) trp-1Δ1 leu2-Δ1 TELadh4::URA3(VIIL Telomere)

value: ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TELadh4::URA3(VIIL Telomere)


title: Con_lung-1


title: Treated_2

city: Nantong

first: YU

last: WU

address: Nantong, 226001, PR China;

institute: Nantong Hospital of Traditional Chinese Medicine

data_processing:
The raw data were quality controlled by removing adapters, Q20 less than 80% to obtain clean reads.
The clean reads were aligned to miRBase (version 22.0). The expression of miRNAs were estimated using transcript per million (TPM).
The miRNAs with |log2FoldChange|≥0.58 and p<0.05 were regarded as differences miRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample

source_name: MHCC97H Hepatoma Cancers Cells

growth_protocol: The human high metastatic liver cells line MHCC97H was purchased from Wuhan University. Cells were cultured in DMEM medium supplemented with 5%fetal bovine serum (FBS) and 5% fetal bovine serum without exosomes (Gibco A2720801), 100 U/ml penicillin, 100 g/ml streptomycin (Life Technologies, Inc., Rockville, MD) in a humidified incubator under 5% CO2 at 37◦C.

extract_protocol:
Cell culture supernatant was collected from the control group and the xanthatin group. Supernatant were collected by differential centrifugation (500xg at 4℃ for 5min, 2000xg at 4℃ for 30min, 10000xg at 4℃ for 60min). Filtrated with a 0.22um sterile filter, added into the ultra-high speed centrifuge tube, centrifuged at 4℃ for 70min at 120000xg and discarded the supernatant. Finally, depending on the amount of precipitation, 200-400 L of pre-cooled sterile PBS was added for resuspended suspension, which was high purity EVs. Total RNA was extracted by TRIzol reagent, and the RNA molecules in a size range of 18–30 nt were enriched by poly-acrylamide gel electrophoresis.
The 3'adapters were added and the 36–44 nt RNAs were enriched. The 5'adapters were then ligated to the RNAs as well. The ligation products were reverse-transcribed by PCR amplification, and the 140–160 bp size PCR products were enriched to generate a cDNA library. The cDNA fragments were purified with PCR extraction kit, poly(A) added and ligated to Illumina sequencing adapters

treatment_protocol: Xanthatin was dissolved in dimethylsulfoxide (DMSO) and with a final concentration of 0.5% in all experiments. Cells were treated with xanthatin (final concentration of 4 μmol/L) for 24h.

value: Xanthatin treatment

tag: molecule subtype

value: exosomal miRNA


title: Treated_1


title: Blank_2

value: Control


title: Blank_3


title: Con_liver-Input3

description: The liver were dissected from twelve-week-old mice

source_name: liver

value: Water


title: 12_a-Set1_Sen1overexpressed_Δswd2_strain_rep2

source_name: Δswd2 strain overexpressing Sen1(202) fragment

tag: chip antibody

value: {delta}swd2 strain overexpressing Sen1(202) fragment


title: 11_a-Set1_Sen1overexpressed_Δswd2_strain_rep1


title: Con_liver-Input2


title: WT_D9_pM_NFIAp_R3

data_processing:
Data was processed using the nf-core rnaseq pipeline with the following options: --genome mm10 --aligner star_salmon --skip_biotype_qc --deseq2_vst -r 3.5.
Assembly: mm10
Supplementary files format and content: normalized counts, columns are samples, rows are gene names

source_name: neural progenitor differentiation

extract_protocol:
Glyoxal fixation The fixation protocol was adapted from published work (Channathodiyil and Houseley, 2021). To prepare ~4 ml of 3% glyoxal solution, 2.835 ml of RNase-free water was combined with 0.789 ml 100% (v/v) EtOH, 0.03 ml acetic acid and 0.313 ml 40% Glyoxal (Sigma-Aldrich, Cat. No. 50649-100ML). All steps were performed on ice and reagents were cooled before mixing. The solution was adjusted to pH 4-5 (with 1M NaOH) if necessary. The solution was always kept on ice and stored for up to 3 days at 4°C. All samples were fixed and stained on the same day. To minimise RNase activity, cells were kept on ice and only pre-chilled reagents were used.  Cells were resuspended in 50 µl PBS + 0.5% BSA first, followed by adding 300 µl 3% glyoxal. Cells were fixed for 15 min with slow side-to-side rocking on ice protected from light. 25 µl of 2M glycine was added for quenching and incubated for 5 min. 1 ml PBS + 0.5 % BSA was added to stop the fixation, and cells were spun down at 2000xg for 5 min at 4°C. 1-2x106 cells were prepared for Flow cytometry staining and resuspended in 100 µl PBS + 0.5% BSA + 0.3% Triton X-100. Cells were incubated on ice for 30 min. Staining was performed as previously described and processed in the same way as described for CaTS-ATAC-seq. 10-15,000 cells of each desired population were sorted into 300 µl TRIzol reagent (Invitrogen, Cat. No. 15596026) and stored at -80°C until further processing. TRIzol RNA extraction and library preparation All steps were performed at room temperature unless otherwise stated. For TRIzol extraction, Phasemaker tubes (Thermo Fisher A33248) were used according to the manufacturer’s instructions. 300 µl of sorted cells in TRIzol were mixed and transferred to Phasemaker tubes and incubated for 5 min at room temperature. 200 µl chloroform per 1 ml TRIzol used for lysis was added and mixed vigorously. Samples were incubated for 10 min and spun for 5 min at 12,000×g and 4°C. The upper phase was transferred to a new RNase-free tube. 8 µg RNase-free GlycoBlue (stock 15 mg/ml) was added to each sample and briefly mixed to see the pellet easier. 150 µl of 100% isopropanol was added (500 µl per initial 1 ml TRIzol). The solution was incubated for 10 min, then centrifuged for 10 min at 12,000xg at 4°C and supernatant was carefully discarded. The pellet was washed in 1 ml of 75% EtOH per 1 ml TRIzol reagent used for lysis. The sample was then centrifuged for 5 min at 7500xg at 4°C. The pellet was air dried for 5-10 min to remove residual EtOH. To solubilise the pellet, it was resuspended in ~17 µl of RNase-free water. The resuspended RNA was incubated in a heat block for 10 min at 55°C. RNA was stored at -80°C until further processing.
paired-end library preparation was performed using the SMART-Seq HT kit (Takara, Cat. No. 634437) followed by Nextera XT DNA Library Preparation Kit (Illumina, Cat. No. FC-131-1096).

value: neural progenitor differentiation

tag: specific progenitors

value: pM

value: WT


title: P-T34823

value: T cell

value: CD19 CAR transducted and TRAC knockout


title: WT_D9_pM_NFIAp_R1


title: Con_liver-Input1

value: twelve-week-old mice

value: Feeding with sterilized food


title: P-T28455


title: 10_a-Set1_Sen1overexpressed_WT_strain_rep2

source_name: WT strain overexpressing Sen1(202) fragment


title: Blank_1


title: WT_D9_p2_NFIAn_R2


title: 9_a-Set1_Sen1overexpressed_WT_strain_rep1

value: WT strain overexpressing Sen1(202) fragment


title: WT_D9_pM_NFIAn_R3


title: Con_kidney-3

description: The kidney were dissected from twelve-week-old mice

source_name: kidney


title: WT_D9_p2_NFIAp_R3


title: Con_kidney-2


title: WT_D9_p1_NFIAn_R2


title: Con_lung-2


title: Treated_3


title: WT_D9_pM_NFIAn_R1


title: WT_D9_p2_NFIAn_R3


title: 8_a-Set1_Δbre1_strain_rep2

source_name: MATa his3∆0 leu2∆0 met15∆0 ura3∆0 bre1Δ::KanMX

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0 bre1{delta}::KanMX


title: 7_a-Set1_Δbre1_strain_rep1


title: WT_D9_p2_NFIAp_R1


title: WT_D9_pM_NFIAp_R2


title: WT_D9_p2_NFIAn_R1


title: 5_a-Set1_Δrad6_strain_rep1

source_name: MAT alpah his3d1 leu2d0 ura3d0 lysd0 rad6Δ::KanMX

value: MAT alpah his3d1 leu2d0 ura3d0 lysd0 rad6{delta}::KanMX


title: Con_intestine-Input3

description: The intestine were dissected from twelve-week-old mice

source_name: intestine


title: WT_D9_p2_NFIAp_R2


title: WT_D9_p1_NFIAn_R3


title: 4_a-Set1_Δset1_strain_rep2

source_name: MAT alpah his3d1 leu2d0 ura3d0 lysd0 set1Δ::HIS3

value: MAT alpah his3d1 leu2d0 ura3d0 lysd0 set1{delta}::HIS3


title: Con_intestine-Input1


title: Con_intestine-Input2


title: WT_D7_pM_NFIAn_R3


title: WT_D9_p1_NFIAn_R1


title: 3_a-Set1_Δset1_strain_rep1


title: WT_D7_pM_NFIAn_R1


title: 2_a-Set1_WT_strain_rep2

source_name: MATa his3∆0 leu2∆0 met15∆0 ura3∆0

value: MATa his3{delta}0 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Con_heart-3

description: The heart were dissected from twelve-week-old mice

source_name: heart


title: WT_D7_pM_NFIAn_R2


title: WT_D7_p2_NFIAn_R3


title: WT_D7_p1_NFIAn_R2


title: Con_kidney-1


title: WT_D7_p1_NFIAn_R3


title: 6_a-Set1_Δrad6_strain_rep2


title: 20_a-HA_Swd2-6HA_Δset1_strain_rep2

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombe spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: fastq, bigwig

source_name: Saccharomyces cerevisiae

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Swd2::6HA::TRP set1{delta}::HIS

value: HA


title: WT_D7_p2_NFIAn_R1


title: 21_a-HA_Notag_WT_strain(Control for removal of background signal of 13~20)

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere))


title: Con_heart-1

value: Water


title: WT_D5_p2_NFIAn_R3


title: Con_heart-2


title: WT_D7_p2_NFIAn_R2


title: Con_brain-Input1

source_name: brain


title: WT_D5_pM_NFIAn_R3


title: 1_a-Set1_WT_strain_rep1


title: WT_D7_p1_NFIAn_R1


title: WT_D5_pM_NFIAn_R2


title: 18_a-HA_Swd2-6HA_WT_strain_rep2

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Swd2::6HA::TRP


title: WT_D5_p2_NFIAn_R1

value: neural progenitor differentiation


title: WT_D5_p1_NFIAn_R3


title: Amp_testis-2

source_name: testis

value: Water with ampicillin


title: Amp_testis-3


title: 17_a-HA_Swd2-6HA_WT_strain_rep1


title: WT_D5_p1_NFIAn_R2

value: WT


title: WT_D5_p1_NFIAn_R1


title: Con_brain-Input3


title: 16_a-HA_Swd2-3HA & Rad6-C88A-9Myc_strain_rep2

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Rad6-C88A::9Myc::TRP Swd2::3HA::HIS


title: WT_D11_pM_NFIAp_R3

value: pM


title: Sample 21-ATACseq

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

library_source: genomic single cell

data_processing:
scRNA-seq libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina). scATAC-seq libraries were sequenced using a NextSeq 500 150-cycle flow cell (Illumina).
For scATAC-seq, reads were aligned to the  human genomes (hg38), and peaks were called using the cellranger-atac count pipeline. Individual samples were merged using the cellranger-atac pipeline to generate the transcription factor activity matrix.
For scRNA-seq,  raw reads were aligned to the  human genomes (hg38), and the digital expression matrix was generated using cellranger count.
Assembly: hg38
Supplementary files format and content: Transcription factor activity matrix for scATAC-seq
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Bone Marrow

extract_protocol:
BM MNCs were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA).
For scATAC-seq, the scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei. The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines. Equal molar concentrations of uniquely indexed samples were pooled together. For scRNA-seq, sample preparation and sequencing were performed at MD Anderson Cancer Center’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10X Genomics, Pleasanton, CA), and single cells were lysed and barcoded for reverse transcription. Equal amounts of each uniquely indexed sample library were pooled together.

value: Bone Marrow

value: Lin-CD34+ cells

value: NRAS G12D

value: Untreated


title: WT_D11_p2_NFIAp_R2


title: Sample 23-ATACseq

value: NRAS G12R


title: Con_brain-Input2

value: twelve-week-old mice

value: Feeding with sterilized food


title: 12_a-Myc_Notag_WT_strain(Control for removal of background signal of 6~11)

value: MATa ura3-52 leu2{delta}1 trp1{delta}63

value: MYC


title: WT_D11_p1_NFIAp_R3


title: WT_D5_p2_NFIAn_R2


title: Amp_testis-1


title: 19_a-HA_Swd2-6HA_Δset1_strain_rep1

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Swd2::6HA::TRP set1{delta}::HIS

value: HA


title: WT_D11_p2_NFIAp_R3


title: 15_a-HA_Swd2-3HA & Rad6-C88A-9Myc_strain_rep1


title: Sample 24-ATACseq

value: NRAS G12R, BRAF D594H

value: Azacitidine


title: Amp_spleen-3

source_name: spleen

value: Water with ampicillin


title: 14_a-HA_Swd2-3HA & Rad6-9Myc_strain_rep2

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Rad6::9Myc::TRP Swd2::3HA::HIS


title: WT_D11_pM_NFIAp_R2

value: neural progenitor differentiation

value: WT


title: Amp_lung-2

source_name: lung


title: Sample 4-ATACseq

value: Bone Marrow

value: KRAS T58I, NRAS G12R, KRAS T58K


title: Sample 22-ATACseq

value: Lin-CD34+ cells

value: NRAS G12D


title: 10_a-Myc_Swd2-3HA&Rad6-C88A-9Myc_strain_rep1

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Rad6-C88A::9Myc::TRP Swd2::3HA::HIS


title: 13_a-HA_Swd2-3HA & Rad6-9Myc_strain_rep1


title: Amp_spleen-2

value: twelve-week-old mice


title: WT_D11_p1_NFIAp_R2


title: Sample 3-ATACseq

value: Untreated


title: Amp_spleen-1

value: Feeding with sterilized food


title: MUT_D9_pM_NFIAn_R3

value: pM

value: MUT


title: Amp_lung-1


title: MUT_D9_p2_NFIAn_R3


title: MUT_D9_pM_NFIAn_R1


title: 11_a-Myc_Swd2-3HA&Rad6-C88A-9Myc_strain_rep2

value: MYC


title: Amp_liver-Input3

source_name: liver


title: Amp_lung-3


title: WT+veh, liver 2

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

institute: Seoul National University

data_processing:
FastQC v0.11.7 used for base-calling and quality check.
Trimmomatic 0.38 performs trimming and alignment with various parameters for Illumina paired-end or single-end.
HISAT2 version 2.1.0, Bowtie2 2.3.4.1 is a tool that quickly and accurately maps high throughput sequencing data to the reference genome.
StringTie version 2.1.3b is a tool that assembles sequencing information mapped to a reference to quickly and accurately generate potential transcripts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Expression_Profile.mm10.gene.txt: Tab-delimited text file includes Read_Count, FPKM (normalized value), and TPM (normalized value) values for each sample.

extract_protocol:
TruSeq Stranded mRNA LT Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols and TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E.

value: liver

value: 10-12 weeks

value: wild type

value: vehicle


title: MUT_D9_p1_NFIAn_R1

value: neural progenitor differentiation


title: WT+veh, liver 3


title: 8_a-Myc_Swd2-3HA&Rad6-9Myc_strain_rep1

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Rad6::9Myc::TRP Swd2::3HA::HIS


title: MUT_D9_p1_NFIAn_R3


title: WT+veh, liver 1


title: Amp_liver-Input2

value: Water with ampicillin


title: 7_a-Myc_Rad6-9Myc_strain_rep2

value: MATa ura3-52 leu2{delta}1 trp1{delta}63 Rad6::9Myc::TRP


title: 6_a-Myc_Rad6-9Myc_strain_rep1


title: Amp_kidney-3


title: MUT_D7_pM_NFIAn_R2


title: 5_a-HA_Notag_WT_strain(Control for removal of background signal of 1~4)

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere))

value: HA


title: WT+APAP, liver 2

value: acetaminophen


title: Amp_kidney-2

value: twelve-week-old mice


title: Amp_liver-Input1


title: MUT_D7_pM_NFIAn_R3


title: 4_a-HA_Swd2-3HA_Δrad6_strain_rep2

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Swd2::3HA::HIS rad6{delta}::KanMX4


title: 9_a-Myc_Swd2-3HA&Rad6-9Myc_strain_rep2


title: WT+APAP, liver 3


title: WT+APAP, liver 1


title: Gα12KO+veh, liver 3

description:
8Ga12KO_veh
Gα12-/-


title: MUT_D7_p2_NFIAn_R3


title: MUT_D7_p2_NFIAn_R2


title: 1_a-HA_Swd2-3HA_WT_strain_rep1

value: MATa ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TEladh4:L:URA3(VIIL Telomere)) Swd2::3HA::HIS


title: 2_a-HA_Swd2-3HA_WT_strain_rep2


title: Gα12KO+veh, liver 2

description:
7Ga12KO_veh
Gα12-/-


title: MUT_D7_p2_NFIAn_R1


title: Amp_intestine-Input2

value: Feeding with sterilized food


title: Gα12KO+veh, liver 1

description:
5Ga12KO_veh
Gα12-/-


title: MUT_D7_p1_NFIAn_R3

value: MUT


title: Amp_heart-3


title: Gα12KO+APAP, liver 2

description:
3Ga12KO_APAP
Gα12-/-


title: Amp_heart-2


title: MUT_D7_p1_NFIAn_R1


title: MUT_D7_p1_NFIAn_R2


title: BM Sample 20

value: Bone Marrow

value: BM MNCs

value: Wildtype

value: Decitabine


title: BM Sample 17


title: 3_a-HA_Swd2-3HA_Δrad6_strain_rep1


title: 14_a-Set1_551WT_strain_rep2

source_name: ura3-52 his3Δ200 ade2-101(ochre) lys2-80(1m) trp-1Δ1 leu2-Δ1 TELadh4::URA3(VIIL Telomere)

value: ura3-52 his3{delta}200 ade2-101(ochre) lys2-80(1m) trp-1{delta}1 leu2-{delta}1 TELadh4::URA3(VIIL Telomere)


title: Amp_heart-1


title: MUT_D5_pM_NFIAn_R3

source_name: neural progenitor differentiation

value: neural progenitor differentiation

value: pM


title: Gα12KO+APAP, liver 1

description:
2Ga12KO_APAP
Gα12-/-

value: liver

value: 10-12 weeks


title: MUT_D7_pM_NFIAn_R1


title: Gα12KO+APAP, liver 3

description:
4Ga12KO_APAP
Gα12-/-


title: Amp_brain-Input3

value: Water with ampicillin


title: Amp_intestine-Input3


title: Small Intestine, delta_FliC

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

department: Institut für Molekulare Medizin

institute: RWTH Aachen University Hospital

data_processing:
Raw sequencing data were processed by CellRanger pipeline with default parameters.
Assembly: mm10-2020-A
Supplementary files format and content: H5

source_name: small intestine

extract_protocol:
Single epithelial cells were isolated from pooled small intestines (n=4) of 7 day-old mice. Epithelial cells were stained with EpCam-APC (1:500 dilution) (eBioscienceTM) for 20 min on ice. DAPI (1:200 dilution) (Roth) was then added to stain dead cells. Single epithelial cells were sorted with FACS ARIA II (BD) equipped with a 100 mm nozzle.
Live epithelial cells were further processed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s instruction. Single-cell sequencing on High-Output flow cells using 150 cycles was performed on an Illumina NextSeq 500 platform. The fragment size of the final libraries was determined using the Bioanalyzer High-Sensitivity DNA Kit (Agilent). Library concentration was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

value: small intestine

value: epithelial cells


title: Amp_brain-Input2

value: twelve-week-old mice


title: MUT_D5_pM_NFIAn_R2


title: Small Intestine, E.coli

value: Ecoli


title: BM Sample 19

value: Untreated


title: BM Sample 18


title: Amp_intestine-Input1

value: Feeding with sterilized food


title: Amp_brain-Input1


title: H9 cells, 8d, replicate 1

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.2.0.28691 and real-time base calling was performed using Real Time Analysis v4.6.7. Then the Illumina DRAGEN BCL Convert 07.021.645.4.0.3 pipeline was used to generate the sequence data.
Assembly: hg38
Supplementary files format and content: count_matrix.rds
Supplementary files format and content: metadata.txt

source_name: organoid

extract_protocol:
Organoid dissociation was carried out using the Neurosphere Dissociation Kit (Miltenyi, 130-095-943). Twenty organoids were used.
Single cell libraries were prepared in accordance with Chromium Single Cell 3' Reagent Kit v3.1 Dual Index user guide

value: organoid

value: WT

value: neural differentiation


title: Small Intestine, OMM9


title: BM Sample 15

value: Bone Marrow

value: BM MNCs

value: Wildtype


title: MUT_D5_pM_NFIAn_R1

value: neural progenitor differentiation

value: MUT


title: MUT_D5_p2_NFIAn_R3


title: Abx_testis-3

value: Water with multiple antibiotics


title: Abx_testis-2


title: MUT_D5_p2_NFIAn_R2


title: CD34 Sample 9

value: Lin-CD34+ cells

value: PTPN11 A72T


title: CD34 Sample 6

value: CBL C384Y, CBL F378fs

value: Azacitidine


title: Cardiac allograft, d14, GIL, aIL6 3

city: Vienna

first: Moritz

last: Muckenhuber

state: Vienna

address: Währinger Gürtel 18-20

department: General Surgery

country: Austria

institute: Medical university of vienna

data_processing:
Reads in fastq format were aligned to the mouse reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode
Reads per gene were counted by STAR
differential gene expression was calculated using DESeq2 version 1.22.2.
TPM were generated by RSEM
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Graft infiltrating leukocytes (cardiac allograft)

extract_protocol:
RNA was extracted from flow sorted graft infiltrating leukocytes isolated from explanted cardiac allograft tissue using an Rneasy micro kit (Qiagen)
Sequencing libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (E6420) according to manufacturer's protocols (New England Biolabs)

treatment_protocol: BL6 recipients of a BALB/c cardiac allograft were treated with ATG induction and CTLA4-Ig with or without additional IL6 blockade

value: wt

value: ATG/CTLA4-Ig and aIL6


title: Cardiac allograft, d14, GIL, aIL6 4

value: Graft infiltrating leukocytes (cardiac allograft)


title: MUT_D5_p2_NFIAn_R1


title: Abx_testis-1

value: twelve-week-old mice

value: Feeding with sterilized food


title: BM Sample 16

value: Untreated


title: Cardiac allograft, d14, GIL, aIL6 2


title: Amp_kidney-1

source_name: kidney

value: Water with ampicillin


title: MUT_D5_p1_NFIAn_R3


title: Abx_spleen-3


title: CD34 Sample 5

value: Bone Marrow

value: CBL C384Y


title: MUT_D5_p1_NFIAn_R2


title: CD34 Sample 4

value: KRAS T58I, NRAS G12R, KRAS T58K


title: Abx_spleen-2


title: Abx_spleen-1


title: Abx_lung-3


title: MUT_D11_pM_NFIAn_R2

value: neural progenitor differentiation

value: pM


title: CD34 Sample 3


title: MUT_D5_p1_NFIAn_R1

value: MUT


title: MUT_D11_pM_NFIAn_R3


title: Cardiac allograft, d14, GIL, control 3


title: CD34 Sample 2

value: Lin-CD34+ cells

value: CBL Y371H, NRAS G13V

value: Decitabine


title: Cardiac allograft, d14, GIL, control 1


title: CD34 Sample 11

value: BRAF G469A, CBL K382E, CBL C384Y


title: MUT_D11_p2_NFIAn_R2


title: CD34 Sample 12

value: BRAF G469A

value: Guadecitabine


title: Cardiac allograft, d14, FFPE, aIL6 8

source_name: cardiac allograft (FFPE)

extract_protocol:
RNA was extracted from FFPE sections (30 5µm sections) of explanted cardiac allograft tissue using an Rneasy FFPE kit (Qiagen)
RNA libraries for RNAseq were constructed using a NebNext Ultra II Directional RNA Library Prep Kit (E7760) and NEBNext rRNA Depletion Kit v2 (E7400) according to manufacturer's protocols (New England Biolabs)

value: cardiac allograft (FFPE)

value: wt

value: ATG/CTLA4-Ig and aIL6


title: Cardiac allograft, d14, GIL, aIL6 1

value: Graft infiltrating leukocytes (cardiac allograft)


title: Cardiac allograft, d14, FFPE, aIL6 7


title: CD34 Sample 10

value: PTPN11 A72T

value: Azacitidine


title: Abx_liver-Input2

value: twelve-week-old mice

value: Feeding with sterilized food

value: Water with multiple antibiotics


title: Abx_lung-2


title: Abx_lung-1


title: Cardiac allograft, d14, FFPE, aIL6 6


title: MUT_D11_p1_NFIAn_R2

value: neural progenitor differentiation


title: CD34 Sample 1

value: Bone Marrow

value: CBL Y371H, NRAS Y64_S6, NRAS G13V, NRAS G12S

value: Untreated


title: MUT_D11_p2_NFIAn_R3

value: MUT


title: MUT_D11_p1_NFIAn_R3


title: Cardiac allograft, d14, GIL, control 4


title: Abx_liver-Input3


title: Abx_liver-Input1


title: BM Sample 13

value: BM MNCs

value: NRAS G12V, NRAS G12D, PTPN11 A72V


title: Cardiac allograft, d14, FFPE, aIL6 4


title: BM Sample 9


title: Abx_kidney-3


title: Cardiac allograft, d14, GIL, control 2


title: BM Sample 8

value: NRAS G13R, PTPN11 A72D


title: Abx_kidney-2


title: Cardiac allograft, d14, FFPE, aIL6 3

value: cardiac allograft (FFPE)


title: HER2.eSPR transduced BMDM replication 1

city: Duarte

first: Siqi

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

description:
1 ug of RNA was used for cDNA library construction atNovogeneusing an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 20 M raw reads were generated from each library.
eSPR-1

data_processing:
sequencing reads were aligned to the mouse or human genome using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a).
Aligned reads were then quantified to transcriptome (mm10; Ensembl Transcripts release 100), and normalized (Median Ratio normalization).
Differentiated gene expression analysis (DESeq2) were performed to generate raw counts
Assembly: mm10
Supplementary files format and content: tab delineated text file include raw counts

source_name: bone marrow differentiated cells

extract_protocol:
e extracted with an RNA extraction kit (Qiagen).
RNA was used for cDNA library construction using a NEBNext® Ultra RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s protocol.

value: bone marrow differentiated cells

value: bone marrow derived macrophages

value: Adenvirus transduced


title: Abx_kidney-1


title: Cardiac allograft, d14, FFPE, aIL6 2

value: wt

value: ATG/CTLA4-Ig and aIL6


title: empty vector transduced BMDM replication 2

description:
1 ug of RNA was used for cDNA library construction atNovogeneusing an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 20 M raw reads were generated from each library.
EmptyVec-2


title: BM Sample 7

value: Wildtype


title: BM Sample 14

value: Decitabine and venetoclax


title: BM Sample 6

value: CBL C384Y, CBL F378fs

value: Azacitidine


title: Abx_intestine-Input2

source_name: intestine

value: twelve-week-old mice

value: Feeding with sterilized food

value: Water with multiple antibiotics


title: empty vector transduced BMDM replication 1

description:
1 ug of RNA was used for cDNA library construction atNovogeneusing an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 20 M raw reads were generated from each library.
EmptyVec-1


title: Cardiac allograft, d14, FFPE, aIL6 5


title: Cardiac allograft, d14, FFPE, control 7


title: Abx_intestine-Input3


title: Abx_intestine-Input1


title: BM Sample 4

value: Bone Marrow

value: KRAS T58I, NRAS G12R, KRAS T58K


title: untreated BMDM replication 2

description:
1 ug of RNA was used for cDNA library construction atNovogeneusing an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 20 M raw reads were generated from each library.
UTD-2

value: untransduced


title: BM Sample 5

value: BM MNCs

value: CBL C384Y

value: Untreated


title: Cardiac allograft, d14, FFPE, control 6

value: cardiac allograft (FFPE)


title: Cardiac allograft, d14, FFPE, control 8


title: HER2.eSPR transduced BMDM replication 2

description:
1 ug of RNA was used for cDNA library construction atNovogeneusing an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randomly by adding fragmentation buffer. The first strand cDNA was synthesized using random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA , USA) using a paired-end 150 run (2×150 bases). 20 M raw reads were generated from each library.
eSPR-2

value: bone marrow differentiated cells

value: bone marrow derived macrophages

value: Adenvirus transduced