title: MDST8 rep1 RNA

description: MDST8 rep1


title: Sample 8_PyMT_PCBP1_WT(2)

status: Public on Oct 15 2025

type: SRA

city: Charleston

first: Cécile

last: Fréreux

state: SC

address: 173 Ashley Avenue

country: USA

institute: Medical University of South Carolina

description: Library name: Sample 8

library_source: transcriptomic

data_processing:
Read quality was assessed with FastQC and reads were aligned with Bowtie2. Differential expression analysis was performed in Partek Flow using the Gene Specific Analysis algorithm.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes normalized CPM for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Mammary tumor

extract_protocol:
RNA was extracted by Trizol/phenol chloroform and analyzed for quality (RIN) by a Bioanalyzer (Agilent 2100)
Libraries were generated by the Medical University of South Carolina core facility using a poly(A)-enrichment mRNA-seq protocol (Illumina-compatible stranded mRNA library preparation) according to the manufacturer’s instructions

tag: tissue

value: Mammary tumor

tag: genotype

value: WT

tag: batch


title: Sample 7_PyMT_PCBP1_WT(1)

description: Library name: Sample 7


title: Car-1 rep2 RNA

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

description: Car-1 rep2

data_processing:
Adapter sequences were removed using cutadapt
Trimmed sequences were mapped to the human genome (GRCh38) with STAR 2.7.10a using GENCODE v43
Gene counts were determined during the STAR mapping procedure with the ‘–quantMode GeneCounts’ setting
Gene counts were normalised to log2 transformed TPM values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Cells were cultured in DMEM/F12  supplemented with 10% v/v fetal bovine serum and 50 units/mL of penicillin/streptomycin. Cells were maintained at 37 °C in humidified air containing 5% CO2.

extract_protocol:
Ultrafiltration was performed prior to SEC. SEC with the Automated Fraction Collector (AFC-V1, Izon) was performed to isolate vesicles using 2 qEV original / 70 nm gen 2 columns (IZON) per sample. Using a buffer volume of 2.70 ml, and a fraction volume of 0.5 ml, the particles of interest were collected in fractions 3 and 4 (between 1 and 2 ml of the Purified Collection Volume (PCV)). Both fractions of the 2 isolations were pooled, resulting in a volume of 2 ml per sample. 1 ml of the vesicle isolate was concentrated with an Amicon Ultra-2 Centrifugal Filter Unit (Millipore) to 250 µl. Total RNA from the EVs was isolated using the miRNeasy serum/plasma kit (QIAgen) according to the manufacturers' protocol with minor adjustments.
mRNA libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio Inc.) according to the manufacturers' protocol, including ribosomal cDNA depletion

value: cell line

tag: cell line

tag: cell type

value: CRC


title: Gag-hnRNP K-rep1

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
FeatureCounts was used to summarize and count mapped RNA-seq reads for genomic features.
Assembly: hg19 and NL4-3
Supplementary files format and content: Counts files showing summarization of reads (i.e. chromosomal locations and counts).

growth_protocol: 293T cells grown in 6-well dishes were transfected with 2 μg of the indicated PR- NL4-3-derived proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
Trizol extraction
TruSeq Stranded Total RNA Sample Prep Kit (Illumina) was used to generate libraries following manufacturer's protocol.

treatment_protocol: No treatments

value: 293T cells transfected

tag: treatment

value: Gag-hnRNP K


title: Gag-CNBP4-rep2


title: WT-Gag-rep2

value: WT-Gag


title: Patient_16

city: Aachen

first: Mohamed

last: Saad

address: Pauwelsstraße 30

department: Institut für Zell- und Tumorbiologie

country: Germany

institute: Uniklinik RWTH Aachen

description:
Library name: EV_423
column name in raw_counts_All_samples.txt : Patient_16

data_processing:
The sequencing data was initially trimmed using TrimGalore (version 0.6.6), followed by alignment with STAR software (version 2.7.9)
Read quantification was conducted using Kallisto to generate a raw count matrix.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimated txt file includes raw count for each sample

source_name: Preipheral blood

extract_protocol:
16 patients peripheral blood samples were collected using EDTA as an anticoagulant. The samples were centrifuged at 1500 xg for 15 minutes, and the supernatant was subsequently collected. This supernatant underwent a second centrifugation at 2500 xg for 15 minutes to obtain Platelet-Poor Plasma (PPP). A volume of 350 μl PPP was mixed with 28 ml of phosphate-buffered saline (PBS) and then ultracentrifuged at 100000 xg for 1 hour at 4°C using a Beckman Optima XPN-100.
The resulting pellet upon ultracentrifugation , containing extracellular content, was dissolved in 100 μl of PBS and then combined with 800 μl of TRIZOL LS Reagent (ThermoFisher). RNA was extracted through a phenol-chloroform method and cDNA libraries were prepared using the Smart-Seq V4 ultra-low input RNA kit from Clontech Laboratories, following the manufacturer’s instructions. The amplified cDNA was further processed to create Illumina-compatible libraries according to the TruSeq Nano DNA sample preparation guide (Illumina). These libraries were then subjected to paired-end sequencing (2x75 cycles) on an Illumina HiSeq2500 platform.

value: Preipheral blood

tag: reticulin grade


title: Gag-dNC-rep2

value: Gag-dNC


title: Car-1 rep1 RNA

description: Car-1 rep1


title: Sample 6_PyMT_PCBP1_KO(6)

description: Library name: Sample 6

value: PCBP1 KO


title: Gag-bZIP-rep2

value: Gag-bZIP


title: Gag-CNBP6-rep2


title: Gag-hnRNP F-rep1

value: Gag-hnRNP F


title: Patient_15

description:
Library name: EV_418
column name in raw_counts_All_samples.txt : Patient_15


title: HT55 rep2 RNA

description: HT55 rep2


title: Gag-hnRNP A1-rep1

value: Gag-hnRNP A1


title: Sample 5_PyMT_PCBP1_KO(5)

description: Library name: Sample 5


title: Sample 10_PyMT_PCBP1_WT(4)

description: Library name: Sample 10


title: Sample 4_PyMT_PCBP1_KO(4)

description: Library name: Sample 4


title: Gag-SRSF5-rep1


title: Patient_14

description:
Library name: EV_416
column name in raw_counts_All_samples.txt : Patient_14


title: Patient_13

description:
Library name: EV_415
column name in raw_counts_All_samples.txt : Patient_13


title: RCM-1 rep2 miRNA

description: RCM-1 rep2

data_processing:
Data processing and UMI correction was done using sRNAbench. (Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res. 2022 Jul 5;50(W1):W710-W717. doi: 10.1093/nar/gkac363. PMID: 35556129; PMCID: PMC9252802.)
Gene counts were normalised to log2 transformed CPM values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

growth_protocol: Cells were cultured in DMEM/F12 supplemented with 10% v/v fetal bovine serum and 50 units/mL of penicillin/streptomycin. Cells were maintained at 37 °C in humidified air containing 5% CO2.

extract_protocol:
Ultrafiltration was performed prior to SEC. SEC with the Automated Fraction Collector (AFC-V1, Izon) was performed to isolate vesicles using 2 qEV original / 70 nm gen 2 columns (IZON) per sample. Using a buffer volume of 2.70 ml, and a fraction volume of 0.5 ml, the particles of interest were collected in fractions 3 and 4 (between 1 and 2 ml of the Purified Collection Volume (PCV)). Both fractions of the 2 isolations were pooled, resulting in a volume of 2 ml per sample. 1 ml of the vesicle isolate was concentrated with an Amicon Ultra-2 Centrifugal Filter Unit (Millipore) to 250 µl. Total RNA from the EVs was isolated using the miRNeasy serum/plasma kit (QIAgen) according to the manufacturers' protocol with minor adjustments.
Small RNA libraries were prepared using the costum IsoSeek protocol described in the STAR protocol. (van Eijndhoven, M.A.J., Scheepbouwer, C., Aparicio-Puerta, E., Hackenberg, M., and Pegtel, D.M. (2023). IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution. STAR Protoc 4, 102645. 10.1016/j.xpro.2023.102645.)


title: Gag-SRSF4-rep1


title: Sample 3_PyMT_PCBP1_KO(3)

description: Library name: Sample 3


title: RCM-1 rep1 miRNA

description: RCM-1 rep1


title: Gag-SRSF1-rep1


title: Patient_12

description:
Library name: EV_411
column name in raw_counts_All_samples.txt : Patient_12


title: Sample 2_PyMT_PCBP1_KO(2)

description: Library name: Sample 2


title: Patient_11

description:
Library name: EV_420
column name in raw_counts_All_samples.txt : Patient_11


title: Patient_10

description:
Library name: EV_413
column name in raw_counts_All_samples.txt : Patient_10


title: Hutu80 rep2 miRNA

description: Hutu80 rep2


title: Hutu80 rep1 miRNA

description: Hutu80 rep1


title: Gag-NCx2-rep1


title: Gag-NCx3-rep1


title: Mutant_female

city: Boston

first: Rhian

last: Stavely

state: MA

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

description:
Library name: MF
10x Genomics

library_source: transcriptomic single cell

data_processing:
Output data were processed using the 10X genomics Cell Ranger pipeline to generate barcode and feature count matrices for downstream analysis
Assembly: mm10
Supplementary files format and content: CellRanger output data_barcodes_features_matrix.tsv

source_name: Muscularis propria of colon

extract_protocol:
Nuclei were isolated from the muscularis propria of the colon using the 10X Chromium Nuclei Isolation Kit as of the manufacturer’s instructions. Briefly, colons were collected and pinned in a silicone-lined petri dish to remove the mucosa and submucosa. The muscularis propria was then minced into 2-5mm fragments before conducting the nuclei isolation procedure.
snRNA-seq - Chromium Single Cell 3' Reagent Kit (v3.1)

value: Muscularis propria of colon

tag: Sex

value: female


title: SW1116 rep2 miRNA

description: SW1116 rep2


title: Gag-CNBP7-rep1


title: HT55 rep1 RNA

description: HT55 rep1


title: Patient_8

description:
Library name: EV_332
column name in raw_counts_All_samples.txt : Patient_8


title: SW1116 rep1 miRNA

description: SW1116 rep1


title: Control_female

description:
Library name: CF
10x Genomics


title: Patient_7

description:
Library name: EV_331
column name in raw_counts_All_samples.txt : Patient_7


title: Gag-CNBP4-rep1


title: MDST8 rep2 miRNA

description: MDST8 rep2


title: Control_male

description:
Library name: CM
10x Genomics

value: male


title: Patient_6

description:
Library name: EV_65
column name in raw_counts_All_samples.txt : Patient_6


title: MDST8 rep1 miRNA

description: MDST8 rep1


title: Gag-CNBP3-rep1


title: Sample 1_PyMT_PCBP1_KO(1)

description: Library name: Sample 1


title: Car-1 rep2 miRNA

description: Car-1 rep2


title: Patient_5

description:
Library name: EV_305
column name in raw_counts_All_samples.txt : Patient_5


title: whole mouse embryonic heads, 12ss, dcko, biological replicate 3

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample-12 12ss dcko (animal 3123.09)

data_processing:
Kallisto 0.50.1 pseudoalignment
tximport 1.34.0 import into DESeq2
Assembly: GRCm39
Supplementary files format and content: kallisto output pseudoalignment abundance processed by tximport into TPMs; csv file format broken by stage; one sample per column

source_name: Whole mouse embryonic heads

extract_protocol:
Whole embryonic heads were cut caudal to the first pharyngeal arch, snap frozen in a dry ice/MeOH slurry, and stored at -80C until extracted using the Rneasy kit (Qiagen 74004)
Library preparation was completed by the CCHMC Genomics Sequencing Facility where RNA was polyA-selected, reverse-transcribed using Illumina's TruSeq stranded mRNA library preparation kit. Amplification was accomplished with 15 cycles of PCR.

value: Whole mouse embryonic heads


title: Gag-CNBP2-rep1


title: whole mouse embryonic heads, 12ss, dcko, biological replicate 2

description: Library name: Sample-11 12ss dcko (animal 3123.07)


title: Patient_4

description:
Library name: EV_30
column name in raw_counts_All_samples.txt : Patient_4


title: Patient_3

description:
Library name: EV_29
column name in raw_counts_All_samples.txt : Patient_3


title: Patient_9

description:
Library name: EV_408
column name in raw_counts_All_samples.txt : Patient_9


title: HT55 rep2 miRNA

description: HT55 rep2


title: whole mouse embryonic heads, 12ss, dcko, biological replicate 1

description: Library name: Sample-10 12ss dcko (animal 3065.05)


title: Gag-dNC-NC-rep1

value: Gag-dNC-NC


title: Patient_2

description:
Library name: EV_28
column name in raw_counts_All_samples.txt : Patient_2


title: whole mouse embryonic heads, 12ss, control, biological replicate 3

description: Library name: Sample-09 12ss ctrl (animal 3123.03)

value: Control


title: Gag-dNC-rep1

value: cell line

value: WT


title: Gag-CNBP5-rep1

value: 293T cells transfected


title: Patient_1

description:
Library name: EV_26
column name in raw_counts_All_samples.txt : Patient_1


title: Mutant_male

description:
Library name: MM
10x Genomics


title: HT55 rep1 miRNA

description: HT55 rep1

value: CRC


title: whole mouse embryonic heads, 12ss, control, biological replicate 2

description: Library name: Sample-08 12ss ctrl (animal 3093.03)


title: T-24

city: Wuhan

first: Jinfeng

last: Xiong

address: 1095 JiefangAnv. Wuhan, Hubei 430030, China

country: China

institute: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China

data_processing:
We selected Hisat2 as the mapping tool
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package.
Genome_build: Genome_build: hg38

source_name: cervix

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pathology

tag: hpv integration

value: positive


title: WT-Gag-rep1

value: WT-Gag


title: whole mouse embryonic heads, 12ss, control, biological replicate 1

description: Library name: Sample-07 12ss ctrl (animal 2989.03)


title: T-23


title: Car-1 rep1 miRNA

description: Car-1 rep1


title: whole mouse embryonic heads, 8ss, dcko, biological replicate 3

description: Library name: Sample-06 8ss dcko (animal 3066.02)


title: ex vivo isolated, cultured non-classic Th1 cells, donor nc1-2

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

description: Library name: ncTh1_2

library_source: genomic

data_processing:
The sequenced 2 × 100 bp paired-end libraries were assessed for sufficient sequencing quality and potential adapter contamination using the programs FastQC (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trim_galore (version 0.6.5; Babraham Bioinformatics, https://www.bioinformatics.ac.uk/projects/trim_galore/) and cutadapt (Martin, M., EMBnet, 2011, 17.1:10-12). Quality-controlled libraries were  mapped against the human reference genome (assembly GRCh38) using the bisulfite short read mapping software BSMAP (Xi, Y. and Li, W., BMC Bioinformatics, 2009, 10:232). Only unique, properly paired reads (methratio.py parameters: --unique, --paired, --remove-duplicate) were used to determine CpG methylation levels and coverage. CpG motifs with a minimum coverage of five mapped reads in at least two replicates of a condition served as input for methylation level smoothing and DMR detection using the Bioconductor package bsseq (version 1.16) (Hansen et al., Genome Biol., 2012, 13:R83). Regions were classified as differentially methylated between two conditions if (1) they contain at least three CpG motifs with (2) a maximum distance of 200 bases, (3) a mean methylation difference of at least 0.25, and (4) all CpGs in the region have an associated t-statistic (computed with the bsseq function Bsmooth.tstat) within the 0.01 to 0.99 quantile interval (parameter qcutoff of the bsseq function dmrFinder).
Assembly: GRCh38
Supplementary files format and content: csv file includes chromosomal location, number of CpG motifs, region width, areaStat, mean methylation difference, mean methylation group1, mean methylation group2, methylation direction (direction), nearest tss, distance to nearest tss, nearest gene id, nearest gene name, nearest gene description, preceding tss, following tss

molecule: genomic DNA

source_name: culture cells

growth_protocol: Th1, Th17, non-classic Th1 cell clones were isolated and cultivated as described in Mazzoni et al.2015 (PMID: 25740946). Genomic DNA of naive CD4+ T cells was isolated directly after fluorescence-activated cell sorting (CD3+CD4+CD45RA+CD31+CD45RO-) from donor material.

extract_protocol:
Genomic DNA was extracted by using a DNeasy Blood & Tissue Kit (QIAGEN).
Genomic DNA was sheared by using a Covaris S220 system (Duty Cycle: 5%, Intensity: 3, Cycles per Burst: 200, Time: 70 sec). The DNA sequencing library was generated from sheared DNA using a NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) and the NEBNext® Multiplex Oligos for Illumina® (Methylated Adaptor, Index Primers Set 1). Generated libraries were bisulfite converted by using the EZ DNA Methylation Kit (Zymo Research). Bisulfite converted libraries were PCR amplified by utilizing the KAPA Hot Start Uracil PCR Master Mix (Kapa Biosystems) for 9 cycles. Finally, libraries were sequenced on Illumina HiSeq 2500 using the TruSeq SBS Kit v3 – HS (Illumina).

value: culture cells

value: CD4+ non-classical T helper 1 cell


title: ex vivo isolated, cultured non-classic Th1 cells, donor nc1-3

description: Library name: ncTh1_3


title: Demyelination, S4, R2

city: Singapore

first: Catherine Wei Min

last: Ong

state: Singapore

address: 14 Medical Drive, MD6, Centre for Translational Medicine, #15-02

country: Singapore

institute: National University of Singapore

description: microdissected RNA-Seq

data_processing:
Alignment was performed using Kallisto (version 0.46), with sequence based bias correction.
Data was annotated using ensembldb package (version 2.24.0). The transcript abundance was summarized to gene level using Sleuth (version 0.30).
Raw counts from RNA sequencing were processed using edgeR, Bioconductor version 3.17, with 3 variance estimated and size factor normalised using Trimmed Mean of M-values (TMM).
Assembly: GRCh38
Supplementary files format and content: CSV table with counts and TPM as estimated by Kallisto

source_name: Demyelination brain tissue

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: Demyelination brain tissue


title: Demyelination, S4, R1

description: microdissected RNA-Seq


title: whole mouse embryonic heads, 8ss, dcko, biological replicate 2

description: Library name: Sample-05 8ss dcko (animal 3065.07)


title: Gag-bZIP-rep1

value: Gag-bZIP


title: ex vivo isolated, cultured non-classic Th1 cells, donor nc1-1

description: Library name: ncTh1_1


title: Demyelination, S3, R2

description: microdissected RNA-Seq


title: whole mouse embryonic heads, 8ss, dcko, biological replicate 1

description: Library name: Sample-04 8ss dcko (animal 3065.04)


title: ex vivo isolated, cultured Th17 cells, donor 17-3

description: Library name: Th17_3

value: CD4+ T helper 17 cell


title: T-22


title: Demyelination, S3, R1

description: microdissected RNA-Seq


title: T-17


title: whole mouse embryonic heads, 8ss, control, biological replicate 3

description: Library name: Sample-03 8ss ctrl (animal 3275.02)


title: Demyelination, S2

description: microdissected RNA-Seq


title: ex vivo isolated, cultured Th17 cells, donor 17-2

description: Library name: Th17_2


title: T-16


title: whole mouse embryonic heads, 8ss, control, biological replicate 2

description: Library name: Sample-02 8ss ctrl (animal 3068.02)


title: ex vivo isolated, cultured Th17 cells, donor 17-1

description: Library name: Th17_1


title: T-15


title: CNSTB, S6, normal2

description: microdissected RNA-Seq

source_name: CNSTB brain tissue

value: CNSTB brain tissue


title: ex vivo isolated, cultured Th1 cells, donor 1-3

description: Library name: Th1_3

value: CD4+ T helper 1 cell


title: whole mouse embryonic heads, 8ss, control, biological replicate 1

description: Library name: Sample-01 8ss ctrl (animal 2989.10)


title: knock-out mouse, proximal colon 3

description:
Library name: KOP3
10x Genomics

source_name: digested cells from muscularis propria

extract_protocol:
Cells were prepared by digestion of colonic muscularis propria for 60 minutes at 37° C in dispase and collagenase XI. Samples were filtered through a 40 μm filter, stained with DAPI, and underwent FACS sorting for DAPI negativity to obtain live cells.
Single cells (scRNAseq) 10X Genomics Cell Ranger pipeline

value: digested cells from muscularis propria

tag: colon region

value: Proximal

tag: ganglia status

value: Ganglionated

tag: strain

tag: age


title: CNSTB, S6, granuloma3

description: microdissected RNA-Seq


title: T-21


title: ex vivo isolated, cultured Th1 cells, donor 1-1

description: Library name: Th1_1


title: ex vivo isolated, cultured Th1 cells, donor 1-2

description: Library name: Th1_2


title: knock-out mouse, distal colon 3

description:
Library name: KOD3
10x Genomics

value: Distal

value: Aganglionic


title: T-12

value: negative


title: T-10


title: knock-out mouse, proximal colon 2

description:
Library name: KOP2
10x Genomics


title: CNSTB, S6, granuloma1

description: microdissected RNA-Seq


title: ex vivo, naive T cells, donor 2

description: Library name: Tn_2

source_name: peripheral blood

value: peripheral blood

value: naive CD4+ T cell


title: knock-out mouse, distal colon 2

description:
Library name: KOD2
10x Genomics


title: ex vivo, naive T cells, donor 3

description: Library name: Tn_3


title: T-6


title: CNSTB, S5, granuloma5

description: microdissected RNA-Seq


title: T-4

value: positive


title: Spheroid

city: Philadelphia

first: Francesca

last: Costabile

address: 3400 Civic Center BLVD

institute: University of Pennsylvania

description: Library name: B16 Spheroid

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to mm10 genome using STAR.
Read quantification and feature annotation were performed using featureCounts.
Differential expression analysis was performed using NOISeq.
Assembly: mm10
Supplementary files format and content: text file includes mapped reads to genomic features for all samples

extract_protocol:
RNA was extracted sing Rneasy mini plus kit (quiagen) and 1.3 ug of total RNA was used for the contruction of sequencing libraries
The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA 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 PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Melanoma

value: WT


title: T-3


title: T-14


title: CNSTB, S5, granuloma4

description: microdissected RNA-Seq


title: ex vivo, naive T cells, donor 1

description: Library name: Tn_1


title: wild-type mouse, distal colon 2

description:
Library name: WTD2
10x Genomics


title: wild-type mouse, proximal colon 1

description:
Library name: WTP1
10x Genomics


title: CNSTB, S5, granuloma3

description: microdissected RNA-Seq


title: CNSTB, S6, normal1

description: microdissected RNA-Seq


title: T-8


title: Mouse tumor in vivo

description: Library name: Tumor snap frozen

source_name: tumor

value: tumor


title: CNSTB, S6, granuloma2

description: microdissected RNA-Seq


title: CNSTB, S5, granuloma2

description: microdissected RNA-Seq


title: T-2


title: CNSTB, S5, granuloma1

description: microdissected RNA-Seq


title: B16-control

description: Library name: B16 Control


title: GM4_HiC

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Library name: GM4_HiC

data_processing:
Illumina sequencing reads were de-multiplexed using bcl2fastq/2.20.0.
Individual FASTQ files were processed using juicer_tools pre option (juicer/1.6) was used to make .hic files at multiple resolutions with MAPQ scores ≥ 30 and Arima provided fragment-delimited maps. Individual .hic files were combined with juicer/1.6’s mega.sh script.
Differential loops were called at 5kb resolution using KR normalization with mustache’s diffmustache.py package in python/3.1 (detection FDR < 0.01 and difference FDR < 0.001).
Assembly: GRCm38/mm10
Supplementary files format and content: .hic contact matrix files

source_name: muscle

extract_protocol:
MuSCs were lysed, digested with restriction enzymes, labeled with biotin, and subjected to proximity ligation. Proximally ligated DNA was purified and fragmented. The fragments were enriched by biotin enrichment beads.
Hi-C library was prepared on-bead using the Accel-NGS 2S Plus kit (Swift Biosciences). After adaptor ligation, ligated products were PCR-amplified using KAPA Library Amplification Kit (Roche) and purified. Libraries were combined, and the pooled library was quantified by qPCR using a NEBNext Library Quant Kit (NEB). The final pooled library was paired-end sequenced with read lengths of 150 bp on a NovaSeq 6000 platform (Illumina) using an S2 300-cycle kit.

value: muscle

value: FISC/MuSC


title: Coculture

description: Library name: B16 Coculture


title: wild-type mouse, distal colon 1

description:
Library name: WTD1
10x Genomics


title: CNSTB, S4, granuloma4

description: microdissected RNA-Seq

source_name: CNSTB spinal tissue

value: CNSTB spinal tissue


title: wild-type mouse, proximal colon 2

description:
Library name: WTP2
10x Genomics


title: Mandarin duck, female, early growth, in season, blue+black flight feather, H3K27ac, Rep 2

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description: Library name: Chuong-ChIP-180

data_processing:
Raw reads were quality filtered and aligned to the Mandarin duck reference genome (BioProject PRJNA787744) using Bowtie2.
Peaks were called with MACS2; replicate concordance was assessed and peak sets merged for downstream analyses.
Normalized coverage tracks (bigWig) were generated with deepTools; peak BED files were produced with MACS2 and bedtools.
Motif enrichment was performed using HOMER; differential binding analysis was carried out using DiffBind (FDR ≤ 0.05).
Assembly: Mandarin duck reference genome (BioProject PRJNA787744).
Supplementary files format and content: Processed files include peak calls in BED format and normalized coverage tracks (bigWig).
Supplementary files format and content: Differential binding result tables (TSV) with peak intensities, fold changes, and adjusted p-values.

organism: Aix galericulata

source_name: feather

growth_protocol: Mandarin ducks (Aix galericulata) were maintained at the National Chung Hsing University poultry farm under standard housing and feeding conditions. Regenerating sail and flight feathers were plucked and collected approximately four weeks later during the breeding season (“in season”).

extract_protocol:
Feather follicles (sail and adjacent flight feathers) were dissected. Chromatin was crosslinked, isolated, and sheared. Immunoprecipitation was performed with anti-H3K27ac antibody (Abcam # ab4729), alongside input controls.
ChIP and input DNA were end-repaired, A-tailed, adapter-ligated, size-selected, and PCR-amplified using Illumina-compatible ChIP-seq protocols. Libraries were sequenced on Illumina HiSeq/NextSeq platforms.

treatment_protocol: No experimental treatment was applied; samples reflect natural seasonal growth and sex-specific feather development.

value: feather

value: feather follicle

value: wild-type

value: female

tag: body region

value: blue+black flight feather

tag: chip antibody

value: H3K27ac (abcam #ab4729)


title: Mandarin duck, male, early growth, in season, blue+brown flight feather, H3K27ac, Rep 2

description: Library name: Chuong-ChIP-165

value: male

value: blue+brown flight feather


title: Mandarin duck, female, early growth, in season, blue+black flight feather, H3K27ac, Rep 1

description: Library name: Chuong-ChIP-177


title: shNT_H2az_chipseq_IP2

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

institute: IMCB

data_processing:
ChIP-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
ChIP-seq data processing included sequencing reads filtering based on quality and adapter sequences removal using Trim_galore (https://github.com/FelixKrueger/TrimGalore) with the default options.
The resulting fastq files were aligned to the human reference genome (mm10) using bowtie2 (Langmead& Salzberg, 2012) with the following parameters:” -N 1 -L 25 -X 500 --no-mixed --no-discordant”; the rest of the options were set to the default. Duplicated reads were removed from the bam files using were removed using SAMtools (v.1.10).
Dmtf1 and H2az ChIP-seq peak calling was done with Macs2 (q-value < 0.01). DeepTools software (https://deeptools.readthedocs.io/en/develop/) was used to generate BigWig files (“bamCoverage” function) and produce ChIP-seq heatmaps (“computeMatrix” and “plotHeatmap” functions).
Assembly: mm10
Supplementary files format and content: bigwig format; processed data.

source_name: mouse neural stem cells

growth_protocol: The mNSCs were cultured in NeuroCult Proliferation mouse NSC media (STEMCELL), which was supplemented with 20ng/ml human epidermal growth factor (human EGF), 20ng/ml human basic fibroblast growth factor (human FGF), and 1% PS.  The mNSCs were passaged using Accutase (Sigma). All cells were cultured in a 5% CO2 incubator at 37°C.

extract_protocol:
The histones of mNSCs were crosslinked to DNA with 1% formaldehyde for 10 minutes at room temperature. The fixation was stopped by 0.25M glycine. Cells were lysed using SDS CHIP Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8). The lysate was then performed sonication for 40 cycles at the Bioruptor sonicator (Diagenode) (30s ON and 30s OFF). After sonication, the samples were diluted by ChIP dilution buffer (0.01% SDS, 1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, 167 mM NaCl). After pre-clear, 10% of the lysates were used as input. All the left lysates were used for immunoprecipitation with antibodies and protein A/G agarose beads overnight. The samples were immunoprecipitated with V5 Tag (Thermo Fisher Scientific, Cat#A190-120A) or H2AZ antibody (Abcam, Cat# Ab4174). After immunoprecipitation, the bound DNA was washed with following buffers sequentially to remove nonspecific sequences: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20mM Tris-HCl pH 8, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20 mM Tris-HCl pH 8, 500mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8) and TE wash buffer (10 mM Tris-HCl pH 8, 1mM EDTA). The pellet was then eluted in the fresh elution buffer (84 mg NaHCO3, 1 ml 10% SDS, 9 ml H2O). The eluted samples were then reverse crosslinked with NaCl at 65 °C overnight for library preparation
Library preparation was performed as previously described as described in Bowman et al. BMC Genomics 2013. Briefly, end repair with NEBNext End Repair enzyme (NEB, E6050) and clean-up with 2.4x volume AMPure XP beads (Beckman Coulter, A63880). A-tailing with Klenow Fragment (NEB, M0212) and purified with 2.4x volume AMPure XP beads. Adapter ligation reactions contained annealed universal adapter and T4 rapid ligase (NEB, B0202) and clean-up with 1.8x volume AMPure XP beads. Chromatin was amplified using KAPA Real-time Library Amplification Kit (KAPABIOSYSTEMS, KK2701) with universal primer and barcoded primer. Amplified chromatin was purified with QIAquick Gel Extraction Kit (Qiagen) and sequenced paired-end with Illumina NextSeq 500.

treatment_protocol: DMTF1 ChIP-seq in mNSCs following treatment with V5-DMTF1 overexpression. H2AZ ChIP-seq in mNSCs following treatment either non-targeting shRNA (shNT, was provided by Dr. Ronald A. DePinho lab), or shRNA targeting DMTF1 sh823 (Sigma TRCN0000077823) and sh826 (Sigma TRCN0000077826).

value: mouse neural stem cells

value: wild type

value: shNT

tag: antibody


title: GM3_HiC

description: Library name: GM3_HiC

tag: tissue


title: CNSTB, S4, granuloma5

description: microdissected RNA-Seq


title: GM2_HiC

description: Library name: GM2_HiC

tag: genotype


title: GM1_HiC

description: Library name: GM1_HiC


title: shNT_H2az_chipseq_IP1


title: CNSTB, S4, granuloma3

description: microdissected RNA-Seq


title: shNT_H2az_chipseq_IN2

value: input


title: Mandarin duck, female, early growth, in season, black sail feather, H3K27ac, Rep 2

description:
Library name: Chuong-ChIP-168
Column name in H3K27ac_Sail_FemaleSpecific_FDR.05_1058_add-ID.xlsx: FSailH3K27ac_C168

value: black sail feather


title: Mandarin duck, male, early growth, in season, blue+brown flight feather, H3K27ac, Rep 1

description: Library name: Chuong-ChIP-159


title: OM2_HiC

description: Library name: OM2_HiC


title: CNSTB, S4, granuloma2

description: microdissected RNA-Seq


title: CNSTB, S4, granuloma1

description: microdissected RNA-Seq


title: Mandarin duck, female, early growth, in season, black sail feather, H3K27ac, Rep 1

description:
Library name: Chuong-ChIP-171
Column name in H3K27ac_Sail_FemaleSpecific_FDR.05_1058_add-ID.xlsx: FSailH3K27ac_C171


title: sh826_H2az_chipseq_IP2


title: Mandarin duck, male, early growth, in season, blue+brown sail feather, H3K27ac, Rep 2

description:
Library name: Chuong-ChIP-156
Column name in H3K27ac_Sail_FemaleSpecific_FDR.05_1058_add-ID.xlsx: MSailH3K27ac_C156

value: blue+brown sail feather


title: CNSTB, S4, inflammatory4

description: microdissected RNA-Seq


title: sh826_H2az_chipseq_IP1


title: Mandarin duck, male, early growth, in season, blue+brown sail feather, H3K27ac, Rep 1

description:
Library name: Chuong-ChIP-153
Column name in H3K27ac_Sail_FemaleSpecific_FDR.05_1058_add-ID.xlsx: MSailH3K27ac_C153


title: CNSTB, S4, inflammatory3

description: microdissected RNA-Seq


title: YM1_HiC

description: Library name: YM1_HiC

value: muscle


title: shNT_H2az_chipseq_IN1


title: sh826_H2az_chipseq_IN2


title: Mandarin duck, male, early growth, in season, brown sail feather, epithelium, Rep 1

description: Library name: Chuong-149

data_processing:
Raw reads were quality checked and trimmed; high-quality reads were aligned to the Mandarin duck reference genome (BioProject PRJNA787744) using STAR v2.4.1d.
Aligned reads were quantified at the gene level using HTSeq-count v0.6.0.
Library size normalization was performed using the TMM method.
Differential expression analysis was conducted using edgeR; results include normalized counts and gene-level statistics.
Assembly: Mandarin duck reference genome (BioProject PRJNA787744).
Supplementary files format and content: Tab-delimited text files containing raw gene counts and normalized expression matrices.
Supplementary files format and content: Differential expression result tables (TSV) including log fold-change, p-values, and FDR-adjusted significance.

growth_protocol: Mandarin ducks (Aix galericulata) were maintained at the National Chung Hsing University poultry farm under standard housing and feeding conditions. Regenerating sail feathers were plucked and collected approximately four weeks later during the breeding season (“in season”).

extract_protocol:
Feather follicles were dissected into pulp (mesenchymal) and epithelium (epidermal) compartments. Total RNA was extracted using the TRIzol protocol (Invitrogen, Cat #15596026) following manufacturer’s instructions.
Libraries were prepared from 1 µg of total RNA per sample using the Illumina TruSeq RNA Prep Kit v2 (RS-122–2001/-2002). Poly(A)+ mRNA was enriched, fragmented, converted to cDNA, end-repaired, adapter-ligated, and PCR-amplified according to manufacturer’s protocol.

tag: tissue type

value: brown sail feather, epithelium

value: Epithelium / Epidermal


title: CNSTB, S4, inflammatory1

description: microdissected RNA-Seq

value: CNSTB spinal tissue


title: Mandarin duck, male, early growth, in season, brown sail feather, epithelium, Rep 2

description: Library name: Chuong-247

value: feather


title: Mouse skin, DMBA/TPA treated, R3

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

description:
Library name: MusDT3
counts_mus_dt.tsv

data_processing:
Trimming: TrimGalore!
Alignment:Hisat2
Counting: featureCounts
Assembly: Mouse: GRCm39, Acomys: https://doi.org/10.5281/zenodo.7761277
Supplementary files format and content: csv files with unnormalized counts

source_name: Skin

extract_protocol:
Purelink RNA extraction kit, according to manufacturer instructions
Stranded mRNA library

value: Skin

value: DMBA/TPA


title: Mouse skin, DMBA/TPA treated, R4

description:
Library name: MusDT4
counts_mus_dt.tsv


title: sh826_H2az_chipseq_IN1


title: CNSTB, S4, inflammatory2

description: microdissected RNA-Seq


title: Mouse skin, DMBA/TPA treated, R2

description:
Library name: MusDT2
counts_mus_dt.tsv


title: CNSTB, S3, inflammatory1

description: microdissected RNA-Seq


title: Mouse skin, DMBA/TPA treated, R1

description:
Library name: MusDT1
counts_mus_dt.tsv


title: Mandarin duck, male, early growth, in season, blue sail feather, epithelium, Rep 1

description: Library name: Chuong-150

value: blue sail feather, epithelium

value: wild-type


title: sh823_H2az_chipseq_IP1


title: CNSTB, S3, granuloma4

description: microdissected RNA-Seq


title: Mandarin duck, male, early growth, in season, blue sail feather, epithelium, Rep 2

description: Library name: Chuong-250

value: male


title: OM1_HiC

description: Library name: OM1_HiC

value: FISC/MuSC


title: Mandarin duck, male, early growth, in season, brown sail feather, pulp, Rep 2

description: Library name: Chuong-248

value: brown sail feather, pulp

value: Pulp / Mesenchymal


title: sh823_H2az_chipseq_IN2

value: mouse neural stem cells

value: wild type


title: CNSTB, S3, granuloma3

description: microdissected RNA-Seq


title: Mouse skin, untreated, R4

description:
Library name: MusCtrl4
counts_mus_dt.tsv

value: Untreated


title: sh823_H2az_chipseq_IN1

value: input


title: CNSTB, S3, granuloma2

description: microdissected RNA-Seq


title: Mandarin duck, male, early growth, in season, blue sail feather, pulp, Rep 2

description: Library name: Chuong-251

value: blue sail feather, pulp


title: Mandarin duck, male, early growth, in season, brown sail feather, pulp, Rep 1

description: Library name: Chuong-151


title: sh823_H2az_chipseq_IP2


title: CNSTB, S3, granuloma1

description: microdissected RNA-Seq


title: Dmtf1_chipseq_IP2


title: Dmtf1_chipseq_IP1


title: Mouse skin, untreated, R1

description:
Library name: MusCtrl1
counts_mus_dt.tsv


title: Mandarin duck, male, early growth, in season, blue sail feather, pulp, Rep 1

description: Library name: Chuong-152


title: CNSTB, S2, granuloma6

description: microdissected RNA-Seq


title: CNSTB, S2, granuloma5

description: microdissected RNA-Seq


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 26 deg, replicate 3

city: Wien

first: Stela

last: Jelenic

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

description: Library name: WAGO4Y611E_26_3

library_source: other

data_processing:
RNA sequencing data have been analysed using the RNA-Seq pipeline of the IMP/IMBA Bioinfo core facility (ii-bioinfo@imp.ac.at). The pipeline is based on the nf-core/rnaseq pipeline [doi: 10.5281/zenodo.1400710] and is built with nextflow (Ewels et al. 2020)
Assembly: WBcel235
Supplementary files format and content: Differential gene-expression result tables showing fold-change and p-values

molecule: other

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were grown at 20 or 26 deg (indicated), synchronized and harvested as young adults

extract_protocol:
TRIzol extraction and DNaseI treatment
automated ribonucleic depletion using rRNA depletion kit Ribovanish;  library preparation using Ultra II Directional RNA Library Prep Kit (NEB, Cat #E7765)

value: Whole worm


title: Wild mouse fibroblasts, 20 gy, 12d, R4

description:
Library name: MUSW_12d_WM19_20Gy
counts_mus_irrad.tsv

source_name: Primary skin fibroblasts

value: Primary skin fibroblasts

value: 20 gy

tag: timepoint

tag: batch


title: Dmtf1_chipseq_IN1

tag: cell type

tag: treatment


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 26 deg, replicate 2

description: Library name: WAGO4Y611E_26_2


title: CNSTB, S2, granuloma4

description: microdissected RNA-Seq

value: CNSTB spinal tissue


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 26 deg, replicate 1

description: Library name: WAGO4Y611E_26_1


title: YM2_HiC

description: Library name: YM2_HiC

value: muscle


title: CNSTB, S2, granuloma3

description: microdissected RNA-Seq


title: shNT_rnaseq_3

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trim_galore with default parameters.
Mapping of RNA-seq reads was done using bowtie2 with default parameters for RNA-seq data.
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Assembly: mm10
Supplementary files format and content: txt format; raw counts for three experimental conditions with 3 replicates each.

extract_protocol:
Total RNA from cells was extracted using the RNeasy® Mini or Micro Kit (Qiagen).
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: The shRNAs against mouse Dmtf1 (sh823 #1, (#TRCN0000077823) and sh826 #2, (#TRCN0000077826) were purchased from Sigma.  Lentivirus was produced using a 3rd generation system. HEK 293T cells were co-transfected with pMD2.G, pRSV-Rev, pMDVSVG, and shRNA plasmids. After 72 hours, the lentivirus was harvested and concentrated by ultracentrifuge. The lentiviral particles were then resuspended using DMEM/F12 media (Nacalai tesque). The mNSCs were infected with lentivirus when splitting, the fresh media was replaced 24 hours after infection.

value: shNT

tag: time


title: Wild mouse fibroblasts, 10 gy, 12d, R4

description:
Library name: MUSW_12d_WM19_10Gy
counts_mus_irrad.tsv

value: 10 gy


title: shNT_rnaseq_2


title: rRNA depletion RNA from WAGO-4 KO worms grown at 26 deg, replicate 3

description: Library name: WAGO4KO_26_3

value: WAGO-4 KO


title: CNSTB, S2, normal2

description: microdissected RNA-Seq


title: Mouse skin, untreated, R3

description:
Library name: MusCtrl3
counts_mus_dt.tsv

value: Skin


title: shNT_rnaseq_1


title: Wild mouse fibroblasts, untreated passaged, 12d, R4

description:
Library name: MUSW_12d_WM19_ConP
counts_mus_irrad.tsv

value: Untreated passaged


title: rRNA depletion RNA from WAGO-4 KO worms grown at 26 deg, replicate 2

description: Library name: WAGO4KO_26_2


title: Wild mouse fibroblasts, 20 gy, 12d, R3

description:
Library name: MUSW_12d_WM15_20Gy
counts_mus_irrad.tsv


title: Mouse skin, untreated, R2

description:
Library name: MusCtrl2
counts_mus_dt.tsv


title: sh826_rnaseq_3


title: CNSTB, S2, normal1

description: microdissected RNA-Seq


title: rRNA depletion RNA from WAGO-4 KO worms grown at 26 deg, replicate 1

description: Library name: WAGO4KO_26_1


title: CNSTB, S2, granuloma2

description: microdissected RNA-Seq


title: Dmtf1_chipseq_IN2


title: sh826_rnaseq_2


title: rRNA depletion RNA from 3xFG worms grown at 26 deg, replicate 3

description: Library name: 3XFG_26_3

value: 3xFG; 3xFLAG::GFP::WAGO-4


title: Wild mouse fibroblasts, untreated, 12d, R3

description:
Library name: MUSW_12d_WM15_Con
counts_mus_irrad.tsv


title: CNSTB, S2, granuloma1

description: microdissected RNA-Seq


title: sh826_rnaseq_1


title: Wild mouse fibroblasts, 10 gy, 12d, R3

description:
Library name: MUSW_12d_WM15_10Gy
counts_mus_irrad.tsv


title: rRNA depletion RNA from 3xFG worms grown at 26 deg, replicate 2

description: Library name: 3XFG_26_2


title: Wild mouse fibroblasts, untreated, 12d, R4

description:
Library name: MUSW_12d_WM19_Con
counts_mus_irrad.tsv


title: Wild mouse fibroblasts, untreated passaged, 12d, R3

description:
Library name: MUSW_12d_WM15_ConP
counts_mus_irrad.tsv


title: sh823_rnaseq_3


title: rRNA depletion RNA from 3xFG worms grown at 26 deg, replicate 1

description: Library name: 3XFG_26_1


title: Wild mouse fibroblasts, 20 gy, 12d, R2

description:
Library name: MUSW_12d_WM14_20Gy
counts_mus_irrad.tsv


title: CNSTB, S1,inflammatory1

description: microdissected RNA-Seq


title: TILs from CT26 tumors 6 days after 12 Gy treatment 4

city: San Diego

first: Tao

last: Xie

address: 10770 Science Center Dr

institute: Pfizer

description:
Library name: CT26 16
10x genomics

data_processing:
Raw sequencing reads were processed into count data using the Cell Ranger v4 (10X Genomics) and then further analyzed using Seurat 3 for data normalization and filtering. Canonical correlation analysis was performed using the top 20 CCA components. Visualization of single-cell RNA-Seq data was performed using Seurat or ggplot2 function in R.
Assembly: Mouse mm10
Supplementary files format and content: matrix files

source_name: Tumor infiltrating immune cells

extract_protocol:
Tumors from treated mouse models were harvested on day 6 after radiotherapy. To obtain single-cell suspensions, tumors were processed using the Tumor Dissociation Kit, mouse (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Following dissociation, cells were resuspended in autoMACS® Rinsing Solution with MACS® BSA Stock Solution diluted 1:20 and the cell suspensions were passed through a 70-µm cell strainer. Immune cells were isolated from cell suspensions using CD45 (TIL) MicroBeads, mouse (Miltenyi Biotec, Cat. No. 130-110-618) following manufacturer’s instructions.
Isolated cells were counted using Cellaca MX Cell Counter (Nexcelom Bioscience, Lawrence, MA). Cells were processed for scRNAseq using the 10x Genomics chromium v3 3' chemistry pipeline according to the manufacturer’s instructions. Cells were resuspended in 0.04% BSA in PBS at a concentration of 1 × 10⁶ cells/ml. Cells were loaded onto a Chromium Single Cell B Chip (10x Genomics, Pleasanton, CA) to aim for target cell recovery of 8 × 10³ cells. Library construction was performed according to Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 protocol (10x Genomics). Libraries were sequenced using the NovoSeq 6000 platform (Illumina; San Diego, CA) aiming for a minimum of 200 × 10⁶ reads per library (25,000 reads per cell).

treatment_protocol: An X-Rad 225 biological irradiator (Precision X-Ray, Madison, CT) was used at a dose output of 225 kV, 10 mA. Targeted irradiation of tumor bearing mice was performed using a 0.3 mm Copper filter with a 5 × 5 mm collimator.

value: Tumor infiltrating immune cells

tag: cell line

value: cancer cells

value: 12 Gy


title: sh823_rnaseq_2

value: mouse neural stem cells

value: wild type


title: rRNA depletion RNA from WT worms grown at 26 deg, replicate 3

description: Library name: WT_26_3


title: Wild mouse fibroblasts, 10 gy, 12d, R2

description:
Library name: MUSW_12d_WM14_10Gy
counts_mus_irrad.tsv


title: TILs from CT26 tumors 6 days after 12 Gy treatment 3

description:
Library name: CT26 15
10x genomics


title: sh823_rnaseq_1


title: Wild mouse fibroblasts, untreated, 12d, R2

description:
Library name: MUSW_12d_WM14_Con
counts_mus_irrad.tsv

value: Untreated


title: TILs from CT26 tumors 6 days after 12 Gy treatment 2

description:
Library name: CT26 14
10x genomics


title: rRNA depletion RNA from WT worms grown at 26 deg, replicate 1

description: Library name: WT_26_1

value: Whole worm


title: Wild mouse fibroblasts, untreated passaged, 12d, R2

description:
Library name: MUSW_12d_WM14_ConP
counts_mus_irrad.tsv

value: Primary skin fibroblasts


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 20 deg, replicate 3

description: Library name: WAGO4Y611E_20_3


title: Patient 1, scRNAseq from skin and blood

city: Vienna

first: Georg

last: Stary

address: Waehringer Guertel 18-20, 1090 Wien

department: Department of Dermatology

institute: Medical University Of Vienna

description:
Library name: EM_MA
10x Genomics single cell RNA-seq using cell hashing technique for blood and skin cell distinction

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files., Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Assembly: hg38
Supplementary files format and content: Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

source_name: Skin and peripheral blood

extract_protocol:
Human skin tissue was digested for 2h in Collagenase and DNAse passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Peripheral blood mononuclear cells were isolated from the blood using Ficoll gradients.
Single-Cell 5’ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s instructions

value: Skin and peripheral blood

value: Skin cells, peripheral blood leukocytes

value: naïve

tag: disease

value: Lyme disease


title: TILs from CT26 tumors 6 days after 12 Gy treatment 1

description:
Library name: CT26 13
10x genomics


title: Patient 2, scRNAseq from skin and blood

description:
Library name: EM_GS
10x Genomics single cell RNA-seq using cell hashing technique for blood and skin cell distinction


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 20 deg, replicate 2

description: Library name: WAGO4Y611E_20_2


title: Wild mouse fibroblasts, 20 gy, 12d, R1

description:
Library name: MUSW_12d_WM11_20Gy
counts_mus_irrad.tsv

value: 20 gy


title: Wild mouse fibroblasts, 10 gy, 12d, R1

description:
Library name: MUSW_12d_WM11_10Gy
counts_mus_irrad.tsv

value: 10 gy


title: TILs from CT26 tumors 6 days after sham treatment 2

description:
Library name: CT26 11
10x genomics

value: Sham (0 Gy)


title: atrx_c

city: Uppsala

first: Miyuki

last: Nakamura

address: Ulls Grand1

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
Original files were filter with sequence quality with the FASTX-toolkit software (-q 20 -p 80 -Q 33). Adaptor sequences were removed. Read1 and read2 files were paired using the BBmap software. Paired sequences were mapped using Hisat2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig format. For Bigwig formating, mapped reads were processed by the deepTools with the RPGC normalization (number of reads per bin / scaling factor for 1x average coverage) in 10 bp bin.

organism: Arabidopsis thaliana

source_name: seedling atrx mutant

growth_protocol: Sterilized seeds were sown to x1/2 Murashige and Skoog medium plate with 1% sucrose. Plants were grown for 10 days under long-day conditions. Seedlings were harvested 30 minutes before turning off lights.

extract_protocol:
Total RNA was extracted by RNeasy Plant mini kit (Qiagen, Germany #74904)
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) was used to enrich Poly-A tail RNA from total RNA. RNA-seq libraries were prepared with NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7709). For indexing, NEBNext Multiplex Oligos for Illumina (NEB #E7760) was used.

treatment_protocol: Sown seeds were kept 2 days at 4˚C in dark before moving to 22˚C under long-day conditions.

tag: ecotype background

value: atrx mutant

value: 10 days seedlings


title: atrx_b


title: TILs from CT26 tumors 6 days after sham treatment 3

description:
Library name: CT26 12
10x genomics

value: Tumor infiltrating immune cells


title: Wild mouse fibroblasts, untreated passaged, 12d, R1

description:
Library name: MUSW_12d_WM11_ConP
counts_mus_irrad.tsv

value: Untreated passaged


title: rRNA depletion RNA from WAGO-4 KO worms grown at 20 deg, replicate 3

description: Library name: WAGO4KO_20_3

value: WAGO-4 KO


title: Wild mouse fibroblasts, untreated, 12d, R1

description:
Library name: MUSW_12d_WM11_Con
counts_mus_irrad.tsv


title: atrx_a


title: TILs from B16F10 tumors 6 days after 12 Gy treatment 4

description:
Library name: B16F10 8
10x genomics

value: cancer cells

value: 12 Gy


title: TILs from B16F10 tumors 6 days after 12 Gy treatment 3

description:
Library name: B16F10 7
10x genomics


title: rRNA depletion RNA from WT worms grown at 26 deg, replicate 2

description: Library name: WT_26_2


title: C56BL6 mouse fibroblasts, 20 gy, 12d, R4

description:
Library name: MUS_12d_M32_20Gy
counts_mus_irrad.tsv


title: rRNA depletion RNA from WAGO-4 KO worms grown at 20 deg, replicate 1

description: Library name: WAGO4KO_20_1


title: TILs from CT26 tumors 6 days after sham treatment 1

description:
Library name: CT26 10
10x genomics


title: lhp1dekT_b

source_name: seedling lhp1;dek2,3;4 quadruple mutant

value: lhp1;dek1;2;3 quadruple mutant


title: lhp1dekT_a


title: C56BL6 mouse fibroblasts, 10 gy, 12d, R4

description:
Library name: MUS_12d_M32_10Gy
counts_mus_irrad.tsv


title: TILs from B16F10 tumors 6 days after 12 Gy treatment 2

description:
Library name: B16F10 6
10x genomics


title: lhp1_c

source_name: seedling lhp1 mutant

value: lhp1 mutant


title: rRNA depletion RNA from 3xFG worms grown at 20 deg, replicate 2

description: Library name: 3XFG_20_2

value: Whole worm

value: 3xFG; 3xFLAG::GFP::WAGO-4


title: TILs from B16F10 tumors 6 days after 12 Gy treatment 1

description:
Library name: B16F10 5
10x genomics


title: lhp1_b


title: rRNA depletion RNA from WAGO-4(Y611E) worms grown at 20 deg, replicate 1

description: Library name: WAGO4Y611E_20_1


title: C56BL6 mouse fibroblasts, untreated, 12d, R4

description:
Library name: MUS_12d_M32_Con
counts_mus_irrad.tsv

value: Primary skin fibroblasts

value: Untreated


title: TILs from B16F10 tumors 6 days after sham treatment 3

description:
Library name: B16F10 4
10x genomics


title: C56BL6 mouse fibroblasts, 20 gy, 12d, R3

description:
Library name: MUS_12d_M29_20Gy
counts_mus_irrad.tsv


title: rRNA depletion RNA from 3xFG worms grown at 20 deg, replicate 1

description: Library name: 3XFG_20_1


title: rRNA depletion RNA from WAGO-4 KO worms grown at 20 deg, replicate 2

description: Library name: WAGO4KO_20_2


title: dekQ_c

source_name: seedling dek1;2;3;4 quadruple mutant

value: dek quadruple mutant


title: TILs from B16F10 tumors 6 days after sham treatment 1

description:
Library name: B16F10 1
10x genomics


title: lhp1_a


title: rRNA depletion RNA from WT worms grown at 20 deg, replicate 3

description: Library name: WT_20_3


title: TILs from B16F10 tumors 6 days after sham treatment 2

description:
Library name: B16F10 2
10x genomics


title: rRNA depletion RNA from WT worms grown at 20 deg, replicate 1

description: Library name: WT_20_1


title: dekQ_a


title: rRNA depletion RNA from WT worms grown at 20 deg, replicate 2

description: Library name: WT_20_2


title: CD48 KO3

first: Kei

last: Sakano

state: CALIFORNIA

address: 1450 Biggy Street NRT5509

department: Molecular Microbiology and Immunology

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: sorted ILC2s


title: dekQ_b


title: C56BL6 mouse fibroblasts, untreated passaged, 12d, R3

description:
Library name: MUS_12d_M29_ConP
counts_mus_irrad.tsv


title: Wt_c

source_name: seedling wild-type

value: wild-type


title: CD48 KO2


title: rRNA depletion RNA from 3xFG worms grown at 20 deg, replicate 3

description: Library name: 3XFG_20_3


title: C56BL6 mouse fibroblasts, 20 gy, 12d, R2

description:
Library name: MUS_12d_M24_20Gy
counts_mus_irrad.tsv

value: 20 gy


title: CD48 KO1


title: Wt_b

value: 10 days seedlings


title: WT3

value: WT


title: C56BL6 mouse fibroblasts, 10 gy, 12d, R2

description:
Library name: MUS_12d_M24_10Gy
counts_mus_irrad.tsv

value: 10 gy


title: T cells, Helenalin-treated and costimulated_donor5

type: RNA

city: Heidelberg

first: Yvonne

last: Samstag

address: INF 305

department: Institute of Immunology

institute: Heidelberg University Hospital

description: total RNA was isolated from T cells pretreated with Helenalin for 1 h  and costimulated for 4 h

hyb_protocol: hybridization of the sample mixed with reporter codeset and capture probeset was done at 65°C for 20 h (according to manufacture's protocol)

scan_protocol: samples were purified, immobilized on cartridges and scanned on the nCounter® SPRINT Profiler (nanoString Technologies)

data_processing: the raw RCC files were uploaded onto the nSolver software, raw counts were measured, stable houskeeping genes for normalization was identified using NormFinder, an excel plug-in software, and data were subsequently normalized to obtain normalized counts. The normalized counts were used for the final evaluations.

label: nCounter® Reporter Codeset and Capture Probeset

source_name: T cells, CD3x28 costimulated, 4 h

label_protocol: for each sample, 5uL of total RNA was mixed with 3uL of reporter codeset and 2uL of capture probeset (according to manufacture's protocol)

extract_protocol: total RNA was extracted using Direct-zol RNA isolation following manufacture's protocol

tag: cells

value: T cells

tag: donor id

value: Donor 5


title: C56BL6 mouse fibroblasts, untreated passaged, 12d, R4

description:
Library name: MUS_12d_M32_ConP
counts_mus_irrad.tsv

value: Untreated passaged


title: C56BL6 mouse fibroblasts, untreated, 12d, R3

description:
Library name: MUS_12d_M29_Con
counts_mus_irrad.tsv


title: T cells, Thymol-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with Thymol for 1 h  and costimulated for 4 h


title: C56BL6 mouse fibroblasts, 10 gy, 12d, R3

description:
Library name: MUS_12d_M29_10Gy
counts_mus_irrad.tsv


title: C56BL6 mouse fibroblasts, untreated, 12d, R2

description:
Library name: MUS_12d_M24_Con
counts_mus_irrad.tsv


title: ebs1Δ biol rep 3

city: Martinsried

first: Fabien

last: Bonneau

address: Am Klopferspitz 18

department: Structural Cell Biology

institute: Max Planck Institute of Biochemistry

description:
Library name: dEBS1_3
dEBS1_3

data_processing:
Reads were aligned with STAR (v2.7.11a)
Read count extraction on sgdGene annotations was performed with featureCounts (Subread v 2.0.5) with parameters -p --countReadPairs -B -C -s 2
Assembly: sacCer3
Supplementary files format and content: raw_gene_counts.tsv is a tab-delimited text file or raw counts for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown in SD-LEU to an absorbance between 0.6 and 0.7 at 600 nm

extract_protocol:
Total RNA was extracted with the hot-phenol method and subsequently treated with Dnase
Library was prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after poly(A) enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module

tag: strain

value: ebs1delta::KlURA3, pRS415


title: C56BL6 mouse fibroblasts, untreated passaged, 12d, R2

description:
Library name: MUS_12d_M24_ConP
counts_mus_irrad.tsv


title: T cells, DMSO-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with DMSO for 1 h  and costimulated for 4 h


title: CNSTB, ATT, S5, granuloma2

description: microdissected RNA-Seq

data_processing:
Alignment was performed using Kallisto (version 0.46), with sequence based bias correction.
Data was annotated using ensembldb package (version 2.24.0). The transcript abundance was summarized to gene level using Sleuth (version 0.30).
Raw counts from RNA sequencing were processed using edgeR, Bioconductor version 3.17, with 3 variance estimated and size factor normalised using Trimmed Mean of M-values (TMM).
Assembly: GRCm39, M. tb strain H37Rv transcriptome
Supplementary files format and content: CSV table with counts and TPM as estimated by Kallisto

source_name: M.tb H37Rv-infected brain tissue

value: M.tb H37Rv-infected brain tissue

value: Rifampicin (10mg/kg), Isoniazid (25mg/kg), Ethambutol (100mg/kg), Pyrazinamide (150mg/kg); Five days a week for a duration of eight weeks.


title: WT1


title: T cells, Radix-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with Radix for 1 h  and costimulated for 4 h


title: CNSTB, ATT, S5, granuloma1

description: microdissected RNA-Seq


title: C56BL6 mouse fibroblasts, 20 gy, 12d, R1

description:
Library name: MUS_12d_M16_20Gy
counts_mus_irrad.tsv


title: C56BL6 mouse fibroblasts, 10 gy, 12d, R1

description:
Library name: MUS_12d_M16_10Gy
counts_mus_irrad.tsv


title: T cells, EtOH-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with EtOH for 1 h  and costimulated for 4 h


title: T cells, Tota-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with Tota for 1 h  and costimulated for 4 h


title: nmd4Δ biol rep 6

description:
Library name: dNMD4_6
dNMD4_6

value: nmd4delta::KlURA3, pRS415


title: C56BL6 mouse fibroblasts, untreated, 12d, R1

description:
Library name: MUS_12d_M16_Con
counts_mus_irrad.tsv

value: Primary skin fibroblasts


title: T cells, Ferm-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with Ferm for 1 h  and costimulated for 4 h


title: nmd4Δ biol rep 5

description:
Library name: dNMD4_5
dNMD4_5


title: CNSTB, ATT, S4, granuloma1

description: microdissected RNA-Seq


title: C56BL6 mouse fibroblasts, untreated passaged, 12d, R1

description:
Library name: MUS_12d_M16_ConP
counts_mus_irrad.tsv


title: CNSTB, ATTSB, S3, granuloma2

description: microdissected RNA-Seq

value: Rifampicin (10mg/kg), Isoniazid (25mg/kg), Ethambutol (100mg/kg), Pyrazinamide (150mg/kg), SB-3CT (50mg/kg); Five days a week for a duration of eight weeks.


title: Wt_a


title: nmd4Δ biol rep 4

description:
Library name: dNMD4_4
dNMD4_4


title: T cells, H2O-treated and costimulated_donor5

description: total RNA was isolated from T cells pretreated with H2O for 1 h  and costimulated for 4 h


title: Wild mouse fibroblasts, 20 gy, 24h, R4

description:
Library name: MUSW_24h_WM19_20Gy
counts_mus_irrad.tsv


title: WT2


title: nmd4Δ biol rep 3

description:
Library name: dNMD4_3
dNMD4_3


title: CNSTB, ATTSB, S3, granuloma1

description: microdissected RNA-Seq


title: CNSTB, ATTDO, S4, granuloma1

description: microdissected RNA-Seq

value: Rifampicin (10mg/kg), Isoniazid (25mg/kg), Ethambutol (100mg/kg), Pyrazinamide (150mg/kg), Doxycycline (100mg/kg); Five days a week for a duration of eight weeks.


title: ebs1Δ biol rep 2

description:
Library name: dEBS1_2
dEBS1_2


title: T cells, untreated and unstimulated_donor5

description: total RNA was isolated from T cells kept untreated and unstimulated for 4 h

source_name: T cells, unstimulated, 4 h


title: ebs1Δ biol rep 1

description:
Library name: dEBS1_1
dEBS1_1


title: Wild mouse fibroblasts, 10 gy, 24h, R4

description:
Library name: MUSW_24h_WM19_10Gy
counts_mus_irrad.tsv


title: nmd4Δ biol rep 1

description:
Library name: dNMD4_1
dNMD4_1


title: nmd4Δ biol rep 2

description:
Library name: dNMD4_2
dNMD4_2


title: T cells, Thymol-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with Thymol for 1 h  and costimulated for 4 h

value: Donor 4


title: T cells, Helenalin-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with Helenalin for 1 h  and costimulated for 4 h


title: Wild mouse fibroblasts, untreated, 24h, R4

description:
Library name: MUSW_24h_WM19_Con
counts_mus_irrad.tsv

value: Untreated


title: Wild mouse fibroblasts, 20 gy, 24h, R3

description:
Library name: MUSW_24h_WM15_20Gy
counts_mus_irrad.tsv


title: Wild mouse fibroblasts, 10 gy, 24h, R3

description:
Library name: MUSW_24h_WM15_10Gy
counts_mus_irrad.tsv


title: CNSTB, ATTDO, S2, granuloma1

description: microdissected RNA-Seq


title: CNSTB, ATTDO, S1, granuloma2

description: microdissected RNA-Seq


title: T cells, DMSO-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with DMSO for 1 h  and costimulated for 4 h


title: upf1Δ biol rep 3

description:
Library name: dUPF1_3
dUPF1_3

value: upf1delta::KlURA3, pRS415


title: T cells, Radix-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with Radix for 1 h  and costimulated for 4 h


title: upf1Δ biol rep 2

description:
Library name: dUPF1_2
dUPF1_2


title: CNSTB, ATTDO, S1, granuloma1

description: microdissected RNA-Seq


title: T cells, Tota-treated and costimulated_donor4


title: upf1Δ biol rep 1

description:
Library name: dUPF1_1
dUPF1_1


title: CNSTB, ATTSB, S2, granuloma1

description: microdissected RNA-Seq


title: wild type biol rep 5

description:
Library name: WT_5
WT_5


title: CNSTB, ATTDO, S3, granuloma1

description: microdissected RNA-Seq


title: CNSTB, ATTSB, S1, granuloma1

description: microdissected RNA-Seq


title: Wild mouse fibroblasts, 10 gy, 24h, R2

description:
Library name: MUSW_24h_WM14_10Gy
counts_mus_irrad.tsv


title: T cells, Ferm-treated and costimulated_donor4


title: wild type biol rep 4

description:
Library name: WT_4
WT_4


title: CNSTB, ATT, S3, granuloma1

description: microdissected RNA-Seq


title: T cells, H2O-treated and costimulated_donor4


title: CNSTB, ATT, S2, granuloma1

description: microdissected RNA-Seq


title: wild type biol rep 3

description:
Library name: WT_3
WT_3


title: Wild mouse fibroblasts, 20 gy, 24h, R1

description:
Library name: MUSW_24h_WM11_20Gy
counts_mus_irrad.tsv

value: 20 gy


title: wild type biol rep 2

description:
Library name: WT_2
WT_2


title: T cells, untreated and unstimulated_donor4


title: Wild mouse fibroblasts, 10 gy, 24h, R1

description:
Library name: MUSW_24h_WM11_10Gy
counts_mus_irrad.tsv


title: Wild mouse fibroblasts, untreated, 24h, R3

description:
Library name: MUSW_24h_WM15_Con
counts_mus_irrad.tsv


title: CNSTB, ATT, S1, granuloma2

description: microdissected RNA-Seq


title: CNSTB, ATT, S1, granuloma1

description: microdissected RNA-Seq


title: wild type biol rep 1

description:
Library name: WT_1
WT_1


title: Wild mouse fibroblasts, 20 gy, 24h, R2

description:
Library name: MUSW_24h_WM14_20Gy
counts_mus_irrad.tsv


title: Wild mouse fibroblasts, untreated, 24h, R1

description:
Library name: MUSW_24h_WM11_Con
counts_mus_irrad.tsv


title: T cells, EtOH-treated and costimulated_donor4

description: total RNA was isolated from T cells pretreated with EtOH for 1 h  and costimulated for 4 h


title: GF3_RNA

description: Library name: GF3_RNA

data_processing:
Illumina sequencing reads were de-multiplexed, trimmed to remove adapter sequences, and checked for quality using fastqc ad multiqc.
Reads were aligned to the mouse reference genome (assembly GRCm38/mm10) using STAR/2.7.5b.
BAM files were sorted and indexed using samtools/1.10, duplicates were removed using Picard/2.20.8 and filtered to retain alignments with a minimum mapping quality of 10. The featureCounts function of the Rsubread R package/2.6.4 was used to estimate counts.
RPKM normalized bigWig files were generated using the bamCoverage function in deepTools/3.5.0.
For multiple alignments, significantly altered transposable element transcripts were assessed using the TEtranscripts function in TEToolkit/2.2.3.
Assembly: GRCm38/mm10
Supplementary files format and content: Txt files of raw counts for genes and transposable elements (TE)

source_name: muscle

extract_protocol:
Sorted cells were centrifuged at 2500 g for 5 mins at 4°C and stored in -80°C. RNA was extracted from FISCs (~200,000 cells per sample) using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
Reverse transcription was performed with 1-10 ng RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s instructions. After purification of amplified cDNA, quality and quantity was determined using a 2100 Bioanalyzer the DNA high sensitivity kit (Agilent). RNAseq library constructions were performed using the SMART-Seq Library Prep Kit (Takara) according to manufacturer’s instructions. Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (NEB). The RNA-seq libraries were subjected to two rounds of 75 bp paired end sequencing on a NextSeq 550 platform using a 150 cycle kit (Illumina).

value: muscle

value: FISC/MuSC


title: Healthy, S4, normal4

description: microdissected RNA-Seq

source_name: Normal brain tissue

value: Normal brain tissue


title: C56BL6 mouse fibroblasts, 20 gy, 24h, R4

description:
Library name: MUS_24h_M32_20Gy
counts_mus_irrad.tsv


title: T cells, Thymol-treated and costimulated_donor3

value: T cells

value: Donor 3


title: GF4_RNA

description: Library name: GF4_RNA


title: Healthy, S4, normal3

description: microdissected RNA-Seq


title: Wild mouse fibroblasts, untreated, 24h, R2

description:
Library name: MUSW_24h_WM14_Con
counts_mus_irrad.tsv


title: Healthy, S3, normal4

description: microdissected RNA-Seq


title: T cells, DMSO-treated and costimulated_donor3


title: T cells, Radix-treated and costimulated_donor3


title: C56BL6 mouse fibroblasts, untreated, 24h, R4

description:
Library name: MUS_24h_M32_Con
counts_mus_irrad.tsv


title: C56BL6 mouse fibroblasts, 10 gy, 24h, R4

description:
Library name: MUS_24h_M32_10Gy
counts_mus_irrad.tsv

value: 10 gy


title: GF2_RNA

description: Library name: GF2_RNA


title: T cells, Tota-treated and costimulated_donor3

description: total RNA was isolated from T cells pretreated with Tota for 1 h  and costimulated for 4 h


title: Healthy, S3, normal3

description: microdissected RNA-Seq


title: GM4_RNA

description: Library name: GM4_RNA


title: T cells, Helenalin-treated and costimulated_donor3

description: total RNA was isolated from T cells pretreated with Helenalin for 1 h  and costimulated for 4 h


title: GF1_RNA

description: Library name: GF1_RNA


title: C56BL6 mouse fibroblasts, 10 gy, 24h, R3

description:
Library name: MUS_24h_M29_10Gy
counts_mus_irrad.tsv


title: Healthy, S2, normal2

description: microdissected RNA-Seq


title: GM3_RNA

description: Library name: GM3_RNA


title: T cells, EtOH-treated and costimulated_donor3


title: GM2_RNA

description: Library name: GM2_RNA


title: C56BL6 mouse fibroblasts, untreated, 24h, R3

description:
Library name: MUS_24h_M29_Con
counts_mus_irrad.tsv


title: Healthy, S2, normal3

description: microdissected RNA-Seq


title: GM1_RNA

description: Library name: GM1_RNA


title: Healthy, S1, normal1

description: microdissected RNA-Seq


title: CNSTB, S4, normal1

description: microdissected RNA-Seq


title: T cells, H2O-treated and costimulated_donor3

description: total RNA was isolated from T cells pretreated with H2O for 1 h  and costimulated for 4 h


title: C56BL6 mouse fibroblasts, 20 gy, 24h, R2

description:
Library name: MUS_24h_M24_20Gy
counts_mus_irrad.tsv


title: OF4_RNA

description: Library name: OF4_RNA


title: T cells, untreated and unstimulated_donor3

description: total RNA was isolated from T cells kept untreated and unstimulated for 4 h


title: C56BL6 mouse fibroblasts, untreated, 24h, R2

description:
Library name: MUS_24h_M24_Con
counts_mus_irrad.tsv


title: OF3_RNA

description: Library name: OF3_RNA


title: CNSTB, S4, inflammatory1

description: microdissected RNA-Seq


title: C56BL6 mouse fibroblasts, 20 gy, 24h, R1

description:
Library name: MUS_24h_M16_20Gy
counts_mus_irrad.tsv


title: C56BL6 mouse fibroblasts, 20 gy, 24h, R3

description:
Library name: MUS_24h_M29_20Gy
counts_mus_irrad.tsv


title: T cells, Thymol-treated and costimulated_donor2

description: total RNA was isolated from T cells pretreated with Thymol for 1 h  and costimulated for 4 h

value: Donor 2


title: C56BL6 mouse fibroblasts, 10 gy, 24h, R2

description:
Library name: MUS_24h_M24_10Gy
counts_mus_irrad.tsv


title: T cells, Helenalin-treated and costimulated_donor2


title: T cells, DMSO-treated and costimulated_donor2

description: total RNA was isolated from T cells pretreated with DMSO for 1 h  and costimulated for 4 h


title: T cells, Ferm-treated and costimulated_donor3

description: total RNA was isolated from T cells pretreated with Ferm for 1 h  and costimulated for 4 h


title: CNSTB, S4, granuloma6

description: microdissected RNA-Seq

value: M.tb H37Rv-infected brain tissue


title: C56BL6 mouse fibroblasts, 10 gy, 24h, R1

description:
Library name: MUS_24h_M16_10Gy
counts_mus_irrad.tsv


title: CNSTB, S4, granuloma5

description: microdissected RNA-Seq


title: OF1_RNA

description: Library name: OF1_RNA


title: C56BL6 mouse fibroblasts, untreated, 24h, R1

description:
Library name: MUS_24h_M16_Con
counts_mus_irrad.tsv


title: CNSTB, S4, normal2

description: microdissected RNA-Seq


title: T cells, Tota-treated and costimulated_donor2


title: T cells, Radix-treated and costimulated_donor2

description: total RNA was isolated from T cells pretreated with Radix for 1 h  and costimulated for 4 h


title: CNSTB, S3, normal2

description: microdissected RNA-Seq


title: T cells, EtOH-treated and costimulated_donor2

description: total RNA was isolated from T cells pretreated with EtOH for 1 h  and costimulated for 4 h


title: P-2 BO Mice, scRNAseq

city: Shanghai

first: Rui

last: Gao

address: Zhennan rode

department: School of Medicine

institute: Tongji University

description: Singleron GEXSCOPE

data_processing:
The scRNA-seq data was analyzed using Seurat v5. Doublets in single-cell RNA sequencing data were predicted and removed using DoubletFinder. Then 19500 singlets were randomly selected from each tumor using a random number generator.
Assembly: mm10
Supplementary files format and content: barcodes, genes, and matrix files

source_name: Subcutaneous melanoma tumor

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Subcutaneous melanoma tumor

value: C57BL/6 mice

value: all cells isolated from tumor tissue

value: 6-8 weeks old

value: PBS treatment via intratumoral injection


title: OM3_RNA

description: Library name: OM3_RNA


title: CNSTB, S3, normal1

description: microdissected RNA-Seq


title: OM2_RNA

description: Library name: OM2_RNA


title: CNSTB, S3, granuloma8

description: microdissected RNA-Seq


title: P-1 BO Mice, scRNAseq

description: Singleron GEXSCOPE


title: T cells, Ferm-treated and costimulated_donor2


title: M-2 BO Mice, scRNAseq

description: Singleron GEXSCOPE

value: MagRM treatment via intratumoral injection


title: OF2_RNA

description: Library name: OF2_RNA


title: OM1_RNA

description: Library name: OM1_RNA


title: YF3_RNA

description: Library name: YF3_RNA


title: M-1 BO Mice, scRNAseq

description: Singleron GEXSCOPE


title: T cells, H2O-treated and costimulated_donor2


title: CNSTB, S3, granuloma6

description: microdissected RNA-Seq


title: T cells, untreated and unstimulated_donor2


title: HL-2 BO Mice, scRNAseq

description: Singleron GEXSCOPE

value: MagRM via intratumoral injection with IIMT treatment


title: CNSTB, S3, granuloma7

description: microdissected RNA-Seq


title: YF2_RNA

description: Library name: YF2_RNA


title: CNSTB, S3, granuloma5

description: microdissected RNA-Seq


title: YF1_RNA

description: Library name: YF1_RNA


title: OM4_RNA

description: Library name: OM4_RNA


title: HL-1 BO Mice, scRNAseq

description: Singleron GEXSCOPE


title: CNSTB, S2, normal2

description: microdissected RNA-Seq


title: T cells, Thymol-treated and costimulated_donor1

value: Donor 1


title: YM4_RNA

description: Library name: YM4_RNA


title: T cells, DMSO-treated and costimulated_donor1


title: M_WT_1714RE

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV. De-multiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (Bolger et al., 2014) was used for cleaning.
R package “QuasR” (Gaidatzis et al., 2015) was used for the read alignment to the mouse genome (mm10) followed by counting at the gene level.
Assembly: mm10
Supplementary files format and content: Excel file include raw counts

source_name: spinal cord

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: spinal cord

tag: Sex

value: male

value: microglia

value: Wildtype

value: EAE


title: M_cKO_1726LE

value: Kdm6a cKO


title: CNSTB, S2, normal1

description: microdissected RNA-Seq

value: Normal brain tissue


title: T cells, Radix-treated and costimulated_donor1

value: T cells


title: CNSTB, S2, inflammatory4

description: microdissected RNA-Seq

value: M.tb H37Rv-infected brain tissue


title: YM2_RNA

description: Library name: YM2_RNA

value: muscle

value: FISC/MuSC


title: T cells, Helenalin-treated and costimulated_donor1

description: total RNA was isolated from T cells pretreated with Helenalin for 1 h  and costimulated for 4 h


title: F_cKO_1726LC

value: female


title: CNSTB, S2, inflammatory3

description: microdissected RNA-Seq


title: YM1_RNA

description: Library name: YM1_RNA


title: T cells, Tota-treated and costimulated_donor1

description: total RNA was isolated from T cells pretreated with Tota for 1 h  and costimulated for 4 h


title: CNSTB, S2, granuloma4

description: microdissected RNA-Seq


title: T cells, Ferm-treated and costimulated_donor1


title: M_WT_1714LC


title: CNSTB, S2, inflammatory5

description: microdissected RNA-Seq


title: F/F rep1

city: Fukuoka

first: Naoto

last: Haruyama

state: Fukuoka

department: Faculty of Dental Science

country: Japan

institute: Kyushu University

description: Library name: MK.F.1_MK.F.1_R1

data_processing:
raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.7), Trimmomatic (version 0.39), and cutadapt (version 3.7) software.
Trimmed reads were then mapped to the mouse GRCm39 genome using STAR (version 2.7.10a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include count values for each sample.

source_name: skin

extract_protocol:
Separated epidermal layer was washed with PBS and homogenized. Total RNA was isolated with TRIzol reagent and purified using the RNeasy Mini Kit.
RNA sequencing libraries were prepared using the QIAseq UPX 3' Transcriptome Kit (#333088, QIAGEN). Subsequently, the libraries were adapted for the MGI sequencing platform with the MGIEasy Universal Library Conversion Kit (App-A) (#1000004155, MGI).

treatment_protocol: The dorsal whole skin was dissected after shaving, then incubated in 3.8% sodium thiocyanate for 20 min at room temperature to separate the epidermis from the dermis.

value: skin

value: epidermis

value: Flox/Flox


title: F_WT_1696RELP


title: F/F rep2

description: Library name: MK.F.2_MK.F.2_R1


title: T cells, H2O-treated and costimulated_donor1


title: CNSTB, S2, granuloma3

description: microdissected RNA-Seq


title: M_cKO_1695RPLC


title: F_WT_1714RPLC


title: cKO rep2

description: Library name: MK.cKO.2_MK.cKO.2_R1

value: cKO


title: YM3_RNA

description: Library name: YM3_RNA


title: MG shJUNB exp3

type: protein

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
Isaac_Witz__Sivan_Izraely_48
582
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

hyb_protocol: Each slide was probed with one antibody. The detection system used was a GenPoint-based staining kit from Agilent.

scan_protocol: Array-Pro Analyzer

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curve from the “standard curve” (supercurve) of the slide (Ab). Supercurve is constructed by a script in R written by Bioinformatics (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in MD Anderson Cancer Center, http://bioinformatics.mdanderson.org/Software/supercurve). The raw spot intensity data were adjusted to correct spatial bias before model fitting. The protein concentrations of each set of slides were then normalized by median polish, which was corrected across samples by the linear expression values using the median expression levels of all Ab experiments to calculate a loading correction factor for each sample. These values (given as log2 values) are defined as Supercurve Log2 (Raw) values. All the data points were normalized for protein loading and transformed to linear values.

label: DAB

molecule: protein

source_name: Immortalized human microglia-SV40 cells (ABM, Milton, Canada)

label_protocol: Samples were probed with Ab by CSA amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: Cells were maintained in RPMI-1640 medium (Biological Industries, Kibbutz Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS), 2 mmol/ml L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. 0.5% FBS supplemented medium was used for starvation in all the experiments. Cells were cultured in an incubator with humidified air with 5% CO2 at 37°C.

extract_protocol: Cell lysate was extracted using RIPA buffer (Sigma-Aldrich).

treatment_protocol:
The JunBlo microglia cells were established by using a mixture of three different pGIPZ vectors containing shRNA sequences targeting JUNB mRNA (RHS4430-200225817, RHS4430-200229510 and RHS4430-200246702; Dharmacon, Lafayette, CO, USA). A sh-non-silencing pGIPZ vector (RHS4531, Dharmacon) was used as a negative control. The variants are referred as MG conlo, MG JunBlo. All microglia variants were selected using 6 μg/ml puromycin (AG Scientific Inc.) as selection antibiotics, except for GFP-labeled MG conhi and MG JunBhi, which were also selected using 800 μg/ml G-418 disulfate (AG Scientific Inc.)
0.5X10 microglia cells were seeded on collagen coated plates in Prigrow III supplemented with 10% FCS for 24hrs. Then the cells were washed twice with ice cold PBS and frozen at -80° until protein extraction.

value: Microglia cell line

value: shJUNB


title: F_cKO_1695BP

value: spinal cord


title: T cells, EtOH-treated and costimulated_donor1

value: Donor 1


title: cKO rep1

description: Library name: MK.cKO.1_MK.cKO.1_R1


title: CNSTB, S1, normal1

first: Catherine Wei Min

last: Ong

description: microdissected RNA-Seq


title: M_WT_1714RC

value: male

value: microglia

value: Wildtype


title: T cells, untreated and unstimulated_donor1


title: cbpADM - TT E. coli, OD2, rep2

first: Santiago

last: Maya

address: Im Neuenheimer Feld 329

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

description: Library name: Sample 12

data_processing:
In brief, demultiplexed reads were processed as described earlier (Galmozzi and Merker et al. 2019) with the following changes for libraries prepared: The 3’ adaptor was trimmed with cutadapt v2.6 using the modified command cutadapt command 1: cutadapt --cores=0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --nextseq- trim=20 --discard-untrimmed -O 6 -o output.fastq input.fastq.gz.
Unique molecular identifiers (UMI) were extracted using custom Julia scripts (Script 1, Bertolini and Fenzl et al. 2021). julia path_to_input/infile.fastq.gz path_to_output/outfile.fastq.gz --umi3 5 --umi5 2
5’ adaptor was removed using cutadapt with the following command. cutadapt command 2: cutadapt -g ^CCCCCC -g ^CCCCC -g ^CCCC -m 15 -M 45 -o output.fastq.gz input.fastq.gz
To remove ncRNA, trimmed reads that aligned to indexed libraries of E. coli-specific ncRNA using bowtie v1.0.0 were removed using the following command: bowtie --threads 8 -t -n 2 –best ref_file_path -q input.fastq --un ncRNA_depleted.fastq
The trimmed reads were aligned to Escherichia coli genome (build NC_000913-3), with bowtie 1.0.0. Genome derivatives of the Escherichia coli genome (build NC_000913-3) were modified acording to the specific codon mutation. The command used was: bowtie  -m 1 -t -n 2 --best --strata ref_file_path -q input.fastq --un unaligned_reads.fastq --max _multi-mapped_reads.fastq -S _aligned_reads.sam
Samtools was then used to generate bam files using the following command: samtools sort -@ 8 _aligned_reads.sam -o _aligned_reads_sorted.bam
PCR dupliclates were collapsed to single reads and reads were assigned to (a-, p-, e-site) via a custom script (Script2, Bertolini and Fenzl et al. 2021). julia path_to_script/Script2.jl path_to_genome_annotation/annotation.gff' --use_umis --assignment_type 3 -o path_to_output path_to_input/infile.bam
Assembly: build NC_000913-3
Supplementary files format and content: Processed data are stored in HDF5 files, with each file containing one dataset per gene. Datasets consist of a 2-row matrix: the first row lists the 1-based positions within the coding sequence (CDS), and the second row gives the corresponding number of detected P-site reads at each position. Dataset attributes provide additional metadata, including gene and protein names, CDS length, and the gene’s chromosomal location and strand orientation.
Library strategy: Ribo-Seq

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria

growth_protocol: Single colonies of MG1655 and strains encoding DnaJ and CbpA mutant proteins (DnaJF98A - F102A, CbpAF98A - F102A) were inoculated for overnight cultures in LB Medium. On the following day two biological replicates were inoculated in 100 mL and 50 mL of LB medium to an initial OD600 of 0.01. Cells were grown at 37°C in baffled Erlenmeyer flasks with shaking at 110 rpm and harvested during log and early stationary phase (OD600 of 0.5 and 2.0).

extract_protocol:
RNA from ribosomes precipitated via sucrose cushion were extracted using the tri reagent (zymo research) method as described in Koubek et al. 2025.
Libraries were costructed as in Koubek et al. 2025.

treatment_protocol: Prior to harvest, 1 mM chloramphenicol was added, then cells were centrifuged (5 minutes at 4.500 x g) and flash-freezed in liquid nitrogen. Frozen cell pellets were lysed by cryo-milling. Lysates were thawed,and treated with 150U MNase / 40 μg RNA for 30 min at 4 °C. Digestion was stopped by placing samples in ice and supplementing 6 mM EGTA.

value: E. coli MG1655 CbpAF98A - F102A

value: Bacteria


title: CNSTB, S1, inflammatory4

address: 14 Medical Drive, MD6, Centre for Translational Medicine, #15-02

institute: National University of Singapore

description: microdissected RNA-Seq

value: M.tb H37Rv-infected brain tissue


title: CNSTB, S1, inflammatory3

description: microdissected RNA-Seq


title: M_cKO_1675BW

value: Kdm6a cKO

value: EAE


title: F_WT_1698LE

value: female


title: dnaJDM - TT E. coli, OD2, rep2

description: Library name: Sample 10

value: E. coli MG1655 DnaJF98A - F102A


title: MG shJUNB exp2

description:
Isaac_Witz__Sivan_Izraely_46
580
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: MG shControl exp2

description:
Isaac_Witz__Sivan_Izraely_45
579
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

value: shControl


title: F_cKO_1695RPLW


title: cbpADM - TT E. coli, OD2, rep1

description: Library name: Sample 11


title: M_WT_1698LP


title: WT - TT E. coli, OD2, rep2

description: Library name: Sample 8


title: CNSTB, S1, granuloma4

description: microdissected RNA-Seq


title: CNSTB, S1, granuloma5

description: microdissected RNA-Seq


title: MG shJUNB exp1

description:
Isaac_Witz__Sivan_Izraely_44
578
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: CNSTB, S1, normal2

description: microdissected RNA-Seq

value: Normal brain tissue


title: dnaJDM - TT E. coli, OD2, rep1

description: Library name: Sample 9


title: MG shControl exp1

description:
Isaac_Witz__Sivan_Izraely_43
577
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: MG JUNB OE exp3

description:
Isaac_Witz__Sivan_Izraely_42
564
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

value: JUNB OE


title: MG shControl exp3

description:
Isaac_Witz__Sivan_Izraely_47
581
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

value: Microglia cell line


title: cbpADM - TT E. coli, OD05, rep2

description: Library name: Sample 6


title: M_cKO_1675LE


title: CNSTB, S1, granuloma2

description: microdissected RNA-Seq


title: cbpADM - TT E. coli, OD05, rep1

description: Library name: Sample 5


title: F_cKO_1675RE


title: F_WT_1698RC


title: WT - TT E. coli, OD2, rep1

description: Library name: Sample 7


title: MG pQCXIP exp3

description:
Isaac_Witz__Sivan_Izraely_41
563
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.

value: Control


title: MG JUNB OE exp2

description:
Isaac_Witz__Sivan_Izraely_40
562
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: M_WT_1698RW

value: spinal cord


title: dnaJDM - TT E. coli, OD05, rep2

description: Library name: Sample 4


title: Healthy, S3, normal1

description: microdissected RNA-Seq


title: CNSTB, S2, inflammatory2

description: microdissected RNA-Seq


title: MG pQCXIP exp2

description:
Isaac_Witz__Sivan_Izraely_39
561
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: WT - TT E. coli, OD05, rep2

description: Library name: Sample 2


title: Healthy, S2, normal1

description: microdissected RNA-Seq


title: MG JUNB OE exp1

description:
Isaac_Witz__Sivan_Izraely_38
560
The protein of interest was detected by probing with a specific antibody, amplifying the signal via a tyramide amplification system, and visualized via DAB colorimetric reaction.


title: F_cKO_1675LC


title: CNSTB, S2, inflammatory1

description: microdissected RNA-Seq


title: F_WT_1720LC


title: H3K27me3_lhp1dekT_rep2

data_processing:
Following quality trimming, the first 80 nucleotides from the forward reads were aligned to the reference genome using Bowtie2 with the 'best' option.
Processed data files were prepared with the bamCoverage command in the deepTools(v3.3.2) with option '-bs 1 --normalizeUsing CPM  --ignoreDuplicates' to calculate normalized  coverage of reads.
Assembly: TAIR10
Supplementary files format and content: bigWig

source_name: 12 days seedlings

growth_protocol: Plants were grown on1/2 Murashige-Skoog medium plate for 12 days under long-day condition (8h/16h: dark/light) at 22±1 ˚C.

extract_protocol:
Frozen seedlings were ground into fine powder. Suspension in nuclei isolation buffer and then crosslinked with 1% formaldehyde. After fiitering through a 40 µm nylon cell strainer, isolated nuclei were centrifuged and resuspended in nuclear isolation buffer. The nuclear pellets were lysed using a buffer containing detergen and sonicated using a focused-ultrasonicator. Following immunoprecipitation processes, DNA was decrosslinked from the beads by incubating overnight at 65 °C in elution buffer. Genomic DNA were recovered and purified after Proteinase K and RNase treatment.
The  libraryies were made using the ThruPLEX DNA-seq Kit (Takara) with manufacturer's protocol

treatment_protocol: Whole plants were harversted 1 hour before dark.

value: 12 days seedlings

value: lhp1;dek2;3;4 quadruple mutant

value: anti-H3K27me3 antibody


title: CNSTB, S1, granuloma3

description: microdissected RNA-Seq


title: dnaJDM - TT E. coli, OD05, rep1

description: Library name: Sample 3


title: H3K27me3_lhp1dekT_rep1


title: CNSTB, S1, inflammatory2

description: microdissected RNA-Seq