title: SY5Y cells, Con rep2

city: Wuhan

first: Xiao

middle: si

last: Yu

address: Jiefang Avenue

department: Pediatric Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Hisat2 v2.0.5
Index of the reference genome was built using Hisat2 v2.0.5.
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: DMEM/F12, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from tissues and cells by Trizol (Vazyme, R411-01)method.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Neuroblastoma cell line

value: Control


title: SY5Y cells, DLX5 rep3

status: Public on Dec 01 2025

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: DLX5 overexpression


title: SY5Y cells, Con rep1


title: LADY_replicate2.

city: Shanghai

first: Tao

last: Wu

address: Tongji University Siping Road Campus

department: school of life science and technology

institute: Tongji University

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed mRNA-Seq reads were mapped to hg38 genome using HISAT2(v2.2.0). Refseq genes were quantified to rawcount using featureCounts(v2.0.3).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes rawcounts for each sample

molecule: polyA RNA

source_name: induce and maintain in LADY medium

extract_protocol:
the mRNA sequencing libraries were constructed by following the manufacturer’s instructions.
mRNA-seq libraries were prepared for sequencing using standard Illumina protocols

value: pluripotent stem cells

value: naive state

value: WT


title: SY5Y cells, DLX5 rep2


title: SY5Y cells, DLX5 rep1


title: Mixed-Het / 12454-JC-0019

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

country: USA

institute: Vanderbilt University

description:
Library name: 12454-JC-0019
Mouse (in vivo)

data_processing:
Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments. Genialis General RNA-seq analysis pipeline (STAR, v2.7.10b) was used. Analysis steps thus include trimming (BBDuk), mapping (STAR), expression quantification (STAR) and normalization (rnanorm).
Assembly: mm39
Supplementary files format and content: csv file include TPM counts per sample

organism: Mus musculus

source_name: Isolated islets

extract_protocol:
RNA was harvested using RNEasy mini plus kit (Qiagen), 1.3ug used for construction of sequencing libraries
A Quality Control analysis was performed on the RNA samples using the Agilent Bioanalyzer to assess quality and an RNA Qubit assay was used to determine quantity.  Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit (NEB) (P/N: E7765L, NEB, Ipswich, MA) following the manufacturer’s instructions.  End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument.  Prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturer's protocols. 150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 50M reads per sample.  Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment.

tag: tissue

value: Isolated islets

value: Mouse (in vivo)

value: pancreatic islets

value: Mixed male MafA S64F (Het)

tag: Sex

value: male


title: 6hr-Veh-3

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR
Differential analysis was performed by Deseq2
Assembly: hg19
Supplementary files format and content: counts table was generated using STAR using the VIPER pipeline
Supplementary files format and content: bw files were generated using STAR using the VIPER pipeline

extract_protocol:
Isolation of total RNA was performed using the Aurum™ Total RNA Mini-Kit according to the manufacturer’s instructions (Bio-Rad, Hercules, CA). Total RNA concentration and quality were determined using a Nanodrop 1000 (ThermoFisher).
Nextera

value: Immortalized human breast carinoma

tag: time

tag: dosage

value: veh


title: Mixed-WT / 12454-JC-0016

description:
Library name: 12454-JC-0016
Mouse (in vivo)

value: Mixed male MafA WT


title: 6hr-10nM-1


title: 6hr-10nM-3


title: Mixed-WT / 12454-JC-0014

description:
Library name: 12454-JC-0014
Mouse (in vivo)


title: Mixed-WT / 12454-JC-0012

description:
Library name: 12454-JC-0012
Mouse (in vivo)


title: 6hr-Veh-1


title: LAY_replicate1

source_name: induce and maintain in LAY medium


title: C57-Het / 12454-JC-0011

description:
Library name: 12454-JC-0011
Mouse (in vivo)

value: C57 male MafA S64F (Het)


title: C57-Het / 12454-JC-0010

description:
Library name: 12454-JC-0010
Mouse (in vivo)


title: IARS1 healthy control 1

first: Weitao

last: Zhou

state: Minhang district

address: Block 8, Children's Hospital of Fudan University, Wanyuan Road, Minhang District, Shanghai, China

institute: Children's Hospital of Shanghai Jiaotong University

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were analyzed by the Cell Ranger pipeline (v3.0.1, 10x Genomics),
The gene-barcode matrix of UMI counts was then subjected to analysis with Seurat (v3.0.2) for quality control, normalization, dimensional reduction, batch effect removal, clustering and visualization
The uniform manifold approximation and projection (UMAP) was created based on the top 30 dimensions resulted from principal component analysis (PCA).
The cell clusters were identified from PCA-reduced data, and then determined with SingleR (v1.0.6) and automatic assignment.
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
the PBMCs were isolated through density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare) and processed within 1 hour.
With survival rate of over 85%, the single cell suspensions were washed and resuspended at a concetration of 700-1200 cells/ul using the Chromium Next GEM Single Cell V(D)J Reagent Kits(10x Genomics) according to the manufacturer’s instructions. Based on a target cell count of 10,000-13,000, GEMs (Gel Bead in Embusion) were created for single cell isolation.
These GEMs were collected by oil breaking treatment and subjected to reverse transcription PCR for labeling. Subsequently, cDNA, along with cell barcodes, underwent PCR amplification. The single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 5’ Library Kits (PN-1000165, PN-1000020)

value: PBMC

value: primary cells

value: wild type

tag: treatment

value: no treatment


title: SY5Y cells, Con rep3

value: Neuroblastoma cell line

value: Control


title: Mixed-Het / 12454-JC-0021

description:
Library name: 12454-JC-0021
Mouse (in vivo)


title: Mixed-WT / 12454-JC-0013

description:
Library name: 12454-JC-0013
Mouse (in vivo)


title: 6hr-100pM-1


title: Mixed-Het / 12454-JC-0017

description:
Library name: 12454-JC-0017
Mouse (in vivo)


title: 18hr-Veh-3


title: Mixed-WT / 12454-JC-0015

description:
Library name: 12454-JC-0015
Mouse (in vivo)


title: C57-Het / 12454-JC-0007

description:
Library name: 12454-JC-0007
Mouse (in vivo)


title: 18hr-10nM-1


title: 18hr-10nM-3


title: C57-Het / 12454-JC-0006

description:
Library name: 12454-JC-0006
Mouse (in vivo)


title: Mixed-Het / 12454-JC-0018

description:
Library name: 12454-JC-0018
Mouse (in vivo)


title: C57-Het / 12454-JC-0008

description:
Library name: 12454-JC-0008
Mouse (in vivo)


title: 18hr-Veh-1


title: C57-WT / 12454-JC-0005

description:
Library name: 12454-JC-0005
Mouse (in vivo)

value: C57 male MafA WT


title: 18hr-100pM-3


title: 18hr-100pM-1


title: 6hr_Veh_2

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the chips pipeline

molecule: genomic DNA

extract_protocol:
Omni-ATAC was performed as previously described (PMID: 28846090).
See PMID 28846090.


title: C57-WT / 12454-JC-0002

description:
Library name: 12454-JC-0002
Mouse (in vivo)


title: C57-WT / 12454-JC-0001

description:
Library name: 12454-JC-0001
Mouse (in vivo)


title: C57-WT / 12454-JC-0004

description:
Library name: 12454-JC-0004
Mouse (in vivo)


title: 154702-f-iso_mid

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
Library name: 25242
mid mKate2

data_processing:
Alignment with Kallisto 0,48
Assembly: GRCm38.p5
Supplementary files format and content: count_matrix.tsv

source_name: Brain

extract_protocol:
Microglia isolation was performed using the MACS system (Miltenyi Biotec) as described previously. However, no CD11b enrichment step was performed as the intrinsic mKate2 reporter is only expressed in TREM2 expressing (microglia) cells. Hence, FACS was performed based on the mKate2 fluorescence signal and sorted into low, mid and high expressing subpopulations, as a proxy for the TREM2 expression of individual cells. The sorted fractions were spun down and the pellets stored at -80°C before being processed for further analysis.
RNA isolation was performed using the RNeasy Micro kit (Qiagen), following manufacturer's instruction. For the RNA sequencing, both the quantity and integrity of RNA were assessed using the HS RNA assay on a Tapestation 4200 system from Agilent. The Smart‐seq2 protocol, as detailed by Picelli et al. (2014), was employed to create non-strand-specific, full transcript sequencing libraries. In summary, 2 µL of total RNA were transferred to a buffer containing 0.2% TritonX‐100, protein-based RNase inhibitor, dNTPs, and oligo‐dT oligonucleotides for priming the subsequent RT reaction on polyadenylated mRNA sequences. The SMART RT reaction was conducted at 42°C for 90 min using commercial SuperScript II (Invitrogen) and a Template-Switching Oligo. The pre-amplification PCR with 17 cycles was carried out to produce double‐stranded DNA from the cDNA template. After normalization, 100-300 pg of amplified cDNA underwent tagmentation and enrichment using self-loaded Tn5 transposase (Diagenode) to construct the final sequencing libraries. Quantification of libraries was performed using the Qubit HS dsDNA assay, and the distribution of library fragment sizes was determined using the D1000 assay on a Tapestation 4200 system (Agilent). The sequencing was executed in single-end mode (75 cycles) on a NovaSeq 6000 System (Illumina) with a NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) chemistry. Raw sequencing data were demultiplexed using bcl2fastq2 v2.20 and aligned against M. musculus reference genome (M16) using Kallisto 0,48.

treatment_protocol: 8-month-old Trem2-mKate2KI/wt APPSAA/SAA.hTfRKI/KI mice were injected with 1 mg/kg Trem2 agonist, 4D9, coupled to an antibody transport vehicle (ATV:4D9) and an istype control monthly until 11 months. At 12 months, mice were injected with 30 mg/kg FDG, 641 perfused 1 hour later and the extracted microglia were then sorted into low, mid and high mKate2 expressing populations with FACS

value: Brain

tag: strain

value: microglia

value: Trem2-mKate2 Ki/wt X APP-SAA Ki/Ki x hTfR Ki/Ki

value: isotype control

tag: batch


title: 6hr-100pM-3


title: 6hr_10nM_2


title: 154701-f-4D9_high

description:
Library name: 25240
high mKate2

value: 1 mg/kg ATV:4D9


title: C57-WT / 12454-JC-0003

description:
Library name: 12454-JC-0003
Mouse (in vivo)

value: Isolated islets

value: Mouse (in vivo)

value: pancreatic islets

value: male


title: 6hr_Veh_3

value: Immortalized human breast carinoma

value: veh


title: 6hr_100pM_3


title: C57-Het / 12454-JC-0009

description:
Library name: 12454-JC-0009
Mouse (in vivo)

value: C57 male MafA S64F (Het)


title: 154701-f-4D9_mid

description:
Library name: 25239
mid mKate2


title: 6hr_10nM_1


title: 154701-f-4D9_low

description:
Library name: 25238
low mKate2


title: 6hr_100pM_2


title: 6hr_100pM_1


title: 154700-m-iso_mid

description:
Library name: 25236
mid mKate2


title: 18hr_Veh_3


title: 154700-m-iso_low

description:
Library name: 25235
low mKate2


title: 18hr_10nM_3


title: 154698-m-iso_mid

description:
Library name: 25233
mid mKate2


title: 6hr_10nM_3


title: 18hr_Veh_1


title: 154698-m-iso_low

description:
Library name: 25232
low mKate2


title: 6hr_Veh_1


title: 18hr_10nM_2


title: 18hr_Veh_2


title: 18hr_10nM_1


title: 154691-m-4D9_high

description:
Library name: 25228
high mKate2


title: 154691-m-4D9_mid

description:
Library name: 25227
mid mKate2


title: 18hr_100pM_1


title: 154691-m-4D9_low

description:
Library name: 25226
low mKate2


title: 18hr_100pM_2


title: 154697-m-4D9_mid

description:
Library name: 25230
mid mKate2


title: 154700-m-iso_high

description:
Library name: 25237
high mKate2


title: donor4-CM

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

data_processing:
The raw sequencing data was processed by the Cell Ranger software (v3.0.2, 10x Genomics)
Human refence genome (GRCh38) was used for accurate mapping of the sequencing readouts and quantification of gene expression
Assembly: GRCh38

source_name: retinas

extract_protocol:
Macular and peripheral explants were dissociated into single cells following light treatment using Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.Then The single-cell suspension was combined with barcoded gel beads in a microfluidic chip and run on the Chromium Controller (10X Genomics) to create gel bead-in-emulsion (GEMs) droplets (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268, 10×Genomics). The GEMs were incubated, enabling mRNA reverse transcription into cDNA.
The barcoded cDNA was then amplified using PCR to construct a library according to users guide of Chromium Single Cell 3ʹ Reagent Kits v3

treatment_protocol: Macular and peripheral explants were dissociated into single cells following light  treatment. In brief,We employed a custom-built light exposure system situated within the tissue culture incubator to induce light stress in retinal explants.Light stress was accomplished by subjecting explants to intense light at 32k lux, while the control group were exposed to 5k lux light. Retinal explant tissues were placed on 12-well plate transwell inserts (#3460, Corning) with neurobasal medium (#21103049, Gibco), 2% B27 (#17504044, Gibco), 1% N2 (#17502048, Gibco), 1% fetal bovine serum (FBS, #F9423, Sigma‐Aldrich), 1% GlutaMax (#35050, Gibco), 1%ITS (#51500056, Gibco) and 1% penicillin-streptomycin (P/S, #P4333, Sigma‐Aldrich). Macular and peripheral neural retinal explants were exposed to light exposure for 4 hr.Single cell dissociation was achieved using the Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.

value: retinas

value: Macular neural retinas from right donor eyes exposed to dim light


title: donor4-CP

value: Mid-peripheral neural retinas from right donor eyes exposed to dim light


title: 154600-f-4D9_mid

description:
Library name: 25224
mid mKate2


title: donor4-LP

value: Mid-peripheral neural retinas from left donor eyes exposed to intense light


title: donor4-LM

value: Macular neural retinas from left donor eyes exposed to intense light


title: 154599-f-iso_high

description:
Library name: 25222
high mKate2

value: Brain


title: donor3-CP


title: 154600-f-4D9_high

description:
Library name: 25225
high mKate2

value: microglia


title: 154697-m-4D9_high

description:
Library name: 25231
high mKate2

value: Trem2-mKate2 Ki/wt X APP-SAA Ki/Ki x hTfR Ki/Ki


title: 154599-f-iso_low

description:
Library name: 25220
low mKate2

value: isotype control


title: donor3-CM


title: donor3-LP


title: 154598-f-4D9_high

description:
Library name: 25219
high mKate2

value: 1 mg/kg ATV:4D9


title: 154598-f-4D9_mid

description:
Library name: 25218
mid mKate2


title: donor3-LM


title: 154597-f-iso_high

description:
Library name: 25216
high mKate2


title: 18hr_100pM_3


title: 154697-m-4D9_low

description:
Library name: 25229
low mKate2


title: donor2-CP


title: donor2-LP


title: donor2-CM


title: donor2-LM


title: 154596-f-4D9_high

description:
Library name: 25213
high mKate2


title: 154600-f-4D9_low

description:
Library name: 25223
low mKate2


title: donor1-CP


title: 154595-m-iso_mid

description:
Library name: 25209
mid mKate2


title: 154597-f-iso_low

description:
Library name: 25214
low mKate2


title: Steroidogenic adrenal cells, SF1-Cre; mTmG, male 15 week old_Iso21

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description:
Library name: SF1_mTmG
NovaSeq (S4) 300

data_processing:
h5 files generated with cellranger. Reads were aligned to mm10 mouse reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adrenal gland

extract_protocol:
Following dissociation, cells were stained with 2μg/ml DAPI and 5μM Vybrant DyeCycle Ruby (Invitrogen, #V10309). Ruby-positive, DAPI-negative single cells were sorted based on fluorescent properties using the Thermofisher Bigfoot Cell Sorter at the University of Michigan Flow Cytometry Core. Cells were collected in BSA-precoated tubes containing HBSS 1X with 2% FBS and kept on ice. Single-cell droplets with a target capture of 10,000 cells were immediately prepared on the 10x Chromium system
Library was performed according the manufacturer instructions with the Chromium Next GEM Single Cell 3′ Gene Expression Library Construction Kit version 3.1

value: Adrenal gland

value: Steroidogenic - SF1 lineage

value: WT, SF1-Cre ; Rosa mTmG

tag: age

value: 15 week old


title: donor1-LM


title: donor1-LP


title: donor1-CM


title: 154599-f-iso_mid

description:
Library name: 25221
mid mKate2


title: C57mice ears,  paeonol 3

city: Nanjing

first: xin

last: sun

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

description: Library name: Paeonol 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: ear

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: ear

value: tissue


title: 154595-m-iso_low

description:
Library name: 25208
low mKate2


title: control_2

first: Fan

last: Pan

state: Shanghai

address: Ren Ji Hospital, Shanghai Jiao Tong University School Of Medicine, Shanghai  Street Address: 845 Lingshan Road, Pudong New Area

institute: Shanghai jiaotong university

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress
P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
The reads were reassembled using StringTie.
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 files include FPKM values for each Sample

source_name: placenta

growth_protocol: Human primary placental syncytiotrophoblastswere collected and cultured in DMEM containing 10% FBS (Gibco) and 1% antibiotics (Gibco) at 37°C in 5% CO2/95% air to allow spontaneous syncytialization in vitro.

extract_protocol:
Total RNA was extracted from syncytiotrophoblasts treated with or without AZM (10 μΜ; 24 hours) (n=3 each) using Trizol reagent (#15596026, Thermo Fisher, Massachusetts, U.S.). RNA purity and integrity were determined using a NanoDropND-2000
RNA-sequence libraries were constructed using a TruSeq RNA sample preparation kit (Illumina Inc.) according to a manufacturer’s protocol.

treatment_protocol: The cells were treated with 10μM azithromycin  (#S1835, Selleck) for 24 hours following reagents in phenol red- and FBS-free DMEM medium

value: placenta

value: placental syncytiotrophoblasts

value: Epithelial cells

value: WT

value: DMSO


title: control_1


title: control_3


title: C57mice ears,  paeonol 2

description: Library name: Paeonol 2


title: 154597-f-iso_mid

description:
Library name: 25215
mid mKate2


title: Steroidogenic adrenal cells, SF1-Cre; mTmG, male 15 week old_Iso20

description:
Library name: 780-TD-1
NovaSeq (S4) 300

value: male


title: AZ_3

value: azithromycin


title: Carnegie stage 20 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

description:
CS20_02
sn-Multiome-seq fastq raw reads and aligned matrices

library_source: other

data_processing:
*library strategy: snMultiome-seq
Cellranger multiome alignment to hg38 standard build (ATAC and RNA)
Assembly: hg38
Supplementary files format and content: cell x gene matrix (filtered_feature_bc_matrix.h5)
Supplementary files format and content: cell x fragment matrix (atac_fragments.tsv.gz)

molecule: other

source_name: human embryonic orofacial region

extract_protocol:
single nuclei were generated using standard protocols from 10X genomics for generating nuclei.
Chromium Single Cell Multi-ome 3′ Library and Gel Bead kit following the manufacturer’s instructions (10x Genomics)

treatment_protocol: flash frozen primary human embryonic samples were obtained from the HDBR.

value: human embryonic orofacial region

tag: Stage

value: Carnegie stage 20


title: AZ_2


title: 154596-f-4D9_mid

description:
Library name: 25212
mid mKate2

value: Brain

value: microglia

value: Trem2-mKate2 Ki/wt X APP-SAA Ki/Ki x hTfR Ki/Ki


title: C57mice ears,  model 3

description: Library name: Model 3


title: C57mice ears,  paeonol 1

description: Library name: Paeonol 1


title: C57mice ears,  model 2

description: Library name: Model 2


title: C57mice ears,  model 1

description: Library name: Model 1


title: Carnegie stage 20 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS20_01
sn-Multiome-seq fastq raw reads and aligned matrices


title: C57mice ears,  control 1

description: Library name: Control 1

value: absolute ethyl alcohol


title: C57mice ears,  control 3

description: Library name: Control 3


title: Carnegie stage 17 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

description:
CS17_02
sn-Multiome-seq fastq raw reads and aligned matrices

value: Carnegie stage 17


title: C57mice ears,  control 2

description: Library name: Control 2


title: RNA-seq of 0h RSK1 KO BMDM

city: Beijing

first: Xingxian

last: Liu

address: 30 Shuangqing Rd, Haidian District

institute: Tsinghua University

description: Library name: RSK1_KO_0h_RNA

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm39
Supplementary files format and content: xlsx file including FPKM values for each Sample

source_name: BMDM

extract_protocol:
RNA extraction using Trizol
RNA-seq library construction using SMARTER-seq Library Prep Kit following manufacturers' protocol.

value: BMDM

value: RSK1 KO

value: No treatment


title: RNA-seq of 24h RSK1 KO BMDM

description: Library name: RSK1_KO_24h_RNA

value: KS stimulated for 24h


title: Carnegie stage 16 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS16_01
sn-Multiome-seq fastq raw reads and aligned matrices

value: Carnegie stage 16


title: Carnegie stage 14 primary human embryonic orofacial tissue, snMultiome-seq replicate 3

description:
CS14_04
sn-Multiome-seq fastq raw reads and aligned matrices

value: Carnegie stage 14


title: Carnegie stage 17 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS17_01
sn-Multiome-seq fastq raw reads and aligned matrices


title: Carnegie stage 16 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

description:
CS16_02
sn-Multiome-seq fastq raw reads and aligned matrices


title: Carnegie stage 13 primary human embryonic orofacial tissue, snMultiome-seq replicate 4

description:
CS13_04
sn-Multiome-seq fastq raw reads and aligned matrices

value: Carnegie stage 13


title: IL-6 low population sgRNA

description: Library name: IL-6_neg_sorted

data_processing:
The RRA module (default setting) was used to calculate log2 fold changes and p-values of the genes. Custom R (v4.1.3) scripts were used to visualize the data.
Assembly: mm39
Supplementary files format and content: txt file including sgRNA counts for negative population and control group
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA extraction using the NucleoSpin Blood XL kit (MACHEREY-NAGEL 740950.50), following the manufacturer’s instructions.
Amplification of the sgRNA cassettes by PCR was performed according to the broad GPP protocol

value: KS stimulated for 72h and sorted for IL-6 low (top 5%) population


title: Carnegie stage 14 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

description:
CS14_02
sn-Multiome-seq fastq raw reads and aligned matrices


title: Carnegie stage 14 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS14_01
sn-Multiome-seq fastq raw reads and aligned matrices


title: Carnegie stage 13 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

description:
CS13_02
sn-Multiome-seq fastq raw reads and aligned matrices


title: RNA-seq of 72h BMDM

description: Library name: 72h_RNA

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm39
Supplementary files format and content: xlsx file including TPM values for each Sample

extract_protocol:
RNA using Trizol, Ribotagged transcripts in RiboTag-seq using Qiagen RNeasy Mini Kit.
RNA-seq library construction using SMARTER-seq Library Prep Kit following manufacturers' protocol. Ribo-seq library construction following Sanz et al, Proc. Nat. Acad Sci., 2009.

value: WT

value: KS stimulated for 72h


title: Carnegie stage 13 primary human embryonic orofacial tissue, snMultiome-seq replicate 5

description:
CS13_05
sn-Multiome-seq fastq raw reads and aligned matrices

value: human embryonic orofacial region


title: Carnegie stage 13 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS13_01
sn-Multiome-seq fastq raw reads and aligned matrices


title: AZ_1

value: placenta

value: placental syncytiotrophoblasts

value: Epithelial cells

value: azithromycin


title: RNA-seq of 0h WT BMDM

description: Library name: 0h_RNA


title: Input control sgRNA

description: Library name: Input_control


title: Carnegie stage 13 primary human embryonic orofacial tissue, snMultiome-seq replicate 3

description:
CS13_03
sn-Multiome-seq fastq raw reads and aligned matrices


title: RNA-seq of 24h WT BMDM

description: Library name: 24h_RNA


title: RiboTag-seq of 72h BMDM

description: Library name: 72h_RiboTag


title: RiboTag-seq of 0h WT BMDM

description: Library name: 0h_RiboTag


title: Carnegie stage 12 primary human embryonic orofacial tissue, snMultiome-seq replicate 3

description:
CS12_03
sn-Multiome-seq fastq raw reads and aligned matrices

value: Carnegie stage 12


title: RiboTag-seq of 24h WT BMDM

description: Library name: 24h_RiboTag


title: Carnegie stage 12 primary human embryonic orofacial tissue, snMultiome-seq replicate 1

description:
CS12_01
sn-Multiome-seq fastq raw reads and aligned matrices


title: RNA-seq of  LPS stimulated 24h WT BMDM

description: Library name: LPS_24h_RNA

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm39
Supplementary files format and content: txt file including TPM values for each sample

extract_protocol:
RNA using Trizol, RFP in Ribo-seq using Qiagen miRNeasy Mini Kit.
RNA-seq library construction using SMARTER-seq Library Prep Kit following manufacturers' protocol. Ribo-seq library construction following Ingolia et al, Nat. Prot. 2012.

value: LPS stimulated for 24h


title: Carnegie stage 12 primary human embryonic orofacial tissue, snMultiome-seq replicate 2

description:
CS12_02
sn-Multiome-seq fastq raw reads and aligned matrices


title: RNA-seq of 24h WT BMDM

description: Library name: WT_24h_RNA

value: BMDM


title: MCL39

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
The raw sequencing data were preprocessed (demultiplexed cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite provided by 10X Genomics
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Live MCL cells were first enriched by Ficoll-Paque Plus and anti-human CD19 magnetic beads. Depletion of human erythroid precursors and erythrocytes was then performed using CD235a (Glycophorin-A) magnetic beads. 15,000 cells from the resulting suspensions were loaded on a Chromium controller to generate single-cell partitions following the manufacturer’s protocol (10X genomics)
scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and sequenced using the NovaSeq 6000 system (Illumina).

tag: individual

value: patient MCL39

value: Bone marrow

value: before inclusion in the OAsIs trial


title: RNA-seq of  LPS stimulated 6h WT BMDM

description: Library name: LPS_6h_RNA

value: LPS stimulated for 6h


title: Ribo-seq of  LPS stimulated 24h WT BMDM

description: Library name: LPS_24h_Ribo

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm39
Supplementary files format and content: txt file including TPM values for each sample
Library strategy: Ribo-Seq


title: MCL34_incl

value: patient MCL34


title: RNA-seq of 0h BMDM

description: Library name: LPS_0h_RNA

value: No treatment


title: MCL36

value: patient MCL36


title: Ribo-seq of 0h BMDM

description: Library name: LPS_0h_Ribo

value: WT


title: Ribo-seq of  LPS stimulated 6h WT BMDM

description: Library name: LPS_6h_Ribo


title: MCL34_Rel

value: at relapse in the OAsIs trial


title: MCL12

value: patient MCL12


title: RNA-seq of 24h BCAP-deficient BMDM

description: Library name: BCAP_KO_24h_RNA

value: BCAP KO

value: KS stimulated for 24h


title: RNA-seq of 0h BCAP-deficient BMDM

description: Library name: BCAP_KO_0h_RNA


title: MCL10

value: patient MCL10


title: RNA-seq of 24h WT BMDM

description: Library name: WT_24h_RNA


title: 001-124_MLT

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: primary cell

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)
RNA-Seq (3'SRP)

treatment_protocol: treatment 24h with the BTK inhibitor Ibrutinib (500 nM) or the MALT1 inhibitor MLT-748 (1 μM)

value: primary cell

tag: disease

value: mantle cell lymphoma

value: 1 uM MLT-748


title: RNA-seq of 0h WT BMDM

description: Library name: WT_0h_RNA

value: BMDM


title: 001-124_ibru

value: 500nM ibrutinib


title: 001-124 ct

value: untreated


title: RNA-seq of 0h WT BMDM

description: Library name: WT_0h_RNA


title: SUDHL16_MLT

value: DLBCL

value: cell line


title: SUDHL16 ct


title: SUDHL16_ibru


title: OCILY3_ibru


title: Ribo-seq of 24h WT BMDM

description: Library name: WT_24h_Ribo

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm39
Supplementary files format and content: xlsx file including TPM values for each Sample
Library strategy: Ribo-Seq


title: Ribo-seq of 0h WT BMDM

description: Library name: WT_0h_Ribo


title: Ribo-seq of 0h BCAP-deficient BMDM

description: Library name: BCAP_KO_0h_Ribo


title: OCILY3 ct


title: MOG (E071918-8)

city: Sacramento

first: Hyun Kyu

last: Kim

state: CA

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

description:
Library name: Sample 8
EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin

data_processing:
2. Read Mapping: STAR
Assembly: Mus_musculus_mm10
Supplementary files format and content: FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)

source_name: spinal cord

growth_protocol: All animals were from C57BL/6 background and maintained in 12 h light/dark cycle with water and food. Animals and procedures in this study were approved by the Institutional Animal Care and Use Committee at the University of California, Davis.

extract_protocol:
RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit (QIAGEN) with RNase-Free DNase Set (QIAGEN) to remove genomic DNA. The quality of RNA samples was determined by the Bioanalyzer 2100 system (Agilent Technologies). The RNA integrity number (RIN) of all our RNA samples used for RNA-seq was greater than 6.8.
2.1Library construction  Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose.  NEB library: Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.  Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction. Below is the workflow chart:

treatment_protocol: On day 0, three-month-old mice were administrated subcutaneously of 300 µg of rodent MOG peptide (35-55) emulsified in CFA containing 5 mg/mL killed Mycobacterium tuberculosis. On day 2, mice were intraperitoneally administrated of 200 ng of pertussis toxin. CFA control mice received only CFA and pertussis toxin, without MOG peptide.

value: spinal cord

value: wild-type

value: MOG


title: OCILY3_MLT


title: MOG (E071918-12)

description:
Library name: Sample 9
EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin


title: MOG (E071918-4)

description:
Library name: Sample 7
EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin


title: MOG (E071918-14)

description:
Library name: Sample 10
EAE-induced mice administered MOG peptide (amino acids 35–55) emulsified in CFA with pertussis toxin


title: REC_ibru

source_name: REC

value: REC


title: Ribo-seq of 24h BCAP-deficient BMDM

description: Library name: BCAP_KO_24h_Ribo


title: REC ct


title: NTS3_ibru


title: MCL24

value: patient MCL24

value: Bone marrow

value: at relapse in the OAsIs trial


title: Islets, Akita treated with dapagliflozine, rep3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: Library name: DAPA3_S9_R1_001.fastq.gz

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10. The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: raw_and_DESeq2_norm_counts.xlsx
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol,  raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Pancreatic islets of Langerhans

growth_protocol: Mouse islets were were isolated and maintained for 3 hours in complete RPMI-1640 medium containing 11 mmol/l glucose supplemented with 10% heat-inactivated FBS, 100 IU/mL Pen/Strep. solution, 10 mmol/l HEPES, 2 mmol/l l-glutamine, 1 mmol/l sodium pyruvate and 0.05 mmol/l 2-mercaptoethanol in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
RNA was isolated from mouse islets employing QIAshredders and RNeasy Micro Kit (Qiagen).
Smart-seq v4 ultralow

treatment_protocol: Islets did not receive treatment in vitro

value: Pancreatic islets of Langerhans

value: primary cells

value: pancreatic endocrine cells

value: Akita (C57BL/6-Ins2Akita/J)

value: mice treated for 2 weeks with dapagliflozin


title: NTS3_MLT

value: mantle cell lymphoma

value: 1 uM MLT-748


title: CFA (E031014-6)

description:
Library name: Sample 5
Mice treated with complete Freund’s adjuvant (CFA) and pertussis toxin

value: CFA


title: REC_MLT


title: SP53 ct

value: untreated


title: CFA (E031014-5)

description:
Library name: Sample 4
Mice treated with complete Freund’s adjuvant (CFA) and pertussis toxin


title: Naive (N050218-6)

description:
Library name: Sample 3
Naïve mice,


title: SP53_MLT

value: cell line


title: CFA (E031014-7)

description:
Library name: Sample 6
Mice treated with complete Freund’s adjuvant (CFA) and pertussis toxin

value: spinal cord


title: Naive (N050218-2)

description:
Library name: Sample 1
Naïve mice,

value: wild-type


title: Islets, Akita treated with dapagliflozine, rep1

description: Library name: DAPA1_S7_R1_001.fastq.gz


title: SP53_ibru

value: 500nM ibrutinib


title: S. cerevisiae pus4∆ RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

organism: Saccharomyces cerevisiae

source_name: haploid

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: haploid

value: BY4741 pus4{delta}


title: CDR-7_EPICv2

type: genomic

city: Philadelphia

first: Yee Hoon

last: Foong

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-7
208767510001_R06C01

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Quality control preprocessing were done using Minfi package. Probes with signal lower than background in >25% of the samples were eliminated using Minfi's detectionP() function. Background and dye correction were done using Minfi's preprocessFunnorm function (funnorm + noob). Only probes that are common between EPICv1 (GPL21145) and EPICv2 are included in the downstream analyses
Minfi's getBeta() was used to extract Beta values after the quality control preprocessing steps. Only probes that are common between EPICv1 (GPL21145) and EPICv2 are included in the downstream analyses

label: Cy3 and Cy5

source_name: Sacrum/ Coccyx

label_protocol: not provided

extract_protocol: Genomic DNA was extracted using standard Phenol:Chloform extraction

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: F

value: Bisulfite treated


title: Naive (N050218-4)

description:
Library name: Sample 2
Naïve mice,


title: Islets, Akita treated with dapagliflozine, rep2

description: Library name: DAPA2_S8_R1_001.fastq.gz

value: Pancreatic islets of Langerhans

value: primary cells

value: pancreatic endocrine cells


title: S. cerevisiae pus4∆ RNA002 chemistry

description: tRNA sequencing (RNA002)


title: Islets, Akita untreated, rep3

description: Library name: AK3_S6_R1_001.fastq.gz

value: Akita (C57BL/6-Ins2Akita/J)

value: untreated mice


title: CDR-8_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-8
209148960089_R08C01

value: M


title: Islets, Akita untreated, rep2

description: Library name: AK2_S5_R1_001.fastq.gz


title: Islets, Akita untreated, rep1

description: Library name: AK1_S4_R1_001.fastq.gz


title: CDR-6_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-6
209107000016_R06C01


title: Islets, WT rep3

description: Library name: WT3_S3_R1_001.fastq.gz

value: WT


title: CDR-5_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-5
209217440149_R05C01


title: Islets, WT rep2

description: Library name: WT2_S2_R1_001.fastq.gz


title: CDR-4_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-4
209148960089_R07C01


title: Islets, WT rep1

description: Library name: WT1_S1_R1_001.fastq.gz


title: CDR-3_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-3
208767510013_R08C01


title: DT 5

description: Library name: YasminN_11_S23_R1_001.fastq.gz

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: raw_and_norm_counts.xlsx
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol,  raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Tongue

extract_protocol:
Mice were sacrificed and the tongue was excised and injected at several sites along the tongue with 0.5 mL of 4mg/ml Dispase in PBS + 2% FCS until fully distended. After incubation in PBS+ 2% FCS for 10 min at 37°C the epithelium was carefully separated using forceps and then rinsed with PBS. Epithelial tissues were then minced and treated with a Collagenase type II (2 mg/mL; Worthington Biochemicals) and DNase I (1 mg/mL; Sigma) solution in PBS plus 2% FCS for 25 min at 37 °C in a shaker bath. A total of 20 μL of 0.5 M EDTA per 2 mL sample was added to the digested tissues and incubated for an additional 10 min. The cells were washed, filtered with 70-μM filter.
mRNA kapa stranded kit done by Abed

value: Tongue

value: Epithelium

value: Diphtheria toxin injection


title: CDR-1_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-1
208767300163_R07C01


title: DT 6

description: Library name: YasminN_12_S24_R1_001.fastq.gz


title: CDR-2_EPICv2

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
CDR-2
208767510023_R08C01


title: DT 4

description: Library name: YasminN_10_S22_R1_001.fastq.gz


title: DT 3

description: Library name: YasminN_9_S21_R1_001.fastq.gz


title: ΔlasR at 37°C stationary replicate C

city: Atlanta

first: Rachel

middle: Evans

last: Robinson

state: GA

address: 1510 Clifton Road NE

department: Pediatrics

institute: Emory University

description: Library name: lasR_37_stat_C

data_processing:
Demultiplexing, quality control, and adaptor trimming using bcl-convert (v4.1.5) (this step only performed by SeqCenter)
Read mapping using bowtie2 (v2.4.5) to reference genome NC_002516.2 for P. aeruginosa PAO1
Raw read quantification using htseq-count (v2.0.2)
Differential gene expression analysis using DESeq2 (v1.38.3)
Assembly: NC_002516.2
Supplementary files format and content: Tab-delimited text file containing raw counts produced by htseq-count for all samples. Note, the first column provides the PA locus number (gene/transcript unique identifier corresponding to reference genome).

organism: Pseudomonas aeruginosa

source_name: Bacterial

growth_protocol: Bacteria were grown at 37°C or 25°C, as indicated, in LB shaking at 200 rpm. Samples were collected from the same cultures at stationary phase (OD ~2.0).

extract_protocol:
Standard TRI reagent protocol (phenol/chloroform based) for RNA extraction
Library construction was performed by SeqCenter (Pittsburgh, PA, USA) using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus depletion kit and 10 bp unique dual indices.

treatment_protocol: Cells were harvested by centrifugation and immediately used in RNA extraction protocol (below).

value: Bacterial

value: {delta}lasR

tag: temperature

tag: growth phase

value: stationary - OD ~ 2.0


title: ΔlasR at 37°C stationary replicate A

description: Library name: lasR_37_stat_A


title: DT 1

description: Library name: YasminN_7_S19_R1_001.fastq.gz


title: ΔlasR at 37°C stationary replicate B

description: Library name: lasR_37_stat_B


title: PBS 6

description: Library name: YasminN_6_S18_R1_001.fastq.gz

value: PBS injection


title: NTS3 ct

value: mantle cell lymphoma

value: cell line

value: untreated


title: ΔlasR at 25°C stationary replicate C

description: Library name: lasR_25_stat_C


title: ΔlasR at 25°C stationary replicate B

description: Library name: lasR_25_stat_B


title: PBS 5

description: Library name: YasminN_5_S17_R1_001.fastq.gz


title: PBS 4

description: Library name: YasminN_4_S16_R1_001.fastq.gz


title: PAO1 at 37°C stationary replicate C

description: Library name: WT_37_stat_C

value: Wild-type


title: PBS 3

description: Library name: YasminN_3_S15_R1_001.fastq.gz


title: ΔlasR at 25°C stationary replicate A

description: Library name: lasR_25_stat_A


title: PBS 2

description: Library name: YasminN_2_S14_R1_001.fastq.gz


title: DT 2

description: Library name: YasminN_8_S20_R1_001.fastq.gz


title: PAO1 at 25°C stationary replicate A

description: Library name: WT_25_stat_A


title: PBS 1

description: Library name: YasminN_1_S13_R1_001.fastq.gz


title: PAO1 at 37°C stationary replicate A

description: Library name: WT_37_stat_A


title: CCI

city: Chengdu

first: Cheng

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

description:
Library name: SAMPLE 2
10x Genomics

data_processing:
Then nuclei were stained with trypan blue and counted using a dual fluorescence cell counter. The suspension was then loaded onto Chromium microfluidic chips using V3 chemistry and barcoded with a 10X Chromium Controller (10X Genomics, San Francisco, USA). Microdissected tissue samples were placed in 1 mL of nuclei lysis buffer and homogenized using 10 strokes with a loose Dounce pestle followed by 10 strokes with a tight pestle. The resulting homogenate was filtered through a 30-μm cell strainer (Miltenyi Biotec, Cologne, Germany) and centrifuged at 400xg for 5 minutes to pellet the nuclei. The nuclei were resuspended in Diluted Nuclei Buffer (10X Genomics, San Francisco, USA). RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed using the Chromium Single Cell V3 reagent kit (10X Genomics, San Francisco, USA) according to the manufacturer’s instructions. Sequencing was carried out on an Illumina NovaSeq 6000 system following the manufacturer’s protocol (Illumina, San Diego, USA).
Raw reads were demultiplexed and aligned to the reference genome using the 10X Genomics Cell Ranger pipeline with default settings. Subsequent single-cell analyses were conducted primarily with Cell Ranger and Seurat, unless stated otherwise. In summary, unique molecule identifiers (UMIs) were quantified for each gene and cell barcode (filtered by Cell Ranger) to generate digital expression matrices. For further filtering in Seurat, genes expressed in more than three cells were retained, and each cell was required to have at least 200 expressed genes. Contaminating cells were removed to enrich the target cell population. Data analysis and visualization were performed using Loupe Cell Browser v3.1.0 (10X Genomics, California, USA).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: VTA

extract_protocol:
Neuropathic pain was induced by CCI of the left sciatic nerve.  The right side was used as the CCI-contralateral side: the sciatic nerve was only exposed but not ligated.  The VTA of mice were minced and then digested using the Adult Brain Dissociation Kit (Miltenyi Biotec, Shanghai, China) and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, Shanghai, China).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: VTA


title: PAO1 at 25°C stationary replicate B

description: Library name: WT_25_stat_B


title: PAO1 at 25°C stationary replicate C

description: Library name: WT_25_stat_C


title: WT_host_lys2_rep2

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

institute: HIRI

description: Library name: WT_host_lys2_rep2

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11/v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422 (Illumina)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT)
Alignment of trimmed read pairs to Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 genome using map_single_fragments.py fom the RILseq software (Melamed et al., 2018) v0.82 (https://github.com/asafpr/RILseq; see https://github.com/yairra/RILseq for latest versions) with default parameters. BWA (Li, 2013) v0.7.17 was used for read alignment with the RILseq software.
Mapping of chimeric fragments with map_chimeric_fragments.py from the RILseq software with default parameters but including a transcript file (TF) based on an ad hoc annotation of Salmonella Typhimurium strain SL1344 described in (Holmqvist et al., 2016) (parameter: -t TF)
Overrepresented interacting regions were identified using the RILseq_significant_regions.py script from the RILseq software with default parameters except for including a BioCyc data folder for Salmonella (--bc_dir), the chromosome ID mapping --BC_chrlist NC_016810.1,NC_016810,NC_017718.1,NC_017718,NC_017719.1,NC_017719,NC_017720.1,NC_017720) and parameters for excluding rRNA interactions (--ribozero --rrna_list rRNA,RRNA). The resulting significant interacting regions (S-chimeras) were reannotated using the Salmonella ad hoc annotation described above.
Assembly: GCF_000210855.2
Supplementary files format and content: Character (TAB) separated value files containing counts of statistically significant chimeras

organism:
Mus musculus
Salmonella enterica

source_name: RAW264.7 (ATCC TIB-71)

growth_protocol: Raw macrophages were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C. Salmonella were cultivated in LB or SPI-2-inducing minimal medium.

extract_protocol:
Trizol
RIL-seq library preparation was conducted using the sRNA NEBNext kit for Illumina. 3 µL of RNA were mixed with 1 µL of 3’ SR Adaptor (1:10 diluted) and incubated at 70°C for 2 min. 6.5 µL of 3’ ligation mix (5 µL of 3’ ligation buffer, 1.5 µL of 3’ enzyme mix) were added and incubated at 25°C for 1 h. 2.75 µL of SR mix (2.5 µL of water, 0.25 µL of SR RT primer) were added to reactions and incubated for three subsequential steps (75°C for 5 min, 37°C for 15 min, 25°C for 15 min). Pre-denatured 5’ adaptor (1:10 diluted) was added to each tube together with 5’ ligation mix (0.5 µL of 5’ ligation reaction buffer, 1.25 µL 5’ ligation enzyme mix) and samples were incubated at 25°C for 1 hour. For first-strand cDNA synthesis, 5 µL of cDNA mix were added (4 µL first-strand buffer, 0.5 µL murine RNase inhibitor, 0.5 µL SuperScript II RT). The reactions were incubated at 50°C for 1 h followed by 15 min at 70°C. 10 µL of cDNA were PCR-amplified with barcoded NEB index primer and SR primer in a 50 µL reaction (25 µL LongAmp Taq 2x mix, 12.5 µL nuclease-free water, 1.25 µL SR primer, 1.25 µL index primer).

treatment_protocol: Infection was carried out following the protocol of PMID: 26789254 with the indicated Salmonella Typhimurium (SL1344) strain. At 20 hours post-infection, cells were harvested and bacterial RNA subjected to RIL-seq as described in PMID: 35063132. Salmonella was cultivated in LB to an OD600 of 2.0, followed by two successive washes with Phosphate-Buffered Saline (PBS). Subsequently, the bacteria were inoculated at a ratio of 1:50 and transferred to SPI-2 medium (170mM MES, 5mM KCl, 7.5mM (NH4)2SO4, 0.5mM K2SO4, 1mM KH2PO4, 8µM MgCl2, 38mM Glycerol,  bacto casamino acid 0.1% and pH of 5.8). This cultivation was conducted at 37 °C with constant shaking at 220 rpm until the cultures attained an OD600 of 0.3.

value: RAW264.7 (ATCC TIB-71)

value: Salmonella, macrophages

tag: infection condition

value: WT Salmonella

tag: timepoint post_infection

tag: biological replicate


title: WT_host_lys2_rep1

description: Library name: WT_host_lys2_rep1

tag: cell line

tag: cell type


title: EAC056_Tumour_Tibia_ATAC

city: Cambridge

first: Elizabeth

last: Cooper

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

description: 10x Genomics Multiome

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger ARC pipeline (v8.0.1) with the mm10 mouse genome reference. FASTQ files were generated and aligned to the mm10 genome for both ATAC and gene expression data. Peaks of accessible chromatin were identified, and feature-barcode matrices for RNA and ATAC data were generated. Quality control metrics, such as fragment size distribution, TSS enrichment, and barcode counts, were assessed to filter low-quality nuclei. Gene expression and chromatin accessibility data were integrated for multimodal analysis. Processed data were exported as filtered feature matrices for downstream analysis using Seurat or other bioinformatics tools.
Assembly: mm10
Supplementary files format and content: Cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell ranger output files: *atac_peaks.bed, *atac_fragments.tsv.gz

source_name: Tibia Bone Marrow

extract_protocol:
Age-matched 6-8 week-old EPZFTA-RELA and NestinCreERT2 mice were intravenously injected with CD45-PE 3 minutes prior to schedule 1. For skulls the dura was peeled and removed with fine forceps. The skull were then cut into small pieces using sterile scissors and mechanically dissociated in FACS buffer with a pestle, followed by a filtration step through a 70-μm cell strainer. Samples were centrifuged for 5 minutes at 420 x g. For peripheral bone marrow, both tibia were flushed with 0.05% BSA PBS with 0.05% EDTA, filtered through 7- µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-CD45 APC and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM
Chromatin accessibility was captured using Tn5 transposase to tag accessible DNA regions, while nuclear RNA was reverse transcribed into cDNA with unique barcodes and UMIs. Nuclei were partitioned into GEMs using the 10x Genomics Chromium Controller for simultaneous ATAC and cDNA amplification. Libraries were constructed separately for ATAC and gene expression: ATAC fragments underwent adapter ligation and PCR amplification, while cDNA was fragmented, ligated, and amplified. Libraries were quality-checked (Bioanalyzer/Qubit) and sequenced on an Illumina platform for paired-end reads

tag: tissue

value: Tibia Bone Marrow

value: CD34 +ve FACS sorted cells

tag: genotype


title: WT

description:
Library name: SAMPLE 1
10x Genomics


title: EAC056_Tumour_Tibia_GEX

description: 10x Genomics Multiome


title: Hfq_host_lys2_rep1

description: Library name: Hfq_host_lys2_rep1

value: Hfq::3xflag Salmonella


title: EAC056_Non-Tumour_Tibia_ATAC

description: 10x Genomics Multiome


title: PAO1 at 37°C stationary replicate B

description: Library name: WT_37_stat_B


title: EAC056_Non-Tumour_Skull_GEX

description: 10x Genomics Multiome

source_name: Skull Bone Marrow

value: Skull Bone Marrow


title: Hfq_host_lys2_rep2

description: Library name: Hfq_host_lys2_rep2


title: Streptomyces coelicolor A3(2) wild type replicate 2

city: Norwich

first: Leah

last: McPhillips

address: Colney Lane

department: Molecular microbiology

institute: John Innes Centre

description: Library name: WT2

data_processing:
Raw sequencing reads were received as FASTAq files which were aligned to the reference FASTA file (S. coelicolor A3(2) reference genome, GenBank: AL645882.2, where the chromosome, SCP1 and SCP2 FASTA files were combined to form a single FASTA file) using Bowtie on the Galaxy platform to give BAM files.
Coverage was determine for each BAM file using the BEDtools genomecov tool.
Coverage analysis was performed using custom R scripts by calculating the mean sequencing coverage for the chromosome (spanning only from positions 1060620–8667507 bp to exclude the TIRs due to the TIR duplication of S. coelicolor A3(2) chromosome compared to the reference sequence, which is actually the S. coelicolor M145 chromosome), SCP1 and SCP2.
The plasmid copy number per chromosome was determined by calculating the ratio of plasmid coverage to chromosomal coverage.
Assembly: Streptomyces coelicolor A3(2) reference genome, GenBank: AL645882.2
Supplementary files format and content: WTX_coverage.csv files contain read coverage at each position of the combined S. coelicolor A3(2) reference genome FASTA file (containing the chromosome, SCP1 and SCP2)
Supplementary files format and content: WTX_mean_coverage.csv files contain the average coverage for each genetic element in S. coelicolor A3(2), which was then used to calcuate the plasmid copy number of SCP1 and SCP2 per chromosome.

organism: Streptomyces coelicolor

growth_protocol: 5 µL of S. coelicolor A3(2) wild type spores were plated onto soyaflour mannitol (SFM) agar in triplicate and incubated at 30°C for 5 days.

extract_protocol:
Spores were collected in 3 mL of dH2O. Spores were spun down at 13,000 rpm for 1 minute, supernatant was discarded and the spores were resuspended in 978 uL of Sodium Phosphate Buffer from the FastDNA Spin Kit for Soil (MP Biomedicals Germany GmbH). DNA was extracted as per the manufacturers’ protocols for the kit except homogenization in the FastPrep Instrument was performed for 40 seconds at speed setting 6, twice.
Illumina sequencing libraries were prepared using the tagmentation-based and PCR-based Illumina DNA Prep kit and custom IDT 10 bp unique dual indices (UDI) with a target insert size of 280 bp. No additional DNA fragmentation or size selection steps were performed.

value: spores

value: wild type


title: EAC056_Non-Tumour_Tibia_GEX

description: 10x Genomics Multiome


title: EAC056_Tumour_Skull_GEX

description: 10x Genomics Multiome


title: Streptomyces coelicolor A3(2) wild type replicate 1

description: Library name: WT1


title: WT_host_lys1

description: Library name: WT_host_lys1


title: EAC030_Non-Tumor_DCLN_TCR

description:
10x Genomics 5' TCR
SITTD2

data_processing:
The 10X Genomics Cell Ranger (v8.1.0) software was used to demultiplex samples and generate fastq files using the ‘fastq’ command, map and quantify the GEX data to the mouse genome (mm10-3.0.0) using the ‘count’ command, and map the VDJ sequence to a curated mouse VDJ reference (vdj_GRCm38_alts_ensembl-2.2.0) using the ‘vdj’ command.
Raw counts for the GEX and HTO data were processed using the R-based Seurat package (v 5.1.0). The first processing step included filtering out multiplets (GEMS with >1 cell), and the second processing step included normalization, principal components analysis, clustering of cells and differential gene expression with the filtered expression data. The VDJ data was processed using custom R scripts to filter out only the T-cell receptor alpha amino acid sequences (labeled as numbered CDR3). The TCR alpha sequence data was then merged with the final single cell gene expression data. The same was done for BCR.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Assembly: mm10
Supplementary files format and content: Cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell ranger output files: all_contig_annotations.csv
Library strategy: scTCR-Seq

source_name: Deep cervical lymph nodes

extract_protocol:
Age-matched 6-8 week-old EPZFTA-RELA and NestinCreERT2 mice were intravenously injected with CD45-PE 3 minutes prior to schedule 1. For skulls the dura was peeled and removed with fine forceps. Both the tibia and skull were then cut into small pieces using sterile scissors and mechanically dissociated in FACS buffer with a pestle, followed by a filtration step through a 70-μm cell strainer. Samples were centrifuged for 5 minutes at 420 x g. For peripheral bone marrow, both tibia were flushed with 0.05% BSA PBS with 0.05% EDTA, filtered through 7- µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended on 0.05% BSA PBS solution. The whole intact deep cervical lymph nodes were mashed through a 70 μm cell strainer, using a sterile syringe plunger, and washed with 5 mL of FACS buffer. Deep cervical lymph node samples were then filtered through 70 µm meshes. Samples were centrifuged for 5 minutes at 420 x g.. Brains were macrodissected based on TdTomato fluorescent signal to harvest the tumor and region-matched brain in non-tumor bearing animals. Tumor/brain samples were mechanically dissociated using sterile surgical scalpels into ∼1 mm3 cubes, and dissociated using the mouse tumor dissociation kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100 µm meshes and washed with 2% fetal bovine serum in RPMI, spun down 420 g for 5 minutes. Samples were resuspended in 40% percoll and centrifuged at 600 x g for 10 minutes. Samples were stained with DAPI (0.2 µg/ml). Samples were centrifuged, resuspended in FACS buffer with anti-CD16/32 (FC block; Biolegend) diluted 1:50 in FACS buffer and fluorescently conjugated antibodies (anti-CD45 APC and anti-Ter 119 FITC)  at 4°C, followed by for 20 minutes. Cells were sorted using the Influx Cell Sorter (BD Biosciences) or FACsAria II (BD Biosciences) into 1% BSA coated 1.5 mL Eppendorf tubes with 500 μL of DMEM.
Single-cell gene expression (GEX) and TCR/BCR libraries were constructed using the 10x Genomics Chromium platform. Cells were partitioned into Gel Bead-In-Emulsions (GEMs) with barcoded oligonucleotides for cell and molecular indexing. For GEX libraries, mRNA was reverse-transcribed, cDNA was amplified, and sequencing libraries were prepared. For TCR/BCR libraries, cDNA was enriched for V(D)J regions using target-specific primers before library preparation. Libraries were indexed, quantified, and sequenced on an Illumina platform. Paired-end sequencing enabled capture of transcriptomes and full-length V(D)J sequences, linking receptor information to gene expression profiles for each cell. Data were processed with 10x Genomics Cell Ranger pipelines.

value: Deep cervical lymph nodes

value: CD45 +ve FACS sorted cells


title: EAC056_Tumour_Skull_ATAC

description: 10x Genomics Multiome


title: EAC056_Non-Tumour_Skull_ATAC

description: 10x Genomics Multiome


title: Streptomyces coelicolor A3(2) wild type replicate 3

description: Library name: WT3


title: EAC030_Non-Tumor_DCLN_BCR

description:
10x Genomics 5' BCR
SITTF5

data_processing:
The 10X Genomics Cell Ranger (v8.1.0) software was used to demultiplex samples and generate fastq files using the ‘fastq’ command, map and quantify the GEX data to the mouse genome (mm10-3.0.0) using the ‘count’ command, and map the VDJ sequence to a curated mouse VDJ reference (vdj_GRCm38_alts_ensembl-2.2.0) using the ‘vdj’ command.
Raw counts for the GEX and HTO data were processed using the R-based Seurat package (v 5.1.0). The first processing step included filtering out multiplets (GEMS with >1 cell), and the second processing step included normalization, principal components analysis, clustering of cells and differential gene expression with the filtered expression data. The VDJ data was processed using custom R scripts to filter out only the T-cell receptor alpha amino acid sequences (labeled as numbered CDR3). The TCR alpha sequence data was then merged with the final single cell gene expression data. The same was done for BCR.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Assembly: mm10
Supplementary files format and content: Cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell ranger output files: all_contig_annotations.csv
Library strategy: scBCR-Seq


title: Hfq_host_lys1

description: Library name: Hfq_host_lys1


title: EAC030_Non-Tumor_Dura_BCR

description:
10x Genomics 5' BCR
SITTA4

source_name: Dura

value: Dura


title: EAC030_Non-Tumor_Brain_BCR

description:
10x Genomics 5' BCR
SITTB4

source_name: Brain

value: Brain


title: EAC030_Non-Tumor_Dura_TCR

description:
10x Genomics 5' TCR
SITTG2


title: EAC030_Non-Tumor_Brain_TCR

description:
10x Genomics 5' TCR
SITTH2


title: EAC030_Non-Tumor_Brain_GEX

description:
10x Genomics 5' GEX
SITTA12

data_processing:
The 10X Genomics Cell Ranger (v8.1.0) software was used to demultiplex samples and generate fastq files using the ‘fastq’ command, map and quantify the GEX data to the mouse genome (mm10-3.0.0) using the ‘count’ command, and map the VDJ sequence to a curated mouse VDJ reference (vdj_GRCm38_alts_ensembl-2.2.0) using the ‘vdj’ command.
Raw counts for the GEX and HTO data were processed using the R-based Seurat package (v 5.1.0). The first processing step included filtering out multiplets (GEMS with >1 cell), and the second processing step included normalization, principal components analysis, clustering of cells and differential gene expression with the filtered expression data. The VDJ data was processed using custom R scripts to filter out only the T-cell receptor alpha amino acid sequences (labeled as numbered CDR3). The TCR alpha sequence data was then merged with the final single cell gene expression data. The same was done for BCR.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Assembly: mm10
Supplementary files format and content: Cell ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell ranger output files: all_contig_annotations.csv


title: TX PAX_1136185_04

type: RNA

city: La Jolla

first: SUNIL

last: KURIAN

address: 10666 N Torrey Pines Rd

institute: Scripps Health

description:
TX
GSM2869692

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained in the Affymetrix Gene Titan MC.

scan_protocol: GeneChips were scanned in the Affymetrix Gene Titan MC.

data_processing: All samples were processed using the Affymetrix Gene Titan MC instrument following the standard procedure outlined in the user guide for the HT HG-U133 Plus PM Array Plate. https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2Fgenetitan_mc_user_guide.pdf

label: Biotin

source_name: Peripheral Whole Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: PAXgene extraction of total RNA was performed using the PAXgene RNA extraction kit according to the manufacturer's instructions.

tag: tag

value: Well Functioning Transplant


title: EAC030_Non-Tumor_Skull_BCR

description:
10x Genomics 5' BCR
SITTH5


title: EAC030_Non-Tumor_Skull_TCR

description:
10x Genomics 5' TCR
SITTF2


title: EAC030_Non-Tumor_Skull_GEX

description:
10x Genomics 5' GEX
SITTG11


title: EAC030_Non-Tumor_DCLN_GEX

description:
10x Genomics 5' GEX
SITTE11


title: EAC030_Non-Tumor_Tibia_TCR

description:
10x Genomics 5' TCR
SITTE2


title: EAC030_Non-Tumor_Dura_GEX

description:
10x Genomics 5' GEX
SITTH11


title: EAC030_Non-Tumor_Tibia_GEX

description:
10x Genomics 5' GEX
SITTF11


title: EAC030_Non-Tumor_Tibia_BCR

description:
10x Genomics 5' BCR
SITTG5


title: TX PAX_1134571_04

description:
TX
GSM2869689


title: TX PAX_1134586_04

description:
TX
GSM2869691


title: EAC030_Tumor_DCLN_TCR

description:
10x Genomics 5' TCR
SITTG1


title: cAR PAX_1136158_04

description:
cAR
_

value: Clinical acute rejection


title: ADNR PAX_1134560_04

description:
ADNR
_

value: Acute dysfunction no rejection


title: subAR PAX_1133645_06

description:
subAR
_

value: Subclinical acute rejection


title: TX PAX_1133779_04

description:
TX
GSM2869687


title: subAR PAX_1133109_04

description:
subAR
GSM2869686


title: cAR PAX_1134583_04

description:
cAR
_


title: subAR PAX_1134584_04

description:
subAR
GSM2869690


title: TX PAX_1131615_04

description:
TX
GSM2869685


title: ADNR PAX_1134570_04

description:
ADNR
_


title: EAC030_Tumor_Dura_TCR

description:
10x Genomics 5' TCR
SITTB2


title: EAC030_Tumor_DCLN_BCR

description:
10x Genomics 5' BCR
SITTA5


title: EAC030_Tumor_DCLN_GEX

description:
10x Genomics 5' GEX
SITTF10


title: subAR PAX_1131609_04

description:
subAR
GSM2869947


title: EAC030_Tumor_Dura_GEX

description:
10x Genomics 5' GEX
SITTC11


title: subAR PAX_1131598_04

description:
subAR
GSM2869946


title: EAC030_Tumor_Dura_BCR

description:
10x Genomics 5' BCR
SITTD5


title: subAR PAX_1133100_04

description:
subAR
GSM2869948


title: EAC030_Tumor_Brain_TCR

description:
10x Genomics 5' TCR
SITTC2


title: TX PAX_1131592_04

description:
TX
GSM2869683


title: EAC030_Tumor_Brain_BCR

description:
10x Genomics 5' BCR
SITTE5


title: EAC030_Tumor_Brain_GEX

description:
10x Genomics 5' GEX
SITTD11


title: TX PAX_1131595_04

description:
TX
GSM2869684


title: EAC030_Tumor_Skull_BCR

description:
10x Genomics 5' BCR
SITTC5


title: ADNR PAX_1134564_06

description:
ADNR
_


title: TX PAX_1129891_04

description:
TX
GSM2869682


title: EAC030_Tumor_Skull_GEX

description:
10x Genomics 5' GEX
SITTB11


title: EAC030_Tumor_Skull_TCR

description:
10x Genomics 5' TCR
SITTA2


title: EAC030_Tumor_Tibia_BCR

description:
10x Genomics 5' BCR
SITTB5


title: ADNR PAX_1129886_06

description:
ADNR
_


title: U2af1-WT 32D cells, rep2

city: Tianjin

first: Yishuang

last: Li

address: 288 Nanjing Road, Tianjin 300020, P. R. China

institute: State Key Laboratory of Experimental Hematology

data_processing:
Clean reads were mapped to mm10 using hisat2
Read count extraction were performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 32D cells were maintained in IMDM containing 10% FBS and 5ng/ml mIL-3.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (QIAGEN).
Libraries were prepared with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina.

treatment_protocol: The fragments of human wild type U2AF1 (U2AF1-WT) and mutant U2AF1 (U2AF1 S34F) were amplified via PCR and then subcloned into retroviral vector MSCV-IRES-GFP. Retrovirus containing these constructs was used to transduce 32D cells.

value: myeloblast-like cell lines

tag: library type

value: mRNA


title: TX PAX_1129703_04

description:
TX
GSM2869681


title: subAR PAX_1130242_04

description:
subAR
GSM2869945


title: EAC030_Tumor_Tibia_GEX

description:
10x Genomics 5' GEX
SITTA11


title: U2af1-WT 32D cells, rep1


title: EAC030_Tumor_Tibia_TCR

description:
10x Genomics 5' TCR
SITTH1


title: Muscle tissues,   Mck-Cre+; Igf2f/f (Igf2 cKO),cKO3-1

city: Hangzhou

first: Xihua

last: Lin

address: 3 East Qingchun Road

department: Department of Endocrinology and Metabolism

institute: Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University

data_processing:
The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool. The differential expression cut-off threshold was determined relied on |log2fold change (log2FC) | > 1 and p-value < 0.05.
Assembly: RNA was extracted, sequenced, and analyzed by a custom service provided by Novogene using an Illumina NovaSeq 6000. The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool.
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include baseMean values for each Sample

source_name: Muscle tissues

growth_protocol: All mice used in the study were bred on a C57BL/6 background. Mice were maintained under standard conditions of 22±2 °C, 50% to 60% relative humidity, and a 12-h light–dark diurnal cycle, and had free access to water and food. Animal care and experiments were conducted in accordance with the guidelines of the Animal Care Committee of Zhejiang University.

extract_protocol:
The Trizol reagent (Invitrogen) was used to isolate total RNA from the treated cells, followed by reverse transcription utilizing a reverse transcription reagents kit (TaKaRa) to produce a cDNA template.
RNA was extracted, sequenced, and analyzed by a custom service provided by Novogene using an Illumina NovaSeq 6000. The bioinformatics analysis was conducted utilizing the OmicStudio tools available at the following website: https://www.omicstudio.cn/tool.

treatment_protocol: To selectively inactivate the Igf2 gene in the muscle, CRISPR-Cas9 technology was used to insert loxP sites on flanking exons 2 of the Igf2 gene in fertilized mouse eggs to generate Igf2 foxed (Igf2f/f) mice (Cyagen Biosciences). Igf2f/f mice were crossbred with Mck-Cre mice (Strain #006475) to generate Mck-Cre+; Igf2f/+ mice. Then, Mck-Cre+; Igf2f/+ mice were crossbred with Igf2f/f mice to generate muscle-specific Igf2-defcient mice, termed as Mck-Cre+; Igf2f/f (Igf2 cKO). The Mck-Cre-; Igf2f/f littermates were used as controls (Igf2f/f; Ctrl). Genotyping for the Igf2 foxed allele, and Mck-Cre gene was performed by PCR and genome sequencing using DNA extracted from tails.

value: Muscle tissues

tag: strain background

value: Igf2 cKO

tag: treatment

value: Mck-Cre+; Igf2f/f (Igf2 cKO)


title: U2af1-WT 32D cells, rep3


title: Muscle tissues,   Mck-Cre+; Igf2f/f (Igf2 cKO),cKO2-1


title: U2af1 S34F 32D cells, rep3

value: U2af1 S34F


title: U2af1 S34F 32D cells, rep2


title: ADNR PAX_1129334_04

description:
ADNR
_


title: TX PAX_1129216_04

description:
TX
GSM2869678


title: TX PAX_1129215_04

description:
TX
GSM2869677


title: subAR PAX_1128585_05

description:
subAR
GSM2869672


title: Muscle tissues,  Control Igf2f/f , WT3-1

value: Control

value: Control Igf2f/f


title: subAR PAX_1128861_04

description:
subAR
GSM2869944


title: TX PAX_1127728_04

description:
TX
GSM2869671


title: subAR PAX_1127878_04

description:
subAR
GSM2869943


title: TX PAX_1128877_04

description:
TX
GSM2869675


title: TX PAX_1127503_04

description:
TX
GSM2869670


title: U2af1 S34F 32D cells, rep1


title: Muscle tissues,  Control Igf2f/f , WT2-1


title: TX PAX_1128865_04

description:
TX
GSM2869674


title: TX PAX_1129681_04

description:
TX
GSM2869679


title: TX PAX_1127208_04

description:
TX
GSM2869669


title: subAR PAX_1126940_04

description:
subAR
GSM2869942


title: TX PAX_1129212_04

description:
TX
GSM2869676


title: Muscle tissues,   Mck-Cre+; Igf2f/f (Igf2 cKO),cKO1-1


title: ADNR PAX_1128583_04

description:
ADNR
_


title: LIPUS3

city: Chongqing

first: Li

last: houxuan

address: Medical College Road, Yuzhong District,

institute: Chongqing Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: osteoclast

growth_protocol: Bone marrow cells were obtained from the tibias and femurs of 7-week-old WT and db/db mice, followed by overnight culture in α-MEM medium supplemented with 10% fetal bovine serum.   The bone marrow cells that did not adhere to the culture were subsequently incubated with 50ng/ml M-CSF for a duration of 3 days in order to generate bone marrow-derived macrophages (BMM).   To generate osteoclast, complete medium containing 100ng/mL receptor activator forRANKL and 50ng/mL M-CSF was used with 10ng/mL TNF-α.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The cells were further treated with LIPUS or left untreated.

value: osteoclast

value: db/db

value: LIPUS stimulation


title: Muscle tissues,  Control Igf2f/f , WT1-1


title: ADNR PAX_1126318_04

description:
ADNR
_


title: subAR PAX_1126487_04

description:
subAR
GSM2869941


title: CN3

value: No LIPUS stimulation


title: ADNR PAX_1126325_04

description:
ADNR
_


title: CN2


title: CN1


title: subAR PAX_1125904_04

description:
subAR
GSM2869668


title: LIPUS2


title: ADNR PAX_1126921_04

description:
ADNR
_


title: LIPUS1


title: MIN6, re+AA+Rap 3h, Input

city: New Brunswick

first: Jialin

last: Fan

state: NJ

address: 195 Little Albany St, Room 3527

institute: The Cancer Institute of New Jersey (CINJ)

data_processing:
Samples were quantified with Qubit 2.0, and the insertion size of the library is detected with NGS3K.
Sequencing was performed according to the concentration and the demand of data amount on Illumina NovaSeq platform. Raw reads from PDX1 ChIP-seq were trimmed to remove low quality bases and potential adapter sequences.
Next, the clean reads after trimming were mapped to the Mus musculus reference genome (GRCm38.p6) using BWA (0.7.12) considering the small fragment size of ChIP-seq, and duplicates were removed using SAMBLASTER.
MACS2 (2.1.0)  was used for PDX1 peak calling and then peaks were annotated by HOMER for their locations relative to nearby genes. Peak visualization was performed using IGV software.
Assembly: GRCm38.p6

growth_protocol: DMEM, 15%FBS, 2mM Glutamine, cells were cultured at 37 degree at 5% CO2

extract_protocol:
standard ChIP protocol using CST kit
Immunoprecipitated and purified DNA was prepared as a standard Illumina library using NEBNext® Ultra™ II DNA Library Prep Kit according to the manufacturer’s protocol by Novogene

treatment_protocol: ctrl, no AA for 16h, readd AA for 3h, readd AA and Rap for 3h

value: pancreatic beta cell

tag: chip antibody

value: readd AA and Rap 3h


title: MIN6, -AA 16h, Input

value: no AA 16h


title: MIN6, re+AA 3h, Input

value: readd AA 3h


title: subAR PAX_1125795_04

description:
subAR
GSM2869667

value: Subclinical acute rejection


title: MIN6, ctrl, Input

value: ctrl


title: MIN6, re+AA+Rap 3h, rep1, ChIP

value: Rabbit polyclonal antibody anti-Pdx1, made in Genescript


title: MIN6, re+AA+Rap 3h, rep2, ChIP


title: MIN6, re+AA 3h, rep3, ChIP


title: MIN6, re+AA 3h, rep2, ChIP


title: MIN6, re+AA 3h, rep1, ChIP


title: subAR PAX_1124979_06

description:
subAR
GSM2869940


title: TX PAX_1125792_04

description:
TX
GSM2869666

value: Well Functioning Transplant


title: TX PAX_1124364_04

description:
TX
GSM2869661


title: TX PAX_1124720_04

description:
TX
GSM2869662


title: MIN6, -AA 16h, rep2, ChIP


title: MIN6, -AA 16h, rep3, ChIP


title: TX PAX_1124759_04

description:
TX
GSM2869663


title: MIN6, -AA 16h, rep1, ChIP


title: ADNR PAX_1125899_05

description:
ADNR
_

value: Acute dysfunction no rejection


title: TX PAX_1124951_06

description:
TX
GSM2869939


title: ADNR PAX_1125365_04

description:
ADNR
_


title: cAR PAX_1124952_06

description:
cAR
_

value: Clinical acute rejection


title: MIN6, re+AA+Rap 3h, rep3, ChIP


title: MIN6, ctrl, rep3, ChIP


title: subAR PAX_1124371_04

description:
subAR
GSM2869937


title: MIN6, ctrl, rep2, ChIP


title: MIN6, ctrl, rep1, ChIP


title: subAR PAX_1124267_04

description:
subAR
GSM2869936


title: subAR PAX_1124254_05

description:
subAR
GSM2869935


title: subAR PAX_1124251_04

description:
subAR
GSM2869934


title: TX PAX_1124253_04

description:
TX
GSM2869660


title: TX PAX_1124245_04

description:
TX
GSM2869658


title: TX PAX_1124246_04

description:
TX
GSM2869659


title: TX PAX_1124085_04

description:
TX
GSM2869656


title: cAR PAX_1123830_06

description:
cAR
_


title: Macrophage, H3K4me3, infected, biol rep 1

city: Houston

first: Brandon

middle: T

last: Tran

email: Brandon.Tran@bcm.edu, brttran@gmail.com

state: Texas

address: 1 Moursund St

institute: Baylor College of Medicine

description:
Macrophage_H3K4me3_infected_1
Macrophage_Diffbind_H3K4me3.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K4me3_GREAT_UP.tsv
Macrophage_H3K4me3_GREAT_DOWN.tsv
Macrophage_H3K4me3_infected_peaks.broadPeak
Macrophage_H3K4me3_infected_1vsIgG_peaks.xls

data_processing:
FASTQ files were preprocessed using HTS stream
File alignment (BWA, samtools
Peakcalling done using MACS v2.2 in python, cut-off FDR < 0.01
Differential analysis using bioconductor package Diffbind in R, with cutoff FDR < 0.05.  GRanges generated as final object from Diffbind package
Granges exported as csv files for differential analysis
Gene ontology was performed on Granges using bioconductor rGREAT and GREAT v4.04 in Rstudio. Outputs were converted to dataframes and then exported as tsv files
Assembly: mm10
Supplementary files format and content: bigWig genomic tracks, broadpeak for peakcalling, xls files of identified peaks
Supplementary files format and content: csv files of differential analysis between infected vs naïve cell states, tsv files of GO analysis of both significantly  increased and decreased gene loci
Library strategy: CUT&RUN

source_name: bone marrow

growth_protocol: Cell subpopulations (HSCs, MPP3s, GMPs, Macrophages) were isolated from whole bone marrwo from naïve or M. avium infected mice

extract_protocol:
tibias, femurs, and pelvic bones were isolated from mice and cell subpopulations (HSCs, MPP3s, GMPs, and Macrophages) were purified via FACS following cKit+ magnetic separation. Markers were for the following: HSCs (Lin-,cKit+, CD150+, CD48-), MPP3s (Lin-, cKit+, CD150-, CD48+, Flk2-, CD34+), GMPs (Lin-, ckit+, CD34+, CD16/32+), Macrophages (CD3-, B220-, NK1.1-, CD11b+, Ly6g-, Ly6c+). Cells were washed with wash buffer (50 mL  total, 20mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and a Roche Complete protein inhibitor tablet), incubated with Concanavalin A-coated magnetic beads (Bang Laboratories L200731C) for 15 minutes at room temperature. Samples slurries were then magnetically separated, washed once more, and then incubated in primary antibody at respective dilutions (1:50 dilution for all) in wash buffer added with 0.05% Digtonin (Digitonin Wash Buffer) at 4C overnight. Samples were washed with Digitonin Wash buffer three times then incubated with pAG-MNase (142.5 Digitonin Wash Buffer + pAG-MNase, Epicypher 15-1016) for 1 hour at 4C. Slurries were then magnetically separated and washed three more times and resuspended in 150 uL Digtonin Wash buffer. 1 uL of 100mM CaCl2 was added to activate enzymatic cleaving, to which samples were stored on ice in 4C for 45 minutes. After time, one equal volume of 2X Stop buffer ( 340mM NaCl, 20 mM EDTA, 4mM EGTA, 0.05 Digtonin, 0.05 mg/mL glycogen. 5ug/mL RNase A, 2pg/mL heterologus spike-in DNA) was added to end the reaction. Samples were incubated for 30 minutes at 37C to release CUT&RUN fragments and then magnetically separated. Supernatant was collected for DNA fragments, and DNA was purified through phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in molecular grade water for frozen until library preparation.
DNA libraries were prepared for sequecning per standard Illumina protocols

treatment_protocol: Mice were systemically infected or sham treated with 1-month of M. avium, at 2.0e6 colony forming units of M. avium per mouse

value: bone marrow

value: murine macrophage

value: wildtype

tag: strain

value: M. avum infection, 4 weeks

tag: chip anitbody

value: H3K4me3 (Cell Signaling Technologies, #9751)


title: Macrophage, H3K27ac, infected, biol rep 2

description:
Macrophage_H3K27ac_infected_2
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K27ac_infected_peaks.broadPeak
Macrophage_H3K27ac_infected_2vsIgG_peaks.xls

value: H3K27ac (Cell Signaling Technologies, #8173)


title: TX PAX_1123947_04

description:
TX
GSM2869654


title: Macrophage, H3K27ac, naive, biol rep 2

description:
Macrophage_H3K27ac_naive_2
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K27ac_naive_peaks.broadPeak
Macrophage_H3K27ac_naive_2vsIgG_peaks.xls

value: naïve


title: Macrophage, H3K4me3, naive, biol rep 1

description:
Macrophage_H3K4me3_naive_1
Macrophage_Diffbind_H3K4me3.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K4me3_naive_peaks.broadPeak
Macrophage_H3K4me3_naive_1vsIgG_peaks.xls


title: TX PAX_1124885_04

description:
TX
GSM2869664


title: Macrophage, IgG, naive

description:
Macrophage_igG_naive
Macrophage_Diffbind_H3K4me3.csv
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K4me3_naive_peaks.broadPeak
Macrophage_H3K27ac_naive_peaks.broadPeak

value: IgG (Jackson ImmunoResearch 315-005-003)


title: TX PAX_1123660_04

description:
TX
GSM2869653


title: Macrophage, H3K4me3, naive, biol rep 2

description:
Macrophage_H3K4me3_naive_2
Macrophage_Diffbind_H3K4me3.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K4me3_naive_peaks.broadPeak
Macrophage_H3K4me3_naive_2vsIgG_peaks.xls


title: Macrophage, H3K27ac, naive, biol rep 1

description:
Macrophage_H3K27ac_naive_1
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K27ac_naive_peaks.broadPeak
Macrophage_H3K27ac_naive_1vsIgG_peaks.xls


title: Macrophage, IgG, infected

description:
Macrophage_IgG_infected
Macrophage_Diffbind_H3K4me3.csv
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K4me3_infected_peaks.broadPeak
Macrophage_H3K27ac_infected_peaks.broadPeak


title: Macrophage, H3K4me3, infected, biol rep 2

description:
Macrophage_H3K4me3_infected_2
Macrophage_Diffbind_H3K4me3.csv
Macrophage_H3K4me3_DBA_report_0.05.csv
Macrophage_H3K4me3_GREAT_UP.tsv
Macrophage_H3K4me3_GREAT_DOWN.tsv
Macrophage_H3K4me3_infected_peaks.broadPeak
Macrophage_H3K4me3_infected_2vsIgG_peaks.xls


title: TX PAX_1123658_04

description:
TX
GSM2869652


title: TX PAX_1123655_04

description:
TX
GSM2869650


title: TX PAX_1123534_04

description:
TX
GSM2869648


title: GMP, H3K4me3, infected, biol rep 2

description:
GMP_H3K4me3_infected_2
GMP_Diffbind_H3K4me3.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K4me3_GREAT_UP.tsv
GMP_H3K4me3_GREAT_DOWN.tsv
GMP_H3K4me3_infected_peaks.broadPeak
GMP_H3K4me3_infected_2vsIgG_peaks.xls

value: murine granulocyte-monocyte progenitor


title: GMP, H3K4me3, infected, biol rep 1

description:
GMP_H3K4me3_infected_1
GMP_Diffbind_H3K4me3.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K4me3_GREAT_UP.tsv
GMP_H3K4me3_GREAT_DOWN.tsv
GMP_H3K4me3_infected_peaks.broadPeak
GMP_H3K4me3_infected_1vsIgG_peaks.xls


title: Macrophage, H3K27ac, infected, biol rep 1

description:
Macrophage_H3K27ac_infected_1
Macrophage_Diffbind_H3K27ac.csv
Macrophage_H3K27ac_DBA_report_0.05.csv
Macrophage_H3K27ac_infected_peaks.broadPeak
Macrophage_H3K27ac_infected_1vsIgG_peaks.xls


title: GMP, H3K27ac, infected, biol rep 2

description:
GMP_H3K27ac_infected_2
GMP_Diffbind_H3K27ac.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K27ac_GREAT_DOWN.tsv
GMP_H3K27ac_infected_peaks.broadPeak
GMP_H3K27ac_infected_2vsIgG_peaks.xls


title: TX PAX_1123654_04

description:
TX
GSM2869649


title: ADNR PAX_1123528_04

description:
ADNR
_


title: subAR PAX_1123765_06

description:
subAR
GSM2869933


title: GMP, IgG, naive

description:
GMP_IgG_naive
GMP_Diffbind_H3K4me3.csv
GMP_Diffbind_H3K27ac.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K4me3_naive_peaks.broadPeak
GMP_H3K27ac_naive_peaks.broadPeak


title: TX PAX_1123657_04

description:
TX
GSM2869651


title: GMP, H3K4me3, naive, biol rep 2

description:
GMP_H3K4me3_naive_2
GMP_Diffbind_H3K4me3.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K4me3_GREAT_UP.tsv
GMP_H3K4me3_GREAT_DOWN.tsv
GMP_H3K4me3_naive_peaks.broadPeak
GMP_H3K4me3_naive_2vsIgG_peaks.xls


title: GMP, H3K27ac, infected, biol rep 1

description:
GMP_H3K27ac_infected_1
GMP_Diffbind_H3K27ac.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K27ac_GREAT_DOWN.tsv
GMP_H3K27ac_infected_peaks.broadPeak
GMP_H3K27ac_infected_1vsIgG_peaks.xls


title: GMP, H3K27ac, naive, biol rep 1

description:
GMP_H3K27ac_naive_1
GMP_Diffbind_H3K27ac.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K27ac_GREAT_DOWN.tsv
GMP_H3K27ac_naive_peaks.broadPeak
GMP_H3K27ac_naive_1vsIgG_peaks.xls


title: GMP, IgG, infected

description:
GMP_IgG_infected
GMP_Diffbind_H3K4me3.csv
GMP_Diffbind_H3K27ac.csv
GMP_H3K4me3_DBA_report_0.05.csv
GMP_H3K27ac_DBA_report_0.05.csv
GMP_H3K4me3_infected_peaks.broadPeak
GMP_H3K27ac_infected_peaks.broadPeak


title: cAR PAX_1123264_04

description:
cAR
_


title: TX PAX_1123263_04

description:
TX
GSM2869646


title: subAR PAX_1123271_04_2

description:
subAR
GSM2869932


title: TX PAX_1123022_05

description:
TX
GSM2869644


title: TX PAX_1122532_04

description:
TX
GSM2869643


title: MPP3, H3K4me3, infected, biol rep 2

description:
MPP3_H3K4me3_infected_2
MPP3_Diffbind_H3K4me3.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K4me3_GREAT_UP.tsv
MPP3_H3K4me3_infected_peaks.broadPeak
MPP3_H3K4me3_infected_2vsIgG_peaks.xls

value: murine multipotent progenitor 3


title: MPP3, IgG, infected

description:
MPP3_IgG_infected
MPP3_Diffbind_H3K4me3.csv
MPP_Diffbind_H3K27ac.csv
MPP3_H3K4me3_DBA_report_0.05.csv
MPP3_H3K27ac_DBA_report_0.05.csv
MPP3_H3K4me3_infected_peaks.broadPeak
MPP3_H3K27ac_infected_peaks.broadPeak


title: TX PAX_1122219_04

description:
TX
GSM2869642


title: cAR PAX_1123261_04

description:
cAR
_