title: H3K27me3_kaku4_6wk

data_processing:
All clean ChIP-seq reads were mapped to the Arabidopsis genome TAIR10 using BOWTIE2 software with default parameters. The MACS program was used to shift the reads to identify peaks.
Assembly: Arabidopsis reference genome (TAIR10)
Supplementary files format and content: wig files

source_name: 6-week-old leaves

extract_protocol:
A native chromatin immunoprecipitation (ChIP) was performed using antibody of histone modification essentially as described with minor modification (Nagaki et al. 2003).
ChIP-seq libraries were constructed by Shanghai Jiayin Biotechnology Co., Ltd and sequenced using the Illumina system Novaseq 6000 with a 150-bp read length.

value: 6-week-old leaves

tag: chip antibody


title: LP, chill,  100h,  rep2

status: Public on Feb 09 2024

type: SRA

city: Kearneysville

first: Jianyang

last: Liu

state: WV

address: 2217 Wiltshire Road

country: USA

institute: USDA-ARS

library_source: transcriptomic

data_processing:
Illumina paired-end bisulfite sequences were evaluated for quality using FastQC (version 0.11.9)
Trim reads with Trimmomatic to remove adapter sequence or poor quality sequence from raw reads
FASTQ files were aligned to Prunus persica NCBIv2 genome (Cheng et al. 2017) using the STAR (v2.6.0) software
Mapped read counts were transformed to Counts per Million (CPM) using the Bioconductor package edgeR (Robinson et al., 2010
Differentially expressed genes (DEGs) were identified on genes with false discovery rate (FDR) < 0.05 and log fold-changes (logFC) > 1.5 between LFP and JB at each time point.

molecule: total RNA

organism: Prunus persica

source_name: Floral bud

growth_protocol: Peach cuttings (shoots with floral buds attached) were kept with the base submersed in water, which was changed periodically.

extract_protocol:
RNA was extract from the floral buds using a RNA Isolation Kit (Norgen BiotecK Corp, Ontario, Canada)
Truseq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Peach cuttings were kept in chilling condition (4℃) for 1000 h, and then moved to warm condition (22℃) for 20 d for JB and 28 for LFP until they started to bloom.

tag: tissue

value: Floral bud

tag: genotype

tag: treatment

value: Chilling (4 C)


title: Ribo_Proargdrop_DFMO_5825

city: Zurich

first: Sarah

last: Cherkaoui

address: August-Forel-Strasse 51

department: Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: Ribosome Profiling

data_processing:
Fastq files were adaptor stripped using cutadapt with a minimum length of 15 and a quality cutoff of 2 (parameters: -a CTGTAGGCACCATCAAT –minimum-length = 15 –quality-cutoff = 2).
Resulting reads were mapped, using default parameters, with HISAT2 (PMID: 25751142), using a GRCm38, release 101 genome and index. Ribosome profiling: reads were removed if they mapped to rRNA or tRNA according to GRCm38 RepeatMasker definitions from UCSC. A full set of transcript and CDS sequences for Ensembl release 101 was then established. Only canonical transcripts [defined by knownCanonical table, downloaded from UCSC] were retained with their corresponding CDS. Reads were then mapped to the canonical transcriptome with bowtie2 using default parameters.
Assembly: GRCm38, release 101

organism: Mus musculus

source_name: Tumor tissue

extract_protocol:
Mouse tumors were mechanically disrupted in liquid nitrogen and homogenized in a lysis buffer (LB, 50 mM Tris, pH 7.4, 100 mM KCl, 1.5 mM MgCl2, 1.0% Triton X-100, 0.5% Na-Deoxycholate, 25 U/ml Turbo DNase I, 1mM DTT, 100 µg/ml cycloheximide, and Protease inhibitors) 3 ml of LB per 1 g of tissue. Ribosome profiling: Mouse tumors were mechanically disrupted in liquid nitrogen and homogenized in a lysis buffer (LB, 50 mM Tris, pH 7.4, 100 mM KCl, 1.5 mM MgCl2, 1.0% Triton X-100, 0.5% Na-Deoxycholate, 25 U/ml Turbo DNase I, 1mM DTT, 100 µg/ml cycloheximide, and Protease inhibitors) 3 ml of LB per 1 g of tissue. To obtain ribosome footprints 0.12 ml of total extracts containing 300 µg of total RNA were treated with RNAse I (Epicentre) (25U/1 mg of total RNA), for 45 min at 20ºC with slow agitation. 10 ml SUPERaseIn RNase inhibitor was added to stop nuclease digestion. Monosomes were isolated using S-400 columns. For isolation of mRNA protected fragments (RPF) 3 volumes of QIAzol® were added to the S-400 eluate, mixed thoroughly and proceed to RNA purification with Direct-Zol RNA Mini Prep Plus kit. RNA-seq: Total RNA were isolated from the same extracts, that were used to obtain RPF (bellow, RiboSeq). 3 volumes of QIAzol® (Qiagen, Cat. No. 79306) were added to 80 µl of cell extracts, mixed thoroughly and proceed to RNA purification with Direct-Zol RNA Mini Prep Plus kit.
Ribosome Profiling: RPF libraries were prepared as described (PMID: 28579404, PMID: 19213877). Briefly, RPFs (25-34 nt) were size-selected by electrophoresis using a 15% TBE-Urea polyacrylamide gel electrophoresis (PAGE) and two RNA markers, 25-mer (5’ AUGUACACGGAGUCGAGCACCCGCA 3’) and 34-mer (5’AUGUACACGGAGUCGAGCACCCGCAACGCGAAUG 3’). After dephosphorylation with T4 Polynucleotide Kinase (NEB, #M0201S) the adapter Linker-1 (5' rAppCTGTAGGCACCATCAAT/3ddC/ 3') was ligated to the 3′ end of the RPF using T4 RNA Ligase 2. Ligated products were purified using 10% TBE-Urea PAGE. Ribosomal RNA was subtracted using RiboCop rRNA Depletion Kit V2 H/M/R. The adapter Linker-1 was used for priming reverse transcription (RT) with the RT primer Ni-Ni-9 (5’AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC5CACTCA5TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG 3’) using ProtoScript® II Reverse Transcriptase. RT products were purified using 10% TBE-Urea PAGE. The cDNA was circularized with CircLigase™ II ssDNA Ligase. The final libraries were generated by PCR using forward index primer NI-N-2 (5’ AATGATACGGCGACCACCGAGATCTACAC 3’) and one of the reverse index primers. Amplified libraries were purified using 8% TBE-PAGE and analyzed by Qubit and TapeStation. RNAseq: RNA were sent to Genomic Platform (UNIGE) for stranded mRNA libraries preparation. Libraries were sequenced on an Illumina NovaSeq 6000, SR 100 bp, 10 libraries in 1 pool.

treatment_protocol: Pharmalogical (treament with/wihtout difluoromethylornithine DFMO) and dietary intervention (with/without proline and arginine in the diet)

value: Tumor tissue

tag: cell line

value: neuroblastoma cancer cells

tag: cell type

value: Neuroblast

value: MYCN Amplified

value: Proline Arginine Dropout Diet with DFMO Treatment(ProArg DFMO)


title: SIC_32_Colon_128_TST_Nuclei_5p_GEX

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

library_source: transcriptomic single cell

data_processing:
We used Cell Ranger v3.1.0 for generating gene count matrices from sequencing reads (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). We used R scripts to analyze the count matrices.
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 files, anndata h5ad files, HTML files, CSV files

organism: Homo sapiens

source_name: Colon mucosal biopsy

extract_protocol:
Please see the methods in the associated publication.
Please see the methods in the associated publication.

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: channel

tag: pcr primer

tag: chemistry


title: Ribo_Proargdrop_DFMO_5805

description: Ribosome Profiling


title: LP, chill,  100h,  rep1


title: LP, chill,  0h,  rep3


title: AAV_SYN_rMBD3_GFP_24h_Mg_(2) [KSZ_F83_0054]

city: Warsaw

first: Kinga

last: Szydlowska

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
Adapter and quality trimming (Trim Galore!)
Mapping of reads to a reference genome (STAR-Salmon)
Sort and index alignments (SAMtools)
Counting reads mapped to genomic genes (FeatureCounts)
Differential analysis of gene expression (DeSeq2, R, pvalue<0.05)
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: coma-separated value text file includes FPKM log2+1 read counts for all Samples (result from DeSeq2)

organism: Rattus norvegicus

source_name: cortex

extract_protocol:
RNA isolation from cell culture: To isolate RNA from the cell culture, the plate was washed twice with sterile, cold PBS buffer. After the buffer was drawn off, 400 µl of Qiazole (#79306, Qiagen) was added to the well of a plate, and incubated 5 minutes at room temperature with shaking. Next, the homogenate was pipetted several times and transferred to new tubes. Eighty µl of chloroform (#C0549-1PT, Sigma) was added to the homogenate. The samples were vortexed and incubated 10-15 minutes at room temperature until phase separation. The upper phase was used for further RNA isolation, which was performed according to the protocol of the RNA isolation kit: RNeasy Mini Kit (#74104, Qiagen). The RNA was measured on a Nanodrop Spectrophotometer (DS-11 Spectrophotometer, DeNovix) at λ= 260 nm and 280 nm. The isolated RNA was stored at -80°C.
RNA-seq libraries were prepared by KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Kapa Biosystems, MA, USA) as previously described (Grabowska et al., 2022). Transcriptomic data analysis was done as follows: FASTQ files were aligned to rn6 rat reference genome with STAR program (Dobin et al., 2013), reads were counted to genes using feature Counts algorithm (Liao et al., 2014). Gene counts were normalized with FPKM method and differential analysis was performed by DESeq2 (Love et al., 2014). Genes were considered to be differentially expressed (DE) with adjusted p value < 0.05(Yu et al., 2012).  In order to examine gene expression patterns, cluster analysis was performed in cultures after transfection with the respective viral constructs, in R software using the Mfuzz Clustering package.

tag: development stage

value: cortex

value: neurons

tag: condition

value: Standard

value: medium with Mg

tag: treatment 2

tag: cell culture

value: biol rep 2

tag: time point_[h]


title: SIC_196_Colon_612_TST_Nuclei_5p_GEX

tag: tissue

value: Control - Healthy


title: AAV_SYN_GFP_24h_Mg_(2) [KSZ_F83_0053]


title: LP, chill,  0h,  rep2

tag: genotype


title: Ctrl_24h_Mg_(2) [KSZ_F83_0052]

tag: treatment

value: non transfected


title: Ribo_Proargdrop_DFMO_5736

description: Ribosome Profiling

tag: cell line


title: Ribo_Proargdrop_DFMO_5732

description: Ribosome Profiling

tag: cell type


title: RNA_Proargdrop_DFMO_5732

description: RNA Sequencing


title: JB, warm,  20d,  rep3

value: John Boy

value: Warm (22 C)


title: SIC_188_Colon_585_TST_Nuclei_5p_GEX

tag: patient id


title: LP, chill,  0h,  rep1

value: Floral bud

value: Chilling (4 C)


title: H3K27me3_WT_6wk

city: Beijing

first: Zhen

last: Su

address: #2 Yuanmingyuan Xilu

department: College of Biological Sciences

country: China

institute: China Agricultural University

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

value: 6-week-old leaves

value: col

tag: chip antibody


title: Ribo_CD_DFMO_135

description: Ribosome Profiling

value: Tumor tissue

value: neuroblastoma cancer cells

value: Neuroblast

value: MYCN Amplified

value: DFMO Treatment (CD DFMO)


title: SIC_187_Colon_584_TST_Nuclei_5p_GEX

value: Colon mucosal biopsy

tag: simplified patient_id

tag: disease state


title: Ribo_CD_DFMO_5823

description: Ribosome Profiling


title: Ctrl_24h_(2) [KSZ_F83_0049]

value: cortex

value: neurons

value: Epileptic

value: medium without Mg


title: JB, warm,  20d,  rep1


title: SIC_186_Colon_584_TST_Nuclei_5p_GEX

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

tag: channel


title: JB, warm,  20d,  rep2

value: John Boy


title: Ribo_CD_DFMO_5806

description: Ribosome Profiling


title: JB, warm,  16d,  rep3

value: Warm (22 C)


title: SIC_31_Colon_128_TST_Nuclei_5p_GEX

value: Control - On ICI Therapy

tag: pcr primer

tag: chemistry


title: AAV_SYN_rMBD3_GFP_24h_Mg_(1) [KSZ_F83_0048]

tag: development stage

tag: condition

value: Standard

value: medium with Mg

value: biol rep 1


title: SIC_172_Colon_529_TST_Nuclei_5p_GEX


title: Ribo_Proargdrop_DFMO_5746

description: Ribosome Profiling

value: Tumor tissue

value: Proline Arginine Dropout Diet with DFMO Treatment(ProArg DFMO)


title: SIC_141_Colon_438_TST_Nuclei_5p_GEX

value: irColitis Case

value: Prednisone 3mg


title: Ribo_CD_DFMO_5802

description: Ribosome Profiling

value: neuroblastoma cancer cells

value: Neuroblast

value: MYCN Amplified

value: DFMO Treatment (CD DFMO)


title: AAV_SYN_GFP_24h_Mg_(1) [KSZ_F83_0047]

value: cortex

value: neurons

tag: treatment 2

tag: cell culture


title: JB, warm,  16d,  rep2

tag: tissue

value: Floral bud


title: SIC_140_Colon_441_TST_Nuclei_5p_GEX

value: Colon mucosal biopsy


title: Ctrl_24h_Mg_(1) [KSZ_F83_0046]

value: non transfected

tag: time point_[h]


title: Ribo_CD_DFMO_5747

description: Ribosome Profiling

tag: genotype

tag: treatment


title: AAV_SYN_rMBD3_GFP_24h_(2) [KSZ_F83_0051]

tag: cell type

value: Epileptic

value: medium without Mg

value: biol rep 2


title: AAV_SYN_GFP_24h_(2) [KSZ_F83_0050]


title: SIC_140_Colon_441_CST_Nuclei_5p_GEX

tag: patient id


title: Ribo_Proargdrop_5828

description: Ribosome Profiling

tag: cell line

value: Proline Arginine Dropout Diet (ProArg)


title: JB, warm,  12d,  rep3

value: John Boy

value: Warm (22 C)


title: AAV_SYN_GFP_24h_(1) [KSZ_F83_0044]

value: biol rep 1


title: AAV_SYN_rMBD3_GFP_24h_(1) [KSZ_F83_0045]


title: Ribo_Proargdrop_5785

description: Ribosome Profiling

value: Tumor tissue


title: SIC_13_Colon_78_TST_Nuclei_5p_GEX_A

tag: simplified patient_id

value: Control - Healthy


title: JB, warm,  12d,  rep2


title: Ribo_Proargdrop_5784

description: Ribosome Profiling

value: neuroblastoma cancer cells

value: Neuroblast


title: SIC_134_Colon_417_TST_Nuclei_5p_GEX

tag: disease state

value: irColitis Case


title: AAV_SYN_rMBD3_GFP_6h_Mg_(1) [KSZ_F83_0042]

value: cortex

value: Standard

value: medium with Mg


title: Ctrl_24h_(1) [KSZ_F83_0043]

value: neurons


title: JB, warm,  12d,  rep1

value: Floral bud


title: Ribo_Proargdrop_5705

description: Ribosome Profiling

value: MYCN Amplified


title: JB, warm,  8d,  rep3


title: AAV_SYN_GFP_6h_Mg_(1) [KSZ_F83_0041]


title: SIC_132_Colon_410_TST_Nuclei_5p_GEX

value: Colon mucosal biopsy

value: Control - On ICI Therapy

tag: steroids at_the_time_of_biopsy


title: SIC_126_Colon_398_TST_Nuclei_5p_GEX

tag: channel


title: Ctrl_6h_Mg_(1) [KSZ_F83_0040]

value: non transfected


title: JB, warm,  8d,  rep2

value: John Boy


title: SIC_121_Colon_382_TST_Nuclei_5p_GEX

tag: pcr primer


title: AAV_SYN_rMBD3_GFP_6h_(1) [KSZ_F83_0039]

value: Epileptic

value: medium without Mg


title: JB, warm,  16d,  rep1

value: Warm (22 C)


title: Ribo_CD_5840

description: Ribosome Profiling

value: Tumor tissue

value: Control Diet (CD)


title: SIC_13_Colon_78_TST_Nuclei_5p_GEX_B

value: Control - Healthy

tag: chemistry


title: JB, warm,  4d,  rep3


title: SIC_109_Colon_368_TST_Nuclei_5p_GEX


title: Ribo_CD_5812

description: Ribosome Profiling

value: neuroblastoma cancer cells

value: Neuroblast


title: AAV_SYN_GFP_6h_(1) [KSZ_F83_0038]

tag: development stage

value: cortex

value: biol rep 1


title: SIC_109_Colon_368_CST_Nuclei_5p_GEX


title: Ribo_CD_5781

description: Ribosome Profiling


title: Ribo_CD_5778

description: Ribosome Profiling


title: JB, warm,  4d,  rep2


title: SIC_100_Colon_332_TST_Nuclei_5p_GEX_B

value: irColitis Case


title: JB, warm,  4d,  rep1

value: Floral bud


title: Ctrl_6h_(1) [KSZ_F83_0037]

value: neurons

tag: condition


title: SIC_100_Colon_332_TST_Nuclei_5p_GEX_A

value: Colon mucosal biopsy


title: AAV_SYN_GFP_2h_Mg_(1) [KSZ_F83_0035]

value: Standard

value: medium with Mg

tag: treatment 2


title: AAV_SYN_rMBD3_GFP_2h_Mg_(1) [KSZ_F83_0036]

tag: cell culture


title: Ribo_Proargdrop_5702

description: Ribosome Profiling

tag: tissue

value: MYCN Amplified

value: Proline Arginine Dropout Diet (ProArg)


title: Ribo_CD_5696

description: Ribosome Profiling

value: Neuroblastoma Cancer Cells


title: G3

city: Stanford

first: Edward

middle: N.

last: Wilson

state: CA

address: 1201 Welch Road MSLS P254

department: Neurology

institute: Stanford University

description:
G3
AD_diffexpr-results.csv

data_processing:
Raw data (raw reads) in FASTQ format were processed through fastp.
Paired-end clean reads were mapped to the reference genome using hisat2 version 2.0.5.
FeatureCounts (v1.5.0-p3) was used to count read numbers mapped for each gene.
Differential expression analysis between two conditions/groups was performed using DESeq2 (v1.20.0) using default settings
Assembly: GRCm38
Supplementary files format and content: .csv matrix file included

source_name: Primary brain microglia

extract_protocol:
RNA extracted using Rneasy mini plus kit (Qiagen).
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Primary brain microglia

value: Microglia

tag: age

value: ADULT


title: JB, warm,  8d,  rep1

tag: genotype

value: John Boy

value: Warm (22 C)


title: G2

description:
G2
AD_diffexpr-results.csv


title: SIC_100_Colon_332_TST_Nuclei_5p_GEX


title: MC_9_Colon_661_TST_Nuclei_5p_GEX

value: Control - Healthy


title: Ctrl_2h_Mg_(1) [KSZ_F83_0034]

value: cortex

tag: treatment

value: non transfected

tag: time point_[h]


title: AAV_SYN_rMBD3_GFP_2h_(1) [KSZ_F83_0033]

tag: cell type

value: Epileptic

value: medium without Mg

value: biol rep 1


title: JB, warm,  1d,  rep1

value: Floral bud


title: G1

description:
G1
AD_diffexpr-results.csv


title: JB, warm,  1d,  rep2


title: JB, chill,  1000h,  rep3

value: Chilling (4 C)


title: MC_2_Colon_576_TST_Nuclei_5p_GEX

value: Colon mucosal biopsy

tag: patient id


title: MC_1_Colon_555_TST_Nuclei_5p_GEX

tag: simplified patient_id


title: F3

description:
F3
AD_diffexpr-results.csv


title: Ctrl_2h_(1) [KSZ_F83_0031]

value: neurons


title: AAV_SYN_GFP_2h_(1) [KSZ_F83_0032]


title: SIC_140_Colon_441_TST_Nuclei_3p_V3_GEX

tag: disease state

value: irColitis Case


title: F1

description:
F1
AD_diffexpr-results.csv


title: JB, chill,  1000h,  rep2


title: JB, chill,  800h,  rep3


title: JB, warm,  1d,  rep3


title: SIC_140_Colon_441_CST_Nuclei_3p_V3_GEX

tag: steroids at_the_time_of_biopsy


title: E3

description:
E3
AD_diffexpr-results.csv

value: Wild Type


title: SIC_97_Colon_318_CD45pos_5p_TCR

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)


title: AAV_SYN_GFP_24h_Mg_(3) [KSZ_F83_0029]

tag: development stage

tag: condition

value: Standard

value: medium with Mg

tag: treatment 2

tag: cell culture

value: biol rep 3


title: E2

description:
E2
AD_diffexpr-results.csv

tag: tissue

value: Primary brain microglia

value: Microglia

tag: genotype

tag: age

value: ADULT


title: Ctrl_24h_Mg_(3) [KSZ_F83_0028]

value: cortex

tag: cell type

tag: treatment

value: non transfected

tag: time point_[h]


title: JB, chill,  800h,  rep1

value: Floral bud

value: John Boy

value: Chilling (4 C)


title: SIC_97_Colon_318_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: pcr primer

tag: chemistry


title: AAV_SYN_rMBD3_GFP_24h_(3) [KSZ_F83_0027]

value: neurons

value: Epileptic

value: medium without Mg


title: JB, chill,  600h,  rep3


title: AAV_SYN_GFP_24h_(3) [KSZ_F83_0026]


title: D3

description:
D3
Aging_diffexpr-results.csv

value: Aged


title: E1

description:
E1
AD_diffexpr-results.csv

value: Wild Type


title: JB, chill,  600h,  rep2


title: SIC_94_Colon_340_CD45pos_5p_BCR

value: Control - On ICI Therapy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)


title: SIC_94_Colon_340_CD45pos_5p_TCR

tag: tissue


title: JB, chill,  600h,  rep1

tag: genotype


title: SIC_89_Colon_310_CD45pos_5p_TCR

value: Prednisone 2.5mg


title: AAV_SYN_rMBD3_GFP_6h_Mg_(3) [KSZ_F83_0024]

tag: development stage

value: cortex

tag: cell type

tag: condition

value: Standard

value: medium with Mg

tag: treatment 2

tag: cell culture

value: biol rep 3


title: D2

description:
D2
Aging_diffexpr-results.csv

value: Primary brain microglia

value: Microglia

tag: age


title: F2

description:
F2
AD_diffexpr-results.csv

value: ADULT


title: SIC_89_Colon_310_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy


title: JB, chill,  1000h,  rep1

value: Floral bud

value: John Boy

tag: treatment

value: Chilling (4 C)


title: D1

description:
D1
Aging_diffexpr-results.csv

value: Aged


title: JB, chill,  400h,  rep3


title: AAV_SYN_rMBD3_GFP_24h_Mg_(3) [KSZ_F83_0030]

value: neurons

tag: time point_[h]


title: JB, chill,  800h,  rep2


title: Ctrl_6h_Mg_(3) [KSZ_F83_0022]

value: non transfected


title: C3

description:
C3
Aging_diffexpr-results.csv

value: Wild Type


title: SIC_76_Colon_273_CD45pos_5p_BCR

value: irColitis Case - B Cell-Depleted Patient

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)

tag: chemistry


title: JB, chill,  400h,  rep2

tag: tissue

tag: genotype


title: SIC_76_Colon_273_CD45pos_5p_TCR

tag: dead cell_depletion_method

tag: cd45 positive_selection


title: AAV_SYN_rMBD3_GFP_6h_(3) [KSZ_F83_0021]

tag: development stage

value: cortex

tag: cell type

tag: condition

value: Epileptic

value: medium without Mg

tag: treatment 2

tag: cell culture

value: biol rep 3


title: JB, chill,  400h,  rep1

value: Floral bud

tag: treatment


title: C1

description:
C1
Aging_diffexpr-results.csv

value: Primary brain microglia

value: Microglia

tag: age


title: SIC_71_Colon_241_CD45sort_5p_TCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Frozen

value: CD235 negative FACS sorting

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: JB, chill,  200h,  rep3

value: John Boy

value: Chilling (4 C)


title: AAV_SYN_GFP_6h_(3) [KSZ_F83_0020]

value: neurons

tag: time point_[h]


title: Ctrl_24h_(3) [KSZ_F83_0025]

tag: tissue

value: non transfected


title: SIC_71_Colon_241_CD45pos_5p_BCR

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

tag: rbc depletion_methods

tag: chemistry


title: B3

description:
B3
Aging_diffexpr-results.csv

tag: cell type

tag: genotype

value: Young


title: JB, chill,  200h,  rep2


title: Ctrl_6h_(3) [KSZ_F83_0019]

tag: development stage

value: cortex

tag: condition

value: Epileptic

value: medium without Mg

tag: treatment 2

tag: cell culture


title: B2

description:
B2
Aging_diffexpr-results.csv

value: Primary brain microglia

tag: age


title: AAV_SYN_GFP_6h_Mg_(3) [KSZ_F83_0023]

value: Standard

tag: treatment

value: medium with Mg

value: biol rep 3


title: SIC_40_Colon_282_CD45pos_5p_TCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case - Follow Up Colitis Resolution Biopsy

tag: steroids at_the_time_of_biopsy

value: Budesonide 6mg

value: Follow Up

value: Fresh

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)


title: JB, chill,  100h,  rep3

tag: tissue

value: Floral bud

value: John Boy

value: Chilling (4 C)


title: JB, chill,  200h,  rep1


title: B1

description:
B1
Aging_diffexpr-results.csv

value: Microglia

value: Young


title: SIC_40_Colon_282_CD45pos_5p_BCR

tag: initial vs_follow_up_sample

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

tag: rbc depletion_methods


title: AAV_SYN_GFP_2h_Mg_(3) [KSZ_F83_0017]

tag: development stage

value: cortex

tag: cell type

value: neurons

tag: condition

tag: time point_[h]


title: SIC_32_Colon_178_CAP_unselect_5p_TCR

value: irColitis Case - Follow Up Steroid Resistant Biopsy

value: Follow up

value: Frozen

tag: chemistry


title: A3

description:
A3
Aging_diffexpr-results.csv

value: Primary brain microglia

tag: genotype

value: Wild Type

tag: age


title: C2

description:
C2
Aging_diffexpr-results.csv

value: Aged


title: A2

description:
A2
Aging_diffexpr-results.csv


title: SIC_32_Colon_178_CAP_unselect_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: Budesonide 6mg


title: JB, chill,  100h,  rep1

tag: treatment


title: A1

description:
A1
Aging_diffexpr-results.csv

tag: tissue


title: AAV_SYN_rMBD3_GFP_2h_(3) [KSZ_F83_0015]

value: Epileptic

value: medium without Mg

tag: treatment 2

tag: cell culture

value: biol rep 3


title: JB, chill,  0h,  rep3

value: Floral bud

value: John Boy


title: SIC_32_Colon_128_CAP_unselect_5p_TCR

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: dead cell_depletion_method

tag: cd45 positive_selection


title: T3

data_processing:
Raw data (raw reads) in FASTQ format were processed through fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d).
FeatureCounts (v1.5.0-p3) was used to count read numbers mapped for each gene.
Differential expression analysis between two conditions/groups was performed using DESeq2 (v1.20.0) using default settings
Assembly: Mus_musculus_grcm38
Supplementary files format and content: .csv matrix file includes FPKM values for each sample

source_name: Primary peritoneal macrophage

extract_protocol:
RNA extracted using Rneasy mini plus kit (Qiagen).Total mRNA was transcribed into full length cDNA using Takara V3 Stranded Prep kit
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: Primary peritoneal macrophage

tag: cell type

value: macrohage


title: AAV_SYN_GFP_2h_(3) [KSZ_F83_0014]

tag: development stage

value: cortex

value: neurons

tag: condition

tag: time point_[h]


title: SIC_32_Colon_128_CAP_unselect_5p_BCR

tag: patient id

tag: processed from_fresh_or_frozen_blood

value: Frozen

tag: rbc depletion_methods

tag: chemistry


title: JB, chill,  0h,  rep2

tag: tissue

tag: genotype

tag: treatment

value: Chilling (4 C)


title: SIC_196_Colon_612_CD45sort_5p_TCR_B

tag: simplified patient_id

tag: disease state

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

value: Fresh

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: Ctrl_2h_(3) [KSZ_F83_0013]

value: Epileptic

value: medium without Mg

tag: treatment 2

value: non transfected

tag: cell culture


title: T2

tag: age

value: Aged


title: JB, chill,  0h,  rep1

value: Floral bud

value: John Boy


title: SIC_196_Colon_612_CD45sort_5p_TCR_A

value: Colon mucosal biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: dead cell_depletion_method

tag: cd45 positive_selection


title: AAV_SYN_rMBD3_GFP_2h_Mg_(2) [KSZ_F83_0012]

tag: development stage

value: cortex

tag: cell type

tag: condition

value: Standard

value: medium with Mg

value: biol rep 2

tag: time point_[h]


title: AAV_SYN_rMBD3_GFP_2h_Mg_(3) [KSZ_F83_0018]

tag: tissue

value: neurons

value: biol rep 3


title: JB, chill,  100h,  rep2

tag: genotype

tag: treatment

value: Chilling (4 C)


title: MSH7-crispr-aa-14DAP-rep3

first: Luguang

last: Jiang

state: Beijing

address: No.2 Yuanmingyuan West Road, Haidian, Beijing

description:
MSH7-aa-14-rep3
MSH7-14DAP-genecounts.txt

data_processing:
Sequencing reads were processed with trimmomatic-0.39 to remove adaptor sequence and low-quality sequence, and then mapped to B73 RefGen_v4 reference genome (https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-50/plants/fasta/zea_mays/dna/) using HISAT2 (version: 2.2.1).
Uniquely mapped reads were kept for subsequent gene expression quantification using featureCounts (v1.6.4).
DEGs analysis was performed using the DESeq2 R package.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie (version: 1.3.6).
Assembly: B73 RefGen_v4 reference genome
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Zea mays

source_name: Seed (14 DAP)

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Plus kit,treated with RNase-free DNaseI and purified using the RNAclean Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit following manufacturer's protocols.

value: Seed (14 DAP)

value: MSH7 knockout


title: O6

value: Primary peritoneal macrophage

value: macrohage

value: Wild Type


title: AAV_SYN_GFP_2h_Mg_(2) [KSZ_F83_0011]


title: SIC_196_Colon_612_CD45sort_5p_BCR_B

tag: patient id

tag: simplified patient_id

tag: disease state

value: Control - Healthy

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)

tag: chemistry


title: Ctrl_2h_Mg_(2) [KSZ_F83_0010]

value: cortex

tag: treatment 2

value: non transfected

tag: cell culture


title: MSH7-crispr-aa-14DAP-rep1

description:
MSH7-aa-14-rep1
MSH7-14DAP-genecounts.txt


title: SIC_196_Colon_612_CD45sort_5p_BCR_A

value: Colon mucosal biopsy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: dead cell_depletion_method


title: O4

tag: cell type

tag: age

value: Aged


title: O3

tag: tissue

tag: genotype


title: AAV_SYN_rMBD3_GFP_2h_(2) [KSZ_F83_0009]

tag: development stage

value: neurons

tag: condition

value: Epileptic

tag: treatment

value: medium without Mg

value: biol rep 2

tag: time point_[h]


title: AAV_SYN_GFP_2h_(2) [KSZ_F83_0008]


title: MSH7-WT-AA-14DAP-rep3

description:
MSH7-AA-14-rep3
MSH7-14DAP-genecounts.txt

value: Seed (14 DAP)

value: WT


title: MSH7-WT-AA-14DAP-rep2

description:
MSH7-AA-14-rep2
MSH7-14DAP-genecounts.txt


title: YWTE

description: YWTE

value: Primary peritoneal macrophage

value: macrohage

value: Wild Type

value: Young


title: Ctrl_2h_(2) [KSZ_F83_0007]


title: AAV_SYN_rMBD3_GFP_6h_Mg_(2) [KSZ_F83_0006]

value: Standard

value: medium with Mg


title: SIC_188_Colon_585_CD45sort_5p_BCR_B_siPCR_relabel

tag: patient id

tag: simplified patient_id

tag: disease state

value: Control - Healthy

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)


title: T1

value: Aged


title: SIC_188_Colon_585_CD45sort_5p_TCR_A

value: Colon mucosal biopsy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: chemistry


title: MSH7-crispr-aa-7DAP-rep3

description:
MSH7-aa-7-rep3
MSH7-7DAP-genecounts.txt

source_name: Seed (7 DAP)

value: Seed (7 DAP)

value: MSH7 knockout


title: YWTB

description: YWTB

tag: cell type

tag: age


title: AAV_SYN_GFP_6h_Mg_(2) [KSZ_F83_0005]

tag: tissue

value: cortex

value: neurons

tag: treatment 2

tag: cell culture

value: biol rep 2


title: YWTA

description: YWTA

value: Primary peritoneal macrophage

value: macrohage

tag: genotype

value: Wild Type


title: SIC_187_Colon_584_CD45sort_5p_TCR

tag: pcr primer

tag: dead cell_depletion_method


title: SIC_187_Colon_584_CD45sort_5p_BCR

tag: patient id

tag: simplified patient_id


title: AAV_SYN_rMBD3_GFP_6h_(2) [KSZ_F83_0003]

tag: development stage

tag: condition

value: Epileptic

tag: treatment

value: medium without Mg

tag: time point_[h]


title: SIC_186_Colon_584_CD45sort_5p_TCR

tag: disease state

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

tag: cd45 positive_selection


title: Ctrl_2h_Mg_(3) [KSZ_F83_0016]

tag: tissue

tag: cell type

value: Standard

value: medium with Mg

tag: treatment 2

value: non transfected

value: biol rep 3


title: MSH7-WT-AA-7DAP-rep2

description:
MSH7-AA-7-rep2
MSH7-7DAP-genecounts.txt

tag: genotype

value: WT


title: SIC_172_Colon_529_CD45sort_5p_TCR

value: Colon mucosal biopsy

value: Control - On ICI Therapy

value: Initial

tag: channel

tag: pcr primer

value: Frozen

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)

tag: chemistry


title: SIC_188_Colon_585_CD45sort_5p_TCR_B

tag: patient id

tag: simplified patient_id


title: SIC_186_Colon_584_CD45sort_5p_BCR


title: MSH7-WT-AA-7DAP-rep3

description:
MSH7-AA-7-rep3
MSH7-7DAP-genecounts.txt

value: Seed (7 DAP)


title: YWTC

description: YWTC

value: Primary peritoneal macrophage

value: macrohage

value: Wild Type

tag: age

value: Young


title: AAV_SYN_GFP_6h_(2) [KSZ_F83_0002]

tag: development stage

value: cortex

value: neurons

tag: condition

value: Epileptic

tag: treatment

value: medium without Mg

tag: cell culture

value: biol rep 2

tag: time point_[h]


title: MSH7-crispr-aa-14DAP-rep2

description:
MSH7-aa-14-rep2
MSH7-14DAP-genecounts.txt

value: Seed (14 DAP)

value: MSH7 knockout


title: MSH7-crispr-aa-7DAP-rep2

description:
MSH7-aa-7-rep2
MSH7-7DAP-genecounts.txt


title: MSH7-crispr-aa-7DAP-rep1

description:
MSH7-aa-7-rep1
MSH7-7DAP-genecounts.txt


title: Ctrl_6h_Mg_(2) [KSZ_F83_0004]

value: Standard

value: medium with Mg

value: non transfected


title: SIC_188_Colon_585_CD45sort_5p_BCR_A

value: Colon mucosal biopsy

tag: disease state

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection


title: s3_cNrxn3_KD

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

data_processing:
Raw data of fastq format were processed through fastp software. Reads containing adapters, poly-N and low quality reads from raw data.
Hisat2 v2.0.5 software was used to map reads to the reference genome.
Stringtie v1.3.3b was used for assembly of mapped reads
featureCounts v1.5.0-p3 was sed to count the read numbers mapped to each gene and then FKPM (Fragments per Kilobase of transcript sequence per Millions base pairs sequenced) was calculated based on the length of the gene and read count mapped to each gene.
Assembly: rn6
Supplementary files format and content: Raw read counts in .xls format
Supplementary files format and content: FPKM in .xls format

source_name: orbitofrontal cortex

extract_protocol:
Total RNA was isolated used the Rneasy kit from Qiagen, according to the manufacturer's protocol.
RNA sequencing was performed on four biological replicate samples per group by Novogene (Sacramento, CA). Messenger RNA was purified from total RNA using poly-T oligo-attached beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification.

treatment_protocol: Adult male Sprague Dawley rats were ages 8 weeks on arrival. Animals received infusion of 1ul of siRNA complex dissolved in JetPEI transfection reagent containing 5ng scrambled control siRNA (Horizon Discorvery catalog # D-001810-10-20) or an siRNA targeted to the backsplice junction of rno_circRNA_013711, circular neurexin 3 gene (circNrxn3; sequence: Sense: 5':U.C.C.A.A.A.G.G.C.U.A.G.A.C.A.G.G.A.A.U.U 3'; Antisense: 5' U.U.C.C.U.G.U.C.U.A.G.C.C.U.U.U.G.G.A.U.U 3') into the orbitofrontal cortex in the following coordinates: Anterior/Posterior +3.2, Medial/Lateral +/- 2.6, and Dorsal/Ventral -4 relative to Bregma. Animals were euthanized 7 days after siRNA infusion and orbitofrontal cortex collected for RNA sequencing analysis.

tag: tissue

value: orbitofrontal cortex

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: adult

value: cNrxn3 siRNA


title: MSH7-WT-AA-14DAP-rep1

description:
MSH7-AA-14-rep1
MSH7-14DAP-genecounts.txt

tag: genotype

value: WT


title: Fcgr4- macrophages, mouse 3

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
trim reads using Trimommatic
map reads to mm10 using STAR
count aligned reads using featureCounts from SubRead
Assembly: mm10
Supplementary files format and content: tab-delimited table of read counts assigned to features

source_name: Epididymal adipose

extract_protocol: Cells were sorted directly into trizol. Extraction was done using the Zymo Research Microprep kit

value: Epididymal adipose

tag: cell type

value: Macrophage

tag: population

value: 24 weeks of ad libitum high fat diet feeding, followed by 2 weeks of caloric restriction (reducing the amount of food by 30%)


title: Fcgr4- macrophages, mouse 4


title: s4_cNrxn3_KD

tag: age


title: Ctrl_6h_(2) [KSZ_F83_0001]

tag: development stage

value: cortex

value: neurons

tag: condition

value: Epileptic

value: medium without Mg

tag: treatment 2

value: biol rep 2


title: SIC_172_Colon_529_CD45sort_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

value: Control - On ICI Therapy

value: Initial

tag: channel

tag: pcr primer

value: Frozen

tag: dead cell_depletion_method

value: Flow Cytometry (CD45+)

tag: chemistry


title: Fcgr4+ macrophages, mouse 3

tag: treatment


title: s2_cNrxn3_KD

tag: tissue

value: orbitofrontal cortex

value: Sprague-Dawley

value: male


title: Fcgr4+ macrophages, mouse 4


title: P28 mouse cerebellum tissue, GFP astrocytes, rep 3

city: Houston

first: Dongjoo

last: Choi

state: TX

address: 1 baylor plaza

institute: BCM

description: Column name in processed data file UK_count.txt: UKP28CB12

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPM values

molecule: polyA RNA

source_name: cerebellum

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen #74004)
cDNA synthesis and library construction with 8-bp single indices were done from 10 ng total RNA using Trio RNASeq System (NuGEN #0507-96).
A final library dilution of 1.3 pM was subjected to paired-end sequencing.

value: cerebellum

value: astrocyte


title: P28 mouse cerebellum tissue, GFP astrocytes, rep 1

description: Column name in processed data file UK_count.txt: UKP28CB10


title: SIC_141_Colon_438_CD45pos_5p_TCR_B

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: Prednisone 3mg

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)


title: SIC_141_Colon_438_CD45pos_5p_TCR_A


title: Fcgr4- macrophages, mouse 2

value: Epididymal adipose

tag: cell type

value: Macrophage

tag: genotype

tag: population

value: 24 weeks of ad libitum high fat diet feeding, followed by 2 weeks of caloric restriction (reducing the amount of food by 30%)


title: s1_cNrxn3_KD

tag: strain

tag: Sex

tag: age

value: adult

value: cNrxn3 siRNA


title: SIC_141_Colon_438_CD45pos_5p_BCR_B

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

value: Initial

tag: channel

tag: pcr primer


title: P14 mouse cerebellum tissue, GFP astrocytes, rep 3

description: Column name in processed data file UK_count.txt: UKP28CB9

tag: tissue


title: MSH7-WT-AA-7DAP-rep1

description:
MSH7-AA-7-rep1
MSH7-7DAP-genecounts.txt

value: Seed (7 DAP)

value: WT


title: SIC_140_Colon_441_CD45sort_5p_TCR

tag: disease state

value: Frozen

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)

tag: chemistry


title: s5_scr

value: orbitofrontal cortex

value: Sprague-Dawley

value: male

tag: treatment

value: Scrambled siRNA


title: SIC_141_Colon_438_CD45pos_5p_BCR_A

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: Prednisone 3mg

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: Fcgr4+ macrophages, mouse 2

value: Epididymal adipose

tag: cell type

value: Macrophage

tag: genotype

tag: population

value: 24 weeks of ad libitum high fat diet feeding, followed by 2 weeks of caloric restriction (reducing the amount of food by 30%)


title: P14 mouse cerebellum tissue, GFP astrocytes, rep 2

description: Column name in processed data file UK_count.txt: UKP28CB8

value: cerebellum

value: astrocyte

tag: age


title: P14 mouse cerebellum tissue, GFP astrocytes, rep 1

description: Column name in processed data file UK_count.txt: UKP28CB7


title: s4_scr

tag: strain

tag: Sex

value: adult


title: SIC_140_Colon_441_CD45sort_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

value: Initial

tag: channel

value: Frozen

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)


title: Fcgr4+ macrophages, mouse 1

tag: tissue


title: P7 mouse cerebellum tissue, GFP astrocytes, rep 3

description: Column name in processed data file UK_count.txt: UKP28CB6


title: Fcgr4- macrophages, mouse 1


title: s3_scr

value: orbitofrontal cortex

value: Sprague-Dawley

value: male

value: Scrambled siRNA


title: P28 mouse cerebellum tissue, GFP astrocytes, rep 2

description: Column name in processed data file UK_count.txt: UKP28CB11


title: SIC_134_Colon_417_CD45pos_5p_TCR

tag: disease state

value: irColitis Case

tag: pcr primer

value: Fresh

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)

tag: chemistry


title: t4_2

city: liaocheng

first: zhaoyong

last: lv

state: shandong

address: dong chang west Road

institute: Liaocheng People's Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnel
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

extract_protocol:
Macrophages stimulated by CaP Zn, CaP Zn0.8Mn, CaP Zn0.8Mn0.1Li were lysed with TRIzol reagent and rapidly frozen on dry ice, and RNA was harvested using Trizo reagent llumina TruSeq RNA Sample Prep Kit(Cat#FC-122-10).
RNA libraries were prepared for sequencing using standard illumina protocolsmRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: RAW264.7 cells were inoculated with 5×105 cells/mL onto the surface of CaP Zn0.8Mn0.1Li . After 3 days of culture, the culture medium was absorbed and rinsed with PBS, and 1 mL TRIzol reagent was added. After the cells were fully digested, The RNA samples were transferred into 1.5mL EP tubes and sequenced by transcriptome sequencing technology.scaffolds.

tag: cell line

value: macrophage

tag: treatment

value: CaP Zn0.8Mn0.1Li


title: P1 mouse cerebellum tissue, GFP astrocytes, rep 3

description: Column name in processed data file UK_count.txt: UKP28CB3

value: cerebellum

tag: cell type

value: astrocyte


title: t3_2

treatment_protocol: RAW264.7 cells were inoculated with 5×105 cells/mL onto the surface of CaP Zn0.8Mn. After 3 days of culture, the culture medium was absorbed and rinsed with PBS, and 1 mL TRIzol reagent was added. After the cells were fully digested, The RNA samples were transferred into 1.5mL EP tubes and sequenced by transcriptome sequencing technology.scaffolds.

value: CaP Zn0.8Mn


title: P7 mouse cerebellum tissue, GFP astrocytes, rep 1

description: Column name in processed data file UK_count.txt: UKP28CB4

tag: genotype


title: t4_1

treatment_protocol: RAW264.7 cells were inoculated with 5×105 cells/mL onto the surface of  CaP Zn0.8Mn0.1Li . After 3 days of culture, the culture medium was absorbed and rinsed with PBS, and 1 mL TRIzol reagent was added. After the cells were fully digested, The RNA samples were transferred into 1.5mL EP tubes and sequenced by transcriptome sequencing technology.scaffolds.


title: SIC_134_Colon_417_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: processed from_fresh_or_frozen_blood

tag: rbc depletion_methods


title: HRAS, 24hpi, biological replicate 1

city: Edinburgh

first: Yi

last: Feng

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

description:
10x Genomics
Cell_Metadata.csv
Gene_Metadata.csv
Raw_counts.mtx
Normalised_log_counts.mtx

data_processing:
First, each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing, UMI processing, cell barcode processing, genome alignment, gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts, low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections (UMAP) were calculated. A priori markers of keratinocytes, macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph-based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally, all samples were aggregated and the data was re-normalised and re-clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes (Welch’s T-test, FDR <0.05, FC > 1.5). The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets.
Assembly: Danio_rerio.GRCz11.101
Supplementary files format and content: Comma-separated values files and matrix files

organism: Danio rerio

source_name: whole larvae

extract_protocol:
Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS (no mag, no cal, plus phenol red), HEPES 15mM , D-Glucose 25mM, 2% Sterile Goat Serum, Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes, followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample, 5 wells were pooled into a single falcon tube, then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion (Becton Dickson). Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs (gel beads in emulsion). A poly-A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier (UMI), cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries, further rounds of PCR were carried out, in which the Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: whole larvae

tag: cell types

value: keratinocytes and myeloid cells

tag: strain


title: SIC_126_Colon_398_CD45pos_5p_TCR

tag: patient id

tag: simplified patient_id

tag: channel


title: HRAS, 24hpi, biological replicate 2

tag: tissue


title: HRAS, 8hpi


title: t3_1


title: P1 mouse cerebellum tissue, GFP astrocytes, rep 2

description: Column name in processed data file UK_count.txt: UKP28CB2

tag: age


title: CAAX control, 24hpi, biological replicate 2


title: t6_1

treatment_protocol: RAW264.7 cells were inoculated with 5×105 cells/mL onto the surface of CaP Zn. After 3 days of culture, the culture medium was absorbed and rinsed with PBS, and 1 mL TRIzol reagent was added. After the cells were fully digested, The RNA samples were transferred into 1.5mL EP tubes and sequenced by transcriptome sequencing technology.scaffolds.

value: CaP Zn


title: CAAX control, 24hpi, biological replicate 1


title: t6_2


title: SIC_121_Colon_382_CD45pos_5p_BCR

tag: disease state

tag: pcr primer

tag: dead cell_depletion_method

tag: cd45 positive_selection


title: s1_scr

value: orbitofrontal cortex

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment


title: SIC_109_Colon_368_CD45pos_5p_TCR

value: Control - On ICI Therapy

tag: steroids at_the_time_of_biopsy

value: Fresh

value: CD235 Bead Depletion

tag: chemistry


title: P1 mouse cerebellum tissue, GFP astrocytes, rep 1

description: Column name in processed data file UK_count.txt: UKP28CB1

tag: cell type

tag: genotype


title: LNCaP/AR sgUBE2J1 3

city: Dallas

first: Ping

last: Mu

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Cente

data_processing:
The alignment of the reads to the human reference genome (GRCh38) was executed using STAR (v2.7.2b), while FeatureCounts (v1.6.4) was employed for gene counts, biotype counts, and rRNA estimation. The differential expression analysis was conducted using the R package DEseq2 (v1.26), with selected cutoff values of an absolute fold change greater than 2 and a false discovery rate of less than 0.1. The differentially expressed genes were then identified, and GSEA was performed using the R package fgsea (v1.14.0) in conjunction with the 'Hallmark' libraries from MsigDB.
Assembly: GRCh38
Supplementary files format and content: deseq2_normalized_counts.xlsx: DESeq normalized reads are stored in xlsx file and contains gene counts normalized by DESeq2.

source_name: LNCaP/AR

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol:
RNA was extracted from LNCaP/AR cells using Trizol (Ambion, 15596018).
RNA-seq libraries were then prepared using the stranded Illumina TruSeq mRNA kit. The preparation began with 500 ng of total RNA and included 10 cycles of PCR amplification.
These barcoded RNA-seq libraries were run as paired-end, 50-nucleotide reads on an Illumina HiSeq 2500 and were selectively filtered by poly(A).

treatment_protocol: For RNAseq samples: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% Full serum.

tag: cell line

value: LNCaP/AR

value: prostate cancer cell line


title: snRNA, Cerebrum, Cdca7G305V/G305V, rep1

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

country: Netherlands

institute: Leiden Univeristy Medica Center

data_processing:
UMI (Unique molecular Identifiers) containing reads were mapped and counted with Cell Ranger 6.0.1 using a custom pre-mRNA GTF built on mm10 to include intronic reads. Due to an error of annotation in Cell Ranger, Pcdha10 and Pcdha11 read counts were combined together as Pcdha10_Pcdha11 throughout the analysis.
Datasets were processed individually using Seurat v4.1.0 (Hao and Hao et al, 2021) to filter out low-quality nuclei (Features > 1000, Features < 7500, Percentage of Mitochondrial genes < 5 %). Filtered libraries were normalized using the method « LogNormalize » and scale factor = 10000. Clustering was performed for all libraries using the Seurat functions FindNeighbors() and FindClusters() with the respective parameters dims = 50 and resolution = 0.5. UMAP representations were created using the Seurat function RunUMAP(). Read counts for individuals Pcdha isoforms were extracted from the Seurat object from each file using the Seurat function GetAssayData().
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: nuclear RNA

source_name: Cerebrum

extract_protocol:
Nuclei were isolated as previously described (Krishnaswami et al, 2016). Briefly, tissue was chopped, flash frozen and stored at -80 ºC. The Dounce homogenizer (2 ml one), pestles and all the buffers (NIM1 – 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris pH 8; NIM2 – NIM1, 1 µM DTT, protease inhibitor; Homogenization buffer – NIM2, 0,4 U/µl RiboLock (ThermoFisher, EO0384)) were precooled. The tissue was homogenized in 1 ml homogenization buffer with five strokes of the loose pestle, followed by 15 strokes of the tight pestle. Homogenate was filtered through a BD Falcon tube with a 35-μm nylon cell strainer cap (352235, Corning). The number of nuclei was counted by staining an aliquot with trypan blue and using TC10 Automated Cell Counter (BioRad). The nuclei were resuspended in 1 ml NIM2 buffer and sample was centrifugated (500 g, 5 min, 4 ºC). The washing step was repeated 2-3 times.
snRNA-seq libraries were obtained using Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 (10x Genomics , PN-1000165) chemistry and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000120). Two libraries were prepared per genotype.
5' snRNA-seq

value: Cerebrum

tag: strain

value: FVB


title: SIC_121_Colon_382_CD45pos_5p_TCR

tag: patient id

value: irColitis Case

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood

tag: rbc depletion_methods

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: snRNA, Cerebrum, Cdca7G305V/G305V, rep2

tag: tissue

tag: age


title: 20TGF_scRNA_MM48_NPG_S8

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

data_processing:
For Dropseq data, FASTQ sequencing reads were processed, aligned to the mouse genome (mm10), and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2, January 2016 http://mccarrolllab.com/dropseq/)
Assembly: mm10
Supplementary files format and content: Processed data is provided in the .txt file format containing the normalized gene count matrix for each sample.

source_name: Cortex

growth_protocol: THY1-Tau22 breeders were obtained from Luc Buée (University of Lille, France) under a Material Transfer Agreement. The line was rederived and bred by crossing heterozygous male breeders with commercially obtained C57Bl6/J females. The mice were kept in specialized facilities maintained under specific pathogen-free conditions. They were provided with unrestricted access to standard mouse food (Ssniff, # V 1534-300) and water at all times. Offspring was let age until 28 weeks.

extract_protocol:
RNA was extracted from the cortex using RNeasy Universal Kit (Qiagen). RNA samples were deemed of acceptable quality when their RNA integrity value exceeded 8.5, and their absorbance ratios at 260/230 and 260/280 were equal to or greater than 1.8 and 2, respectively. These high-quality RNA samples were subsequently preserved at -80°C until they were utilized. For single cell gene expression profiling, freshly dissected mouse cortex was disrupted with the Adult - Brain Dissociation (Miltenyi Biotec).
The 3′ end enriched cDNA libraries were prepared by tagmentation reaction of 600 pg cDNA library using the standard Nextera XT tagmentation kit (Illumina). Reactions were performed according to the manufacturer’s instructions. The PCR amplification cycling programme used was 95 °C 30 s, and 12 cycles of 95 °C (10 s), 55 °C (30 s), and 72 °C (30 s), followed by a final extension step of 72 °C (5 min). Libraries were purified twice to reduce primers and short DNA fragments with 0.6 × and 1 × Agencourt AMPure XP beads (Beckman Coulter), respectively, in accordance with the manufacturer’s protocol. Finally, purified libraries were eluted in 10 μl Molecular Grade Water. Quality and quantity of the tagmented cDNA library were evaluated using Bioanalyzer High Sensitivity DNA Chip. The average size of the tagmented libraries prior to sequencing was between 400 and 700 bps.
Purified Drop-seq cDNA libraries were sequenced using an Illumina NextSeq 500 machine with the recommended sequencing protocol, except for 6 pM of custom primer (GCCTGTCCGCGGAAGCAGTGGTATCAACG CAGAGTAC) applied for priming of read 1. Paired-end sequencing was performed for the read 1 of 20 bases (covering the random cell barcode 1–12 bases and the rest 13–20 bases of random unique molecular identifier (UMI) and for read 2 of 60 bases of the genes. Raw reads were further demultiplexed and processed using a dedicated Drop-seq computational pipeline

value: Cortex

value: female

value: TG


title: P7 mouse cerebellum tissue, GFP astrocytes, rep 2

description: Column name in processed data file UK_count.txt: UKP28CB5

value: cerebellum

value: astrocyte


title: SIC_109_Colon_368_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: simplified patient_id

tag: disease state

value: Initial

tag: channel

tag: pcr primer


title: CAAX control, 8hpi

value: whole larvae

tag: cell types

value: keratinocytes and myeloid cells

tag: treatment


title: 19WTF_scRNA_MM48_NPG_S7

tag: Sex

value: WT


title: 17WTM_scRNA_MM48_NPG_S5

value: male


title: LNCaP/AR sgUBE2J1 2

value: LNCaP/AR

tag: cell type

value: prostate cancer cell line


title: LNCaP/AR sgUBE2J1 1


title: snRNA, Cerebrum, WT, rep2

value: Cerebrum

value: FVB

tag: genotype


title: SIC_100_Colon_332_CD45sort_5p_BCR

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: Frozen

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)

tag: chemistry


title: 16TGF_scRNA_MM48_NPG_S8

value: Cortex

value: female

value: TG


title: SIC_126_Colon_398_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: patient id

tag: initial vs_follow_up_sample

value: Initial

tag: processed from_fresh_or_frozen_blood

value: Fresh

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: LNCaP/AR sgNT 3

tag: cell line

value: LNCaP/AR

value: prostate cancer cell line

value: sgNT


title: Spleen, RNA, Cdca7G305V/G305V, rep3

description: 1882-RNA-3 Missense

data_processing:
Quality assessment of the raw sequencing reads was done using FastQC  v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters were removed by TrimGalore v0.4.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters for paired-end Illumina reads, after which, quality filtering was performed by the same software. Reads smaller than 20bps and those with an error rate (TrimGalore option "-e") higher than 0.1 were discarded, after which a final quality assessment of the filtered reads was done with FastQC to identify possible biases left after filtering.
The remaining reads were mapped to  the mouse reference genome (build mm10) using the STAR aligner v2.5.1 (Dobin et al., 2013) using default parameters with the following exceptions: “–outputMultimapperOrder random” and  “–twopassMode basic”. Before mRNA quantification, duplicated reads were marked with Picard tools v2.17 (http://broadinstitute.github.io/picard/). Quantification was done by HTSeq-count v0.91 (Anders et al., 2015), using the GENCODE MV16 annotation with the option “–stranded no”. Statistical analysis was done using DESeq2 v1.2.0 (Love et al., 2014) (R package). For transposable elements analysis, trimmed reads were mapped to the mouse reference genome (GRCm38/mm10) using the STAR aligner v2.7.0e with the same parameters as above for unique mapping. Annotation for TEs was obtained from: http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/GRCm38_Ensembl_rmsk_TE.gtf.gz.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of RNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: count table, DESEQ2 table

source_name: Spleen

extract_protocol:
Total RNA was isolated with QIAzol (Qiagen 5346994). About 1µg of total RNA was used for reverse transcription using RevertAid H Minus First Strand cDNA Synthesis Kit (Thermoscientific K1632).
Truseq RNA seq library PE101 following manufacturer's protocol

tag: tissue

value: Spleen

tag: age


title: SIC_100_Colon_332_CD45sort_5p_TCR

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: channel

value: Frozen

tag: rbc depletion_methods


title: MC_9_Colon_661_CD45sort_5p_TCR

value: Control - Healthy

tag: pcr primer

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)


title: snRNA, Cerebrum, WT, rep1

value: Cerebrum

tag: strain

value: FVB


title: 14TGF_scRNA_MM48_NPG_S6

value: Cortex

tag: Sex

value: female

tag: genotype

value: TG


title: 18TGM_scRNA_MM48_NPG_S6

value: male


title: 15TGF_scRNA_MM48_NPG_S7


title: Spleen, RNA, Cdca7G305V/G305V, rep2

description: 1882-RNA-2 Missense


title: LNCaP/AR sgNT 2

tag: cell type

tag: treatment


title: LNCaP/AR sgNT 1


title: MC_2_Colon_576_CD45sort_5p_TCR_B

value: Colon mucosal biopsy

tag: steroids at_the_time_of_biopsy

value: Initial

value: Fresh

tag: dead cell_depletion_method

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)

tag: chemistry


title: Spleen, RNA, Cdca7G305V/G305V, rep1

description: 1882-RNA-1 Missense


title: MC_9_Colon_661_CD45sort_5p_BCR

tag: patient id

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood


title: 13WTF_scRNA_MM48_NPG_S5

tag: tissue

value: WT


title: Spleen, RNA, WT, rep3

description: 1882-RNA-6 WT

value: Spleen

tag: age


title: MC_2_Colon_576_CD45sort_5p_TCR_A

tag: simplified patient_id

tag: disease state

tag: channel


title: i-TERTci + GSK2830371 Rep5 on doxycycline for 28 days

city: Nice

first: Marina

last: Shkreli

address: 28 av de Valombrose

department: Faculty of Medicine

country: France

institute: IRCAN

description:
MS2702
i-TERTci_GSK2830371_Rep5

data_processing:
Paired-end sequencing (2x100bp) was performed by BGI Global services.
Quality of raw reads was assessed with FastQC. Clipping adaptor sequences were carried out using Trimmomatic and the trimmed reads were aligned to the mouse genome reference (mm10) downloaded from ENSEMBL using the STAR read aligner.
Differentially expressed genes (DEGs) were identified using the Bioconductor package DESeq2. DEGs were considered statistically significant at an adjusted p-value (Padj) < 0.05.
Assembly: Genome_build: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Kidney

growth_protocol: Double transgenic i-TERTci mice are maintained at a heterozygous status for each transgene. All mice were treated in accordance with the Institutional Animal Care and Use Committee approved guidelines at the Université Côte d’Azur (UCA, Nice, France) (CIEPAL-AZUR Agreements APAFIS#15232-2018051116515863v3, APAFIS#28252-2020111812195508v2, and APAFIS#33000-2021091515568721v2).

extract_protocol:
Total RNA was extracted from whole kidney using RNeasy Micro Kit with DNase treatment (Qiagen, Ref# 74004). RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Only samples with RNA Integrity Number (RIN) >7 were further submitted to high throughput sequencing.
Libraries were prepared by BGI Global services.

treatment_protocol: Double transgenic i-TERTci mice encompass both actin-rtTA+ and tetop-TERTci+ transgenes, allowing doxycycline-regulated and ubiquitous expression of TERTci in those mice. In order to induce TERTci overexpression in adult i-TERTci mice, doxycycline was administered in drinking water in light-protected bottles and changed biweekly. The actin-rtTA+ control mice followed the same treatment than i-TERTci mice. Doxycycline-treated i-TERTci mice show high proteinuira levels (above 10mg/mL) at about 15 days of doxycycline treatment. At that time, daily IP injection of GSK2830371 or DMSO was administered to the mice until the end of the experiment.

value: Kidney

value: Whole organ

value: i-TERTci (actin-rtTA+;TetOp-TERTci+)

value: Doxycycline + GSK


title: i-TERTci + GSK2830371 Rep4 on doxycycline for 49 days

description:
MS2701
i-TERTci_GSK2830371_Rep4


title: Spleen, RNA, WT, rep2

description: 1882-RNA-5 WT


title: MC_2_Colon_576_CD45sort_5p_BCR_B

value: Control - Healthy

tag: pcr primer

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)


title: 11WTF_scRNA_MM48_NPG_S3

value: Cortex

tag: Sex

tag: genotype


title: Spleen, RNA, WT, rep1

description: 1882-RNA-4 WT


title: i-TERTci + GSK2830371 Rep3 on doxycycline for 49 days

description:
MS2700
i-TERTci_GSK2830371_Rep3

tag: cell type

tag: treatment


title: i-TERTci + GSK2830371 Rep2 on doxycycline for 49 days

description:
MS2699
i-TERTci_GSK2830371_Rep2


title: MC_2_Colon_576_CD45sort_5p_BCR_A

tag: steroids at_the_time_of_biopsy

tag: dead cell_depletion_method


title: 10TGM_scRNA_MM48_NPG_S2


title: Spleen, input, H3K27me3

data_processing:
After preprocessing with TrimGalore to remove low quality reads, reads were aligned to the mouse genome (mm10) using bowtie2 v2.3.4.2 (Langmead and Salzberg, 2012) with parameters -very sensitive.
Peaks were called using SICER (Xu et al, 2014) for H3K9me3 (parameters - W200, G600) and H3K27me3 (parameters – W 1000, G 4000). For ChIP-seq peaks were called using input fractions as control.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig,broadPeak (except for Input sample)

source_name: Spleen P21

growth_protocol: Spleen was flash frozen and stored at -80 ºC

extract_protocol:
For chromatin preparation, frozen tissue was smashed using pestle and mortar (done in liquid nitrogen), and cross linked with 1% formaldehyde (344198; Calbiochem) in 9 ml of 1% PBS for 15 min at room temperature. Glycine (125 mM) was used to quench cross-linking for 5 min, and tissue was washed twice with cold PBS containing proteinase inhibitors (cOmplete™, EDTA-free Protease Inhibitor Cocktail, 5056489001, Roche). For lysis 1 ml of Cytoplasmic lysis buffer (10 mM Tris (pH 8), 10 mM NaCl, 0,2 % Igepal, and freshly added Protease Inhibitor Cocktail (05056489001; Roche)) was used. Tissue was homogenized 2 times for 10 sec (IKA model - T10 basic, at max speed – 6). Samples were spun down at 4000 rpm for 8-10 min at 4°C, and the pellets were resuspended in 1 ml SDS lysis buffer (1% SDS, 50 mM Tris-HCl (pH 8.1), 10 mM EDTA and freshly added Protease Inhibitor Cocktail). Lysed samples were sheared by sonication (Diagenode Biorupter Pico, - 30 sec ON/ 30 sec OFF, 15-25 cycles). Sheared chromatin was centrifuged at 12,000 g for 15 min at 4°C to discard the pellets
For library preparation the Kapa Hyper Prep Kit (Roche, KK8504, 07962363001) was used, following the manufacturer’s instructions

tag: strain

value: FVB

tag: chip antibody


title: MC_1_Colon_555_CD45pos_5p_TCR

tag: patient id

tag: initial vs_follow_up_sample

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)

tag: chemistry


title: 09TGM_scRNA_MM48_NPG_S1

tag: tissue

value: male

value: TG


title: MC_1_Colon_555_CD45pos_5p_BCR

value: Colon mucosal biopsy

tag: simplified patient_id

tag: disease state

value: Initial

tag: processed from_fresh_or_frozen_blood

value: Fresh


title: i-TERTci + GSK2830371 Rep1 on doxycycline for 31 days

description:
MS2697
i-TERTci_GSK2830371_Rep1

value: Kidney


title: i-TERTci + DMSO Rep5 on doxycycline for 31 days

description:
MS2698
i-TERTci_DMSO_Rep5

value: Whole organ

value: Doxycycline + DMSO


title: Spleen, Cdca7G305V/G305V, H3K27me3, rep1

value: Spleen

tag: age

value: Millipore 17-622


title: 08TGM_scRNA_MM48_NPG_S12

tag: Sex


title: Spleen, Cdca7G305V/G305V, H3K27me3, rep2

tag: genotype


title: 07WTM_scRNA_MM48_NPG_S11

value: WT


title: SIC_94_Colon_340_CD45pos_5p_GEX

value: Control - On ICI Therapy

tag: channel

tag: pcr primer

tag: rbc depletion_methods


title: Spleen, WT, H3K27me3, rep2


title: i-TERTci + DMSO Rep3 on doxycycline for 29 days

description:
MS2694
i-TERTci_DMSO_Rep3

tag: cell type

value: i-TERTci (actin-rtTA+;TetOp-TERTci+)

tag: treatment


title: 06WTM_scRNA_MM48_NPG_S10

value: Cortex


title: SIC_97_Colon_318_CD45pos_5p_GEX

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: CD235 Bead Depletion

tag: dead cell_depletion_method


title: 12WTF_scRNA_MM48_NPG_S4

value: female


title: Spleen, WT, H3K27me3, rep1

tag: strain

value: FVB

tag: chip antibody


title: i-TERTci + DMSO Rep2 on doxycycline for 29 days

description:
MS2693
i-TERTci_DMSO_Rep2


title: Spleen, input, H3K9me3


title: 04TGF_scRNA_MM48_NPG_S4

value: TG


title: SIC_89_Colon_310_CD45pos_5p_GEX

value: Colon mucosal biopsy

tag: patient id

value: Prednisone 2.5mg

tag: initial vs_follow_up_sample

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)

tag: chemistry


title: i-TERTci + DMSO Rep1 on doxycycline for 29 days

description:
MS2692
i-TERTci_DMSO_Rep1

tag: tissue

value: Kidney

value: Whole organ


title: 05WTM_scRNA_MM48_NPG_S9

value: male


title: Spleen, Cdca7G305V/G305V, H3K9me3, rep2

value: Spleen

tag: age

value: Active motif 39161


title: 03WTF_scRNA_MM48_NPG_S3

tag: Sex

value: WT


title: SIC_40_Colon_282_CD45pos_5p_GEX

tag: simplified patient_id

tag: disease state

value: irColitis Case - Follow Up Colitis Resolution Biopsy

value: Budesonide 6mg

value: Follow Up

tag: processed from_fresh_or_frozen_blood

value: Fresh


title: Spleen, Cdca7G305V/G305V, H3K9me3, rep1

tag: genotype


title: Actin-rtTA control mice Rep3 on doxycycline for 30 days

description:
MS2486
CTL_Rep3

tag: cell type

value: Actin-rtTA+

value: Doxycycline


title: 02TGM_scRNA_MM48_NPG_S2

value: Cortex

value: TG


title: SIC_71_Colon_241_CD45sort_5p_GEX

value: Colon mucosal biopsy

value: irColitis Case

value: Initial

tag: channel

tag: pcr primer

value: Frozen

tag: rbc depletion_methods

value: CD235 negative FACS sorting

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: 01WTM_scRNA_MM48_NPG_S1

value: male


title: SIC_32_Colon_128_CAP_unselect_5p_GEX

tag: steroids at_the_time_of_biopsy

tag: dead cell_depletion_method


title: SIC_32_Colon_178_CAP_unselect_5p_GEX

tag: patient id

value: irColitis Case - Follow Up Steroid Resistant Biopsy

value: Follow up


title: Actin-rtTA control mice Rep2 on doxycycline for 30 days

description:
MS2485
CTL_Rep2

value: Kidney

value: Whole organ

tag: treatment


title: i-TERTci + DMSO Rep4 on doxycycline for 38 days

description:
MS2695
i-TERTci_DMSO_Rep4

value: i-TERTci (actin-rtTA+;TetOp-TERTci+)

value: Doxycycline + DMSO


title: TOPBP1B5/B5 testes,rep2,scRNA-seq

city: Ithaca

first: Andrew

last: Grimson

address: 526 Campus Rd

department: Molecular and Cell Biology

institute: Cornell University

data_processing:
10X Genomics cellranger(v6.1.1) mkfastq was used with defaut parameters to generate demultiplexed fastq files
10X Genomics cellranger(v7.0.0) count was used with default parameters to map reads to the reference genome and generate gene-barcode matrices
Seurat(v4.3.0) was used to merge gene-barcode matrices from different libraries
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis

extract_protocol:
Mice testis were collected from 8-12 weeks old mice (n = 5 mouse, 10 testis for Topbp1+/+ , and  n = 20-30 mice, 40-60 testis for  Topbp1B5/B5). Decapsulated testes were held in 10 ml of DMEM-F12 buffer containing 2mg of Collagenase 1A and DNAse 7 mg/ml at 35°C in a shaker water-bath at 150 rpm for 5 min. 40 ml of DMEM-F12 was added and the tubules were left to settle for 1 min. The supernatant was removed and tubules were washed again with 40 ml of DMEM-F12. The tubules were digested using 10 ml of DMEM-F12 buffer containing 5 mg of trypsin in a 35°C shaker water-bath, 150 rpm for 5 min. Digested tubules were strained on a 100 μm strainer containing 3 ml of FBS. Cells were centrifuged at 300xg for 5 min, 4°C and checked for single cells and viability. Cells were stained with Vybrant dye cycle 100 μM for 30 min at room temperature. After staining, cells were sorted to enrich for spermatocytes using the Sony MA900 sorter, tuned to emit at 488 nm and with a 100 μm nozzle. Laser power was set to collect VDG-emitted fluorescence in FL1. Sorted cells were collected on 1.5 ml tubes containing 0.5ml of DMEM-F12 buffer + 10% FBS.
10X Genomics Chromium Single Cell 3′ RNA-seq v2

value: testis

tag: strain

value: 8-12 weeks

value: TOPBP1 B5/B5

tag: batch


title: Spleen, WT, H3K9me3, rep1

tag: tissue

value: Spleen

value: FVB

tag: chip antibody

value: Active motif 39161


title: Actin-rtTA control mice Rep1 on doxycycline for 30 days

description:
MS2484
CTL_Rep1

value: Actin-rtTA+

value: Doxycycline


title: Wildtype testes,rep2,scRNA-seq

tag: age

value: Wildtype


title: Cerebrum, input, H3K4me3

data_processing:
After preprocessing with TrimGalore to remove low quality reads, reads were aligned to the mouse genome (mm10) using bowtie2 v2.3.4.2 (Langmead and Salzberg, 2012) with parameters -very sensitive.
Peaks were called using MACS2 (Zhang et al, 2008; -f BAMPE, -g mm). For ChIP-seq peaks were called using input fractions as control.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Nuclei were isolated as previously described (Krishnaswami et al, 2016). Briefly, tissue was chopped, flash frozen and stored at -80 ºC. The Dounce homogenizer (2 ml one), pestles and all the buffers (NIM1 – 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris pH 8; NIM2 – NIM1, 1 µM DTT, protease inhibitor; Homogenization buffer – NIM2, 0,4 U/µl RiboLock (ThermoFisher, EO0384)) were precooled. The tissue was homogenized in 1 ml homogenization buffer with five strokes of the loose pestle, followed by 15 strokes of the tight pestle. Homogenate was filtered through a BD Falcon tube with a 35-μm nylon cell strainer cap (352235, Corning). The number of nuclei was counted by staining an aliquot with trypan blue and using TC10 Automated Cell Counter (BioRad). The nuclei were resuspended in 1 ml NIM2 buffer and sample was centrifugated (500 g, 5 min, 4 ºC). The washing step was repeated 2-3 times. Further ULI-ChIP-seq protocol was followed (Brind'Amour, 2015). Briefly, around 1 million nuclei per IP were diluted in 50 µl Nuclear storage buffer (15% sucrose, 10 mM Tris pH 7,2, 70 mM KCl, 2 mM MgCl2 and proteinase inhibitors) and fragmented using MNase at 37 ºC for 7,5 min. Upon fragmentation reaction was stopped with 6,6 µl 100 mM EDTA and 6,6 µl 1% Triton/1% DOC. The samples were then diluted up to 200 µl with Complete immunoprecipitation buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 15 mM NaCl, 0.1% Triton X-100, 1x EDTA-free protease inhibitor cocktail, 1mM PMSF).
The eluted DNA was purified by phenol–chloroform, precipitated with EtOH, and resuspended in 20 µl MQ. For library preparation the Kapa Hyper Prep Kit (Roche, KK8504, 07962363001) was used, following the manufacturer’s instructions.
ULI-ChIP-seq

value: Cerebrum


title: SST_FixedCells_scRNAseq_P5

city: Leuven

first: Elia

last: Micoli

address: Herestraat 49

department: VIB - Center for Brain and Disease Research

country: Belgium

institute: VIB - KU Leuven

description: 10X Genomics

library_source: genomic single cell

data_processing:
Fastq files from 10X experiments were processed and mapped to the mouse genome (mm10-2020-A with the v1.0.1 probe set, provided by 10X genomics). To generate the counts matrix we use cellranger multi (v7.1.0).
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
The neocortex of P5SstCre/+;RCEfl/+mice were dissected in ice-cold HBSS buffer supplement with 25 mM of glucose. Tissues were cut into small pieces and digested at 34°C with carbogen oxygenation using 20 ml of pronase dissociation buffer solution, with the following composition: 0.2 mg/ml Pronase, 25mM of Trehalose, 10 mM glucose, 0.8 mM kynurenic acid, 0.05 mM APV, 0.09M Na2SO4, 0.03M K2SO4 and 0.014M MgCl2. After 10 minutes of incubation, 500 μl 2.5mg/ml Liberase and 400 μl of 10mg/ml DNAseI were added and incubated at 34°C for 5 more minutes. Post enzymatic digestion, tissues were washed once in ice-cold dissociation buffer without enzyme and the mechanically triturated into single cells in 5 ml of OptiMEM supplement with 1% Trehalose, 10 mM glucose, 0.8 mM kynurenic acid and 0.05 mM APV using 5 ml volumetric pipette with 1 ml not filtered tip. We removed myelin by overlaying single cell suspension on top of a 20% percoll and centrifuge at 700 g for 10 mins. The cell pellet was resuspended in 300-500 μl of OptiMEM with 1% Trehalose, 10mM glucose, 0.8 mM kynurenic acid, 0.05 mM APV and the Fixable Viability Dye eFluor 780 1:1000 was added for 5 minutes. Cells were then transferred to 1.5 ml LoBind tubes precoated with 3% BSA overnight and centrifuged at 400g for 7 minutes. The Fixable Viability Dye was removed, pellet cells were resuspended with Fixation buffer (check protocol below for detailed information) overnight at 4°C. The day after the cells were centrifuged at 850g for 7 minutes and resuspended in 700 uL of DPBS with 1% BSA, tissue chunks were eliminated by passing cells suspension through a 40 μm cell strainer (BD).
For Probe Hybridization, GEM barcoding, GEM recovery and pre-amplification, and library construction we followed the Chromium Fixed RNA Profiling protocol (Chromium Fixed RNA Profiling kit; CG000477|Rev C).

value: Brain

tag: cell line

value: Cortical neurons

value: Somatostatin (SST) neurons

value: SST-cre/+;RCEfl/+

value: Probe based RNAseq


title: SIC_76_Colon_273_CD45pos_5p_GEX

data_processing:
We used Cell Ranger v3.1.0 for generating gene count matrices from sequencing reads (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). We used R scripts to analyze the count matrices.
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 files, anndata h5ad files, HTML files, CSV files

source_name: Colon mucosal biopsy

extract_protocol:
Please see the methods in the associated publication.
Please see the methods in the associated publication.

value: Colon mucosal biopsy

tag: simplified patient_id

tag: disease state

value: irColitis Case - B Cell-Depleted Patient

tag: initial vs_follow_up_sample

value: Initial

value: Fresh

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)

tag: chemistry


title: TOPBP1B5/B5 testes,rep1,scRNA-seq

value: testis

value: 8-12 weeks

tag: genotype

value: TOPBP1 B5/B5


title: Cerebrum, Cdca7G305V/G305V, H3K4me3,rep2

value: FVB

value: Millipore 17-614


title: SIC_19_Colon_217_CAP_unselect_5p_GEX

value: Control - On ICI Therapy

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Frozen

tag: rbc depletion_methods


title: SIC_196_Colon_612_CD45sort_5p_GEX_B

tag: patient id

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: Actin-rtTA control mice Rep4 on doxycycline for 30 days

description:
MS2487
CTL_Rep4

tag: tissue

value: Kidney

tag: cell type

value: Whole organ

value: Actin-rtTA+

tag: treatment

value: Doxycycline


title: Cerebrum, Cdca7G305V/G305V, H3K4me3 rep1

tag: strain

value: Cerebrum

tag: age

tag: chip antibody


title: SIC_196_Colon_612_CD45sort_5p_GEX_A

value: Colon mucosal biopsy

tag: simplified patient_id

tag: disease state

tag: initial vs_follow_up_sample

value: Initial

value: Fresh


title: Wildtype testes,rep1,scRNA-seq

value: testis

value: 8-12 weeks

tag: genotype

value: Wildtype

tag: batch


title: AB7152

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: bone marrow

extract_protocol:
LSK cells were single-cell sorted from mice 4 weeks after transplantation by flow cytometry.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: control (CD45.1) and Regnase-1–/–Regenase-3–/– (CD45.2) fetal liver cells were 1:1 mixed and transfered into lethally-irradiated mice (CD45.1/CD45.2).

value: LSK

value: bone marrow


title: Dataset D9 lib7

city: New York City

first: Itai

last: Yanai

address: 435 East 30th Street

institute: NYU Langone Health

description:
B. subtilis grown in LB
D9 lib7

data_processing:
All analysis was performed using the Tavazoie lab computational pipeline (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/PETRI_Seq_Computational.pdf).
Initial QC was performed using FastQC then unique molecular identifiers were extracted with UMI tools. Initial demultiplexing by cell barcode was performed iteratively using Cutadapt.
After selecting barcodes associated with the highest number of reads, reads from individual barcodes were aligned to the E. coli MG1655 or B. subtilis 168 reference genome using BWA.
Numbers of reads mapping to individual genes were quantified using FeatureCounts before counts were collapsed into unique reads based on UMI and used to make the final counts matrix.
Sample annotations were extracted from the number of barcode 1, since this corresponds to the way samples were added in the initial plate during reverse transcription.
Assembly: E. coli reads were aligned to the K-12 MG1655 reference assembly (GCA_000005845.2). B. subtilis reads were aligned to the 168 reference assembly (GCF_000009045.1).
Supplementary files format and content: Counts matrices: gzip-compressed tab-separated text files of counts by genes (columns) by cell barcode (rows) ("_counts.txt.gz")
Supplementary files format and content: Metadata files: tab-separated files containing library and sample information for each cell barcode ("_metadata.txt").

organism: Bacillus subtilis

source_name: Whole bacteria

growth_protocol: Bacteria were streaked out onto agar from frozen stocks overnight then grown overnight in LB. Samples were then diluted back to grow in the medium and to the densities indicated. There was an initial "back-dilution" step prior to harvesting to improve population homogeneity.

extract_protocol:
Samples were fixed and processed according to the protocol of Blattman et al. (PMID: 32451472). Briefly, cells were fixed overnight with 4% formaldehyde, permeabilized with 50% ethanol followed by enzymatic cell wall digestion (100 µg/ml lysozyme, 15 min), then treated with DNase to remove genomic DNA.
Reverse transcription and split-pool barcode ligation were carried out in situ in fixed cells according to the protocol of  Blattman et al. (PMID: 32451472). After barcoding, cells were separated into aliquots of ~20,000 cells for further processing. After lysis and reversal of crosslinking, second strand synthesis was performed using the NebNext Second Strand Synthesis module (New England Biolabs) and tagmentation was carried out using the EZ-Tn5 transposase (Lucigen), before final amplification with multiplex indexing primers.

treatment_protocol: B. subtilis cells were not subject to further treatment besides growth. For E. coli, cells were either harvested in balanced growth or after 1:1 dilution into 2x LB medium.

value: Whole bacteria

tag: cell line

value: Bacteria

value: WT

value: LB


title: Dataset D9 lib6

description:
B. subtilis grown in LB
D9 lib6


title: Spleen, WT, H3K9me3, rep2

value: Spleen

value: FVB

value: Active motif 39161


title: Dataset D9 lib8

description:
B. subtilis grown in LB
D9 lib8


title: SIC_188_Colon_585_CD45sort_5p_GEX_B

city: Charlestown

first: Kamil

last: Slowikowski

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

value: Control - Healthy

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)

tag: chemistry


title: AB7151

description: MARSseq

tag: tissue


title: Cerebrum, WT, H3K4me3, rep1

value: Cerebrum

value: Millipore 17-614


title: SIC_188_Colon_585_CD45sort_5p_GEX_A

value: Colon mucosal biopsy

tag: patient id

tag: steroids at_the_time_of_biopsy

value: Initial

value: Fresh

tag: rbc depletion_methods

tag: dead cell_depletion_method


title: Dataset D9 lib4

description:
B. subtilis grown in LB
D9 lib4

tag: cell type

tag: treatment


title: Dataset D9 lib5

description:
B. subtilis grown in LB
D9 lib5


title: Spleen, WT, ATAC

data_processing:
After preprocessing with TrimGalore to remove low quality reads, reads were aligned to the mouse genome (mm10) using bowtie2 v2.3.4.2 (Langmead and Salzberg, 2012) with parameters -very sensitive.
Peaks were called using SICER (Xu et al, 2014) for H3K9me3 (parameters - W200, G600) and H3K27me3 (parameters – W 1000, G 4000). For ChIP-seq peaks were called using input fractions as control.
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, ATAC_P21_spleen.xlsx

extract_protocol:
In brief, single cell suspensions were prepared by squeezing the tissues through a 35-μm nylon cell strainer (352235, Corning). 50,000 mouse splenic cells were resuspended in 50 µL transposition mix (Nextera) and incubated for 30 min at 37 °C
ATAC-seq libraries were prepared as previously described (Buenrostro et al, 2013). Libraries were amplified by PCR with barcoded Nextera primers.

tag: age


title: SIC_31_Colon_128_CD45sort_5p_GEX

tag: simplified patient_id

tag: disease state

value: Control - On ICI Therapy

tag: initial vs_follow_up_sample

value: Frozen


title: SIC_187_Colon_584_CD45sort_5p_GEX


title: AB7149

description: MARSseq

value: LSK

value: bone marrow

tag: strain


title: AB7150

description: MARSseq


title: Dataset D9 lib3

description:
B. subtilis grown in LB
D9 lib3

value: Whole bacteria

tag: cell line

value: Bacteria

tag: genotype

value: WT

value: LB


title: Scar, lacZTR, 3

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

data_processing:
The bases with low quality were removed using fastp software (version 0.20.0).
Alignment was performed by hisat2 software (version 2.1.0) with a reference of GRCm38.
Reads were counted by featureCounts software (version 2.0.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw reads for each sample

source_name: scar

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

value: Traction

value: hypertrophic scar-like animal model using traction force

value: scar


title: SIC_186_Colon_584_CD45sort_5p_GEX

value: Control - Healthy

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: Dataset D9 lib2

description:
B. subtilis grown in LB
D9 lib2

tag: tissue


title: AB7147

description: MARSseq


title: Scar, lacZTR, 2


title: Cerebrum, WT, H3K4me3, rep2

value: FVB

value: Cerebrum

tag: chip antibody

value: Millipore 17-614


title: SIC_172_Colon_529_CD45sort_5p_GEX

value: Colon mucosal biopsy

tag: patient id

value: Control - On ICI Therapy

tag: steroids at_the_time_of_biopsy

value: Initial

value: Frozen

tag: cd45 positive_selection

tag: chemistry


title: Dataset D9 lib1

description:
B. subtilis grown in LB
D9 lib1

value: Whole bacteria

tag: cell type

value: Bacteria

tag: treatment


title: Scar, lacZTR, 1


title: AB7100

description: MARSseq

value: LSK

value: bone marrow


title: SIC_141_Colon_438_CD45pos_5p_GEX_B

tag: simplified patient_id

value: irColitis Case

value: Prednisone 3mg

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: SIC_141_Colon_438_CD45pos_5p_GEX_A

tag: disease state

tag: initial vs_follow_up_sample


title: AB7099

description: MARSseq

tag: strain


title: Scar, WTTR, 2

tag: genotype

value: Traction

value: hypertrophic scar-like animal model using traction force

value: scar


title: Spleen, Cdca7G305V/G305V, ATAC

value: Spleen

tag: age


title: dorsal root ganglia, CCI, rep1

city: Shanghai

first: Li

last: Liu

state: Please select...

address: Shanghai Pudong New Area Renji Hospital

institute: shanghai jiaotong university

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: Ø MT% < 30%;  Ø Cell Gene Number < Median Gene Number * 2; Ø Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

organism: Mus

source_name: dorsal root ganglia

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

value: dorsal root ganglia

value: Neuron

value: wildtype

value: sciatic chronic construction injury


title: dorsal root ganglia, CCI, rep2


title: AB7098

description: MARSseq


title: AB7097

description: MARSseq


title: Scar, lacZSH, 3

value: Sham


title: dorsal root ganglia, naïve, rep2

value: naive group


title: AB7148

description: MARSseq

value: LSK

value: bone marrow


title: SIC_134_Colon_417_CD45pos_5p_GEX

value: Colon mucosal biopsy

value: irColitis Case

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood


title: AB7096

description: MARSseq

tag: tissue


title: Scar, WTTR, 1


title: SIC_13_Colon_78_CD45sort_5p_GEX

tag: patient id

value: Control - Healthy

tag: steroids at_the_time_of_biopsy

value: Frozen

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: dorsal root ganglia, naïve, rep1