title: Neuro2a cells treated with CRISPRa_Rep1

city: San Francisco

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

data_processing:
Sequencing of libraries was performed using an Illumina novaseq 6000 platform
Sequences are mapped to mm10 with STAR 2.5.1b
Counts were computed using featureCounts with gtf provided from genecode gencode.vM25.primary_assembly.annotation.gtf
Genes with differential expression are identified using DESeq2 R version 4.1.2 (2021-11-01) software.
Assembly: mm10
Supplementary files format and content: featurecounts

source_name: Neuroblastoma 2a

growth_protocol: cells were grown and maintained in EMEM with 10% FBS and 1% Pen/Strep

extract_protocol:
RNA was extracted with Qiagen Rneasy Mini Kit
Novogene - mRNA library preparation (poly A enrichment)

treatment_protocol: treated with either 750 ng of sgRNA and 750 ng of sadCas9-VP64 plasmid, or only sadCas9-VP64

tag: transfection

value: CRISPRa

value: Neuroblastoma


title: N10_Seedling_Rep1 [ncRNA-Seq]

status: Public on Apr 01 2022

type: SRA

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

library_source: transcriptomic

data_processing:
Adapter was removed and low quality reads were removed using UEA small RNA workbench (Stocks, M. B., 2018).
The small RNA reads of length 18nt-25nt filtered and miRNA analysis was performed using miRProf.
Supplementary_files_format_and_content: Text file containing 18nt-25nt long unique reads and their raw abundance after removal of adapter.

molecule: total RNA

organism: Oryza sativa

source_name: 14 day old seedlings

extract_protocol:
Total RNA from seedlings and roots were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)

tag: agent

value: Control (10 mM)

tag: tissue

value: seedlings


title: TPE-2

type: RNA

city: Chengdu

first: Yanyun

last: Wang

address: No. 20 Ren Min Nan Lu

country: China

institute: West China Second University Hospital, Sichuan University

description: circRNA expression in exosomes of TPE

hyb_protocol: One microgram cRNA was then fragmented with 5μl 10 × Blocking Agent and 1μl 25× Fragmentation Buffer at 60°C for 30 min. After diluting the reaction mix with 25μl 2× Hybridization buffer, 50μl solution was dispensed into the gasket slide and assembled into the circRNA expression microarray slide. After incubating for 17h at 65°C in an Agilent Hybridization Oven

scan_protocol: the hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C. The scanned images were imported into Agilent Feature Extraction software

data_processing:
the raw data was quantile normalized and low intensity signals were filtered. The fold change of each circRNA between the two groups was calculated, and the statistical significance was estimated by t-test.
The differentially expressed circRNAs (DECs) were screed based on fold changes ≥ 2 and p-values ≤ 0.05.

organism: Homo sapiens

source_name: exosomes

label_protocol: Total RNA from each sample was digested with Rnase R (Epicentre, Inc., USA), and amplified with fluorescent-labeled random primers using the Arraystar Super RNA Labeling kit. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Germany), and their concentration and specific activity (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (ThermoFisher Scientific, USA).

extract_protocol: Exosomal RNA was extracted from 7 ml PE fluid using exoRNeasy Serum/Plasma Maxi Kit

treatment_protocol: Fifteen milliliter PE samples were collected into 15 mL tubes and centrifuged at 1600 rpm for 30 min at 4℃ (5810R, Eppendorf, Germany). After removing the debris, the supernatants were filtered through a 0.22 mm membrane and stored at -20℃.

tag: fluid

value: pleural effusion

tag: disease

value: TPE

tag: age


title: human liver CD31+ CD45-

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

state: NY

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medicine

data_processing:
Illumina SureCell v1.2app
Genome_build: hg19
Supplementary_files_format_and_content: UMI counts for each gene and bead-barcode combination

molecule: polyA RNA

source_name: Liver CD31+ CD45-

growth_protocol: Cells were isolated from  a human liver sample

extract_protocol:
human liver CD31+ CD45- were isolated by fluorescence-activated cell sorting and subjected to single cell processing using a 10X Chromium.
RNA-seq cDNA libraries were constructed using the 10X Chromium single-cell 3′ Library Kit according to the manufacturer’s original protocol.

treatment_protocol: CD31+ CD45- cells were sorted and processed for single cell analysis in 10X Chromium.

value: Liver

tag: cell population


title: hyl1_1

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
We trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 20-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 cDNAs, using Bowtie2 (Langmead and Salzberg, 2012).
Analysis of the PARE data vas done using CleaveLand v4.5
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Count files

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h-light/8h-dark (20,5/17°C, 70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965).

extract_protocol:
RNA was extracted in Tri-Reagent according to the manufacturer’s protocol, and aqueous phase was left in 1 volume of isopropanol over-night at -20°C, precipitated 30 minutes at 16000g (4°C). Pellets were rinsed in 1 ml 70% ethanol and centrifuged an additional 10 minutes. For AGO1-loaded small RNA samples, IPs were performed as described above from 500mg of 1-week-old Arabidopsis seedlings grown on MS-agar plates. AGO1-loaded small RNA were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was then performed according to the manufacturer’s instructions.
Small RNA libraries were constructed using Real-Seq-AC kit (RealSeq®-AC, USA) according to manufacturer’s instructions with 500ng as starting material. Libraries were sequenced using Illumina Next-Seq 500 technology at University of Delaware (Delaware, USA).

treatment_protocol: No treatment

tag: ecotype

value: Columbia 0

tag: replicate

tag: genotype


title: samAx43

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

data_processing:
The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth.
Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited gene expression data of each sample

extract_protocol:
Total RNA was extracted from  skin biopsies by the Qiagen miRNeasy Mini Kit (Valencia, CA, USA). DNA was removed with on-column DNase digestion by the Qiagen RNase-free DNase Set. The quality of extracted RNA was examined using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
Libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA), according to the manufacture’s instructions. The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth. Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.

tag: timepoint

value: Baseline

tag: subytpe

value: Lesional

tag: skin condition

value: hidradenitis suppurativa


title: Neuro2a cells treated with VP64, no sgRNA control_Rep 5

organism: Mus musculus

tag: cell line

value: VP64, no sgRNA

tag: cell type


title: samAx39

value: Nonlesional


title: LA-MPE-1

description: circRNA expression in exosomes of LA-MPE

value: LA-MPE


title: samAx37


title: aged

city: Rochester

first: Andrew

last: McDavid

address: 265 Crittenden Boulevard, CU 420630

institute: University of Rochester

data_processing:
scRNA-seq reads were processed with Cell Ranger v2.1,  which demultiplexed cells from different samples and quantified transcript counts per putative cell.
The quality control was performed with SingleCellExperiment/R package. After filtering out low-quality cells (<1,000 unique genes, >8% mitochondrial reads) and potential doublets (>12,000 unique molecular identifiers (UMIs))
Assembly: mm10
Supplementary files format and content: 10x genomics hdf5 output from Cell Ranger 2.1, umi counts of genes for all barcodes

source_name: tibial callus tissue

growth_protocol: Young (4-month-old, equivalent to 26-year-old in human) and aged (21-month-old, equivalent to 62-year-old in human) C57BL/6J mice from National Institution of Aging were used. Mice were housed in micro-isolator technique rodent rooms. All animal procedures were approved by the University Committee on Animal Research at the University of Rochester.

extract_protocol:
Two soft calluses were dissected from the fractured tibiae at  day 10 of young or aged mice and pooled as a sample, cut into small pieces (<1 mm3 62 ) and digested in 10 ml of Accumax solution (STEMCELL, 1 hour, room temperature). Cells were passed through a 35um-filter and red blood cells were lysed with ammonium chloride (5 minutes, room temperature). Cells were resuspended in staining medium (PBS with 2% fetal bovine serum) and stained with APC-anti-CD45 (Biolegend, clone 30-F11), FITC-anti-CD31 (eBioscience, clone 390), PerCP/Cy5.5-anti Ter119 (Biolegend, clone TER-119) antibodies and Dapi. Callus SSPC cells (CD45-CD31-Ter119-Dapi-) were sorted (85-micron nozzle) by FACS with a BD Aria II Instrument.
Cells were loaded onto a Chromium chip (10X Genomics) followed by  encapsulation in a lipid droplet (Single Cell 3′ kit, 10X Genomics) to generate cDNA and library  according to the manufacturer’s protocol. cDNA libraries were sequenced to an average of 100,000 reads per cell using Illumina Nextseq 500.

treatment_protocol: Open tibial fractures were performed according to standard operation procedure established in Center for Musculoskeletal Research: an incision of 6 mm in   length was made in the skin on the anterior side of the tibia after anesthesia. A sterile 27 G x 1.25-   inch needle was inserted into the marrow cavity of the tibia from the proximal end, temporarily   withdrawn to facilitate transection of the tibia using a scalpel at midshaft, and then reinserted to stabilize the fracture. The incision was closed with 5-0 nylon sutures. Fractures were confirmed by radiograph.

tag: strain

tag: developmental stage

value: 21 months

value: tibial callus tissue


title: MM_Hyp48_6

city: Hangzhou

first: Yuyu

last: Li

address: Xiaoying

institute: Zhejiang University

library_source: genomic

data_processing:
library strategy: 16s rDNA-sequencing
Vsearch software (v2.3.4) was used for basecalling
dereplication using DADA2
Chao1, Observed species, Goods coverage, Shannon, Simpsonin our samples were calculated with QIIME2.
Blast was used for sequence alignment
feature sequences were annotated with SILVA database
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: genomic DNA

source_name: murine feces

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
DNA V3+V4 region; The libraries were sequenced on Illumina NovaSeq PE250 platform

tag: treatment

value: hypoxia

value: 49 day

tag: molecule

value: rDNA


title: N10_Root_Rep2 [ncRNA-Seq]

source_name: Roots of 14 day old seedlings

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)

tag: agent

value: Control (10 mM)

tag: tissue

value: Roots


title: MM_Hyp48_5

tag: age


title: samAx38

value: Perilesional


title: N10_Seedling_Rep2 [ncRNA-Seq]

value: seedlings


title: N10_Root_Rep1 [ncRNA-Seq]


title: samAx36


title: N100_Seedling_Rep1 [ncRNA-Seq]

value: high N stress (100 mM)


title: samAx34

value: Lesional


title: MM_Hyp48_2


title: N100_Seedling_Rep2 [ncRNA-Seq]


title: Placenta SG 8

city: Jerusalem

first: Liron

last: Hefetz

address: Ein Kerem Campus

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Reads containing adapters and poly-A sequences were trimmed using Cutadapt.
Genome mapping was performed using Tophat2, and read counts summarized through HTSeq count.
Differential expression with DESeq2, after discarding genes with less than 10 reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed_data_Hefetz_et_al.txt: Tab-delimited text file with expression data. The first row is a header line. Columns include general gene details, raw counts, normalized counts, the baseMean, and the DESeq2 analysis results for each comparison.

source_name: Placenta

extract_protocol:
Placentas were harvested at e18.5, flash frozen in liquid nitrogen, and RNA was extracted using TRI reagent (Sigma-Aldrich, Cat. No. T9424).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Hsd:ICR (CD-1)

value: Sleeve gastrectomy (SG)

value: Placenta


title: N100_Root_Rep1 [ncRNA-Seq]


title: MM_Hyp48_1


title: MM_Hyp48_4


title: samAx33

value: Nonlesional

value: hidradenitis suppurativa


title: Placenta Sham 6

value: Sham


title: Placenta SG 10


title: N100_Root_Rep2 [ncRNA-Seq]


title: MM_Hyp48_3

value: hypoxia


title: N0_Seedling_Rep2 [ncRNA-Seq]

value: low N stress (0 mM)


title: MM_Nor_5

value: normoxia

value: 49 day

value: rDNA


title: MM_Nor_4


title: Placenta Sham 4


title: samAx32


title: N0_Root_Rep1 [ncRNA-Seq]

value: Indica

value: Pusa Basmati 1 (PB1)


title: young

value: 4 months

value: tibial callus tissue


title: MM_Nor_6


title: Placenta SG 7


title: samAx31


title: samAx30

value: Baseline


title: samAx35

value: Perilesional


title: Placenta Sham 5

value: Hsd:ICR (CD-1)


title: MM_Nor_2


title: N10_Seedling_Rep1

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The processed reads were aligned to the rice genome, Oryza sativa IRGSP-1 using Hisat2 (Kim, D., 2019).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as xlsx format

value: Control (10 mM)

value: seedlings


title: samAx28

value: Lesional


title: Placenta SG 3

value: Sleeve gastrectomy (SG)

value: Placenta


title: Placenta Sham 1

value: Sham


title: MM_Nor_3


title: samAx23

value: hidradenitis suppurativa


title: Placenta SG 9


title: N0_Root_Rep2 [ncRNA-Seq]

value: low N stress (0 mM)

value: Roots


title: N10_Seedling_Rep2


title: E11_799_192_MGE_10x_cDNA_S6_L002 (RNA)

first: Alex

middle: S

last: Nord

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

data_processing:
Base-calling was performed using Illumina bcl2fastq.
10x MULTI-seq samples were processed using CellRanger v3.0.2 using GRCm38 appended with a custom chromosome containing the individual sequences for CreERT2, IRES, EGFP, and tdTomato.
For 10x samples, the function SCTransform was used for normalization.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw UMI counts for each sample.
Supplementary files format and content: LMOlist.csv: contains the sample barcodes used in this study and the associated enhancer for each barcode.

source_name: Medial ganglionic eminence

extract_protocol:
Tissue was microdissected from E11.5 mouse brain and immediately dissociated and processed for single-cell RNA-seq via standard protocols.
Single-cell RNA-seq libraries were prepared by standard methods for MULTI-seq using the 10x Chromium platform.

value: MGE

tag: enhancer

value: multiplexed sample:hs192,hs799


title: N0_Seedling_Rep1 [ncRNA-Seq]

value: Indica

value: Pusa Basmati 1 (PB1)


title: N10_Root_Rep1


title: E11_799_192_MGE_10x_BC_S5_L002 (Barcodes)

description:
Demultiplexing barcode for MULTI-seq.
Sample barcodes are stored in BC_R2 file, with cell barcodes and    UMIs stored in R1.


title: samAx24

value: Nonlesional


title: N10_Root_Rep2


title: Placenta Sham 2


title: samAx29

value: Baseline


title: MNK3_WT_RNA, 2

city: Philadelphia

first: John James

last: Tello-Cajiao

address: Curie Blvd 421

department: Genetics

institute: university of Pennsylvanya

data_processing:
Bulk RNA data was aligned to the mm10 reference genome using STAR_2.7.8a with parameters; --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outSAMtype BAM SortedByCoordinate --alignEndsType Local --outReadsUnmapped Fastx. Additionally, we counted reads using HTseq-count with parameters; -f bam -r name -s no -t exon -i gene_id -m intersection-nonempty. Next, we transformed read counts into RPKM for subsequent analyses.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: tab-delimited text files with read count

growth_protocol:
ILC2 were expanded using 10ng/ml of IL-2, IL-7, IL-33, IL-25
MNK3 were cultured with IL-7 and IL-15 (10ng/ml)

extract_protocol:
total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen). RNA integrity numbers were determined using a TapeStation 2200 (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9. Libraries were prepared using the SMARTer® Stranded Total RNA-seq Kit v2-Pico Input Mammalian kit (Takara). Two technical replicates were generated for each experiment. Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 500 (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NIH-Swiss mouse fetal day-15

value: MNK-3 originated from day-15 fetal thymocytes

value: Cell line

value: wild type (Cell line)


title: samX9


title: MNK3_WT_RNA


title: MM_Nor_1

value: normoxia

value: 49 day

value: rDNA


title: samX8

value: Perilesional


title: ILC2_WT_RNA

value: Bone Marrow

value: from pooled 8-12 weeks mice

value: wild type


title: N100_Seedling_Rep1

value: high N stress (100 mM)

value: seedlings


title: N100_Seedling_Rep2

value: Indica


title: samAx22

value: Lesional

value: hidradenitis suppurativa


title: S65816

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

country: Germany

institute: Heidelberg University Hospital

description: Sample 31

data_processing:
Demultiplexed using the JE demultiplexer (v1.2) standard operation
Data quality was checked using FastQC (v.11.9)
Reads were mapped using Salmon quasimapper (v.1.5)
Reads normalized using DESeq2 (v.1.32)
Genome_build: Mouse genome from Ensemble (v.GRCm39)
Supplementary_files_format_and_content: Processed data in CSV format with raw gene counts

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were cultured overnight in complete RPMI 1640 medium (+10% FCS, 1% Pen/Strep, 2mM L-Ala-L-Glu and 1 mM sodium pyruvate). Non-adherent cells were transferred to 10 cm petri dishes and differentiated for 6 days in complete RPMI medium containing 30% L929 supernatant. Fresh differentiation medium was added after 3 days.

extract_protocol:
Total RNA was isolated using NucleoSpin RNA Kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 2.5x10^5 cells were seeded onto 6-wells plates and treated with 2 µg/ml (Z)-4-Hydroxytamoxifen (Sigma) for 22h.

value: bone marrow derived macrophages

value: Trex1 FL/FL

tag: time point after tam treatment

value: day 4


title: samX7


title: N100_Root_Rep2

value: Pusa Basmati 1 (PB1)

value: Roots


title: MNK3_WT_ATAC, 2

data_processing:
ATAC-seq fastq files were aligned to the mm10 reference genome using the mem function of the software bwa-0.7.17 with additional parameters; -M. ATAC-seq peaks were subsequently called using MACS2 software with additional parameters; –nomodel -f BAM -B --keep-dup all --broad --broad-cutoff   0.1 -q 0.1. ATAC-seq profiles between primary ILC3s and the MNK3 cell line were compared by first creating a reference peak catalog. The reference peak catalog consisted of the pool of peaks called in each cell type with the corresponding raw counts in each sample. Next, we performed differential analysis using DESeq2.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million

growth_protocol: MNK3 were cultured with IL-7 and IL-15 (10ng/ml)

extract_protocol:
Fifty thousand cells were pelleted at 550 x g and washed with 50 μL ice-cold 1X PBS, followed by treatment with 50 μL of lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2,0.1% IGEPAL CA-630). Nuclei pellets were resuspended in a 50 μL transposition reaction containing 2.5μL Tn5  transposase (FC-121-1030; Illumina). The reaction was incubated in a 37°C heat block for 45min. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (Qiagen) and amplified with varying cycles, depending on the side reaction results. Libraries were purified using a QIAQuick PCR Purification Kit (Qiagen). Libraries were validated for quality and size distribution using a TapeStation2200 (Agilent). Libraries were paired-end sequenced (38bp+38bp) on a NextSeq 500 (Illumina)
DNA libraries were prepared for sequencing using standard Illumina protocols

value: NIH-Swiss mouse fetal day-15

value: MNK-3 originated from day-15 fetal thymocytes

value: Cell line

tag: genotype

value: wild type (Cell line)


title: S65815

description: Sample 29

value: day 3


title: S65831

description: Sample 30


title: NK_WT_RNA

source_name: ILC1 (NK cell)

value: Spleen

value: from pooled 8-12 weeks mice


title: N100_Root_Rep1

value: high N stress (100 mM)


title: MNK3_WT_ATAC


title: S65830

description: Sample 28

value: day 2


title: samX5

tag: timepoint

value: Perilesional


title: S65832

description: Sample 32


title: N0_Seedling_Rep1

value: Indica

value: low N stress (0 mM)

value: seedlings


title: HiC_MNK3

data_processing:
All samples were aligned using the HiC-Pro pipeline with recommended parameters.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Next, Hi-C matrices were converted into the m.cool format and normalized by matrix balancing with default parameters using the cooler tools.

extract_protocol:
Hi-C libraries were generated on up to 1x106 cells using Arima-Hi-C kit (Arima Genomics) and Accel-NGS Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen,Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (43bp+43bp) on NextSeq 500 (Illumina).
DNA libraries were prepared for sequencing using standard Illumina protocols


title: samX4

tag: subytpe

value: Lesional

value: hidradenitis suppurativa


title: samX3

value: Baseline

value: Nonlesional

tag: skin condition


title: S65814

description: Sample 27

value: bone marrow derived macrophages

value: Trex1 FL/FL


title: samX21


title: N0_Seedling_Rep2

value: Pusa Basmati 1 (PB1)


title: S65813

description: Sample 25

value: day 1


title: N0_Root_Rep1

value: Roots


title: N0_Root_Rep2


title: MuSC.D1.DTR_rep3 [DTR 4]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the human reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: MuSCs isolated from cardiotoxin-injured skeletal muscle

extract_protocol: For MuSC and Vg6+ gdT cell samples, cells were isolated by enzymatic digestion of the indicated tissue and cells were purified by fluoresence activated cell sorting. 1000 cells were sorted in TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing. For whole muscle samples, tissue was homogenized in Trizol, and then RNA was isolated per the manufacterure protocl and cleaned up by ethanol precipitation. 2ng of purified RNA were added to TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

value: Tcrd-DTR

value: i.p. diptheria toxin

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: samX20


title: HiC_ILC2

value: Bone Marrow

value: from pooled 8-12 weeks mice

value: wild type


title: WT_PB1_Rep1

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The processed reads were aligned to the rice genome, Oryza sativa IRGSP-1 using Hisat2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as xlsx format

extract_protocol:
Total RNA from seedlings were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Indica

value: wildtype


title: MuSC.D1.DTR_rep2 [DTR 3]


title: S65829

description: Sample 26


title: samX19

value: Lesional


title: WT_PB1_Rep2


title: S65823

description: Sample 22

value: untreated

value: day 3


title: MADS27OE_Rep2


title: MuSC.D1.DTR_rep1 [DTR 2]


title: S65808

description: Sample 23

value: day 4


title: HiC_NK

value: Spleen


title: samX15

value: Nonlesional

value: hidradenitis suppurativa


title: samX6


title: MuSC.D1.WT_rep2 [WT 5]

value: wild-type


title: samX14

value: Perilesional


title: S65807

description: Sample 21

value: bone marrow derived macrophages

value: Trex1 FL/FL


title: S65824

description: Sample 24


title: MADS27OE_Rep1

value: Pusa Basmati 1 (PB1)


title: MADS27_ChIP-seq_Rep2

description: Pulled down DNA fraction

data_processing:
The reads obtained were trimmed using cutadapt and aligned to IRGSP rice genome with parameters -q -v 1 -m 100 -y -a --best –strata
The alignment files are taken for peak calling using MACS2. The parameters used are -g 4.0e08 -s 50 -q 0.05 -B
Supplementary_files_format_and_content: Bedgraph track files and peaks in xls format

source_name: Young seedlings

growth_protocol: The regenerating seedlings grown in half-strength Murashige-Skoog media was used as tissue source.

extract_protocol:
Chromatin from the lysed nuclei was sheared using ultrasonicator (Covaris) at 4 degrees till the DNA fragments accumulate substantially in the size range of 200-500bp. The sheared cromatin was diluted ten times using ChIP dilution buffer (Song et al., 2016) and incubated overnight at 4oC with ~50ul of pre-equilibriated Myc-Trap Magnetic Agarose (Chromotek, ytma10). Washes, elution, de-crosslinking and DNA purification was done as described. The purified DNA was taken for library preparation.
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. The sequencing was done in single end mode in a Illumina HiSeq2500 platform.

treatment_protocol: No treatment.

value: Transgenic plant overexpressing 3xMyc tagged (N-ter) OsMADS27

tag: antibody

value: Myc-Trap from Chromotek Chromotek, ytma10


title: MuSC.D1.WT_rep3 [WT 6]

value: i.p. diptheria toxin

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: MuSC.D1.WT_rep1 [WT 2]


title: samX13


title: MADS27_ChIP-seq_Rep1

description: Pulled down DNA fraction

value: Indica


title: samX12

value: Baseline


title: D7.rIL-17A_rep3

source_name: Tibialis anterior muscle

value: i.p and i.m. rIL-17A


title: S65822

description: Sample 20

tag: cell type

value: untreated

value: day 2


title: D7.rIL-17A_rep1


title: Input_ChIP-seq_Rep2

description: Sheared Chromatin


title: samX2


title: samX10

value: Lesional


title: S65805

description: Sample 17

value: day 1


title: samX11

value: hidradenitis suppurativa


title: S65864

description: Sample 16

value: Trex1 WT/FL

value: day 4


title: sir2delta2-2

city: Buffalo

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
C neoformans genome sequence in fasta and gene annotations in GFF format were downloaded from NCBI (CNA3 https://www.ncbi.nlm.nih.gov/assembly/GCF_000149245.1/)
The CNA1 genome library and gene annotations for mapping and gene counting were compiled using STAR v2.7.0f (--runMode genomeGenerate --sjdbOverhang 50) and RSEM v1.2.15 (rsem-prepare-reference)
Then reads were mapped to CNA1 genome annotation using STAR v2.7.0f with parameters “--outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000  --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --readFilesCommand zcat”
RSEM v1.2.15 (rsem-calculate-expression) was used to count reads on genes based on STAR alignment on each sample, then a combined count matrix of expected gene counts was built using “rsem-generate-data-matrix”.
Genome_build: CNA3 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000149245.1/)
Supplementary_files_format_and_content: Matrix table with expected gene counts for every gene and every sample from STAR-RSEM pipeline
Supplementary_files_format_and_content: CNA3.gtf: GTF file for gene annotations
Supplementary_files_format_and_content: ALL.mat.txt: expected gene counts from STAR/RSEM; Check CNA3.gtf for gene name of each gene id

organism: Cryptococcus neoformans

source_name: sir2 delta mutant clone 2 in H99 replicate 2

extract_protocol:
Total RNA was harvested from cell pellets by bead-beating (5 min, 30 sec on and off cooling on ice) followed by RNA extraction using the Qiagen RNEasy Mini Kit protocol.
The samples were prepared using the Illumina TruSeq RNA library prep kit, starting with isolated mRNA since the organism was yeast. Approximately 1 ug of total RNA was used and polyA mRNA selected using the Illumina TruSeq RNA library prep kit. After multiplexing, the samples were pooled and sequenced on a HiSeq2500 in one lane, single read, 50 cycles.

tag: strain

value: sir2 delta mutant

tag: growth phase

value: Mid-log

tag: temperature

value: 30 degrees C

tag: stress condition

value: unstressed


title: Input_ChIP-seq_Rep1

description: Sheared Chromatin

tag: subspecies

value: Pusa Basmati 1 (PB1)

value: Transgenic plant overexpressing 3xMyc tagged (N-ter) OsMADS27


title: S65806

description: Sample 19

value: bone marrow derived macrophages

value: Trex1 FL/FL

tag: treatment


title: samX1

value: Baseline


title: D14.DTR_rep3

value: Tcrd-DTR

value: i.p. diptheria toxin

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: S65848

description: Sample 15


title: D7.PBS_rep1

value: wild-type

value: i.p and i.m. PBS


title: S65821

description: Sample 18

value: untreated

value: day 1


title: sir2delta2-1

source_name: sir2 delta mutant clone 2 in H99 replicate 1


title: s2_H12: 623950 T18 V4

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human airway epithelial cells

growth_protocol: Primary human lung bronchial-airway epithelial basal cells (Lonza, cat. no. CC2540; obtained from healthy donors 655308, 623950, 672447, and 626776) were expanded in 75-cm2 tissue-culture flasks using airway epithelial cell growth medium (Promocell) to 60-70% confluency. Primary diseased human lung bronchial-airway epithelial basal cells (Lonza, cat. no. 00195275; obtained from donors 18TL343179, 18TL103224, 436083, 440551, 430905) were expanded in 75-cm2 tissue-culture flasks using airway epithelial cell growth medium (Promocell) to 60-70% confluency. Primary human pulmonary microvascular endothelial cells (Cell Biologics) were expanded in 75-cm2 tissue-culture flasks using human endothelial cell growth medium (Cell Biologics) to 70-80% confluency. To create human airway transwells, 6.5mm transwells with 0.4μm pores (Sigma-Aldrich) were coated with collagen type IV from human placenta (0.5mg ml-1 in water; Sigma-Aldrich) at room temperature overnight. The solution was aspirated from the transwell, which was then used for seeding cells. Lung bronchial-airway epithelial basal cells (1.0 X 105 cells ml-1) were first seeded in the apical chamber of transwell in airway epithelial growth medium (Promocell) and incubated at 37 ˚C with 5% CO2 until 100% confluent. The adherent cells were maintained using airway epithelial growth medium (Promocell). Once confluent, the apical medium was removed and the basal chamber received PneumaCult-ALI medium (StemCell) to establish ALI. The airway epithelial cells were cultured for 3-4 additional weeks at 37oC with 5% CO2, and the apical surface of the epithelium was washed with PBS once a week to remove mucus and cellular debris. Prior to infection experiment, human pulmonary microvascular endothelial cells (1.5 X 106 cells ml-1) were seeded on the basal side of the membrane and incubated for 2 hours at 37˚C with 5% CO2. The transwells were then returned to ALI using PneumaCult-ALI media (StemCell) supplemented with 0.1% VEGF, 0.01% EGF, and 1mM CaCl2.

extract_protocol:
total RNA were prepared using Qiagen Rneasy mini plus kit
RNA libraries were prepared for sequencing using standard Illumina Illumina NovaSeq 6000 with 150-bp pair-ended reads

treatment_protocol: Prior to infection, human airway transwells were equilibrated for 24 hours in reduced hydrocortisone (10nmol/L) differentiation media (StemCell). The airway epithelial cells were infected with influenza virus (MOI=0.1) in 50ul PBS for 1.5 hours at 37 ˚C with 5% CO2. After the incubation period, the apical solution was aspirated and the transwells were returned to 37oC with 5% CO2. The apical surface of the epithelium was washed with PBS 4 hours and 18 hours post-infection and collected for analysis. The basal supernatant was collected 4 hours and 18 hours post-infection and analyzed for cytokines and chemokines.

tag: donor

tag: time point

value: 18 hr

tag: condition

value: NHB

tag: infection

value: influenza A virus

value: Human airway epithelial cells


title: S65863

description: Sample 14

value: Trex1 WT/FL

tag: time point after tam treatment

value: day 3


title: S65847

description: Sample 13

tag: genotype


title: sir2delta1-2

source_name: sir2 delta mutant clone 1 in H99 replicate 2

value: sir2 delta mutant

value: Mid-log

value: 30 degrees C

value: unstressed


title: D7.PBS_rep3


title: D14.DTR_rep2

value: Tcrd-DTR


title: H99-2

source_name: wild type strain H99 replicate 2

value: WT


title: s2_H11: 623950 T18 V3


title: D14.DTR_rep1

value: i.p. diptheria toxin

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: D14.WT_rep3

value: wild-type


title: s2_A1: 18TL 103224 T4 C1

value: 4 hr

value: COPD

value: control


title: sir2delta1-1

source_name: sir2 delta mutant clone 1  in H99 replicate 1


title: H99-1

source_name: wild type strain H99 replicate 1


title: S65862

description: Sample 12

value: bone marrow derived macrophages

value: day 2


title: S65846

description: Sample 11


title: D14.WT_rep2


title: s1_H12: 436083 T18 V4

value: 18 hr

value: influenza A virus

value: Human airway epithelial cells


title: D14.WT_rep1


title: S65845

description: Sample 9

value: Trex1 WT/FL

value: day 1


title: D7.DTR_rep2


title: s2_H8: 623950 T18 P4

value: NHB


title: 28C mo 2 days rep1

first: Jiehua

last: Qiu

state: 省/直辖市

address: shuidaosuo 28 road,fuyang District, Hangzhou city

institute: CNRRI

data_processing:
RNAs were sequenced separately at oebiotech, using Illumina Hiseq X-Ten with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of MSU release 7 using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test
Genome_build: NCBI_ASM465v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: rice leaves

growth_protocol: The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 4-5 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
Total RNA was extracted from mycelia cultured in the liquid CM for 2 days from three biological repeats using the TRIzol (Invitrogen, USA) reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: leaves

tag: infected with

value: Magnaporthe oryzae

tag: time

value: 2 days

tag: growth temperature


title: D7.DTR_rep1

value: Tcrd-DTR

value: i.p. diptheria toxin


title: 28C mo 2 days rep3


title: 28C mo 2 days rep2


title: s2_H9: 623950 T18 V1

tag: cell type


title: S65840

description: Sample 7

value: untreated

value: day 4


title: 28C mock 2 days rep3

tag: strain

value: mock


title: D7.WT_rep3

value: wild-type

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: 28C mock 2 days rep2


title: D7.WT_rep2


title: S65855

description: Sample 6

value: bone marrow derived macrophages

value: day 3


title: s1_H10: 436083 T18 V2

value: 18 hr

value: COPD

value: influenza A virus


title: S65854

description: Sample 4

value: Trex1 WT/FL

value: day 2


title: S65839

description: Sample 5


title: s1_H9: 436083 T18 V1

value: Human airway epithelial cells


title: D7.WT_rep1


title: 22C mo 2 days rep3

value: leaves

value: Magnaporthe oryzae


title: s1_H8: 436083 T18 P4


title: s2_H7: 623950 T18 P3

value: NHB


title: D3.DTR_rep3

value: Tcrd-DTR

value: i.p. diptheria toxin


title: s1_H11: 436083 T18 V3


title: 22C mo 2 days rep2

value: 2 days


title: S65838

description: Sample 3

value: untreated


title: D3.DTR_rep2


title: S65856

description: Sample 8

value: day 4


title: D3.DTR_rep1

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: 22C mo 2 days rep1


title: 22C mock 2 days rep3

value: mock


title: S65853

description: Sample 2

value: bone marrow derived macrophages

value: day 1


title: s1_H7: 436083 T18 P3

value: 18 hr

value: COPD


title: 28C mock 2 days rep1


title: s2_H5: 623950 T18 P1


title: S65837

description: Sample 1

value: Trex1 WT/FL


title: 22C mock 2 days rep2


title: D3.WT_rep3

value: wild-type


title: s2_H10: 623950 T18 V2

value: influenza A virus

value: Human airway epithelial cells


title: D3.WT_rep2


title: Neuro2a cells treated with VP64, no sgRNA control_Rep 4

data_processing:
Sequencing of libraries was performed using an Illumina novaseq 6000 platform
Sequences are mapped to mm10 with STAR 2.5.1b
Counts were computed using featureCounts with gtf provided from genecode gencode.vM25.primary_assembly.annotation.gtf
Genes with differential expression are identified using DESeq2 R version 4.1.2 (2021-11-01) software.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts

source_name: Neuroblastoma 2a

extract_protocol:
RNA was extracted with Qiagen Rneasy Mini Kit
Novogene - mRNA library preparation (poly A enrichment)

tag: cell line

tag: transfection

value: VP64, no sgRNA


title: s2_H4: 623950 T18 C4

value: NHB

value: control


title: D3.WT_rep1

value: i.p. diptheria toxin


title: s1_H6: 436083 T18 P2


title: Neuro2a cells treated with VP64, no sgRNA control_Rep 3


title: Neuro2a cells treated with VP64, no sgRNA control_Rep 2


title: WMJJ rkn replicate 2

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

description: Mildly RKN-resistant Genotype

data_processing:
We first performed quality assessment of the resulting reads from the Illumina platform using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and processed sequencing libraries using Trimmomatic (version 0.39; ) to remove adapter read sequences.
We then quantified gene expression using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1. The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
We then integrated transcript-level abundances from kallisto to  count-based statistical analysis in edgeR (version 3.13) to produce the table of read counts per locus.
Genome_build: The G. hirsutum TM-1 UTx v2.1 genome release was used as a reference genome to align the reads (www.cottongen.org ; https://doi.org/10.1038/s41588-020-0614-5 )
Supplementary_files_format_and_content: The table of counts is a tab-separated plaint text file (.txt) which contains the counts per million reads corresponding to each locus per library (rows), and each RNA-seq library sample (columns) is named according to genotype, condition and biological replicate (for example SJ2_ctl1 would be Acala SJ2-control conditions-replicate 1; rkn means root-knot nematode infested).

organism: Gossypium hirsutum

source_name: Root tissue (23 days-old-plants)

growth_protocol: Cotton plants were grown in a Greenhouse in pots with soil. Air temperatures in the greenhouse were maintained between 280 C and 350 C during the day and 240 C at night.

extract_protocol:
The root samples from each genotype were grounded in liquid nitrogen, and total RNA was isolated three biological replicates following the manufacturer’s instructions using Spectrum TM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). The yield and purity of RNA were analyzed with a ND-1000 Spectrophotometer (Nano Drop Technology, Wilmington, DE, USA). Only RNA samples with 1.8 - 2.2 ratio of absorbance 260/280 nm were used for analysis.
For each genotype, 2 mg of RNA from each of the three biological-replicates used for cDNA library preparation. The cDNA libraries were prepared following the TruSeq RNA Sample Preparation v2 low sample (LS) protocol guide (Illumina Inc., San Diego, CA USA)
Illumina Platform, MiSeq and HiSeq2500

treatment_protocol: Two treatments control (ctl) and root-knot nematode M. incognita infested (rkn). Control plants were not infested. For root-knot nematode (RKN) infestated plants, the roots of 12 days old seedlings of three genotypes NemX (resistant), SJ2 (susceptible) and WMJJ (moderately resistant) were infected with 5000 J2/plant RKN. The disease progression was noted for 10 days and infected roots from 23-day old plant were collected from each of the five plants, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

value: Root-knot nematode infested (M. incognita) (rkn)

value: Wild Mexico Jack Jones (WMJJ)


title: D1.DTR_rep2

value: Tcrd-DTR


title: D1.DTR_rep3

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: s2_H3: 623950 T18 C3


title: 22C mock 2 days rep1

value: leaves

value: mock

value: 2 days


title: Neuro2a cells treated with CRISPRa_Rep5

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

value: CRISPRa


title: WMJJ rkn replicate 1

description: Mildly RKN-resistant Genotype


title: Neuro2a cells treated with CRISPRa_Rep3


title: WMJJ control replicate 2

description: Mildly RKN-resistant Genotype

value: Control (ctl)


title: s2_H6: 623950 T18 P2

value: 18 hr


title: D1.DTR_rep1


title: WMJJ control replicate 1

description: Mildly RKN-resistant Genotype


title: s1_H5: 436083 T18 P1

value: COPD


title: D1.WT_rep3

value: wild-type


title: s1_H3: 436083 T18 C3

value: Human airway epithelial cells


title: s1_H4: 436083 T18 C4


title: LCR1_KO scRNA

data_processing:
Cellranger v(3.1.0) pipeline with default parameters
ScRNA-sequencing normalization and clustering. First, we filtered out low quality or dead cells by excluding any cell that had less than 1100 UMI and more than 8% of mitochondrial genes, also, we excluded genes expressed in less than 10 cells. Next, we processed the data following the steps recommended in the SCTransform tutorial73. Briefly, we computed the percentage of mitochondrial genes (percent.mt) in addition to the cell cycling score (S.score, g2m.score) of each cell, and then called the SCTransform function of the Seurat package74.  For the SCTransform function we selected the following parameters: method=’GlmGamPoi’,var.to.regress=(’percent.mt’,’S.score’,’g2m.score’).  Subsequently, we applied dimensional reduction using the RunPCA, RunUMAP, RunTSNE functions and created a Shared Nearest Neighbors (SNN) graph using the FindNeighbors function with default parameters. Finally, we called the function FindClusters with parameters; resolution=0.8, algorithm=4, method=’igraph’, to obtain the clusters reported in this work.
Cellranger v(3.1.0) pipeline with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Output of CellRanger software : Features, Barcodes and Matrix

source_name: Bone Marrow

extract_protocol:
BM progenitors (Live,CD45+, Lin-, CD127+) were obtained by pooling LCR1+/+ or LCR1-/- animals (same number of males and females; between 8 and 12 weeks old). After cell sorting cells were washed two times with PBS containing 0.01% of Bovine Serum Albumin (BSA, Sigma #A8806) cell viability and cell counts were assessed using an hemacytometer and a trypan blue staining.
Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics) according to the manufacturer’s protocol for 10000 cells recovery. Briefly, cellular suspension was added to the master mix containing RT Reagent B, Template Switch Oligo, Reducing Agent B and RT Enzyme C. 70mL of master mix with cell suspension was then loaded to the Row 1, while Row 2 and Row 3 were filled with 50mL of Gel Beads 45mL of Partitioning Oil respectively. After run completion, 100mL of GEM mix was used for reverse transcription and was performed using a C1000 Touch Thermal cycler (Bio-Rad) at the following conditions: 53°C for 45 min, 85°C for 5 min, held at 4°C. Post GEM-RT cleanup was performed with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min, 12 cycles of (90°C for 15 s, 67°C for 20 s and 72°C for 1 min), 72°C for 1 min, held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit (Beckman Coulter) and quality was assessed using a TapeStation (Agilent). Libraries were constructed following the manufacturer’s protocol and sequenced with a targeted sequencing depth of 20.000 read pairs per cell on pair-end mode on either a NextSeq 500/550 or a NovaSeq with recommended loading concentration (1.8pM and 300pM for NextSeq and NovaSeq respectively).

value: Progenitors (viab, Lineage-, CD45+, CD127+)

value: LCR1 knocked-out


title: D1.WT_rep2


title: LCR1_WT scRNA

value: Wild Type


title: Acala SJ2 rkn replicate 2

description: RKN susceptible Genotype

value: Acala SJ2


title: D1.WT_rep1

value: i.p. diptheria toxin


title: s2_H1: 623950 T18 C1

value: NHB

value: control


title: s2_H2: 623950 T18 C2


title: Vg6.Muscle-d3 rep3

source_name: Vg6+ T cells from cardiotoxin-injured skeletal muscle

value: cardiotoxin-induced hindlimb skeletal muscle injury


title: Acala SJ2 control replicate 1

description: RKN susceptible Genotype


title: Vg6.Muscle-d3 rep2


title: s2_G12: 672447 T4 C4

value: 4 hr


title: Acala NemX rkn replicate 2

description: RKN-resistant Genotype

value: Root-knot nematode infested (M. incognita) (rkn)

value: Acala NemX


title: Vg6.Muscle-d3 rep1


title: s1_H2: 436083 T18 C2


title: Neuro2a cells treated with CRISPRa_Rep2

value: CRISPRa


title: Acala NemX control replicate 2

description: RKN-resistant Genotype

value: Control (ctl)


title: Vg6.C-LP rep2

source_name: Vg6+ T cells from colonic lamina propria


title: s2_G8: 623950 T4 V4

value: influenza A virus


title: Acala NemX rkn replicate 1

description: RKN-resistant Genotype


title: Acala NemX control replicate 1

description: RKN-resistant Genotype


title: s2_G7: 623950 T4 V3


title: Acala SJ2 rkn replicate 1

description: RKN susceptible Genotype


title: airway epithelial cells, STAT3-cKO, PBS, rep2

city: Chiba

first: Masaya

last: Yokota

address: 1-8-1 Inohana

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Graduate school of Medicine, Chiba University

description: total RNA

data_processing:
Illumina adapters and low-quality reads were trimmed using FASTX-toolkit (ver 0.0.13).
Quality-controlled reads were mapped to mouse mm10 genome.
Raw read counts on each gene were calculated using Homer.
Normalized expresson levels were calculated using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes normalized expression levels for each Sample.

source_name: airway epithelial cells

extract_protocol:
Airway epithelial cells were isolated from lung by FACS sorting. Total RNA was extracted from the isolated cells by using a TRIzol reagent. NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used with 1 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: lung

value: isolated airway epithelial cells from lung

value: PBS


title: s1_G8: 436083 T4 V4

value: COPD

value: Human airway epithelial cells


title: Acala SJ2 control replicate 2

description: RKN susceptible Genotype


title: airway epithelial cells, STAT3-WT, PBS, rep2

description: total RNA


title: s1_H1: 436083 T18 C1

value: 18 hr


title: hyl1_3 (AGO1-IP RNA)

data_processing:
We trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 34-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 blastsets for all the features, using Bowtie2 (Langmead and Salzberg, 2012).
Differential accumulation was done using DESeq2 (Love et al., 2014) and all plots were generated using ggplot2 (Wickham, 2016) packages in R environment.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Count files

source_name: AGO1-IP RNA

extract_protocol:
RNA was extracted in Tri-Reagent according to the manufacturer’s protocol, and aqueous phase was left in 1 volume of isopropanol over-night at -20°C, precipitated 30 minutes at 16000g (4°C). Pellets were rinsed in 1 ml 70% ethanol and centrifuged an additional 10 minutes. For AGO1-loaded small RNA samples, IPs were performed as described above from 500mg of 1-week-old Arabidopsis seedlings grown on MS-agar plates. AGO1-loaded small RNA were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was then performed according to the manufacturer’s instructions.
Small RNA libraries were constructed using Real-Seq-AC kit (RealSeq®-AC, USA) according to manufacturer’s instructions with 500ng as starting material. Libraries were sequenced using Illumina Next-Seq 500 technology at University of Delaware (Delaware, USA).

value: Seedlings

tag: ecotype

value: Columbia 0

tag: replicate


title: hyl1fbw2_3 (AGO1-IP RNA)


title: Vg6.C-LP rep3

value: wild-type


title: s1_G7: 436083 T4 V3


title: hen1fbw2_3 (AGO1-IP RNA)


title: s2_G6: 623950 T4 V2

value: NHB


title: hen1_3 (AGO1-IP RNA)


title: s2_G5: 623950 T4 V1


title: airway epithelial cells, STAT3-cKO, PBS, rep1

description: total RNA

tag: treatment


title: fbw2_3 (AGO1-IP RNA)


title: s1_G6: 436083 T4 V2

tag: donor


title: Vg6.C-LP rep1


title: Col0_3 (AGO1-IP RNA)


title: airway epithelial cells, STAT3-cKO, HDM, rep2

description: total RNA

value: HDM


title: airway epithelial cells, STAT3-cKO, HDM, rep1

description: total RNA


title: s2_G4: 623950 T4 C4

tag: time point

value: 4 hr

value: control


title: s1_G5: 436083 T4 V1

tag: condition


title: airway epithelial cells, STAT3-WT, PBS, rep1

description: total RNA


title: hen1fbw2_2 (AGO1-IP RNA)


title: airway epithelial cells, STAT3-WT, HDM, rep2

description: total RNA


title: s1_G4: 436083 T4 C4

tag: infection


title: airway epithelial cells, STAT3-WT, HDM, rep1

description: total RNA


title: hen1_2 (AGO1-IP RNA)


title: s1_G3: 436083 T4 C3


title: hyl1fbw2_2 (AGO1-IP RNA)


title: airway epithelial cells, SCD1 inhibitor, HDM, rep2

description: total RNA

extract_protocol:
Airway epithelial cells were isolated from lung by FACS sorting. Total RNA was extracted from the isolated cells by using a TRIzol reagent. NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used with 5 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: WT

value: HDM + SCD1 inhibitor


title: s2_G2: 623950 T4 C2


title: airway epithelial cells, SCD1 inhibitor, HDM, rep1

description: total RNA


title: airway epithelial cells, DMSO, HDM, rep2

description: total RNA

value: HDM + DMSO


title: fbw2_2 (AGO1-IP RNA)


title: hyl1_2 (AGO1-IP RNA)


title: hen1fbw2_1 (AGO1-IP RNA)


title: Col0_2 (AGO1-IP RNA)


title: s1_G1: 436083 T4 C1


title: H4K20me1Dam - mESC (KIN3764_KIN4394_index13)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Raw data files include both DamID and CEL-seq reads
single-end run contains cell-specific barcode and the gDNA sequence to determine the DamID signal. Paired-end run is of the same library, sequenced later to get R1 with barcode and R2 with transcript sequence.

data_processing:
Library strategy: scDam&T-seq
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq reads are aligned using GRCm38 (v. 89) transcript models and tophat2 (v. 2.1.1) with the following paramters: : “--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: celseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; damid count table: count table containing UMI-unique GATC counts per 10-kb interval for all single-cell samples; sample annotation: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. Barcodes follow a 3-NNN-3-NNN format, where "N" positions indicate the barcode-specific sequence, and the "3" indicates positions of a 3nt UMI sequence.

source_name: mouse hybrid F1 embryonic stem cells

growth_protocol: F1 hybrid 129/Sv:Cast/Eij mouse embryonic stem cells (mESCs) were cultured on irradiated primary mouse embryonic fibroblasts (MEFs), in ES cell culture media CM+/+; G-MEM (Gibco) supplemented with 10% FBS (Hyclone, Sigma lot no), 1% Pen/Strep, 1x GlutaMAX (Gibco), 1x non-essential amino acids (Gibco), 1x sodium pyruvate (Gibco), 0.1mM β-mercaptoethanol (Sigma) and 10^3U/ml ESGROmLIF (EMD Millipore ESG1107). Cells were split every 3 days and medium was changed every other day.

extract_protocol:
F1ES cells were  trypsinized and harvested in medium with 20 μg/mL Hoechst 34580 (Sigma 63493) per 1x10^6 cells for 45 minutes at 37°C. The cells were stained for live/dead gating with 1ug/ml propidium iodide and singlets were index sorted based on their Hoechst profile. One cell per well was sorted into 384-well plates (Biorad, HSP3801) using the BD FACS Jazz cell sorter. Wells contained 5 μL filtered mineral oil (Sigma) and 50nL of 0.5uM unique CELseq primer.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Expression of the Dam-POI constructs was suppressed by addition of 0.5mM indole-3-acetic acid (IAA; Sigma, I5148). When plated for targeting or experiments the cells were passaged at least 2 times in feeder free conditions on plates coated with 0.1% gelatin in 60% BRL conditioned medium (40% CM+/+ medium and 60% of CM+/+ medium conditioned on Buffalo Rat Liver cells) with 1mM IAA. For timed induction of the constructs the IAA is washed out at different clone specific optimized times before single cell sorting.

value: 129S1/SvImJ x CAST/Eij

tag: dam-fusion protein

value: anti-H4K20me1 (mintbody)

tag: molecule subtype

value: genomic DNA; mRNA


title: airway epithelial cells, DMSO, HDM, rep1

description: total RNA

tag: tissue

value: lung

value: isolated airway epithelial cells from lung

tag: genotype


title: s2_G1: 623950 T4 C1

value: Human airway epithelial cells


title: s2_F12: 626776 T18 V4

value: 18 hr

value: influenza A virus


title: s2_F11: 626776 T18 V3


title: s1_F12: 440551 T18 V4

value: COPD


title: hyl1fbw2_1 (AGO1-IP RNA)

value: Seedlings

value: Columbia 0


title: s1_G2: 436083 T4 C2


title: s1_F11: 440551 T18 V3


title: H4K20me1Dam - mESC (KIN3764_KIN4394_index10)


title: H4K20me1Dam - mESC (KIN3764_KIN4394_index11)


title: S65861

description: Sample 10

source_name: bone marrow derived macrophages

value: bone marrow derived macrophages

value: Trex1 WT/FL

tag: time point after tam treatment

value: day 1


title: H4K20me1Dam - mESC (KIN3764_KIN4394_index12)


title: DamOnly - mESC (KIN4214_KIN4394_index21)

value: untethered Dam


title: DamOnly - mESC (KIN4117_KIN4836_index32)


title: Col0_1 (AGO1-IP RNA)


title: hen1_1 (AGO1-IP RNA)


title: hen1fbw2_3 (total RNA)

source_name: Total RNA


title: s2_F10: 626776 T18 V2

value: NHB


title: hyl1_1 (AGO1-IP RNA)


title: s2_F9: 626776 T18 V1


title: s1_F10: 440551 T18 V2


title: s2_F8: 626776 T18 P4


title: fbw2_1 (AGO1-IP RNA)


title: DamH3K27me3 - mESC (KIN3764_KIN4394_index23)

value: anti-H3K27me3 (mintbody)


title: hyl1fbw2_3 (total RNA)


title: hen1_3 (total RNA)


title: s2_F7: 626776 T18 P3


title: DamH3K27me3 - mESC (KIN4117_index34)

description: Raw data files include only DamID reads

data_processing:
Library strategy: scDamID
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq reads are aligned using GRCm38 (v. 89) transcript models and tophat2 (v. 2.1.1) with the following paramters: : “--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: celseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; damid count table: count table containing UMI-unique GATC counts per 10-kb interval for all single-cell samples; sample annotation: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. Barcodes follow a 3-NNN-3-NNN format, where "N" positions indicate the barcode-specific sequence, and the "3" indicates positions of a 3nt UMI sequence.

value: 129S1/SvImJ x CAST/Eij


title: s1_F8: 440551 T18 P4


title: fbw2_3 (total RNA)


title: s1_F9: 440551 T18 V1


title: s2_F6: 626776 T18 P2


title: DamH3K27me3 - mESC (KIN3764_index21)

description: Raw data files include only DamID reads


title: Col0_3 (total RNA)


title: DamH3K27me3 - mESC (KIN3764_index22)

description: Raw data files include only DamID reads


title: DamH3K27me3 - mESC (KIN3577_index34)

description: Raw data files include only DamID reads


title: s1_F7: 440551 T18 P3


title: hen1fbw2_2 (total RNA)


title: hyl1_3 (total RNA)


title: hen1_2 (total RNA)


title: DamH3K27me3 - mESC (KIN3764_KIN4394_index20)


title: hyl1fbw2_2 (total RNA)


title: s1_F6: 440551 T18 P2


title: DamH3K27me3 - mESC (KIN3577_index33)

description: Raw data files include only DamID reads


title: DamH3K27me3 - mESC (KIN4214_KIN4394_index27)


title: hyl1_2 (total RNA)


title: DamH3K27me3 - mESC (KIN3577_index32)

description: Raw data files include only DamID reads


title: DamH3K27me3 - mESC (KIN3577_index31)

description: Raw data files include only DamID reads


title: s2_F4: 626776 T18 C4

value: control


title: fbw2_2 (total RNA)


title: Col0_2 (total RNA)


title: DamH3K27me3MUT - mESC (KIN3764_index33)

description: Raw data files include only DamID reads

value: anti-H3K27me3-mutated (mintbody)

value: genomic DNA; mRNA


title: hen1fbw2_1 (total RNA)


title: s1_F5: 440551 T18 P1


title: DamH3K27me3MUT - mESC (KIN3764_index30)

description: Raw data files include only DamID reads


title: s1_F4: 440551 T18 C4


title: hyl1fbw2_1 (total RNA)


title: s1_F3: 440551 T18 C3


title: DamH3K27me3MUT - mESC (KIN3764_index31)

description: Raw data files include only DamID reads


title: DamH3K27me3MUT - mESC (KIN3764_index32)

description: Raw data files include only DamID reads


title: hen1_1 (total RNA)


title: s2_F3: 626776 T18 C3


title: DamCbx7 - mESC (KIN4117_index33)

description: Raw data files include only DamID reads

value: Cbx7 (chromodomain trimer)


title: fbw2_1 (total RNA)


title: s2_F1: 626776 T18 C1

value: Human airway epithelial cells


title: DamCbx7 - mESC (KIN4214_KIN4394_index22)


title: s2_F5: 626776 T18 P1

value: 18 hr


title: DamCbx7 - mESC (KIN2966_index30)

description: Raw data files include both DamID and CEL-seq reads


title: hyl1_1 (total RNA)


title: s1_F1: 440551 T18 C1


title: s1_F2: 440551 T18 C2


title: s2_E12: 672447 T4 C3

value: 4 hr


title: DamCbx7 DamH3K27me3 DamH3K27me3MUT DamOnly H4K20me1Dam - mESC (KIN3443_index03)

value: Cbx7 (chromodomain trimer); anti-H3K27me3 (mintbody); anti-H3K27me3-mutated (mintbody); anti-H4K20me1 (mintbody); untethered Dam


title: DamCbx7 DamH3K27me3 DamH3K27me3MUT DamOnly H4K20me1Dam - mESC (KIN3443_index04)


title: s2_F2: 626776 T18 C2


title: 4-1

city: Wuhan

first: Youquan

last: Zhong

state: hubei

address: NO.115, Donghu road, Wuchang district, Wuhan city, Hubei province, China.

department: TaiKang Medical School,

institute: Wuhan University

data_processing:
Paired-end sequencing reads in fastq format were mapped to the HBVcircle genome with Bowtie2 in no-discordant and no-mixed mode
Sequencing reads from transfected cells were aligned to the HBVcircle genome and generated  the alignment output files (SAM format)
The alignment output files (SAM format) were conversed into the files (BAM format) by using the Samtools
The files (BAM format)  were conversed into the files (BW format)  by using the Deeptools
ChIP-seq density profiles were generated by operating the alignment output files (BAM format) in the IGV genome browser.
Assembly: reference_sequence.txt
Supplementary files format and content: bam files was generated by using  Bowtie2, the files (BAM format)  were conversed into the files (BW format)  by using the deeptools

organism:
Homo sapiens
Hepatitis B virus

extract_protocol:
The cccDNA ChIP-Seq assay was performed according to previously described procedures, with slightly modifications. Huh7 cells transfected HBVcircle were cross-linked by 1% formaldehyde (Invitrogen, USA) for 10 min at room temperature, and fixation was quenched by adding 125 mM glycine final concentration for 5 min. Next, the cells were permeated in nuclei isolation buffer [1× PBS with 0.1% Triton X-100, 0.1% NP-40, 1 mM DTT, 10 mM sodium butyrate, 1× protease inhibitor (Roche)] for 10 min at 4℃. Nuclei were pelleted after centrifugation at 9000g for 3 min at 4℃, resuspended and digested in Mnase digestion buffer [50 mM Tris pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 10% (vol/vol) glycerol, 10 mM sodium butyrate, 1× protease inhibitor] with 1500 U/mL Mnase (New England Biolabs, Ipswich, Massachusetts) at 37℃ for 1 h. and digestion was quenched with 10 mM EGTA final concentration on ice. Then, the digested nuclei were harvested by centrifugation at 9000g for 3 min at 4℃, and resuspended by ChIP lysis buffer (50 mM Tris-HCl pH 8.0, 5 mM EDTA, 150 mM NaCl, 1% NP-40, 0.1% SDS, 10 mM sodium butyrate, protease inhibitor) with occasional mixing for 2 h at 4℃. The sample was centrifugated at 6500g for 5 min, and the supernatant was collected for immunoprecipitation. For ChIP, the above lysis supernatant was added into protein A/G-conjugated agarose beads after protein A/G-conjugated agarose beads was incubated with indicated antibodies in a rotator overnight at 4℃, and followed by collecting beads and washing five times. Immunocomplexes was eluted in elution buffer (1% SDS, 100 mM NaHCO3), and decross-linked at 65 °C for 5–6 h, the DNA fragments were purified by a TIANamp Genomic DNA Kit (TIANGEN Biotech Co., Beijing, China). For sequencing, the DNA fragments were sent to sequencing company (Annoroad Genomics Company, China).
Repair the ends of DNA fragments, add A to the end of the DNA fragment, adaptors were added into the end of the DNA fragments, PCR amplification,  DNA fragments purification.

treatment_protocol: Huh7 cells were transfected with either HBVcircle-WT or HBVcircle-Δcore, and the cells were harvested at day 3 for HBV cccDNA chromatin immunoprecipitation followed by massive parallel sequencing.

value: transfected HBVcircle-WT

tag: chip antibody

value: anti-H3K4me3 (Cell Signaling Technology, #9751)


title: DamCbx7 DamH3K27me3 DamH3K27me3MUT DamOnly H4K20me1Dam - mESC (KIN3443_index02)


title: 4-2

value: transfected HBVcircle-Δcore


title: Col0_1 (total RNA)

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

institute: University of California - Davis

value: Seedlings

value: Columbia 0


title: DamRing1B  - EB day14 (KIN5156_index42)

source_name: Embryoid Bodies (day 14)

growth_protocol: For the EB differentiation the stable knockin F1ES lines were cultured for 2 weeks on 0.1% gelatin coated plates in 2i ES cell culture medium: 48% DMEM/F12 (Gibco) and 48% Neurobasal (Gibco), supplemented with 1x N2 (Gibco), 1x B27 supplement + vitA (Gibco), 1x non-essential amino acids, 1% FBS, 1% Pen/Strep, 0.1mM β-mercaptoethanol, 1 μM PD0325901 (Axon Medchem, PZ0162-5MG), 3 μM CHIR99021 (Tocris, SML1046-5MG) and 10^3U/ml ESGRO mLIF medium before plating for EB differentiation according to ATCC protocol. On day1 of the differentiation 2x10^6 cells are grown in suspension on a non-coated bacterial 10cm dish with 15ml CM +/- (with β-mercaptoethanol without LIF) and 0.5mM IAA. The next day half the cell suspension is divided over 5 non-coated bacterial 10cm dishes with 15ml CM+/- medium and 0.5mM IAA and plates are refreshed every other day.

extract_protocol:
Cells were trypsinized and harvested in medium with 20 μg/mL Hoechst 34580 (Sigma 63493) per 1x10^6 cells for 45 minutes at 37°C. The cells were stained for live/dead gating with 1ug/ml propidium iodide and singlets were index sorted based on their Hoechst profile. One cell per well was sorted into 384-well plates (Biorad, HSP3801) using the BD FACS Jazz cell sorter. Wells contained 5 μL filtered mineral oil (Sigma) and 50nL of 0.5uM unique CELseq primer.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Two days before single cell sorting the EB’s are shifted to CM+/- medium with 1mM IAA, and before single cell sorting on day 7, 10 and 14 the Dam-POI constructs are induced in the following way: 6hrs no IAA (Ring1B), 20hrs no IAA + 7hrs 1uM 4-OH Tamoxifen (Dam-ScFv-H3K27me3) and 7hrs no IAA + 4hrs 1uM 4-OH Tamoxifen (Dam-only), and the best developed embryonic bodies were handpicked and pooled together.

value: Ring1B (full protein)

tag: molecule subtypes


title: s1_E8: 440551 T4 V4

source_name: Human airway epithelial cells

value: COPD

value: influenza A virus

tag: cell type


title: s2_E8: 626776 T4 V4

value: NHB


title: 3-2

tag: cell line

value: anti-H3K27me3 (Cell Signaling Technology, #9733)


title: 3-1


title: 1-2

value: anti-RNA polymerase 2 (self-made)


title: s1_E7: 440551 T4 V3


title: DamH3K27me3 DamOnly DamRing1B  - EB and ESC day14 (KIN5434_index33)

source_name: Embryoid Bodies and 2i-cultured ESC (day 14)

value: 129S1/SvImJ x CAST/Eij

value: anti-H3K27me3 (mintbody); untethered Dam; Ring1B (full protein)

value: genomic DNA; mRNA


title: s1_E6: 440551 T4 V2

value: Human airway epithelial cells


title: DamRing1B  - EB day14 (KIN5156_index27)


title: 2-1

value: anti-H3K27ac (self-made)


title: s2_E6: 626776 T4 V2

value: 4 hr


title: DamOnly  - EB and ESC day10 (KIN5434_index15)

source_name: Embryoid Bodies and 2i-cultured ESC (day 10)

value: untethered Dam


title: mouse ESC Input ChIP-seq

data_processing:
Reads were aligned using bowtie2  (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
Indexes for the alignments were then generated using “samtools index” and genome coverage tracks were computed using the “bamCoverage” utility from DeepTools with the following parameters: “--ignoreDuplicates --minMappingQuality 10”.
For marks that exist in broad domains in the genome, domains were called using MUSIC according to the suggested workflow (https://github.com/gersteinlab/MUSIC). For marks that form narrow peaks in the genome, peaks were called using MACS2 (v. 2.1.1.20160309) using the “macs2 callpeak” utility with the following parameters: “-q 0.05”.
Genome_build: mm10 (mouse) / hg19 (human)
Supplementary_files_format_and_content: bedGraph files were generated using DeepTools and contain the unnormalized, deduplicated read counts across the genome at a resolution indicated by the bin size.
Supplementary_files_format_and_content: broadPeak files were generated using MUSIC and indicate domains of enriched signal for the given mark.
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2 and indicate peaks of enriched signal for the given mark.

source_name: mouse embryonic stem cells

growth_protocol: Human hTERT-immortalized RPE-1 cells were grown in DMEM: F12 supplemented with 10% fetal bovine serum and 1% Pen/Strep (100 U/mL penicillin and 100 ug/mL streptomycin). Mouse embryonic stem cells were cultured on mouse embryonic fibroblasts and replated on 0.1% gelatin for two passages before harvest.

extract_protocol:
Cells were harvested by trypsinization, and chemically crosslinked with fresh formaldehyde solution (1% in PBS) for 8 minutes while rotating at room temperature. Crosslinking was quenched with glycine on ice. Cells were then lysed, sonicated, treated with RNase A and Proteinase K to reverse the crosslink, and cleared using DNA purification columns. Chromatin was incubated with antibodies, after which beads were added for antibody binding. After extensive washing, samples were cleared using purification columns and eluate was measured.
Libraries were prepared according to the Illumina TruSeq DNA LT kit and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: F1 hybrid ESC


title: s2_E5: 626776 T4 V1


title: s2_E7: 626776 T4 V3


title: DamCbx7 DamH3K27me3 DamH3K27me3MUT DamOnly H4K20me1Dam - mESC (KIN3443_index01)

value: Cbx7 (chromodomain trimer); anti-H3K27me3 (mintbody); anti-H3K27me3-mutated (mintbody); anti-H4K20me1 (mintbody); untethered Dam


title: s2_E3: 626776 T4 C3

value: control


title: s2_E4: 626776 T4 C4


title: DamH3K27me3 DamOnly DamRing1B  - EB and ESC day10 (KIN5434_index32)


title: 1-1

value: transfected HBVcircle-WT


title: DamH3K27me3 DamOnly DamRing1B  - EB and ESC day07 (KIN5434_index31)

source_name: Embryoid Bodies and 2i-cultured ESC (day 7)


title: s1_E4: 440551 T4 C4


title: 0h

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

description: microRNAs of L. migratoria response to M. robertsii infection for 0h

data_processing:
Raw reads were converted from very basic figure in sequencing,
clean reads were obtained by removing impurities of raw data such as insert tags, oversized insertion, low quality reads, poly A reads and small reads.
Then the analysis of types, number and length distribution of small RNAs sequences were on the basis of above clean reads.
The expression and distribution of sRNAs on genome was analyzed by mapping clean reads to L. migratoria genome with SOAP
The non-coding RNAs including rRNA, scRNA, snoRNA, snRNA and tRNA were discarded in order to acquire clean sRNAs with the alignment to GenBank and Rfam
Genome_build: Locusta migratoria (migratory locust)
Supplementary_files_format_and_content: Processed data.txt; abundance, all miRNAs and targets were analyzed

organism: Locusta migratoria

growth_protocol: Locusts were fed with a mixture artificial diet of wheat bran, fresh wheat seedlings and water, which provided three times a day at 30±2℃, with a photoperiods of 14L:10D

extract_protocol:
Total RNA was extracted from four abdomens samples by using of TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions.
small RNA was the 18-30 nt stripe and recovered from the different size RNA segments which separated by the PAGE gel.
Then the 3’ and 5’ ligation, reverse transcription and polymerase chain reaction amplification were conducted. PCR products were purified by PAGE gel and cDNA libraries of small RNAs were sequenced using an Illumina/Solexa high-throughput sequencing technology

treatment_protocol: Abdomens from uninfected locusts (0h) and infected 12h、24h and 36h locusts were collected respectively, flash frozen in liquid nitrogen, and stored at -80℃ until RNA extraction

tag: time

value: whole body


title: 24h

description: microRNAs of L. migratoria response to M. robertsii infection for 24h


title: hfd_5_7_BSseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Adapters and low quality bases (-q 20) were trimmed with Trim Galore (v0.6.2). Reads were also trimmed by 9 bp from the 5' ends to remove pull-down biases (--clip_r1 9).
Alignment was performed in single-end, non-directional mode followed by deduplication (deduplicate_bismark) and methylation calling (bismark_methylation_extractor) using Bismark (v0.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Bismark coverage report; tab-delimited text files include methylated and unmethylated calls

source_name: MII oocyte_high fat diet

extract_protocol:
The lysate containing genomic DNA was purified on AMPureXP beads
Libraries were prepared according to the scBS-seq protocol

value: MII oocyte

tag: diet

value: high fat diet


title: hfd_5_6_BSseq


title: 36h

description: microRNAs of L. migratoria response to M. robertsii infection for 36h


title: s1_E5: 440551 T4 V1

value: COPD

value: influenza A virus


title: s1_E2: 440551 T4 C2


title: WT methionine 1, rep 1

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Trans Per Million (TPM) were calculated using a custom script
Genome_build: Streptococcus pneumoniae D39 (accession NC_008533.2, assembly  GCA_000014365.2) was used directly in the analysis.
Supplementary_files_format_and_content: Transcriptome_of pneumococcus_D39_and_metE_mutant_in_1ug_per_ml_methionine.xlsx (TPM values for each sample)

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 1 µg/ml methionine for 6 hours

growth_protocol: Both strains were grown in 5 ml of THY to OD620-0.5; spin in microfuge (1.8 ml/tube x 3) and wash 2 times with Ringer's solution; suspended the final pellet in 1 ml of ringer's solution and adjusted the OD620 to 0.5 with ringer's solution  in a 20-ml glass tube. Mixed 300 ul of  bacterial suspension with 30 ml of fresh (not prewarmed) chemically defined medium supplemented with 1 ug/ml methionine. Split the suspension into four 20-ml glass tubes (7 ml/tube). Incubated at 37 ℃ with 5 % CO2 for 6hrs.

extract_protocol:
Total RNA was purified from cultures at the 6 hrs point. Total RNA was extracted using TIANGEN kit (TIANGEN, Beijing, China) and purified using QIAGEN kit (QIAGEN, Beijing, China).
The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

tag: strain

value: WT

tag: antibiotic resistance

value: rpsL1 (StreptomycinR)

value: cultured for 6 hours


title: 12h

description: microRNAs of L. migratoria response to M. robertsii infection for 12h


title: ΔmetE methionine 1, rep 2

source_name: Streptococcus pneumoniae D39 ΔmetE cultured in CDM with 1 µg/ml methionine for 6 hours

value: {delta}metE


title: s1_E3: 440551 T4 C3

tag: donor

value: Human airway epithelial cells


title: s2_E2: 626776 T4 C2

tag: time point

value: NHB


title: s2_D11: 655308 T18 V3

value: 18 hr

tag: condition


title: s1_D11: 18TL 343179 T18 V3

tag: infection


title: hfd_4_5_BSseq


title: mouse ESC H4K20me1 ChIP-seq

value: 129S1/SvImJ x CAST/Eij

value: H4K20me1 (Abcam ab9051)


title: 2-2

tag: treatment

value: transfected HBVcircle-Δcore

value: anti-H3K27ac (self-made)


title: hfd_5_8_BSseq


title: ΔmetE methionine 1, rep 1


title: DamRing1B  - EB day07 (KIN5156_index25)

source_name: Embryoid Bodies (day 7)

tag: dam-fusion protein

value: Ring1B (full protein)

value: genomic DNA; mRNA


title: hfd_4_2_BSseq

value: MII oocyte


title: s1_D12: 18TL 343179 T18 V4


title: s1_E1: 440551 T4 C1

value: 4 hr

value: control


title: hfd_5_1_BSseq

value: high fat diet


title: WT methionine 1, rep 2

value: WT


title: hfd_5_5_BSseq


title: hfd_5_4_BSseq


title: s2_D8: 655308 T18 P4


title: s2_E1: 626776 T4 C1


title: hfd_5_2_BSseq


title: s1_D8: 18TL 343179 T18 P4

value: COPD


title: hfd_4_9_BSseq


title: hfd_4_7_BSseq


title: s2_D12: 655308 T18 V4

value: influenza A virus


title: s2_D10: 655308 T18 V2


title: hfd_4_4_BSseq


title: s1_D10: 18TL 343179 T18 V2


title: s2_D9: 655308 T18 V1


title: s1_D9: 18TL 343179 T18 V1


title: hfd_4_16_BSseq


title: hfd_4_15_BSseq


title: hfd_3_5_BSseq


title: hfd_3_3_BSseq


title: s1_D6: 18TL 343179 T18 P2


title: s2_D3: 655308 T18 C3


title: hfd_3_2_BSseq


title: s2_D7: 655308 T18 P3


title: s2_D6: 655308 T18 P2


title: hfd_4_14_BSseq


title: hfd_4_10_BSseq


title: hfd_4_11_BSseq


title: s1_D2: 18TL 343179 T18 C2


title: hfd_3_7_BSseq


title: s2_D5: 655308 T18 P1


title: hfd_1_7_BSseq


title: hfd_4_13_BSseq


title: s1_D5: 18TL 343179 T18 P1


title: s2_D2: 655308 T18 C2


title: s1_D4: 18TL 343179 T18 C4


title: hfd_3_6_BSseq


title: hfd_3_1_BSseq


title: hfd_1_5_BSseq


title: hfd_4_12_BSseq


title: s2_D1: 655308 T18 C1


title: s1_D7: 18TL 343179 T18 P3


title: hfd_1_4_BSseq


title: s1_D3: 18TL 343179 T18 C3


title: s1_C7: 18TL 343179 T4 V3


title: hfd_1_1_BSseq


title: s2_C7: 655308 T4 V3


title: hfd_1_8_BSseq


title: hfd_1_6_BSseq


title: s2_C8: 655308 T4 V4


title: s1_C6: 18TL 343179 T4 V2


title: s1_D1: 18TL 343179 T18 C1


title: hfd_1_12_BSseq


title: hfd_1_11_BSseq


title: hfd_1_10_BSseq


title: s2_C6: 655308 T4 V2


title: s2_D4: 655308 T18 C4


title: s2_C4: 655308  T4 C4


title: s2_C5: 655308 T4 V1


title: P0190L2: Drug-treated replicate 3

city: Madison

first: Paul

last: Marker

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

data_processing:
Fastq files generated with bcl2fastq v2.20.422
Alignment to Mus musculus GRCm38 genome with STAR aligner v 2.5.3a with defulat settings
Read counts calculated with RSEM v. 1.3.0 with default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM files that contain expected read counts, TPM and FPKM

source_name: Mouse prostate epithelium

growth_protocol: PTEN-CaP2 (3.5 x 10^5) were combined with collagen mix containing 6 mg/mL rat tail collagen (BD Bioscience), 1X phosphate buffered saline (PBS), 1 N NaOH, and distilled H2O to make 25 μL collagen pellets for xenograft surgery. Pellets were surgically grafted under the kidney capsules of 10-week-old male Balb/C nu/nu mice (Charles River). Xenografts were grown in vivo for 3 weeks at which time mice were treated with 100 mg/kg pegvisomant suspended in sterile saline or a sterile saline vehicle control three times per week for three weeks. Three days after the final injection, mice were sacrificed for organ and xenograft collection.

extract_protocol:
RNA was extracted from flash frozen tissue using a NuceloSpin® RNA extraction kit (740955, Machery-Nagel, Düren, Germany) per the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA Sample Preparation Guide

tag: host age

value: 16 weeks

tag: host sex

value: Male

tag: graft strain

tag: tissue

value: prostate epithelium renal graft


title: s1_C8: 18TL 343179 T4 V4

value: Human airway epithelial cells


title: s2_C12: 672447 T4 C2

value: NHB


title: P0189R2: Drug-treated replicate 2

treatment_protocol: Xenografts were grown in vivo for 3 weeks at which time mice were treated with 100 mg/kg pegvisomant suspended in sterile saline or a sterile saline vehicle control three times per week for three weeks. Three days after the final injection, mice were sacrificed for organ and xenograft collection.


title: CD_3_7_BSseq

source_name: MII oocyte_control diet

value: control diet


title: s1_C3: 18TL 343179 T4 C3


title: hfd_1_15_BSseq


title: s1_C2: 18TL 343179 T4 C2


title: s1_C4: 18TL 343179 T4 C4


title: hfd_1_3_BSseq


title: V0204L2: Vehicle-treated replicate 3

value: PBS vehicle 3X weekly for 3 weeks


title: s2_C3: 655308  T4 C3


title: CD_3_5_BSseq


title: hfd_3_4_BSseq


title: CD_3_6_BSseq


title: CD_3_1_BSseq


title: CD_3_8_BSseq


title: s2_C2: 655308  T4 C2


title: β-glucan coated 25 µm beads 3

city: Los Angeles

first: Seeun

last: Oh

address: 8700 Beverly Blvd

department: Biomedical Science

institute: Cedars-Sinai Medical Center

data_processing:
The quality control of library consists of three steps: (1) Qubit 2.0: tests the library concentration preliminarily. (2) Agilent 2100: tests the insert size. (3) Q-PCR: quantifies the library effective concentration precisely.
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (Galaxy Version 2.7.7a) on the Galaxy server (1) with default parameters, using a custom mouse GRCm38 transcriptome reference downloaded from https://www.ncbi.nlm.nih.gov, containing all protein coding and long non-coding RNA genes based on NCBI mm10 annotation.
Aligned files were imported in R (version 4.0.2), and FeatureCounts of Rsubread (version 2.2.6) was used to count the reads for each gene in all samples.
Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and fitted into a negative binomial generalized linear model with DESeq2 (version 1.28.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow derived dendritic cells

growth_protocol: Bone marrow cells were cultured with RPMI with GM-CSF

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen) and the quality and quantify of total RNA was measured by using Nanodrop, Agarose Gel Electrophoresis, and Agilent 2100.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: 8 days of BMDCs were stimulated with indicated stimuli overnight

tag: sitmulation

value: β-glucan coated 25 µm beads

tag: age

value: Mice were 8-10 weeks


title: s1_B12: 43905 T18 V4

extract_protocol:
total RNA were prepared using Qiagen Rneasy mini plus kit
RNA libraries were prepared for sequencing using standard Illumina Illumina NovaSeq 6000 with 150-bp pair-ended reads

value: 18 hr

tag: cell type


title: s2_C1: 655308  T4 C1


title: β-glucan coated 25 µm beads 1


title: CD_3_4_BSseq

value: MII oocyte


title: s1_C5: 18TL 343179 T4 V1

value: 4 hr


title: P0186L2: Drug-treated replicate 1


title: CD_3_3_BSseq


title: V0203L2: Vehicle-treated replicate 2


title: CD_3_2_BSseq


title: CD_2_4_BSseq


title: V0194L2: Vehicle-treated replicate 1


title: s1_C1: 18TL 343179 T4 C1

value: control


title: CD_2_2_BSseq


title: s1_B10: 43905 T18 V2


title: CD_2_6_BSseq


title: Hyphae locked C. albicans 3

value: Hyphae locked C. albicans


title: β-glucan coated 25 µm beads 2


title: CD_2_5_BSseq


title: CD_2_16_BSseq


title: β-glucan coated 6 µm beads 3

value: β-glucan coated 6 µm beads


title: CD_2_1_BSseq


title: CD_2_8_BSseq


title: s2_B10: 18TL 103224 T18 V2

value: COPD


title: s1_B11: 43905 T18 V3

value: influenza A virus


title: Hyphae locked C. albicans 1


title: s2_B11: 18TL 103224 T18 V3


title: CD_2_3_BSseq


title: s2_B9: 18TL 103224 T18 V1


title: s2_B8: 18TL 103224 T18 P4


title: β-glucan coated 6 µm beads 2


title: s2_B7: 18TL 103224 T18 P3


title: s1_B9: 43905 T18 V1


title: Yeast locked C. albicans 3

value: Yeast locked C. albicans


title: s1_B8: 43905 T18 P4


title: β-glucan coated 6 µm beads 1


title: CD_2_13_BSseq


title: Hyphae locked C. albicans 2


title: CD_2_15_BSseq


title: s1_B7: 43905 T18 P3


title: CD_2_11_BSseq


title: Yeast locked C. albicans 2


title: Unstimulated 3

value: Unstimulated control


title: Yeast locked C. albicans 1


title: Unstimulated 1


title: Unstimulated 2


title: s2_B6: 18TL 103224 T18 P2


title: s1_B6: 43905 T18 P2


title: CD_2_10_BSseq


title: HPmECC, WT-4

city: Kyoto

first: mise

last: yuka

address: 54 Kawahara-cho, Shogoin, Sakyo-ku,

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequencing reads using Trim_Galore (RRID: SCR_011847)
The resulting reads were aligned to the mouse reference genome (GRCm38) using STAR v2.6.1a (RRID: SCR_004463)
Read counts and gene expression values were calculated using RSEM v1.3.1 (RRID:SCR_013027)
Genome_build:  GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing expected read counts, FPKM, and TPM values from RSEM

source_name: murine endometrial cancer cells

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit and Micro Kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraly Kit was TruSeq standared mRNA.

tag: cell line

value: HPmECC

value: murine endometrial cancer cells


title: CD_1_7_BSseq

tag: diet


title: s1_B4: 43905 T18 C4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: Human airway epithelial cells


title: s2_B4: 18TL 103224 T18 C4


title: CD_2_14_BSseq

value: control diet


title: CD_1_6_BSseq


title: HPmECC, WT-1

tag: strain


title: s2_B5: 18TL 103224 T18 P1


title: CD_1_4_BSseq


title: mECC, DM-3

value: mECC


title: mECC, DM-4


title: CD_1_24_BSseq


title: CD_1_8_BSseq


title: CD_2_12_BSseq


title: HPmECC, WT-3


title: s1_B2: 43905 T18 C2


title: s2_B3: 18TL 103224 T18 C3


title: CD_1_5_BSseq


title: s1_B5: 43905 T18 P1


title: primary cultured normal endometrium cells, B6-4

source_name: murine endometrium cells

value: murine endometrium cells


title: CD_1_22_BSseq


title: s1_B1: 43905 T18 C1


title: primary cultured normal endometrium cells, B6-3


title: CD_1_9_BSseq


title: primary cultured normal endometrium cells, B6-2


title: CD_1_19_BSseq


title: mECC, DM-2


title: s1_A8: 43905 T4 V4


title: CD_1_2_BSseq


title: s2_B2: 18TL 103224 T18 C2


title: mECC, DM-1


title: HPmECC, WT-2


title: s2_B1: 18TL 103224 T18 C1


title: CD_1_21_BSseq


title: CD_1_16_BSseq


title: CD_1_20_BSseq


title: primary cultured normal endometrium cells, B6-1


title: s1_B3: 43905 T18 C3


title: s2_A7: 18TL 103224 T4 V3


title: s2_A12: 672447 T4 C1

value: NHB


title: CD_1_13_BSseq


title: s1_A6: 43905 T4 V2


title: s2_A8: 18TL 103224 T4 V4


title: CD_1_15_BSseq