title: bnafah, SD2, rep3

city: yichun

first: tiantian

last: zhi

state: jiangxi

address: 576 Xuefu Road, Yichun City, Jiangxi Province

institute: College of Life Sciences and Resources and Environment, Yichun University

data_processing:
trim-galore software was used to remove the Adapter in the sequence, remove low-quality and N-containing sequences, and then remove sequences shorter than the length threshold (20bp by default) (as long as one sequence in a fragment is shorter than the threshold, the corresponding two sequences are removed).
There is the possibility of machine errors in the sequencing process, and the sequencing quality distribution evaluation can reflect the sequencing quality. We use QPhred score to measure the sequencing quality. When the average sequencing quality is Q20≥85%, and the average Q30≥80%, the sequencing quality is considered qualified.
We used the HISAT2 software to compare the sequence to the reference genome. Obtain sequence location information on the reference genome.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Brassica_napus/latest_assembly_versions/GCF_020379485.1_Da-Ae/.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Brassica napus

source_name: leaves

growth_protocol: The seeds of Brassica napus.L wild type and mutants(bnaa06fah and bnafah) was plated on MS medium grown under long day (16h light/8h dark) for 5 days, seedlings were transplant to soil and growth under long day (16h light/8h dark) condition for 2 weeks, then transferred to SD (16h light/8h dark) condition for 3 days for PCD phenotypic observation.

extract_protocol:
The total RNA was extracted using a TRIzol reagent (TIANGEN, Beijing, China) following the procedure of the manufacturer. Subsequently, the total RNA was qualified and quantified using a Agilent 2100 bioanalyzer. TruSeq RNA Sample Preparation kit v2 (Illumina, San Diego, CA, USA) was used for library construction with the instructions of the manufacturer. All the samples were sequenced using an Illumina HiSeq 2000 sequencer by Biomac Inc.(Beijing, China).
The total RNA was qualified and quantified using a Agilent 2100 bioanalyzer. TruSeq RNA Sample Preparation kit v2 (Illumina, San Diego, CA, USA) was used for library construction with the instructions of the manufacturer.

treatment_protocol: transferred from long day (LD) to short day (SD)for 0, 1 and 2 days

value: leaves

value: BnaA06FAH and BnaC05FAH knock down


title: Cortex_cytoplasm_mTLE+HS13

status: Public on Nov 06 2024

type: SRA

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE+HS(W4)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E07-28.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

library_source: transcriptomic

data_processing:
(tRFs) Quality control of the small RNA-seq raw reads was performed using FastQC (Andrews S, 2010). Adapters were removed using Cutadapt (1.18; (Martin, EMBnet.journal. 2011)) with default settings for single end reads. Trimmed reads were aligned to the hg19 pre-tRNA and mature tRNA (https://github.com/sararselitsky/tDRmapper) with tDRmapper (Selitsky and Sethupathy, BMC Bioinformatics. 2015). All fragments >14 nt and <40 nt were included to further analysis. Only sequences counted >99 times were considered to be expressed.
(tRFs) Differentially expressed (DE) tRFs were identified with DESeq (Anders and Huber, Genome Biol. 2010) R package (R version 4.0.3). Data (only DE tRFs) was visualized with a clustering heatmap (gplots R package) using correlation distance, and principal component analysis (all detected tRFs; PCA; stats R package).
(miRNAs) Following trimming of low-quality bases and adapter sequences with FASTQ-MCF (version 0.0.13), processed reads were mapped using Bowtie. MiRNA alignment was performed against the human reference from miRBase (release v21).
(miRNAs) For differential expression analysis, count data for miRNAs were analysed for differential expression in R using the Bioconductor package EdgeR version 3.12.1 (Robinson et al., Bioinformatics. 2010) with the trimmed mean of M-values (TMM) normalisation method (Robinson and Oshlack., Genome Biol. 2010). Adjusted P-values for multiple testing were calculated using the Benjamini-Hochberg false discovery rate (FDR) and only genes with an FDR < 0.05 were considered significantly differentially expressed.
(miRNAs) IsomiRs analysis was performed using the IsomiRage Java tool (Muller et al., Front Bioeng Biotechnol. 2014). Briefly, .map bowtie output files were used as inputs for the Isomirage pipeline that returned a table containing the number of reads for each isoform in each biological sample. Significant changes in isoform expression were detected using EdgeR, as described above.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab-delimited text files contain raw read counts of different samples, list of differentially expressed genes.
Supplementary files format and content: countTable_edgeR.txt files (The order of the samples (sample IDs) is specified in the file name starting with "guide" for each group of samples for all the comparisons. The unique sample IDs are consecutively ordered as per the guide, for e.g., first with CTL (control samples IDs) and W4 (test tissue samples, mTLE+HS IDs) in this condition. )

molecule: total RNA

organism: Homo sapiens

source_name: Cortex

extract_protocol:
Complete details can be found on in our recent study (Vangoor et al., MedRxiv. 2021). Briefly, sub cellular fractionation was performed isolating pure cytosolic and nuclei cell compartments. Isolated cytoplasmic and nuclei samples were stored in Qiazol (Qiagen) at -80oC until RNA extraction was performed. Total RNA was extracted using miRNeasy kit (Qiagen), according to manufacturer’s protocol.
For small RNA library construction and sequencing, small RNAs of <200 nucleotides were purified using the miRVana microRNA isolation kit (Ambion, Life Technologies). 100 ng of small RNA was prepared for sequencing using the TruSeq Small RNA preparation kit (Illumina, San Diego, California, USA). Small RNA sequencing was performed on an Illumina HiSeq 4000 sequencer at the Beijing Genomics Institute (BGI) (Hongkong, China).

tag: tissue

value: Cortex

tag: Sex

value: Male

tag: cell compartment

value: Cytoplasm

tag: disease state

value: mTLE+HS

tag: fraction

value: Small RNAs


title: PbIMC1gckD, control 2

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

country: China

institute: China Medical University

data_processing:
Reads counts were obtained with HTSeq v0.9.1. Differential expression analysis of genes between the PbIMC1gcKD parasites cultured in both [+] and [-] TMP conditions were determined using the DESeq R package (1.18.0). The p-values were adjusted using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR). Genes with an adjusted P value <0.05 found by DESeq were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: readscount values for each Sample

organism: Plasmodium berghei

source_name: gamete

growth_protocol: activated gametocytes from PbIMC1gcKD [+]/[-] TMP parasite were maintained in gametocyte activation buffer

extract_protocol:
activated gametocytes from PbIMC1gcKD [+]/[-] TMP parasite were purified with 48% Nycodenz and activated in gametocyte activation buffer at 25℃ for 15 min
mRNA was enriched using poly-T oligo-attached magnetic beads. Reverse transcription was performed with SuperScript II (Invitrogen) using random primers. The reaction was then treated with RNaseH to remove the RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced using the Illumina platform.
RNA-seq raw data were initially filtered by fastq to obtain high-quality, clean data. Adapter trimming was performed using cutadapt version 1.13 (http://cutadapt.readthedocs.io/en/stable/guide.html). Processed reads were aligned to the P. berghei ANA genome (assembly PlasmoDB-67) with Hisat2 v2.0.4 [108] and deduplicated according to UMI using UMI-tools (v1.0.0)

value: gamete

tag: cell line

value: Plasmodium berghei ANKA

tag: cell type

tag: genotype

value: WT

tag: treatment

value: trimethoprim treatment


title: Cortex_cytoplasm_mTLE non-HS15_pre

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
processed data file names description (miRNAs):  Cx_cytoplasm_PRE_vs_POST_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-06_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Female

value: mTLE non-HS


title: Cortex_cytoplasm_mTLE non-HS15_post

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_PREvsPOST
processed data file names description (miRNAs):  Cx_cytoplasm_PRE_vs_POST_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_PREvsPOST.txt
miRNA processed data file (Raw count tables):  Cx_cyt_PREvsPOST_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_PREvsPOST_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_PREvsPOST_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E15-02_Post.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnafah, SD2, rep2


title: bnafah, SD1, rep3


title: Cortex_cytoplasm_mTLE+HS12

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE+HS(W4)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E06-19.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_mTLE+HS10

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE+HS(W4)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E06-21.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_mTLE+HS11

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE+HS (W4)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE+HS(W4)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E08-17.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnafah, LD(SD0), rep2


title: bnafah, SD1, rep2


title: Cortex_cytoplasm_mTLE non-HS8

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E11-18.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnafah, SD2, rep1


title: Cortex_cytoplasm_mTLE+HS9

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW4.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW4_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW4_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW4_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E05-03.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnafah, SD1, rep1


title: Cortex_cytoplasm_mTLE non-HS7

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E07-24.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_mTLE non-HS6

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E07-21.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_mTLE non-HS3

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E06-13.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnafah, LD(SD0), rep1


title: Cortex_cytoplasm_mTLE non-HS1

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E05-33.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnaa06fah, SD2, rep3

value: BnaA06FAH knock down


title: bnaa06fah, LD(SD0), rep3


title: Cortex_cytoplasm_mTLE non-HS2

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_E05-35.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_control7

description:
file category:  not applicable
processed data file names description (miRNAs):  not applicable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_S11-028.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable

value: Postmortem controls


title: bnaa06fah, SD2, rep2


title: bnafah, LD(SD0), rep3


title: Cortex_cytoplasm_control6

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE non-HS(W0)_isomiRs_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_S10-109.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnaa06fah, SD1, rep2


title: Cortex_cytoplasm_control5

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE non-HS(W0)_rawcounttable_isomiRs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_S12-002.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: bnaa06fah, SD2, rep1


title: bnaa06fah, LD(SD0), rep2


title: bnaa06fah, SD1, rep1


title: Cortex_cytoplasm_control1

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cortex (Cx)_cytoplasm (cyt)_Control (CTL)_vs_mTLE non-HS(W0)_guide_ordered IDs
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_C02-05.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_control3

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE non-HS(W0)_rawcounttable
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_C05-93.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Cortex_cytoplasm_control4

description:
file category:  Cortex(Cx)_Cytoplasm(cyt)_Control(CTL) and mTLE non-HS (W0)
processed data file names description (miRNAs):  Cx_cytoplasm_CTL_vs_mTLE non-HS(W0)_sigGenes_FDR005
miRNA processed data file (Guide for the files (sample IDs)):  guide_Cx_cyt_CTLvsW0.txt
miRNA processed data file (Raw count tables):  Cx_cyt_CTLvsW0_countTable_edgeR.txt
miRNA processed data file (Significant genes):  Cx_cyt_CTLvsW0_sigGenesFDR005.txt
miRNA processed data file (rawdata-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_countTable_edgeR.txt
miRNA processed data file (significant-IsomiRs):  Cx_cyt_CTLvsW0_isomiRs_sigGenesFDR005.txt
tRFs processed data file (raw counts):  Cx_cyt_S02-071.txt
tRFs processed data file (normalized counts):  not applicable
tRFs processed data file (significant  genes):  not applicable


title: Control, LD(SD0), rep3


title: PAH patient derived circulating endothelial cells 7

city: Cleveland

first: Kulwant

middle: Singh

last: Aulak

state: Ohio

address: 9500 Euclid Ave

department: Immunology and Immunity

country: USA

institute: cleveland Clinic

data_processing:
The original image data file from high-throughput sequencing platforms (using Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data containing sequences of reads and corresponding base quality are stored in FASTQ(fq) format files.
Remove reads with adaptor contamination.
Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Assembly: hg38
Supplementary files format and content: excel file includes fpkm values for each sample

source_name: Blood

growth_protocol: All endothelial cells were grown on fibronectin coated plates (50ng/ml) using endothelial cell media, (EGM-2)

extract_protocol:
RNA was isolated using the RNeasy kit
sequencing libraries using NEBNext Ultra RNA library prep kit for Illumina using manufacturers instructions

value: Blood

value: circulating endothelial cells

value: Endothelial cells

value: PAH


title: Control, SD1, rep3

value: leaves


title: bnaa06fah, SD1, rep3


title: PAH patient derived circulating endothelial cells 8


title: PAH patient derived circulating endothelial cells 5


title: PAH patient derived circulating endothelial cells 6


title: PAH patient derived circulating endothelial cells 4


title: Control, SD2, rep2


title: bnaa06fah, LD(SD0), rep1


title: Control, LD(SD0), rep2


title: PAH patient derived circulating endothelial cells 1


title: PAH patient derived circulating endothelial cells 2


title: Control, SD1, rep1


title: Control, SD1, rep2


title: Control, SD2, rep1


title: Control, LD(SD0), rep1


title: PAH pulmonary artery endothelial cells 5

source_name: pulmonary artery endothelial

value: pulmonary artery endothelial

value: PAEC


title: PAH pulmonary artery endothelial cells 4


title: WT-BMDM-H3K27ac

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

library_source: genomic

data_processing:
Genome mapping was performed using Bowtie (version:0.12.8) and clean reads were compared to reference genome mm10. MACS (version 2.2.7.1) was applied to call peak.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameter was set as fold change ≥ 2 or≤ 1/2 and P value < 0.05, and the differences between the obtained peakswere annotated.
The annotation program was the same as the above peak annotation program, including different peak location information, annotation information, etc. The motif analysis was conducted using “HOMER” tool. And the result of HOMER motif is the motif information predicted based on the existing database within the peak.
Supplementary files format and content: narrowPeak file that includes information of histone modification
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: BMDM

extract_protocol:
CUT&Tag was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions. Briefly, WT and Rbm25-deficiency BMDMs were stimulated with LPS and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibody against H3K9ac or H3K27ac (Millipore) at 4 °C overnight. On next day, samples were incubated with second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

value: bone marrow

value: Mouse primary bone marrow-derived macrophages

value: LPS(100ng/ml) for 4h


title: PAH pulmonary artery endothelial cells 3


title: KO-BMDM-H3K27ac


title: Control, SD2, rep3


title: PAH pulmonary artery endothelial cells 2


title: PAH pulmonary artery endothelial cells 1


title: WT-BMDM-H3K9ac


title: Control pulmonary artery endothelial cells 5

value: Wt


title: KO-BMDM-H3K9ac


title: PAH patient derived circulating endothelial cells 3


title: Control pulmonary artery endothelial cells 4


title: Control pulmonary artery endothelial cells 3


title: Control pulmonary artery endothelial cells 1


title: GSC3565 cells, shSUV39H1_4

city: Bloomington

first: QIQI

last: XIE

state: IN

address: 3209 E 10th St Apt E6

department: Biology

institute: Indiana University Bloomington

data_processing:
total RNA isolated from GSC3565 and GSC1914 cells with control KD or SUV39H1 KD was subjected to RNA-seq at Novogene Corporation. Quality control of the raw RNA-seq reads was performed using FastQC, and adapter sequences were removed with TrimGalore.
Trimmed reads were aligned to the human reference genome (hg19) using STAR aligner. Quantification of transcript abundance was performed using Salmon in quasi-mapping mode, and the resulting quantification files were imported into R for differential expression analysis using the DESeq2 package. Differentially expressed genes (DEGs) were identified with a cutoff of log2 fold change > 1 or < -1 and an adjusted p-value < 0.05.
The DEGs were visualized using volcano plots generated with GraphPad Prism. Gene set enrichment analysis (GSEA) was performed using the preranked list of DEGs based on the log2 fold change and adjusted p-value. Enriched pathways and gene ontology terms were represented as bubble plots using Cytoscape.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: GBM

growth_protocol: Lenti-X-293T cells (Takara Bio, cat# 632180) were cultured in DMEM media (Gibco, cat# 11995065) supplemented with 10% FBS (Corning, cat# 35015CV).

extract_protocol:
Lenti-X-293T cells cultured in DMEM media were transfected with lentivirus packaging plasmids (pMD2.g and psPAX2), along with either control or SUV39H1 shRNA vectors (Sigma-Aldrich Mission shRNA, #1 TRCN0000285355 and #2 TRCN0000275322), or pHAGE PGK-GFP-IRES-LUC-W (Addgene, cat# 46793) using the jetPRIME transfection reagent (Polyplus, cat# 101000001). After 24 hrs, the DMEM media was replaced with GSC culture media, and the cells were incubated for an additional 48 hrs at 37°C to produce lentivirus. The supernatant containing the lentivirus was harvested and saved in -80°C. For lentivirus infection, GSCs (4 x 10^5 cells per well in a 6-well plate) were exposed to the lentivirus for 18 hrs, followed by a media change to GSC culture media and a further 48 hrs incubation.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: GBM

value: GSC

value: SUV39H1 knockdown

value: NO


title: SYO-1 cellline treated with 100nM TAK-981, replicate2

city: La Jolla

first: Aniruddha

middle: J.

last: Deshpande

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed from raw reads using Cutadapt version 2.3.
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
Assembly: hg38
Supplementary files format and content: Tab-delimited file with raw counts from RSEM.
Supplementary files format and content: Tab-delimited file with normalized expression (TPM) from RSEM.

growth_protocol: SYO1 cells were cultured in DMEM supplemented with 10% FBS, 1 % penicillin-streptomycin and 1% L-glutamine. HS-SY-II cells were additionally supplemented with 0.5% Sodium Pyruvate.

extract_protocol:
Cells were pelleted and RNA was extracted with concentration determined by Qubit (Thermo Scientific).
PolyA RNA was isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA)

treatment_protocol: HS-SY-II and SYO1 cells were treated with either TAK-981 at concentrations of 25nM and 100nM respectively for the treatment arm or DMSO for the control arm for 48 hours.

value: Synovial sarcoma


title: SYO-1 cellline treated with DMSO, replicate2

value: DMSO


title: SYO-1 cellline treated with DMSO, replicate3


title: SYO-1 cellline treated with 100nM TAK-981, replicate1


title: GSC3565 cells, shControl_3

value: WT


title: HS-SY-II cellline treated with 25nM TAK-981, replicate1

source_name: HS-SY-II

value: HS-SY-II


title: GSC3565 cells, shSUV39H1_3


title: GSC3565 cells, shControl_4


title: HS-SY-II cellline treated with 25nM TAK-981, replicate2


title: HS-SY-II cellline treated with 25nM TAK-981, replicate3


title: GSC3565 cells, untreated_2

description: untreated.bw

data_processing:
Sequencing reads were trimmed for adapter sequences using Trim Galore and aligned to the human reference genome (hg19) using Bowtie2. Aligned reads were filtered to remove duplicate reads, mitochondrial reads, and low-quality reads using SAMtools and Picard tools.
Peaks were called using MACS2 to identify regions of open chromatin. The resulting peak files were further processed to generate a high-confidence set of peaks by filtering out blacklist regions and peaks overlapping with ENCODE blacklisted regions. The number of reads within each peak was quantified using featureCounts from the Subread package.
Differentially accessible regions between conditions were identified using DESeq2, with an adjusted p-value < 0.05 considered significant. Peaks were annotated to the nearest genes using HOMER, and gene ontology (GO) enrichment analysis was performed on the annotated genes using the GOseq package.
Heatmaps and average signal profiles of ATAC-seq data were generated using DeepTools. The bigWig files for visualization were created using bedGraphToBigWig. The Integrative Genomics Viewer (IGV) was used to visualize the ATAC-seq signal tracks across the genome.
Assembly: hg19
Supplementary files format and content: bw
Supplementary files format and content: bed

growth_protocol: GSC3565 cells treated with vehicle or chaetocin 50 nM for 48 hrs were subjected to ATAC-seq at the Center for Medical Genomics at Indiana University School of Medicine.

extract_protocol:
Nuclei were collected by centrifugation and resuspended in the transposition reaction mix containing Tn5 transposase (Illumina, cat# FC-121-1030) and incubated at 37°C for 30 mins. The transposed DNA was purified using the DNA Clean & Concentrator-5 (Zymo, cat# D4003) and PCR amplified using Nextera PCR primers. The amplified libraries were purified with the KAPA HiFi HotStart ReadyMix (Roche, cat#KK2602) and quantified using a Qubit fluorometer (Thermo Fisher Scientific). Libraries were sequenced on an Illumina platform to generate paired-end reads.
ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, GSCs were washed with cold PBS and lysed in ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630).

value: GBM stem cell

value: untreated


title: HS-SY-II cellline treated with DMSO, replicate2


title: SYO-1 cellline treated with DMSO, replicate4


title: GSC3565 cells, untreated_1

description: untreated.bw


title: GSC1914 cells, shSUV39H1_1


title: GSC1914 cells, shControl_2


title: Control pulmonary artery endothelial cells 2

value: Endothelial cells


title: SYO-1 cellline treated with DMSO, replicate1


title: SYO-1, SS18-SSX Fusion CUT&RUN, TAK-981 Treated, Rep2

data_processing:
Paired-end reads were trimmed using Cutadapt version 2.3 with parameters “-j 12 -m 20 -O 5 -q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT”. Trimmed reads were aligned against E. coli genomic sequence (GCF_000005845.2_ASM584v2_genomic) using Bowtie2 version 2.2.5 with parameters “--local” to quantify spike-in amount. Unmapped reads were subsequently aligned against hg38 chrM to remove mitochondrial reads using Bowtie2 with parameters “--local -X 2000”. Remaining unaligned reads were mapped against human genome version hg38 (without chrM) using Bowtie2 with parameters “--very-sensitive --no-discordant -X 2000”. Multimapping and improperly paired reads were removed using Deeptools alignmentSieve version 3.4.3 with parameters “--minMappingQuality 30 --samFlagInclude 2”. Duplicate reads were removed using Picard MarkDuplicates version 2.22.0. Peak calling was performed in DMSO treated samples using Macs2 version 2.2.9.1 with parameters “--nomodel --shift -75 --extsize 150 --keep-dup all -q 0.01 --broad --broad-cutoff 0.1 --gsize 2700000000.0 --format BAMPE”. Overlapping peaks in DMSO replicates were determined using Bedtools intersect version 2.29.2. Overlapping peaks were merged using Bedtools merge and parameter “-d 500”. Peaks overlapping Encode blacklist regions were removed. Peaks were annotated and peak tags were counted in each sample using Homer annotatePeaks.pl with parameters “hg38 -raw”. Bigwig signal files were generated using Deeptools bamCoverage with parameters “--binSize 20 --smoothLength 500 -p 12 --normalizeUsing RPGC --extendReads --ignoreForNormalization chrX --effectiveGenomeSize 2913022398 –scaleFactor [spike-in scale factor]”.
Assembly: hg38
Supplementary files format and content: Spike-in normalized bigwig file
Library strategy: CUT&RUN

growth_protocol: SYO1 cells were cultured in DMEM supplemented with 10% FBS, 1 % penicillin-streptomycin and 1% L-glutamine.

extract_protocol:
CUT&RUN samples were generated using CUTANA kit according to manufacturere's instructions.
CUT&RUN sample libraries were generated using CUTANA kit according to manufacturere's instructions.

treatment_protocol: SYO1 cells were treated with either TAK-981 or DMSO for 48 hours.


title: GSC3565 cells, Chaetocin_treated_2


title: GSC1914 cells, shControl_1


title: SYO-1, SS18-SSX Fusion CUT&RUN, DMSO Treated, Input


title: SYO-1, SS18-SSX Fusion CUT&RUN, DMSO Treated, Rep2


title: GSC3565 cells, Chaetocin_treated_1


title: SYO-1, SS18-SSX Fusion CUT&RUN, DMSO Treated, Rep1


title: SYO-1, TAK-981 Treated, Input

data_processing:
Mouse spike-in reads were classified and separated from SYO-1 ChIP-seq reads using Xenome version 1.0.0. First mate (read1) of each sample were trimmed using Cutadapt version 2.3 with parameters “-j 12 -m 30 -O 5 -q 15 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”. Trimmed reads were aligned against hg38 chrM to remove mitochondrial reads using Bowtie2 with parameters “--local”. Remaining unaligned reads were mapped against human genome version hg38 (without chrM) using Bowtie2 with parameters “--local”. Multimapping reads were removed using Deeptools alignmentSieve version 3.4.3 with parameters “--minMappingQuality 30”. Duplicate reads were removed using Picard MarkDuplicates version 2.22.0. Peak calling was performed using Macs2 version 2.2.9.1 with parameters “--keep-dup all -q 0.01 --broad --broad-cutoff 0.1 --gsize 2700000000.0 --format BAM”. Overlapping peaks in DMSO replicates were determined using Bedtools intersect version 2.29.2. Overlapping peaks were merged using Bedtools merge. Peaks overlapping Encode blacklist regions were removed. Peaks were annotated and peak tags were counted in each sample using Homer annotatePeaks.pl with parameters “hg38 -raw”. Bigwig signal files were generated using Deeptools bamCoverage with parameters “--binSize 20 --smoothLength 500 -p 12 --normalizeUsing RPGC --ignoreForNormalization chrX --effectiveGenomeSize 2913022398”.
Assembly: hg38
Supplementary files format and content: Read-depth normalized bigwig file

extract_protocol:
Cells were fixed with 1% formaldehyde. Chromatic was sinicated using Covaris.
ChIP-seq libraries were prepared using standard protocol.


title: SMYD1 knockout cells, KO1.Day5

city: Beijing

first: Yun

last: Chang

address: 167 Beilishi Road, Xicheng District

institute: Fuwai hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapedto GrcM38/mm10 using CLc genomic benchwork (parameters- mismath cost: 2 inserion cost. 3 deletion cost:3 ength facion: 0.8 simantyfaction.0 .8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: nm10
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions. 1 ug oftotal RNA was used for the construction of sequencing librarie
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: human embryonic stem cells

value: SMYD1 KO

value: cardiac differentiation


title: D574 TCR library 3

city: New York

first: Alex

last: George

state: NY

address: 960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.TCR.txt.gz

data_processing:
scRNA-seq reads were analyzed by pseudoalignment using kallisto v0.46.2 (GRCh38 with Gencode v24 annotation) and bustools v0.40.0. CITE-seq and hashtag barcodes were demultiplexed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8). GEX count matrix was filtered for cell barcodes with >1000 molecules/cell. These cell barcodes were used to filter ADT hashtag/CITE-seq count matrix from DropSeq8. Hashtags were demultiplexed on filtered HTO/ADT count matrix using the HashSolo (https://github.com/calico/solo/blob/master/solo/hashsolo.py) implementation in ScanPy (https://github.com/scverse/scanpy, scanpy.external.pp.hashsolo function) where prior cell frequency arguments for HashSolo function were based on theoretical doublet rate in 5’v2 HT 10x chip based on cell input (e.g. 0.08 doublet rate, 0.01 negative, 0.91 singlet rate, for 20k cell input).
Immune receptor libraries (TCR and BCR) were aligned using Cell Ranger 7.0.1 (vdj function) using reference vdj_GRCh38_alts_ensembl-7.0.0.
A mitochondrial gene filter was applied for any cells above a 95% confidence interval for MT pseudo-alignment rate on a per library basis. A hemoglobin gene filter was applied to all libraries for cells > 0.01 pseudo-alignment rate for HB genes.
MultiModal Classifier Hierarchy (MMOCHI, https://github.com/donnafarberlab/MMoCHi), which is trained using events selected by thresholding of user-defined marker genes and proteins, was implemented to define immune cell subsets across sites. MMOCHI classification legend: (CD4N = Naive CD4 T cell, CD4Treg = CD4 Regulatory T cell, CD4CM = Central Memory CD4 T Cell, CD4EM = Effector Memory CD4 T cell, CD8EM = Effector Memory CD8 T cell, CD8N = Naive CD8 T Cell, CD8CM = Central Memory CD8 T Cells, B_cell_N = Naive B Cells, B_cell_Innate_M = Innate Memory B Cells (IgD+CD27+), B_cell_CD27-IgD- =  CD27-IgD- B cells, Plasma_cluster = Plasma Cells identified by GEX clustering, Myeloid_cluster = Myeloid Cells identified by GEX clustering, NK_Cluster = NK Cells identified by GEX clustering). Memory B cell classifications are subtyped by receptor isotype.
Assembly: GRCh38/Ensembl93
Supplementary files format and content: GEX and ADT libraries: tab-delimited text files with cell-identifying barcodes, hashtags, donor, tissue site, MMOCHI immune cell classification, stimulation condition (w/ applicable sort information), and count matrix
Supplementary files format and content: TCR and BCR libraries: tab-delimited text files with cell-identifying barcodes, immune receptor chain, VDJ genes, cdr3 amino acid sequence, cdr3 nucleotide sequence, raw clonotype id and other alignment statistics/metadata outputted from CellRanger.
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

source_name: various

extract_protocol:
Organ donor samples in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 2 to 4 hours of procurement. Single cell suspensions were obtained from blood, bone marrow, spleen, lungs, and associated lymph nodes (LN) using mechanical and enzymatic digestion as previously described (Nat Med 22, 72-77. 10.1038/nm.4008). Blood and bone marrow samples were diluted with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS (GeminiBio, cat #100-106)), and mononuclear cells were isolated by density centrifugation using Ficoll-Paque PLUS (GE Healthcare, catalog no. 17-1440-03). Lymph nodes were isolated by dissection from the mesentery of the small and large intestine, the tracheobronchial tree of the lung, and inguinal fat. Tissue samples were first mechanically disrupted with scissors. Isolated LNs and lung were then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNAse 0.1mg/mL (Millipore Sigma cat# DN25-5G)) on a shaker at 37C for 30 minutes followed by addition of 0.5M EDTA (pH 8.0). Digested LNs and lung as well as mechanically disrupted spleen were then pushed through 100m filters and washed with buffers. The samples then underwent density centrifugation as above to isolate live leukocytes. For healthy blood samples, we obtained peripheral blood from a consenting, healthy volunteers by venous puncture. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque PLUS, following manufacturer's protocols for density gradient centrifugation. Single cell mononuclear suspensions isolated from blood and tissue samples prepared as above were plated in 96 well U-bottom plates (1X10^6 cells per well) in 200uL of complete media (RPMI (Corning, catalog no. 10-040-CM), 10% inactivated human AB serum (Gemini, catalog no. 507533010) and penicillin-streptomycin-glutamate (Thermo Fisher Scientific, catalog no. 10378016)) and incubated overnight at 37C in 5% CO2. The next day, the wells were split (5x10^5 cells per well) and topped up with complete media to 200uL. Cells were then blocked for 15 minutes with anti-CD40 monoclonal antibody (0.5g/mL) (Miltenyi Biotec, catalog no. 130-094-133). Subsequently, a SARS-CoV-2 Spike Megapool (S MP) (1g/mL), designed and synthesized as previously described (Cell 181, 1489-1501 e1415. 10.1016/j.cell.2020.05.015), was added to the cell culture for 24 hours. The S MP consists of 253 15-mer peptides overlapping by 10 residues and covering the entire S protein. As controls, additional cells were stimulated with an equimolar amount of DMSO, or a combination of 3 Influenza peptide Mega pools at 1g/mL (CD4 HA, CD4 Other, and CD8), synthesized as previously described (Curr Protoc. 2023 Nov;3(11):e934. doi: 10.1002/cpz1.934.). Following 24-hour stimulation, each tissue and stimulation condition combination for a particular donor was combined, treated with 10uL each of Trustain FcX (BioLegend) and FcR Blocking Reagent (Miltenyi) at 4C for 10 minutes, and then incubated with 2 uL (1 ug) of a unique TotalSeq-C anti-human DNA-barcoded hashtag for 30 minutes at 4C and washed 3 times with FACS buffer) as described. Subsequently all peptide-stimulated samples from a single donor were combined and all DMSO-stimulated samples from a single donor were combined. These samples were stained with BV421 labeled full length Spike protein and a panel of fluorescently labeled antibodies and washed as described above. These samples were sorted using the BD FACSAria III Cell Sorter. Peptide-stimulated samples were sorted for AIM+ CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB++), AIM+ CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB++), and Spike B cells (Live, CD45+, CD19+, CD3-, Spike-BV421+). DMSO-stimulated cells were sorted for AIM-CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB--), AIM-CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB--), and Total B cells (Live, CD45+, CD19+, CD3-, Spike-BV421-). Each sample of sorted cells was counted, and for each donor, a fraction of AIM-CD4 T, AIM-CD8 T, and Total B cells were spiked into the AIM+CD4+T, AIM+CD8+T, and Spike B cell samples to reach ~80K cells for per donor to have adequate cell numbers to manipulate for CITE-seq staining and have sufficient cell numbers after washing for input into 10x microfluidics chip (e.g. spike in cells to achieve 80k cells, yielding ~50k out post-wash for 33.3k cell requirement to achieve 20k cell capture on chip). The samples were then stained with TotalSeq C Human Universal Cocktail V1.0 and washed 3 times with FACS buffer by centrifugation or with a Curiox HT2000 Laminar Wash System (Curiox, 5 uL/sec speed, 27 cycles, 50 uL loading volume). The resultant stained cells (33.3K) were resuspended in 10x genomics recommended loading buffer (1X DPBS w/ 0.04% BSA) for loading into 10x Genomics single sequencing workflows with a target of 20K cell captured per lane on chip. To investigate the role of Tregs in the AIM assay, we performed CD25 depletion on our single cell LLN suspension from D616 prior to the above peptide stimulation and sorting protocols. For depletion, single cell suspensions were pre-incubated with 10uL each of Trustain FcX (BioLegend, catalog no. 422322) and FcR Blocking Reagent (Miltenyi, catalog no. 130-059-901) at 4C for 10 minutes followed by addition of 10uL of biotinylated anti-CD25 for 30 minutes on ice and washed with FACS buffer three times. Washed BioMag Plus Streptavidin Beads (BangsLabs catalog no. BP628) were resuspended in 100uL of FACS buffer and incubated with the single cell suspension at room temperature for 5 minutes. 1.5mL of DPBS was added to the tube and placed on the EasySep magnet (STEMCELL Technologies catalog no. 18000) for 5 minutes. The supernatant was collected and set aside. The remaining beads were combined with DPBS and placed back on the magnet for an additional 5 minutes prior to collecting the supernatant and combining with the supernatant from the first separation. This sample was then plated at 1X10^6 cells per well in 96-well U bottom plates for in vitro peptide stimulations as above. DMSO control, SARS or Flu peptide stimulated, and CD25 depleted SARS or Flu stimulated were FACS sorted with AIM+ gates described above. SARS or Flu peptide stimulated CD4 T cells were also sorted using an altenative AIM+ gating strategy (Live, CD45+, CD19-, CD3+, CD4+, OX40 & CD40LG) while maintaining original CD8 gating strategy. Stimulated and sorted single cell-suspensions were loaded onto a 5v2 high throughput (HT) Chromium Next GEM Single Cell Chip N (10x Genomics) for co-encapsulation with barcoded GelBeads with a target capture of 20-30k cells per sample.
Organ donor samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). The scTCR-seq and sc-BCRseq libraries for D561 and D574 were sequenced with a 150-cycle high-output kit on an Illumina NextSeq 550 (read 1: 26 bp; read 2: 114 bp; index read 1: 10 bp; index read 2: 10 bp). Hashtag IDs for D534,D559,D561,D564,D568,D574: (HTO1: Donor blood AIM+ SARS, HTO2: Donor blood AIM+ Flu, HTO3: Donor blood AIM- DMSO control, HTO4: Donor bone marrow AIM+ SARS, HTO5: Donor bone marrow AIM+ Flu, HTO6: Donor bone marrow AIM- DMSO control, HTO7: Donor spleen AIM+ SARS, HTO8: Donor spleen AIM+ Flu, HTO9: Donor spleen AIM- DMSO control, HTO10: Donor lung AIM+ SARS, HTO12: Donor lung AIM+ Flu, HTO13: Donor lung AIM- DMSO control, HTO14: Donor lung lymph node AIM+ SARS, HTO15: Donor lung lymph node AIM+ Flu, HTO16: Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Healthy blood samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane).  Hashtag IDs for healthy blood donors FLD032,FLD040,FLD015,FLD041,FLD029,FLD030: (HTO1: Donor 1 blood AIM+ SARS, HTO2: Donor 1 blood AIM+ Flu, HTO3: Donor 1 blood AIM- DMSO control, HTO4: Donor 2 blood AIM+ SARS, HTO5: Donor 2 blood AIM+ Flu, HTO6: Donor 2 blood AIM- DMSO control, HTO7: Donor 3 blood AIM+ SARS, HTO2: Donor 3 blood AIM+ Flu, HTO3: Donor 3 blood AIM- DMSO control). Donors 1-3 in hashtag IDs correspond to FLD-prefixed donors in corresponding order in library ID. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Donor 616: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification. The scRNA-seq gene expression (GEX) libraries and antibody derived tag (ADT) CITE-seq/hashtag libraries libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). Hashtag IDs for D616: (HTOs 1,3,4,5,6,7: Donor 616 LLN AIM- DMSO control, HTO8: Donor 616 LLN AIM+ Flu peptide stimulation, HTO9: Donor 616 LLN AIM+ SARS peptide stimulation, HTO13: Donor 616 LLN CD25 depletion AIM+ Flu peptide stimulation, HTO14: Donor 616 LLN CD25 depletion AIM+ SARS peptide stimulation, HTO10: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate Flu peptide stimulation, HTO12: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate SARS peptide stimulation).  (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).

value: various

value: mononuclear cells (MNCs)

tag: library type

value: mRNA


title: D574 TCR library 4


title: SYO-1, H2AK119ub ChIP-seq, TAK-981 Treated, Rep1


title: hESCs,WT2. Day5


title: GSC1914 cells, shSUV39H1_2

value: GBM


title: D574 TCR library 2


title: HS-SY-II cellline treated with DMSO, replicate1


title: HS-SY-II cellline treated with DMSO, replicate3


title: SYO-1, H2AK119ub ChIP-seq, DMSO Treated, Rep2


title: SYO-1, SS18-SSX Fusion CUT&RUN, TAK-981 Treated, Input


title: hESCs,WT1. Day5


title: SYO-1, SS18-SSX Fusion CUT&RUN, TAK-981 Treated, Rep1


title: D574 TCR library 1


title: SYO-1, H2AK119ub ChIP-seq, DMSO Treated, Rep1


title: SME3

first: Yuanjie

last: Tang

state: Shanghai

address: 300 Fenglin Road, Xuhui District

department: CAS Center for Excellence in Molecular Plant Sciences

institute: CHINESE ACADEMY OF SCIENCES

data_processing:
Adapter sequences and low-quality reads were filtered out using Trimmomatic v0.32. The filtered reads were then mapped to the CHA0 genome (ASM39720v1) using STAR 2.7.9a. Differentially expressed genes (DEGs) were analyzed using the R package DESeq2 v.1.38.0.
Assembly: ASM39720v1
Supplementary files format and content: comma-delimited text file includes rawcounts for each samples

organism: Pseudomonas protegens

source_name: CHA0 treated with sgn3 myb36 root exudates for 1h replicate 3

extract_protocol:
Total bacterial RNA was extracted using RNeasy Mini Kit (Qiagen).
The RNA (10 µg) was treated with DNase I (Takara) to remove any residual DNA, followed by purification with the RNeasy MinElute Cleanup Kit (Qiagen). Ribosomal RNA (rRNA) was depleted using the Ribo-off rRNA Depletion Kit (Vazyme), which involved hybridizing the RNA with plant-specific rRNA probes and probe buffer. The RNA was then incubated with RNase H Buffer and RNase H at 37°C for 30 minutes. The ribosome-depleted RNA was purified using VAHTS RNA Clean Beads (Vazyme). The RNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

tag: strain

value: sgn3 myb36 root exudates for 1h


title: D574 BCR library 4

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.BCR.txt.gz


title: PE6

first: Hong

last: Cui

address: 36# Sanhao Street

institute: Shengjing Hospital of China Medical University

data_processing:
Raw reads containing adapters or low quality bases were filtered by Cutadapt (version:cutadapt-1.9) to get high quality clean reads.
Then sequence quality was verified using FastQC (0.11.9).
Trimmed reads were mapped to the reference genome using HISAT2 (version:hisat2-2.0.4) package.
Expression abundance for mRNAs was calculated by FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: h38
Supplementary files format and content: Processed Data.xlsx

source_name: placenta

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following the manufacturer's protocols.

value: placenta


title: hNSC, CHD8, ChIP

city: Rotterdam

first: Raymond

middle: A

last: Poot

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus MC

data_processing:
The reads were first trimmed by removing the Illumina adapters, followed by alignment to the reference genome GRCh38 using HISAT2.
After alignment, low-quality, duplicated fragments and fragments that exceeded 150 bases in length were removed.
Peaks were called using MACS2 (version 2.1.1.20160309) with FDR thresholds 1e-4 (CHD8) and 1e-3 (TRRAP).
Peaks overlapping with ENCODE Blacklist have been removed using GenomicRanges package v.1.48 in R. Subsequently, the peaks longer than 1kb have been filtered as they are mostly artefacts not presenting narrow peaks for TF binding.
Assembly: GRCh38
Supplementary files format and content: BigWig files: fragment coverage after filtering
Supplementary files format and content: BED files: peaks after filtering

source_name: hNSCs

growth_protocol: hNSCs were cultured on Geltrex-coated dishes (Geltrex LDEV-free reduced growth factor membrane matrix, A1413202, Thermo Fisher Scientific) in KnockOut DMEM/F12 (12660012, Invitrogen) supplemented with 2 mM L-Glutamine (25030024, Thermo Fisher Scientific), 20 ng/ml EGF (315-09, Peprotech), 20 ng/ml FGF (100-18B, Peprotech) and 2% of StemPro Neural Supplement (A1050801, Thermo Fisher Scientific)

extract_protocol:
hNSCs were double crosslinked by incubation with 2 mM disuccinimidyl glutarate solution, followed by an incubation with 1% of buffered formaldehyde solution. Subsequently, the cell pellets were lysed with lysis buffer (1% SDS, 50 mM TrisHCl pH 8.1, 10mM EDTA pH 8.0 and 1x CEF protease inhibitors (Roche)) and sonicated using a Bioruptor Pico sonication device (Diagenode, B01060001) for 14 cycles of 30sec on and 30sec off. The ChIP was performed on the resulting sheared chromatin by incubation overnight at 4°C with ProtG Dynabeads (Invitrogen, #100-04D) that had been pre-coupled to either the CHD8 antibody, TRRAP antibody or IgG antibody (Diagenode, C15410206) as control. Following the overnight incubation, the Dynabeads were washed twice with Low salt wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl), once with High salt wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 500 mM NaCl), once with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 0.5% IGEPAL, 1% NaDeoxycholate) and once with T10E1 (10 mM TrisHCl pH 8.0, 1 mM EDTA). The bound complexes were eluted of the beads by incubation for 1 hour at 65°C in ChIP elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS) with occasional gentle vortexing. The samples were de-crosslinked overnight by incubation at 55°C. DNA was extracted from the elutions by the Phenol:Chloroform:Isoamyl alcohol (PCI) method and diluted in water.
The DNA libraries for the input, IgG, CHD8 and TRRAP ChIP samples were prepared using the ThruPLEX V2 DNA sample preparation protocol from Takara Bio.

value: hNSCs

value: H9 human embryonic stem cell-derived neural stem cells

tag: chip antibody

value: CHD8 (Bethyl, A301-225A)


title: SMYD1 knockout cells, KO2.Day5


title: PE4


title: D574 BCR library 3


title: PE3


title: PE2


title: SYO-1, H2AK119ub ChIP-seq, TAK-981 Treated, Rep2

value: Synovial sarcoma


title: SYO-1, DMSO Treated, Input

value: DMSO


title: hNSC, IgG, ChIP

value: WT

value: IgG (Diagenode, C15410206)


title: D574 BCR library 2


title: PE1


title: hNSC shSCR KD 72h #3: I21-1460-09

data_processing:
The Illumina adapter and poly-A sequences were removed from the reads.
The trimmed reads were alligned to the reference genome GRCh38 using HISAT2.
Quantification of the reads was performed using HT-seq count.
Differential gene expression was calculated using EdgeR.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited  file including raw counts for each sample

growth_protocol: hNSCs were cultured on Geltrex-coated dishes (GeltrexÔ LDEV-free reduced growth factor membrane matrix, A1413202, Thermo Fisher Scientific) in KnockOutÔ DMEM/F12 (12660012, Invitrogen) supplemented with 2 mM L-Glutamine (25030024, Thermo Fisher Scientific), 20 ng/ml EGF (315-09, Peprotech), 20 ng/ml FGF (100-18B, Peprotech) and 2% of StemProÒ Neural Supplement (A1050801, Thermo Fisher Scientific)

extract_protocol:
RNA was isolated using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, RTN350-1KT)
Total RNA was prepped using the Illumina TruSEq Stranded mRNA library Prep kit according to the manufacturer's protocol

value: WT, Control knockdown

tag: time

value: 72h after transfection


title: N6


title: N4


title: hNSC shSCR KD 72h #2: I21-1460-08


title: D574 BCR library 1


title: N3


title: N5


title: D561D564 TCR library 2


title: D561D564 TCR library 1


title: N1


title: hNSC shSCR KD 72h #1: I21-1460-07


title: hNSC shMYC KD 72h #3: I21-1460-12

value: MYC knockdown


title: N2


title: hNSC, TRRAP, ChIP

value: TRRAP (Invitrogen, PA5-78246)


title: PE5


title: Cells_culture medium_24hs, replicate 3

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

data_processing:
BaseCall Conversion Illumina's official basecalling program, the bcl2fastq conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads. Adaptor Clipping Adaptors are short nucleotide sequences which have to be ligated to every single DNA molecule during library preparation, and allow DNA fragments to bind to a flow cell for next generation sequencing. Removal of adapter sequences, a process called 'adaptor trimming', or clipping, is one of the first steps in analyzing NGS data. Predict circRNAs using CIRI2 (packaged in CIRIquant) Sequence Quality Trimming Quality trimming was proformed to remove low quality reads/bases. Lower quality bases from the the 3' end were removed using a sliding-window approach as the per base quality gradually drops toward the 3' end of reads. Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Predict circRNAs using CIRI2 (packaged in CIRIquant) CIRI2 is extensively optimized for the key steps in circRNA detection, including inferring original region for sequencing read segments based on seed matching, and distinguishing BSJ reads from forward-spliced junction (FSJ) reads based on an adapted MLE. CIRI2 is applicable to sequencing data with mixed read lengths, and can be run with multiple thread
Prepare CIRIquant output files Study with biological replicates, a customed analysis pipeline of edgeR is recommended and we provide prep_CIRIquant to generate matrix of circRNA expression level / junction ratio and CIRI_DE_replicate for DE analysis
Prepare StringTie output The output of StringTie should locate under output_dir/gene/prefix_out.gtf. You need to use prepDE.py from stringTie to generate the gene count matrix for normalization.
Differential expression analysis For differential analysis using CIRI_DE_replicate, you need to install a R environment and edgeR package from Bioconductor.
Assembly: GRCh38.p6
Supplementary files format and content: The Excel file includes the read counts for each sample in the 'Number of BSJ Reads' sheet
Supplementary files format and content: The Excel file includes TPM values for each sample

source_name: cell line

growth_protocol: Jurkat cells culture in RPMI-1640 medium

extract_protocol:
The total RNAs of treated Jurkat cells were isolated by using the QIAamp RNA Blood Mini Kit (QIAGEN GmbH, Germany)
The SureSelect XT HS2 mRNA Library Preparation kit (Agilent, Santa Clara, CA, USA) was used for Circular RNA/ RNA IP samples to construct nonpoly-A select step RNA libraries, followed by HighPrep PCR clean-up system. Input of 10 ul Circular RNA/ RNA IP sample was directly mixed with 10 ul priming buffer in enzymatic fragmentation steps and subsequently then subjected to cDNA construction. After adaptor ligation, unique dual indexes were introduced and each library was amplified in a PCR with 10 cycles. Library quality and quantity Final libraries were quantified using Nanodrop,Qubit dsDNA HS Assay and Agilent 4200 TapeStation System.

treatment_protocol: Jurkat cells were cultured in medium with or without the presence of PMA(20 ng/mL) and inomycin (500 ng/mL).

value: cell line

value: Jurkat cell

value: T cell

value: Cells_coulture medium_24hrs, replicate 3


title: Cells_culture medium_24hs, replicate 2

value: Cells_coulture medium_24hrs, replicate 2


title: D561D564 BCR library 2

value: various

value: mononuclear cells (MNCs)

value: mRNA


title: Cells_culture medium_24hs, replicate 1

value: Cells_coulture medium_24hs, replicate 1


title: D561D564 BCR library 1


title: hNSC shMYC KD 72h #2: I21-1460-11

value: hNSCs

value: H9 human embryonic stem cell-derived neural stem cells


title: hNSC shMYC KD 72h #1: I21-1460-10


title: Cells_PMA 20ng/ml_ inomycin 500 ng/m_24hrs, replicate 3


title: Cells_PMA 20ng/ml_ inomycin 500 ng/mL_24hrs, replicate 2


title: Cells_PMA 20ng/ml_ inomycin 500 ng/mL_24hrs, replicate 1


title: H1299, 2, HOXD1, TBS

city: Ji'nan

first: Lianlian

last: Li

address: No. 6699 Qingdao Road

institute: Shandong First Medical University(Shandong Academy Of Medical Sciences)

data_processing:
FastQC v0.11.7 was used to perform basic statistics on the raw data.
The raw data is processed with the software Trimmomatic[1] v0.36 according to the following standards: (1)Cut off low-quality reads, using a sliding window, 4 bases as a window, if the average base mass value of the window is less than 15, the reads is truncated from there (2)Remove reads with a quality of less than 3 or containing N. (3)Remove adapters. Remove the reads that alignment with the adapter sequence. (4)Remove reads shorter than 36nt after pruning. (5)Remove reads that do not form paired.
Use BSMAP[2] v2.7.3 to mapping target sequences.
BSMAP v2.7.3 is used to detect methylation levels at various sites on the amplicon.
We counted methylated C sites under sequence environments (CG) . To study between-group differences, a t-test was used to detect the site of each amplicon in each comparison group.
Assembly: hg38
Supplementary files format and content: txt

source_name: Lung

extract_protocol:
1 μg of genomic DNA was converted using the ZYMO EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA) and one twentieth of the elution products were used as templates for PCR amplification with 35 cycles using KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (Kapa Biosystems, Wilmington, MA, USA)
For each sample, BSP products of multiple genes were pooled equally, 5'-phosphorylated, 3'-dA-tailed and ligated to barcoded adapter using T4 DNA ligase (NEB). Barcoded libraries from all samples were sequenced on Illumina platform.

value: Lung

value: Epithelial


title: hNSC shSCR KD 72h #3: I20-1331-13

value: WT, Control knockdown


title: H1299, 3, HOXD1, TBS


title: H1299, 1, HOXD1, TBS


title: control BR3

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

description: reference.cnn

data_processing:
Adapter trimming and quality filtering of the sequencing libraries was done using fastp (0.21.0) with the default parameters.
The sequencing libraries were mapped against mm10 using Bowtie 2 (2.4.5) (--very-sensitive -X 2000).
The copy number variant detection was done using CNVkit (0.9.10) from whole-genome sequencing data (-m wgs).
Assembly: mm10
Supplementary files format and content: Bin-level and segmented log2 ratios.
Library strategy: Whole Genome Sequencing

source_name: Spleen

extract_protocol:
Genomic DNA was isolated from sorted wild type CD4 cells, or sorted expanded CD45.2+ Tet2/3 DKO cells after one or two transplantations  in congenic CD45.1+ recipient mice using the PureLink genomic DNA mini kit (Invitrogen, catalogue number K182001). DNA was quantified (after dilution) using Qubit 1X dsDNA High Sensitivity (HS) (Invitrogen, catalogue number: Q33230) in a Qubit 4 fluorometer (Invitrogen).
DNA was provided to the UNC High Throughput Sequencing Facility and libraries were prepared using Illumina PCR free DNA library prep kit. Paired end, 2x150 bp length sequencing was performed using Illumina NextSeq2000 P1 system

value: Spleen

value: CD4 T cells

value: Wild type


title: control BR2

description: reference.cnn


title: LCKFREE_IAV_D10 targeted scRNAseq

city: Clayton

first: Justin

middle: Boxuan

last: Zhang

state: VIC

address: Willington road

country: Australia

institute: Monash University

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Parsing and base calling performed using Dragen BCLConvert 3.7.4. R1 and R2 reads were analyzed using the Seven Bridges Genomics platform, which includes quality control steps including read quality filtering, recursive substitution error correction (RSEC), distribution-based error correction (DBEC), and cell label filtering by sample multiplexing.
Supplementary files format and content: Comma separated value files and matrix files

extract_protocol:
Spleens were harvested into Hank's balanced salt solution (HBSS) and mashed through a 70μm cell strainer. Red blood cell lysis was performed by resuspending cells in 1ml red blood cell lysing buffer (Sigma Aldrich, Cat. 11814389001) for 4 min before quenching with 9ml HBSS. Cells were then filtered with 70μm cell strainer
Library was performed according to manufacter's instructions (BD Rhapsody Single-cell Analysis System)

value: CD8 and CD4 T cells

value: 3xC57Bl/6 and 3x LckC20.23A

value: 10E4 pfu HKx31 IAV infection


title: A549, 3, HOXD1, TBS


title: A549, 1, HOXD1, TBS


title: A549, 2, HOXD1, TBS


title: control BR1

description: reference.cnn


title: hNSC shSCR KD 72h #1: I20-1331-03

value: 72h after transfection


title: hNSC shTRRAP KD 72h #3: I20-1331-14

value: TRRAP knockdown


title: Beas2B, 1, HOXD1, TBS


title: Tet2/3 DKO CD4 1st transfer BR3

value: Expanded CD45.2+ T cells

value: Tet2/3 DKO


title: Beas2B, 3,  HOXD1, TBS


title: A549, LV-HOXD1, 3, Input

data_processing:
Trimmomatic (version 0.36) was used to filter out low-quality reads. Clean reads were mapped to the human genome using BWA (version 0.7.15-r1140).
Samtools (version 1.3.1) was used to remove potential PCR duplicates.
MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth,300 bp; model fold, 5, 50;q value, 0.05). If the midpoint of a peak located closest to the TSS of one gene, the peak will be assigned to that gene.
HOMER (version3) was used to predict motif occurrence within peaks with default settings for a maximum motif length of 12 base pairs.
ClusterProfiler (http://www.bioconductor.org/packages/release/ bioc/html/clusterProfiler.html) in R package was employed to perform GO (Gene Ontology, http://geneontology.org/) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) enrichment analysis. The GO and KEGG enrichment analysis were calculated using hypergeometric distribution with a q value cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: txt, bw

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

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor (Diagenode).
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method.

value: HOXD1 overexpression


title: Tet2/3 DKO CD4 2nd transfer BR2


title: hNSC shTRRAP KD 72h #2: I20-1331-08


title: hNSC shTRRAP KD 72h #1: I20-1331-04


title: hNSC shSCR KD 72h #3: I21-1241-12


title: A549, LV-HOXD1, 1, Input


title: A549, LV-HOXD1, 3, ChIP

value: DYKDDDDK Tag (D6W5B) Rabbit mAb (CST, #14793)


title: A549, LV-HOXD1, 2, Input


title: Tet2/3 DKO CD4 1st transfer BR2


title: hNSC shSCR KD 72h #2: I20-1331-07

value: hNSCs


title: Beas2B, 2, HOXD1, TBS


title: A549, LV-HOXD1, 2, ChIP


title: A549, LV-HOXD1, 1, ChIP


title: Tet2/3 DKO CD4 1st transfer BR1


title: hNSC shSCR KD 72h #2: I21-1241-11

value: H9 human embryonic stem cell-derived neural stem cells


title: Cal27, Input

city: Nanjing

first: Jin

address: 140, Hanzhong Road

department: OMFS

institute: Nanjing Medical University

data_processing:
Raw ChIP-seq reads were trimmed using Trimmomatic (version 0.39).
Trimmed seuqence reads were  aligned using Bowtie2 algorithm (version 2.5.2) to the human reference genome hg19/GRCh37 using the following parameters: -t -p 36 --local --very-sensitive-local --no-discordant --no-mixed.
BAM format data were sorted and indexed with SAMtools (version 1.18).
Peaks calling were utilization the MACS2 (version 2.2.9) algorithm using the following parameters:  -g hs -B -f BAM --SPMR --keep-dup all -p 1e-5.
Pileup signal (.bed files) were converted to binary big-wig files (.bw file) and Reads Per Kilobase per Million mapped reads (RPKM) normalized by DeepTools (version 3.5.4) using bamCoverage command.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak (exprect for Input)

extract_protocol:
Cal27 cells (~1×107) in a logarithmic growth phase with monolayer growth were washed and collected. All samples were fixed with 1% formaldehyde at room temperature for 15 min, followed by 0.125 M glycine treatment for 5 min. The sample was then pelleted, washed and re-suspended in ChIP lysis buffer (25 mM Tris-HCl pH 7.5, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, 1×Proteinase Inhibitor Cocktail). Then, samples were sonicated by Bioruptor® Plus sonication device (Shearing condition: 20 cycles on cooling condition, 30 seconds ON, 30 seconds OFF), immunoprecipitated with antibody against H3K27ac, BRD4, EP300, SOX2, SMAD3 or Rabbit IgG on ChIP-Grade Protein G Agarose Beads (#9007, Cell Signaling Technology, USA) and purified by Universal DNA Purification Kit (#DP214, TIANGEN Biotech, China).
The ChIP-Seq library was prepared using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (#E7645L, New England Biolabs, USA) according to the manufacturer’s instructions.

value: Head and neck squamous cell carcinoma


title: hNSC shSCR KD 72h #1: I21-1241-10


title: Cal27, p300, ChIP

value: p300 (Active Motif, #61401)


title: hNSC shCHD8 KD 72h #3: I21-1241-09

value: CHD8 knockdown


title: Cal27-CSC, ATAC-seq

data_processing:
Raw ATAC-seq reads were trimmed using Trimmomatic (version 0.39).
Trimmed seuqence reads were  aligned using Bowtie2 algorithm (version 2.5.2) to the human reference genome hg19/GRCh37 using the following parameters: -t -p 36 --local --very-sensitive-local --no-discordant --no-mixed.
BAM format data were sorted and indexed with SAMtools (version 1.18).
Peaks calling were utilization the MACS2 (version 2.2.9) algorithm using the following parameters:  -g hs -B -f BAM --shift 100 --extsize 200 --SPMR -q 0.01. chrM reads were removed.
Pileup signal (.bed files) were converted to binary big-wig files (.bw file) and Reads Per Kilobase per Million mapped reads (RPKM) normalized by DeepTools (version 3.5.4) using bamCoverage command.
Assembly: hg19
Supplementary files format and content: BigWig, narrowPeak

value: CSC


title: Tet2/3 DKO CD4 2nd transfer BR3

value: Spleen


title: Tet2/3 DKO CD4 2nd transfer BR4


title: Cal27-nonCSC, ATAC-seq

value: nonCSC


title: SAT00199

city: Los Angeles

first: Seung Hyuk

middle: T.

last: Lee

address: 695 Charles E. Young Drive South

institute: UCLA

data_processing:
Sequence reads were aligned to the GRCh38 human genome reference with Gencode v42 gene annotations using STARSolo in STARv2.7.10b with the the ‘--soloFeatures GeneFull’ parameter to account for full pre-mRNA transcripts.
We assigned each droplet to the one of the pooled donors for each library using demuxlet, implemented in the popscle software tool.
Assembly: GRCh38
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names).

source_name: subcutaneous adipose tissue

extract_protocol:
Frozen subcutaneous adipose tissue biopsies were minced over dry ice and incubated in 5mL ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 15-minute incubation, the lysate was filtered through a 30-μm MACS smart strainer (Miltenyi Biotec #130-110-915) and centrifuged at 500 x g for 7 minutes at 4 °C. The nuclei pellet was gently re-suspended in 1mL of wash buffer consisting of 1X PBS, 1.0% BSA, and 0.2 U/ul RNase inhibitor (Sigma #3335402001) and filtered through a 30-μm MACS smart strainer (Miltenyi Biotec #130-110-915). Lastly, the nuclei were centrifuged at 500 x g for 7 minutes at 4 °C, re-suspended in 70 μL wash buffer, and proceeded with library construction.
Libraries were prepared using the 10x Chromium Single Cell 3’ Reagent Kit v3.1.

value: subcutaneous adipose tissue

tag: ethnicity

value: Finnish

tag: cohort

value: Roux-en-Y versus one-anastomosis gastric bypass (RYSA)


title: Tet2/3 DKO CD4 2nd transfer BR1


title: SAT00196


title: SAT00195


title: FVB x BALB/c Tg(Kat6b) sample 4

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Sequence reads were trimmed for adapter sequence.
Reads were aligned to the Mus musculus (mm39) and Drosophila melanogaster (Dme1R6.32) genomes by Rsubread version 2.12.3.
Read counts were summed over technical replicates and summarized by genomic regions - Promoters (TSS - 1 kb to TSS), Transcription end sites (TES to TES + 1 kb) of protein coding genes, and H3K4me1+/H3K27ac+ enhancer enriched regions - using the Rsubread's featureCounts function and Rsubread's inbuilt mm39 NCBI annotation.
Assembly: mm39, Dme1R6.32
Supplementary files format and content: Tab-delimited text files for Promoter region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for Transcription end site region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for H3K4me1+/H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Supplementary files are also supplied containing regions counts for all samples as count matrices.

source_name: Dorsal telencephalon

growth_protocol: Neural stem and progenitor cells were isolated from the dorsal telencephalon of E12.5 mouse embryos and cultured in neurosphere medium at 37 degree C and 5% CO2.

extract_protocol:
Using 50,000 NSPCs from mouse dorsal telencephalon tissue, combined with 50,000 Drosophila melanogaster S2 cells spike-in, ATAC-sequencing was performed as described in (Buenrostro et al., 2015, Current Protocols in Molecular Biology).
Samples were amplified using NEBNext High-Fidelity PCR master mix (M0541S) and P5/P7 indexing primer combinations under the following conditions: 72 deg C, 5 min, 98 deg C, 30 sec, 10x cycles, 98 deg C, 10 sec, 63 deg C, 30 sec, 72oC, 1 min. Amplified samples were size-selected using 1.3x volumes AMPure beads (Beckman Coulter, A63880), eluted in 20 microliter nuclease-free H2O and analysed using a D1000 Tape and 4200 Tapestation (Agilent). Samples were processed on a high-throughput sequencing machine (NextSeq 2000, Illumina).

value: FVB x BALB/c

value: Dorsal telencephalon

value: Neural stem and progenitor cells


title: hNSC shCHD8 KD 72h #1: I21-1241-07

value: 72h after transfection


title: FVB x BALB/c Tg(Kat6b) sample 3


title: SAT00198


title: SAT00193


title: SAT00192


title: FVB x BALB/c Tg(Kat6b) sample 2


title: SAT00190


title: shPAF1 Pol II ChIP

first: Aiwei

last: Wu

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. ChIP-seq reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: Hg38
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins).

source_name: HEL cell line

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
For immunoprecipitation, on day 1 antibodies were diluted in RIPA-0.3 and bound to Dynabeads protein A (Thermo, cat. no. 10002D) by incubating at 4 °C for 3 hours. Afterwards, the bead-antibody complexes were washed twice with RIPA-0.3 and then incubated with sonicated chromatin at 4 °C overnight. On day 2, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 1 mM EDTA, 0.25 M LiCl, 0.25% NP-40, and 0.25% NaDOC, pH 7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, 0.2 M NaCl, and 1% SDS, pH 7.4) supplemented with 10 µg/ml RNase A for both elution and RNA digestion, and incubated at 55 °C for 1 hour. Then Proteinase K was added to a final concentration of 200 µg/ml, and after 30 min incubation the temperature was increased to 65 °C for crosslink reversal. After incubation for 4 to 6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205).
The libraries were constructed with 2–10 ng immunoprecipitated DNA. After end-repair, A-tailing, and barcode ligation, barcoded DNA was amplified by 16-cycle PCR. Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

treatment_protocol: For double fixation with DMA (Thermo, cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For sonication, fixed cells were washed twice with PBS and resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH 7.4) supplemented with Protease Inhibitor Cocktail (Millipore, cat. no. 535140) at a concentration of 40 million cells/ml; genomic DNA was disrupted to a size range of 100 to 500 bp.

tag: antibody

value: Pol II

tag: fixation

value: DMA+FA


title: shCtrl for PAF1 data Pol II ChIP

value: shCtrl


title: SAT00191

tag: tissue


title: FVB x BALB/c Tg(Kat6b) sample 1


title: SAT00189


title: shCtrl for PAF1 data input

value: input


title: Cal27, BRD4, ChIP

value: Head and neck squamous cell carcinoma

value: BRD4 (Active Motif, #91301)


title: hNSC shCHD8 KD 72h #2: I21-1241-08

value: hNSCs

value: H9 human embryonic stem cell-derived neural stem cells

value: CHD8 knockdown


title: SAT00188


title: SAT00187


title: SAT00186


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_60min, rep2

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

library_source: other

data_processing:
Adapters in raw reads were trimmed, and reads shorter than 20 were filtered with Trim Galore (v0.6.1).
Then reads were mapped to 60-nt and 32-nt oligonucleotides sequences with bowtie2 (v2.4.1).
RT-stop rates of all bases in oligonucleotides sequences were calculated using custom scripts.
Assembly: 60nt_mix_32nt_oligonucleotide
Supplementary files format and content: txt, RT-stop rate result

molecule: other

organism: synthetic construct

source_name: 60nt oligo

extract_protocol:
The oligonucleotides were purchased.
RNA oligonucleotides were RNA was reverse transcribed by Superscript III reverse transcriptase (Thermo scientific). The 5’ adaptor was ligated by T4 RNA ligase high concentration 1 (NEB). The amplification cycles of the cDNA were determined by qPCR (generally 10-15 cycles). The cDNA was amplified by PCR with Q5 High-Fidelity 2×Master Mix (NEB). Library PCR products were purified twice by 0.9x XP beads (Beckman).


title: FVB x BALB/c WT sample 3

value: Wild-type


title: FVB x BALB/c WT sample 4


title: SAT00185

value: subcutaneous adipose tissue


title: SAT00184

value: Finnish


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_60min, rep1


title: SAT00182

value: Roux-en-Y versus one-anastomosis gastric bypass (RYSA)


title: SAT00181


title: FVB x BALB/c WT sample 1

value: FVB x BALB/c


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_30min, rep1


title: SAT00183


title: FVB x BALB/c WT sample 2

value: Dorsal telencephalon


title: C57BL/6 Kat6b KO sample 4

value: Neural stem and progenitor cells


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_15min, rep2


title: SAT00180


title: SAT00176


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_15min, rep1


title: C57BL/6 Kat6b KO sample 3


title: SAT00174


title: C57BL/6 Kat6b KO sample 2


title: SAT00170


title: SAT00169


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_0min, rep1


title: C57BL/6 Kat6b KO sample 1


title: SAT00168


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_30min, rep2


title: C57BL/6 WT sample 4


title: 60nt_mix_32nt_oligo, CMC_treated, blocked, XRN1_treated_60min, rep1

source_name: 60nt mix 32nt oligo

extract_protocol:
The oligonucleotides were purchased.
RNA oligonucleotides were RNA was reverse transcribed by Superscript III reverse transcriptase (Thermo scientific). The  5’ adaptor was ligated by T4 RNA ligase high concentration 1 (NEB). The amplification cycles of the cDNA were determined by qPCR (generally 10-15 cycles). The cDNA was amplified by PCR with Q5 High-Fidelity 2×Master Mix (NEB). Library PCR products were purified twice by 0.9x XP beads (Beckman).

value: blocked


title: C57BL/6 WT sample 3


title: SAT00167


title: SAT00166


title: SAT00164


title: SAT00177


title: SAT00163


title: SAT00162


title: C57BL/6 WT sample 2


title: 60nt_mix_32nt_oligo, CMC_treated, blocked, no_XRN1_treated_60min, rep1


title: 60nt_mix_32nt_oligo, CMC_treated, blocked, XRN1_treated_30min, rep1


title: C57BL/6 WT sample 1


title: SAT00158


title: SAT00159


title: SAT00175


title: SAT00171


title: SAT00160


title: 60nt_oligo, CMC_treated, not_blocked, XRN1_treated_0min, rep2


title: 60nt_mix_32nt_oligo, CMC_treated, blocked, no_XRN1_treated_30min, rep1


title: SAT00154


title: H3K14ac, Kat6b-/-, sample 4

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the Mus musculus (mm39) and Drosophila melanogaster (Dme1R6.32) genomes by Rsubread version 2.12.3.
Read counts were summarized by genomic regions - Promoters (TSS - 1 kb to TSS), Gene body and Transcription end sites (TES to TES + 1 kb) of protein coding genes, and H3K4me1+/H3K27ac+ enhancer enriched regions - using the Rsubread's featureCounts function and Rsubread's inbuilt mm39 NCBI annotation.
Assembly: mm39 and Dme1R6.32
Supplementary files format and content: Tab-delimited text files for Promoter region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of sequence reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for Gene body counts of protein coding genes; columns represent Entrez Gene ID, gene length in base counts, and the number of reads mapping to that gene.
Supplementary files format and content: Tab-delimited text files for Transcription end site region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for H3K4me1+/H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Supplementary file containing sequence read counts for all samples in matrix form are also provided.
Library strategy: CUT&Tag

growth_protocol: Neural stem and progenitor cells were isolated from the dorsal telencephalon of E12.5 mouse embryos and cultured as free-floating neurosphere colonies as described in Rietze et al. (Nature 2001).

extract_protocol:
All NSPCs were primary cells, derived from freshly dissected tissue. All molecular assays were performed at passages 3-5.
CUT&Tag sequencing was performed using 50,000 NSPCs combined with 50,000 Drosophila melonagaster S2 cells, as described in Kaya-Okur et al. (Nature Communications 2019), with minor modifications as described in Wichmann et al. (Cell Death and Disease 2022).

tag: cut&tag antibody


title: SAT00151


title: H3K14ac, Kat6b-/-, sample 3


title: 60nt_mix_32nt_oligo, no_CMC_treated, blocked, no_XRN1_treated, rep1


title: 60nt_oligo, CMC_treated, blocked, no_XRN1_treated, rep2


title: SAT00149


title: SAT00148


title: H3K14ac, Kat6b-/-, sample 2


title: SAT00147


title: SAT00144


title: 60nt_oligo, CMC_treated, blocked, no_XRN1_treated, rep1


title: H3K14ac, Kat6b-/-, sample 1


title: 60nt_oligo, CMC_treated, not_blocked, no_XRN1_treated, rep2


title: H3K14ac, C57BL/6 Wildtype, sample 4

value: Wildtype


title: SAT00142


title: SAT00138


title: 60nt_oligo, CMC_treated, not_blocked, no_XRN1_treated, rep1


title: SAT00141


title: 60nt_oligo, no_CMC_treated, blocked, no_XRN1_treated, rep2


title: H3K14ac, C57BL/6 Wildtype, sample 3


title: SAT00136


title: SAT00131


title: SAT00133


title: 60nt_oligo, no_CMC_treated, not_blocked, no_XRN1_treated, rep2


title: H3K14ac, C57BL/6 Wildtype, sample 1


title: SAT00129


title: 60nt_oligo, no_CMC_treated, blocked, no_XRN1_treated, rep1


title: 60nt_oligo, no_CMC_treated, not_blocked, no_XRN1_treated, rep1


title: SAT00126


title: SAT00143


title: H3K14ac, C57BL/6 Wildtype, sample 2


title: SAT00125


title: RNA.Pol.II, Kat6b-/-, sample 3


title: SAT00127


title: SAT00124


title: RNA.Pol.II, Kat6b-/-, sample 2


title: H3K27Ac E12.5 TrkC Cut&Run rep3

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Sequence reads were trimmed for adaptor with cutadapt
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie with ‘--no-mixed --no-discordant’
After alignment, fragments with size ≤ 90 bp were selected for peak calling of Runx3/Brn3a/Islet1 samples. No size selection was applied to the H3K27Ac.
Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Runx3 samples we also used '-p e-5'.
Assembly: mm10
Supplementary files format and content: bed file for every experiment with the genomic regions of the consensus peaks.
Supplementary files format and content: Peak calling was performed with MACS2 against the control samples using ‘--keep-dup all’, For the Brn3a samples we also used '-p e-5'

source_name: dorsal root ganglia (DRG)

extract_protocol:
DRG were dissected from E12.5 BacE-GFP expressing embryos (Appel et al 2016) and dissociated with Trypsin B/Collagenase H.  GFP positive cells were FACS isolated and 300,000-600,000 cells were used for Cut&Run analysis with anti-Brn3a (1:200) (kindly provided by E.Turner), home made anti-Runx3 (1:200), anti-H3K27Ac (1:50) (Abcam 4729) antibodies or Normal Rabbit Serum (NRS, 1:200). GFP positive TrkC neurons were bound to ConA beads, permeabilized, incubated with anti-Brn3a, anti-Runx3, anti-H3K27Ac or NRS and targeted by MNase cleavege. Antibody bound DNA was extracted by phenol chloroform.
Library was prepared using NEBNEXT Ultra II DNA Library Prep Kit for Illumina (#E7645). DNA fragments were PCR amplified with Illumina primers for no more than 15 cycles and library fragments up to ~250 bp (insert plus adaptor and PCR primer sequences) were SPRI (x0.8) purified. Libraries were sequenced on the Illumina NextSeq 500/550 following the manufacturer's protocols.

value: dorsal root ganglia (DRG)

value: TrkC proprioceptive neurons

value: Runx3-BAC-GFP-CB6 transgenic mice


title: SAT00137


title: SAT00128


title: SAT00119


title: SAT00121


title: H3K27Ac E12.5 TrkC Cut&Run rep2


title: RNA.Pol.II, Kat6b-/-, sample 4


title: SAT00118


title: RNA.Pol.II, Kat6b-/-, sample 1


title: RNA.Pol.II, C57BL/6 Wildtype, sample 4


title: SAT00116


title: SAT00117


title: H3K27Ac E12.5 TrkC Cut&Run rep1


title: SAT00111


title: SAT00109


title: RNA.Pol.II, C57BL/6 Wildtype, sample 2


title: Brn3a E12.5 TrkC Cut&Run rep4


title: RNA.Pol.II, C57BL/6 Wildtype, sample 3


title: Brn3a E12.5 TrkC Cut&Run rep3


title: Normal Rabbit Serum E12.5 TrkC Cut&Run

description: NRS sample


title: SAT00107


title: SAT00123


title: SAT00108


title: SAT00105


title: SAT00104


title: Brn3a E12.5 TrkC Cut&Run rep2


title: RNA.Pol.II, C57BL/6 Wildtype, sample 1


title: Brn3a E12.5 TrkC Cut&Run rep1


title: H3K9ac, Kat6b-/-, sample 4


title: SAT00101


title: SAT00100


title: Runx3 E12.5 TrkC Cut&Run rep3


title: H3K9ac, Kat6b-/-, sample 2