title: Ops_37_3

city: Umeå

first: Joram

last: Waititu

address: 67 umea

country: Sweden

institute: Umeå University

data_processing:
CLC-Bio Genomic Workbench
The CLC-Bio Genomic Workbench was used with default parameters to perform quality, ambiguity, and length trimming of the reads.
Trimmed sequence reads were mapped to the reference genome of Y. pseudotuberculosis YPIII (NC_010465 for chromosome and NC_006153 for pYV plasmid)
Read count extraction and normalization were performed using the CLC-Bio Genomic Workbench
Assembly: Yersinia pseudotuberculosis YPIII
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text files includes TPM for each sample

organism: Yersinia pseudotuberculosis YPIII

source_name: Y. pseudotuberculosis YPIII/pIBX

growth_protocol: All the strains were cultured overnight at 26oC in LB supplemented with 50 μg/ml kanamycin for in vitro growth as well as total RNA purification.

extract_protocol:
TRIzol Reagent was used to isolate total RNA according to the manufacturer’s instructions followed by DNase I treatment. The NanoDrop 1000  and Agilent 2100 Bioanalyzer were used to assess RNA concentration and integrity, respectively.
RNA libraries for RNA-seq were prepared using using the ScriptSeq Complete Bacteria Kit according to the manufacturer’s instructions while the library concentrations were measured with Qubit 2.0 Fluorometer (

treatment_protocol: For stress conditions, the LB was supplemented with 125 mM NaCl, 0.5% bile, 0.2% glucose and a combination of all three (LB-BNG).For infection, the bacteria were grown overnight in LB at 26°C and concentrations were estimated by absorbance at OD600nm. Cultures were re-suspended to 107 CFUs/ml in sterilized tap water supplemented with 150 mM NaCl. The infection dose was determined by viable count and drinking volume. Eight weeks old female FVB/N (Taconic Farms, Inc) mice were deprived of food and water for 16 hours before oral infection with ~107 CFUs of wt Y. pseudotuberculosis YPIII (pIBX; harboring the luxCDBAE operon in the virulence plasmid pYV) or the corresponding ΔrfaH mutant strain, which were supplied in their drinking water for 6 hours

value: 6 single nucleotide substitutions in ops region

value: 37 degrees Celsius


title: Ops_37_2

status: Public on Sep 10 2025

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: treatment


title: Vestibular epithelium, R00965LF_Control

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

country: Spain

institute: Universitat de Barcelona

description: Library name: AN0791

data_processing:
RNAseq reads were mapped to the rat reference genome (Rnor6.0) with STAR/2.5.3a with ENCODE parameters
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was ensembl92
Assembly: Rnor6.0
Supplementary files format and content: text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Vestibular epithelium

extract_protocol:
Vestibular epithelia were quickly dissected in ice-cold PBS. Two utricles and six crista from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Subchronic ototoxicity rats were given 20 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 4 weeks; control rats received plain drinking water.

tag: tissue

value: Vestibular epithelium

tag: Sex

value: male

tag: strain

value: Long-Evans

value: Control

tag: batch


title: scRNA_KO0069mouse_Stomach

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

description: Updated Microwell-seq_scRNA-seq

library_source: transcriptomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The data were aligned to a GRCm38.88 reference genome. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat.
Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq1.1 protocol

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml PBS.

value: Stomach

tag: age

value: 14 weeks

value: Female


title: scRNA_KO0069mouse_Spleen

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: scRNA_KO0058mouse_Gallbladder-BileDuct

description: Updated Microwell-seq_scRNA-seq

value: Gallbladder-BileDuct

value: 15 weeks


title: Lag3-/-; 5xFAD+, 3 month, female, rep1

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

country: USA

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

description: Library name: Q183

data_processing:
STAR Alignment to Mm10 genome
Subread featureCounts to summarize read counts across genes. Genes without read counts in all samples were excluded. The edgeR package was used for analysis.
Assembly: Mm10
Supplementary files format and content: Counts.Raw.txt
Supplementary files format and content: RPKM.values.txt

source_name: hippocampus

growth_protocol: Animals were maintained on a 12-hour light/ 12-hour dark cycle with ad libitum access to water and standard chow.

extract_protocol:
Total RNA from FACS purified CD11b+; CD45low hippocampal microglia was isolated using RNeasy Plus Mini Kit (Qiagen) and stored at -80°C. cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
The cDNA libraries were prepared using the Nextera XT DNA Library Prep Kit and Nextera XT index Kit (Illumina) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Facility using a NextSeq 500 NGS system (Illumina).

value: hippocampus

tag: cell type

value: microglia

value: 3 month

value: female


title: Ops_37_1


title: scRNA_KO0069mouse_Pancreas

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: TEQUILA-seq on T47D for 468 actionable cancer genes, replicate 1 and 2

city: Philadelphia

first: Lan

last: Lin

state: PA

address: CTRB 9054 3501 Civic Center Blvd

department: Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine

institute: The Children’s Hospital of Philadelphia

description:
Library name: T47D_TEQUILA
Column='T47D_TEQUILA_downsampled_ontarget'
T47D_ESPRESSO_downsampled_abundance.esp
T47D_ESPRESSO_downsampled_updated.gtf

data_processing:
For adaptive sampling experiments, reference FASTA files were uploaded and selected under “Enrich or deplete sequences” in the “Adaptive Sampling” section of the experiment set up within MinKNOW. When indicated, adaptive sampling was performed only on channels 1-1500, while channels 1501-3000 performed standard 1D cDNA or direct RNA sequencing.
Basecalling of raw nanopore data was performed using super-high accuracy dorado (v.0.6.0) with the following settings: --emit-fastq --device cuda:all’. The ‘dna_r10.4.1_e8.2_400bps_sup@v4.3.0’ model was used for basecalling of cDNA sequencing data, and ‘rna004_130bps_sup@v3.0.1’ was used for basecalling of direct RNA data. Where adaptive sampling was performed on only a portion of channels on a flow cell, pod5 files were split according to channel number before basecalling was performed.
Basecalled reads were aligned to either the GRCh38/hg39 primary reference genome or to the SIRV-Set4 reference genome using minimap2 (v2.25) with parameters: ‘-ax splice -ub --secondary=no -t 8 -k 14 -w 4’. A bed file containing annotated splice junctions was created using minimap2’s ‘paftools.js gff2bed’ tool and supplied to the aligner with ‘--junc-bed’.
Data from SH-SY5Y, BT549, and T47D cell lines were downsampled to an equal number of on-target reads in each condition, where indicated.
Novel and annotated transcripts were quantified using ESPRESSO (v1.4.0) guided by a gene annotation GTF file using default parameters.
Assembly: GRCh38
Supplementary files format and content: *_abundance.esp files contain transcript isoform quantifications for each sample.
Supplementary files format and content: *_updated.gtf files contain all novel and annotated transcript isoforms output by ESPRESSO.

organism: Homo sapiens

source_name: T47D human breast cancer cells

growth_protocol: SH-SY5Y human neuroblastoma cells (ATCC, CRL-2266) were cultured in DMEM/F-12 (Gibco, 11330032) with 10% fetal bovine serum (FBS, Corning, MT35010CV) and 100 U/ml penicillin-streptomycin (Gibco, 15140122) at 37°C in 5% CO2. BT459 and T47D breast cancer cell lines were cultured according to ATCC recommendations in RPMI-1640 Medium (Gibco, 11875093) with 10% fetal bovine serum (FBS, Corning, MT35010CV), 0.023 units/mL human insulin (BT549) (Sigma Aldrich, I2643) or 0.2 units/mL bovine insulin (T47D) (Cell Applications, 128100) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from SH-SY5Y, BT549, and T47D cell lines using TRIzol reagent (Invitrogen, 15596018).
Spike-in RNA variants (SIRV) were added to total SH-SY5Y RNA at a ratio of 1:1200. For whole transcriptome cDNA sequencing, reverse transcription was performed on 300ng of total SH-SY5Y RNA with 250pg SIRV-Set4 spike-in RNA (Lexogen, 141.01) using Maxima H minus reverse transcriptase (Thermo Fisher, EP0752), dNTP (Invitrogen, 18427088), template-switching oligo (TSO) (IDT), and RNase inhibitor (Promega, N2615) at 42°C for 90 min, followed by enzymatic inactivation at 85°C for 5 min. PCR amplification was performed with KAPA HiFi HotStart ReadyMix (Fisher Scientific, 50-196-5217) using the following program: 95°C initial denaturing for 3 minutes, followed by 12 cycles of 98 °C for 20 seconds, 67°C for 20 seconds, 72°C for 5 minutes, and a final extension at 72°C for 8 minutes. Amplified cDNA was purified using 0.7X SPRIselect beads (Beckman Coulter, B23318). Nanopore direct RNA libraries were prepared from 3600ng of total RNA from SY5Y cells with 3ng of spike-in RNAs following the standard SQK-RNA004 protocol. First-strand cDNA was synthesized by incubating RNA with T4 DNA Ligase (2M U/ml - NEB, M0202), Quick Ligation Reaction Buffer (NEB, B6058), RNAseOUT (Invitrogen, 10777019), and the supplied RT Adapter at room temperature for 10 minutes, then 50°C for 50 minutes with 10 mM dNTP mix (Thermo Scientific, 18427013), SuperScript III Reverse Transcriptase and the associated 5X First-strand buffer (Invitrogen, 18080093), and the supplied DTT, followed by a 10 minute enzymatic inactivation at 70°C. The resulting RNA-DNA hybrid was purified with 1.8X Agencourt RNAClean XP beads (Beckman Coulter, A63987). The supplied RNA Ligation Adapter was ligated for at room temperature with NEBNext Quick Ligation Reaction Buffer (NEB, E6056) and T4 DNA Ligase (2M U/ml - NEB, M0202) for 10 minutes, then purified with 0.4X Agencourt RNAClean XP beads (Beckman Coulter, A63987) and supplied Wash Buffer, then eluted with the supplied RNA Elution Buffer. Libraries were immediately loaded onto RNA PromethION flow cells (FLO-PRO004RA) and sequenced on a P2 Solo. Nanopore whole transcriptome libraries were prepared from 200ng of amplified cDNA following the standard ONT SQK-LSK114 protocol. The cDNA products underwent end-repair and dA-tailing with the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, E7546) by incubating at 20°C for 5 minutes and 65°C for 5 minutes. The cDNA was then purified with 1X AMPure XP beads (Beckman Coulter, A63881). Adapter ligation was carried out at room temperature for 10 minutes using NEBNext Quick T4 DNA ligase (NEB, E6056). The ligated libraries were purified with 0.4X volumes of AMPure XP beads (Beckman Coulter, A63881) and the supplied Ligation Adapter and Short Fragment Buffer, then eluted with the supplied Elution Buffer. Replicates for each SY5Y+SIRV-Set4 experiment (cDNA control, gene-based cDNA-AS, master-transcript-based cDNA-AS, transcript-based cDNA-AS, exon-based cDNA-AS, and TEQUILA-seq) as well as BT549/T47D experiments (cDNA control, gene-based cDNA-AS, and master-transcript-based cDNA-AS) were performed on a single R10.4.1 PromethION flow cell (FLO-PRO114M) on a P2 Solo or P24. Flow cells were washed in between replicates using the flow cell wash kit (ONT, EXP-WSH004). BT549 and T47D TEQUILA-seq experiments were sequenced on R9.4.1 flow cells (FLO-MIN106) on a GridION. Unless otherwise specified, 20fmol of each cDNA library was loaded onto the flow cell.

tag: cell line

value: T47D human breast cancer cells


title: Lag3-/-, 3 month, female, rep3

description: Library name: Q245


title: Ops_26_3

value: 6 single nucleotide substitutions in ops region

value: 26 degrees Celsius


title: WT, 6 month, female, rep1

description: Library name: A187

value: 6 month


title: TEQUILA-seq on BT549 for 468 actionable cancer genes, replicate 1 and 2

description:
Library name: BT549_TEQUILA
Column='BT549_TEQUILA_downsampled_ontarget'
BT549_ESPRESSO_downsampled_abundance.esp
BT549_ESPRESSO_downsampled_updated.gtf

source_name: BT549 human breast cancer cells

value: BT549 human breast cancer cells


title: scRNA_KO0069mouse_Ovary

description: Updated Microwell-seq_scRNA-seq

value: Ovary


title: Lag3-/-, 3 month, female, rep2

description: Library name: Q244


title: Eef1g cKO leptotene/zygotene spermatocytes_rep3

city: Jinan

first: Jianze

last: Xu

state: Shandong

address: Jinan

institute: Shangdong university

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. HISAT2 were  used to align paired-end clean reads to the reference genome.featureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of p value < 0.05 and log2 fold change > 1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw_counts for each Sample

source_name: testis

extract_protocol:
Cell lysis, mRNA reverse transcription, and cDNA amplification were performed using the Single Cell Full Length mRNA-Amplification Kit (Vazyme,N712).
cDNA fragmentation and adapter ligation were carried out with the TruePrep Flexible DNA Library Prep Kit for Illumina (Vazyme, TD504).

value: testis

value: spermatocytes

value: Eef1g cKO


title: Lag3-/-, 3 month, female, rep1

description: Library name: Q243


title: Ops_26_2


title: Eef1g cKO leptotene/zygotene spermatocytes_rep2

description: Library name: Sample 5


title: scRNA_KO0069mouse_Uterus

description: Updated Microwell-seq_scRNA-seq

value: Uterus

value: 14 weeks

value: Female


title: Ops_26_1


title: 5xFAD+, 3 month, female, rep3

description: Library name: A211

value: hippocampus


title: scRNA_KO0069mouse_LymphNodes

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: 5xFAD+, 3 month, female, rep2

description: Library name: A201

value: microglia

value: 3 month


title: Oanti_37_2

value: gmd, fcl, manC, wbyq, gne, manB, and wzz deletion

value: 37 degrees Celsius


title: scRNA_KO0069mouse_Lung

description: Updated Microwell-seq_scRNA-seq

value: Lung


title: Lag3-/-; 5xFAD+, 3 month, female, rep2

description: Library name: Q184

value: female


title: scRNA_KO0069mouse_Heart

description: Updated Microwell-seq_scRNA-seq

value: Heart


title: 5xFAD+, 3 month, female, rep1

description: Library name: A197


title: Oanti_37_3


title: Control leptotene/zygotene spermatocytes_rep3

description: Library name: Sample 3

value: Wild type


title: Control leptotene/zygotene spermatocytes_rep2

description: Library name: Sample 2


title: WT, 3 month, female, rep3

description: Library name: A225


title: Oanti_26_3

value: 26 degrees Celsius


title: Control leptotene/zygotene spermatocytes_rep1

description: Library name: Sample 1

value: testis


title: scRNA_KO0069mouse_BoneMarrow

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow


title: WT, 3 month, female, rep2

description: Library name: A212


title: WT, 3 month, female, rep1

description: Library name: A200


title: 6-month-old Ctns-/-  (cys7)

type: genomic

city: Rome

first: Giusi

last: Prencipe

address: Viale di San Paolo 15

country: Italy

institute: Bambino Gesù Children's Hospital

hyb_protocol: DNA was amplified, fragmented and hybridized to the Infinium Mouse Methylation BeadChip using the standard protocol.

scan_protocol: Illumina iScan microarray platform

data_processing:
Data analysis was performed by means of an in-house pipeline using R programming language (v.4.1.2), mainly based on the ENmix package (v.1.30.03) for importing IDAT files, performing data quality control, and correcting for background and dye-bias noise (Xu et al., 2021).
Matrix_processed.csv represents Normalized beta-values

molecule: genomic DNA

source_name: kidney

label_protocol: standard protocol

extract_protocol: Genomic DNA was extracted using standard techniques from paraffine embedded mouse kidney.

value: kidney


title: 6-month-old Ctns-/-  (cys6)


title: scRNA_KO0069mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine


title: dengue_2

city: Guangzhou

first: zheng

last: wenjiang

state: Guangdong

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

data_processing:
Libraries were sequenced on the Illumina HiSeq X Ten platform, and 150 bp paired-end reads were generated.
The raw data were first pre-processed by removing primer splice sequences and double-checking and screening the base quality and length of sequenced fragments.
We used cutadapt software (version 1.14) to remove the splice sequences and screen out sequences between 15 and 41 nt in length, and then used fastx toolkit software (version 0.0.13) to perform Q20 quality control on the sequences, retaining those with 80% Q20 and above.
NGSQCToolkit (version 2.3.3) was used to filter out reads containing N bases, and the obtained high-quality CleanReads were distributed according to the type, quantity, and sequence length, and finally the sequences were annotated against databases (Rfam database (version 10.0) , cDNA sequences, RepeatMasker, miRBase database) using bowtie software to obtain the final small RNA distribution data for the six mice samples.
We used the TPM formula (transcript per million) to calculate the expression of known miRNAs and newly predicted miRNAs. “N” is the number of reads per miRNA, “M” is the total number of reads compared to the sample (CleanReads). For the TPM result see the document named: "TPM.xls"
Differential gene expression analysis was performed using the DESeq2 (2014) R package
Assembly: http://www.mirbase.org/cgi-bin/browse.pl?org=mmu
Supplementary files format and content: tab-delimited text files include TPM and count values for each Sample
Supplementary files format and content: A total of 1172 known miRNAs were found in these six samples. For the annotation result see the document named: "1172 miRNAs annotation.xls"

source_name: kidney tissue, Dengue, Day8 2

growth_protocol: IFNAR-/- mice on the C57BL/6J background were generated and bred in-house under specific pathogen-free conditions in our laboratory at 21 °C in 55% humidity on a 12:12 h light: dark cycle.

extract_protocol:
Total RNA was extracted from mouse kidney tissue using mirVana™ miRNA ISOlation Kit (Ambion) according to the manufacturer’s protocol. 0.5 ug of total RNA was used for the construction of sequencing libraries.
samall RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.) following the manufacturer’s recommendations.  Briefly, total RNA was ligated to adapters at each end. Then the adapter-ligated RNA was reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140-160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol:
Male mice (6-8 weeks old) were challenged intraperitoneally (i.p.) with the DENV-2 TSV01 strain (dengue virus infection group, n=3, 1×105 PFU)
Mice injected with an equivalent volume of PBS (mock infection) were used as negative controls (n=3).

value: IFNAR knockdown

value: dengue virus serotypes -2 (TSV01) i.p.

tag: time

value: Day 8


title: dengue_3

source_name: kidney tissue, Dengue, Day8 3


title: Ptdss1 KD#3, replicate 3

city: Houston

first: Jielin

last: Liu

state: TX

address: 7455 Fannin St

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

description: Library name: KD3_3

data_processing:
The NextSeq RTA was used for base calling
bcl2fastq was used to convert the .bcl files into .fastq files
Fastq files were aligned to the mouse reference genome (mm10) using HISAT2 and assembled using StringTie
R and R package DESeq2 was used for data normalization and differential expression analysis
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol:
Total RNA was extracted from cells using Quick-RNA miniprep kit (ZYMO research).
Libraries were generated using Illumina’s TruSeq Kit

value: mouse bladder cancer cell line

value: Ptdss1 KD_3


title: 6-month-old Ctns-/-  (cys5)


title: dengue_1

source_name: kidney tissue, Dengue, Day8 1


title: rfaH_37_3

value: rfaH deletion mutant


title: 6-month-old Ctns-/-  (cys4)


title: Ptdss1 KD#3, replicate 2

description: Library name: KD3_2


title: Ptdss1 KD#3, replicate 1

description: Library name: KD3_1


title: Oanti_37_1

value: gmd, fcl, manC, wbyq, gne, manB, and wzz deletion


title: 6-month-old Ctns-/-  (cys3)


title: scRNA_KO0069mouse_Brain

description: Updated Microwell-seq_scRNA-seq

value: Brain

value: 14 weeks

value: Female


title: Ptdss1 KD#2, replicate 3

description: Library name: KD2_3

value: Ptdss1 KD_2


title: control_2

source_name: kidney tissue, Control, Day8 2

value: PBS i.p.


title: rfaH_26_3

value: 26 degrees Celsius


title: rfaH_37_1

value: 37 degrees Celsius


title: 6-month-old Ctns-/-  (cys2)

value: female


title: control_1

source_name: kidney tissue, Control, Day8 1

value: kidney


title: Ptdss1 KD#2, replicate 2

description: Library name: KD2_2


title: Eef1g cKO leptotene/zygotene spermatocytes_rep1

description: Library name: Sample 4

value: testis

value: spermatocytes

value: Eef1g cKO


title: Oanti_26_1


title: rfaH_26_2


title: 6-month-old Ctns-/-  (cys1)


title: LM1

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: biotin

source_name: ALK-positive large B-cell lymphoma, cell line

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions


title: Ptdss1 KD#2, replicate 1

description: Library name: KD2_1


title: 6-month-old wild type  (wt7)


title: wt_37_3

value: WT


title: ALKpos LBCL case 6

source_name: ALK-positive large B-cell lymphoma

value: ALK-positive large B-cell lymphoma


title: ALKpos LBCL case 5


title: control_3

source_name: kidney tissue, Control, Day8 3

value: IFNAR knockdown

value: Day 8


title: rfaH_37_2

value: rfaH deletion mutant


title: Ptdss1 KD#1, replicate 3

description: Library name: KD1_3

value: mouse bladder cancer cell line

value: Ptdss1 KD_1


title: wt_37_2


title: 6-month-old wild type  (wt5)


title: Ptdss1 KD#1, replicate 1

description: Library name: KD1_1


title: ALKpos LBCL case 4


title: ALKpos LBCL case 3


title: 6-month-old wild type  (wt4)


title: WT, replicate 3

description: Library name: WT_3_


title: wt_26_3


title: ALKpos LBCL case 2


title: WT, replicate 2

description: Library name: WT_2


title: 6-month-old wild type  (wt2)


title: wt_26_2


title: ALKpos LBCL case 1


title: WT, replicate 1

description: Library name: WT_1


title: rfaH_26_1


title: 6-month-old wild type  (wt1)


title: 6-month-old wild type  (wt6)


title: Ptdss1 KD#1, replicate 2

description: Library name: KD1_2


title: 220722_BrdUTP_methcontrols.50_BrdUTP_meth

status: Public on Sep 09 2025

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description:
Library name: Sample 175
PCR control for model training

library_source: genomic

data_processing:
Reads are demultiplexed using lima to produce a .bam file for subreads for each sample.
Circular consensus sequences (CCS) were generated for each sample using ccs to produce a corresponding .bam file per sample.
Assembly: mm10
Supplementary files format and content: Processed data is shared in .pickle format.

source_name: mESCs

growth_protocol: K562 cells (ATCC) were grown for at least three days in standard media containing RPMI 1640 + L-Glutamine (Hyclone) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). mESC E14 cells were grown on 0.2% gelatin and maintained in standard media containing DMEM + Glutamax (ThermoFisher 10566-016), 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 1X Non-Essential Amino Acids (ThermoFisher 11140-50), 1 mM Sodium Pyruvate (ThermoFisher 11360-070), 0.128mM 2-Mercaptoethanol (BioRad 1610710XTU), and 1X Leukemia Inhibitory Factor (purified and gifted by Barbara Panning Lab at UCSF). mESCs were passaged every 1-2 days using TrypLE Express Enzyme (1X) (12605010). Media was changed daily when cells were not passaged. All cell lines were regularly tested negative for mycoplasma contamination. Standard media was added to mESC E14 or K562 cells with a final concentration of 10 uM BrdU (abcam ab142567). Cells were incubated in BrdU-containing media for between 5 minutes and 24 hours. After labeling, mESC E14 plates were rinsed three times with 1x PBS and collected using TrypLE Express Enzyme (1X) (12605010). K562s were collected and spun down (300xg, 5 minutes) immediately after labeling.

extract_protocol:
To the methylation reaction, 2.65 uL 10% SDS and 2.65 uL of 20 mg/mL Proteinase K (Thermo Scientific AM2548) were added and incubated at 65oC for at least 2 hours and up to overnight. To extract the DNA, an equal volume of Phenol-Chloroform was added and mixed vigorously by shaking. The samples were then spun at max speed for 2 min and the aqueous portion was removed. To the aqueous extraction, 0.1x volumes of 3M NaOAc, 1 uL GlycoBlue, and 3x volumes of cold 100% EtOH were added, mixed by inversion and incubated overnight at -20oC or for 2 hours at -80oC. Samples were then spun at max speed for 30 minutes at 4oC, washed with 500 uL 70% EtOH, spun again at max speed for 2 minutes at 4oC. The resulting pellet was air dried and resuspended in 40 uL EB.
Purified DNA from mESCs and K562s was sheared using a Covaris g-tube (520079) in a 5424 rotor at 7,000 RPM for 6 passes for a target size between 6,000 and 8,000 bp. Sheared DNA was used as input for the PacBio HiFi SMRTbell Library Preparation protocol using the SMRTbell Express Template Prep Kit 2.0. Briefly, samples underwent removal of single stranded overhangs, DNA damage repair, end-repair, A-tailing, barcoded SMRTbell adapter ligation, and exonuclease cleanup according to manufacturer’s protocol followed by a 1X AMPure PB bead cleanup. Final sample concentration was measured via Qubit High Sensitivity DNA Assay and library size was measured on an Agilent Bioanalyzer DNA chip. Libraries were sequenced on PacBio Sequel II 8M SMRTcells.

treatment_protocol: Briefly, all nuclei were collected by centrifugation (300xg, 5 min), washed in ice cold 1X PBS, spun again (300xg, 5 min), and resuspended in 1 mL Nuclear Isolation Buffer (20mM HEPES, 10mM KCl, 1mM MgCl2, 0.1% Triton X-100, 20% Glycerol, and 1X Protease Inhibitor (Roche 4693132001)) per 10 million cells by gently pipetting 5x with a wide-bore pipette tip. The suspension was incubated on ice for 5 minutes, and nuclei were pelleted (600xg, 4oC, 5 min), washed with Buffer M (15mM Tris-HCl pH 8.0, 15 mM NaCl, 60mM KCl, 0.5mM Spermidine), and spun once again (600xg, 4oC, 5 min). Nuclei were resuspended in 200 uL of Methylation Reaction Buffer (Buffer M containing 1mM S-adenosylmethionine (SAM; New England BioLabs B9003S)). 10uL high-concentration EcoGII was added per 1e6 nuclei and the nuclei suspension was incubated at 37oC for 30 minutes. An additional 1 uL of 32 mM SAM was supplemented after 15 minutes. Any unmethylated controls were treated similarly with the addition of SAM, but EcoGII was excluded from those reactions.

value: mESCs

value: yes EcoGII / 50% BrdUTP in PCR


title: 210930_MO_E14_K562_BrdU.E14_BrdU

description:
Library name: Sample 171
PCR control for model training

value: no EcoGII / 100% BrdUTP in PCR


title: 220722_BrdUTP_methcontrols.100_BrdUTP_meth

description:
Library name: Sample 176
PCR control for model training

value: yes EcoGII / 100% BrdUTP in PCR


title: wt_37_1

value: 37 degrees Celsius


title: 210930_MO_E14_K562_BrdU.E14_dNTP

description:
Library name: Sample 170
PCR control for model training

value: no EcoGII / no BrdUTP in PCR


title: 220722_BrdUTP_methcontrols.50_BrdUTP_naked

description:
Library name: Sample 174
PCR control for model training

value: no EcoGII / 50% BrdUTP in PCR


title: 6-month-old wild type  (wt3)

value: kidney

value: female


title: MOC1 Fuso-1

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

description: Library name: MOC1 Fuso-1

data_processing:
Data were quantified as transcripts per million reads mapped (TPM) using kallisto
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each sample

extract_protocol:
RNA was extracted using a Qiagen RNeasy Mini Kit per manufacturer's instructions.
Poly-A RNA libraries for RNA-seq were prepared by CCF core facilities

treatment_protocol: Cells were either mock infected or infected with Fusobacterium or Prevotella at an MOI of 200 for four hours.

value: HNSCC cell line

tag: replicate

value: Fusobacterium


title: MOC1 Control-3

description: Library name: MOC1 Control-3

value: Mock


title: MOC1 Fuso-3

description: Library name: MOC1 Fuso-3


title: MOC1 Prevotella-3

description: Library name: MOC1 Prevotella-3

value: Prevotella


title: MOC1 Control-2

description: Library name: MOC1 Control-2


title: MOC1 Prevotella-2

description: Library name: MOC1 Prevotella-2


title: Ventricle, WT mouse 5, 7 weeks old

city: Hefei

first: Yuchen

last: Wang

state: Anhui

address: 81 Meishan Road

department: School of Basic Medical Sciences

institute: Anhui Medical University

description:
Library name: WT5
WT5

data_processing:
The quality information of raw data in FASTQ  format was calculated and then the raw data was filtered using fastp(0.22.0) software.
Reference genome index was built by HISAT2 (v2.1.0) and the filtered reads were mapping to the reference genome using HISAT2.
The gene read count value was counted using HTSeq (v0.9.1) as the original expression level of the gene.
FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
Assembly: GRCm39 (Genome Reference Consortium Mouse Reference 39)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Heart

growth_protocol: All animal experiments were approved by the University of Science and Technology of China (USTC) Ethics Committee. All mice were purchased from the GemPharmatech Co., Ltd. and maintained on a 12-h light/dark cycle from 8 am to 8 pm.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: Mice were fed on chow diet.

value: Heart

value: 7 weeks old

value: WT

value: Chow diet


title: MOC1 Fuso-2

description: Library name: MOC1 Fuso-2


title: Ventricle, WT mouse 4, 7 weeks old

description:
Library name: WT4
WT4


title: MOC1 Prevotella-1

description: Library name: MOC1 Prevotella-1


title: Oanti_26_2

source_name: Y. pseudotuberculosis YPIII/pIBX

value: gmd, fcl, manC, wbyq, gne, manB, and wzz deletion

value: 26 degrees Celsius


title: MOC1 Control-1

description: Library name: MOC1 Control-1


title: Ventricle, WT mouse 6, 7 weeks old

description:
Library name: WT6
WT6


title: Ventricle, WT mouse 3, 7 weeks old

description:
Library name: WT3
WT3


title: wt_26_1


title: Ventricle, WT mouse 2, 7 weeks old

description:
Library name: WT2
WT2


title: Ventricle, WT mouse 1, 7 weeks old

description:
Library name: WT1
WT1


title: Ventricle, Vps13c-cKO mouse 6, 7 weeks old

description:
Library name: V_cKO6
V_cKO6

value: Vps13c knockout


title: Ventricle, Vps13c-cKO mouse 4, 7 weeks old

description:
Library name: V_cKO4
V_cKO4


title: Ventricle, Vps13c-cKO mouse 5, 7 weeks old

description:
Library name: V_cKO5
V_cKO5


title: Ventricle, Vps13c-cKO mouse 2, 7 weeks old

description:
Library name: V_cKO2
V_cKO2


title: Ventricle, Vps13c-cKO mouse 1, 7 weeks old

description:
Library name: V_cKO1
V_cKO1


title: Enh-CBS_NPC_Cap-C_Gata6

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

description: Library name: Sample 3

data_processing:
Capture-C data was processesd and analyze according to PMCID: PMC7613269
Assembly: mm10 based custom refence genomes corresponding to each of the genotypes was generated using reform tool (https://gencore.bio.nyu.edu/reform/)
Supplementary files format and content: Bigwig; for each sample the bigwig files show the average Capture-C signals obtained for two independent biological replicates (rep1 and rep2)
Library strategy: Capture-C

source_name: Mouse ESCs (E14Tg2a)

growth_protocol: Mouse ESCs (E14Tg2a) were cultured on gelatin-coated plates at 37°C with 5% CO2 in the presence of Knock-out DMEM, supplemented with 15% FBS , 0.1 mM 2-mercaptoethanol, 1x Glutamax, 1× penicillin–streptomycin, 1× MEM non-essential amino acids and leukemia inhibitory factor (LIF).

extract_protocol:
Capture-C data was processed and analyzed according to PMCID: PMC7613269. Briefly, 5 × 106 cells were crosslinked with 2% paraformaldehyde for 10 min. Subsequently, cells were quenched with 0.125 M glycine for 10 min. After washing three times with PBS, cells were resuspended in lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% NP-40 and 1× protease inhibitors) for 30 min on ice. Afterwards, nuclei were pelleted by centrifugation and resuspended in NEB Buffer DpnII (B0543S, NEB) for subsequent chromatin digestion with DpnII (R0543S, NEB) followed by proximity ligation (Life Tech, cat. no. EL0013). Next, de-crosslinking was performed with Proteinase K (3U; Thermo Fisher, cat. no. EO0491) and subsequent incubation with RNase A (7.5 mU; Roche: 1119915).
DNA was purified using the Qiagen kit (28506). Purified DNA was sonicated using Covaris S220 Focused-ultrasonicator (time, 180 s; duty factor, 10%; peak incident power, 175 W; cycles per burst, 200) to an average size of 200 bp. Sheared DNA was purified using AMPure XP SPRI beads (Beckman Coulter, cat. no. A63881). 3C libraries were generated using the NEBNext Ultra II kit (New England Biolabs, cat. no. E7645S/L). Index primers set 1 and 2 from the NEBNext Multiplex Oligos for Illumina kit (New England Biolabs, E7335S/L E7500S/L) were incorporated using Herculase II Fusion Polymerase Kit (Agilent, cat. no. 600677). Enrichment of ligated fragments containing the viewpoints of interest was performed using 120bp long probes in two consecutive rounds, as described for MCC in PMID: 34108683. Isolation of hybridized DNA was performed using M-270 Streptavidin Dynabeads (Invitrogen, 65305) and amplified by PCR (11 cycles). The second enrichment reaction was performed using the pulled down material from the first enrichment reaction as input. The quality of the final libraries was assessed with a fragment analyzer and sequenced using the the Novaseq6000 sequencing system (150bp paired-end reads;15 Mreads/lib).

treatment_protocol: Differentiation towards Neural Progenitor cells was performed by growing mESC for six days in N2B27 medium, supplemented with FGF and XAV

value: Mouse ESCs (E14Tg2a)

value: NPC

value: Enh-CBS

value: Double hybridization capture using ssDNA probes at the Gata6 locus


title: 4xEnh_NPC_Cap-C_Gata6

description: Library name: Sample 4


title: WT_NPC_Cap-C_Gata6

description: Library name: Sample 1

value: Wild type


title: Sh2-Thap-rep3

city: Shanghai

first: Peipei

last: Jiang

state: Shanghai

address: No. 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong University

description: Library name: Sh2-Thap-rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence using trim_galore with the default parameters
Trimmed sequence reads were mapped to mm10 genome using STAR (v2.5.3a ) with default parameters
All mapped bam files were converted to bigwig using bedtools (v2.31.0) for visualization in IGV
Diferentially expressed genes were analyzed by DEseq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO₂ at 37℃

extract_protocol:
RNA was harvested using MolPure Cell RNA Kit (YEASEN, 19231ES50)
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: CEBPγ knock down, Thap 6h


title: C2C12_Thap6h_ATF4_SCBT_rep1

description: Library name: C2C12_Thap6h_ATF4_SCBT_rep1

data_processing:
The raw reads were trimmed by Trim Galore (v0.6.10)
Trimmed reads were mapped to the mouse transcriptome (mm10) by Bowtie2
CUT&Tag peaks were identified using MACS2 (v2.2.7.1, -f BAMPE) with p<0.05.  Pronounced ATF4 peaks were then filter with the summit>400
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% C02 at 37℃

extract_protocol: The CUT&Tag assay was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme #TD903)

treatment_protocol: C2C12 cells were treated with 100nM DMSO and 100nM Thap respectively for 6h.

value: Thap 6h


title: C2C12_DMSO6h_ATF4_SCBT_rep2

description: Library name: C2C12_DMSO6h_ATF4_SCBT_rep2

value: DMSO 6h


title: C2C12_DMSO6h_ATF4_SCBT_rep1

description: Library name: C2C12_DMSO6h_ATF4_SCBT_rep1


title: C2C12_Thap6h_ATF4_SCBT_rep2

description: Library name: C2C12_Thap6h_ATF4_SCBT_rep2


title: Sh2-DMSO-rep1

description: Library name: Sh2-DMSO-rep1

value: CEBPγ knock down, DMSO 6h


title: Sh2-Thap-rep1

description: Library name: Sh2-Thap-rep1


title: Sh2-DMSO-rep3

description: Library name: Sh2-DMSO-rep3


title: Ctrl-Thap-rep2

description: Library name: Ctrl-Thap-rep2


title: Sh2-DMSO-rep2

description: Library name: Sh2-DMSO-rep2


title: Ctrl-Thap-rep1

description: Library name: Ctrl-Thap-rep1


title: Ctrl-DMSO-rep3

description: Library name: Ctrl-DMSO-rep3


title: Ctrl-DMSO-rep2

description: Library name: Ctrl-DMSO-rep2


title: Ctrl-DMSO-rep1

description: Library name: Ctrl-DMSO-rep1


title: els, adult, non-activated, replicate 3

city: Princeton

first: Catherine

middle: Jensen

last: Peña

state: NJ

address: Princeton Neuroscience Institute, Washington Road, Lot 20

institute: Princeton Neuroscience Institute

description:
Library name: elsF4_VTA_NB
SP 100nt Chemistry to yield ~325-400M read depth

data_processing:
read trimming with fastp (v0.23.4) with base correction enabled
alignment to mm39 with bowtie2 (v2.4.5) ("--no-unal --no-mixed --no-discordant")
unique reads selected (MAPQ>30) using samtools (v1.13)
samtools (v1.13) collate, fixmate, sort, markdup
MACS2 (v2.2.9.1) call narrowpeaks for each sample (ignoring duplicates)
R (v4.4.2) package BRGenomics (v1.17.1) "import_bam" (field=NULL), unique reads selected, GenomicRanges (v1.58.0) coverage, cpm/rpm normalization, rtracklayer (v1.66.0) export.bw
Assembly: mm39
Supplementary files format and content: bigWig (cpm normalized), macs2 narrowpeaks

source_name: brain

extract_protocol:
all nuclei were extracted by iodixanol gradient and centrifugation at 500g for 5 min at 4C. Nuclei with nuclear Sun1-myc-sfGFP tag were separated from total nuclear population by magnetic immunoprecipitation.
Accessible chromatin for all nuclei were excised and adapters were bound by Illumina transposition kit (Illumina). (Tn5 transposition)
DNA fragments were recovered with a Qiagen MinElute kit (Qiagen) and barcoded with Illumina UD indexes. DNA fragments were PCR amplified according to Buenrostro et al and Corces et al. Post amplification libraries were cleaned up by AMPure XP beads (ThermoFisher). Libraries were validated by Agilent High Sensitivity DNA kit.
ATAC-seq

treatment_protocol: nuclei were extracted from VTA cells of mice in adulthood after either early-life stress or standard rearing

value: brain

tag: region

value: ventral tegmental area

value: ArcCreERT2 x Sun1/+

value: adult (>60 PND)

tag: activation

value: non-activated

value: Female

tag: stress

value: early life stress

tag: pooled or_single_animal

value: single animal


title: els, adult, non-activated, replicate 2

description:
Library name: elsM6_VTA_NB
SP 100nt Chemistry to yield ~325-400M read depth

value: Male


title: els, adult, non-activated, replicate 1

description:
Library name: elsM5_VTA_NB
SP 100nt Chemistry to yield ~325-400M read depth


title: Ventricle, Vps13c-cKO mouse 3, 7 weeks old

description:
Library name: V_cKO3
V_cKO3

value: Heart

value: 7 weeks old

value: Vps13c knockout

value: Chow diet


title: std, adult, non-activated, replicate 1

description:
Library name: stdF5_VTA_NB
SP 100nt Chemistry to yield ~325-400M read depth

value: standard-reared


title: std, adult, non-activated, replicate 2

description:
Library name: stdF6_VTA_NB
SP 100nt Chemistry to yield ~325-400M read depth


title: els, adult, activated, replicate 3

description:
Library name: elsF4_VTA_BB
SP 100nt Chemistry to yield ~325-400M read depth

value: activated


title: els, adult, activated, replicate 2

description:
Library name: elsM6_VTA_BB
SP 100nt Chemistry to yield ~325-400M read depth


title: std, adult, activated, replicate 2

description:
Library name: stdF5_VTA_BB
SP 100nt Chemistry to yield ~325-400M read depth


title: Enh_NPC_Cap-C_Gata6

description: Library name: Sample 2

value: Mouse ESCs (E14Tg2a)

value: NPC

value: Enh

value: Double hybridization capture using ssDNA probes at the Gata6 locus


title: els, adult, activated, replicate 1

description:
Library name: elsM5_VTA_BB
SP 100nt Chemistry to yield ~325-400M read depth

value: brain

value: ventral tegmental area

value: ArcCreERT2 x Sun1/+


title: Ctrl-Thap-rep3

description: Library name: Ctrl-Thap-rep3

value: Thap 6h


title: Sh2-Thap-rep2

description: Library name: Sh2-Thap-rep2

value: CEBPγ knock down, Thap 6h


title: C57BL/6_multiplex

city: London

first: Anne

last: O'Garra

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: C57BL/6_uninf_HN878_multiplex

data_processing:
CellRanger7.0.1: default params
Scripts for analysis post-Cell Ranger available at https://github.com/aspides-js/ogarra_lab
Assembly: mm10-2020-A
Supplementary files format and content: Tar archive of Cell Ranger output directory including filtered output matrix
Supplementary files format and content: Data slot from Seurat object integrated across all samples

source_name: Lung

extract_protocol:
Cells were thawed and hybridised for 22 hours to probes from the Mouse 16-Plex Fixed Cell Profiler kit (10X Genomics), as per manufacturer’s instructions. All samples were split in two and hybridised to two different barcoded probes to increase cell recovery, except for two out of three uninfected control samples from each mouse strain.
Cells from C57BL/6 and C3HeB/FeJ mice were combined in equal numbers per barcode into individual pools, which were washed, concentrated and loaded on 10x chip Q where the fixed and probe-hybridized single cell suspensions were partitioned into nanolitre-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes was sampled separately to index the contents of each partition. Inside the GEMs, probes were ligated and the 10x GEM Barcode was added, and all ligated probes within a GEM share a common 10x GEM Barcode. Barcoded and ligated probes were then pre-amplified in bulk, after which gene expression libraries were generated.

value: Lung

value: Mixed sample (Uninf, HN878_d14. HN878_d20)

tag: library type

value: mRNA

tag: kit

value: 10X Flex Gene


title: std, adult, activated, replicate 1

description:
Library name: stdM4_VTA_BB
SP 100nt Chemistry to yield ~325-400M read depth

tag: genotype

value: adult (>60 PND)

value: Male

value: single animal


title: C3HeB/FeJ_Mtb_HN878_d21_lung_3

description: Library name: C3H_d21_Lung_3

data_processing:
nf-core/rnaseq pipeline v3.16.1; default parameters
Assembly: mm10
Supplementary files format and content: csv of DESeq2 noramalised expression values

extract_protocol:
RNA was extracted from lung homogenates using the DirectZol Mini Kit with on-column DNase I digestion (Zymo), as per manufacturer’s instructions. BAL cell pellets were resuspended in TRI reagent and vortexed at high speed for ≥10 seconds to lyse. RNA was extracted from BAL lysates using the DirectZol Mini Kit with on-column DNase I digestion (Zymo), as per manufacturer’s instructions. RNA integrity of all samples was determined to range from 5.7 – 9.4 (median 7.9)
RNA-seq libraries from whole BAL and lung of HN878-infected C57BL/6 and C3HeB/FeJ mice and from lung tissue samples obtained from anti-IFNAR-treated HN878-infected C3HeB/FeJ mice were prepared using the total RNA library prep kit with Polaris ribosomal RNA depletion (Watchmaker Genomics)

tag: treatment

value: HN878 Infected Day 21


title: C3HeB/FeJ_Mtb_HN878_d21_lung_2

description: Library name: C3H_d21_Lung_2

tag: tissue


title: C3HeB/FeJ_multiplex

description: Library name: C3HeB/FeJ_uninf_HN878_multiplex


title: C3HeB/FeJ_Mtb_HN878_d14_lung_4

description: Library name: C3H_d14_Lung_4

value: HN878 Infected Day 14


title: C3HeB/FeJ_uninfected_lung_4

description: Library name: C3H_uninf_Lung_4

value: Uninfected


title: C3HeB/FeJ_uninfected_lung_5

description: Library name: C3H_uninf_Lung_5


title: C3HeB/FeJ_uninfected_lung_2

description: Library name: C3H_uninf_Lung_2


title: C3HeB/FeJ_Mtb_HN878_d14_lung_3

description: Library name: C3H_d14_Lung_3


title: C3HeB/FeJ_uninfected_lung_3

description: Library name: C3H_uninf_Lung_3


title: C3HeB/FeJ_Mtb_HN878_d21_lung_5

description: Library name: C3H_d21_Lung_5


title: C3HeB/FeJ_Mtb_HN878_d21_lung_1

description: Library name: C3H_d21_Lung_1


title: C3HeB/FeJ_Mtb_HN878_d14_lung_5

description: Library name: C3H_d14_Lung_5


title: C57BL/6_Mtb_HN878_d21_lung_5

description: Library name: B6_d21_Lung_5


title: C57BL/6_Mtb_HN878_d21_lung_3

description: Library name: B6_d21_Lung_3


title: C57BL/6_Mtb_HN878_d21_lung_2

description: Library name: B6_d21_Lung_2


title: C57BL/6_Mtb_HN878_d21_lung_4

description: Library name: B6_d21_Lung_4


title: C3HeB/FeJ_Mtb_HN878_d21_lung_4

description: Library name: C3H_d21_Lung_4


title: C3HeB/FeJ_uninfected_lung_1

description: Library name: C3H_uninf_Lung_1


title: C57BL/6_Mtb_HN878_d14_lung_5

description: Library name: B6_d14_Lung_5


title: C3HeB/FeJ_Mtb_HN878_d14_lung_1

description: Library name: C3H_d14_Lung_1


title: inC-scRNA-seq of hPBMCs processed in CAGEs, all and T/N/K cell subset (PBMCs)

city: Boston

first: Ignas

last: Mazelis

state: MA

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

description:
Library name: hPBMCs_all and hPBMCs_TNK
inC-scRNA-seq of hPBMCs processed in CAGEs
inC-scRNA-seq of hPBMCs processed in CAGEs, T/N/K cell subset

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used:CTTAATAG, ATAGCCTT, TAAGGCTC, TCGCATAA), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5.
Count matrices were generated using STARsolo pipeline (2) (STAR 2.7.9a) with the with parameters (--soloFeatures Gene, GeneFull, --genomeSAsparseD 3, --outSAMtype BAM SortedByCoordinate, --outSAMattributes CB CR UR UB UY GN GX, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR, --soloMultiMappers EM, --soloCellFilter EmptyDrops_CR, --quantMode TranscriptomeSAM GeneCounts) Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly was used.
Count matrices were filtered by selecting barcodes with >1000 UMIs and fraction of mitochondrial counts being below 0.4. UMI and Gene sampling were perfomed on aligned and sorted BAM files. Count marices were analyzed using scanpy python packages
Assembly: Mixed Human GRCh38.101 genome assembly
Supplementary files format and content: h5ad cell x genes expression matrix

source_name: Blood

growth_protocol: Human Peripheral Blood Mononuclear Cells were obtained from Lonza (CC-2704). The cryo-preserved cell vials were stored in liquid Nitrogen until use, and then thawed in a 37ºC metal bead bath for 7 minutes. The thawed cell suspension was transferred into a 15 mL falcon tube. 1 mL of 37ºC pre-warmed DMEM (ThermoFisher, 10566016) with 10% FBS (ATCC, 30-2020) and 1x Penicillin/Streptomycin (ThermoFisher, 10378016) was slowly added into the original cryopreservation tube. This media was then added one drop at a time into the falcon tube. Additional 8 mL of pre-warmed media were added slowly onto the cell suspension. Cells were resuspended gently and centrifuged at room temperature at 300g for 4 mins. All of the media was aspirated from the cell pellet and cells were suspended in 5 mL of fresh, 37ºC appropriate media with 10% FBS and 1x Penicillin/Streptomycin and transferred into 25 cm2 culture flask with a filter cap (Corning). Cells were cultured in a 37ºC incubator with 5% CO2. In the case of PBMCs, cells were washed one more time with IMDM + 10% FPBS +1x Pen/Strep and were passed through a 40μm strainer. Following this, cells were washed with ice cold plain IMDM with 0.5% BSA

extract_protocol:
PBMCs  were washed twice with IMDM with 0.5% BSA and were encapsulated into CAGEs at a final concentration of 1.4e6 cells/mL in core mix. Next, the CAGE core dextran was removed using dextranase enzyme. Following this, all steps were performed on ice. First, capsules were washed three times with an ice-cold 3X SSCI buffer with 800g spins for 1 min. Cells were lysed by washing with ice-cold 7.5pH TEIS with 5 min incubations on ice. After lysis, capsules were imaged, washed three times with 3X SSCI and three times with HI10, packed at 800g for 1 min and stored on ice. Reverse-transcription reaction was set on ice and performed in 14x PCR strip tubes. A single 60μL reaction was composed out of 36.3μL of packed capsules, 1.5μL of 10μM RT poly(T) primer housing a 10nt UMI and 6nt barcode (1 out of 14), 1.8μL of 10% Igepal CA-630 (Millipore Sigma, I8896-50ML), 12μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 3μL of 10mM dNTPs (NEB, N0447L), 1.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 0.9μL of 50μM TSO, 3μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). To set up the reaction, capsules, RT primer and Igepal CA-630 (Millipore Sigma, I8896-50ML) were mixed on ice in a PCR tube, with each housing a different RT barcode. Capsules were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. Reactions were left at room temperature overnight and processed the next day. After the RT reaction, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with ice-cold TI100 (pH 8.0) with 2 min incubations on ice and twice with TI10 (pH 8.0). Next, Capsule dU PCR was performed to carry out cDNA amplification. After the cDNA amplification, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with TI100 (pH 8.0), twice with TI10 (pH 8.0). Washed capsules were subjected to tree rounds of split-and-pool barcoding. Following split-and-pool barcoding, capsules were split into 4 tubes and were dissolved  using 10M NaOH. DNA was purified using MinElute PCR purification kit and barcoded cDNA was eluted into 20μL of the elution buffer. Barcoded and purified DNA was amplified using PCR. After the reaction, amplified barcoded cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer.
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7 binding primer, 4 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

value: Blood

value: PBMCs


title: C57BL/6_Mtb_HN878_d14_lung_4

description: Library name: B6_d14_Lung_4


title: SCC25 Prevotella-1

description: Library name: SCC25 Prevotella-1

value: HNSCC cell line

value: Prevotella


title: SCC25 Prevotella-2

description: Library name: SCC25 Prevotella-2


title: C3HeB/FeJ_Mtb_HN878_d14_lung_2

description: Library name: C3H_d14_Lung_2


title: SCC25 Fuso-2

description: Library name: SCC25 Fuso-2

value: Fusobacterium


title: SCC25 Fuso-1

description: Library name: SCC25 Fuso-1


title: C57BL/6_Mtb_HN878_d14_lung_2

description: Library name: B6_d14_Lung_2


title: C57BL/6_Mtb_HN878_d14_lung_3

description: Library name: B6_d14_Lung_3


title: C57BL/6_Mtb_HN878_d14_lung_1

description: Library name: B6_d14_Lung_1


title: C57BL/6_uninfected_lung_5

description: Library name: B6_uninf_Lung_5


title: C57BL/6_uninfected_lung_3

description: Library name: B6_uninf_Lung_3


title: PCI-15B Prevotella-2

description: Library name: PCI-15B Prevotella-2


title: SCC25 Control-1

description: Library name: SCC25 Control-1

value: Mock


title: C57BL/6_uninfected_lung_4

description: Library name: B6_uninf_Lung_4


title: C57BL/6_uninfected_lung_2

description: Library name: B6_uninf_Lung_2


title: SCC25 Control-2

description: Library name: SCC25 Control-2


title: C57BL/6_Mtb_HN878_d21_lung_1

description: Library name: B6_d21_Lung_1


title: PCI-15B Fuso-2

description: Library name: PCI-15B Fuso-2


title: C3HeB/FeJ_Mtb_HN878_d21_BAL_4

description: Library name: C3H_d21_BAL_4

source_name: Bronchoalveolar lavage

value: Bronchoalveolar lavage


title: PCI-15B Fuso-1

description: Library name: PCI-15B Fuso-1


title: PCI-15B Control-2

description: Library name: PCI-15B Control-2


title: OQO1 Prevotella-2

description: Library name: OQO1 Prevotella-2


title: C3HeB/FeJ_Mtb_HN878_d21_BAL_3

description: Library name: C3H_d21_BAL_3


title: C3HeB/FeJ_Mtb_HN878_d21_BAL_2

description: Library name: C3H_d21_BAL_2


title: OQO1 Prevotella-1

description: Library name: OQO1 Prevotella-1


title: C3HeB/FeJ_Mtb_HN878_d21_BAL_5

description: Library name: C3H_d21_BAL_5


title: C3HeB/FeJ_Mtb_HN878_d21_BAL_1

description: Library name: C3H_d21_BAL_1


title: PCI-15B Control-1

description: Library name: PCI-15B Control-1


title: OQO1 Fuso-2

description: Library name: OQO1 Fuso-2


title: C3HeB/FeJ_Mtb_HN878_d14_BAL_5

description: Library name: C3H_d14_BAL_5


title: OQO1 Fuso-1

description: Library name: OQO1 Fuso-1


title: C3HeB/FeJ_Mtb_HN878_d14_BAL_4

description: Library name: C3H_d14_BAL_4


title: PCI-15B Prevotella-1

description: Library name: PCI-15B Prevotella-1


title: OQO1 Control-2

description: Library name: OQO1 Control-2


title: OQO1 Control-1

description: Library name: OQO1 Control-1


title: C3HeB/FeJ_Mtb_HN878_d14_BAL_3

description: Library name: C3H_d14_BAL_3


title: C57BL/6_uninfected_lung_1

description: Library name: B6_uninf_Lung_1

value: Lung


title: C3HeB/FeJ_Mtb_HN878_d14_BAL_2

description: Library name: C3H_d14_BAL_2


title: C3HeB/FeJ_Mtb_HN878_d14_BAL_1

description: Library name: C3H_d14_BAL_1


title: FaDu Prevotella-2

description: Library name: FaDu Prevotella-2

source_name: FaDu

value: FaDu


title: FaDu Prevotella-1

description: Library name: FaDu Prevotella-1


title: C3HeB/FeJ_uninfected_BAL_5

description: Library name: C3H_uninf_BAL_5


title: C3HeB/FeJ_uninfected_BAL_4

description: Library name: C3H_uninf_BAL_4


title: C3HeB/FeJ_uninfected_BAL_3

description: Library name: C3H_uninf_BAL_3


title: FaDu Fuso-1

description: Library name: FaDu Fuso-1


title: C3HeB/FeJ_uninfected_BAL_2

description: Library name: C3H_uninf_BAL_2


title: FaDu Fuso-2

description: Library name: FaDu Fuso-2


title: FaDu Control-2

description: Library name: FaDu Control-2


title: FaDu Control-1

description: Library name: FaDu Control-1


title: C3HeB/FeJ_uninfected_BAL_1

description: Library name: C3H_uninf_BAL_1


title: C57BL/6_Mtb_HN878_d21_BAL_3

description: Library name: B6_d21_BAL_3


title: C57BL/6_Mtb_HN878_d21_BAL_4

description: Library name: B6_d21_BAL_4


title: IFNα_24h_3

city: Changchun City

first: Le

state: Jilin Province

address: No. 1 Xinmin Street

institute: the First Hospital of Jilin University

description:
Library name: sample 12
HepG2 cells treated with IFNα (20 ng/mL) for 8 h

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform.
Clean reads were processed with Bowtie to remove annotated sequences and obtain unannotated reads containing miRNAs.
The unannotated reads were aligned to mm10 genome using Bowtie to determine their genomic positions.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes miRNA counts for each sample
Supplementary files format and content: tab-delimited text file includes miRNA expression for each sample

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Small RNA Library Prep Kit following the manufacturer’s protocol.

treatment_protocol: Cells were treated with IFNα (20 ng/mL) for 3 h, 8 h, or 24 h. Control cells were treated with PBS.

value: liver cancer cells

value: WT

value: batch 1


title: IFNα_8h_3

description:
Library name: sample 9
HepG2 cells treated with IFNα (20 ng/mL) for 8 h


title: IFNα_24h_1

description:
Library name: sample 10
HepG2 cells treated with IFNα (20 ng/mL) for 8 h


title: C57BL/6_Mtb_HN878_d21_BAL_2

description: Library name: B6_d21_BAL_2


title: IFNα_8h_1

description:
Library name: sample 7
HepG2 cells treated with IFNα (20 ng/mL) for 8 h


title: IFNα_8h_2

description:
Library name: sample 8
HepG2 cells treated with IFNα (20 ng/mL) for 8 h


title: C57BL/6_Mtb_HN878_d21_BAL_5

description: Library name: B6_d21_BAL_5


title: C57BL/6_Mtb_HN878_d14_BAL_5

description: Library name: B6_d14_BAL_5


title: IFNα_3h_3

description:
Library name: sample 6
HepG2 cells treated with IFNα (20 ng/mL) for 3 h


title: C57BL/6_Mtb_HN878_d14_BAL_4

description: Library name: B6_d14_BAL_4


title: IFNα_3h_2

description:
Library name: sample 5
HepG2 cells treated with IFNα (20 ng/mL) for 3 h


title: C57BL/6_Mtb_HN878_d14_BAL_2

description: Library name: B6_d14_BAL_2


title: IFNα_3h_1

description:
Library name: sample 4
HepG2 cells treated with IFNα (20 ng/mL) for 3 h


title: C57BL/6_Mtb_HN878_d21_BAL_1

description: Library name: B6_d21_BAL_1


title: IFNα_0h_3

description:
Library name: sample 3
untreated HepG2 cells

value: untreated HepG2 cells


title: C57BL/6_Mtb_HN878_d14_BAL_1

description: Library name: B6_d14_BAL_1


title: IFNα_0h_2

description:
Library name: sample 2
untreated HepG2 cells


title: IFNα_0h_1

description:
Library name: sample 1
untreated HepG2 cells


title: Organoid IN only part 2

city: Lund

first: Daniella

last: Rylander Ottosson

address: Sölvegatan 19, BMC A11.

department: Exp Med Science Department

institute: Lund University

description:
Library name: Seq270_12
Culture condition: FACS-sorted transplanted hESC-derived interneurons in forebrain organoids, transduced with nuclear GFP at 100 DIV (Days in vitro)

data_processing:
The raw fastq files were processed with Cell Ranger (v7.1.0).
Assembly: As reference, the GRCh38-2020 human reference transcriptome from 10X Genomics was used.
Supplementary files format and content: H5DF files contain UMI counts for each sample

molecule: nuclear RNA

growth_protocol: Human interneuron differentiation was initiated from the hESC lines RC17 (RCe021-A, p35-40) hESCs were expanded in 6-well plates coated with LN521 (0.5 mg/cm2; BioLamina, Sundbyberg, Sweden) in iPS Brew XF medium (Miltenyi Biotec, Bergisch Gladbach, Germany). Cells were passaged at 80% confluency using EDTA (0.5 mM; MA, USA). The interneuron differentiation protocol was adapted from Nicholas et. al 2013.

extract_protocol:
Spheroids and organoids were collected at 100 DIV, snap-frozen and stored at -80°C until processed. Nuclei isolation was performed according to (Södersten et al., 2018) with modifications (Fiorenzano et al., 2024).
Single nuclei suspensions were loaded onto 10x Genomics Single Cell 3′ Chips along with the mastermix according to 10X protocols.


title: C57BL/6_uninfected_BAL_4

description: Library name: B6_uninf_BAL_4


title: IFNα_24h_2

description:
Library name: sample 11
HepG2 cells treated with IFNα (20 ng/mL) for 8 h


title: C57BL/6_uninfected_BAL_3

description: Library name: B6_uninf_BAL_3


title: 210930_MO_E14_K562_BrdU.K562_dNTP

description:
Library name: Sample 173
PCR control for model training

value: no EcoGII / no BrdUTP in PCR


title: Organoid IN only part 1

description:
Library name: Seq270_11
Culture condition: FACS-sorted transplanted hESC-derived interneurons in forebrain organoids, transduced with nuclear GFP at 100 DIV (Days in vitro)


title: 210930_MO_E14_K562_BrdU.K562_BrdU

description:
Library name: Sample 172
PCR control for model training

value: no EcoGII / 100% BrdUTP in PCR


title: C57BL/6_uninfected_BAL_2

description: Library name: B6_uninf_BAL_2


title: Spheroid IN + hGPC

description:
Library name: Seq258_2
Culture condition: 3D spheroids of hESC-derived interneurons in co-culture with humanglial progenitor cells (hGPCs) at 100 DIV (Days in vitro)


title: Spheroid IN + mAST

description:
Library name: Seq258_3
Culture condition: 3D spheroids of hESC-derived interneurons in co-culture with mouse astrocytes (mAst) at 100 DIV (Days in vitro)


title: C57BL/6_uninfected_BAL_1

description: Library name: B6_uninf_BAL_1


title: Shredded carrots (Daucus carota) with 24 h of storage

city: Monterrey

first: Edwin

last: Reza

state: Nuevo Leon

address: ve. Ignacio Morones Prieto 3000

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tec de Monterrey

description: Library name: T24.1.L4

data_processing:
Cutadapt and fqtrim were used for data quality filtering to remove adapter sequences, and reads with an average base quality >Q20  and read longer than 18 nt were retained.
Reads count and normalization were performed using miRDeep software
Assembly: miRBase(v22)
Supplementary files format and content: xls file includes TPM for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Daucus carota

source_name: vegetable tissue

extract_protocol:
RNA extraction was performed using a TRIzol-based method following the manufacturer's instructions.
Sequencing libraries were constructed using 1 μg of RNA per sample and SMARTer smRNA-Seq Kit according to the manufacturer's protocol

treatment_protocol: comercial-grade carrots were rinsed with tap water, disinfected with a chlorine solution (200 ppm, pH 6.5-7.0) for 5 minutes, then peeled by hand and shredded using a mechanical food processor. Excess of moisture was removed by manual spinning in a salad spinner. Samples were stored at 20 ± 2 °C, and subsamples were collected at 24 and 48 h for total RNA isolation

value: vegetable tissue


title: Shredded carrots (Daucus carota) with 24 h of storage_2

description: Library name: T24.1.L5


title: Shredded carrots (Daucus carota) with 48 h of storage_2

description: Library name: T48.1.L6


title: Shredded carrots (Daucus carota) with 48 h of storage

description: Library name: T48.1.L1


title: Shredded carrots (Daucus carota) with not storage time_2

description: Library name: T0.1.L5


title: Shredded carrots (Daucus carota) with not storage time

description: Library name: T0.1.L4


title: Spheroid IN only

description:
Library name: Seq258_1
Culture condition: 3D spheroids with hESC-derived interneurons only at 100 DIV (Days in vitro)


title: Tekt3_ko_heart

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description:
Library name: Sample 7
10x Genomics

data_processing:
Raw sequencing data (FASTQ files) were demultiplexed and aligned to the mouse reference genome (GRCm38/mm10) using Cell Ranger (v6.1.1) pipeline with default parameters, generating a feature-barcode expression matrix.
Downstream analysis was performed in R using the Seurat package (v4.1.3). Genes expressed in fewer than 3 cells, as well as cells with <200 genes or >10% mitochondrial gene content, were excluded.
Doublets were identified and removed using the DoubletFinder package (v2.0.3).
Batch correction was conducted using the Harmony package (v0.1.1) to minimize potential sample-specific effects.
Assembly: GRCm38/mm10
Supplementary files format and content: matrix files

source_name: cardiac OFTs

extract_protocol:
E10.5 wild-type and homozygous ciliary gene knockout/mutant mouse embryos were isolated and dissected for cardiac OFTs. The obtained tissues were washed for 2-3 times with DPBS pre-cooled at 4℃ and then was transferred to a 2 mL centrifuge tube with tissue storage buffer (Miltenyi Biotec, #130-100-008). The tube was centrifuged at 50 × g for 1 min at 4 °C, after which the tissue storage buffer was discarded and 1 ml of pre-warmed digestion solution (Miltenyi Biotec, #130-110-203; 37 °C) was added to the OFT tissue. The tissues were incubated in a 37 °C water bath and gently pipetted every 5 min, for a total digestion time of approximately 15 min. Enzymatic digestion was terminated by adding 10% FBS (Pricella, #164210-50), and the cell suspension was filtered through a 40 µm cell strainer (Corning, #CLS431750). The filtered suspension was centrifuged at 300 × g for 3 min at 4 °C, and the pellets were resuspended in PBS containing 0.01% Bovine Serum Albumin (Sigma, #A1933).
Libraries were constructed using the High Throughput Single Cell 3’RNA-Seq Kit v2.0 (MobiDrop, #S050200201) and indexed using the 3' Single Index Kit (MobiDrop, #S050300201).

value: cardiac OFTs

value: Tekt3 KO


title: MDA-MB-231 G579S cells, 100nM OTS964, rep 2

city: Palo Alto

first: Jason

last: Sheltzer

address: 1651 Page Mill Road

department: Radiation Oncology

institute: Stanford University

description: Library name: Sample 32

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 mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: A375 cells were maintained in DMEM, Cal51 cells were maintained in DMEM, DLD1 cells were maintained in DMEM and MDA-MB-231 were maintained in DMEM. All media was supplemented with 10% fetal bovine serum (FBS) and pen-strep. Cells were kept in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO control or OTS964 (100 nM) for 6 hours

value: Human breast cancer cell line

value: CDK11 inhibition (OTS964)


title: C57BL/6_uninfected_BAL_5

description: Library name: B6_uninf_BAL_5

value: Uninfected


title: A006

first: Tong

last: Fu

address: DongAn Road

institute: Fudan University

description: Library name: A006

data_processing:
The FASTQ files were processed and aligned to GRCh38 human reference genome using Cell Ranger software (version 8.0.1) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Breast cancer

extract_protocol:
GEM Generation & Barcoding: Prepare Master Mix, mix with cell suspension, and add Gel Beads. Dispense Partitioning Oil into wells and run the Chromium Controller to generate GEMs. GEM-RT Incubation: Store GEMs on ice for up to 1 hour or at 4°C for up to 72 hours, or at −20°C for longer storage.
Post GEM-RT Cleanup & cDNA Amplification: Clean up cDNA using Dynabeads and amplify using cDNA amplification mix. cDNA Cleanup: Clean up the amplified cDNA using SPRIselect reagent. Library Construction: Fragment cDNA, perform end repair and A-tailing, then ligate adaptors. Post Ligation Cleanup: Clean the library using SPRIselect reagent to remove excess adaptors. Sample Index PCR: Perform PCR to add sample indexes for multiplexing. Post PCR Cleanup: Clean the PCR product using SPRIselect reagent.

value: Breast cancer

tag: Stage

value: advanced TNBC


title: MDA-MB-231 G579S cells, 100nM OTS964, rep 1

description: Library name: Sample 31


title: MDA-MB-231 wild-type cells, 100nM OTS964, rep 2

description: Library name: Sample 30


title: C57BL/6_Mtb_HN878_d14_BAL_3

description: Library name: B6_d14_BAL_3

value: Bronchoalveolar lavage

value: HN878 Infected Day 14


title: Sptbn5_ko_heart

description:
Library name: Sample 6
10x Genomics

value: Sptbn5 KO


title: MDA-MB-231 wild-type cells, 100nM OTS964, rep 1

description: Library name: Sample 29


title: A005

description: Library name: A005


title: MDA-MB-231 G579S cells, DMSO control, rep 1

description: Library name: Sample 27

value: DMSO control


title: Ppef2_ko_heart

description:
Library name: Sample 5
10x Genomics

value: Ppef2 KO


title: Pkhd1l1_ko_heart

description:
Library name: Sample 4
10x Genomics

value: Pkhd1l1 KO


title: A004

description: Library name: A004


title: MDA-MB-231 G579S cells, DMSO control, rep 2

description: Library name: Sample 28


title: MDA-MB-231 wild-type cells, DMSO control, rep 2

description: Library name: Sample 26

value: WT


title: A003

description: Library name: A003


title: Mlf1_ko_heart

description:
Library name: Sample 3
10x Genomics

value: Mlf1 KO


title: MDA-MB-231 wild-type cells, DMSO control, rep 1

description: Library name: Sample 25


title: DLD1 G579S cells, 100nM OTS964, rep 2

description: Library name: Sample 24

value: Human colorectal cancer cell line


title: A002

description: Library name: A002


title: DLD1 G579S cells, 100nM OTS964, rep 1

description: Library name: Sample 23


title: Agbl2_ko_heart

description:
Library name: Sample 2
10x Genomics

value: Agbl2 KO


title: DLD1 wild-type cells, 100nM OTS964, rep 1

description: Library name: Sample 21


title: DLD1 G579S cells, DMSO control, rep 2

description: Library name: Sample 20


title: DLD1 G579S cells, DMSO control, rep 1

description: Library name: Sample 19


title: DLD1 wild-type cells, 100nM OTS964, rep 2

description: Library name: Sample 22


title: WT_heart

description:
Library name: Sample 1
10x Genomics

value: cardiac OFTs

value: wild-type


title: DLD1 wild-type cells, DMSO control, rep 2

description: Library name: Sample 18


title: E025

description: Library name: E025

value: early-stage TNBC


title: blood, day 44, group 9 #9

city: shimogyo-ku

first: Tomohiro

last: Sensui

address: chudoji, awatacho

country: Japan

institute: Maruho

description: Library name: PR3287_189_b

data_processing:
rRNA was filtered using RiboPicker, and mapped to the mouse genome GRCm39 using the DRAGEN Bio-IT Platform (Illumina).
Assembly: GRCm39
Supplementary files format and content: txt file including raw counts for each sample
Supplementary files format and content: txt file including TPM for each sample

source_name: whole blood

extract_protocol:
Blood samples were collected from the tail vein (approximately 0.1 mL) using EDTA-2K-coated capillary tubes without anesthesia. Total RNA was isolated from blood using a NucleoSpin RNA Blood Kit (Macherey-Nagel, Easton, PA, USA), according to the manufacturer’s instructions.
Libraries were prepared using TruSeq Stranded Total RNA with RiboZero Globin (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: whole blood

tag: strain

value: NC/Nga

tag: Sex

value: male

tag: condition

value: conventional

tag: group

value: group 9

tag: dermatitis score

value: day 44


title: blood, day 44, group 9 #10

description: Library name: PR3287_190_b

tag: time


title: Cal51 G579S cells, 100nM OTS964, rep 2

description: Library name: Sample 16

tag: cell line

value: Human breast cancer cell line

tag: cell type

value: CDK11 inhibition (OTS964)


title: Cal51 G579S cells, 100nM OTS964, rep 1

description: Library name: Sample 15


title: blood, day 44, group 9 #8

description: Library name: PR3287_188_b


title: E024

description: Library name: E024

value: Breast cancer


title: DLD1 wild-type cells, DMSO control, rep 1

description: Library name: Sample 17

value: DMSO control


title: E023

description: Library name: E023


title: blood, day 44, group 9 #7

description: Library name: PR3287_187_b

value: WT


title: Cal51 wild-type cells, 100nM OTS964, rep 1

description: Library name: Sample 13


title: Cal51 G579S cells, DMSO control, rep 2

description: Library name: Sample 12


title: E022

description: Library name: E022


title: Cal51 G579S cells, DMSO control, rep 1

description: Library name: Sample 11


title: blood, day 44, group 9 #6

description: Library name: PR3287_186_b


title: blood, day 44, group 9 #5

description: Library name: PR3287_185_b


title: Cal51 wild-type cells, DMSO control, rep 2

description: Library name: Sample 10


title: blood, day 44, group 9 #4

description: Library name: PR3287_184_b


title: A001

description: Library name: A001

value: advanced TNBC


title: E021

description: Library name: E021


title: E026

description: Library name: E026


title: A375 G579S cells, 100nM OTS964, rep 2

description: Library name: Sample 8

value: Human melanoma cell line


title: Cal51 wild-type cells, DMSO control, rep 1

description: Library name: Sample 9


title: E020

description: Library name: E020


title: A375 wild-type cells, 100nM OTS964, rep 2

description: Library name: Sample 6


title: Cal51 wild-type cells, 100nM OTS964, rep 2

description: Library name: Sample 14


title: blood, day 44, group 9 #3

description: Library name: PR3287_183_b


title: A375 G579S cells, DMSO control, rep 2

description: Library name: Sample 4


title: A375 wild-type cells, 100nM OTS964, rep 1

description: Library name: Sample 5


title: A375 G579S cells, DMSO control, rep 1

description: Library name: Sample 3


title: blood, day 44, group 9 #1

description: Library name: PR3287_181_b


title: A375 wild-type cells, DMSO control, rep 2

description: Library name: Sample 2


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (RNA-seq)

city: Huntsville

first: Richard

middle: M.

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: iTF-Microglia_LPS_IFNG_rep1

data_processing:
PE150 raw reads were quality-checked with FastQC before and after trimming. Trim Galore [paired-end mode, --illumina flag] was used to remove adapter sequences and low-quality bases.
Trimmed reads were quantified using Salmon [--validateMappings, --seqBias, --gcBias] by mapping to the GENCODE v46 human transcriptome (hg38) and using a k-mer size of 31.
Transcript-level quantifications were imported into R with tximeta, and summarized to gene-level using summarizeToGene().
Assembly: hg38
Supplementary files format and content: tab-delimited text include raw gene counts for each sample

source_name: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2

growth_protocol: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2 iPSCs were maintained at 37°C with 5% CO2 in mTeSR Plus medium on dishes coated with Growth Factor Reduced (GFR), LDEV-Free Matrigel. Medium was changed every other day. Cells were passaged at 70–80% confluency using ReLeSR, resuspended in room-temperature mTeSR Plus, and transferred to freshly coated dishes.

extract_protocol:
Total RNA was extracted from untreated and LPS+IFNG-treated iTF-iPSCs and iTF-Microglia (three replicates per condition) using the Total RNA Purification Plus Kit (Norgen).
Eukaryotic RNA-Seq (non-stranded) libraries were prepared by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol:
KOLF2.1J iTF-iPSCs were washed with D-PBS, dissociated with Accutase, and centrifuged at 300×g for 5 minutes. Cell pellets were resuspended in Essential 8 Basal Medium supplemented with 10 μM Y-27632 ROCK Inhibitor and 2 μg/mL doxycycline, then seeded onto double-coated plates with Poly-D-Lysine-precoated Bio plates and GFR Matrigel. On day 2, cells were switched to differentiation medium (Advanced DMEM/F12 supplemented with 1× GlutaMAX, 2 μg/mL doxycycline, 100 ng/mL human IL-34 and 10 ng/mL human GM-CSF). On day 4, the medium was replaced with iTF-Microglia medium (Advanced DMEM/F12 supplemented with 1× GlutaMAX, 2 μg/mL doxycycline, 100 ng/mL human IL-34, 10 ng/mL human GM-CSF, 50 ng/mL human M-CSF and 50 ng/mL human TGF-β1). On day 8, fresh iTF-Microglia medium was added. Cells were maintained for 9 more days with full medium changes every 2–3 days.
KOLF2.1J iTF-iPSCs and Day 18 iTF-Microglia were either untreated or stimulated with 100 ng/mL LPS (Invitrogen) and 20 ng/mL IFNG (Gibco) in fresh mTeSR Plus (for iTF-iPSCs) or iTF-Microglia medium (for iTF-Microglia) for 24 hours before harvesting.

value: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2

value: iTF-Microglia Day18

value: LPS 100 ng/ml + IFNG 20 ng/ml

value: 24 hours


title: A375 wild-type cells, DMSO control, rep 1

description: Library name: Sample 1


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep3 (RNA-seq)

description: Library name: iTF-Microglia_LPS_IFNG_rep3


title: E016

description: Library name: E016

value: early-stage TNBC


title: E005

description: Library name: E005


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (RNA-seq)

description: Library name: iTF-Microglia_LPS_IFNG_rep2


title: E006

description: Library name: E006


title: E132

description: Library name: E132


title: blood, day 30, group 9 #9

description: Library name: PR3287_179_b

value: whole blood

value: NC/Nga

value: day 30


title: blood, day 30, group 9 #10

description: Library name: PR3287_180_b

value: male

value: conventional

value: group 9


title: blood, day 44, group 9 #2

description: Library name: PR3287_182_b

value: day 44


title: E015

description: Library name: E015

value: Breast cancer


title: iTF-Microglia Day 18, untreated, rep3 (RNA-seq)

description: Library name: iTF-Microglia_rep3

value: Untreated


title: E014

description: Library name: E014


title: iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep3 (RNA-seq)

description: Library name: iTF-iPSCs_LPS_IFNG_rep3

value: iPSCs


title: A375 G579S cells, 100nM OTS964, rep 1

description: Library name: Sample 7

value: CDK11 inhibition (OTS964)


title: iTF-Microglia Day 18, untreated, rep1 (RNA-seq)

description: Library name: iTF-Microglia_rep1


title: iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (RNA-seq)

description: Library name: iTF-iPSCs_LPS_IFNG_rep2


title: blood, day 30, group 9 #8

description: Library name: PR3287_178_b

value: WT


title: E013

description: Library name: E013


title: iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (RNA-seq)

description: Library name: iTF-iPSCs_LPS_IFNG_rep1

value: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2


title: blood, day 30, group 9 #6

description: Library name: PR3287_176_b


title: E012

description: Library name: E012


title: blood, day 30, group 9 #5

description: Library name: PR3287_175_b


title: iTF-iPSCs, untreated, rep2 (RNA-seq)

description: Library name: iTF-iPSCs_rep2


title: iTF-iPSCs, untreated, rep1 (RNA-seq)

description: Library name: iTF-iPSCs_rep1


title: iTF-Microglia Day 18, untreated_rep1

description: Library name: iTF-Microglia_rep1

data_processing:
Hi-C PE150 reads were processed using the ENCODE Hi-C pipeline (v1.15.1) following ENCODE standards. Sequencing reads were aligned to the hg38 genome using BWA-MEM. Low-quality, secondary, and duplicate reads were removed, and valid interaction pairs were retained to construct contact matrices at multiple resolutions.
Reads were trimmed with Cutadapt, aligned to the hg38 reference genome using Bowtie2, and filtered to remove duplicates and mitochondrial reads using Picard and Samtools. High-quality, properly paired reads were retained.
Hi-C contact matrices at multiple resolutions were generated by merging all samples across cell types (iTF-iPSCs and iTF-Microglia) and conditions (untreated and LPS+IFNG-treated), and using Juicer and normalized with Knight-Ruiz (KR) matrix balancing.
Chromatin loops were identified using HiCCUPS, as implemented in the ENCODE Hi-C pipeline. Loops were called from the combined .hic file. Final loop coordinates were extracted from the 30.bedpe.gz output file.
Assembly: hg38
Supplementary files format and content: Hi-C contact matrix after filtering out all alignments with mapQ <30 (binary .hic format)
Supplementary files format and content: Bedpe file with called loops after filtering out all alignments with mapQ <30

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 min at RT. Cells were lysed and homogenized before chromatin was digested with Arima enzyme cocktail.
Libraries were prepared using the Arima-HiC+ Genome-Wide Hi-C kit (Arima Genomics) following the manufacturer’s protocol

treatment_protocol:
KOLF2.1J iTF-iPSCs were washed with D-PBS, dissociated with Accutase, and centrifuged at 300×g for 5 minutes. Cell pellets were resuspended in Essential 8 Basal Medium supplemented with 10 μM Y-27632 ROCK Inhibitor and 2 μg/mL doxycycline, then seeded onto double-coated plates with Poly-D-Lysine-precoated Bio plates and GFR Matrigel. On day 2, cells were switched to differentiation medium (Advanced DMEM/F12 supplemented with 1× GlutaMAX, 2 μg/mL doxycycline, 100 ng/mL human IL-34 and 10 ng/mL human GM-CSF). On day 4, the medium was replaced with iTF-Microglia medium (Advanced DMEM/F12 supplemented with 1× GlutaMAX, 2 μg/mL doxycycline, 100 ng/mL human IL-34, 10 ng/mL human GM-CSF, 50 ng/mL human M-CSF and 50 ng/mL human TGF-β1). On day 8, fresh iTF-Microglia medium was added. Cells were maintained for 9 more days with full medium changes every 2–3 days.
KOLF2.1J iTF-iPSCs were untreated and Day 18 iTF-Microglia were either untreated or stimulated with 100 ng/mL LPS (Invitrogen) and 20 ng/mL IFNG (Gibco) in fresh mTeSR Plus (for iTF-iPSCs) or iTF-Microglia medium (for iTF-Microglia) for 24 hours before harvesting.

value: iTF-Microglia Day18


title: E011

description: Library name: E011


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h_rep2

value: LPS 100 ng/ml + IFNG 20 ng/ml


title: E009

description: Library name: E009


title: iTF-Microglia Day 18, untreated, rep2 (RNA-seq)

description: Library name: iTF-Microglia_rep2


title: blood, day 30, group 9 #4

description: Library name: PR3287_174_b


title: E010

description: Library name: E010


title: iTF-Microglia Day 18, untreated_rep2

description: Library name: iTF-Microglia_rep2


title: iTF-iPSCs, untreated_rep1

description: Library name: iTF-iPSCs_rep1


title: blood, day 30, group 9 #7

description: Library name: PR3287_177_b


title: iTF-iPSCs, untreated_rep2

description: Library name: iTF-iPSCs_rep2


title: blood, day 30, group 9 #1

description: Library name: PR3287_171_b


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (Input)

description: Library name: iTF-Microglia_LPS_IFNG_rep2_input

data_processing:
PE150 raw reads were pre-processed with clumpify (BBMap v38.42) to remove optical duplicates [dedupe=t optical=t dupedist=12000]
Pre-processed reads were run with the ENCODE chip-seq-pipeline2 with histone-specific settings [-type histone].
Reads were trimmed with Trimmomatic, aligned to the hg38 reference genome using Bowtie2, and PCR duplicates removed with Picard.
Peaks were called with MACS2, and reproducible peaks identified via naive overlap.
Assembly: hg38
Supplementary files format and content: Optimal set of reproducible ChIP-seq peaks identified by overlapping peak calls from two replicates. Peaks were called using MACS2 with narrowPeak output format.
Supplementary files format and content: Genome-wide –log10 p-value signal track calculated from the pooled ChIP-seq replicates compared to pooled input controls. It was generated using MACS2. The values indicate the statistical significance of enrichment for open chromatin.

extract_protocol:
Chromatin was extracted following protocols from ENCODE Consortium. Chromatin was immunoprecipitated with an anti-H3K27ac antibody (ActiveMotif).
Libraries were prepared by end-repair, adapter ligation, and PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] ×15 cycles; 5 min at 72°C).

value: 24 hours


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (Input)

description: Library name: iTF-Microglia_LPS_IFNG_rep1_input


title: blood, day 40, group 8 #10

description: Library name: PR3287_170_b

value: group 8

value: day 40


title: iTF-Microglia Day 18, untreated, rep1 (Input)

description: Library name: iTF-Microglia_rep1_input


title: E004

description: Library name: E004

value: early-stage TNBC


title: iTF-Microglia Day 18, untreated, rep2 (Input)

description: Library name: iTF-Microglia_rep2_input


title: E131

description: Library name: E131


title: iTF-iPSCs, untreated, rep3 (RNA-seq)

description: Library name: iTF-iPSCs_rep3


title: iTF-iPSCs, untreated, rep2 (Input)

description: Library name: iTF-iPSCs_rep2_input


title: blood, day 40, group 8 #9

description: Library name: PR3287_169_b

value: whole blood

value: NC/Nga


title: iTF-iPSCs, untreated, rep1 (Input)

description: Library name: iTF-iPSCs_rep1_input


title: blood, day 30, group 9 #3

description: Library name: PR3287_173_b

value: male

value: conventional

value: day 30


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h_rep1


title: E128

description: Library name: E128

value: Breast cancer


title: blood, day 40, group 8 #8

description: Library name: PR3287_168_b


title: E127

description: Library name: E127


title: E008

description: Library name: E008


title: blood, day 30, group 9 #2

description: Library name: PR3287_172_b

value: group 9


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (ChIP)

tag: chip antibody

value: H3K27ac (ActiveMotif, #39034)


title: iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (ChIP)


title: iTF-Microglia Day 18, untreated, rep2 (ChIP)

description: Library name: iTF-Microglia_rep2

value: Untreated


title: iTF-iPSCs, untreated, rep2 (ChiP)

description: Library name: iTF-iPSCs_rep2

value: iPSCs


title: blood, day 40, group 8 #6

description: Library name: PR3287_166_b

value: WT


title: blood, day 40, group 8 #7

description: Library name: PR3287_167_b


title: iTF-Microglia Day 18, untreated, rep1 (ChiP)

description: Library name: iTF-Microglia_rep1

value: KOLF2.1J CLYBL_6-TF-iMG_KI1/KI2

value: iTF-Microglia Day18


title: E003

description: Library name: E003


title: iTF-iPSCs, untreated, rep1 (ChIP)

description: Library name: iTF-iPSCs_rep1


title: E002

description: Library name: E002


title: Thap12h_RNAseq_rep3

description: Library name: Thap12h_RNAseq_rep3

source_name: HeLa

value: HeLa

value: Human Cervical Carcinoma Cell

value: CCCP 12h