title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 8

status: Public on Apr 16 2026

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway #C0930, Patterson Lab 607A

institute: University of Texas at Austin

description: Library name: CL-8

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

organism: Labroides dimidiatus

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

treatment_protocol: Whole heads were transferred into 30 mL conical tubes with RNAlater (ThermoFischer, Waltham, MA, USA) to preserve the integrity of the RNA. The elapsed time between capture and death ranged from 6 to 28 minutes. After 3 hours (on average) in RNAlater, the samples were transferred into O.C.T. Compound (Sakura, Torrance, CA, USA) and flash frozen in liquid nitrogen and shipped to The University of Texas at Austin for RNA isolation.frozen heads were sectioned on a cryostat microtome into 300µm thick slices. The second most rostral slice of the brain, containing pallial areas Dl and Dm (i.e., the putative teleost homologs of the mammalian hippocampus and basolateral amygdala (areas Dl and Dm, respectively), along with partial portions of septal and striatal territories, was collected and stored in 200ul of ice-cold homogenization buffer with 1-thioglycerol (Promega Corporation, Madison, WI, USA) and stored at -80C until further processing.

value: Female, forebrain section

value: high density; Clam Gardens


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 5

type: SRA

country: USA

description: Library name: CL-5

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment

value: low density; Osprey collection


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 7

description: Library name: CL-7


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 4

description: Library name: CL-4


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 9

description: Library name: CL-9


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 3

description: Library name: CL-3


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 2

description: Library name: CL-2


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 20

description: Library name: CL-20

value: low density; Watson's Bay


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 1

description: Library name: CL-1


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 15

description: Library name: CL-15

value: high density; The Crest


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 19

description: Library name: CL-19


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 8

description: Library name: TUB-8

organism: Labrichthys unilineatus


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 14

description: Library name: CL-14


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 13

description: Library name: CL-13


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 7

description: Library name: TUB-7


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 5

description: Library name: TUB-5


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 12

description: Library name: CL-12


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 11

description: Library name: CL-11


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 4

description: Library name: TUB-4


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 2

description: Library name: TUB-2


title: P1

status: Public on Aug 01 2026

city: chengdu

first: yujie

last: xie

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

country: China

institute: West China Hospital, Sichuan University

description:
Library name: sample1
Column name in raw_counts_All_Samples.txt: P1

data_processing:
Raw Data Quality Control and Trimming: Raw paired-end sequencing reads were processed using fastp (v 0.23.2) to remove adapter sequences (auto-detected), trim low-quality bases (Phred score <20 at read ends), and discard reads containing >5% poly-N nucleotides or shorter than 50 bp. Quality metrics (Q20, Q30, GC content) were calculated for both raw and clean data.
Alignment to Reference Genome: Clean reads were aligned to the human reference genome GRCh38 using HISAT2 (v 2.2.1)
Gene Expression Quantification: Gene-level read counts were generated using featureCounts (v 2.0.6), Final outputs included raw count matrix and FPKM-normalized expression matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: Esophageal squamous cell carcinoma

extract_protocol:
Total RNA was extracted from esophageal squamous cell carcinoma tissue using TRIzol reagent (Invitrogen, Catalog #: 15596026) following the manufacturer's protocol. RNA concentration and purity (A260/A280 ratio > 1.9, A260/A230 ratio > 2.0) were measured using a NanoDrop 2000 spectrophotometer. RNA integrity was confirmed by 1% agarose gel electrophoresis showing distinct 18S and 28S rRNA bands.
Stranded RNA sequencing libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

value: Esophageal squamous cell carcinoma

value: primary tumor stage T2 patients without lymph node metastasis


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 9

description: Library name: MEL-9

organism: Halichoeres melanurus


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 1

description: Library name: TUB-1


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 8

description: Library name: MEL-8


title: Cancer_167_2

status: Public on May 26 2026

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description:
Library name: 167_2
2

data_processing:
The reads were base-called using Illumina Bcl2fastq version 1.8.4 base-calling software.
The reads were aligned against the human hg19 reference genome using STAR version 2.4.2a.
Then, reads were assigned to known genes, and the number of reads per gene was counted using the subreads package
Assembly: Illumina iGenome hg19
Supplementary files format and content: Text file containing genewise raw read counts
Supplementary files format and content: csv file containing the anonymized clinical data of the patients

source_name: prostate

extract_protocol:
RNA-sequencing was carried out on fresh-frozen samples, alongside validation samples containing at least 50% Gleason score (GS) ≥6 carcinoma (malignant sample) or morphologically benign prostatic tissue (benign control sample) from the same patient. Samples were homogenized using an Ultra Turrax homogenizer, and total RNA was extracted using NucleoSpin® RNA kit and NucleoSpin® RNA/DNA buffer set (Macherey-Nagel, Düren, Germany). Proper RNA quality was detected using a Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, IA).
The samples were prepared for sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation Kit and sequenced on the HiSeq 3000 instrument with paired-end chemistry and 100 bp read length.

value: prostate

tag: group

value: Cancer

tag: biochemical recurrance

value: Yes

tag: ggg

tag: pn


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 7

description: Library name: MEL-7


title: Benign_167_1

description:
Library name: 167_1
1

value: Benign


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 9

description: Library name: LYR-9

organism: Thalassoma lunare


title: LA2

city: Hangzhou

first: Min

last: Li

address: Yuhang

department: School of Public health and Nursing

institute: HangZhouNomal University

description:
Library name: sample5
count.LA2

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm39
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: connective tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: connective tissue

tag: cell line

tag: cell type

value: Fibrosarcoma cells

tag: genotype

value: cell line

value: LA

tag: batch


title: Labrichthys unilineatus, non-cleaner, forebrain section, sample 10

description: Library name: TUB-10


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 6

description: Library name: MEL-6


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 8

description: Library name: LYR-8


title: Cancer_138_2

description:
Library name: 138_2
2


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 7

description: Library name: LYR-7


title: Cancer_136_1

description:
Library name: 136_1
1

value: No


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 3

description: Library name: MEL-3


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 4

description: Library name: LYR-4


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 1

description: Library name: MEL-1


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 3

description: Library name: LYR-3


title: Halichoeres melanurus, facultative cleaner, forebrain section, sample 2

description: Library name: MEL-2


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 6

description: Library name: LYR-6


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 2

description: Library name: LYR-2


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 1

description: Library name: LYR-1


title: Blood from patient 2 month post-treatment with Omaveloxolone at a dose of 50 mg PO daily, replicate 3

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

description:
Library name: treated_2mo_3
plasma_oma_conc.csv
Plasma omaveloxolone concentration for this timepoint is in row with timepoint = 2

data_processing:
Raw reads were aligned using Kallisto with bootstrapping (number of bootstraps = 100).
Assembly: GRCh38
Supplementary files format and content: Tab separated files containing transcript ID, transcript length, effective length (the adjusted transcript length used in abundance estimation, taking into account the fragment length distribution), est_counts (raw counts) and tpm (counts normalized by eff_length)

molecule: polyA RNA

source_name: blood

growth_protocol: Blood samples were collected from a 12 year old male patient diagnosed with Leigh Syndrome caused by heterozygous NM_003172.4(SURF1):c.312_321delinsAT (p.Pro104_Leu105insTer); NM_003172.4(SURF1):c.574C>T (p.Arg192Trp) mutations in the SURF1 gene. The patient was  enrolled in an approved research protocol (WCG IRB Protocol #2001-01). Blood was collected in PAXgene tubes and shipped at room temperature to the sequencing facility for processing within 24 hours for RNA sequencing. Whole blood samples were collected at approximately 1 month intervals between July 2024 to November 2024.

extract_protocol:
The RNA was extracted using the PAXgene RNA extraction kit.
Barcoded libraries for RNA-seq were prepared with 100 ng of RNA using NEBNext Ultra II RNA Library Prep Kit (NEB, Ipswich, MA) for Illumina with QIAGEN QIAseq FastSelect -rRNA HMR Kit (QIAGEN, Germany) per manufacturer’s protocol.

treatment_protocol: Omaveloxolone was originally prescribed at 50 mg PO, daily and dose was increased to 100 mg PO, daily after 2 months. Concentration of Omaveloxolone in plasma was estimated using mass spectrometry.

value: blood

value: 50 mg Omaveloxolone

tag: time

value: 2 months


title: Thalassoma lunare, facultative cleaner, forebrain section, sample 10

description: Library name: LYR-10

value: Female, forebrain section


title: Coris batuensis, non-cleaner, forebrain section, sample 9

description: Library name: CHO-9

organism: Coris batuensis


title: Coris batuensis, non-cleaner, forebrain section, sample 8

description: Library name: CHO-8


title: Benign_0275_1

description:
Library name: 0275_1
1


title: Coris batuensis, non-cleaner, forebrain section, sample 5

description: Library name: CHO-5


title: Coris batuensis, non-cleaner, forebrain section, sample 6

description: Library name: CHO-6


title: Coris batuensis, non-cleaner, forebrain section, sample 4

description: Library name: CHO-4


title: Coris batuensis, non-cleaner, forebrain section, sample 1

description: Library name: CHO-1


title: Coris batuensis, non-cleaner, forebrain section, sample 2

description: Library name: CHO-2


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 9

description: Library name: BLA-9

organism: Hemigymnus melapterus


title: Coris batuensis, non-cleaner, forebrain section, sample 3

description: Library name: CHO-3


title: Coris batuensis, non-cleaner, forebrain section, sample 10

description: Library name: CHO-10


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 7

description: Library name: BLA-7


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 6

description: Library name: BLA-6


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 8

description: Library name: BLA-8


title: P. promelas larvae, UP, biological replicate UP_FIELD31, lane 1, time step = NA, analyzed on 20160930

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20160930_ UP_FIELD_31_ACAGTG_L001_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

value: whole larvae

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 5

description: Library name: BLA-5


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 1

description: Library name: BLA-1


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 10

description: Library name: BLA-10


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 2

description: Library name: BLA-2


title: LP1 multiple myeloma celll line with SCR GapmeR replicate D

status: Public on Apr 15 2026

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: LP1-SCR-D

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed with featureCounts (v1.6.4) to obtain raw read counts. For gene expression analysis, we applied the voom/limma pipeline. Genes with fewer than 10 reads in more than 95% of samples were excluded to reduce background noise. Normalization was conducted using the trimmed mean of M-values (TMM) method to account for differences in library size and reduce technical variability. The data were then transformed using voom, which converts raw counts into log2 counts per million (log2-CPM) and assigns precision weights to each observation. Differential expression analysis was performed using these transformed values, and P values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method. Differential expressed genes were selected at 10% FDR adjusted p-value and 1.5 fold change cut off values.
Assembly: hg38
Supplementary files format and content: counts.txt

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer’s instructions. The purity and concentration of total RNA was determined by the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). The ratios of absorption (260 nm/280 nm) of all samples were between 1.8 and 2.0.
Before library preparation, RNA concentration was evaluated through Qubit™ RNA Broad Range Assay Kit (Invitrogen, Walthman, MA, USA) while RNA quality was established on 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) using RNA Screen tape kit (Agilent Technologies, Santa Clara, CA, USA). According to the TruSeq Stranded Total RNA (San Diego, CA, USA) protocol, 500 ng of RNA for each sample with RIN value between 9 and 10, were used for RNA sequencing. Final libraries with optimal quality and quantity criteria, assessed by D1000 Screen tape kit (Agilent Technologies) and by Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen), respectively, were run on NextSeq 500 sequencer (Illumina) using a 2 × 150 high-output flow cell with 8 samples/run.

treatment_protocol: NEAT1 knock-down (KD) with specific GapmeR at 48h was obtained by gymnosis.

value: Multiple myeloma cell line

value: SCR GapmeR


title: LP1 multiple myeloma celll line with SCR GapmeR replicate B

description: Library name: LP1-SCR-B


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate A

description: Library name: AMO1-SCR-A


title: LP1 multiple myeloma celll line with SCR GapmeR replicate A

description: Library name: LP1-SCR-A


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate C

description: Library name: AMO1-SCR-C


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate D

description: Library name: AMO1-SCR-D


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 17

description: Library name: CL-17

value: low density; Watson's Bay


title: Arabidopsis, asf1a1b, Rep2

status: Public on Apr 08 2026

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description: Library name: asf1a1b R2

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Txt files include TPM values for each sample.
Supplementary files format and content: Txt file includes differential gene analysis between asf1a1b and Columbia.

organism: Arabidopsis thaliana

source_name: fresh seeds

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°.

extract_protocol:
total RNA was extracted by using RNAprep Pure Polysaccharide Polyphenol Plant Total RNA Extraction Kit (TIANGEN, DP441) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

treatment_protocol: freshly seeds were harvested within 24 hours.

value: fresh seeds


title: Arabidopsis, Columbia-0, Rep3

description: Library name: columbia R3


title: Arabidopsis, Columbia-0, Rep1

description: Library name: columbia R1


title: Neutrophils, Donor Siglec14-NULL, Fn-stimulated

status: Public on Mar 11 2026

city: Bellinzona

first: Giandomenica

last: Iezzi

address: via chiesa 5

department: Department of Surgery and Gut Division

country: Switzerland

institute: Institute for Translational Research USI-EOC (IRT)

description: Library name: Sample 5

library_source: transcriptomic single cell

data_processing:
Raw FASTQ data were processed using the BD Rhapsody™ Sequence Analysis Pipeline (v2.2.1), with the pre-built RhapRef_Human_WTA_2025-03 reference. All parameters were left at their default settings.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood neutrophils

extract_protocol:
Peripheral blood neutrophils (PBNs) from the healthy donor and Siglec14-NULL donor were isolated by negative sorting with magnetic beads. Freshly isolated PBNs were resuspended into phenol red- and serum-free RPMI and plated at a 0.5x106/ml concentration. They were then cocultured alone or in the presence of live bacteria at a 50:1 bacteria: neutrophil ratio.
Reverse transcription was performed on mRNA captured by BD Rhapsody™ Cell Capture Beads usingthe BD Rhapsody™ cDNA Kit, following the manufacturer’s instructions. This step generatedbead-bound cDNA via oligo(dT)-primed reverse transcription. Whole transcriptomeamplification (WTA) was then carried out using the BD Rhapsody™ WTA Amplification Kit,which amplifies 3ʹ end transcript fragments through targeted PCR to produce whole-transcriptome libraries. Purification steps were conducted using SPRIselect magnetic beadsaccording to the recommended ratios for each step of the protocol. Final libraries werequantified using the Qubit™ dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific), and39size distribution was assessed on an Agilent 2100 Bioanalyzer using the High Sensitivity DNAkit (Agilent Technologies).

value: Peripheral blood neutrophils

value: Donor Siglec14-NULL


title: Neutrophils, Donor Siglec14-NULL, unstimulated

description: Library name: Sample 4


title: Arabidopsis, Columbia-0, Rep2

description: Library name: columbia R2


title: Neutrophils, Donor WT, Bf-stimulated

description: Library name: Sample 3

value: Donor WT


title: Neutrophils, Donor WT, Fn-stimulated

description: Library name: Sample 2


title: Neutrophils, Donor WT, unstimulated

description: Library name: Sample 1


title: V4624

status: Public on Mar 04 2026

city: Evanston

first: Christina

last: Thapa

state: Illinois

address: 1001 University Place

department: Center for Psychiatric Genetics (CPG)

institute: Endeavor Health

description: Library name: V4624

data_processing:
Trimmomatic was used to trim adapters and low quality reads and read ends. Then, both Spliced Transcripts Alignment to a Reference (STAR) and Burrows-Wheeler Aligner (BWA) was used for alignment resulting in gene expression counts tables and bam files, respectively. Final processed counts is provided.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values

source_name: iPS Cells

extract_protocol:
Cells were lysed with 800ul of Buffer RLT Plus (QIAGEN #1053393). Cell lysates were processed using RNeasy Plus Mini Kit (QIAGEN #74134) to extract purified RNA.
Library was constructed by Novogene using Illumina NovaSeq X.

value: iPS Cells

value: iPSC

tag: Sex

value: Male

tag: lof target_gene

tag: ancestry

value: EA


title: V4642

description: Library name: V4642

tag: tissue


title: Neutrophils, Donor Siglec14-NULL, Bf-stimulated

description: Library name: Sample 6


title: V4621

description: Library name: V4621


title: CW20107

description: Library name: CW20107

value: Female

value: Negative Control


title: V4618

description: Library name: V4618


title: V4614

description: Library name: V4614


title: V4610

description: Library name: V4610


title: V4605

description: Library name: V4605


title: V4603

description: Library name: V4603


title: V4613

description: Library name: V4613


title: V4601

description: Library name: V4601


title: V4598

description: Library name: V4598


title: V4596

description: Library name: V4596


title: V4579

description: Library name: V4579


title: V4573

description: Library name: V4573


title: V4484

description: Library name: V4484

value: DSCAM


title: V4572

description: Library name: V4572


title: V4483

description: Library name: V4483


title: V4475

description: Library name: V4475


title: V4472

description: Library name: V4472


title: V4474

description: Library name: V4474


title: V4471

description: Library name: V4471


title: V4469

description: Library name: V4469


title: V4458

description: Library name: V4458


title: V4454

description: Library name: V4454


title: V4452

description: Library name: V4452


title: V4449

description: Library name: V4449


title: V4440

description: Library name: V4440

value: TRIO


title: V4447

description: Library name: V4447


title: V4441

description: Library name: V4441


title: V4442

description: Library name: V4442


title: V4438

description: Library name: V4438


title: V4436

description: Library name: V4436


title: V4434

description: Library name: V4434


title: V4431

description: Library name: V4431


title: V4424

description: Library name: V4424


title: V4404

description: Library name: V4404

value: NIPBL


title: V4383

description: Library name: V4383


title: V4380

description: Library name: V4380


title: V4364

description: Library name: V4364


title: V4355

description: Library name: V4355


title: V4353

description: Library name: V4353


title: V4345

description: Library name: V4345


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description: Library name: V4342


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description: Library name: V4334


title: V4332

description: Library name: V4332


title: V4330

description: Library name: V4330


title: V4326

description: Library name: V4326

value: AA


title: V4323

description: Library name: V4323


title: V4317

description: Library name: V4317


title: V4312

description: Library name: V4312


title: V4308

description: Library name: V4308


title: V4303

description: Library name: V4303


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description: Library name: V4301


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description: Library name: V4300


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description: Library name: V4290


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description: Library name: V4588


title: V4481

description: Library name: V4481


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description: Library name: V4480


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description: Library name: V4270


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description: Library name: V4271


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description: Library name: V4267


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description: Library name: V4266


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description: Library name: V4259


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description: Library name: V4253


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description: Library name: V4251


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description: Library name: V4246


title: V4410

description: Library name: V4410


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description: Library name: V4394


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description: Library name: V4396


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description: Library name: V4245


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description: Library name: V4239


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description: Library name: V4366


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description: Library name: V4363


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description: Library name: V4232


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description: Library name: V4229


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description: Library name: V4357


title: V4225

description: Library name: V4225


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description: Library name: V4221


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description: Library name: V4220


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description: Library name: V4213


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description: Library name: V4172


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description: Library name: V4170


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description: Library name: V4159


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description: Library name: V4147


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description: Library name: V4141


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description: Library name: V4140


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description: Library name: V4130


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description: Library name: V4119


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description: Library name: V4095


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description: Library name: V4093


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description: Library name: V4089


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description: Library name: V4088


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description: Library name: V4059


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description: Library name: V4061


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description: Library name: V4054


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description: Library name: V4321


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description: Library name: V4053


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description: Library name: V4049


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description: Library name: V4043


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description: Library name: V4033


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description: Library name: V4032


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description: Library name: V4037


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description: Library name: V4031


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description: Library name: V4030


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description: Library name: V4006


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description: Library name: V4016


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description: Library name: V4008


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description: Library name: V4005


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description: Library name: V3595


title: V3588

description: Library name: V3588


title: V3585

description: Library name: V3585


title: V3583

description: Library name: V3583


title: V3581

description: Library name: V3581


title: V3579

description: Library name: V3579


title: V3578

description: Library name: V3578


title: V3571

description: Library name: V3571

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title: V3565

description: Library name: V3565


title: V3568

description: Library name: V3568


title: V3564

description: Library name: V3564


title: V3559

description: Library name: V3559


title: Benign_104_2

description:
Library name: 104_2
2

value: prostate

tag: group

value: Benign

value: No

value: Unknown


title: V3561

description: Library name: V3561


title: V3554

description: Library name: V3554


title: V3546

description: Library name: V3546


title: V3543

description: Library name: V3543

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description: Library name: V3540


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description: Library name: V3535


title: V3542

description: Library name: V3542


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description: Library name: V3533


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title: V3452

description: Library name: V3452


title: V3528

description: Library name: V3528


title: V3519

description: Library name: V3519

value: SPAST


title: V3442

description: Library name: V3442

value: iPS Cells

value: SKI


title: V3440

description: Library name: V3440

value: iPSC

value: POGZ


title: V3272

description: Library name: V3272

value: Male

value: EA


title: Labroides dimidiatus, obligate cleaner. forebrain section, sample 6

description: Library name: CL-6

value: Female, forebrain section

tag: treatment

value: low density; Osprey collection


title: V3271

description: Library name: V3271

value: NIPBL


title: V3259

description: Library name: V3259


title: V3266

description: Library name: V3266


title: V3262

description: Library name: V3262

value: Female

value: AA


title: V3261

description: Library name: V3261


title: V3255

description: Library name: V3255


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description: Library name: V3242


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description: Library name: V3233


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description: Library name: V3237


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description: Library name: V3219


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description: Library name: V3214


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description: Library name: V3212


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description: Library name: V3210


title: V3211

description: Library name: V3211

value: DSCAM


title: V3208

description: Library name: V3208


title: V3200

description: Library name: V3200


title: V3196

description: Library name: V3196

value: Negative Control


title: V3185

description: Library name: V3185


title: V3180

description: Library name: V3180


title: V3179

description: Library name: V3179


title: V3178

description: Library name: V3178


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description: Library name: V3175


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description: Library name: V3193


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description: Library name: V3163


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description: Library name: V3168


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description: Library name: V3159


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description: Library name: V3145


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description: Library name: V3155


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description: Library name: V3143


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description: Library name: V3137


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description: Library name: V3134


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description: Library name: V3132


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description: Library name: V3128


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description: Library name: V3127


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description: Library name: V3121


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description: Library name: V3123


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description: Library name: V3126


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description: Library name: V3107


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description: Library name: V3101


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description: Library name: V3098


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description: Library name: V3100


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description: Library name: V3095


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description: Library name: V3093


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description: Library name: V3091


title: V3089

description: Library name: V3089


title: V3090

description: Library name: V3090


title: V3085

description: Library name: V3085


title: V3088

description: Library name: V3088


title: V3087

description: Library name: V3087


title: V3086

description: Library name: V3086


title: V3073

description: Library name: V3073


title: V3071

description: Library name: V3071


title: V3056

description: Library name: V3056


title: V3051

description: Library name: V3051


title: V3049

description: Library name: V3049


title: V3048

description: Library name: V3048


title: V3036

description: Library name: V3036


title: V3042

description: Library name: V3042


title: V3035

description: Library name: V3035


title: WT8_wt_low, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 15 μg/L

status: Public on Jan 22 2026

city: Buffalo

first: Charikleia

last: Karageorgiou

state: NY

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

description:
Library name: WT8
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

data_processing:
Mutltiple tools (FastQC, MultiQC, cutadapt, Bowtie2, samtools, featureCounts, DESeq2)
Sequence reads were assessed with FastQC and MultiQC
RNA-seq reads were mapped to Kluyveromyces lactis CBS 2359 reference (Klac_CBS2359_s29) using bowtie2
RNA-seq reads were quantified using featureCounts
The differential expression analysis was carried out using DESeq2
Assembly: Kluyveromyces lactis CBS 2359; RefSeq assembly accession GCF_000002515.2_ASM251v1.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include Deseq2 normalized values for each Sample

organism: Kluyveromyces lactis

source_name: LRY2992 (MATa SIR2 hmldelta hmrdelta)

growth_protocol: Kluyveromyces lactis strains LRY2992 (WT, MATa SIR2 hmlΔ hmrΔ) and LRY2993 (sir2Δ, MATα sir2Δ hmlΔ hmrΔ) were streaked on YPD, then inoculated into 10 mL YM minimal medium (yeast nitrogen base lacking niacin + 5 g/L (NH₄)₂SO₄ + 20 g/L glucose) supplemented with 400 µg/L nicotinic acid and grown overnight at 30 °C. Overnight cultures were diluted to OD₆₀₀ ≈ 0.3 in the same medium containing the indicated nicotinic-acid concentration (15, 45, 135 or 400 µg L⁻¹) and incubated 4 h (OD₆₀₀ ≈ 1.0) before harvest.

extract_protocol:
Ten OD₆₀₀ units of log-phase cells were washed in 500μl AE buffer (50mM NaoAc, ph=5.3; 10mM EDTA) and stored at -80°C. Frozen pellets were resuspended in 500μl AE/SDS buffer (10 parts AE: 1 part 10% SDS) and an equal amount of phenol-equilibrated with citrate (pH 4.5), vortexed and incubated at 65 °C for 4 min as per Schmitt et al., 1990. A second extraction with phenol/chloroform was followed by ethanol precipitation. Residual DNA was removed with DNase I (NEB M0303S).
Poly(A)⁺ RNA selection and library preparation were completed by Azenta sequencing services. Paired-end 150 bp reads were generated on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: Intracellular NAD⁺ was modulated solely by the precursor concentration. No other treatments were applied. WT and sir2Δ strains were grown in parallel at each nicotinic-acid level to separate genotype from metabolic effects.

value: LRY2992 (MATa SIR2 hmldelta hmrdelta)

value: yeast cells

value: nicotinic acid 15 μg/L


title: WT6_wt_lmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: WT6
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 45 μg/L


title: WT7_wt_low, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: WT7
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: WT5_wt_lmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: WT5
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: WT4_wt_hmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: WT4
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 135 μg/L


title: WT3_wt_hmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: WT3
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: RESUB_WT1R_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: RESUB-WT1R
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 400 μg/L


title: WT2_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: WT2
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 3

description: Library name: BLA-3


title: RESUB_DEL8_del_low, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: RESUB-DEL8
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

source_name: LRY2993 (MATalpha sir2delta hmldelta hmrdelta)


title: RESUB_WT1_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: RESUB-WT1
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: DEL7_del_low, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: DEL7
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: LRY2993 (MATalpha sir2delta hmldelta hmrdelta)


title: DEL5_del_lmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: DEL5
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: DEL6_del_lmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: DEL6
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: DEL4_del_hmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: DEL4
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: DEL3_del_hmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: DEL3
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: DEL1_del_high, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: DEL1
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: DEL2_del_high, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: DEL2
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: PFD-006-T0-N

status: Public on Jan 20 2026

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description:
Library name: PFD-006-T0-N
10x Genomics

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.1.0)
Background and non-cellular barcodes are removed
Assembly: GRCh38
Supplementary files format and content: .tsv: barcodes, genes, .mtx: count matrix

source_name: rectum

extract_protocol:
Tissue digestion with Liberase
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.

value: rectum

tag: subject status

value: patients with Crohn's Disease (CD) with and without perianal fistulizing disease (PFD)

value: CD+PFDun

value: Uninvolved

tag: ethnicity

value: caucasian

value: ileal

tag: phenotype

value: Inflammatory/Stricturing/Penetrating

value: Adalimumab

tag: immunosuppressors

tag: chemistry

tag: technology

value: 10x Genomics


title: PFD-008-T0-N

description:
Library name: PFD-008-T0-N
10x Genomics

value: CD+PFDinf

value: Inflamed

value: Female

value: ileocolonic

value: Penetrating

value: Tofacitinib


title: PFD-039-T0-N

description:
Library name: PFD-039-T0-N
10x Genomics

value: CDinf

value: Male

value: colonic

value: Inflammatory

value: Steroids


title: PFD-038-T0-N

description:
Library name: PFD-038-T0-N
10x Genomics

value: rectum

value: arab


title: PFD-036-T0-N

description:
Library name: PFD-036-T0-N
10x Genomics

value: CD+PFDre

value: Remission

value: caucasian

value: Infliximab

value: Azathioprine/Mercaptopurine


title: PFD-035-T0-N

description:
Library name: PFD-035-T0-N
10x Genomics

value: CD+PFDun

value: Uninvolved

value: 10x Genomics


title: PFD-034-T0-N

description:
Library name: PFD-034-T0-N
10x Genomics

value: ileal

value: Ustekinumab

value: Tacrolimus


title: PFD-031-T0-N

description:
Library name: PFD-031-T0-N
10x Genomics

value: CD+PFDinf

value: Inflamed

value: Male


title: PFD-032-T0-N

description:
Library name: PFD-032-T0-N
10x Genomics

value: Inflammatory


title: PFD-030-T0-N

description:
Library name: PFD-030-T0-N
10x Genomics

value: rectum

value: Female

value: ileocolonic


title: PFD-029-T0-N

description:
Library name: PFD-029-T0-N
10x Genomics

value: CDinf

value: colonic

value: Inflammatory/Penetrating

value: Steroids


title: PFD-028-T0-N

description:
Library name: PFD-028-T0-N
10x Genomics

value: CD+PFDre

value: Remission

value: caucasian

value: Penetrating


title: PFD-025-T0-N

description:
Library name: PFD-025-T0-N
10x Genomics

value: Vedolizumab

value: 10x Genomics


title: PFD-026-T0-N

description:
Library name: PFD-026-T0-N
10x Genomics


title: PFD-027-T0-N

description:
Library name: PFD-027-T0-N
10x Genomics

value: Ustekinumab


title: PFD-023-T0-N

description:
Library name: PFD-023-T0-N
10x Genomics

value: CD+PFDun

value: Uninvolved

value: ileal

value: Infliximab

value: Azathioprine/Mercaptopurine


title: PFD-022-T0-N

description:
Library name: PFD-022-T0-N
10x Genomics

value: rectum

value: CD+PFDinf

value: Inflamed

value: Male

value: ileocolonic

value: Adalimumab


title: PFD-020-T0-N

description:
Library name: PFD-020-T0-N
10x Genomics

value: Stricturing/Penetrating


title: PFD-021-T0-N

description:
Library name: PFD-021-T0-N
10x Genomics

value: N

value: caucasian


title: PFD-024-T0-N

description:
Library name: PFD-024-T0-N
10x Genomics

value: Female

value: Inflammatory


title: PFD-019-T0-N

description:
Library name: PFD-019-T0-N
10x Genomics

value: CD+PFDre

value: Remission

value: Inflammatory/Stricturing/Penetrating

value: Ustekinumab

value: 10x Genomics


title: PFD-018-T0-N

description:
Library name: PFD-018-T0-N
10x Genomics

value: Vedolizumab


title: PFD-015-T0-N

description:
Library name: PFD-015-T0-N
10x Genomics

value: rectum

value: CDun

value: Uninvolved

value: Methotrexate


title: PFD-014-T0-N

description:
Library name: PFD-014-T0-N
10x Genomics

value: CD+PFDinf

value: Inflamed

value: hindu

value: ileocolonic


title: PFD-013-T0-N

description:
Library name: PFD-013-T0-N
10x Genomics

value: CD+PFDun

value: Male

value: caucasian

value: colonic

value: Azathioprine/Mercaptopurine


title: PFD-012-T0-N

description:
Library name: PFD-012-T0-N
10x Genomics

value: Female

value: ileal

value: Inflammatory/Stricturing

value: Infliximab


title: PFD-011-T0-N

description:
Library name: PFD-011-T0-N
10x Genomics

value: rectum

value: Inflammatory

value: Adalimumab

value: 10x Genomics


title: PFD-004-T0-N

description:
Library name: PFD-004-T0-N
10x Genomics

value: CDun

value: Uninvolved


title: PFD-002-T0-N

description:
Library name: PFD-002-T0-N
10x Genomics

value: Ustekinumab


title: bone_marrow_reads

status: Public on Aug 09 2025

city: Ann Arbor

first: Lindsey

middle: A

last: Muir

state: MI

address: 1600 Huron Parkway B520

institute: University of Michigan

description: Library name: bone_marrow

data_processing:
Raw reads were processed with EPI2ME Labs `wf-single-cell' (https://github.com/epi2me-labs/wf-single-cell)
Assembly: GRCh38
Supplementary files format and content: Processed files are scanpy compliant AnnData objects.

source_name: bone marrow

growth_protocol: All cells were cultured at 37°C with 5% CO₂. Neonatal human foreskin fibroblasts (BJ, ATCC CRL-2522, RRID:CVCL_3653) were used as the initial cell type for reprogramming. Cells used for control and reprogramming cultures were at an initial passage number between 2 and 4, and were at 10 or fewer passages for endpoints. Fibroblasts were cultured in high glucose DMEM containing sodium pyruvate + 10% fetal bovine serum + 1% penicillin/streptomycin (P/S) + 1% L-glutamine. For reprogramming cultures, plates were coated with 0.1% porcine gelatin (Millipore #SF008). Primary human bone marrow CD34+ cells (ATCC PCS-800-012TM) were cultured in complete MyeloCult H5100 (STEMCELL Technologies 05150).

extract_protocol:
Adherent cells were dissociated using 1x TrypLE Express Enzyme (Gibco #12604-021)
Full-length barcoded cDNA amplicons were obtained from single cells using the 10X Genomics Next GEM Single Cell 3' Kit V3.1. Briefly, 20,000 sorted CD34+ cells and 2,000 control fibroblasts were loaded onto the 10X Genomics Chromium Controller (X) to partition single cells into Gel Beads-In Emulsion (GEMs). cDNA was generated from polyadenylated mRNA transcripts, incorporating a unique molecular identifier (UMI) and a cell-specific barcode for each transcript. Barcoded cDNA was pooled, purified with SILANE magnetic beads (10X Genomics #PN-2000048), and amplified by PCR. Barcoded cDNA libraries were prepared for sequencing according to the Oxford Nanopore Technologies (ONT) 3' cDNA protocols. Briefly, cDNA amplicons were biotin tagged by PCR with the primers shown in the ONT protocols. Biotinylated cDNA was purified with Dynabeads™ M-280 Streptavidin beads (Invitrogen #11205D), followed by secondary PCR amplification and Agencourt AMPure XP bead clean-up (Beckman Coulter #A63881). Products were assessed for quality following ONT recommendations. Long-read cDNA libraries were prepared for sequencing as in ONT protocols and sequenced on an ONT GridION or PromethION Solo 2 (P2) sequencer. Raw reads were base-called with guppy using the High Accuracy basecalling model and stored as fastq files.

treatment_protocol: Lentiviral transductions were carried out in complete medium without penicillin/streptomycin in the presence of 8 µg/mL polybrene (Millipore Sigma TR-1003-G). Integrated TF expression cassettes were induced with 1 µg/mL doxycycline hyclate (Dox, Millipore Sigma D9891) supplemented in the culture medium for 48 hours. Control fibroblasts were untransduced for single cell transcriptomics experiments. Reprogramming cells were switched to complete MyeloCult H5100 with 10e-6 M hydrocortisone (Millipore Sigma #H0888) and 1% P/S for 48 hours after the initial Dox treatment.

value: bone marrow

tag: cell type

value: various


title: PFD-003-T0-N

description:
Library name: PFD-003-T0-N
10x Genomics

tag: age

value: Male

value: arab

value: Stricturing

value: Mercaptopurine


title: PFD-010-T0-N

description:
Library name: PFD-010-T0-N
10x Genomics

value: Female

value: caucasian

value: ileocolonic

value: Methotrexate


title: Chip-seq of Runx3 with Tbet KO 1

status: Public on Jul 19 2025

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 34

library_source: genomic

data_processing:
Library construction and the quality inspection was carried out using Illumina HiSeq 4000 for sequencing
Assembly: T-bet,Runx3
Supplementary files format and content: .txt
Supplementary files format and content: .bw

molecule: genomic DNA

organism: Mus musculus

source_name: CD8+T cells

extract_protocol:
T-bet and Runx3 CUT&RUN:We adopted Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for genome-wide mapping of Runx3 in WT and Tbx21–/–.In brief, FACS-sorted live cells (1 × 105 cells per reaction) were bound to concanavalin A-coated magnetic beads (Bangs Laboratories) and permeabilized with 0.05% (w/v) digitonin and then incubated with anti-Runx3 antibody (Active Motif, 1 µl per reaction) or IgG overnight. After removal of unbounded antibodies with proper washing, the nuclei were incubated with protein A/G-micrococcal nuclease (MNase) fusion protein (plasmid obtained from Addgene) for 1hr at 4 °C. CaCl2 was then added to activate MNase activity and incubated on ice for 30 min. ATAC-seq:WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells cells were sorted on 4 dpi. Three biological replicates for each cell type, and 50,000 cells for each replicate were used to prepare ATACseq libraries as previously described71. Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice. The extracted nuclei were resuspended in transposition mix containing 2.5 µl Transposase (Illumina) and incubated at 37oC for 30 min. The products were purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina). DNA fragments in the range of 150-1,000 bp were recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific). RNA-seq:Total RNA was extracted from the sorted WT, Runx3–/–, Tbx21–/–, or Runx3–/–Tbx21–/– cells on 4 dpi, and triplicates were obtained for each genotype. cDNA synthesis and amplification were performed using SMARTer Ultra Low Input RNA Kit (Clontech).
T-bet and Runx3 CUT&RUN:The reaction was quenched with stopping buffer and the DNA fragments were purified with MinElute Reaction Cleanup kit (QIAGEN) and then amplified by PCR for 10–14 cycles with barcoded Nextera primers (Illumina). ATAC-seq:The libraries were quantified using a KAPA Library Quantification kit and sequenced on Illumina HiSeq 4000 sequencing systems in paired end 150 bp reads at the Admera Health. RNA-seq:Libraries were sequenced on Illumina’s HiSeq4000 in paired read mode with the read length of 150 nucleotides. Sequence data in fastq format were generated using CASAVA 1.8.2 processing pipeline from Illumina.

value: CD8+T cells


title: Chip-seq of Runx3 with Tbet KO 2

description: Library name: Sample 35


title: Chip-seq of Runx3 with Tbet KO 3

description: Library name: Sample 36


title: Chip-seq of Tbet 3

description: Library name: Sample 33


title: Chip-seq of Tbet 2

description: Library name: Sample 32


title: Chip-seq of Runx3 3

description: Library name: Sample 27


title: Chip-seq of Tbet 1

description: Library name: Sample 31


title: Chip-seq of Runx3 2

description: Library name: Sample 26


title: ATAC-seq of Tbet KO 2

description: Library name: Sample 23


title: ATAC-seq of Tbet KO 3

description: Library name: Sample 24


title: Chip-seq of Runx3 1

description: Library name: Sample 25


title: ATAC-seq of Tbet KO 1

description: Library name: Sample 22


title: ATAC-seq of Cpntrol 3

description: Library name: Sample 15


title: ATAC-seq of Cpntrol 2

description: Library name: Sample 14


title: ATAC-seq of Cpntrol 1

description: Library name: Sample 13


title: Brain_patient_81

status: Public on Apr 01 2025

city: Pessac

first: Andreas

last: Bikfalvi

address: Allée Geoffroy St-Hilaire

country: France

institute: University of Bordeaux

description: Library name: 19025084

data_processing:
Read alignment software : Salmon / version 0.8.2 / parameters : --threads : "20" --libType : "A"
Assembly: HG38
processed data files format and content: raw and normalized counts

source_name: Brain

extract_protocol:
RNAs were isolated using RNeasy kit (Qiagen, 74134) and DNA was removed using RNase-free DNase (Qiagen, 79254). Overall, 500 ng was used as input material for a Low Input Ribozero treatment using the Epicentre Ribo-Zero Gold Kit–Low Input (HMR). The integ
The depleted RNA was used as input material for the ScriptSeq v2 RNA-Seq Library Preparation protocol. Following 14 cycles of amplification, the libraries were purified using Ampure XP beads. Each library was quantified using Qubit, and the size distribut

value: Brain

tag: patient id

tag: pet

value: pos

value: female

tag: first intervention

tag: histology

value: Astrocytoma

tag: grade

tag: eor

value: Total

tag: recurrence

tag: adjuvant

tag: type of_adjuvant

tag: lost in_follow_up

tag: recurrence free_survival

tag: os

tag: follow up


title: Brain_patient_27

description: Library name: 18048737

tag: tissue

tag: Sex


title: Brain_patient_146

description: Library name: 19009831

value: Oligodendroglioma


title: Brain_patient_96

description: Library name: 18030421


title: Brain_patient_30

description: Library name: 19023570

value: male

value: Subtotal


title: Brain_patient_42

description: Library name: 18020382

value: RT


title: Brain_patient_15

description: Library name: 18016784

tag: proteomic id


title: Brain_patient_138

description: Library name: 17045191

value: neg

tag: age


title: Brain_patient_37

description: Library name: 17012894

tag: patient id


title: Brain_patient_56

description: Library name: 17017593

tag: pet


title: Brain_patient_62

description: Library name: 17036942

tag: first intervention

value: Partial


title: Brain_patient_98

description: Library name: 17011758

tag: histology


title: Brain_patient_111

description: Library name: 17011553

tag: grade


title: Brain_patient_105

description: Library name: 17012663

tag: eor

value: CT


title: Brain_patient_35

description: Library name: 17010047

tag: recurrence


title: Brain_patient_94

description: Library name: 16045177

tag: adjuvant


title: Brain_patient_80

description: Library name: 16034236

tag: type of_adjuvant


title: Brain_patient_71

description: Library name: 16047595

tag: lost in_follow_up


title: Brain_patient_82

description: Library name: 16027194

tag: recurrence free_survival


title: Brain_patient_158

description: Library name: 16040530

tag: os


title: Brain_patient_79

description: Library name: 16023746

tag: follow up


title: Brain_patient_86

description: Library name: 16018296

tag: tissue


title: Brain_patient_148

description: Library name: 16022653

tag: Sex


title: Brain_patient_49

description: Library name: 16014865

tag: proteomic id


title: Brain_patient_58

description: Library name: 16013815

tag: age


title: Brain_patient_134

description: Library name: 16013509

tag: patient id


title: Brain_patient_1

description: Library name: 16006308

tag: pet


title: Brain_patient_112

description: Library name: 16017831

tag: first intervention


title: Brain_patient_95

description: Library name: 16002282

tag: histology


title: Brain_patient_16

description: Library name: 16004660

tag: grade


title: Brain_patient_17

description: Library name: 16000179

tag: eor


title: Brain_patient_124

description: Library name: 16001264

tag: recurrence


title: Brain_patient_44

description: Library name: 15046128

tag: adjuvant


title: Brain_patient_25

description: Library name: 16000363


title: Brain_patient_59

description: Library name: 15045036

tag: type of_adjuvant


title: Brain_patient_110

description: Library name: 15043188

tag: lost in_follow_up


title: Brain_patient_152

description: Library name: 15035335

tag: recurrence free_survival


title: Brain_patient_93

description: Library name: 15028249

tag: os


title: Brain_patient_104

description: Library name: 15026630

tag: follow up


title: Brain_patient_34

description: Library name: 15022703

tag: tissue


title: Brain_patient_65

description: Library name: 15019883

tag: Sex


title: Brain_patient_74

description: Library name: 15019231

tag: proteomic id


title: Brain_patient_130

description: Library name: 15023880

tag: age


title: Brain_patient_39

description: Library name: 15009881

tag: patient id


title: Brain_patient_73

description: Library name: 15004956

tag: pet


title: Brain_patient_5

description: Library name: 15003867

tag: first intervention


title: Brain_patient_2

description: Library name: 14037657

tag: histology


title: Brain_patient_60

description: Library name: 14024445

tag: grade


title: Brain_patient_57

description: Library name: 14023172

tag: eor


title: Brain_patient_32

description: Library name: 14040111

tag: recurrence


title: Brain_patient_19

description: Library name: 14018354

tag: adjuvant


title: Brain_patient_77

description: Library name: 14016025


title: Brain_patient_46

description: Library name: 14014240


title: Brain_patient_157

description: Library name: 14012645

tag: type of_adjuvant


title: Brain_patient_89

description: Library name: 13024846

tag: lost in_follow_up


title: Brain_patient_47

description: Library name: 14011660

tag: recurrence free_survival


title: scARC library, group 44, 6hr_ATAC

status: Public on Feb 20 2025

first: Jubao

last: Duan

state: IL

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description:
Library name: scARC_Library_44_6
Library 44, 6 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031

library_source: genomic single cell

data_processing:
10x Genomics Chromium single cell Multiome sequencing libraries were sequenced at UMGC on Novaseq S4 platform targeting pair-end (2 x 150bp) 50k reads per nuclei for ATAC library and 25K reads per nuclei for gene expression library. Briefly, after raw data collection, Illumina’s BCL2FASTQ software was used to de-multiplex and assemble the fastq files corresponding to reads (R1/R2) and indices (i5/i7) for Cell Ranger ARC. The fastq files were subsequently processed by 10x Genomics Cell Ranger ARC (v2.0.2) and aligned twice to both the human GRCh38.p14 genome and a contingent of human GRCh38.p14 and mouse GRCm38 provided by 10x Genomics for efficient identification and removal of rodent astrocytes. For snATAC-seq, the per-library Transcription Start Sites (TSS) enrichment score is usually between 7-9 and the Fraction of high-quality Reads overlapping Peaks (FRiP) is usually between 40%-80%. We excluded cells with >15% of the reads mapped to mitochondrial genes, cells with > 8,000 or < 400 number of features, and cells with > 40,000 or <500 number of UMI counts (filtered by 400 < nCount < 8,000 using Seurat).
For each library that contains cells derived from 3-4 iPSC lines, barcode-level identification was performed separately for snRNA-seq (GEX) and snATAC-seq data with genotyping information of all donors. Briefly, the BAM files generated from GEX and ATAC assays (gex_possorted_bam.bam and atac_possorted_bam.bam) were processed by demuxlet (Kang et al., 2018) with known genotype information provided as .vcf files. Barcodes (cells) identified as singlets with P1 likelihood (p1LLK) < 1x10-8 were collected, and only barcodes positively identified in both GEX and ATAC assays were retained for downstream analysis.
snRNA-seq (GEX) data were processed by extracting gene expression data from the .h5 files generated by Cell Ranger ARC. Only barcodes (cells) confidently assigned to individual iPSC lines were retained. With Seurat 5.1.0(Hao et al., 2024), for cell type assignmentsTo assign cell type identity, Leiden clustering was performed at the library level based on the first 30 PCs (or appropriate as determined by the elbowplot) and subsequently by comparing cell clusters and their marker gene expressions (GAD1, GAD2, SLC17A6, SLC17A7, NEFM) and added as metadata. The library-level gene expression matrices were subsequently collated in Seurat 5.1.0(Hao et al., 2024) as one large object with cell line-specific metadata assigned. Harmony (Korsunsky et al., 2019) was used to integrate the library-level gene matrices and removed sequencing batch-derived effects.
For snATAC-seq data, the aggregation function of Cell Ranger ARC was used to merge and generate new fragment files for MACS2-based peak calling with the CallPeaks() function in Signac(Stuart et al., 2021) with default settings. We made two merged fragment files, one containing all libraries from batch 024 (18 cell lines) and the other from batch 018, 024, 025, and 029 (76 cell lines). From each fragment file, we iterated througugh the combinations of cell types (NEFM+ glut, NEFM- glut, GABA) and stimulation stages (0 hr, 1 hr, 6 hr), which generated nine peak sets (cell type x time). We further generated a union peak set from batch 024 by setting CallPeaks(combine.peaks = TRUE) for peak analysis across different cell types. Finally, peaks that fell within the ENCODE blacklisted regions were removed. We also removed peaks that fall within chromosomes X and Y and the mitochondrial genome regions.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger 2.0.2 output directory sans .bam files
Supplementary files format and content: h5, count matrices snATAC and snRNA-seq
Supplementary files format and content: .cloupe, 10x Genomics Loupe data file

source_name: Neuron

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rate glial cells. For excitatory neuron differentiation, we used the method to derive Ngn2-glutamatergic neuron {Zhang, 2013 #6824}  with minor modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 5 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor, together with appropriate amount of rtTA virus and Ngn2-puro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. On DIV2 - DIV4, cells were treated with neural culture media (Neuralbasal media with 1x B27Plus and 1x Glutamax) supplemented with 2g/ml puromycin, 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, puromycin was withdrawn and cells were treated with neural culture media with 2ug/ml doxycycline. On DIV7, cells would be ready for replating. For generating excitatory neurons, we used the method to derive Ascl1/Dlx2-GABAergic neurons {Yang, 2017 #7817} with minopr modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 7 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor together with rtTA virus, Ascl1-puro virus and Dlx2-hygro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. From DIV2 - DIV4, cells were treated with neural culture media supplemented with 2g/ml puromycin, 150g/ml hygromycin and 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, cells were treated with neural culture media with 2g/ml doxycycline and 2M AraC. Cells would be ready for replating on DIV7. To co-culture the excitatory and inhibitory neurons,  on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using accutase at 37C for 15-20min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2g/ml doxycycline, 10ng/ml BDNF, 10ng/ml GDNF, 10ng/ml NT-3 and 1% FBS. For each co-culture,  we pooled cells from 3-4 donor lines with equal proportion. On DIV8, we refilled cells with more media. From DIV9 – DIV33, media was refreshed every three days with half volume change. Doxycycline was withdrawn at DIV14 and 1uMµM AraC was added in the media from DIV8-DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
After stimulation, cells were briefly washed with 1x PBS and dissociated in accutase at 37C for 40min with gentle shaking. After accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40m tip filter (Sigma# BAH136800040-50EA) to obtain single cells. The washed cells were subjected to fresh nuclei isolation following 10x Genomics’ protocols (CG000365 and CG000338). For each library, around 15,000 freshly isolated nuclei were loaded for GEM capture targeting 10,000 nuclei recovery.
The pre-amplified DNAs (for snATAC-seq) and cDNAs (for snRNA-seq) were shipped to University of Minnesota Genomics Center  (UMGC) for sn-multiomics sequencing library construction following 10x Genomics’ standard protocol.

treatment_protocol: To model neuron activation, we followed previously used protocol to treat the cells with KCI {Boulting, 2021 #8234}. Briefly, 24hr before stimulation, old media was aspirated and DIV33 neuron co-culture were silenced in neural culture media supplemented with 1M TTX and 100M DL-AP5. The next day, we added fresh culture media with warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) to initiate KCI stimulation. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr). After stimulation, cells were dissociated for 10x Genomics’ sn-Multiomics sequencing library preparation.

value: Neuron

tag: cell line

tag: cell type

value: cultured glutamatergic and GABAergic neurons derived from iPS cells

tag: batch


title: Brain_patient_3

description: Library name: 14000798

tag: tissue

tag: Sex

tag: os

tag: follow up


title: scARC library, group 49, 0hr_ATAC

description:
Library name: scARC_Library_49_0
Library 49, unstimulated, contains cell lines CD0000049, CD000058, CD000032, CD000061


title: Brain_patient_107

description: Library name: 12030697

tag: patient id

tag: proteomic id

tag: pet

tag: age


title: scARC library, group 44, 0hr_ATAC

description:
Library name: scARC_Library_44_0
Library 44, unstimulated, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: Brain_patient_114

description: Library name: 12017980

tag: first intervention

tag: histology

tag: grade

tag: eor


title: scARC library, group 44, 1hr_ATAC

description:
Library name: scARC_Library_44_1
Library 44, 1 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 39, 6hr_ATAC

description:
Library name: scARC_Library_39_6
Library 39, 6 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 39, 0hr_ATAC

description:
Library name: scARC_Library_39_0
Library 39, unstimulated, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 36, 1hr_ATAC

description:
Library name: scARC_Library_36_1
Library 36, 1 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: scARC library, group 36, 0hr_ATAC

description:
Library name: scARC_Library_36_0
Library 36, unstimulated, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: Sample 29, EHC3, healthy

status: Public on Jan 27 2025

city: Kalyani

first: Kartiki

middle: V.

last: Desai

state: West Bengal

address: N.S.S kalyani

country: India

institute: National Institute of Biomedical Genomics

data_processing:
NovaSeq software used for base calling and FASTQC was used for quality check.
Sequence reads were trimmed for adaptor sequence using CutAdapt, and masked for low-complexity or low-quality sequence, then mapped with the human genome (GrCh38.1) by Hisat2.0 with parameters  -q -x -1 -2 -S
Aligned sequences were processed by Featurecounts package to get transcript specific counts with parameters -p s 2 -t -g
Assembly: GrCh38.1
Supplementary files format and content: Tab-delimited text files include single normalized count matrix from featureCounts for each Sample

source_name: Serum derived Evs

extract_protocol:
EV RNA was isolated by EXOQUICK® Exosome isolation and RNA purification kit for serum/plasma (System Biosciences,CA) and was reverse transcribed to make amplified cDNA by SMART seq v4 ultra-low input RNA kit (Takara Bio Inc, USA).
Low Input Library Prep Kit v2 (Takara Bio Inc, USA). DNA unique Dual index kit was used to combine libraries for sequencing (Takara Bio Inc, USA).  NOVASEQ 6000 was used for sequencing to generate 25 million paired end reads per sample.

value: Serum derived Evs

tag: genotype

value: Healthy


title: Sample 30, EHC4, healthy


title: Sample 27, EHC1, healthy


title: Sample 28, EHC2, healthy


title: Sample 26, E282, Tumor

value: Tumor


title: Sample 25, E278, Tumor


title: Sample 24, E266, Tumor


title: Sample 21, E258, Tumor


title: Sample 22, E263, Tumor


title: Sample 20, E252, Tumor


title: Sample 19, E248, Tumor


title: Sample 18, E245, Tumor


title: Sample 16, E236, Tumor


title: Sample 17, E237, Tumor


title: Sample 15, E233, Tumor


title: Sample 14, E232, Tumor


title: Sample 11, E211, Tumor


title: Sample 13, E229, Tumor


title: Sample 12, E222, Tumor


title: Sample 10, E207, Tumor


title: Sample 9, E204, Tumor


title: Sample 8, E202, Tumor


title: Sample 7, E198, Tumor


title: Sample 6, E197, Tumor


title: Sample 5, E189, Tumor


title: Sample 4, E183, Tumor


title: Sample 2, E176, Tumor


title: Sample 3, E177, Tumor


title: Sample 1, E168, Tumor


title: reprogram_reads

status: Public on Dec 09 2024

description: Library name: ihsc_gridion

data_processing:
Raw reads were processed with EPI2ME Labs `wf-single-cell' (https://github.com/epi2me-labs/wf-single-cell)
genome build/assembly GRCh38
processed data files format and content: Processed files are scanpy compliant AnnData objects.

source_name: induced hematopoietic stem cells

value: reprogrammed fibroblast

tag: treatment

value: Doxycycline-inducible lentiviral vectors to express GATA2, GFI1B, FOS, STAT5A, and REL


title: fibroblast_reads

description: Library name: bj_fibroblast

source_name: neonatal foreskin

value: neonatal foreskin

tag: cell line

value: BJ fibroblast

value: fibroblast


title: reprogram_reads2

description: Library name: ihsc_p2

tag: cell type


title: CD4, CITE-seq group 6

status: Public on Jul 01 2024

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

library_source: other

data_processing:
Raw reads were processed using the Cellranger arc pipeline (version 2.0.1) with default parameters, CITE reads were processed with Kite (https://github.com/pachterlab/kite) and Kallisto (version 0.48.0).
Assembly: hg38
Supplementary files format and content: Matrix files and fragments.tsv files from the cellranger pipeline or Kallisto
Supplementary files format and content: Morphine.Meta.csv contains hashkey, treatment conditions, and timepoint keys
Library strategy: DOGMA-seq

molecule: other

source_name: Peripheral Blood

extract_protocol:
cDNA, transposed cDNA, and CITE cDNA were extracted according to the 10X multiome protocol with the modifications described in Mimitou et al.Nat. Biotechnol. 2021.
Libraries were constructed using the 10X multiome protocol with the modificaitons described in Mimitou et al. Nat. Biotechnol. 2021.

treatment_protocol: Dead cells were removed using a bead based kit (STEMCELL Technologies #17899), and hashed using TotalSeq-A antibodies. Each sample was pooled in equal ratios and stained with the TotalSeq™-A Human Universal Cocktail, V1.0 (Bioledgend #399907). Pools were then lysed on ice with DIG lysis buffer for 5 minutes before washing. Cells werethen loaded into the 10X Chromium controller (10x Genomics) according to the manufacturer protocol. CD4+ T cells samples were additionally negatively selected using Miltenyi Biotech #130-096-533.

value: Peripheral Blood


title: CD4, CITE-seq group 5


title: PBMC, CITE-seq group 3

value: PBMC


title: CD4, CITE-seq group 4


title: CD4, CITE-seq group 3


title: CD4, CITE-seq group 1


title: PBMC, CITE-seq group 2


title: CD4, CITE-seq group 2


title: PBMC, CITE-seq group 1


title: CD4, scATAC-seq group 6


title: CD4, scATAC-seq group 5


title: PBMC, scATAC-seq group 3


title: CD4, scATAC-seq group 4


title: CD4, scATAC-seq group 3


title: CD4, scATAC-seq group 2


title: PBMC, scATAC-seq group 1


title: CD4, scRNA-seq group 6


title: CD4, scATAC-seq group 1


title: CD4, scRNA-seq group 5


title: scARC library, group 39, 1hr_ATAC

description:
Library name: scARC_Library_39_1
Library 39, 1 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042

tag: batch


title: CD4, scRNA-seq group 4

tag: tissue


title: PBMC, scATAC-seq group 2


title: CD4, scRNA-seq group 3


title: PBMC, scRNA-seq group 2


title: PBMC, scRNA-seq group 3


title: CD4, scRNA-seq group 2


title: scARC library, group 36, 6hr_ATAC

description:
Library name: scARC_Library_36_6
Library 36, 6 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: CD4, scRNA-seq group 1


title: PBMC, scRNA-seq group 1


title: Sample 23, E265, Tumor


title: DOT1LKO input

status: Public on Apr 30 2024

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
Aligned bam files were then filtered to remove reads in black-listed regions, duplicate reads were marked using Picard MarkDuplicates
Bam files were filtered again to remove low quality reads (samtools view -q 10 -F 1800)
Bamcoverage was performed under standard parameters and visualised on IGV
Assembly: UCSC mm10
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

source_name: splenic NK cells, cultured

extract_protocol:
input only contains secondary antibody (NBP1-72763), H3K4me3 was targeted using αH3K4me3  (Cell Signalling #9727), H3K27me3 was targeted using αH3K27me3 (Cell Signalling #9733)
Tn5-digested DNA underwent PCR witrh universal i5 primer and sample-specific, unique i7 primer, followed by SBS V2.5 chemistry

value: splenic NK cells

value: NK cells

tag: chip antibody

value: none (input)

value: NK cell enrichment followed by culturing for 5 days


title: DOT1LKO H3K27me3


title: DOT1LKO H3K4me3


title: WT H3K4me3

value: WT


title: WT input


title: NK cells, cultured, d5, rep1, IP sample

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with Bowtie2 (parameters: --no-mixed --no-discordant -X 1000)
Aligned bam files were then filtered to remove reads in black-listed regions, duplicate reads were marked using Picard MarkDuplicates
Bam files were filtered again to remove low quality reads (samtools view -q 10 -F 1800)
Bamcoverage was applied on Bam files
Assembly: UCSC mm10
Supplementary files format and content: bigwig

source_name: spleen

growth_protocol: Splenic NK cells isolated with STEMCELL NK cell isolation kit; cultured in IMDM (10% FCS), P/S, Glutamax, β-ME for 5 days.

extract_protocol:
2 µg of anti-H3K79me2 (ab3594) was used to perform ChIP. DNA was purified using the NucleoSpin Gel and PCR Clean-up kit according to the manufacturer's specifications
MGITech MGIEasy DNA FS Library preparation kit V3 (according to the manufacturer's instructions: document revision A0)

value: spleen

value: NK cell

value: IMDM (10% FCS) + 50 ng/ml IL-15


title: NK cells, cultured, d5, rep2, input

value: no primary


title: NK cells, cultured, d5, rep2, IP sample


title: WT H3K27me3


title: NK cell, cultured, d5, knockout, rep2

description: column 6

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with RNAStar, followed by featureCounts and DESeq2 (standard parameters)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: enriched splenic NK cells

growth_protocol: cultured for 5 days in complete IMDM containing 50 ng/ml recombinant human IL15

extract_protocol:
Macherey Nagel NucleoSpin RNA kit according to manufacturer's instructions
MGIEasy V3 chemistry

value: enriched splenic NK cells

value: DOT1L KO

value: 5 days in culture (50 ng/ml IL-15)


title: NK cell, cultured, d5, knockout, rep3

description: column 7


title: NK cells, cultured, d5, rep1, input


title: NK cell, cultured, d5, knockout, rep1

description: column 5


title: NK cell, cultured, d5, wild type, rep3

description: column 4


title: NK cell, cultured, d5, wild type, rep2

description: column 3


title: splenic sorted NK cells, knockout, d2 MCMV, rep2

description: column 11

data_processing:
Raw paired end fastq files were aligned to the UCSC mm10 genome with RNAStar, followed by featureCounts and DESeq2 (standard parameters)
Assembly: UCSC mm10
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: sorted splenic NK cells

extract_protocol:
bulk RNA was isolated from sorted, splenic NK1.1+ CD3/TCRβ- Ly49H+ cells using the Nucleospin RNA isolation kit
MGIEasy V3 chemistry

value: sorted splenic NK cells

value: NK cells (Ly49H+)

tag: time

value: NK cell enrichment followed by FACS sort for Ly49H+ NK1.1+ CD3-


title: splenic sorted NK cells, knockout, d2 MCMV, rep3

description: column 12


title: NK cell, cultured, d5, wild type, rep1

description: column 2


title: splenic sorted NK cells, wild type, d2 MCMV, rep2

description: column 9


title: splenic sorted NK cells, knockout, rep2

description: column 6


title: splenic sorted NK cells, knockout, rep3

description: column 7


title: splenic sorted NK cells, knockout, rep1

description: column 5


title: splenic sorted NK cells, wild type, d2 MCMV, rep1

description: column 8


title: splenic sorted NK cells, wild type, rep2

description: column 3


title: splenic sorted NK cells, wild type, rep3

description: column 4


title: splenic sorted NK cells, wild type, rep1

description: column 2


title: Hi-C_NeuN-_H4

status: Public on Mar 26 2024

city: Moscow

first: Ilya

middle: Andreevich

last: Pletenev

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skoltech

data_processing:
Fastq files were preprocessed with trimmomatic (Bolger, A. M., Lohse, M., & Usadel, B., 2014)
Preprocessed files were provided as input for distiller pipeline (https://github.com/open2c/distiller-nf) with default parameters to obtain mcool files(https://github.com/open2c/distiller-nf, v.0.3.3)
Most of the Hi-C analysis was performed on Hi-C matrices merged by cell type. Merging was done at 1 kbp resolution using cooler.merge_coolers() function of a cooler library (Abdennur and Mirny 2020), v.0.8.11.
The resulting merged Hi-C maps were sampled to the equal number of contact pairs using cooltools.sample() function of a cooltools library (Open2C et al. 2022), v.0.5.1.
To avoid possible bias due to Hi-C ligation artifacts, the values at the main diagonal were removed prior to sampling using cooler and custom python code.
Resulting .cool files with Hi-C matrices were ICE normalized (Imakaev et al. 2012) using “cooler balance” command with default parameters.
Assembly: hg38
Supplementary files format and content: *.mcool – Hi-C matrix (see https://github.com/open2c/cooler)
Supplementary files format and content: PC1* - values of an eigenvector that defines compartments
Supplementary files format and content: fithic.h3k27me3.NeuN+.hi-c_merged.res-100kb.bedpe.gz – coordinates of neuronal H3K27me3-enriched polycomb contacts
Supplementary files format and content: Loops* - coordinates of chromatin loops
Supplementary files format and content: TAD_boundaries_* - coordinates of TAD boundaries

source_name: Left posterior superior temporal gyrus (Wernicke's area - BA22p)

extract_protocol:
Post-mortem human brain samples were obtained via National BioService Russian Biospecimen CRO (St. Petersburg, Russia). Informed consent for using human tissues for research was obtained in writing form from all donors or their next of kin by the tissue provider bank. Sampled brain tissue of all subjects was defined as healthy by medical pathologists. All subjects had sudden death with no prolonged agony state and had no history of neurologic and psychiatric disorders or alcohol and drug abuse. Post-mortem brain frontal blocks 1-1,5 cm thick were stored at -80°C warped in a foil, in zip-lock packages. For sample dissection, The Atlas of the Human Brain (AHB) (Mai 2016) was used to locate the area of interest, a posterior part of the superior temporal gyrus of the left hemisphere (posterior Brodmann area 22 (BA22p), Wernicke's area). Frontal blocks with surfaces nearest to AHB level: 60 (MNI: -36.57; ICL: 34.82; MCP: 20.08) were placed into the cryostat Leica CM1950 chamber with -20°C before dissection for 15-20 min on custom-made aluminum support. A tissue piece of approximately 150 mg weight was cut out from a selected area using a metal scalpel. Dissected samples were then collected with tweezers, put into tubes, and placed in dry ice immediately. All materials used during dissection (scalpels, tweezers, tubes) were sterile and chilled using dry ice before use.
Preparation of bulk Hi-C libraries from 11 samples of human brain tissue was performed as previously described (Lieberman-Aiden et al. 2009; Ulianov et al. 2016) with optimal changes to brain tissue (Eremenko et al. 2021). Approximately 200,000-400,000 sorted nuclei for the sample were lysed in a solution of lysis buffer containing 150 mM Tris-HCI pH7.5-8, 150 mM NaCI, 0.5% (v/v) NP-40, 1% (v/v), Triton-X100, 1x Protease Inhibitor (CALBIOCHEM, #539137) on ice for 15 min, centrifuged at +4 °C 5000g for 7 min, the pellet was resuspended and washed in 1.12Х restriction enzyme DPN II buffer. After the final wash, the pellet suspension in 1.12Х DPN II buffer with added 0.3% SDS has incubated for 60 min 1400 rpm at +37°C. Further, the reaction was quenched with 1.8% Triton X-100 for 60 min at 1400 rpm at +37°C, and the 500U DPN II restriction enzyme was added, the suspension was left overnight at 1400 rpm at +37°C. After that, the additional amount of 200U DPN II restriction enzyme was added to the digested nuclei and incubated for the next 120 min at 1400 rpm at +37°C. After that, the restriction was unactivated at +65°C for 20 min. The digested DNA samples were washed and resuspended in 1.2XNEB2, and after that digested ends were marked with biotin during the incubation in the mix of 1М biotin-14dATP, 10x NEB2, 10mM dCTP, 10mM dGTP, 10mM dTTP, 5U/ul Klenow (NEB #M0210S) for 90 min 900 rpm at +37 °C. The resulting blunt ends were washed with 1X T4 DNA ligase buffer and chromatin fragments were proximally ligated with 50 U T4 DNA ligase (Fermentas) for 6 h 1400 rpm at +37 °C. Then the 0.5% SDS with 20 μg/ml proteinase K was added to samples for overnight incubation at +65 °C. The following step was DNA purification with phenol–chloroform extraction and precipitation with 2.5 volumes of 96% ethanol, 0.1 volumes of 3M sodium acetate, 20 μg/ml glycogen, and 9.4 μg/ml tRNA for 60 min at −80 °C. After the centrifugation step at 20000g for 20 min, +4°C the pellet was dissolved in 10 mM Tris-HCl pH 8.0 with the addition of RNase A and incubated for 45 min at +37°C. The next step was DNA sample purification on 2.5 volumes of magnetic AMPure XP beads with the following DNA elution in 10 mM Tris-HCl for 15 min at +55°C. Eluted DNA was fragmented by sonication with Power 15 regime, 4 repeats for 30 s with 3 min break. Sonicated DNA samples were then concentrated on Amicon columns 14000g/5 min with double 10 10 mM Tris-HCl pH 8.0 washing. The resulting biotin-marked fragments were isolated using Dynabeads MyOne Streptavidin C1 (Invitrogen #65001) and diluted in TWB buffer (1M Tris-HCl pH 8.0, 50 mM EDTA, 5M NaCl, 1% Tween). All subsequent steps were performed on that bead-bound DNA fraction including DNA ends repair with repair mix (10Х ligase NEB buffer, 10 mM dNTP mix, T4 DNA Pol, T4 PNK, 1 ul Klenow) for 30 min at room temperature, and PolyA tail adding reaction with a mix containing 10Х NEB2, 10 mМ dATP, Klenow (exo-) and incubation for 30 min at +37°C and then for 20 min at +65°C. Then beads were washed with 1X T4 ligase buffer for 3 min at room temperature 900 rpm, and the ligation reaction was performed with a ligation mix of 10X T4 ligase buffer, adapter, 5 U T4 ligase (Fermentas) for 2.5 h at room temperature. Finally, libraries were PCR amplified using Illumina  forward  and reverse primers and KAPA HiFi HotStart for 16 cycles to select the appropriate cycle for amplified DNA fragments collection (the 6, 9, 12, and 15 cycles were collected and checked for DNA quantity on chosen cycle). Last, up to the chosen number of cycles Hi-C libraries were PCR amplified, and resulting fragments were purified using 1.5 volumes AMPure XP magnetic beads.

value: NeuN-


title: Hi-C_NeuN-_H3

value: Left posterior superior temporal gyrus (Wernicke's area - BA22p)


title: Hi-C_NeuN-_H2


title: Hi-C_NeuN+_H4

value: NeuN+


title: Hi-C_NeuN+_H3


title: Hi-C_NeuN+_H2


title: visium_sham_male

status: Public on Jan 17 2024

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

description: 10X Visium

data_processing:
Visium data processing: Sequencing was performed on a NovaSeq S4, targeting 125 million reads using dual indexing. Resulting FASTQ files were aligned to mm10 reference, manually aligned to respective hematoxylin and eosin stained images. The counts were normalized using 10× Genomics Space Ranger (spatial 3′ v1; spaceranger-1.2.1). The gene-by-count matrix was input to CellScopes.jl for downstream analysis.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
Assembly: mm10
Library strategy: spatial transcriptomics

extract_protocol: 10X Visium protocol: After removing the renal capsule, the kidneys were bisected in a coronal manner to prepare for 10x Genomics Visium sample preparation. To preserve the high quality of RNA for processing, the fresh tissue was immersed in a bath of 2-methylbutane equilibrated with liquid nitrogen. The tissue samples were then stored at -80°C prior to embedding them in optimal cutting temperature compound (OCT). The remaining kidney tissue was fixed overnight in 10% formalin at room temperature, before being transferred to 70% ethanol for storage at 4°C. The tissue was subsequently embedded in paraffin by the Washington University Musculoskeletal Research Center Core. Frozen kidney samples were embedded in cryomolds using OCT on dry ice. The blocks were then stored at -80°C. For preparation of Visium, the blocks were equilibrated to -18°C, and 10 μm sections were mounted onto the active sequencing areas of the 10× Genomics Visium slides. The slides were stored in airtight containers at -80°C until used for spatial library generation. Hemotoxylin and eosin staining were performed according to the 10× Genomics Visium protocol. Visium libraries were prepared according to 10× Genomics Visium manufacturer’s instructions (PN-1000185, Lot No. 155614, Rev D).

tag: Sex

value: male

tag: surgery

value: sham

value: Kidney


title: Hi-C_NeuN+_H1


title: cartana_iri6w_male

type: RNA

description: ISS by Cartana

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
ISS data processing: ISS data was processed using our in-house pipeline called CellScopes https://github.com/TheHumphreysLab/CellScopes.jl.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
genome assembly: mm10

label: not applicable

label_protocol: not applicable

extract_protocol: RNA hybridization-based in situ sequencing protocol: Fresh kidneys were incubated in 2-methylbutane (Millipore, Sigma) equilibrated in liquid nitrogen to maintain RNA integrity. Tissues were then stored at −80°C and embedded in cryomolds using OCT (Tissue-Tek 4583) on dry ice. For frozen sectioning, OCT blocks were equilibrated to −18°C, and 10 μm-thick sections were mounted onto the glass slides (1358W; Globe Scientific). Libraries were prepared using the high sensitivity (HS) library preparation kit provided by CARTANA (Sweden) per manufacturer’s instruction. In brief, slides were fixed in freshly prepared formaldehyde diluted in 0.01% DEPC treated PBS, followed by permeabilization in 0.1M HCl (DEPC treated). After dehydration and rehydration in series of alcohol gradients, slides were incubated in RM1-mix (provided by the library kit) overnight at 37°C. Kidney sections were incubated in WB4 (library kit) at 37°C for 30 min. Gene probes were ligated in ligases dissolved in RM2 (library kit) at 37°C for 2 hours. Transcripts were amplified in RM3-mix (library kit) at 30°C overnight. Slides were stained with DAPI for quality control imaging and shipped to 10x Genomics for in situ sequencing.

value: IRI 6 weeks


title: Hi-C_NeuN-_H1


title: cartana_iri2d_male

description: ISS by Cartana

value: IRI 2 days


title: cartana_iri12h_male

description: ISS by Cartana

value: IRI 12 hours


title: cartana_iri4h_male

description: ISS by Cartana

value: IRI 4 hours


title: splenic sorted NK cells, knockout, d2 MCMV, rep1

description: column 10


title: female Poecilia latipinna 17, whole brain, Ff treatment

status: Public on Jul 01 2023

city: Austin

first: Rebecca

last: Young

address: 2415 Speedway #C0930, Patterson Lab 607A

institute: University of Texas at Austin

data_processing:
Libraries were demultiplexed using a custom python script. Raw 101 bp reads were trimmed to remove low quality base pairs (Phred quality score < 20), reads with few contiguous high-quality base pairs (fewer than 30 bp) using a python script.
python script (http://genomics-pubs.princeton.edu/prv/resources/scripts/TQSfastq.py)
Adapter sequences were trimmed using the program cutadapt (https://cutadapt.readthedocs.io/en/stable/).
To evaluate the quality of the trimmed reads, we ran FastQC (Andrew, 2010) using TACC (Texas Advanced Computing, The University of Texas at Austin).
Reads were pseudoaligned to the Sailfin molly Poecilia latipinna (assembly GCA_001443285.1, retrieved from Ensembl January 2019) with Kallisto (version 0.43.0) using the single-end reads option with a length of 100bp (-l 100), standard deviation of 20 (-s 20).
Assembly: GCA_001443285.1
Supplementary files format and content: tab-delimited Kalisto abundance text files include estimated counts and transcripts per million

organism: Poecilia latipinna

source_name: whole brain

growth_protocol: Fish were maintained in semi-natural on-campus outdoor ponds at the Brakenridgen Field Laboratory at the University of Texas, Austin

extract_protocol:
Immediately following the 30-minute behavioral trial, focal females were immediately decapitated, whole brains were removed and individually immersed in RNAlater solution (Applied Biosystems, Carlsbad, CA, USA) at 4˚ Celsius with gentle shaking for 24 hours, then stored at -80 C (without RNAlater) for subsequent RNA profiling. 1-4 μg of total RNA were used as input for RNA library preparation and sequencing.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq mRNA Sample Prep Kit.

treatment_protocol: Sexually experienced P. latipinna females were collected from a semi-natural environment and socially isolated for two weeks to ensure sexual receptivity. Each female was subjected to short-term (30min) non-contact dichotomous choice assays. Females were randomly assigned to one of two social choice treatment groups (mate preference with male stimuli to female shoaling partner with female stimuli) without a non-social control. Focal females made preference decisions based on stimuli size differences in both treatments.Each focal female was acclimatized in an opaque cylinder for 5 minutes in the central neutral zone before being released. Following release from habituation, focal females were observed for 15 minutes and position and behavior in tank recorded.  After the first 15 minutes of observations, focal females were brought back to the neutral area and placed in the opaque habituation cylinder while the stimulus fish were switched to opposite sides to ensure that our preference measures were directed at a specific fish rather than a location preference in our experimental tank. Following the stimulus switch, focal females were observed for an additional 15 minutes.

value: whole brain

tag: preference behavior

value: Ff social context


title: female Poecilia latipinna 13, whole brain, Mm treatment

value: Mm mate choice context


title: female Poecilia latipinna 11, whole brain, Mm treatment