title: hxk2 ko_TCM+cAMP_Rep3

city: Hyderabad

first: Sriram

last: Varahan

state: Telangana

address: Habsiguda

department: Microbes and biology of infection

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

description: Library name: hxk2 ko_TCM+cAMP_Rep3

data_processing:
The reference genome was indexed with Hisat2 (v 2.2.1), and Samtools (v 1.20) was used to filter out multi-mapped reads and convert SAM files to BAM format. Read counting for uniquely mapped reads was done with FeatureCounts, using gene annotation data from the reference C. neoformans var. grubii H99 genome.
Normalization and differential gene expression analysis were performed using R (v 4.3.2). Genes with a log2 fold change of ≥ 1 were considered to be upregulated, indicating at least a doubling in expression under the given condition, while those with a log2  fold change of ≤ -1 were considered to be downregulated.
ASM14924v2 (Cryptococcus neoformans var. grubii H99)
Assembly: Tab-delimited text file containing raw gene counts for each sample
Supplementary files format and content: Tab-delimited text files containing DESeq2 differential gene expression results for the H99 vs. hxk2Δ and H99 vs. hxk2Δ + cAMP comparisons.

organism: Cryptococcus neoformans

source_name: Fungal cell

growth_protocol: Wild-type,  hxk2Δ (with and without exogenous supplementation of cAMP) strains of C. neoformans were cultured in TCM at cell density of 106 CFU per ml for 24 hours at 37 °C under 5% CO2.

extract_protocol:
RNA libraries for RNA-seq were prepared using Qiagen Yeast depletion kit and Illumina Standard Total RNA kits following manufacturer's protocols.
Raw sequencing reads were obtained in FASTQ format. The reference genome and annotation files for the C. neoformans var. grubii H99 were downloaded from the NCBI site (Sample ID: SAMN03081441). Quality assessment of the raw reads was performed using FastQC (v 0.12.1). Adapter sequences were trimmed using Cutadapt (v 5.2).

treatment_protocol: Total RNA was isolated from cells harvested after 24 hours of incubation using the hot acid-phenol method. For cell disruption, zirconium beads were used with a bead-beating protocol consisting of 10-second pulses interspersed with 1-minute rests on ice to prevent thermal degradation.

value: Fungal cell

tag: genotype

value: HXK2 knockout

tag: treatment

value: Growth in titan cell inducing medium supplemented with cAMP


title: Rpl41 KO mouse kidney RNA-seq replicate 1

status: Public on Jul 27 2026

type: SRA

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

description: Library name: Sample 66

library_source: transcriptomic

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: HEK293T cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
Extract protocol for RNA-seq Total RNA was extracted from cell lysates with the use of a PureLink RNA Mini Kit (Thermo Fisher Scientific), and the quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent). Extract protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay For the harringtonine run-off assay, cells were treated with 2 μg/ml harringtonine (MedChemExpress) at 37 °C for 60, 120, or 180 s, followed by treatment with 100 μg/ml cycloheximide for 1 minute to halt translation. Cells were then immediately harvested. Cell and tissue lysate supernatants were assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen) to a concentration of 20 U/ml. The samples were then loaded on a 1 M sucrose cushion (containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)), and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. Ribosome footprints were purified using ISOGEN (Fujifilm). The recovered RNA was size-selected by electrophoresis on a 15% polyacrylamide TBE–urea gel (SuperSep RNA, Fujifilm), isolating fragments of 17–34 nucleotides for Ribo-seq and 50–80 nucleotides for Disome-seq. Extract protocol for SLAM-seq To label newly synthesized RNA, cells were incubated for 24 h in culture medium containing 50 μM 4-thiouridine (4sU, Merck). The medium was then replaced with fresh medium containing 50 μM uridine, and cells were harvested at 0, 3, 6, 12, and 24 h after the switch. Total RNA was extracted using ISOGEN (NIPPON GENE) according to the manufacturer’s instructions.
Library construction protocol for RNA-seq For RNA-seq, after mRNA selection via the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), and the libraries were sequenced with a NovaSeq (Illumina). Library construction protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina). Library construction protocol for SLAM-seq The purified RNA was alkylated by adding iodoacetamide (IAA) to a final concentration of 10 mM, followed by incubation at 50 °C for 15 min. The reaction was quenched by adding DTT to a final concentration of 20 mM. RNA was then purified, and libraries were prepared using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit (Forward) with Unique Dual Indices (12 nt) (Lexogen). Sequencing was performed on a NovaSeq platform (Illumina).

tag: cell line

value: Kidney


title: VPA_326_C5_H_R1

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Library name: Sample 127
raw cell lysate and Illumina NextSeq 2126

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: 260722_count_table_GEO.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

molecule: total RNA

organism: Homo sapiens

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRG cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRG cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 10e6 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRG Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRG Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building.
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRG cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70C followed by a temperature gradient with a ramp rate of 0.5C/min to 45C over a 50 min period, followed by a nuclease digestion at 37C for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37C, immediately followed with a 15 min enzyme denaturation at 80C to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37C for 10 min, 95C for 2 min; 6 cycles of 95C for 30 sec, 54C for 30 sec, 72C for 120 sec; 16 cycles of 95C for 30 sec; 72C for 2 min; 72C for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRG Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to trichostatin A ( 0.018811, 0.056433, 0.1693, 0.5079, 1.5237 µM), panobinostat (0.001468, 0.004403, 0.01321, 0.03963, 0.084 µM), valproic acid (0.100478, 0.301433, 0.9043, 2.7129, 3.038 µM), mocetinostat (0.177222, 0.531667, 1.595, 2.5, 3.9 µM), apicidin (0.041722, 0.125167, 0.3755, 0.5, 0.86 µM), tacedinaline (1.143333, 3.43, 10.29, 30.87, 44 µM), scriptaid  (4.94, 14.82, 44.46, 60, 94.5 µM), vorinostat (0.404778, 1.214333, 3.643, 10.929, 23.5 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

tag: tissue

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

value: VPA

tag: chemical longname

tag: dose

tag: well

tag: dose group

tag: plate

value: H

tag: index

value: TCAGCTAAT

value: GCTGCGTAT

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: hxk2 ko_TCM+cAMP_Rep2

description: Library name: hxk2 ko_TCM+cAMP_Rep2

tag: genotype


title: WT mouse kidney RNA-seq replicate 3

description: Library name: Sample 65


title: VPA_303_C4_H_R3

description:
Library name: Sample 126
raw cell lysate and Illumina NextSeq 2125

value: liver tumor associated with chronic hepatitis C

value: ATCGCGACT

value: TAAGTTACG


title: FE-4602-7-START

city: New York

first: Ezequiel

middle: Carlos

last: Dantas

state: Y

address: 550E First Street

country: USA

institute: NYU Langone

data_processing:
Read alignments were done using Galaxy (https://usegalaxy.org/), where paired-end FASTQ files were processed with Cutadapt for adapter removal.
Reads were mapped using STAR (2-pass mapping) with the GENCODE v43 basic annotation was performed on genome assembly GRCh38 (hg38).
Counts were obtained with featureCounts, and quality control was performed with FastQC and MultiQC
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Fixated Whole Blood

extract_protocol:
Total RNA was extracted from fixed whole blood using Qiagen PAXgene Blood RNA Kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA quality control was performed using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina.Enriched RNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized and fragments were end-repaired and adenylated at 3’ends.  Universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Sugar


title: hxk2 ko_TCM+cAMP_Rep1

description: Library name: hxk2 ko_TCM+cAMP_Rep1

tag: cell type

value: Fungal cell

value: HXK2 knockout

tag: treatment


title: WT mouse kidney RNA-seq replicate 2

description: Library name: Sample 64

tag: cell line

value: Kidney


title: FE-4602-7-POS

tag: tissue

value: POS

value: Post randomization


title: VPA_330_C4_H_R2

description:
Library name: Sample 125
raw cell lysate and Illumina NextSeq 2124

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: VPA

tag: chemical longname

tag: dose

tag: well

value: TAGCGACAA

value: AATAGGTGC


title: hxk2 ko_TCM_Rep3

description: Library name: hxk2 ko_TCM_Rep3

value: Growth in titan cell inducing medium


title: FE-3675-2-START

value: VLCD


title: WT mouse kidney RNA-seq replicate 1

description: Library name: Sample 63


title: VPA_326_C4_H_R1

description:
Library name: Sample 124
raw cell lysate and Illumina NextSeq 2123

value: liver tumor associated with chronic hepatitis C

tag: dose group

tag: plate

value: H

tag: index

value: TGCTTATTC

value: GCTGCGTAT

tag: group

value: test


title: hxk2 ko_TCM_Rep2

description: Library name: hxk2 ko_TCM_Rep2

value: Fungal cell


title: FE-3675-2-POS

value: Fixated Whole Blood


title: Rpl41 KO mouse kidney Ribo-seq replicate 3

description: Library name: Sample 62

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Library strategy: Ribo-Seq

value: Kidney


title: VPA_303_C3_H_R3

description:
Library name: Sample 123
raw cell lysate and Illumina NextSeq 2122

value: TGGAACGCT

value: TAAGTTACG

tag: replicate

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: hxk2 ko_TCM_Rep1

description: Library name: hxk2 ko_TCM_Rep1

tag: genotype

value: HXK2 knockout


title: FE-3671-5-START

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Sugar


title: VPA_330_C3_H_R2

description:
Library name: Sample 122
raw cell lysate and Illumina NextSeq 2121

tag: tissue

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

value: VPA

value: GCTATCGAT

value: AATAGGTGC


title: H99_TCM_Rep3 (Control)

description: Library name: H99_TCM_Rep3

value: Wild-type (H99)

tag: treatment

value: Growth in titan cell inducing medium


title: FE-3671-5-POS

value: POS

value: Post randomization


title: Rpl41 KO mouse kidney Ribo-seq replicate 2

description: Library name: Sample 61


title: Rpl41 KO mouse kidney Ribo-seq replicate 1

description: Library name: Sample 60


title: VPA_326_C3_H_R1

description:
Library name: Sample 121
raw cell lysate and Illumina NextSeq 2120

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

tag: dose

tag: well

value: H

value: ATTCGAATC

value: GCTGCGTAT

value: test


title: H99_TCM_Rep2 (Control)

description: Library name: H99_TCM_Rep2

value: Fungal cell


title: FE-3239-3-START

value: Fixated Whole Blood

value: START

value: Before randomization

value: VLCD


title: H99_TCM_Rep1 (Control)

description: Library name: H99_TCM_Rep1


title: WT mouse kidney Ribo-seq replicate 3

description: Library name: Sample 59

value: Kidney


title: WT mouse kidney Ribo-seq replicate 1

description: Library name: Sample 57


title: WT mouse kidney Ribo-seq replicate 2

description: Library name: Sample 58


title: VPA_303_C2_H_R3

description:
Library name: Sample 120
raw cell lysate and Illumina NextSeq 2119

value: HepaRG

value: liver progenitor cells

value: VPA

tag: dose group

tag: plate

tag: index

value: GATAGCGGA

value: TGCCGGTAT

tag: group


title: FE-3239-3-POS

value: POS

value: Post randomization


title: Cervical lymph node-live_attenuated_vaccine-rep-3

city: Daejeon

first: Woohyun

last: Kwon

address: expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: Sample_Li3
10x Genomics

library_source: transcriptomic single cell

data_processing:
10x genomics Cell Ranger (version 8.0.1)
Assembly: ASM1176430v1.1 combined with H5N1 influenza GA/W22-145E isolate
Supplementary files format and content: matrix files

organism: Mustela putorius furo

source_name: Cervical lymph node

extract_protocol:
Male influenza-seronegative ferrets (16-18 weeks old, INSCIENCE) were immunized under anesthesia with either LAIV (106 TCID50/ml) via the intranasal route or a killed vaccine (15 mg) administered intramuscularly. Two weeks after the primary immunization, only the killed-vaccine group received a homologous booster dose. Ferrets were intranasally challenged with A/Lesser Scaup/Georgia/W22-145E/2022 (H5N1, clade 2.3.4.4b) at a dose of 105.5 TCID50/ml (PMID: 41004584). For scRNA-seq, cervical lymph nodes were collected from two ferrets per group at 5 days post-infection (dpi) for single-cell RNA sequencing.
10x Genomics Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3.1 (PN-1000121; 10X Genomics)

value: Cervical lymph node

value: Live attenuated vaccine


title: VPA_330_C2_H_R2

description:
Library name: Sample 119
raw cell lysate and Illumina NextSeq 2118

value: liver tumor associated with chronic hepatitis C

value: H

value: ATTGGTTGC

value: AATAGGTGC

tag: replicate

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: FE-3169-1-START

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

tag: diet group


title: Postnatal Day10, Pax7 Progeny cells3

city: Paris

first: Takuto

last: HAYASHI

address: 160 Rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

description: Library name: Sample3-3/4

data_processing:
feature-barcode matrices were generated by aligning the reads to the mouse genome (mm10 Ensemble: version 92) with CellRanger v8.0.1.
Assembly: mm10
Supplementary files format and content: The Cell Ranger output includes three files: features.tsv, barcodes.tsv, and matrix.mtx, which together represent the gene expression count matrix. The matrix contains UMI counts for each gene (features) in each cell (barcodes)., For 10X genomics: data processing pipeline Cell Ranger version 8.0.1 Data analysis for 10X genomics using Seurat version 5.2.2

molecule: nuclear RNA

source_name: Skeletal muscle

extract_protocol:
Approximately 10,000 cells were processed using the Chromium Next GEN Single Cell 3’Reagent Kits v3.1
RNA libraries were prepared using a chromium controller from10X Genomics, according to the manufacturer’s instructions.

tag: tissue

value: Skeletal muscle

tag: cell type

value: Pax7 progeny

tag: genotype

value: Pax7CreERT2; Rosa26HTB::GFP

value: Two administrations of tamoxifen were performed starting two days prior to sampling.


title: Cervical lymph node-live_attenuated_vaccine-rep-2

description:
Library name: Sample_Li2
10x Genomics

tag: treatment


title: MDS_AZA_007

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

library_source: genomic

data_processing:
Reads were trimmed using Trim Galore (version 0.6.2) and aligned to a bisulfite-converted human genome (hg19) using Bowtie2 and Bismark (versions 2.4.1 and 0.23.1, respectively).
After strand collapsing and filtering by coverage (keep loci with reads between 10-400), methylation loci were tiled by window (25bp) and a methylDiff object was created using MethylSig (version 1.5.0) for regions that were present in at least 3 samples per group.
Significant differentially methylated regions (DMRs) were identified as those with an absolute mean methylation difference of ≥ 25 and a DMR q-value of ≤ 0.05.
Assembly: hg19
Supplementary files format and content: genome-wide cytosine report output from bismark
Supplementary files format and content: tab-delimited text files include base-pair resolution information of the read strand and coverage of the methylated and unmethylated Cs in the sequenced DNA for each Sample

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
For the isolation of CD34+ cells from human bone marrow samples, we utilized the Miltenyi MACS magnetic bead purification kit. In a nutshell, 2 mL frozen vials of human mononuclear cells (MNC) were thawed at 37°C, followed by treatment with 200 µL of DNase-I (Roche) at a concentration of 1 mg/mL for 90 seconds. Subsequently, the cells were gently resuspended in Iscove's Modified Dulbecco's Medium (IMDM) containing 40% fetal bovine serum (FBS) to minimize primary human cell mortality. All centrifugation steps were performed at 1500 rpm. After an 8-minute centrifugation, the cells were resuspended in 15 mL of MACS buffer and then incubated with magnetic beads for 50 minutes at 4°C. Following three consecutive washes with MACS buffer (each for 10 minutes at 4°C), the cells were resuspended in 6 mL of MACS buffer and passed through an AUTOMACS instrument using the Posseld program. After another 8-minute centrifugation at 4°C, the cells were resuspended in RTL buffer with beta-mercaptoethanol. DNA and RNA were extracted from the CD34+ fraction using the AllPrep Micro kit (QIAGEN), while the CD34+ depleted fraction was processed with the AllPrep Mini kit.
Prior to adapter ligation, the methylated adapters were diluted to a concentration of 150 nmol/L. During the gel size selection step, fragments falling within the range of 150 to 450 base pairs were excised from the gel.

value: Bone marrow

tag: cell line

tag: individual

value: MDS patient

tag: age

tag: Sex

value: Male

tag: responder

value: NonResp


title: VPA_326_C2_H_R1

description:
Library name: Sample 118
raw cell lysate and Illumina NextSeq 2117

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: VPA

tag: chemical longname

tag: dose

tag: well

tag: dose group

tag: plate

tag: index

value: GATAGCGGA

value: ATGGTTAGA

tag: group

value: test


title: VPA_303_C1_H_R3

description:
Library name: Sample 117
raw cell lysate and Illumina NextSeq 2116

tag: tissue

value: liver tumor associated with chronic hepatitis C

value: H

value: AGCCGATTA

value: TGCCGGTAT

tag: replicate

tag: chemical type

tag: cas-nr

tag: batch nr_heparg


title: Rpl41 KO mouse brain RNA-seq replicate 3

description: Library name: Sample 56

source_name: Brain

tag: cell line

value: Brain


title: Cervical lymph node-live_attenuated_vaccine-rep-1

description:
Library name: Sample_Li1
10x Genomics

value: Cervical lymph node

tag: treatment

value: Live attenuated vaccine


title: VPA_330_C1_H_R2

description:
Library name: Sample 116
raw cell lysate and Illumina NextSeq 2115

tag: cell type

value: TGATTAAGC

value: AATAGGTGC


title: Cervical lymph node-Inactivated_vaccine-rep-3

description:
Library name: Sample_k3
10x Genomics

value: Inactivated vaccine


title: FE-3105-8-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: Starch


title: FE-3169-1-POS

value: VLCD


title: Rpl41 KO mouse brain RNA-seq replicate 1

description: Library name: Sample 54


title: FE-2982-6-START

value: START

value: Before randomization


title: Cervical lymph node-Inactivated_vaccine-rep-2

description:
Library name: Sample_k2
10x Genomics


title: WT mouse brain RNA-seq replicate 3

description: Library name: Sample 53


title: Rpl41 KO mouse brain RNA-seq replicate 2

description: Library name: Sample 55


title: FE-3105-8-START


title: Cervical lymph node-Inactivated_vaccine-rep-1

description:
Library name: Sample_k1
10x Genomics


title: VPA_326_C1_H_R1

description:
Library name: Sample 115
raw cell lysate and Illumina NextSeq 2114

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: VPA

tag: chemical longname

tag: dose

value: ATGGTTAGA

value: test


title: TSA_303_C5_H_R3

description:
Library name: Sample 114
raw cell lysate and Illumina NextSeq 2113

value: TSA

tag: well

tag: dose group

tag: plate

value: H

value: ATTCGAATC

value: TGCCGGTAT


title: WT mouse brain RNA-seq replicate 2

description: Library name: Sample 52

value: Brain


title: TSA_330_C5_H_R2

description:
Library name: Sample 113
raw cell lysate and Illumina NextSeq 2112

tag: tissue

tag: index

value: ACCTGAGGC

value: TGTAACGGC

tag: group


title: FE-2982-6-POS

value: Fixated Whole Blood

value: POS

value: Post randomization

value: Starch


title: HCR voluntary-running aged soleus RNA-seq He2

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: UPL26-002514
Aged female rat soleus muscle; group=HCR + Exercise; original sample name=He 2; count matrix column=UPL26-002514.

data_processing:
Raw reads were assessed using FastQC and MultiQC.
The first six nucleotides of each read were extracted as unique molecular identifiers using UMI-tools.
Reads were trimmed using Cutadapt to remove library-derived bases, Illumina adapters, poly(A) tails, ambiguous bases, and low-quality sequences.
Trimmed reads were aligned to the rat mRatBN7.2 reference genome using STAR, and coordinate-sorted BAM files were generated.
PCR duplicates were removed using UMI-tools, and gene-level counts were obtained from deduplicated BAM files using featureCounts in stranded mode.
Assembly: mRatBN7.2 (Rattus norvegicus; rn7)
Supplementary files format and content: gene_count_matrix_clean.tsv is a tab-delimited text file containing raw gene-level counts generated by featureCounts from UMI-deduplicated BAM files. Rows correspond to genes (Geneid) and columns correspond to RNA-seq libraries UPL26-002492 through UPL26-002517.

organism: Rattus norvegicus

source_name: soleus muscle

growth_protocol: Selectively bred low- and high-running-capacity rats (LCR and HCR; 44th generation) were used. Female rats were housed in temperature-controlled rooms under a 12:12 h light-dark cycle with ad libitum access to standard chow and water.

extract_protocol:
Rats were deeply anesthetized, and soleus muscle samples were rapidly excised, snap-frozen, and stored at -80 C. Total RNA was extracted from soleus muscle using the Quick-RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer's instructions.
RNA-seq libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD v2 for Illumina (Lexogen). Briefly, 100 ng of total RNA was used for first-strand cDNA synthesis using an oligo(dT) primer, followed by RNA removal. Second-strand synthesis was initiated by random priming, and products were purified using magnetic beads. Libraries were amplified and barcoded by PCR, quality assessed using an Agilent 4200 TapeStation, and sequenced to generate single-end reads.

treatment_protocol: Sedentary LCR and HCR animals were maintained without wheel access. For the voluntary exercise cohort, female rats were pair-housed in cages equipped with a running wheel for more than five months.

value: soleus muscle

tag: genotype

value: selectively bred HCR rat

value: voluntary wheel running


title: MDS_AZA_086

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts  files

extract_protocol:
RNA extracted from the CD34+ fraction was employed for RNA-seq. To guarantee RNA quality, Tapestation was utilized prior to library preparation. The RNA was treated with Illumina Ribo-Zero
For library preparation, we used the Nugen Ovation Solo RNA-seq ultra-low input kit, following the manufacturer's instructions. Subsequently, the prepared libraries were sequenced on an Illumina NextSeq platform. These libraries were paired-end and they were strand-specific.

value: Bone marrow

tag: individual

value: MDS patient

tag: age

tag: Sex

value: Female

tag: responder

value: Responder


title: FE-2635-2-START

tag: timepoint

value: START

value: Before randomization

value: Sugar


title: MDS_AZA_089

tag: cell line

value: Male


title: WT mouse brain RNA-seq replicate 1

description: Library name: Sample 51

value: Brain


title: TSA_326_C5_H_R1

description:
Library name: Sample 112
raw cell lysate and Illumina NextSeq 2111

value: liver tumor associated with chronic hepatitis C

value: HepaRG

tag: cell type

value: liver progenitor cells

value: TSA

value: H

value: TCAGCTAAT

value: ATGGTTAGA

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: BHK-21 4 days 4C no rewarm rep3

city: Cambridge

first: Tara

last: Thakurta

state: MA

address: 455 Main Street

institute: Whitehead Institute

description:
Library name: L511_172
core WO6; count-matrix column WO06

data_processing:
Read alignment with STAR v2.7.1a (paired-end; --outSAMtype BAM SortedByCoordinate).
Gene-level read quantification with featureCounts (Subread).
Differential expression analysis with DESeq2 (R).
Assembly: Human (K562): GRCh38, Ensembl release 93 (Homo_sapiens.GRCh38.93.canonical). Hamster (BHK-21): BCM_Maur_2.0, GCF_017639785.1 (Mesocricetus auratus).
Supplementary files format and content: Tab-delimited gene-level raw count matrices (genes x samples): BHK21_featureCounts.matrix.txt (hamster BHK-21, 6 samples) and K562_raw_counts.matrix.txt (human K562, 9 samples). DESeq2 differential expression result tables (cold vs 37 C) are provided as supplementary processed files.

organism: Mesocricetus auratus

growth_protocol: Cell lines were maintained at 37 C, 5% CO2, and 95% relative humidity.

extract_protocol:
Cell pellets were lysed and homogenized using QIAshredder columns (Qiagen), and RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion, according to the manufacturer's instructions.
Libraries were prepared using the NEBNext Ultra II kit. In brief, 1 ug of RNA per sample underwent Poly(A) selection before fragmentation and random priming followed by first- and second-strand complementary DNA synthesis. Following cDNA synthesis, NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB E6441A) were ligated before PCR enrichment. All libraries were pooled to a final concentration of 2 nM and sequenced on a NovaSeq 6000.

treatment_protocol: For cold exposure experiments, cells were subsequently transferred to 4 C for up to 5 days. At the time of collection, cells were collected (with gentle scraping for adherent BHK-21 lines) and pelleted by centrifugation. Per-sample timepoints are given in the treatment column.

tag: treatment

value: 4 days 4C no rewarm


title: MDS_AZA_090

value: Bone marrow

value: MDS patient


title: FE-2635-2-POS

value: Fixated Whole Blood

value: POS

tag: randomization

value: Post randomization

tag: diet group


title: 4_HKM7VBGXT.4.CCTAAGAC_TATGCAGT

status: Public on Jul 28 2026

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 4_SM-NBW8A_plate1
DHMT_48hr_LDLR_A_a

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

value: iPSC-derived excitatory neuron, astrocyte

value: LDLR knockdown

tag: day

tag: guide rna

tag: barcode


title: BHK-21 4 days 4C no rewarm rep2

description:
Library name: L511_171
core WO5; count-matrix column WO05


title: BHK-21 4 days 4C no rewarm rep1

description:
Library name: L511_170
core WO4; count-matrix column WO04


title: Rpl41 KO mouse brain Ribo-seq replicate 3

description: Library name: Sample 50

value: Brain


title: TSA_330_C4_H_R2

description:
Library name: Sample 111
raw cell lysate and Illumina NextSeq 2110

tag: tissue

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

tag: dose

tag: well

tag: dose group

tag: plate

tag: index

value: TAGCGACAA

value: TGTAACGGC

tag: group


title: FE-2609-6-POS

tag: timepoint

value: VLCD


title: BHK-21 37C before cold rep2

description:
Library name: L511_168
core WO2; count-matrix column WO02

tag: cell line

value: 37C before cold


title: Rpl41 KO mouse brain Ribo-seq replicate 2

description: Library name: Sample 49


title: FE-2609-6-START

value: START

value: Before randomization


title: BHK-21 37C before cold rep3

description:
Library name: L511_169
core WO3; count-matrix column WO03

tag: treatment


title: TSA_303_C3_H_R3

description:
Library name: Sample 109
raw cell lysate and Illumina NextSeq 2108

value: HepaRG

tag: cell type

value: liver progenitor cells

value: TSA

value: H

value: TGGAACGCT

value: TGCCGGTAT

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: TSA_326_C4_H_R1

description:
Library name: Sample 110
raw cell lysate and Illumina NextSeq 2109

tag: tissue

value: TGCTTATTC

value: ATGGTTAGA


title: FE-2522-2-START

value: Fixated Whole Blood

tag: randomization

tag: diet group

value: Starch


title: Rpl41 KO mouse brain Ribo-seq replicate 1

description: Library name: Sample 48

value: Brain


title: WT mouse brain Ribo-seq replicate 3

description: Library name: Sample 47


title: WT mouse brain Ribo-seq replicate 2

description: Library name: Sample 46


title: FE-2416-4-START


title: HUB-FT-s008

city: Utrecht

first: Iris

last: Gooijers

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: Sample 6

data_processing:
FASTQ files were processed in three sequential steps: adapter trimming and homopolymer removal with Cutadapt (version 4.7) followed by ribosomal RNA filtering with RiboDetector (version 0.3.1). The processed FASTQ files were then aligned to the zebrafish (DanioRerio) GRCz11 reference genome using STARsolo (v2.7.11b). Gene expression count tables were generated with STARsolo by including intronic reads and excluding multigene reads. The resulting count tables were Poisson-corrected and combined across the six SORT-seq plates before being incorporated into a Seurat object and provided as the processed data file.
Assembly: DanioRerio, GRCz11 ENSEMBL release 109 using STARsolo (2.7.11b)
Supplementary files format and content: Format = RDS (R serialized Seurat object); Content = Seurat object containing processed scRNA-seq data for 2304 cells and 27863 genes. Includes RNA assay with six count layers (counts.1-counts.6) and associated cell metadata.

organism: Danio rerio

source_name: Heart

extract_protocol:
Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on myl7:PercevalHR expression in 384 well plates, each well containing 1 cell, containing Vapor-Lock oil with CEL-Seq2 barcoded primers, spike-in mRNA and dNTPs (Single Cell Discoveries). Plates were spun down and frozen at -80oC until ready for library prep.
Single-cell sequencing libraries were prepared by Single Cell Discoveries (Utrecht, The Netherlands) using the SORT-seq protocol. The CEL-Seq2 protocol was used for library prep (Hashimshony et al., 2016)). Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the NovaSeq X Plus Illumina sequencer. In total six 384-well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and three from plna R14del mutant cells.

value: Heart

tag: genotype

value: plna R14del

value: one year

tag: batch


title: TSA_303_C2_H_R3

description:
Library name: Sample 106
raw cell lysate and Illumina NextSeq 2105

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

tag: dose

tag: well

tag: dose group

value: GATAGCGGA

value: AACACAATC


title: NC_1

city: Shanghai

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

country: China

institute: Shanghai First Maternity and Infant Hospital

description: Library name: NC_1

data_processing:
Raw sequencing fastq files stored in Rawdata folder were quality-controlled using FastQC, and low-quality reads/adapters were trimmed by Trim Galore. BigWig coverage signal files normalized by RPM were generated from BAM files and deposited in Bigwig folder for genome browser visualization.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Raw data: gzipped FASTQ paired-end files, deposited under Rawdata directory, containing original sequencing reads for NC and shCHI3L1 replicate samples. Processed data: normalized BigWig files in Bigwig directory, presenting genome-wide read density signal for each sample.

extract_protocol:
Total RNA was extracted from NC (negative control shRNA) and shCHI3L1 knockdown SKOV-3 human ovarian cancer cell lines using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was assessed using Agilent 2100 Bioanalyzer (RIN value ≥7.0 for all samples), and RNA concentration was quantified by Qubit fluorometer. Genomic DNA contamination was removed by DNase I digestion before subsequent library construction.
mRNA was enriched from qualified total RNA using oligo (dT) magnetic beads. Fragmentation buffer was added to interrupt mRNA into short fragments. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, A-tailing and adapter ligation, fragments with suitable size were purified, PCR amplified to construct the final cDNA library. Paired-end sequencing was performed on Illumina sequencing platform.

tag: cell line

value: human ovarian cancer cells


title: BHK-21 37C before cold rep1

description:
Library name: L511_167
core WO1; count-matrix column WO01

tag: treatment

value: 37C before cold


title: MDA-MB-231 siBYSL biological replicate 2

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

institute: The Second Hospital of Dalian Medical University

description:
Library name: MDA_MB_231_siBYSL_2
MDA-MB-231 cells transfected with SI-BYSL-Homo-838; biological replicate 2.

data_processing:
Adapters, random bases introduced for library balancing, and low-quality sequence were removed from raw reads to generate clean reads.
Clean paired-end reads were aligned to the Homo sapiens GRCh38.p13 reference genome with HISAT2 using Gencode release 38 comprehensive gene annotation.
Gene-level unnormalized read counts and FPKM expression values were generated for annotated genes. The submitted processed matrix contains complete gene-level raw read counts for all six libraries.
Differential expression analysis between siBYSL and siNC groups was performed using DESeq2.
Assembly: GRCh38.p13; Gencode release 38
Supplementary files format and content: Tab-delimited matrix containing gene-level unnormalized raw read counts for all six RNA-seq libraries.
Supplementary files format and content: Rows are identified by Gencode v38 gene accessions and include gene symbol, chromosome, gene type, and description. Sample column headers exactly match the corresponding sample library names.

growth_protocol: MDA-MB-231 human breast cancer cells (Procell, CL-0150A; STR authenticated) were maintained in high-glucose DMEM (Procell, PM150210) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 micrograms/mL streptomycin at 37 degrees C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIZOL (Ambion, 15596-018), further purified by phenol-chloroform extraction, and treated with RQ1 DNase (Promega, M6101) to remove DNA. RNA purity and quantity were assessed spectrophotometrically, and integrity was verified by 1% agarose gel electrophoresis.
For each sample, 1 microgram total RNA was treated with RQ1 DNase. Poly(A)+ mRNA was captured using VAHTS mRNA Capture Beads (Vazyme, N401). Directional libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) and VAHTS RNA Multiplex Oligos Set 1 for Illumina (Vazyme, N323). The dUTP-marked second cDNA strand was not amplified, enabling strand-specific sequencing. Libraries were sequenced as 150-nt paired-end reads on an Illumina NovaSeq X Plus system.

treatment_protocol: Cells were seeded at 1.8 x 10^5 cells per well in 12-well plates. Negative-control siRNA or SI-BYSL-Homo-838 (sense 5'-GAGAUGACGUUGCUGAAUATT-3'; antisense 5'-UAUUCAGCAACGUCAUCUCTT-3') was transfected at 160 pmol per well using 4 microliters Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778030). Medium was replaced 6 h after transfection and cells were harvested 48 h after transfection.

value: siRNA-mediated BYSL knockdown using SI-BYSL-Homo-838


title: TSA_330_C2_H_R2

description:
Library name: Sample 105
raw cell lysate and Illumina NextSeq 2104

value: HepaRG

tag: cell type

value: liver progenitor cells

value: TSA

tag: plate

value: H

tag: index

value: ATTGGTTGC

value: TGTAACGGC

tag: group


title: TSA_330_C3_H_R2

description:
Library name: Sample 108
raw cell lysate and Illumina NextSeq 2107

value: GCTATCGAT

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: HFpEF_2

city: Suita

first: Manami

last: Katoh

state: Osaka

address: 6-1 Kishibe-simmachi

department: Department of Heart Failure Pathophysiology  and Therapeutics

institute: National Cerebral and Cardiovascular Center Research Institute

description:
Library name: Sample4
10× Genomics

data_processing:
Raw FASTQ files were processed for each sample using the Cell Ranger software (version 9.0.0, 10× Genomics), against the Cell Ranger GRCm39 mouse reference genome.
Raw mapped counts were used as the input for data processing with the Seurat R package (version 5.2.1).
To exclude ambient RNA contamination, the data were processed using CellBender.
We removed cells with detected genes <1000, detected counts <2000 and >30000, and mitochondrial gene content > 5%.
Following the filtering step, we normalized the read counts using the ‘NormalizeData’ function (10,000 default scale factor), separately for each dataset.
Assembly: GRCm39 mouse reference genome
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz

extract_protocol:
10000 nuclei were prepared to a concentration of 1,000 nuclei/µL and loaded into the Chromium Controller (10× Genomics) and single-cell cDNA libraries were generated using a Chromium GEM-X Single cell 3′ v4 Chemistry Kit (PN-1000691, 10× Genomics).
Libraries were sequenced on a NovaSeq 6000 System, using the NovaSeq S4 Reagent Kit (20027466, Illumina).

tag: tissue

value: Heart

tag: genotype

value: HFpEF mouse model


title: HUB-FT-s004

description: Library name: Sample 4

value: plna R14del

value: one year

tag: batch


title: ASD mouse PFC snRNA-seq [L68P_HvF_2 + L68P_HfF_2 + K5B_HvM_2 + K5B_HfM_2] (4-plex OCM)

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

description:
Library name: 1211-1
10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing; demultiplexed in silico via Cell Ranger multi

data_processing:
Per-library FASTQ files were demultiplexed in silico into the four constituent mice using the Cell Ranger multi pipeline (10x Genomics), with mouse-specific reads assigned via OCM barcodes and aligned to the mouse reference genome to generate per-nucleus gene count matrices.
Downstream processing was performed in Seurat v5.0. Low-quality nuclei were filtered (<750 or >8000 detected genes, <1000 or >30000 UMI counts, >5% mitochondrial reads). Top 3000 highly variable genes per sample were used; expression values were normalised and scaled.
Principal component analysis was performed and sequencing-batch effects were corrected with Harmony. Visualisation used UMAP and clustering used a shared nearest-neighbour graph at resolution 0.3.
Clusters were annotated by reference-based label transfer using Seurat MapQuery against the Allen Brain Cell Atlas scRNA-seq reference (GSE246717; 3 donors, 64,409 isocortex cells, 12 cell classes), followed by manual curation. The 19 clusters were mapped to 10 major cell classes.
Relative cell-class proportions were computed per mouse, stratified by genotype, sex, treatment, and Group 1 / Group 2 transcriptomic class.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Each GSM (tube) is associated with four per-sample MEX triplets (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) produced by Cell Ranger multi `per_sample_outs/`, one set per multiplexed mouse. File naming convention: <mouse_id>__barcodes.tsv.gz, <mouse_id>__features.tsv.gz, <mouse_id>__matrix.mtx.gz (double underscore between mouse_id and file type).
Supplementary files format and content: 10x Genomics Chromium GEM-X Universal 3' v4 with 4-plex On-Chip Multiplexing (OCM). Four mouse-specific nuclei suspensions per GEM well; demultiplexed in silico via Cell Ranger multi. OCM barcodes are hardware-encoded in the chip (not antibody-based CMO/HTO), so feature_reference.csv is not applicable. Mouse <-> OCM-slot mapping per tube is provided in mouse_to_pool.tsv.

source_name: prefrontal cortex

growth_protocol: All mice were housed under a 12 h light/dark cycle with ad libitum access to food and water. Procedures were approved by the Committee of Animal Research and Ethics at KAIST (KA2024-093-v1) and followed the Korean Laboratory Animal Act.

extract_protocol:
Nuclei were isolated from frozen prefrontal cortex tissue using a lysis buffer of 0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 25 mM KCl, 0.1% Triton X-100, 1 mM DTT and 0.2 U/uL RNAse inhibitor (Protector, Sigma). Tissue was homogenised in 1 mL lysis buffer using a Nano pestle, incubated 5 min on ice and filtered through a 70 um strainer (MACS SmartStrainer, Miltenyi). Filtered samples were centrifuged at 500 g for 5 min at 4 C, resuspended in 1 mL lysis buffer, filtered through a 30 um strainer, centrifuged again at 500 g for 5 min at 4 C, and resuspended in PBS with 0.04% BSA. Nuclei were counted on a Countess 3 (Thermo Fisher).
Four mouse-specific nuclei suspensions were tagged with 10x Genomics On-Chip Multiplexing (OCM) barcodes and pooled prior to loading. Libraries were prepared with the Chromium GEM-X Universal 3' Gene Expression kit v4 with 4-plex On-Chip Multiplexing (10x Genomics) according to the manufacturer's instructions, yielding one paired Gene Expression library per GEM well (tube).

treatment_protocol: From P3 to P25, dams received drinking water containing vehicle (0.2% saccharin), fluoxetine (10 mg/L in saccharin water), or lithium carbonate (600 mg/L in saccharin water). Pups were exposed via maternal milk.

value: prefrontal cortex

value: single nucleus from prefrontal cortex (pool of 4 mice via 10x OCM)

tag: age

value: postnatal day 25

tag: sex (pool_composition)

value: female; female; male; male

tag: genotype (pool_composition)

value: heterozygous mutant; heterozygous mutant; heterozygous mutant; heterozygous mutant

tag: treatment (pool_composition)

value: vehicle; fluoxetine; vehicle; fluoxetine

tag: mouse line_(pool_composition)

value: Shank3-L68P; Shank3-L68P; Kmt5b; Kmt5b

tag: multiplexed mouse_ids

tag: n samples_per_pool

tag: sequencing batch


title: HUB-FT-s007

description: Library name: Sample 5

tag: treatment


title: FE-2416-4-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: Starch


title: FE-2071-5-START

value: START

value: Before randomization


title: TSA_326_C3_H_R1

description:
Library name: Sample 107
raw cell lysate and Illumina NextSeq 2106

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

value: TSA

tag: chemical longname

tag: dose

tag: well

tag: dose group

tag: plate

value: H

tag: index

value: ATTCGAATC

value: ATGGTTAGA

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr


title: WT mouse brain Ribo-seq replicate 1

description: Library name: Sample 45

value: Brain


title: FE-2522-2-POS

tag: tissue


title: MDA-MB-231 siBYSL biological replicate 1

description:
Library name: MDA_MB_231_siBYSL_1
MDA-MB-231 cells transfected with SI-BYSL-Homo-838; biological replicate 1.

tag: treatment

value: siRNA-mediated BYSL knockdown using SI-BYSL-Homo-838


title: LCR sedentary aged soleus RNA-seq L3

description:
Library name: UPL26-002494
Aged female rat soleus muscle; group=LCR; original sample name=L3; count matrix column=UPL26-002494.

value: soleus muscle

tag: genotype

value: selectively bred LCR rat

value: sedentary


title: TSA_326_C2_H_R1

description:
Library name: Sample 104
raw cell lysate and Illumina NextSeq 2103

value: ATCGCGACT

tag: batch nr_heparg


title: FE-2071-5-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: Starch


title: HUB-FT-s003

description: Library name: Sample 3

value: Heart

value: WT

value: one year

tag: batch


title: Control_2

description:
Library name: Sample2
10× Genomics

value: control


title: HUB-FT-s002

description: Library name: Sample 2


title: TSA_330_C1_H_R2

description:
Library name: Sample 102
raw cell lysate and Illumina NextSeq 2101

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

tag: cell type

value: liver progenitor cells

tag: chemical shortname

value: TSA

tag: chemical longname

tag: dose

value: H

value: TGATTAAGC

value: TGTAACGGC


title: Control_1

description:
Library name: Sample1
10× Genomics


title: Islets, day 5, DT, biol rep 3

city: Bucharest

first: Ana

last: Vacaru

address: BP Hasdeu 8

country: Romania

institute: ICBP-NS

description:
Library name: K3
total RNA

data_processing:
CLC Genomics Workbench 23.0
Trimming
Alignment
CLC Genomics Workbench was used to extract total counts, RPKM, TPM, CPM
Assembly: mm10
Supplementary files format and content: Tab separated text file with raw counts for each sample

source_name: Pancreatic islets

extract_protocol:
Qiagen RNeasy Mini Kit
polyA enrichment library preparation, performed by Novogene

treatment_protocol: DTR expressing β-cells were ablated by intraperitoneal administration of DT on day 0, 3 and 4.

value: Pancreatic islets

tag: Sex

value: Female

tag: experimental time_point

value: Day 5

value: NSG RIP-DTR Htz

value: DT


title: HFpEF_1

description:
Library name: Sample3
10× Genomics

value: HFpEF mouse model


title: FE-1714-4-START

value: Fixated Whole Blood

value: START

value: Before randomization

value: Starch


title: HCT116 WT cells treated with T144, biological replicate 2

city: Oxford

first: Nicholas

last: La Thangue

state: Oxfordshire

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

description: Library name: HCT116 T144 biol rep 2

data_processing:
RNAseq raw data was processed with fastp software to remove sequencing adaptors and low quality bases.
Processed reads were aligned with human reference genome hg19 using the STAR package (v.2.7.11)
BAM files were analysed by IGV software to visualise the read peaks. Also number of reads within the selected introns was calculated using samtools.
Assembly: hg19
Supplementary files format and content: tabular files include raw number of reads within the selected coordinates

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antiniotics in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was extracted from polysomal fractions (sucrose density gradient ultracentrifugation) using TRIzol, as per the manufacturer's instructions
RNA from HCT116 cells was used to prepare libraries by BGI Genomics. Briefly, mRNAs were isolated using oligo(dT)-based mRNA enrichment. mRNA was fragmented and reverse transcribed with random primer, prior to second strand synthesis with dUTP, end repair and 3' A-tailing. This was followed by adaptor ligation and digestion of U-labelled second strand template with UDG, prior to PCR amplification. Library quality control was performed before circularisation and amplification to make DNA nanoballs.

treatment_protocol: HCT116 cells were treated with 1uM PRMT5 inhibitor (T1-44) for 48h, or with DMSO.

value: colorectal carcinoma

value: WT


title: HUB-FT-s001

description: Library name: Sample 1

value: Heart

value: one year


title: TSA_303_C1_H_R3

description:
Library name: Sample 103
raw cell lysate and Illumina NextSeq 2102

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: 260722_count_table_GEO.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: TSA

tag: well

tag: dose group

tag: plate

value: H

tag: index

value: ACCTGAGGC

value: AACACAATC

tag: group

tag: replicate

tag: chemical type

value: test


title: FE-1739-4-START

data_processing:
Read alignments were done using Galaxy (https://usegalaxy.org/), where paired-end FASTQ files were processed with Cutadapt for adapter removal.
Reads were mapped using STAR (2-pass mapping) with the GENCODE v43 basic annotation was performed on genome assembly GRCh38 (hg38).
Counts were obtained with featureCounts, and quality control was performed with FastQC and MultiQC
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

tag: tissue

tag: timepoint

tag: randomization


title: Islets, day 5, DT, biol rep 1

description:
Library name: K1
total RNA

value: Pancreatic islets

value: Female

value: Day 5

tag: genotype

value: NSG RIP-DTR Htz

tag: treatment

value: DT


title: CI994_330_C5_E_R2

description:
Library name: Sample 99
raw cell lysate and Illumina NextSeq 2098

tag: cell line

tag: cell type

tag: chemical shortname

value: tacedinaline

value: E

value: GTTTATACT

value: AATTCGGAA

tag: cas-nr

tag: batch nr_heparg


title: CI994_303_C5_E_R3

description:
Library name: Sample 100
raw cell lysate and Illumina NextSeq 2099

value: liver tumor associated with chronic hepatitis C

tag: chemical longname

tag: dose

tag: well

value: GGGTTGTTA

value: GACGCGTTA


title: HCT116 WT cells, biological replicate 2

description: Library name: HCT116 WT biol rep 2

value: colorectal carcinoma

value: WT


title: FE-1650-1-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group

value: VLCD


title: Islets, day 3, DT, biol rep 3

description:
Library name: J5
total RNA

value: Pancreatic islets

tag: Sex

value: Female

tag: experimental time_point

value: Day 3


title: CI994_326_C5_E_R1

description:
Library name: Sample 98
raw cell lysate and Illumina NextSeq 2097

value: HepaRG

value: liver progenitor cells

tag: dose group

tag: plate

tag: index

value: CTAATGCAC

tag: group

tag: replicate

tag: chemical type

value: test


title: HCT116 WT cells, biological replicate 1

description: Library name: HCT116 WT biol rep 1

tag: cell line

tag: genotype

tag: treatment


title: FE-1739-4-POS

tag: tissue

tag: timepoint

value: POS

tag: randomization

value: Post randomization

value: Starch


title: FE-1714-4-POS


title: Islets, day 5, DT, biol rep 2

description:
Library name: K2
total RNA

value: Day 5

value: NSG RIP-DTR Htz

value: DT


title: HCT116 WT cells treated with T144, biological replicate 1

description: Library name: HCT116 T144 biol rep 1

tag: cell type

value: colorectal carcinoma

value: WT


title: CI994_303_C4_E_R3

description:
Library name: Sample 97
raw cell lysate and Illumina NextSeq 2096

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

tag: chemical longname

value: tacedinaline

tag: dose

tag: well

value: E

value: AAGACTCTT

value: GACGCGTTA

tag: cas-nr

tag: batch nr_heparg


title: FE-1643-5-START

value: Fixated Whole Blood

value: START

value: Before randomization

tag: diet group


title: InTraSeq, human cord blood HSPC-derived immune cells, ADT

city: Tokyo

first: Satoshi

last: Yamazaki

address: 4 Chome-6-1 Shirokanedai, Minato City

institute: The Institute of Medical Science, The University of Tokyo

description: Library name: ADT

library_source: other

data_processing:
InTraSeq reads were aligned to the human reference genome and gene expression matrices were generated using Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

source_name: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)

growth_protocol: NOG-w41 mouse-derived splenocytes were thawed and maintained in Roswell Park Memorial Institute-1640 (RPMI-1640), 1% bovine serum albumin (BSA) (Wako, Osaka, Japan, catalogue # 019-23293, lot # LKH4780), 1% P/S as the basal medium. Antigen-specific activation was performed with basal medium supplemented with human CD19/Leu-12 protein (His-Tag), biotinylated (Sino Biological, catalogue #11880-H08H-B), added at a concentration of 1µg/ml.

extract_protocol:
RNA was released by cell lysis within gel bead in emulsions (GEMs) and poly(A)+ mRNA was captured using oligodT primers and performed by the 10x Genomics Chromium GEM-X Single Cell 3’ Reagent Kit (10x Genomics).
Library construction was performed using the 10x Genomics Chromium GEM-X Single Cell 3’ Reagent Kit (10x Genomics), following the manufacturer’s instructions. Cells were loaded at a target concentration of approximately 1000 cells / µL (29 µL cell suspension + 7.6µL PBS). cDNA and cell-surface protein library purity and quantity were assessed using an Agilent TapeStation. Sequencing was performed on NovaseqX by Macrogen. Library preparation support and reference genome alignment was conducted using CellRanger.

treatment_protocol: Antigen-specific activation was performed with basal medium supplemented with human CD19/Leu-12 protein (His-Tag), biotinylated (Sino Biological, catalogue #11880-H08H-B), added at a concentration of 1µg/ml for 10 minutes at 37°C.

value: combined hCD45+mCD45-GFP+CD3+CD19-CD33-; hCD45+mCD45-GFP+CD56+CD3-; hCD45+mCD45-GFP+CD19+CD3-CD33-; hCD45+mCD45-GFP+CD33+CD3-CD19-; hCD45+mCD45-GFP-CD3+CD19-CD33-; hCD45+mCD45-GFP-CD56+CD3-; hCD45+mCD45-GFP-CD19+CD3-CD33-; hCD45+mCD45-GFP+CD33+CD3-CD19-

value: 4-1BB/z (GFP+), 4-1BB/z control (GFP-), 2B4/z (GFP+), 2B4/z control (GFP-) (multiplexed samples)

value: CD19 antigen stimulation for 10 minutes at 37°C


title: MDA-MB-231 siNC biological replicate 2

description:
Library name: MDA_MB_231_siNC_2
MDA-MB-231 cells transfected with negative-control siRNA; biological replicate 2.

value: Negative-control siRNA


title: Islets, day 3, DT, biol rep 2

description:
Library name: J4
total RNA

value: Pancreatic islets

tag: Sex

value: Female

tag: experimental time_point

value: Day 3


title: Healthy3

city: Stockholm

first: Cenk

last: Gurdap

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: Karolinska Institute

description:
Library name: Sample 3
10x genomics

data_processing:
cellranger-9.0.1
Assembly: GRCh38
Supplementary files format and content: H5

source_name: PBMCs

extract_protocol:
PBMC samples (four atherosclerosis and four sex- and age-matched healthy controls: A. Healthy) were processed for scRNA-seq using the 10x Genomics Chromium Single Cell 3' v4 platform, following the manufacturer’s protocol. Briefly, after thawing and washing, cells were resuspended in PBS containing 0.04% BSA, counted, and assessed for viability.
Cell suspensions were loaded into the Chromium Controller to generate Gel Bead-In-Emulsions, followed by reverse transcription, cDNA amplification, and library construction using the Single Cell 3' v4 Reagent Kit. Final libraries were quality-checked using an Agilent Bioanalyzer and quantified by qPCR. Sequencing was performed on an Illumina NovaSeq X Plus system (NovaSeq X Series Control Software v1.2.2.48004) using a 151 nt (Read 1) – 10 nt (Index 1) – 10 nt (Index 2) – 151 nt (Read 2) configuration on a ‘25B’ mode flow cell.

value: PBMCs

value: Healthy


title: Islets, day 1, DT, biol rep 3

description:
Library name: I5
total RNA

value: Day 1

value: NSG RIP-DTR Htz

value: DT


title: FE-1643-5-POS

extract_protocol:
Total RNA was extracted from fixed whole blood using Qiagen PAXgene Blood RNA Kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA quality control was performed using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina.Enriched RNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized and fragments were end-repaired and adenylated at 3’ends.  Universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

value: POS

value: Post randomization

value: Starch


title: CI994_330_C4_E_R2

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada

description:
Library name: Sample 96
raw cell lysate and Illumina NextSeq 2095

extract_protocol:
Cell lysates were used directly for TempO-Seq library building.
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRG cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70C followed by a temperature gradient with a ramp rate of 0.5C/min to 45C over a 50 min period, followed by a nuclease digestion at 37C for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37C, immediately followed with a 15 min enzyme denaturation at 80C to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37C for 10 min, 95C for 2 min; 6 cycles of 95C for 30 sec, 54C for 30 sec, 72C for 120 sec; 16 cycles of 95C for 30 sec; 72C for 2 min; 72C for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: tacedinaline

tag: dose group

tag: plate

value: E

tag: index

value: AAGACTCTT

value: AATTCGGAA

tag: group

tag: replicate

tag: chemical type

value: test


title: Islets, day 3, DT, biol rep 1

description:
Library name: J3
total RNA

tag: tissue

value: Pancreatic islets

value: Female

value: Day 3

tag: genotype

tag: treatment


title: TCR_G2

first: Bae-Hyeon

last: Moon

address: 193, Munji-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description:
Library name: TCR_G2
all_contig_annotations_G2.csv

data_processing:
Following tools were used for preprocessing: Cell Ranger software (v9.0.1), GRCh38 human reference genome (refdata-gex-GRCh38-2024-A), R (v4.4.2), Seurat package (v5.3.1), DoubletFinder (v.2.0.6). Donor identification was done with vireo & cellsnp-lite using SNPs from LSMC data. Uncommon genes between LSMCs and PBMCs were filtered out. We applied standard Seurat clustering and UMAP-based dimensional reduction. Batch effects were corrected using Harmony integration.
Assembly: Human reference, GRCh38 (GENCODE v44/Ensembl 110 annotations)
Supplementary files format and content: Seurat object (RDS). TCR (csv)
Library strategy: TCR-Seq

source_name: peripheral blood

extract_protocol:
Sorted γδ T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v3, the 5' Feature Barcode Kit, and Human TCR Amplification Kit (10X Genomics). Primers for γδ TCRs were designed according to previous research by another group. (reference: Song et al., 2023, J Leukoc Biol, 114(6):630-638)
Sorted γδ T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v3, the 5' Feature Barcode Kit, and Human TCR Amplification Kit (10X Genomics). Primers for γδ TCRs were designed according to previous research by another group. (reference: Song et al., 2023, J Leukoc Biol, 114(6):630-638)

value: peripheral blood

tag: cell line

value: Primary cell

tag: cell type

value: gammadelta T cell


title: InTraSeq, human cord blood HSPC-derived immune cells, mRNA

description: Library name: mRNA

value: SPLEEN (NOG-w41 differentiated human cord-blood CD34+ cells)

value: combined hCD45+mCD45-GFP+CD3+CD19-CD33-; hCD45+mCD45-GFP+CD56+CD3-; hCD45+mCD45-GFP+CD19+CD3-CD33-; hCD45+mCD45-GFP+CD33+CD3-CD19-; hCD45+mCD45-GFP-CD3+CD19-CD33-; hCD45+mCD45-GFP-CD56+CD3-; hCD45+mCD45-GFP-CD19+CD3-CD33-; hCD45+mCD45-GFP-CD33+CD3-CD19-

value: 4-1BB/z (GFP+), 4-1BB/z control (GFP-), 2B4/z (GFP+), 2B4/z control (GFP-) (multiplexed samples)

value: CD19 antigen stimulation for 10 minutes at 37°C


title: Islets, day 1, DT, biol rep 2

description:
Library name: I3
total RNA

value: Day 1

value: NSG RIP-DTR Htz

value: DT


title: CI994_303_C3_E_R3

description:
Library name: Sample 94
raw cell lysate and Illumina NextSeq 2093

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: tacedinaline

tag: dose

tag: well

value: E

value: TCCTCAGCC

value: GACGCGTTA


title: FE-1155-2-POS

first: Ezequiel

last: Dantas

address: 550E First Street

institute: NYU Langone

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: VLCD


title: CI994_330_C3_E_R2

description:
Library name: Sample 93
raw cell lysate and Illumina NextSeq 2092

tag: dose group

tag: plate

value: AATTCGGAA

value: test

tag: cas-nr

tag: batch nr_heparg


title: GEX_G2

description:
Library name: GEX_G2
LiverPerfusate_Blood.rds

data_processing:
Following tools were used for preprocessing: Cell Ranger software (v9.0.1), GRCh38 human reference genome (refdata-gex-GRCh38-2024-A), R (v4.4.2), Seurat package (v5.3.1), DoubletFinder (v.2.0.6). Donor identification was done with vireo & cellsnp-lite using SNPs from LSMC data. Uncommon genes between LSMCs and PBMCs were filtered out. We applied standard Seurat clustering and UMAP-based dimensional reduction. Batch effects were corrected using Harmony integration.
Assembly: Human reference, GRCh38 (GENCODE v44/Ensembl 110 annotations)
Supplementary files format and content: Seurat object (RDS). TCR (csv)

value: peripheral blood

value: Primary cell

value: gammadelta T cell


title: FB_G2

description:
Library name: FB_G2
LiverPerfusate_Blood.rds

data_processing:
Following tools were used for preprocessing: Cell Ranger software (v9.0.1), GRCh38 human reference genome (refdata-gex-GRCh38-2024-A), R (v4.4.2), Seurat package (v5.3.1), DoubletFinder (v.2.0.6). Donor identification was done with vireo & cellsnp-lite using SNPs from LSMC data. Uncommon genes between LSMCs and PBMCs were filtered out. We applied standard Seurat clustering and UMAP-based dimensional reduction. Batch effects were corrected using Harmony integration.
Assembly: Human reference, GRCh38 (GENCODE v44/Ensembl 110 annotations)
Supplementary files format and content: Seurat object (RDS). TCR (csv)
Library strategy: CITE-seq

molecule: protein


title: Islets, day 1, DT, biol rep 1

description:
Library name: I2
total RNA

value: Pancreatic islets

tag: Sex

value: Female

tag: experimental time_point

value: Day 1

value: NSG RIP-DTR Htz

value: DT


title: FE-1008-1-START

tag: tissue

value: START

value: Before randomization

value: Sugar


title: Islets, day 0, no DT, biol rep 3

description:
Library name: H4
total RNA

value: Day 0

tag: genotype

tag: treatment


title: FE-1008-1-POS

value: Fixated Whole Blood

value: POS


title: TCR_G1

description:
Library name: TCR_G1
all_contig_annotations_G1.csv

tag: cell line

tag: cell type


title: Islets, day 0, no DT, biol rep 2

description:
Library name: H3
total RNA


title: FD-8339-3-START

value: VLCD


title: Islets, day 0, no DT, biol rep 1

description:
Library name: H2
total RNA


title: CI994_330_C2_E_R2

description:
Library name: Sample 90
raw cell lysate and Illumina NextSeq 2089

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: tacedinaline

value: E

tag: index

value: TAGCTCTTC

value: AAGGTGTTT

tag: group

tag: replicate

tag: chemical type


title: FD-8339-3-POS

tag: timepoint

tag: randomization

value: Post randomization

tag: diet group


title: CI994_326_C2_E_R1

description:
Library name: Sample 89
raw cell lysate and Illumina NextSeq 2088

tag: dose

tag: well

tag: dose group

tag: plate

value: AAGACTCTT

value: CTAATGCAC

value: test

tag: cas-nr

tag: batch nr_heparg


title: FD-8119-3-START

tag: tissue

value: START

value: Before randomization


title: CI994_303_C1_E_R3

description:
Library name: Sample 88
raw cell lysate and Illumina NextSeq 2087

tag: cell line

tag: cell type

value: GACTTCATT

value: TGCATCTGC


title: CI994_330_C1_E_R2

description:
Library name: Sample 87
raw cell lysate and Illumina NextSeq 2086

tag: chemical shortname

tag: chemical longname


title: Eye-skin, MYD88-deficient ft/ft (ft/ftMyD88-/-), rep 4

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 291-XX-34

data_processing:
The CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: GRCm38
Supplementary files format and content: count matrix

source_name: skin

growth_protocol: ft/ftMyD88 /-  mice were generated as an in-house cross between a spontaneous loss-of-function point mutation in filaggrin (ft/ft) and MyD88 deficient (MyD88-/-) mice on a BALB/c background. All mouse strains were bred and maintained under the same specific pathogen-free conditions.

extract_protocol:
Protocol Overview: gentleMACS Octo Dissociator for Isolation of Cells from FFPE [https://cdn.10xgenomics.com/image/upload/v1721078231/support-documents/CG000632_DemonstratedProtocol_SamplePrep_from__FFPETissueSections_RevD.pdf]
Tissue Sections;  https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: skin

value: skin cells

tag: genotype

value: MYD88-deficient ft/ft


title: GBM43 intracranial xenografts, RMC-4550 treated, sample 1

city: San Francsico

first: Sixuan

last: Pan

state: California

institute: UCSF

description:
Library name: shp2-1
PIP-seq

data_processing:
Perturb dataset: Cell Ranger (v6.1.2) was used to align reads to mm10, count UMIs, and assign sgRNAs, while deMULTIplex2 was used to demultiplex MULTI-seq sample hashes. Seurat SCTransform v2 normalization and QC filtering retained only cells with correct dual-sgRNA capture and adequate knockdown. Differential expression was performed with DElegate (DESeq2 pseudoreplicates), followed by fgsea-based pathway analysis. Perturbation signatures were visualized using LDA and UMAP, and interaction modeling between gene perturbations and drug treatment was performed using Theil-Sen regression and random forest-based feature importance.  Xeno dataset: FASTQs were processed with PIPseeker for alignment to a combined human–mouse reference, droplet calling, and UMI matrix generation. Human tumor cells were identified by >85% human read mapping. Subsequent analyses were performed in Seurat using QC filtering, SCTransform v2 normalization, and Scanorama integration. Cell states were assigned with Neftel et al. signatures, and differential gene expression and GSEA were performed to characterize drug-specific transcriptional programs.
Assembly: Perturb dataset: mm10  Xeno dataset: GRCh38
Supplementary files format and content: Feature Barcode Market Exchange Matrices

source_name: brain

extract_protocol:
Perturb datasest: SB28 glioma cells expressing dCas9-KRAB were transduced with a dual-sgRNA CRISPRi library, FACS-sorted, treated with MEK inhibitor, SHP2 inhibitor, or vehicle for five days, then collected by trypsinization. Single-cell suspensions were labeled using MULTI-seq lipid barcodes through sequential incubation with anchor, barcode, and co-anchor oligos, washed in BSA-PBS, pooled, and loaded onto the 10x Chromium Controller for droplet partitioning.  Xeno dataset: Tumors from GBM43 intracranial xenografts were surgically harvested after in vivo drug treatment, mechanically minced, and enzymatically dissociated using the Papain Dissociation System to generate a single-cell suspension. The dissociated cells were filtered through a 70-µm strainer, centrifuged, washed in PBS, and prepared on ice for downstream PIPseq single-cell RNA-sequencing.
Perturb dataset: Dual-sgRNA constructs were cloned with direct-capture tags and used to generate the CRISPRi perturbation pool. Single-cell 3′ transcriptome and sgRNA-capture libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 kit with Feature Barcoding. MULTI-seq barcode libraries were amplified separately from cDNA supernatant after the SPRI cleanup step. All libraries were sequenced on an Illumina NovaSeq X.  Xeno dataset: Single-cell suspensions were processed using the Fluent BioSciences PIPseq T20 3′ Single Cell RNA Kit (v3.0), following the manufacturer’s workflow for barcoding, reverse transcription, amplification, and library preparation. Completed libraries were sequenced on an Illumina NovaSeq X to generate paired-end FASTQ files for downstream processing.

treatment_protocol: Vehicle (DMSO), selumetinib (MEK inhibitor), or RMC-4550 (SHP2 inhibitor)

value: brain

value: glioblastoma

tag: treatment

value: RMC-4550 (SHP2 inhibitor)


title: FD-8032-7-START

city: New York

value: Fixated Whole Blood

value: Sugar


title: CI994_326_C1_E_R1

city: Ottawa

description:
Library name: Sample 86
raw cell lysate and Illumina NextSeq 2085

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: tacedinaline

value: E

tag: index

value: TCCTCAGCC

tag: group

tag: replicate

tag: chemical type


title: FD-8032-7-POS

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group


title: Eye-skin, MYD88-deficient ft/ft (ft/ftMyD88-/-), rep 2

description: Library name: 291-XX-32


title: SPT_303_C5_E_R3

description:
Library name: Sample 85
raw cell lysate and Illumina NextSeq 2084

value: SPT

value: scriptaid

tag: dose

tag: well

tag: dose group

tag: plate

value: TGCATGACA

value: GACGCGTTA

value: test


title: GBM43 intracranial xenografts, selumetinib treated, sample 2

description:
Library name: sel-2
PIP-seq

tag: tissue

value: brain

tag: cell line

value: glioblastoma

value: selumetinib (MEK inhibitor)


title: FD-7985-1-START

value: Fixated Whole Blood

value: START

value: Before randomization

value: Starch


title: Eye-skin, MYD88-deficient ft/ft (ft/ftMyD88-/-), rep 1

description: Library name: 291-XX-31

value: skin

value: skin cells

tag: cell type

value: MYD88-deficient ft/ft


title: SPT_330_C5_E_R2

description:
Library name: Sample 84
raw cell lysate and Illumina NextSeq 2083

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: E

value: AATTCGGAA

tag: cas-nr

tag: batch nr_heparg


title: GBM43 intracranial xenografts, selumetinib treated, sample 1

description:
Library name: sel-1
PIP-seq

tag: genotype

tag: treatment


title: FD-7985-1-POS

value: POS

value: Post randomization


title: Eye-skin, filaggrin-deficient (ft/ft), rep 4

description: Library name: 291-XX-9

value: filaggrin-deficient


title: FD-7910-2-START

value: Sugar


title: GBM43 intracranial xenografts, vehicle control, sample 2

description:
Library name: ctrl-2
PIP-seq

value: brain

value: glioblastoma

value: Vehicle (DMSO)


title: FD-7910-2-POS

value: Fixated Whole Blood


title: Eye-skin, filaggrin-deficient (ft/ft), rep 2

description: Library name: 291-XX-7


title: FD-7779-6-START

value: START

value: Before randomization


title: SPT_326_C4_E_R1

description:
Library name: Sample 80
raw cell lysate and Illumina NextSeq 2079

value: SPT

value: scriptaid

tag: index

value: TAAGGTAGC

value: CTAATGCAC

tag: group

tag: replicate

tag: chemical type

value: test


title: Eye-skin, wildtype balb/c, rep 4

description:
Library name: WT-4
291-XX-18
processed_data_upload.xlsx

data_processing:
FastQC was used to assess quality control parameters before and after read filtering.  After read filtering and quality checks, reads were aligned with the HISAT algorithm to the Mus musculus GCF_000001635.26_GRCm38.p6 reference genome from the NCBI database and with tophat2 to align to reference genes.
Assembly: GRCm38
Supplementary files format and content: xlsx file includes log2 fold change and p-value

source_name: Skin

growth_protocol: Wild-type female BALB/c mice were maintained in-house under pathogen-free conditions.

extract_protocol:
Total RNA was extracted from about 60 mg of tissue per sample with Trizol (Invitrogen) according to the user manual instructions.
Extracted RNA was processed for high throughput sequencing using the Illumina TruSeq mRNA Sample Prep v2 kit. mRNA was generated from approximately 0.1–3.0 μg of total RNA per sample by polyA purification, following converted to cDNA using random primers and reverse transcriptase. Adaptor barcodes were added, and cDNA libraries were purified and enriched by PCR. Samples were run on a 50 cycle single end Illumina HiSeq 2000.

value: Skin

value: wildtype


title: FD-7779-6-POS

tag: timepoint

value: POS

tag: randomization

tag: diet group


title: SPT_326_C5_E_R1

description:
Library name: Sample 83
raw cell lysate and Illumina NextSeq 2082

value: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

tag: dose

tag: well

tag: dose group

tag: plate

value: E

value: TGCATGACA


title: GBM43 intracranial xenografts, vehicle control, sample 3

description:
Library name: ctrl-3
PIP-seq

tag: tissue

value: brain

tag: cell line

tag: cell type

value: glioblastoma

value: Vehicle (DMSO)


title: SPT_303_C3_E_R3

description:
Library name: Sample 79
raw cell lysate and Illumina NextSeq 2078

tag: chemical shortname

tag: chemical longname

value: ACTCATGTA

value: GACGCGTTA

tag: cas-nr

tag: batch nr_heparg


title: Eye-skin, wildtype balb/c, rep 3

description:
Library name: WT-3
291-XX-17
processed_data_upload.xlsx

tag: genotype


title: FD-7428-3-START

value: Fixated Whole Blood

value: START

value: Before randomization

value: VLCD


title: MethylC-seq, pyramidal neurons, P13, Saline, rep5

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: S_AC_01

data_processing:
RNA-seq: Read quality was assessed using FastQC (Andrews, 2010). STAR (2.5.1b; Dobin et al., 2013) was used to map sequence reads and RSEM (version 1.2.31; Li and Dewey, 2011) was used to quantify gene expression.
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequencing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
RNA-seq: Batch correction in P0 samples was performed using ComBat-seq (Zhang et al., 2020). Mitochondrial and lowly expressed genes with fewer than 10 raw counts in all but one sample were removed before differential gene expression analysis. Differential expression analysis was conducted using DESeq2 (Love et al., 2014) with a false discovery rate 0.1. Enrichment analysis was performed by inputting differentially expressed genes into EnrichR (Kuleshov et al., 2016; Chen et al., 2013).
MethylC-seq: CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
Assembly: mm10
Supplementary files format and content: Tab-delimited file contains transcripts per million counts for each RNA-seq sample
Supplementary files format and content: Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosine Context, 5. methylated base call, 6. total mapped base call, 7. indicator of significant methylation (0: unmethylated; 1, methylated)

source_name: brain (frontal cortex)

extract_protocol:
Cortex dissecxtion and nuclei isolation: The frontal cortex tissue was rapidly dissected from perinatal mice on ice. The INTACT method was used to label excitatory neurons and fluoreescence-activated nuclei sorting (FANS) was used to affinity purify GFP+ nuclei. RNA-seq: RNA was extracted by using the RNeasy Mini kit with DNAse I treatment (Qiagen, 74104) for whole frontal cortex, or by using Single-Cell RNA Purification Kit (Norgen, 51800) for nuclei. Bisulfite-Seq (MethylC-seq):  Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
RNA-seq: For whole tissue RNA, strand-specific cDNA libraries were constructed by selecting poly-adenylated mRNA transcripts using Truseq Stranded mRNA High Throughput Library Prep kit (Illumina, 20015963) with TruSeq RNA CD Indexes (Illumina, 20015949). Libraries were sequenced using Illumina NextSeq500, generating 20 million reads (75 bp, paired-end sequencing, whole cortex). INTACT-purified nuclear RNA (Norgen, 51800) was converted to cDNA and amplified with the Ovation RNA-seq System V2 (Nugen, 7102-A01) and libraries prepared with Kapa LTP library preparation kit (Illumina, KK8232) with TruSeq DNA Single Indexes (Illumina, 20015960), generating 40 million reads (150 bp, paired-end sequencing using Illumina HiSeq 4000 or NovaSeq 6000).
Bisulfite-Seq (MethylC-seq):  MethylC-seq libraries were constructed using the snmC-seq2 adapted for Bulk samples (https://dx.doi.org/10.17504/protocols.io.pjvdkn6). 40ng of DNA samples  were subjected to sodium bisulfite conversion using Zymo EZ DNA Methylation-Direct Kit (D5020, D5021), 0.5% of Lambda was added to each sample, resuspended in 9ul of EB buffer, 1ul of random primer was added to each of the samples, denature for 3 min at 95°C, put in ice for 3 min, then 10ul of Random primer was added and mixed, put in thermocycler with at 4°C 5 min,  25°C 5 min, 37°C 60 min. Exonuclease/SAP mix was added next put at 37°C 30min. Samples were subjected to one round of 0.8x SPRI beads clean up. Samples were resuspended in 10ul of EB and denature once again. Adaptase mix was added next, and put at 37°C 30min and 95°C 2min. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart, 1ul of P5 index primer (30uM), and 5ul of P7 index primer (10uM), for a final vol of 50ul. The reaction products were purified using SPRI beads. MethylC-seq libraries were sequenced on Illumina HiSeq 4000 or Novaseq 6000.

treatment_protocol: Dams received IP injection of 0.9% saline or 20 mg/kg polyriboinosinic–polyribocytidylic acid potassium salt (P9582, Lot number 095M4085V, Sigma-Aldrich, St. Louis, MO) in 0.9% saline on embryonic day 12.5.

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment

value: Saline

tag: age

value: Postnatal day 13

tag: Sex

value: male


title: SPT_330_C3_E_R2

description:
Library name: Sample 78
raw cell lysate and Illumina NextSeq 2077

source_name: liver tumor associated with chronic hepatitis C

value: HepaRG

value: liver progenitor cells

value: SPT

value: scriptaid

value: E

tag: index

value: TCAGTACAT

value: AATTCGGAA

tag: group

tag: replicate

tag: chemical type

value: test


title: Eye-skin, wildtype balb/c, rep 2

description:
Library name: WT-2
291-XX-16
processed_data_upload.xlsx

value: Skin

value: wildtype


title: FD-7428-3-POS

source_name: Fixated Whole Blood

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: VLCD


title: MethylC-seq, pyramidal neurons, P13, Saline, rep4

description: Library name: S_HH_02

tag: tissue

value: brain (frontal cortex)

tag: cell type

value: excitatory pyramidal neurons

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline


title: TSA_326_C1_H_R1

description:
Library name: Sample 101
raw cell lysate and Illumina NextSeq 2100

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: TSA

tag: chemical longname

tag: dose

tag: well

tag: dose group

tag: plate

value: H

value: TGGAACGCT

value: ATGGTTAGA


title: SPT_326_C3_E_R1

description:
Library name: Sample 77
raw cell lysate and Illumina NextSeq 2076

value: SPT

value: scriptaid

value: E

value: TCAGTACAT

value: CTAATGCAC

value: test

tag: cas-nr

tag: batch nr_heparg


title: Eye-skin, wildtype balb/c, rep 1

description:
Library name: WT-1
291-XX-15
processed_data_upload.xlsx

value: Skin

tag: genotype

value: wildtype


title: MethylC-seq, pyramidal neurons, P13, Saline, rep6

description: Library name: S_GG_01

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: treatment

tag: age

value: Postnatal day 13

tag: Sex

value: male


title: FE-1650-1-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization

value: Post randomization

tag: diet group

value: VLCD


title: FD-6939-3-START

tag: tissue

value: START

value: Before randomization


title: MethylC-seq, pyramidal neurons, P13, Saline, rep3

description: Library name: S_GG_02

tag: cell type

value: Saline


title: FE-1155-2-START


title: CI994_326_C4_E_R1

description:
Library name: Sample 95
raw cell lysate and Illumina NextSeq 2094

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

tag: chemical longname

value: tacedinaline

value: E

tag: index

value: GAACTGTAT

tag: group

tag: replicate

tag: chemical type


title: SPT_303_C2_E_R3

description:
Library name: Sample 76
raw cell lysate and Illumina NextSeq 2075

value: SPT

value: scriptaid

tag: dose

tag: well

tag: dose group

tag: plate

value: GTTTATACT

value: GACGCGTTA

value: test

tag: cas-nr

tag: batch nr_heparg


title: FD-6939-3-POS

value: Fixated Whole Blood

tag: timepoint

value: POS

tag: randomization


title: HM9Pool_Sort4_Murine CD276

city: Bonn

first: Bianca

last: Broske

address: Venusberg-Campus 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

description:
Library name: HM9Pool_Sort4_Sample5
NGS-Read-Counts_HM9Pool.xlsx

data_processing:
Reads were filtered for a Q-Score > 30 and matched to AI-minibinder sequences using a self-written R script.
Assembly: Read alignment was performed against the designed sequences used for the respective oligo pool.
Supplementary files format and content: The processed data files contain all binder names and sequences present in the respective oligo pool. The target proteins used for staining are indicated in the sheet names, as well as in the header of the respective read column. Technical replicates (file names "*TechRepx") are already pooled and the different sorts indicate replicates of repeated experiments.

organism: synthetic construct

source_name: Transduced HEK293T cells

extract_protocol:
Sorted cells were lysed in direct lysis buffer (1 mM CaCl2, 3 mM MgCl2, 1 mM EDTA, 1% (v/v) Triton X-100, 10 mM Tris pH 7.5) with proteinase K at 65 °C for 10 minutes and 95 °C for 15 minutes.
After lysis, genomically integrated AI-minibinder sequences were PCR amplified using 2x NEBNext High-Fidelity MasterMix (NEB). After second barcoding PCR, product purification, and NanoDrop-based quantification, AI-minibinders were sequenced on Illumina MiSeq platforms.

treatment_protocol: HEK293T cells were lentivirally transduced with plasmid libraries encoding de novo generated minibinder proteins. The HEK293T AI-minibinder libraries were harvested and incubated with respective Fc-tagged recombinant target proteins at 10 µg/mL and secondary APC-labeled anti-human IgG Fc antibody at 250 ng/mL (clone M1310G05, Biolegend). Cells were sorted immediately after staining for distinct APC-signal using the fluorescence-activated cell sorter Sony MA900.

value: Transduced HEK293T cells

tag: treatment

value: Stained with recombinant murine CD276


title: MethylC-seq, pyramidal neurons, P13, Saline, rep2

description: Library name: S_AC_04

tag: tissue

value: brain (frontal cortex)

tag: cell type

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

tag: age

value: Postnatal day 13

tag: Sex

value: male