city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

description:
Library name: Expanded_HSPCs_Flt3L_primed_IgG_CnR_rep4
IgG

data_processing:
Bulk RNAseq was processed using ENCODE pipelines. The adapter trimmed reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v 2.5.1b), and gene expression was calculated with RSEM(v 1.2.31). Then, significant changes in gene expression were determined using DEseq2 (v 1.46.0).
Bulk ATAC-seq and CUT&RUN data was processed by mapping the sequenced reads to the GRCm38/mm10 mouse reference genome using Bowtie 2 following PCR duplicates removal using Picard and mitochondrial reads and blacklist regions filtering using Samtools.  Peak calling was conducted by employing Genrich for ATAC-seq or SEACR for CUT&RUN histone peaks with a stringent mode. Bigwig files were generated using deepTools (v 3.5.1) with binSize 20bp and counts per million (CPM) normalization.
scRNAseq raw reads from cDNA libraries were aligned to the mouse reference genome GRCm38/mm10 using CellRanger and the hashtag oligo (HTO) libraries were quantified and demultiplexed using in-house tools (hashtag tool) as described previously (Zhou et al., 2022 Sci Immunol, PMID: 35594339).
Assembly: GRCm38/mm10
Supplementary files format and content: Raw counts, TPM, and FPKM values from STAR/RSEM outputs (bulk RNAseq)
Supplementary files format and content: Bigwig files (ATAC-seq and CUT&RUN)
Supplementary files format and content: Peak files (ATAC-seq, CUT&RUN) in bed format
Supplementary files format and content: Cell ranger filterted feature barcode matrix output files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
Supplementary files format and content: Binarized HTO counts output
Library strategy: CUT&Run

source_name: bone-marrow

growth_protocol:
In vitro HSPC expansion: CD150+EPCR+Lineage-Kit+Sca1+ HSPCs were cultured in HSPC expansion medium (F12 DMEM , 1 mg/mL of PVA, 1× Insulin–transferrin–selenium–ethanolamine, 10 mM HEPES,  1×  Penicillin–streptomycin–glutamine, 100 ng/mL of recombinant mouse thrombopoietin (TPO) and 10 ng/mL of recombinant mouse stem cell factor (SCF) for 2-4 weeks.
In vitro early T cell development: Freshly isolated bone marrow progenitors or expanded HSPCs were co-cultured with OP9-Dll1 cells in OP9 medium (alphaMEM, 20% FBS, 1×PSQ, and 50 microM beta-mercaptoethanol ) with human Flt3-ligand (Flt3L) and human IL-7 (10 ng/mL each from day0 -day5, 5 ng/mL each for day5-day7, and 1 ng/mL after day 7).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen #74105) with on-column DNase I treatment (Qiagen #1023460)
Bulk RNA-seq library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina.
Bulk ATAC-seq library was constructed after transposition reaction using Tn5 transposases (Illumina #15027916) by following previously published protocol (Corces et al., 2017 Nat Methods, PMID: 28846090).
CUT&RUN library was constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E7645S, #E7500S, #M5505S) by following previously reported protocol ((Liu et al., 2018 Cell, PMID: 29606353)
Single-cell RNA-seq cDNA libraries were prepared using 10X Chromium 3’ capture v3.1 kit.
Single-cell hashtag oligo library was prepared in accordance with the BioLegend TotalseqA guide.

treatment_protocol: Flt3L priming was performed by treating EPCR+ CD150+ Lineage-Kit+Sca1+ expanded HSPCs with 10 ng/mL of human Flt3L in HSPC expansion media for 4 days.

value: bone-marrow

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days

value: wild-type


title: RQ1_IR_4

status: Public on Jan 15 2026

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: HO

hyb_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours.

scan_protocol: Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: RCC format files containing the raw data  were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: NanoString barcodes

molecule: total RNA

organism: Mus

source_name: prefrontal cortex

label_protocol: Per NanoString protocol. Label a 12-tube PCR hybridization strip. The purified RNA is diluted in nuclease-free water to 20 ng/uL. Recommended total RNA samples are 20 ng to 100 ng for hybridization assay. The prepared samples are used as input into nCounter hybridization reactions containing NanoString Reporter and Capture probes. First, remove Reporter CodeSet and Capture ProbeSet tubes from the freezer and thaw at room temperature. Second, after it has thawed, inspect the tube of Reporter CodeSet to make sure no colored precipitate is present. Third, If you see a colored precipitate, heat the entire tube to 75°C for 10 minutes and cool at room temperature before using .The purified RNA was hybridized at thermal cycler at 65°C for 16 to 24 hours into nCounter 15 µL of hybridization buffer containing NanoString Reporter and Capture probes. Add 8 μL of Master Mix to each well of a strip tube. Add 5 µL of sample to each tube containing Master Mix. Add 2 µL of Capture ProbeSet to each tube. Maximum hybridization time should not exceed 48 hours.

extract_protocol: Prefrontal cortexl tissue (10 mg) from the mice were prepared for the extraction of total RNA using a Nucleospin RNA isolation kit (Macherey-Nagel, #740955.250) as per the manufacturer’s protocol.

treatment_protocol: WT (C57BL6/J), RecQ1, WRN, RecQ4 deficient mice were maintained on a 12h light-dark schedule and fed standard NIH chow. Mice were exposed the whole body with γ-irradiation (IR, 6 Gy).

tag: treatment

value: 6 Gy γ-irradiation

tag: Sex

value: F

tag: age

tag: genotype

tag: strain

value: RECQL KO

tag: tissue

value: prefrontal cortex


title: PBMC, Severe COVID-19, pCoV2

type: SRA

city: Farmington

first: Asa

last: Thibodeau

state: CT

address: 10 Discovery Drive

department: Genomic Medicine

institute: The Jackson Laboratory

description:
Library name: pCoV2_snATAC
10x Genomics (scATAC-seq)

library_source: genomic single cell

data_processing:
Data processing was performed using Cell Ranger-ATAC software 2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/overview/welcome)
Assembly: GRCh38-2020-A
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores for all PBMCs.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for CD4+ T Cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for B cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for CD8+ T, cytotoxic T and NK cells.
Supplementary files format and content: H5ad file includes scanpy object containing gene activity scores and chromVAR deviations for myeloid cells.
Supplementary files format and content: Comma separated value file includes single cell read metrics.
Supplementary files format and content: Tab separated value file includes high quality fragment positions on the reference genome with cell barcode and read support information.
Supplementary files format and content: Tab separated value file includes raw cell barcodes.
Supplementary files format and content: Tab separated value file includes raw peak calls.
Supplementary files format and content: Matrix file includes raw read counts for raw peaks and barcodes.
Supplementary files format and content: Tab separated value file includes filtered cell barcodes.
Supplementary files format and content: Tab separated value file includes filtered peak calls.
Supplementary files format and content: Matrix file includes raw read counts for filtered peaks and barcodes.

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Viable single cell suspensions from each sample were used to generate snATAC-seq data using the 10x Chromium platform according to the manufacturer’s protocols (10x Genomics, protocols CG000169; CG000168). Briefly, >100,000 cells from each sample were centrifuged and the supernatant was removed without disrupting the cell pellet. Lysis Buffer was added for 5 minutes on ice to generate isolated and permeabilized nuclei, and the lysis reaction was quenched by dilution with Wash Buffer. After centrifugation to collect the washed nuclei, diluted Nuclei Buffer was used to re-suspend nuclei at the desired nuclei concentration as determined using a Countess II FL Automated Cell Counter and combined with ATAC Buffer and ATAC Enzyme to form a Transposition Mix.
Transposed nuclei were immediately combined with Barcoding Reagent, Reducing Agent B and Barcoding Enzyme and loaded onto a 10x Chromium Chip H for droplet generation followed by library construction. The barcoded sequencing libraries were subjected to bead clean-up and checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and pooled for sequencing on an Illumina NovaSeq 6000 (2x50bp libraries).

value: Blood

tag: cell type

value: Peripheral blood mononuclear cells

tag: age (months)

value: female

tag: race/ethnicity

value: Black

tag: disease state

value: Severe COVID-19


title: RQ1_IR_5

description: HO


title: PBMC, Moderate COVID-19, pCoV3

description:
Library name: pCoV3_snATAC
10x Genomics (scATAC-seq)

value: male

value: Asian

value: Moderate COVID-19


title: PBMC, Convalescent COVID-19, pCoV1

description:
Library name: pCoV1_snATAC
10x Genomics (scATAC-seq)

value: Convalescent COVID-19


title: Micro-C-TALE_rsCBE_rep2

city: Jerusalem

first: Yehudit

last: Bergman

address: Ein Karem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Of Jerusalem

description: Library name: rsCBE2_Micro-C-TALE

library_source: genomic

data_processing:
Reads were mapped, filtered, and balanced using nf-distiller
Assembly: mm10
Supplementary files format and content: mcool file

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Approximately 1.6–4 × 10⁶ CD19⁺ pre-B cells were enriched from WT-Rag1⁻/⁻.hIgM and ΔrsCBE-Rag1⁻/⁻.hIgM mice using anti-CD19 magnetic beads (Miltenyi Biotec) and MACS column separation (Miltenyi Biotec).
Fixed and permeabilized cells were treated with micrococcal nuclease (MNase) (ThermoFisher, #88216) to obtain predominantly mononucleosomal DNA. The DNA was then ligated using T4 DNA ligase (NEB, #M0202L), extracted by phenol–chloroform and ethanol precipitation, and ligation products were enriched by size selection using Ampure XP beads (Beckman Coulter, #A63881). End repair and adaptor ligation were performed using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645S), followed by PCR amplification with indexed primers. Four Micro-C libraries were generated and pooled in equimolar proportions. Capture probes were prepared from fifteen BACs spanning the target genomic region. BAC DNA was mixed equimolarly, sheared to ~200-bp fragments by sonication, end-repaired, and ligated to specialized adaptors using the NEBNext Ultra II kit. The BAC library was then PCR-amplified using biotinylated primers. Hybridization-based capture was performed by incubating the pooled Micro-C libraries with the biotinylated BAC-derived probes in multiple replicates. Hybridized products were pulled down using streptavidin-coated magnetic beads (Dynabeads MyOne sterptavidin C1, Invitrogen, #65001) and amplified by PCR with Illumina-compatible primers. The capture cycle was repeated once, and the final libraries were sequenced on a DNBSEQ-G400 machine using paired-end 150-bp reads.

value: Bone marrow

value: pre-B

value: rsCBE


title: esgts/w1118-UAS-Toll10b/UAS-Bsk-DN replicate 2

city: Oxford

first: Petros

last: Ligoxygakis

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: Toll_Bsk_2

library_source: transcriptomic

data_processing:
SOAP (Short Oligonucleotide Alignment Program), BGI suite for alignment to reference genome
HTSeq-count and futureCounts were used for read counting (quantification).
DESeq2 or differential gene expression
Assembly: DNBSEQ
Supplementary files format and content: BAM files for each sample and ONE xls files with quantification of gene expression for all samples

organism: Drosophila melanogaster

source_name: whole gut

growth_protocol: Fly stocks and crosses were cultured at 18oC (GAL80ts=ON) until adults were emerging and then moved to 29oC (GAL80ts=OFF) for 20 days. Guts were dissected and total RNA was extracted.

extract_protocol:
Total RNA from dissected whole guts was extracted using RNAeasy mini plus kit (Qiagen). 1.5 ul was used to make each sequencing library.
Libraries were generated using the MGIEasy RNA-seq Library Preparation Universal Kit in BGI HongKong.

value: whole gut


title: KC1+cre (Group4)

city: Jinan

first: xiaochen

last: liu

address: Wenhua West Road No.44

country: China

institute: shandong university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung

growth_protocol: Cells were cultured in RPMI-1640 medium (Gibco, #11875093) supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin and 10 μM ROCK inhibitor (146986-50-7, MedChemExpress).

extract_protocol:
RNA was harvested using Trizol (Sigma)
RNA libraries for RNA-seq were prepared by NOVOGENE.

treatment_protocol: After culture for 72 hours, adherent cells were subcultured after detachment using 0.25% trypsin (25200-072, Gibco). For activation of KRASG12D and deletion of CUL4B, K and KC cells were cultured to 70% confluence and were then infected with 1×107 PFU/mL Ad-Cre. After 12 hours, the culture medium was changed.

value: lung

tag: cell line

value: lung epithelial cells

value: primary culture cells

value: KRASG12D and CUL4B knockout

value: Ad-Cre treated


title: esgts/w1118-UAS-Toll10b/UAS-Bsk-DN replicate 3

description: Library name: Toll_Bsk_3


description:
Library name: Expanded_HSPCs_Flt3L_primed_H3K27me3_CnR_rep2
H3K27m3

value: bone-marrow

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days

value: wild-type

tag: batch


title: Micro-C-TALE_rsCBE_rep1

description: Library name: rsCBE1_Micro-C-TALE


title: RQ1_IR_3

description: HO

value: 6 Gy γ-irradiation

value: M

value: RECQL KO

value: prefrontal cortex


title: RQ1_IR_2

description: HO


description:
Library name: d2_OP9_DLL1_unprimed_LSK_progeny_bulk_RNA_rep2
RNA

data_processing:
Bulk RNAseq was processed using ENCODE pipelines. The adapter trimmed reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v 2.5.1b), and gene expression was calculated with RSEM(v 1.2.31). Then, significant changes in gene expression were determined using DEseq2 (v 1.46.0).
Bulk ATAC-seq and CUT&RUN data was processed by mapping the sequenced reads to the GRCm38/mm10 mouse reference genome using Bowtie 2 following PCR duplicates removal using Picard and mitochondrial reads and blacklist regions filtering using Samtools.  Peak calling was conducted by employing Genrich for ATAC-seq or SEACR for CUT&RUN histone peaks with a stringent mode. Bigwig files were generated using deepTools (v 3.5.1) with binSize 20bp and counts per million (CPM) normalization.
scRNAseq raw reads from cDNA libraries were aligned to the mouse reference genome GRCm38/mm10 using CellRanger and the hashtag oligo (HTO) libraries were quantified and demultiplexed using in-house tools (hashtag tool) as described previously (Zhou et al., 2022 Sci Immunol, PMID: 35594339).
Assembly: GRCm38/mm10
Supplementary files format and content: Raw counts, TPM, and FPKM values from STAR/RSEM outputs (bulk RNAseq)
Supplementary files format and content: Bigwig files (ATAC-seq and CUT&RUN)
Supplementary files format and content: Peak files (ATAC-seq, CUT&RUN) in bed format
Supplementary files format and content: Cell ranger filterted feature barcode matrix output files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
Supplementary files format and content: Binarized HTO counts output

value: CD45+Lin-live progeny of unprimed LSK cells after 2days of co-culture with OP9-DLL1 cells

value: Untreated


title: esgts/w1118-UAS-Toll10b replicate 3

description: Library name: Toll_3


title: esgts/w1118-UAS-Toll10b replicate 2

description: Library name: Toll_2


title: esgts/w1118-UAS-Toll10b replicate 1

description: Library name: Toll_1


title: RQ1_IR_1

description: HO


title: esgts/w1118-UAS-Toll10b/UAS-Bsk-DN replicate 1

description: Library name: Toll_Bsk_1


description:
Library name: d2_OP9_DLL1_Flt3L_primed_LSK_progeny_bulk_RNA_rep2
RNA

value: CD45+Lin-live progeny of Flt3L-primed LSK cells after 2 days of co-culture with OP9-DLL1 cells


description:
Library name: d2_OP9_DLL1_unprimed_LSK_progeny_bulk_RNA_rep1
RNA

value: CD45+Lin-live progeny of unprimed LSK cells after 2 days of co-culture with OP9-DLL1 cells


description:
Library name: d1_OP9_DLL1_Flt3L_primed_LSK_progeny_bulk_RNA_rep2
RNA

value: CD45+Lin-live progeny of Flt3L-primed LSK cells after 1 day of co-culture with OP9-DLL1 cells


description:
Library name: d2_OP9_DLL1_Flt3L_primed_LSK_progeny_bulk_RNA_rep1
RNA


title: KO-3

first: Xiao

last: Zhuang

state: Shandong province

address: Shandong University, Wenhuaxi Road 44, Jinan, China

department: Department of Cell Biology

institute: Shandong University

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost:3 length fraction: 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: HT1080 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HT1080 WT and GPR56 KO

value: Human fibrosarcoma

value: GPR56 KO


description:
Library name: d1_OP9_DLL1_Flt3L_primed_LSK_progeny_bulk_RNA_rep1
RNA


title: ESS1-AID, IAA, Ess1-depleted, rep2

city: Shanghai

first: JUXIU

last: CHEN

state: Shanghai

address: 115 Jinzun Road, Pudong New Distract

department: Shanghai Institute of Precision Medicine

institute: Ninth People’s Hospital of Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample4
column name in raw_counts.txt: IAA-2

data_processing:
Raw sequencing data were processed to remove low-quality reads and adapter sequences using FastQC(v0.11.9) and Trimmomatic.
Cleaned reads were then aligned to the S. cerevisiae S288C reference genome R64-1-1 using STAR(v2.7.10a), and the resulting BAM files were sorted using Samtools(v1.10).
Gene expression was quantified with RSEM(v1.3.3), and differential expression analysis was performed using DESeq2.
Assembly: R64
Supplementary files format and content: Tab-separated plain text containing RSEM-estimated raw counts for each Sample.
Supplementary files format and content: csv files include FPKM values for each Sample.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in YPD medium (10 g/L yeast extract, 20 g/L peptone, and 20 g/L glucose) at 30°C.

extract_protocol:
Total RNA was extracted using the Yeast RNA Kit (OMEGA, R6870), including on-column DNase I treatment to remove genomic DNA.
Libraries were prepared according to the manufacturer’s protocol using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: When yeast cells were grown to mid-log phase, cells were then treated with DMSO or 2 mM IAA for 3 hours.

value: IAA


title: Micro-C-TALE_WT_rep2

description: Library name: WT2_Micro-C-TALE

value: Bone marrow

value: pre-B

value: WT


title: KO-1


title: Micro-C-TALE_WT_rep1

description: Library name: WT1_Micro-C-TALE


title: esgts/w118 control replicate 3

description: Library name: esg_3

value: whole gut

value: esg-GAL4, UAS-GFP, tub-GAL80ts/w111


title: esgts/w118 control replicate 1

description: Library name: esg_1

value: esg-GAL4, UAS-GFP, tub-GAL80ts/w1118


description:
Library name: d1_OP9_DLL1_unprimed_LSK_progeny_bulk_RNA_rep2
RNA

value: bone-marrow

value: CD45+Lin-live progeny of unprimed LSK cells after 1 day of co-culture with OP9-DLL1 cells

value: wild-type


title: WT-1


title: Ymu1 bacterial single transcript wRNA expression

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

description: Library name: HS_RNA_1

data_processing:
Paired-end sequencing reads were quality trimmed and merged prior to downstream analysis.
Merged reads of 100–150 nucleotides were selected and aligned to the Ymu1 reference sequence.
Read alignments were sorted and indexed, and coverage tracks were generated for visualization.
Processed alignment files were converted to browser-compatible formats and visualized using standard genome browsers.
Assembly: Ymu1 reference sequence on vector pHS516
Supplementary files format and content: Processed data files are coordinate-sorted BAM files containing aligned RNA-seq reads mapped to the TnpB reference sequence.

organism: Escherichia coli

source_name: E. coli

growth_protocol: Escherichia coli DH10B cells harboring plasmid pHS516 were grown in LB medium at 37 °C to mid-log phase (OD₆₀₀ ≈ 0.6).

extract_protocol:
Total RNA was extracted using a hot formamide lysis method. Cell pellets were resuspended in EDTA and formamide, incubated at elevated temperature to lyse cells, clarified by centrifugation, and RNA was purified using a silica column–based cleanup kit.
Purified total RNA was subjected to bacterial rRNA depletion, followed by end-repaired using phosphatase and polynucleotide kinase treatments. Strand-specific RNA-seq libraries were prepared using the Collibri Stranded RNA Library Prep Kit for Illumina according to the manufacturer’s protocol, followed by PCR amplification, size selection by gel extraction, and sequencing on an Illumina NextSeq 1000/2000.

treatment_protocol: Gene expression was induced by addition of arabinose to the growth medium, followed by overnight incubation at 16 °C.

value: E. coli


title: KO-2


title: OCI-AML22 - LTR12C_3

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
The data is mapped using bowtie2 and called peaks using MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Acute Myeloid Leukemia

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles

value: Acute Myeloid Leukemia

value: LTR12C gRNAs


title: ESS1-AID, IAA, Ess1-depleted, rep1

description:
Library name: Sample3
column name in raw_counts.txt: IAA-1


title: esgts/w118 control replicate 2

description: Library name: esg_2


description:
Library name: d1_OP9_DLL1_unprimed_LSK_progeny_bulk_RNA_rep1
RNA

value: Untreated


title: ESS1-AID, DMSO, control, rep2

description:
Library name: Sample2
column name in raw_counts.txt: DMSO-2

value: DMSO


title: WhiB1 experiment TSS WhiB1 rep2 (RNAP-SigA-RbpA-CarD + WhiB1)

city: New York

first: Ruby

last: Froom

address: 1230 York Avenue

institute: Rockefeller University

description: Library name: Sample 8

data_processing:
After initial Illumina de-multiplexing, reads were further de-multiplexed by inline barcode (the post-demultiplexed raw fastq files are provided here). Reads were filtered using the cutadapt package to trim Illumina adaptors, set a minimum read length of 10, and cumulative quality minimum of 20.
Five-basepair random unique molecular indices (UMIs) were trimmed from the ends of each read and added to the read ID.
Reads were aligned to a concatenated genome (Eco + Mtb) using the bwa-mem algorithm with default parameters.
PCR and optical duplicates were removed using the dedup function from the umi_tools package.
Two separate alignments solely containing the transcript end reads (read 2) for the Eco genome (spike samples) and Mtb genome were generated separately and downsampled to equivalent sequencing depths. These read 2-only alignments were used to create processed bigWig files that were used as input for nonparametric resampling-based TSS and TTS calling.
Assembly: The concatenated genome used was Eco (U00096.3) and Mtb (NC_018143.2.)
Supplementary files format and content: tab-delimited text file includes the transcript end counts ('count' column) for every position in the Mtb genome ('end' column, with the length of the Eco genome added to the genomic position) with at least 2 transcript end counts, with corresponding q-values for how significant the transcript end accumulation is over background within a 200bp window ('qvalue' column).
Supplementary files format and content: bigWig file includes all transcript end counts for every position in the Mtb genome that mapped to the plus strand.
Supplementary files format and content: bigWig file includes all transcript end counts for every position in the Mtb genome that mapped to the minus strand.
Supplementary files format and content: tab-delimited text file includes the transcript end counts ('count' column) for every position in the Eco genome ('end' column) with at least 2 transcript end counts, with corresponding q-values for how significant the transcript end accumulation is over background within a 200bp window ('qvalue' column). Counts with a q-value less than 0.05 were used as input for DESeq2 for size factor estimation.

organism: Mycobacterium tuberculosis

source_name: In vitro transcription of sheared Mtb genomic DNA

extract_protocol:
Genomic DNA was extracted and prepared from Mtb (wildtype H37Rv) using the CTAB-lysozyme method with phenol-chloroform-isoamyl alcohol extraction. RNA was isolated from in vitro transcription reactions using the Zymo Research RNA Clean & Concentrator-5 column purification kit.
5' end libraries were prepared using the following procedure: blocking the 3' ends by ligating a 3'SpC3 ssDNA adaptor; converting 5'PPP to 5'P; ligating a 5' ssDNA adaptor with replicate-specific inline barcodes; pooling samples; fragmenting RNA to Illumina-appropriate size using zinc; repairing transcript ends; degrading non-5' end RNA fragments; ligating a 3' ssDNA adaptor complementary to a specific reverse transcription primer; carrying out reverse transcription and digesting RNA in the RNA-DNA hybrids with RNase H; and amplifying the final library using primers and indices from the NEBNext Small RNA Library Prep Kit. 3' end libraries were prepared using the following procedure: ligating a 3'SpC3 ssDNA adaptor with replicate-specific inline barcodes and reverse transcription primer handle; pooling samples; fragmenting RNA to Illumina-appropriate size using zinc; carrying out reverse transcription and digesting RNA in the RNA-DNA hybrids with RNase H; and amplifying the final library using primers and indices from the NEBNext Small RNA Library Prep Kit. Mtb genomic DNA samples were prepared by the Rockefeller University Genomics Resource Center using their full service library preparation and sequencing option for whole-genome sequencing.

value: Purified components from bacterial cells

value: RNAP-SigA-WhiB1 holoenzyme (including CarD and RbpA)


title: WT-3

value: Human fibrosarcoma


title: WhiB1 experiment TSS WhiB1 rep3 (RNAP-SigA-RbpA-CarD + WhiB1)

description: Library name: Sample 9

value: In vitro transcription of sheared Mtb genomic DNA


description:
Library name: d0_expHSPC_Flt3L_primed_LSK_bulk_RNA_rep2
RNA

value: LSK sorted Flt3L primed expanded HSPC


title: OCI-AML22 - LTR12C_2


title: WT-2

value: WT


description:
Library name: d0_expHSPC_Flt3L_primed_LSK_bulk_RNA_rep1
RNA


title: ESS1-AID, DMSO, control, rep1

description:
Library name: Sample1
column name in raw_counts.txt: DMSO-1


title: OCI-AML22 - LTR12C_1


title: WhiB1 experiment TSS noWhiB1 rep3 (RNAP-SigA-RbpA-CarD)

description: Library name: Sample 6

value: RNAP-SigA holoenzyme (including CarD and RbpA)


title: OCI-AML22 - C3

value: scramble gRNAs


title: Primary neurons of mice, Interfering peptide (100 uM)with DEX, rep4

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

description: Library name: PN-E5-4

data_processing:
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
Assembly: mm10
Supplementary files format and content: .csv

molecule: polyA RNA

source_name: Primary cortical neurons

growth_protocol: L929 cell lines were maintained in DMEM supplemented with 10% FBS and P/S, and primary cultrued neurons in Neurobasal supplemented with B27, Glutamin-Max and P/S with 5% CO2 at 37℃.

extract_protocol:
Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing. The basic principle of sequencing is "Sequencing by Synthesis", where fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

treatment_protocol: Cultured with dexamethasone (Sigma), and peptide with different concentration 4 hours.

value: Primary cortical neurons

value: Interfering peptide (100 uM)with DEX


title: d0_expHSPC_unprimed_LSK_bulk_RNA_rep1

description:
Library name: d0_expHSPC_unprimed_LSK_bulk_RNA_rep1
RNA

value: bone-marrow

value: LSK sorted unprimed expanded HSPC


title: Primary neurons of mice, Interfering peptide (100 uM)with DEX, rep3

description: Library name: PN-E5-3


title: scRNAseq_HTO_library_exp2

description:
Library name: scRNAseq_HTO_library_exp2
Hashtag oligo library 2

library_source: other

molecule: other

source_name: synthetic DNA barcode

value: synthetic DNA barcode


title: Primary neurons of mice, Interfering peptide (100 uM)with DEX, rep2

description: Library name: PN-E5-2


title: scRNAseq_HTO_library_exp1

description:
Library name: scRNAseq_HTO_library_exp1
Hashtag oligo library 1


title: WhiB1 experiment TSS noWhiB1 rep1 (RNAP-SigA-RbpA-CarD)

description: Library name: Sample 4


title: OCI-AML22 - C1

value: Acute Myeloid Leukemia


title: WhiB1 experiment TSS WhiB1 rep1 (RNAP-SigA-RbpA-CarD + WhiB1)

description: Library name: Sample 7


title: Primary neurons of mice, Interfering peptide (30 uM) with DEX, rep4

description: Library name: PN-E4-4

value: Interfering peptide (30 uM) with DEX


title: Graft_10082020

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger™ Single Cell Software Suite v.4.0.0 was used and The reads were aligned to the human transcriptome reference (cellranger GRCh38, Ensembl 98) with STAR 2.6
Assembly: cellranger-GRCh38-3.0.0
Supplementary files format and content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: Kidney transplant

extract_protocol:
PBMC was obtained using ficoll-hypaque gradient centrifugation in accordance with the manufacturer's instructions. Biopsies were cut into small fragments and incubated at 37°C in buffer containing 0.25% trypsin (Gibco) and 40 U/ml DNase I (Thermo Fisher). Dissociated cells were filtered every 10 minutes through a 70 mm cell strainer (Greiner Bio-One) into cold 10% FBS buffer. Residual tissue was dissociated again and passed through the cell strainer. After centrifugation at 400Xg for 5 minutes, cells were resuspended in 2% FBS buffer and strained again through a 40-μm cell strainer
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Kidney transplant

value: CD45+ immune cells

value: Female


title: Primary neurons of mice, Interfering peptide (100 uM)with DEX, rep1

description: Library name: PN-E5-1


title: WhiB1 experiment TSS core RNAP only2

description: Library name: Sample 2

value: Purified components from bacterial cells

value: core RNAP only


title: d0_expHSPC_unprimed_LSK_bulk_RNA_rep2

description:
Library name: d0_expHSPC_unprimed_LSK_bulk_RNA_rep2
RNA

value: wild-type

value: Untreated


title: Graft_07132021

description: 10x Genomics

value: Male


title: WhiB1 experiment TSS core RNAP only3

description: Library name: Sample 3

value: In vitro transcription of sheared Mtb genomic DNA

value: WT


title: scRNAseq_cDNA_library_exp2

description:
Library name: scRNAseq_cDNA_library_exp2
Single-cell RNA library as cDNA 2

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted expanded HSPC,Lin-Kit+Sca1+ (LSK)-sorted Expanded HSPC, LSK-sorted Flt3L-primed expanded HSPC, ELSK or LSK-sorted expanded HSPCs co-cultured with OP9-Dll1 for 5 or 9 days,ELSK-sorted fresh HSPC,LSK-sorted fresh HSPC, ELSK-sorted fresh HSPCs co-cultured with OP9-Dll1 for 5 or 9 days.

value: wild-type and Bcl11b-mCitrine reporter


title: Primary neurons of mice, Interfering peptide (30 uM) with DEX, rep2

description: Library name: PN-E4-2

value: Primary cortical neurons


title: TSS CRP3 (RNAP-SigA-RbpA-CarD + CRP)

value: CRP and cyclic AMP added to RNAP-SigA holoenzyme (including CarD and RbpA)


title: Primary neurons of mice, Interfering peptide (30 uM) with DEX, rep1

description: Library name: PN-E4-1


title: WhiB1 experiment TSS core RNAP only1

description: Library name: Sample 1


description:
Library name: Expanded_HSPCs_Flt3L_primed_IgG_CnR_rep3
IgG

value: bone-marrow

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days


title: Graft_10162020

description: 10x Genomics


title: WhiB1 experiment TSS noWhiB1 rep2 (RNAP-SigA-RbpA-CarD)

description: Library name: Sample 5

value: RNAP-SigA holoenzyme (including CarD and RbpA)


title: scRNAseq_cDNA_library_exp1

description:
Library name: scRNAseq_cDNA_library_exp1
Single-cell RNA library as cDNA 1


title: Primary neurons of mice, Interfering peptide (30 uM) with DEX, rep3

description: Library name: PN-E4-3

value: Interfering peptide (30 uM) with DEX


description:
Library name: Expanded_HSPCs_Flt3L_primed_IgG_CnR_rep2
IgG


title: PBMC_10162020

description: 10x Genomics

source_name: PBMC

value: PBMC

value: CD45+ immune cells


title: TSS CRP2 (RNAP-SigA-RbpA-CarD + CRP)

value: Purified components from bacterial cells


title: TTS NusA_NusG1 (RNAP-SigA-RbpA-CarD + NusG)

value: NusA and NusG added to RNAP-SigA holoenzyme (including CarD and RbpA)


description:
Library name: Expanded_HSPCs_Flt3L_primed_IgG_CnR_rep1
IgG

value: wild-type


title: Primary neurons of mice, Interfering peptide (10 uM) with DEX, rep3

description: Library name: PN-E3-3

value: Interfering peptide (10 uM) with DEX


title: Expanded_HSPCs_unprimed_IgG_CnR_rep1

description:
Library name: Expanded_HSPCs_unprimed_IgG_CnR_rep1
IgG

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in untreated condition for 4 days

value: Untreated


title: Primary neurons of mice, Interfering peptide (10 uM) with DEX, rep1

description: Library name: PN-E3-1


title: TSS noCRP1 (RNAP-SigA-RbpA-CarD)

value: In vitro transcription of sheared Mtb genomic DNA

value: WT


title: Primary neurons of mice, Interfering peptide (10 uM) with DEX, rep2

description: Library name: PN-E3-2


title: TSS noCRP3 (RNAP-SigA-RbpA-CarD)


title: TTS NusG3 (RNAP-SigA-RbpA-CarD + NusG)

value: NusG added to RNAP-SigA holoenzyme (including CarD and RbpA)


title: Primary neurons of mice, Interfering peptide (3 uM) with DEX, rep4

description: Library name: PN-E2-4

value: Primary cortical neurons

value: Interfering peptide (3 uM) with DEX


title: OCI-AML22 - C2

value: Acute Myeloid Leukemia

value: scramble gRNAs


title: TSS CRP1 (RNAP-SigA-RbpA-CarD + CRP)

value: CRP and cyclic AMP added to RNAP-SigA holoenzyme (including CarD and RbpA)


title: Expanded_HSPCs_unprimed_IgG_CnR_rep2

description:
Library name: Expanded_HSPCs_unprimed_IgG_CnR_rep2
IgG

value: bone-marrow


description:
Library name: Expanded_HSPCs_unprimed_H3K27me3_CnR_rep2
H3K27m3


title: Primary neurons of mice, Interfering peptide (3 uM) with DEX, rep3

description: Library name: PN-E2-3


title: TSS core RNAP only2

value: core RNAP only


title: TSS core RNAP only3


description:
Library name: Expanded_HSPCs_Flt3L_primed_H3K27me3_CnR_rep1
H3K27m3

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days


title: TTS NusA_NusG2 (RNAP-SigA-RbpA-CarD + NusG)

value: Purified components from bacterial cells


title: TTS NusA3 (RNAP-SigA-RbpA-CarD + NusA)

value: NusA added to RNAP-SigA holoenzyme (including CarD and RbpA)


title: TTS NusA_NusG3 (RNAP-SigA-RbpA-CarD + NusG)

value: NusA and NusG added to RNAP-SigA holoenzyme (including CarD and RbpA)


description:
Library name: Expanded_HSPCs_unprimed_H3K27me3_CnR_rep1
H3K27m3

value: wild-type


title: Primary neurons of mice, Interfering peptide (10 uM) with DEX, rep4

description: Library name: PN-E3-4

value: Interfering peptide (10 uM) with DEX


title: TTS NusG1 (RNAP-SigA-RbpA-CarD + NusG)


title: TSS core RNAP only1


description:
Library name: Expanded_HSPCs_Flt3L_primed_H3K27ac_CnR_rep2
H3K27ac


title: Primary neurons of mice, Interfering peptide (1 uM) with DEX, rep4

description: Library name: PN-E1-4

value: Interfering peptide (1 uM) with DEX


description:
Library name: Expanded_HSPCs_Flt3L_primed_H3K27ac_CnR_rep1
H3K27ac


title: TSS noCRP2 (RNAP-SigA-RbpA-CarD)

value: In vitro transcription of sheared Mtb genomic DNA

value: RNAP-SigA holoenzyme (including CarD and RbpA)


title: Primary neurons of mice, Interfering peptide (3 uM) with DEX, rep2

description: Library name: PN-E2-2


title: TTS NusG2 (RNAP-SigA-RbpA-CarD + NusG)

value: WT

value: NusG added to RNAP-SigA holoenzyme (including CarD and RbpA)


title: TTS NusA2 (RNAP-SigA-RbpA-CarD + NusA)


title: TTS NusA1 (RNAP-SigA-RbpA-CarD + NusA)


title: Primary neurons of mice, Interfering peptide (1 uM) with DEX, rep3

description: Library name: PN-E1-3

value: Primary cortical neurons


title: WT3

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Library name: WT3

data_processing:
Samples were demultiplexed, quality checked, filtered and aligned genome build GRCm38 using CellRanger v9.0.1. Resulting raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes were processed, analyzed and visualized in R v. 4.3.1 using Seurat v.4 with default parameters in all functions, unless specified. Poor quality cells, with low total unique molecular identifier (UMI) counts and high percent mitochondrial gene expression, were excluded. Filtered samples were normalized using a regularized negative binomial regression (SCTransform) and integrated with Harmony, using 50 principal components. Integrated gene expression matrices were visualized with a UMAP as a dimensionality reduction approach. Resolution for cell clustering was determined by evaluating hierarchical clustering trees at a range of resolutions (0 - 1.2) with Clustree, selecting a value inducing minimal cluster instability. Datasets were subsetted to include only macrophages, based on the expression of key macrophage markers (Adgre1, Csf1r, H2-Ab1, Cd68, Lyz2, Itgam, Mertk). Macrophage only datasets were then split along conditions, and processed anew as described above.
Assembly: mm10
Supplementary files format and content: Raw and filtered counts as Seurat Object in "rds" format

source_name: Lung macrophages

extract_protocol:
Single cells were isolated from digested lungs and LIVE CD45+YFP+ cells were FACS sorted from 3 biological replicates per genotype Dhps+/+ LysM-Cre Rosa26eYFP (control) and Dhps-M Rosa26eYFP mice.
Cells were submitted for 10X Genomics library preparation to the sequencing company OMAPiX using the GEM-X Universal 3’ Gene Expression kit. Libraries were sequenced on NovaSeq 6000 (Illumina).

value: Lung macrophages


title: TTS noTF3 (RNAP-SigA-RbpA-CarD)


description:
Library name: Expanded_HSPCs_unprimed_H3K27ac_CnR_rep2
H3K27ac

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in untreated condition for 4 days

value: Untreated


title: WT1

description: Library name: WT1


title: Primary neurons of mice, Interfering peptide (1 uM) with DEX, rep2

description: Library name: PN-E1-2


description:
Library name: In_vitro_Bcl11bpos_DN2a/b_bulk_ATAC_rep2
genomic accessibility

value: bone-marrow

value: Expanded HSPC-derived Bcl11b+ DN2a/DN2b (Kit high/int CD25+ Bcl11b-mCitrine+) from day9 OP9-Dll1 co-culture


title: Primary neurons of mice, Interfering peptide (1 uM) with DEX, rep1

description: Library name: PN-E1-1


description:
Library name: In_vitro_Bcl11bpos_DN2a/b_bulk_ATAC_rep1
genomic accessibility


title: TTS noTF2 (RNAP-SigA-RbpA-CarD)


description:
Library name: Expanded_HSPCs_unprimed_H3K27ac_CnR_rep1
H3K27ac


title: Primary neurons of mice, Interfering peptide (3 uM) with DEX, rep1

description: Library name: PN-E2-1

value: Interfering peptide (3 uM) with DEX


title: TTS noTF1 (RNAP-SigA-RbpA-CarD)

value: Purified components from bacterial cells


title: Primary neurons of mice, Control peptide (100 uM) with DEX, rep4

description: Library name: PN-E0-4

value: Control peptide (100 uM) with DEX


title: Mtb gDNA3

source_name: Mtb genomic DNA input for in vitro transcription


title: DHPS1

description: Library name: DHPS1

value: KO


title: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep3

description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep3
genomic accessibility

value: Expanded HSPC-derived Bcl11b- DN2a(Kit high CD25+ Bcl11b-mCitrine-) from day5 OP9-Dll1 co-culture


title: Mtb gDNA1

value: Mtb genomic DNA input for in vitro transcription


title: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep2

description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep2
genomic accessibility

value: Expanded HSPC-derived Bcl11b- DN2a(Kit high CD25+ Bcl11b-mCitrine-) from day9 OP9-Dll1 co-culture


title: DHPS3

description: Library name: DHPS3


title: Primary neurons of mice, Control peptide (100 uM) with DEX, rep3

description: Library name: PN-E0-3


title: phm-2(zw93)-3

city: Denton

first: Bojun

last: Chen

address: 1511 W Sycamore St

department: Biological Sciences

institute: University of North Texas

description: Library name: Sample 6

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality. The filtering process is as follows: 1)Discard reads with adaptor contamination.2)Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%). 3)Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
Filtered reads are mapped to the reference genome using Tophat v2.0.12. The mismatch parameter is set to two, and other parameters are set to default.
Gene expression level is estimated by counting the reads that map to exons using DEGSeq 1.12.0. The input data for differential gene expression analysis are readcounts from gene expression level analysis. The differential gene expression analysis contains three steps: 1)Readcounts Normalization; 2)Model dependent p-value estimation; 3)FDR value estimation based on multiple hypothesis testing.
Assembly: ce11
Supplementary files format and content: Tab-delimited text files include Readcount and FPKM.

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Worms were washed off the culture plates and washed three times with M9 buffer. Total RNA was extracted using TRIzol Reagent (Invitrogen) and treated with TURBO DNase (Ambion).
RNA libraries were constructed using standard Illumina protocols.

value: whole worm

value: N2 (Bristol)

tag: developmental stage

value: young adult


title: Primary neurons of mice, Control peptide (100 uM) with DEX, rep2

description: Library name: PN-E0-2


title: Mtb gDNA2

value: WT


title: Primary neurons of mice, Control peptide (100 uM) with DEX, rep1

description: Library name: PN-E0-1

value: Primary cortical neurons


title: DHPS2

description: Library name: DHPS2

value: Lung macrophages


title: HFD-yP-122 I-2

city: Iowa City

first: Ajit

last: Vikram

state: IA

address: 285 Newton Road

department: Internal Medicine

institute: University of Iowa

description: Library name: AV_0846_S14

data_processing:
Primary analysis and de‐multiplexing were performed using Illumina's bcl2fastq v2.20.
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat (v2.1.0) using the mouse (GRCm39) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Assembly: GRCm39
Supplementary files format and content: rawreads.txt raw counts of samples
Supplementary files format and content: These are they rawreads.txt raw counts of samples

source_name: Aorta

growth_protocol: Standard protocol

extract_protocol:
RNA was isolated using Trizol, quantified by the RiboGreen assay, and RNA integrity was assessed using capillary electrophoresis.
RNA samples were used to generate Illumina sequencing libraries using Illumina's TruSeq RNA Sample Preparation Kit or Stranded mRNA Sample Preparation Kit.

treatment_protocol: 8 weeks-old mice (male) were fed a high-fat diet (HFD) for eight weeks. Two weeks after dietary intervention, these mice were intraperitoneally injected with either γPSC, γP-122-I, e-γP-SC, or e-γP-122-I (0.25 μmol.kg-1) for six weeks.

value: Aorta

value: male

value: 8 weeks-old


title: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep1

description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_ATAC_rep1
genomic accessibility

source_name: bone-marrow

value: bone-marrow


title: In_vitro_ETP_bulk_ATAC_rep1

description:
Library name: In_vitro_ETP_bulk_ATAC_rep1
genomic accessibility

value: Expanded HSPC-derived ETP (Kit high CD25- Bcl11b-mCitrine-) from day9 OP9-Dll1 co-culture


title: HFD-yP-SC-4

description: Library name: AV_0937_S16


title: HFD-yP-122 I-3

description: Library name: AV_0847_S15


title: WT2

description: Library name: WT2


title: Primary neurons of mice, Control peptide (100 uM) without DEX, rep3

description: Library name: PN-C0-3

value: Control peptide (100 uM) without DEX


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_ATAC_rep2
genomic accessibility

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days

value: wild-type


title: HFD-e-yP-122 I-4

description: Library name: AV_0740_S11


title: Primary neurons of mice, Control peptide (100 uM) without DEX, rep4

description: Library name: PN-C0-4


title: Primary neurons of mice, Control peptide (100 uM) without DEX, rep2

description: Library name: PN-C0-2


title: Primary neurons of mice, Control peptide (100 uM) without DEX, rep1

description: Library name: PN-C0-1


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_ATAC_rep1
genomic accessibility


title: wild type 2

description: Library name: Sample 2

value: wild type


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_ATAC_rep3
genomic accessibility


title: HFD-e-yP-122 I-2

description: Library name: AV_0738_S9


title: Expanded_HSPCs_unprimed_bulk_ATAC_rep3

description:
Library name: Expanded_HSPCs_unprimed_bulk_ATAC_rep3
genomic accessibility

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in untreated condition for 4 days

value: Untreated


title: HFD-e-yP-122 I-5

description: Library name: AV_0741_S12


title: HFD-yP-122 I-1

description: Library name: AV_0845_S13


title: TCRb, ND580, Cells 49-96

city: Philadelphia

first: Ning

last: Jiang

state: PA

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

description: single cell TCRb amplicon

data_processing:
Cell barcodes were demultiplexed using UMI-tools (version 1.0.1: https://umi-tools.readthedocs.io/en/latest/INSTALL.html). Contigs were assembleda and VDJ genes and CDR3 sequences were assigned using MiXCR (version 4.5.0: https://github.com/milaboratory/mixcr/releases/)
Assembly: N/A
Supplementary files format and content: Processed TCR alpha and beta variable genes and CDR3 sequences are provided in Excel spreadsheet

extract_protocol:
CD8+ T cells and B cells were negatively enriched from cryopreserved PBMCs and cocultured in the presence of peptide, IL2, IL4, IL21, and multimeric CD40L. After 2 weeks, cells were stained with cognate pMHC tetramers and tetramer+ CD8+ T cells were single cell sorted on a BD AriaFusion into lysis buffer. Lysates were snap frozen and stored at -80℃ until use. Reverse transcription and cDNA amplification was done in single cell lysate without RNA extraction
Reverse transcription was performed on lysates with TRBC- and TRAC-specific primers. PCR1 was carried out with the same TRBC/TRAC primers and V-region primers. PCR2 for alpha and beta chains was carried out separately with dual-nested primers binding constant and V-regions with partial Illumina adapters. Index PCR was carried out with Illumina P5 and P7 dual-index primers. Index PCR products for each cell were then pooled and gel purified.

value: Blood

value: In vitro expanded human CD8 T cells

value: in vitro expanded


title: phm-2(zw93)-1

description: Library name: Sample 4

value: whole worm

value: N2 (Bristol)

value: young adult


title: HFD-e-yP-122 I-3

description: Library name: AV_0739_S10

value: Aorta


title: In_vitro_ETP_bulk_ATAC_rep2

first: Boyoung

last: Shin

address: 1200 E. California Blvd

institute: Californial Institute of Technology

description:
Library name: In_vitro_ETP_bulk_ATAC_rep2
genomic accessibility

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen #74105) with on-column DNase I treatment (Qiagen #1023460)
Bulk RNA-seq library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina.
Bulk ATAC-seq library was constructed after transposition reaction using Tn5 transposases (Illumina #15027916) by following previously published protocol (Corces et al., 2017 Nat Methods, PMID: 28846090).
CUT&RUN library was constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E7645S, #E7500S, #M5505S) by following previously reported protocol ((Liu et al., 2018 Cell, PMID: 29606353)
Single-cell RNA-seq cDNA libraries were prepared using 10X Chromium 3’ capture v3.1 kit.
Single-cell hashtag oligo library was prepared in accordance with the BioLegend TotalseqA guide.

value: Expanded HSPC-derived ETP (Kit high CD25- Bcl11b-mCitrine-) from day5 OP9-Dll1 co-culture


title: Expanded_HSPCs_unprimed_bulk_ATAC_rep2

description:
Library name: Expanded_HSPCs_unprimed_bulk_ATAC_rep2
genomic accessibility


title: wild type 3

description: Library name: Sample 3


title: L929, delta-coiled-coil and -LCDs (Isoform 2), rep3

description: Library name: L929-DD-3

source_name: L929 cell line

value: L929 cell line

value: delta-coiled-coil and -LCDs (Isoform 2)


title: HFD-e-yP-122 I-1

description: Library name: AV_0737_S8

value: male

value: 8 weeks-old


title: L929, delta-coiled-coil and -LCDs (Isoform 2), rep2

description: Library name: L929-DD-2


title: L929, delta-IDR combined domain (Isoform 2), rep4

description: Library name: L929-DIDR-4

value: delta-IDR combined domain (Isoform 2)


description:
Library name: In_vitro_Bcl11bpos_DN2a/b_bulk_RNA_d9_rep2
RNA

value: bone-marrow

value: Expanded HSPC-derived Bcl11b+ DN2a/DN2b (Kit high/int CD25+ Bcl11b-mCitrine+) from day9 OP9-Dll1 co-culture


title: L929, delta-coiled-coil and -LCDs (Isoform 2), rep1

description: Library name: L929-DD-1


title: L929, delta-coiled-coil and -LCDs (Isoform 2), rep4

description: Library name: L929-DD-4


title: TCRb, ND602, Cells 49-96

description: single cell TCRb amplicon

source_name: Blood


title: wild type 1

description: Library name: Sample 1

value: wild type


title: HFD-yP-SC-3

description: Library name: AV_0019_S3


title: TCRb, ND580, Cells 1-48

description: single cell TCRb amplicon


title: Expanded_HSPCs_unprimed_bulk_ATAC_rep1

description:
Library name: Expanded_HSPCs_unprimed_bulk_ATAC_rep1
genomic accessibility

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in untreated condition for 4 days

value: wild-type

value: Untreated


title: phm-2(zw93)-2

description: Library name: Sample 5


title: TCRa, ND580, Cells 1-48

description: single cell TCRa amplicon

value: Blood

value: In vitro expanded human CD8 T cells

value: in vitro expanded


title: HFD-e-yP-SC-4

description: Library name: AV_0734_S7


title: TCRa, ND602, Cells 1-48

description: single cell TCRa amplicon


description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_RNA_d9_rep1
RNA

value: Expanded HSPC-derived Bcl11b- DN2a(Kit high CD25+ Bcl11b-mCitrine-) from day9 OP9-Dll1 co-culture


description:
Library name: In_vitro_Bcl11bpos_DN2a/b_bulk_RNA_d9_rep1
RNA


title: L929, delta-IDR combined domain (Isoform 2), rep3

description: Library name: L929-DIDR-3


title: L929, delta-IDR combined domain (Isoform 2), rep1

description: Library name: L929-DIDR-1


title: HFD-e-yP-SC-1

description: Library name: AV_0731_S4

value: Aorta


title: HFD-e-yP-SC-2

description: Library name: AV_0732_S5


title: TCRb, ND602, Cells 1-48

description: single cell TCRb amplicon


description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_RNA_d9_rep2
RNA


title: L929, Full-length (Isoform 2), rep4

description: Library name: L929-F517D-4

value: Full-length (Isoform 2)


title: In_vitro_Bcl11bneg_DN2a_bulk_RNA_d5

description:
Library name: In_vitro_Bcl11bneg_DN2a_bulk_RNA_d5
RNA

value: Expanded HSPC-derived Bcl11b- DN2a(Kit high CD25+ Bcl11b-mCitrine-) from day5 OP9-Dll1 co-culture


title: TCRa, ND580, Cells 49-96

description: single cell TCRa amplicon


title: TCRa, ND602, Cells 49-96

description: single cell TCRa amplicon


title: HFD-yP-SC-2

description: Library name: AV_0018_S2


title: L929, delta-IDR combined domain (Isoform 2), rep2

description: Library name: L929-DIDR-2

value: L929 cell line


title: TCRb, DonorB, Cells 48-96

description:
single cell TCRb amplicon
tcr-combined_final.txt

data_processing:
Cell barcodes were demultiplexed using UMI-tools (version 1.0.1: https://umi-tools.readthedocs.io/en/latest/INSTALL.html). Contigs were assembleda and VDJ genes and CDR3 sequences were assigned using MiXCR (version 4.5.0: https://github.com/milaboratory/mixcr/releases/)
Assembly: IMGT/LIGM-DB
Supplementary files format and content: Combined tab-delimited VDJ and CDR3 features data for each cell from in vitro expanded scTCR-seq experiments
Library strategy: scTCR-seq

extract_protocol:
CD8+ T cells and B cells were negatively enriched from cryopreserved PBMCs and cocultured in the presence of peptide, IL2, IL4, IL21, and multimeric CD40L. After 2 weeks, cells were stained with cognate pMHC tetramers and tetramer+ CD8+ T cells were single cell sorted on a BD AriaFusion into lysis buffer. Lysates were snap frozen and stored at -80℃ until use.
Reverse transcription was performed on lysates with TRBC- and TRAC-specific primers. PCR1 was carried out with the same TRBC/TRAC primers and V-region primers. PCR2 for alpha and beta chains was carried out separately with dual-nested primers binding constant and V-regions with partial Illumina adapters. Index PCR was carried out with Illumina P5 and P7 dual-index primers. Index PCR products for each cell were then pooled and gel purified.

value: CD8+ T cells

tag: library type

value: TCR

tag: condition


title: In_vitro_ETP_bulk_RNA_d5

description:
Library name: In_vitro_ETP_bulk_RNA_d5
RNA

value: Expanded HSPC-derived ETP (Kit high CD25- Bcl11b-mCitrine-) from day5 OP9-Dll1 co-culture


title: TCRb, DonorB, Cells 1-48


title: In_vitro_ETP_bulk_RNA_d9_rep2

description:
Library name: In_vitro_ETP_bulk_RNA_d9_rep2
RNA

value: bone-marrow

value: Expanded HSPC-derived ETP (Kit high CD25- Bcl11b-mCitrine-) from day9 OP9-Dll1 co-culture


title: HFD-yP-SC-1

description: Library name: AV_0016_S1

value: male

value: 8 weeks-old


title: RNA-Seq of C.elegans: day-3 nova-1 mutant hermaphrodite replicate 4

city: Reno

first: Emmanuel

last: Adeyemi

state: NV

address: 1664 N. Virginia Street,

department: Biology

institute: University of Nevada Reno

description: Library name: nova-1_day-3_rep4

data_processing:
CLC Genomics Workbench
Assembly: ce11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole organism

growth_protocol: Day 3 Adults

extract_protocol:
Total RNA was extracted from Day-3 adult worms using the Purelink RNA mini-kit, followed by a DNase I treatment following the manufacturer's protocol. RNA integrity number ranged from 9.6 to 10.0. Samples were stored at -80C prior to RNA-sequencing.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit as recommended by the manufacturer (Illumina) with modified conditions to increase the size of the cloned fragments (fragmentation at 85 °C × 5 min). Barcoded libraries were sequenced at the University of Connecticut genomics center.

value: whole organism

value: Day-3 Adults


title: TCRa, DonorB, Cells 48-96

description:
single cell TCRa amplicon
tcr-combined_final.txt

value: Blood


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_RNA_rep3
RNA

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in Flt3L-priming condition for 4 days

value: wild-type


title: Chip_6, TCR

description:
BD Rhapsody
metadata_totalvi.csv

data_processing:
Cell barcode demultiplexing and TCR umi quantification were done with BD Rhapsody Targeted Analysis Pipeline (Revision 15) available on Seven Bridges Genomics.
Assembly: IMGT/LIGM-DB
Supplementary files format and content: Combined comma-separated matrix where cells are rows and meta data is columns. Contains donor meta data, experiment information, TCR data, pMHC tetramer barcode counts, putative specificity data, phenotype/clustering data, cell phenotype assignment, and more.

extract_protocol:
CD8+ T cells were negatively enriched from cryopreserved PBMC samples and treated with 2.5uM Dasatinib for approximately 30 minutes. Cells were then stained on ice for 1 hour with multiplexed tetramers, then sorted on a BD AriaFusion. Single cells were then isolated and processed using the BD Rhapsody system following manufacturer's instructions.
Libraries were constructed according to manufacturer's instructions (BD Rhapsody Targeted mRNA and TCR/BCR Amplification kit), except full length TCR libraries were not generated. Instead, 10.5ng of PCR2 product was used directly for index PCR.

value: ex vivo


title: HFD-e-yP-SC-3

description: Library name: AV_0733_S6

value: Aorta


title: RNA-Seq of C.elegans: day-3 nova-1 mutant hermaphrodite replicate 2

description: Library name: nova-1_day-3_rep2


title: L929, Control, rep4

description: Library name: L929-F517C-4

value: Control


title: RNA-Seq of C.elegans: day-3 nova-1 mutant hermaphrodite replicate 5

description: Library name: nova-1_day-3_rep5


title: L929, Control, rep3

description: Library name: L929-F517C-3


title: L929, Full-length (Isoform 2), rep1

description: Library name: L929-F517D-1

value: Full-length (Isoform 2)


title: L929, Full-length (Isoform 2), rep2

description: Library name: L929-F517D-2

value: L929 cell line


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_RNA_rep2
RNA


title: RNA-Seq of C.elegans: day-3 nova-1 mutant hermaphrodite replicate 3

description: Library name: nova-1_day-3_rep3


title: RNA-Seq of C.elegans: day-3 nova-1 mutant hermaphrodite replicate 1

description: Library name: nova-1_day-3_rep1


title: Chip_4, TCR

description:
BD Rhapsody
metadata_totalvi.csv

value: CD8+ T cells


title: In_vitro_ETP_bulk_RNA_d9_rep1

description:
Library name: In_vitro_ETP_bulk_RNA_d9_rep1
RNA


title: Expanded_HSPCs_unprimed_bulk_RNA_rep2

description:
Library name: Expanded_HSPCs_unprimed_bulk_RNA_rep2
RNA

value: EPCR+CD150+Lin-Kit+Sca1+ (ELSK)-sorted Expanded HSPCs in untreated condition for 4 days

value: Untreated


title: RNA-Seq of C.elegans: day-3 wild-type hermaphrodite replicate 4

description: Library name: wildtype_day-3_rep4

value: Wildtype


title: RNA-Seq of C.elegans: day-3 wild-type hermaphrodite replicate 5

description: Library name: wildtype_day-3_rep5


title: L929, Control, rep1

description: Library name: L929-F517C-1


description:
Library name: Expanded_HSPCs_Flt3L_primed_bulk_RNA_rep1
RNA

value: bone-marrow


title: L929, Control, rep2

description: Library name: L929-F517C-2


title: L929, Full-length (Isoform 2), rep3

description: Library name: L929-F517D-3


title: RNA-Seq of C.elegans: day-3 wild-type hermaphrodite replicate 3

description: Library name: wildtype_day-3_rep3


title: Chip_5, TCR

description:
BD Rhapsody
metadata_totalvi.csv

value: TCR


title: RNA-Seq of C.elegans: day-3 wild-type hermaphrodite replicate 2

description: Library name: wildtype_day-3_rep2


title: Expanded_HSPCs_unprimed_bulk_RNA_rep3

description:
Library name: Expanded_HSPCs_unprimed_bulk_RNA_rep3
RNA


title: B. fragilis microSPLiT library M30

city: Seattle

first: Dmitry

last: Sutormin

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Library name: M30
microSPLiT library

data_processing:
Reference genome was obtained by combining the reference genomes for  Bacteroides fragilis NCTC 9343 and BF12P1 phage. With the combined reference, barcode lists for each of three indexing rounds, and output sequencing files, STARsolo was run for genome alignment, preserving only the uniquely aligned reads. The raw count matrix was loaded into AnnData; after assigning reads to barcode combinations and sample wells, log-log barcode rank plots were used to determine an initial filtering threshold of 400 UMIs/cell for a reduced likelihood of doubly labeled cells. Remaining ribosomal (r)RNA and transfer (t)RNA reads were filtered out, and the dataset was filtered again by 40 UMIs/cell.
Two F3 libraries were concatenated after filtering, log-normalized by 600 counts per cell, and scaled to unit variance and zero mean. Subsequently, ComBat was run for batch effect correction. Normalized expression data was dimensionally reduced using principal component analysis (PCA). Shared neighbor graphs and uniform manifold approximation representations (UMAP74) were calculated with the first 12 principal components. All subsequent calculations were run in Python using Scanpy documentation for single-cell analysis.
B_fragilis_microSPLiT_supplementary.tar file, associated with this dataset, contains barcode lists, combined reference genome, and plate file for samples deconvolution essential for data analysis.
Assembly: GCF_000025985.1 (Bacteroides fragilis NCTC 9343), Bf12P1 (Bf12P1 siphovirus)
Supplementary files format and content: Tab-separated value and matrix files, generated by STARSolo.

organism: Bacteroides fragilis

source_name: NCTC 9343

growth_protocol: Bacteroides fragilis NCTC 9343 was cultivated in Chopped meat carbohydrate media overnight at 37°C anaerobically (5% H2, 20% CO2, 75% N2).

extract_protocol:
Fixed cells were spun down at 10,000 rcf for 10 min at 4°C, resuspended in cold 100mM Tris-HCl+RI (100mM Tris-HCl pH=8, 20U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)), and spun down again in the same conditions. Cells were resuspended in 250µL permeabilization solution (0.04% Tween-20 in PBS), incubated for 3 min on ice, and after 1mL addition of PBS+RI (1x PBS, 6U/mL SUPERase-In RNase Inhibitor, 24U/mL Enzymatics RNase Inhibitor (Qiagen)), spun down at 10,000 rcf for 10 min at 4°C. Cells were aspirated and resuspended in 200µL digestion mix (100mM Tris-HCl pH=7, 50mM EDTA, 7.5µg of lysozyme (Thermo Fisher Scientific), 250U/mL SUPERase-In RNase Inhibitor), incubated for 15 min at 37°C, immediately added to 1mL PBST (0.01% Tween-20 in PBS+RI), and centrifuged at 10,000 rcf for 10 min at 4°C. Samples were then resuspended in 50µL PBS+RI per sample post-permeabilization. Cells were counted by hemocytometer, and 7 million cells were taken per plate for polyadenylation. 50µL polyadenylate polymerase I solution (1x E. coli Poly(A) polymerase buffer, 800U/mL SUPERase-In RNase Inhibitor, 50mM ATP, 25U of E. coli Poly(A) polymerase) was added, and each sample was incubated at 37°C for 30 min, spun down with 1mL PBST, and resuspended in PBS+RI. Cells were counted again for verification of the number of cells per plate. Reverse transcription (RT) mix was created on ice with final concentrations of 1X reverse transcription buffer, 0.25U/µL Enzymatics RNase Inhibitor, 0.25U/µL SUPERase-In RNase Inhibitor, 500µM dNTPs, 10U/µL Maxima H Minus Reverse Transcriptase, and 7.5% PEG8000 with a final volume of 1320µL for a 96 well plate. Reverse transcription mix was added (12µL) to wells, already containing 4µL mixture of 12.5µM random hexamer and 12.5µM 15dT primer in each well; cells were vortexed and 4µL suspension was added to wells for a final volume of 20µL. Each sample was loaded into different wells of the reverse transcription plate to demultiplex them during analysis. Plates were incubated at 23°C for 10 min and at 50°C for 50 min at 500 rpm. Then, 40µL PBST was added to each well on ice, samples were pooled in a single tube with 24.96µL 10% Tween-20, and the total reaction was centrifuged for 10 min at 10,000 rcf at 4°C. The sample was aspirated and resuspended in 2.2mL PBS+RI and disaggregated with both a 10µm and 1µm pluriStrainer filters. The composition of the 96-well plate and barcoded oligonucleotides used for RT were as previously described in in Gaisser and Skloss et al., 2024. The ligation master mix was made on ice, containing final concentrations of 1X T4 Ligase Buffer 10X, 0.58U/µL Enzymatics RNase Inhibitor, 0.05U/µL SUPERase-In RNase Inhibitor, 7.5% PEG8000, and 8U/µL T4 DNA Ligase, with a final volume of 2040µL. 2mL cell suspension was added to the ligation mix and 40µL aliquots were transferred into each well of a Round 2 ligation barcode plate before incubating for 30 min at 37°C and adding 10µL of round 2 blocking solution (26.4µM BC_0340, 2.5X Ligase Buffer). The plate was incubated again for 30 min at 37oC, and cells were pooled, disaggregated, and barcoded again (Round 3 blocking solution: 11.5µM BC_0066 , 125mM EDTA). After the final filtering step, cells were washed (4000µL 1X PBS, 40µL 10% Tween-20, 10µM SUPERase-In RNase Inhibitor) and aliquoted into libraries with PBS+RI to a final volume of 50µL. Again, the compositions of the 96-well plates and oligonucleotides used for barcoding step were as previously described in in Gaisser and Skloss et al., 2024.
Aliquoted libraries were mixed with 50µL lysis buffer (20mM Tris-HCl pH=8, 400mM NaCl, 100mM EDTA pH=8, 4.4% SDS) and 10µL of 20mg/mL Proteinase K for protein digestion prior to incubation at 55°C for 2 h with 500 rpm shaking. The resulting biotinylated cDNA was captured on MyOne C1 Dynabeads. For template switching, a common 5’ sequence was added to full-length cDNA by resuspending the beads in 200µL Template Switch Mix (1X Maxima RT Buffer, 7.5% PEG8000, 1mM of each dNTP, 500U/mL SUPERase-In RNase Inhibitor, 2.5µM TSO primer, 10U/µL Maxima H minus RT) and incubating at room temperature for 20 min at 600 rpm before further incubation at 42°C for 90 min with agitation. Then, beads were washed in 250µL Tris-T+RI (10mM Tris-HCl, 0.1% Tween-20, 50U/mL SUPERase-In RNase Inhibitor), decanted, and resuspended again with 100µL per sample of terminal deoxynucleotidyl transferase tailing (TdT) master mix (1X TdT buffer, 0.25mM CoCl2, 1.2mM dCTP, 0.06mM ddCTP, 2U/µL TdT enzyme (NEB), 0.1U/µL RNase H (NEB)). Following incubation for 1 h at 37°C and a wash with Tris-T+RI, cDNA was amplified via qPCR using primers BC_0108/M_0002 and BC_0062, fragmented, and ligated with adapters prior to Illumina Sequencing as was described previously in Gaisser and Skloss et al., 2024.  Sequencing was performed on NovaSeq X Plus Series (PE150, Novogene).

treatment_protocol: A turbid 24-h culture of Bacteroides fragilis NCTC 9343 was diluted in Chopped meat carbohydrate media with Bf12P1 phage at an approximate MOI of 0.00004 (total PFU/total CFU as estimated by OD600) and incubated at 37°C. For bile acid samples, a final concentration of 100µM DCA was added to the media. Sample OD600 measurements were monitored every 30 min to ensure lysis had not yet occurred at the time of collection. At 2.5-3 h and OD600 of 0.23, cells were collected on ice, centrifuged, and resuspended in 1.5mL of 4% formaldehyde.

value: NCTC 9343

value: Treated or not-treated with DCA, infected or not infected with lytic phage Bf12P1


title: RNA-Seq of C.elegans: day-3 wild-type hermaphrodite replicate 1

description: Library name: wildtype_day-3_rep1

value: whole organism

value: Day-3 Adults


title: B. fragilis microSPLiT library F3 12k

description:
Library name: F3_12k
microSPLiT library


title: Chip_3, TCR

description:
BD Rhapsody
metadata_totalvi.csv

value: Blood


title: Day7 sample 1

status: Public on Jan 14 2026

city: Hachioji

first: Yo

last: Shinoda

state: Tokyo

address: 1432-1 Horinouchi

department: Pharmacy

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in the dorsal root ganglion on day 7 after the initiation of MeHg administration

hyb_protocol: For each hybridization, 0.60 μg of Cy3-labeled cRNA were fragmented and hybridized at 65˚C for 17 hr to an Agilent SurePrint G3 Rat Gene Expression v2 8×60K Microarray (Design ID: 074036).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent SureScan G4900DA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Day7 sample 1

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using a Low-Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions. cRNA quantity and Cy3 incorporation were determined using a Nanodrop ND-1000 spectrophotometer and Agilent Bioanalyzer.

extract_protocol: The lumbar spinal cord of deeply anesthetized control, Day 7, and Day 14 rats (four per group) were quickly excised and DRGs were removed in cold PBS. At least 6 DRGs were collected from each individual and mixed as an individual sample. Total RNA was extracted from DRGs using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. RNA quantity and quality were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), as recommended.

treatment_protocol: The MeHg solution was administered orally using a gastric tube at a daily dosage of 6.7 mg/kg for 5 days, followed by no administration for 2 days (to obtain Day 7 samples). This cycle was repeated once to obtain Day 14 samples.

value: Dorsal root ganglion

value: male


title: Day14 sample 1

description: Gene expression in the dorsal root ganglion on day 14 after the initiation of MeHg administration

source_name: Day14 sample 1


title: Day14 sample 2

source_name: Day14 sample 2


title: Expanded_HSPCs_unprimed_bulk_RNA_rep1

city: Pasadena

description:
Library name: Expanded_HSPCs_unprimed_bulk_RNA_rep1
RNA

data_processing:
Bulk RNAseq was processed using ENCODE pipelines. The adapter trimmed reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (v 2.5.1b), and gene expression was calculated with RSEM(v 1.2.31). Then, significant changes in gene expression were determined using DEseq2 (v 1.46.0).
Bulk ATAC-seq and CUT&RUN data was processed by mapping the sequenced reads to the GRCm38/mm10 mouse reference genome using Bowtie 2 following PCR duplicates removal using Picard and mitochondrial reads and blacklist regions filtering using Samtools.  Peak calling was conducted by employing Genrich for ATAC-seq or SEACR for CUT&RUN histone peaks with a stringent mode. Bigwig files were generated using deepTools (v 3.5.1) with binSize 20bp and counts per million (CPM) normalization.
scRNAseq raw reads from cDNA libraries were aligned to the mouse reference genome GRCm38/mm10 using CellRanger and the hashtag oligo (HTO) libraries were quantified and demultiplexed using in-house tools (hashtag tool) as described previously (Zhou et al., 2022 Sci Immunol, PMID: 35594339).
Assembly: GRCm38/mm10
Supplementary files format and content: Raw counts, TPM, and FPKM values from STAR/RSEM outputs (bulk RNAseq)
Supplementary files format and content: Bigwig files (ATAC-seq and CUT&RUN)
Supplementary files format and content: Peak files (ATAC-seq, CUT&RUN) in bed format
Supplementary files format and content: Cell ranger filterted feature barcode matrix output files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)
Supplementary files format and content: Binarized HTO counts output

value: wild-type


title: TCRa, DonorB, Cells 1-48

value: in vitro expanded


title: Day7 sample 3

source_name: Day7 sample 3


title: LAD2 CUT&Tag JUND SCF- + imatinib biol rep 2

first: Tianyu

last: Cao

address: No. 100 Haining Road, Hongkou District

department: Urology

institute: Shanghai General Hospital

description:
Library name: IM_2
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control

data_processing:
Adapter trimming and quality filtering were performed with fastp to generate clean reads.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using Bowtie2.
Quality control included assessment of enrichment using strand cross-correlation (SCC; e.g., NSC/RSC) and evaluation of signal-to-background using deepTools fingerprint plots.
Peaks were called using SEACR with the “stringent” strategy. No IgG/input/no-antibody control library was generated; peaks were called per sample without an external background-control track.
Signal tracks were generated from uniquely mapped reads and converted to bigWig format, normalized to RPKM for visualization in genome browsers (e.g., IGV).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data include (i) BED files containing peak coordinates for each sample, and (ii) bigWig files containing genome-wide signal tracks from uniquely mapped reads normalized to RPKM.
Library strategy: CUT&Tag

growth_protocol: LAD2 human mast cell line was maintained in complete culture medium under standard conditions (37°C, 5% CO₂).

extract_protocol:
CUT&Tag was performed using concanavalin A (ConA) magnetic beads to immobilize cells, followed by permeabilization with digitonin. Cells were incubated with primary anti-JUND antibody (Active Motif 61403; RRID:AB_2793621) and secondary antibody, then with pA/pG-Tn5 transposase to tagment chromatin near antibody-bound sites. DNA fragments were released after tagmentation for library amplification.
Libraries were prepared using Hyperactive™ In-Situ ChIP Library Prep Kit for Illumina (Vazyme; TD903–TD904) following the manufacturer’s instructions. Tagmented fragments were PCR-amplified with P5/P7 indexed primers, purified, and assessed on an Agilent 2100 Bioanalyzer. Libraries were sequenced as paired-end reads on an Illumina instrument.

treatment_protocol: Cells were cultured under three conditions prior to CUT&Tag: (i) SCF withdrawal (medium without SCF; EM), (ii) SCF supplementation (medium + SCF; SCF), and (iii) SCF withdrawal plus imatinib treatment (IM). Two biological replicates were prepared per condition.

value: mast cell

value: Medium without SCF (SCF-) + imatinib


title: Control sample 4

description: Gene expression of control dorsal root ganglion

source_name: Control sample 4


title: Day7 sample 4

source_name: Day7 sample 4


title: Control sample 1

source_name: Control sample 1


title: Chip_1, TCR

description:
BD Rhapsody
metadata_totalvi.csv

value: CD8+ T cells

value: ex vivo


title: Expanded_HSPCs_Sca1+_bulk_RNA_rep1

description:
Library name: Expanded_HSPCs_Sca1+_bulk_RNA_rep1
RNA

value: Expanded HSPCs, Sca1+ selected


title: Chip_2, TCR

description:
BD Rhapsody
metadata_totalvi.csv


title: LAD2 CUT&Tag JUND SCF+ biol rep 2

description:
Library name: SCF_2
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control

value: Medium + SCF (SCF+)


title: qd176_advanced tumor

city: Qingdao

first: yuchun

last: wu

state: Shandong Province

address: Laoshan District, Ningxia Road

institute: Qingdao University

description:
Library name: qd176
Bulk RNA-seq of colorectal tissue

data_processing:
Base calling and generation of raw sequencing reads were performed using the Illumina NovaSeq 6000 system with the manufacturer’s default software and parameters. Raw sequencing reads were quality-trimmed using Trimmomatic (v0.39) to remove adapter sequences and low-quality bases. Clean reads were then aligned to the human reference genome (hg38) using STAR (v2.7.7a) with default parameters. Transcript assembly, read counting, and gene expression quantification were performed using Cufflinks (v2.2.1). Differential gene expression analysis was conducted based on the quantified transcript abundance generated by Cufflinks.
Assembly: hg38
Supplementary files format and content: Processed data files include gene expression matrices containing FPKM values for each gene across all samples.

source_name: colorectum

extract_protocol:
Total RNA was extracted from clinical samples using RNAiso Plus (Takara Bio, cat. no. 9109) according to the manufacturer’s instructions. RNA integrity was assessed by agarose gel electrophoresis, and RNA concentration was measured using a Qubit fluorometer (Thermo Fisher Scientific).
RNA-seq libraries were prepared from total RNA according to the standard protocols provided by BGI Genomics (Shenzhen, China). Briefly, mRNA was enriched from total RNA, fragmented, and reverse-transcribed into cDNA. After end repair, adapter ligation, and PCR amplification, the libraries were quality-checked and sequenced using paired-end 2 × 150 bp reads on an Illumina NovaSeq 6000 platform.

value: colorectum


title: LAD2 CUT&Tag JUND SCF- biol rep 2

description:
Library name: EM_2
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control

value: Medium without SCF (SCF-)


title: B. fragilis microSPLiT library F3 6k

description:
Library name: F3_6k
microSPLiT library

value: NCTC 9343


title: LAD2 CUT&Tag JUND SCF- biol rep 1

description:
Library name: EM_1
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control


title: Control sample 2

source_name: Control sample 2


title: qd118_early-stage tumor

description:
Library name: qd118
Bulk RNA-seq of colorectal tissue


title: Day7 sample 2

source_name: Day7 sample 2


title: qd148_advanced tumor

description:
Library name: qd148
Bulk RNA-seq of colorectal tissue


title: Day14 sample 4

source_name: Day14 sample 4


title: qd112_early-stage tumor

description:
Library name: qd112
Bulk RNA-seq of colorectal tissue


title: Day14 sample 3

source_name: Day14 sample 3


title: Expanded_HSPCs_Sca1+_bulk_RNA_rep2

description:
Library name: Expanded_HSPCs_Sca1+_bulk_RNA_rep2
RNA

source_name: bone-marrow

value: bone-marrow


title: qd114_tubular adenomas

description:
Library name: qd114
Bulk RNA-seq of colorectal tissue


title: qd174_normal tissue

description:
Library name: qd174
Bulk RNA-seq of colorectal tissue


title: LAD2 CUT&Tag JUND SCF+ biol rep 1

description:
Library name: SCF_1
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control


title: qd168_villous adenoma

description:
Library name: qd168
Bulk RNA-seq of colorectal tissue


title: qd178_villous adenoma

description:
Library name: qd178
Bulk RNA-seq of colorectal tissue


title: LAD2 CUT&Tag JUND SCF- + imatinib biol rep 1

description:
Library name: IM_1
CUT&Tag for JUND (Active Motif 61403; RRID:AB_2793621); no IgG/input/no-ab control


title: qd172_villous adenoma

description:
Library name: qd172
Bulk RNA-seq of colorectal tissue


title: Control Prolif2

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: Rutland Drive

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

description: Library name: OR9

data_processing:
The raw data were trimmed and filtered by fastp
The clean reads were mapped to the Human reference genome GRCh38 with Hisat2(version 2.2.0)
StringTie(version 2.0.4) and Ballgown(version 2.32.0) were recruited to do the transcript assembly and gene expression analyses with default parameters
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each file

source_name: Eutopic endometrium

growth_protocol: Eutopic human endometrial biopsy were collected from women with and without endometriosis during the proliferative phase.

extract_protocol:
The total RNA from endometrial biopsy were isolated by QIAGEN RNeasy Mini Kit following the vendor's manual.
The library was prepared by University of Missouri Genomic Technology Coe using NEBNext® rRNA Depletion Kit v2

value: Eutopic endometrium


title: qd180_normal tissue

description:
Library name: qd180
Bulk RNA-seq of colorectal tissue


title: Eosis Prolif4

description: Library name: MOSE20


title: Eosis Prolif2

description: Library name: MOSE15


title: Control Prolif3

description: Library name: N3


title: Control sample 3

description: Gene expression of control dorsal root ganglion

source_name: Control sample 3


title: qd150_normal tissue

description:
Library name: qd150
Bulk RNA-seq of colorectal tissue


title: Eosis Prolif3

description: Library name: MOSE13


title: HEK293_dCas13d_gNT_m6A_rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

institute: The University of Chicago

description: Library name: HEK293_dCas13d_gNT_m6A_rep2

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

source_name: Embryonic kidney

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and  100 U/mL penicillin-streptomycin (Gibco). Mouse embryonic stem cells were cultured in DMEM (Invitrogen) supplemented with 20% FBS (GeminiBio), 1 mmol/L L-glutamine (Gibco), 1% nonessential amino acid (Gibco), 100 U/mL penicillin-streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF, Millipore), 0.1 mmol/L 2-mercaptoethanol (Sigma), 3 μmol/L CHIR99021 (Stemcell), 1 μmol/L PD0325901 (Stemcell), and 1% EmbryoMax nucleosides (100×, Millipore). All cell lines were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

value: Embryonic kidney

value: Transformed embryonic kidney cell

value: WT

value: NT ginde RNA

tag: antibody

value: m6A antibody (CST,Cat #56593)


title: HEK293_dCas13d_gNT_noAb_rep1

description: Library name: HEK293_dCas13d_gNT_noAb_rep1


title: qd100_early-stage tumor

description:
Library name: qd100
Bulk RNA-seq of colorectal tissue


title: HEK293_dCas13d_gNT_noAb_rep2

description: Library name: HEK293_dCas13d_gNT_noAb_rep2


title: Control Prolif4

description: Library name: N8


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 6

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: hPM6
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.

data_processing:
Quality Control and Trimming: Raw sequencing reads from all experiments underwent quality control using FastQC. Adapters and low-quality bases were removed using Trim Galore or Trimmomatic.
Alignment: RNA-seq reads were aligned to the mouse (mm10) or human (hg38/GRCh38) reference genome using STAR. CUT&Tag reads were aligned to mm10 using Bowtie2. 4f-SAMMY-seq reads were aligned to mm10 using BWA-mem. Post-alignment filtering removed PCR duplicates and low-quality mapped reads.
Signal Generation and Quantification: For RNA-seq, gene expression was quantified using featureCounts. For CUT&Tag and 4f-SAMMY-seq, normalized signal tracks (bigWig format) were generated using deepTools bamCoverage. For 4f-SAMMY-seq, a log2 ratio of S2S/S3 coverage was calculated to define chromatin accessibility.
Peak Calling and Differential Analysis: For RNA-seq, differential gene expression was analyzed using DESeq2. For CUT&Tag, peaks were called using MACS2 and SEACR, and differential binding analysis was performed using DiffBind. For 4f-SAMMY-seq, differential chromatin regions were identified by comparing log2(S2S/S3) ratios between conditions. Statistical significance was determined using FDR < 0.05.
Annotation and Functional Analysis: CUT&Tag peaks were annotated to genomic features using the ChIPseeker R package. Gene Ontology (GO) functional enrichment analysis was performed on gene lists derived from all experiments using clusterProfiler.
Assembly: mm10 (for mouse samples); GRCh38/hg38 (for human samples)
Supplementary files format and content: For RNA-seq: Raw gene count matrices (genes x samples) and normalized expression tables. Tables of differentially expressed genes include log2 fold change, p-value, and FDR for each gene.
Supplementary files format and content: For CUT&Tag: Peak coordinates in BED format. Normalized signal tracks in bigWig format. Tables of differentially bound regions with associated statistics (fold change, p-value, FDR).
Supplementary files format and content: For 4f-SAMMY-seq: Normalized chromatin accessibility signal as log2(S2S/S3) ratios in bigWig format. Genomic regions defined as euchromatin or heterochromatin in BED format. Tables of differentially accessible genomic regions.

source_name: iPSC-derived NPCs

growth_protocol: Murine Neural Progenitor Cells (NPCs): Derived from the telencephalic cortex of E13.5 mouse embryos, NPCs were cultured in adhesion on flasks coated with 1:100 Matrigel. The culture medium was Neural Inducing Medium (NIM) composed of DMEM/F12, Hormon Mix, penicillin/streptomycin, glutamine, glucose, Heparin, 10 ng/ml bFGF, and 10 ng/ml EGF. Murine Primary Neurons (Ns): Prepared from E18.5 wild-type mouse embryos, neurons were maintained in Neurobasal medium supplemented with glucose, penicillin/streptomycin, L-glutamine, and 1% B27.Human iPSC-derived Neurons (hNs): Wild-type human NPCs were differentiated into cortical neurons. Differentiation was induced in DMEM/F1 with N2 and B27 supplements, SU5402, PD0325901, and DAPT. Following dissociation, cells were plated on Poly-L-Lysine/Laminin/Fibronectin coated plates in neuronal maturation medium (Neurobasal A with B-27, Glutamine, BDNF, Ascorbic acid, Laminin, DAPT, and dbcAMP) for at least 3 weeks before experiments.

extract_protocol:
For RNA-seq: Total RNA was isolated from primary murine NPCs, Ns, and human-derived Ns using Trizol (Sigma-Aldrich) according to the manufacturer's protocol. For CUT&Tag: Nuclei from 100,000 cells were isolated and immobilized on Concanavalin A-coated beads. They were then incubated overnight at 4°C with primary antibodies (anti-MeCP2, anti-V5, or anti-Smarcb1). Following incubation with a secondary antibody, pA-Tn5 transposase was applied to fragment and tag antibody-bound DNA sites. For 4f-SAMMY-seq: 200,000 cells were subjected to DNase I treatment to fragment DNA based on chromatin accessibility. DNA was then fractionated to separate the DNase-sensitive euchromatin fraction (S2S) from the DNase-resistant heterochromatin fraction (S3).
For RNA-seq: Library preparation and paired-end sequencing were performed by a commercial service (Genewiz). For CUT&Tag: Following tagmentation, amplicon libraries were generated using the Nextera® DNA Library Prep Kit (Illumina). Barcoded libraries were pooled and sequenced on the NovaSeq 6000 platform. For 4f-SAMMY-seq: Libraries from S2S and S3 fractions were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina and Unique Dual Index NEBNextMultiplex Oligos. Libraries were pooled and sequenced on an Illumina NextSeq 2000 instrument.

treatment_protocol: Lentiviral particles (LV) were produced in 293T cells and concentrated by ultracentrifugation. Murine NPCs and Ns: Cells were transduced one day after seeding. NPCs were transduced with LV-Mecp2 or LV-EGFP at a Multiplicity of Infection (MOI) of 10. Ns were transduced at an MOI of 5. Cells were harvested for analysis 5 days post-transduction. Human iPSC-derived Neurons: Neurons cultured for 4 weeks were transduced with LV-MECP2 or LV-EGFP at an MOI of 10. Cells were harvested 5 days after infection.

value: iPSC-derived NPCs

value: wild-type

value: MECP2 OE


title: Eosis Prolif1

description: Library name: OR11


title: HEK293_dCas13d_gMYC_m6A_rep1

description: Library name: HEK293_dCas13d_gMYC_m6A_rep1

value: MYC guide RNA


title: qd102_tubular adenomas

description:
Library name: qd102
Bulk RNA-seq of colorectal tissue


title: HEK293_dCas13d_gMYC_m6A_rep2

description: Library name: HEK293_dCas13d_gMYC_m6A_rep2


title: qd170_normal tissue

description:
Library name: qd170
Bulk RNA-seq of colorectal tissue


title: Control Prolif1

description: Library name: OR2


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 5

description:
Library name: hPM5
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.


title: RNA-seq of human iPSC-derived NPCs, MECP2 overexpression, biol rep 4

description:
Library name: hPM4
Transcriptome analysis of human iPSC-derived NPCs transduced with MECP2 to induce overexpression.


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 5

description:
Library name: hPG5
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.

value: EGFP control


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 6

description:
Library name: hPG6
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.


title: RNA-seq of human iPSC-derived NPCs, EGFP control, biol rep 4

description:
Library name: hPG4
Transcriptome analysis of human iPSC-derived NPCs transduced with EGFP as a control.