title: mouse Monocyte rep3

data_processing:
Reads were trimmed using Cutadapt
mapped to mm10  use STAR
Gene count were generated using featureCounts
Gene TPM were generated using kallisto
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM for each Sample

source_name: bone marrow

growth_protocol: Murine HSPCs and monocytes were isolated from C57BL/6 mouse bone marrow cells. Bone marrow cells were collected by flushing the femur with PBS, followed by filtration through a 30 µm nylon mesh (Miltenyi Biotec Pre-Separation Filters, 130-041-407) to eliminate cell clumps. Primary cell isolation used the mouse lineage cell depletion Kit (Miltenyi Biotec, 130-110-470) for HSPCs and the mouse monocyte isolation Kit (Miltenyi Biotec, 130-100-629) for monocytes. Murine B cells, T cells, and NK cells were isolated from C57BL/6 mouse spleen cells. The spleen was isolated, and a single-cell suspension was obtained by passing it through a 100-µm cell strainer. Primary cell isolation utilized specific kits: the B cell isolation Kit (Miltenyi Biotec, 130-90-862) for B cells, the CD8 T cell isolation Kit (Miltenyi Biotec, 130-104-075) for CD8 T cells, and the NK cell isolation Kit (Miltenyi Biotec, 130-115-818) for NK cells. Red blood cell lysis buffer was applied to eliminate red blood cells in all samples.

extract_protocol:
RNAs are amplified in situ, not extracted from the cells.
Cells (> 97% viability) were fixed with 4% PFA and immobilized with Concanavalin A beads. The bead-bound cells underwent three washes with AMOUR-wash buffer (PBS, 1 mM ATP, 0.2 U μL-1 RNase inhibitor). Subsequently, the beads were resuspended in PBS with RNase Inhibitor (40 U μL-1) and annealed with T7N9 oligo (0.25 μM). The reaction mixture was incubated at 42 °C for 2 min, followed by ramping to 25 °C and a 5-min hold. After washing, linear amplification with T7 RNA Polymerase occurred at 37 °C for 2 h with shaking at 1,200 rpm. The resulting RNA was purified using Dynabeads MyOne Silane beads. The purified RNA was ligated to 3'adapter and reverse transcribed. The cDNA was ligated with cDNA adapter and subjected to limited cycle PCR, ready for sequencing.

treatment_protocol: Murine hematopoietic cells were isolated from C57BL/6 mouse bone marrow cells.

value: bone marrow

value: Monocyte

value: WT

value: in situ amplification of surface RNA


title: mouse Monocyte rep2

status: Public on Dec 02 2025

type: SRA

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Plasma_34_ObeseHF

type: RNA

city: Porto Alegre

first: Santiago Alonso

last: Tobar Leitao

state: Rio Grande do Sul

address: Rua Ramiro Barcelos 2350

department: Experimental Research Center

country: Brazil

institute: Hospital de Clínicas de Porto Alegre

hyb_protocol: Samples were hybridized overnight using the GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA) at 48°C. The arrays were then washed and stained in the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).The signal values were evaluated using the Expression Console Software (EC) v1.2 (Affymetrix by Thermo Fisher Scientific). Intensity values (presence/absence values) and signal histograms of each hybridization were quality-checked.

data_processing: Raw data were pre-processed using the Robust Multiarray Average (RMA) method, which applies background correction, log2 transformation, and quantile normalization. The batch effect was adjusted with Surrogate Variable Analysis through the sva R package

label: biotin

organism: Homo sapiens

source_name: Plasma, ObeseHF

label_protocol: Total RNA (160 ng), including miRNAs, was biotin-labeled using the FlashTagTM Biotin HSR RNA Labeling kit (Affymetrix, Genisphere, Hatfield, PA, USA)

extract_protocol: Total RNA was extracted from 396 μL of plasma spiked-in with 4 μL of cel-miR-39-3p. Then, 1.2 mL of Trizol LS reagent was added and incubated for 5 minutes. Next, 0.32 mL of chloroform was added, incubated for 15 minutes, and centrifuged at 12,000 x g at 4ºC for 15 minutes. Then, we removed the supernatant, added 0.8 mL of isopropyl alcohol, incubated for 10 minutes, and centrifuged at 12,000 x g at 4ºC for 10 minutes. After removing the isopropyl alcohol, 1.6 mL of 75% ethanol was added and centrifuged at 7,500 x g, at 4ºC, for 5 minutes. Dry for 10 minutes and resuspend in 16 uL of RNase-free water, placed in a dry bath at 58ºC for 10 min. The concentration of total RNA was determined by spectrophotometric analysis (NanoDrop 1000, Thermo Scientific, Wilmington, DE, USA).

tag: Sex

value: female

value: plasma

tag: condition

value: ObeseHF


title: PEM-CKO-3

city: Jinan

first: Wen

last: Liu

address: 6699 Qingdao Road

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

data_processing:
RNA-Seq
Assembly: mm9
Supplementary files format and content: PEM-CKO-vs-PEM-Control-all.gene.xls file includes raw counts for each sample

source_name: Peritoneal

extract_protocol:
Total RNA was harvested and 1.5ug total RNA was used for the construction of sequcing libraries
RNA-Seq

value: Peritoneal

tag: cell line

value: Peritoneal macrophages (PEMs)

value: macrophages

value: lps


title: C04schilLA4107mock

city: Kiel

first: Severin

last: Einspanier

address: Hermann-Rodewald-Straße 9

department: Department of Plant Pathology and Protection

country: Germany

institute: Christian-Albrechts-University Kiel

description: Library name: sample24

data_processing:
We used cutadapt for trimming&quality filtering
rRNA was depleted using STAR, non-mapping reads were used for further analysis
Reads were mapped to each species' reference genome using STAR.
We used featurecounts for read quantification.
FastQC and MultiQC were used for quality assessment.
Assembly: PRJEB5809, PRJCA008297, PRJNA607731, PRJNA727176, PRJNA1210999
Supplementary files format and content: txt-file contaning read counts per gene (not transcript!).

organism: Solanum chilense

source_name: leaf

growth_protocol: Per accession, a single plant was grown in standard greenhouse conditions and occasionally propagated by cuttings. For the sequencing experiments, single leaflets were sampled from the plants and incubated in a humid envoironment. Sclerotinia sclerotiorum strain 1980 was gron fresh from sclerotioa on cultivated in potato dextrose agar,at 20°C in the dark.

extract_protocol:
RNA was isolated using the Quick-RNA Plant Kit (ZYMO RESEARCH). We pooled 2x2cm parts of two independent leaves into DNA/RNA-shield (ZYMO RESEARCH). 0.5ng/µL RNA was used for library preparation.
We used the 3' mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12nt) with PCR Add-on and Reamplification Kit V2 for Illumina, and the SIRV-Set 3 for in-house library preparation, following the manufacturers iinstructions.

treatment_protocol: Inoculated leaves were treated my a mycelial suspension. For this, potato dextrose broth medium was inoculated with S. Sclerotiorum agar-plugs and incubated for four days on a rotary shaker (120 rpm). The mixture was then mixed, vaccuum-filtered and diluted to an OD=1. Tween80 was added. Empty PDB was used for the mock-treatment

value: leaf

value: mock


title: Plasma_1002_Control

source_name: Plasma, Control

value: Control


title: A04schilLA4107mock

description: Library name: sample4


title: PEM-CKO-2


title: Plasma_22_ObeseHF


title: mouse Monocyte rep1


title: PEM-CKO-1


title: B03schilLA3111mock

description: Library name: sample13


title: Plasma_2_ObeseHF

value: male


title: Plasma_1001_Control


title: Plasma_173_LeanHF

source_name: Plasma, LeanHF

value: LeanHF


title: Control - HFD-Lname 1

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

country: USA

institute: University of Washington

description:
Library name: 1
1

data_processing:
Cleaned reads were aligned to reference genomes (mouse: GRCm38/mm10) using STAR37 with de novo junction discovery and summarized at the gene level using featureCounts. Differential expression analysis was completed using DESeq2 using the standard workflow. Batch correction for different sequencing runs between HFpEF models was performed using limma’s removeBatchEffect function using the standard workflow.
Assembly: mm10
Supplementary files format and content: Normalized count matrix of all genes for all samples following batch correction for sequencing run.

molecule: polyA RNA

source_name: Whole heart

extract_protocol:
Total RNA was extracted from whole-heart lysates using TRIzol and the Qiagen RNeasy kit according to the manufacter's specifications.
RNA-sequencing from whole-heart lysates was performed by BGI Genomics using their standard preparation of PolyA RNA using paired-end 100 nucleotide sequencing with 40 million reads.

treatment_protocol: Adult wild-type (WT, strain #000664) and Leprdb/db (strain #000697) C57BL/6J mice were obtained from The Jackson Laboratory. Animals had unlimited access to sterilized water and food, and were housed in an enriched environment with standard bedding and nesting material, under a 12/12 h day-night cycle in a humidity (40–60%) and temperature (20–22°C) controlled facility. HFpEF was studied in two contemporary two-hit models (Fig. 1A). First, WT mice (10-week-old) were fed with HFD (60 kcal% fat, D12492, Research Diets) and drinking water was supplemented with L-NG-nitroarginine methyl ester (L-NAME, 0.5 g/L, Sigma-Aldrich) for 15 weeks. Age-matched control mice were fed with the standard chow used in the Jackson Laboratory chow (Lab Diet, 5k52). Second, osmotic minipumps (Alzet, 2004) were implanted subcutaneously in 12-wk-old mice that delivered a continuous infusion of d-aldosterone (0.3 μg/h) for 4 weeks in db/db mice. Sham control WT mice were implanted with minipumps filled with vehicle only (saline with 5% ethanol). These mice were fed with normal chow (Teklad, 2918). No difference in cardiac morphometry, echocardiography, cellular electrophysiology, and intracellular Ca2+ handling was found between the two control groups of animals.

value: Whole heart

value: Control - HFD-LName

tag: sequencing run


title: N-113

status: Public on Dec 01 2025

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

description: RMA expression value derived from R Oligo package; core-exon analysis

hyb_protocol: Purified RNA from the blood was processed for gene expression using the Affymetrix HuGene 1.0 ST gene arrays and scanned at the Yale Center for Genome Analysis

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Intensity and quality checks of Affymetrix arrays were performed with R package oligo v1.62.2.  The log2 count normalized matrices of mRNAs in the Affymetrix arrays were batch-adjusted using theComBat function in the sva package (version 3.46.0) and used for all subsequent analyses.

source_name: Control Female

label_protocol: biotin

extract_protocol:
Whole blood was collected in PaxGene RNA tubes
Hemoglobin reduction of blood samples was used to remove hemoglobin gene transcripts (GLOBINclear Kit; Ambion) and samples were checked by Agilent bioanalyzer.
Total RNA from whole blood samples was isolated using a column-based system (total-RNA kit; Norgen)

value: Whole blood

tag: disease

value: Female

tag: endotype


title: A03schilLA3111mock

description: Library name: sample3


title: 000-640

source_name: Asthma Male

value: Asthma

value: Male

value: high


title: A-311

source_name: Asthma Female

value: low


title: 000-634


title: 000-633


title: 000-626


title: 000-621


title: 000-629


title: 000-617


title: 000-593


title: 000-576


title: 000-595

source_name: Control Male


title: 000-579


title: 000-588


title: 000-630


title: 000-561


title: 000-636


title: 000-559


title: 000-558


title: 000-555


title: 000-557


title: 000-598


title: 000-551


title: Plasma_19_ObeseHF

value: plasma

value: ObeseHF


title: 000-546


title: 000-627


title: 000-543


title: 000-552


title: 000-571


title: 000-563


title: 000-540


title: 000-534


title: 000-550


title: 000-526


title: 000-520


title: 000-522


title: 000-601


title: 000-516


title: 000-528


title: 000-537


title: 000-533


title: 000-508


title: 000-511


title: 000-503


title: 000-541


title: 000-499


title: 000-500


title: 000-523


title: 000-495


title: 000-515


title: 000-498


title: 000-484


title: 000-487


title: 000-519


title: 000-480


title: 000-532


title: 000-481


title: 000-483


title: 000-491


title: 000-501


title: 000-477


title: 000-476


title: 000-475


title: 000-473


title: 000-489


title: 000-470


title: 000-469


title: 000-468


title: 000-466


title: 000-464


title: 000-479


title: 000-445


title: 000-455


title: 000-453


title: 000-444


title: 000-432


title: 000-423


title: 000-405


title: 000-331


title: 000-382


title: 000-459


title: 000-324


title: 000-398


title: 000-322


title: 000-386


title: 000-330


title: 000-458


title: 000-300


title: 000-299


title: 000-327


title: 000-420


title: 000-297


title: 000-287


title: 000-350


title: 000-283


title: 000-403


title: 000-253


title: 000-109


title: Homozygous Rbm20/Camk2d double knockout - 3

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

institute: Institute of Experimental Cardiology

description: Library name: DKO_419

data_processing:
RNA-seq reads were aligned to mouse genome reference (mm10 GRCm38) using the Rsubread R package. Quality control of the reads was performed using Fastqcr and Rqc packages, while adapter trimming was conducted with Trimmomatic using standard parameters. For data processing and analysis, we employed a R-based pipeline utilizing BiocManager for package management, ShortRead for sequence manipulation and reading.
Assembly: mm10
Supplementary files format and content: gene_counts_Hesp - Gene counts of analysis of WT_DMSO, HET_DMSO, HET_Hesp2.5, and HET_Hesp5
Supplementary files format and content: gene_counts_DKO.tsv - Gene counts of analysis of WT, Rbm20KO, Camk2dKO and DKO

source_name: heart tissue (LV)

extract_protocol:
RNA was isolated using TRIzol following manufacturers instructions.
Sequence libraries were prepared using SMART-Seq Total RNA pico input (Takara Bio) following manufacturers instructions.

value: heart tissue (LV)


title: Homozygous Camk2d knockout - 5

description: Library name: Camk2dKO_472


title: Homozygous Rbm20/Camk2d double knockout - 4

description: Library name: DKO_475


title: 000-023


title: 000-028


title: Homozygous Rbm20/Camk2d double knockout - 1

description: Library name: DKO_384


title: Homozygous Camk2d knockout - 3

description: Library name: Camk2dKO_470


title: Homozygous Camk2d knockout - 1

description: Library name: Camk2dKO_468


title: Homozygous Rbm20/Camk2d double knockout - 5

description: Library name: DKO_477


title: Homozygous Camk2d knockout - 2

description: Library name: Camk2dKO_469


title: 000-268


title: Homozygous Camk2d knockout - 4

description: Library name: Camk2dKO_471


title: Homozygous Rbm20 knockout - 4

description: Library name: Rbm20KO_570


title: 000-029


title: Homozygous Rbm20 knockout - 3

description: Library name: Rbm20KO_569


title: 000-015


title: 000-254


title: Homozygous Rbm20 knockout - 5

description: Library name: Rbm20KO_571


title: 000-011


title: 000-306


title: Homozygous Rbm20 knockout - 2

description: Library name: Rbm20KO_568


title: Homozygous Rbm20 knockout - 1

description: Library name: Rbm20KO_567


title: Homozygous Rbm20/Camk2d double knockout - 2

description: Library name: DKO_386


title: 000-030


title: Wildtype - 4

description: Library name: WT_576


title: Wildtype - 3

description: Library name: WT_575


title: 000-284


title: Wildtype - 1

description: Library name: WT_548


title: HTO_derived_cDNA

city: ILLKIRCH

first: Mei

last: Li

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

description:
Library name: HTO_derived_cDNA
HTO stored in Custom matrix in the processed data file

library_source: other

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4. Reads were processed with Cell Ranger count (10X Genomics) version 7.1.0 using the Mus musculus genome assembly GRCm39 (mm39).
Assembly: mm39
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: raw_feature_bc_matrix.h5

molecule: protein

source_name: Tumor-draining lymph node

extract_protocol:
At D42, migDC (sorted as alive B220- CD11c+toint MHCIIhi) and CD4+ cells (sorted as alive B220-CD11c-MHCII-CD8a-CD4+) were enriched by FACS sorting from BP and BPT tdLN. BP CD4+ cells were labeled with TotalSeq™ barcoded antibody A0301 Hashtag1 (H1), BP migDC with A0302 Hashtag2 (H2), BPT CD4+ cells were labeled with A0303 Hashtag3 (H3) and BPT migDC with A0304 Hashtag4 (H4). The 4 populations were pooled at the ratio 1:1:1:1 (7500 cells per population) before being processed for multiplex scRNA-seq.
For both librairies, cells were labelled with TotalSeq™-A Cell Hashing antibodies (BioLegend, Amsterdam, The Netherlands) as described. Labelled and washed cells were loaded onto the Chromium iX targeting 16000 captured cells per sample and processed using Single Cell 3' v3.1 (dual index) workflow according to the manufacturer's instructions up until the cDNA amplification step (10X Genomics, Leiden, The Netherlands). The following modifications were made in the next steps. Two picomoles of HTO (5'GTGACTGGAGTTCAGACGTGTGC*T*C) cDNA primers were added into the cDNA amplification PCR, and cDNA was amplified according to the 10x Genomics Single Cell 3' v3.1 protocol using 11 cycles. Following PCR, SPRIselect reagent (Beckman-Coulter, Villepinte, France) at a ratio of 0.6X was used to separate the cDNA fraction derived from cellular mRNAs (retained on beads) from the Cell Hashtag (HTO)-containing fraction (in supernatant). The cDNA fraction was processed according to the 10x Genomics Single Cell 3' v3.1 protocol to generate the transcriptome library. Additional SPRI beads reagent was added to the HTO fraction to bring the ratio up to 2.1X. The beads were washed with 80% ethanol. After final elution in EB buffer, separate PCR was carried out using the 2x KAPA HiFi PCR Master Mix (Roche Sequencing Solutions) to generate dual index cell hashing HTO library according to BioLegend's recommandations. Then surplus PCR primers were further removed by purification using SPRIselect beads. The final mRNA and HTO libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: Primary melanoma tumours were induced on dorsal skin through the topical application of 4-hydroxytamoxifen for three consecutive days, either in TyrCre-ERT2Tg/0BrafLSL–V600E/+Ptenlox/lox mice (BP) or TyrCre-ERT2Tg/0BrafLSL–V600E/+Ptenlox/loxTslp–/– mice (BPT) mice.

value: Tumor-draining lymph node

value: migDC and CD4 cells

value: 4-OH TAM topical treatment to induce local melanoma


title: Wildtype - 2

description: Library name: WT_549


title: 11200023-1-CBX1_S2_L001

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
To process RNA-seq raw data, first obtain the FASTQ files from sequencing providers . Perform quality control using FastQC, and trim low-quality reads and adapter sequences with tools like Trimmomatic or Cutadapt. Align the cleaned reads to a reference genome using HISAT2 , utilizing an appropriate annotation file (GTF/GFF). Quantify transcript abundance with StringTie or count reads per gene with featureCounts.
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample, bw

source_name: liver

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 NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver

value: no

value: hepatocellular carcinoma

value: Cbx5 ko


title: 11200023-1-WT3_S64_L001

value: WT


title: mRNA_derived_cDNA

description:
Library name: mRNA_derived_cDNA
GEX stored in Gene Expression matrix in the processed data file

library_source: transcriptomic single cell


title: 11200023-1-WT1_S62_L001


title: 11200023-1-CBX3_S66_L001


title: E150000474_L01_HC0314741-C1

value: group house


title: E150000474_L01_HC0314743-C3


title: 11200023-1-CBX2_S65_L001


title: 11200023-1-WT2_S63_L001


title: E150000474_L01_HC0314742-C2


title: E150000474_L01_HC0314746-M3

value: social isolation


title: smallRNA-Seq Zeb1_200M_pituitary_1

city: Cambridge

first: David

middle: P

last: Bartel

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute / MIT

description: small RNA

data_processing:
Reads were trimmed of adaptor sequence using cutadapt and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters “-q 30 –p 100” to ensure that all bases had an accuracy of 99.9%. To count the miRNAs in each library, the first 18 nt of each read were string-matched to a dictionary of miRNA sequences. Mouse miRNA dictionaries were based on annotations in miRbase_v20. Matching to the first 18 nt has the advantage of combining all miRNA isoforms into a single count but also can result in ambiguous read assignments for mature miRNAs from distinct loci that are identical for the first 18 nt but differ at one or more positions closer to their 3′ ends (such as let-7a-5p and let-7c-5p). To avoid this ambiguity, these miRNAs (<5% of all annotations) were removed from the dictionary. Differential expression was determined using DESeq2 with the parameter “betaPrior = FALSE”.
Assembly: miRbase_v20
Supplementary files format and content: tab-delimited text file of DESeq2 output includes miRbase name (Feature.ID), baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

molecule: other

source_name: pituitary

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water.
Each small-RNA sequencing libraries was prepared with 0.5 μg of total RNA extracted from mouse pituitary. To minimize loss due to low starting input, 3 ug of total RNA from the budding yeast Naumovozyma castelli was added to each sample prior to size-selection. In addition, 0.5 fmoles of miR-427-5p (X. tropicalis) and 0.5 fmoles of miR-14 (D. melanogaster) were added as spike-ins. From each sample, RNAs that co-migrated within the range of 18 and 32 nt radiolabeled internal standards were isolated on a 15% polyacrylamide urea gel. Purified RNA was ligated to a preadenylated 3′ adapter (AppNNNNTCGTATGCCGTCTTCTGCTTGddC) using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). To reduce ligation biases, this 3′ adapter had 4 random-sequence positions at its 5′ end. After gel purification on a 8% polyacrylamide urea gel, RNA was ligated to a 5′ adapter (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. To reduce ligation biases, this adapter had 4 random-sequence positions at its 3′ end. After gel purification on an 8% polyacrylamide urea gel, RNA was reverse transcribed with SuperScript III (Invitrogen), and the cDNA was amplified ~12 cycles with KAPA HiFi DNA polymerase (Kapa Biosystems). Amplified DNA was purified on a 3% metaphor agarose gel and submitted for sequencing. A step-by-step protocol for constructing libraries for small-RNA sequencing is available at http://bartellab.wi.mit.edu/protocols.html.
small-RNA-seq

value: pituitary

value: female

tag: age

value: 28–36 weeks old

tag: background


title: smallRNA-Seq Zeb1_200M_pituitary_3

description: small RNA


title: Wildtype - 5

description: Library name: WT_577


title: E150000474_L01_HC0314744-M1


title: smallRNA-Seq Zeb1_200M_pituitary_2

description: small RNA


title: E150000474_L01_HC0314745-M2


title: smallRNA-Seq Zeb1_200H_pituitary_3

description: small RNA


title: smallRNA-Seq Zeb1_200H_pituitary_4

description: small RNA


title: smallRNA-Seq Zeb1_WT_pituitary_4

description: small RNA


title: smallRNA-Seq Zeb1_WT_pituitary_3

description: small RNA


title: smallRNA-Seq Zeb1_200H_pituitary_1

description: small RNA


title: smallRNA-Seq Zeb1_WT_pituitary_1

description: small RNA


title: smallRNA-Seq Zeb1_WT_pituitary_2

description: small RNA


title: 000-112

value: Whole blood

value: Asthma

value: Female

value: high


title: Zeb1_200M_ovary_4

description: unstranded

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR v2.7.1a with the parameters “--outFilterType BySJout --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated”. For pituitary and hypothalamus libraries, aligned reads were assigned to genes using htseq-count v0.9.1 with the parameters “-m union -s no” and annotations from Ensembl (Mus_musculus.GRCm38.87.gtf; downloaded May 15, 2017). For ovary libraries, aligned reads were assigned to genes using featureCounts with the parameter “-s 0” and annotations from Gencode (m38.p6 gencode.vM25.basic.annotation.gtf; downloaded 7/10/24). Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.18 (pituitary and hypothalamus) with the parameter “betaPrior = FALSE” and without the lfcShrink function or DESeq2 v1.38.3 (ovary) without the lfcShrink function.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of DESeq2 output includes ENSEMBL gene name (Feature.ID), baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

source_name: ovary

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water.
Each RNA sequencing library was prepared with 1 ug of total RNA extracted from mouse tissue. The TruSeq RNA Sample Prep Kit v2 (Illumina) was used to generate unstranded, poly(A)-selected RNA-seq libraries according to the manufacturer's instructions. Each library was amplified with 15 cycles of PCR.

value: ovary


title: Zeb1_200H_ovary_3

description: unstranded


title: Zeb1_200M_ovary_1

description: unstranded


title: Zeb1_200M_ovary_2

description: unstranded


title: Zeb1_200M_ovary_3

description: unstranded


title: Zeb1_WT_ovary_4

description: unstranded


title: Zeb1_200H_ovary_4

description: unstranded


title: Zeb1_200H_ovary_1

description: unstranded


title: Zeb1_200M_pituitary_2

description: unstranded


title: Zeb1_WT_ovary_1

description: unstranded


title: Zeb1_200M_pituitary_3

description: unstranded


title: Zeb1_WT_ovary_2

description: unstranded


title: Zeb1_200H_ovary_2

description: unstranded


title: Zeb1_200H_pituitary_4

description: unstranded


title: Zeb1_200H_pituitary_1

description: unstranded


title: Zeb1_200M_pituitary_1

description: unstranded


title: Zeb1_200H_pituitary_2

description: unstranded


title: Zeb1_WT_pituitary_3

description: unstranded


title: Zeb1_WT_pituitary_4

description: unstranded


title: Zeb1_200M_hypothalamus_3

description: unstranded

source_name: hypothalamus

value: hypothalamus


title: Zeb1_WT_pituitary_1

description: unstranded


title: Zeb1_200M_hypothalamus_2

description: unstranded


title: Zeb1_200M_hypothalamus_1

description: unstranded


title: Zeb1_200H_hypothalamus_3

description: unstranded


title: Zeb1_200H_hypothalamus_4

description: unstranded


title: Zeb1_WT_pituitary_2

description: unstranded


title: Zeb1_200H_hypothalamus_2

description: unstranded


title: Zeb1_WT_ovary_3

description: unstranded


title: Zeb1_WT_hypothalamus_4

description: unstranded


title: Zeb1_200H_hypothalamus_1

description: unstranded


title: Zeb1_WT_hypothalamus_3

description: unstranded


title: MIN6, re+AA+Rap 3h, rep3

city: New Brunswick

first: Jialin

last: Fan

state: NJ

address: 195 Little Albany St, Room 3527

institute: The Cancer Institute of New Jersey (CINJ)

data_processing:
Raw transcriptome-sequencing reads were aligned to Mus musculus reference genome (GRCm38.p6) using subread-aligner (subread 2.0.1). Differentially expressed genes were determined using limma 3.46.0 with a combination of fold change ≥ 2 and false discovery rate (FDR, by Benjamini-Hochberg algorithm) adjusted P-value ≤ 0.05 (n=3)
Assembly: GRCm38.p6
Supplementary files format and content: text file includes raw counts for each sample

growth_protocol: DMEM, 15%FBS, 2mM Glutamine, cells were cultured at 37 degree at 5% CO2

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo ScientificTM) and RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction
RNA library construction, RNA quality assessment, and sequencing (Illumina, 150bp paired end) were performed by Azenta

treatment_protocol: ctrl, no AA for 16h, readd AA for 3h, readd AA and Rap for 3h

value: pancreatic beta cell

value: readd AA and Rap 3h


title: Zeb1_WT_hypothalamus_2

description: unstranded


title: Zeb1_200H_pituitary_3

description: unstranded


title: MIN6, -AA 16h, rep3

value: no AA 16h


title: MIN6, re+AA 3h, rep1

value: readd AA 3h


title: MIN6, re+AA 3h, rep3


title: MIN6, -AA 16h, rep1


title: MIN6, re+AA+Rap 3h, rep2


title: MIN6, ctrl, rep3

value: ctrl


title: MIN6, -AA 16h, rep2

value: WT


title: MIN6, ctrl, rep2


title: MIN6, ctrl, rep1


title: 168h PH rep2

city: Beijing

first: Xian

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

data_processing:
(data filtering) 1. Remove reads with adaptor sequences. 2. Remove reads in which the percentage of unknown bases (N) is greater than 10%. 3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality.
(alignment) Clean reads were mapped to reference sequences (mm10) and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment
(quantification) The gene expression level is calculated by using RPKM
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs

source_name: 168h PH, liver

extract_protocol:
The liver were removed, flash frozen in liquid nitrogen and then were stored in -70℃. Total RNA were prepared from the liver samples using TRIZOL reagent (Invitrogen), and three RNA samples from the same time point were pooled. There were two pooled samples in each time point.
The total  RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentati on buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3' -end single nucleoti de A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bi oanaylzer and ABI StepOnePl us Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol:
2/3 partial hepatectomy besides sham group
sham group, sham operation

tag: strain

tag: protocol

value: PH

tag: time

value: liver


title: 120h PH rep2

source_name: 120h PH, liver


title: 72h PH rep1

source_name: 72h PH, liver


title: 72h PH rep2


title: 168h PH rep1


title: 120h PH rep1


title: 48h PH rep1

source_name: 48h PH, liver


title: 48h PH rep2


title: 24h PH rep1

source_name: 24h PH, liver


title: 4h PH rep1

source_name: 4h PH, liver


title: Zeb1_WT_hypothalamus_1

description: unstranded


title: 4h PH rep2


title: MIN6, re+AA+Rap 3h, rep1


title: 2h PH rep2

source_name: 2h PH, liver


title: MIN6, re+AA 3h, rep2


title: 2h PH rep1


title: 0.5h PH rep2

source_name: 0.5h PH, liver


title: 0.5h PH rep1


title: sham rep1

source_name: sham, liver

value: sham

value: control


title: Rat H Surgical side 8 week, biol rep 4

city: Boston

first: Lillian

last: Zhu

state: Massachusetts

address: 150 Western Avenue

department: Bioengineering

institute: Harvard University

description:
Library name: Rat H Surgery
Column name in TPM_allSamples.tsv is d15504.H.surg

data_processing:
nf-core/rnaseq workflow revision 3.14.0 with default parameters
Raw data was passed through FastQC and TrimGalore
Trimmed data was aligned and quantified with the star and salmon route
Gene level summaries were prepared from the star_salmon quantitation using tximport version 1.28.0
Additional analysis and plotting was done with the DESeq2 package
Assembly: mRatBN7rat assembly with the Ensembl version 112 annotation
Supplementary files format and content: tab delimited text file with TPM values for each sample
Supplementary files format and content: tab delimited text file with raw counts for each sample

organism: Rattus norvegicus

source_name: Dorsal root ganglia L2-L5

extract_protocol:
RNA was harvested with the Invitrogen PureLink RNA Mini kit. Up to 1 ug of total RNA was used to construct sequencing libraries
polyA RNA libraries were prepared with NEB ribosomal depletion followed by NEB UltraII prep following manufacturer protocols

treatment_protocol: Extensor digitorum longus grafted to saphenous nerve on one hindlimb, unoperated hindlimb left for comparison

value: Dorsal root ganglia L2-L5

value: Male

value: Surgery

value: 8 weeks


title: Rat H Control side 8 week, biol rep 4

description:
Library name: Rat H Control
Column name in TPM_allSamples.tsv is d15503.H.cont

value: Control


title: Rat G Surgical side 8 week, biol rep 3

description:
Library name: Rat G Surgery
Column name in TPM_allSamples.tsv is d15502.G.surg


title: Rat G Control side 8 week, biol rep 3

description:
Library name: Rat G Control
Column name in TPM_allSamples.tsv is d15501.G.cont


title: Rat C Surgical side 8 week, biol rep 1

description:
Library name: Rat D Surgery
Column name in TPM_allSamples.tsv is d15500.D.surg


title: Rat D Control side 8 week, biol rep 1

description:
Library name: Rat C Control
Column name in TPM_allSamples.tsv is d15497.C.cont


title: Rat C Control side 8 week, biol rep 2

description:
Library name: Rat D Control
Column name in TPM_allSamples.tsv is d15499.D.cont


title: Rat D Surgical side 8 week, biol rep 1

description:
Library name: Rat C Surgery
Column name in TPM_allSamples.tsv is d15498.C.surg


title: Rat E Surgical side 6 week, biol rep 3

description:
Library name: Rat E Surgery
Column name in TPM_allSamples.tsv is d15496.E.surg

value: 6 weeks


title: 24h PH rep2


title: Rat E Control side 6 week, biol rep 3

description:
Library name: Rat E Control
Column name in TPM_allSamples.tsv is d15495.E.cont


title: Rat B Surgical side 6 week, biol rep 2

description:
Library name: Rat B Surgery
Column name in TPM_allSamples.tsv is d15494.B.surg


title: Rat A Control side 6 week, biol rep 1

description:
Library name: Rat A Control
Column name in TPM_allSamples.tsv is d15491.A.cont


title: Rat B Control side 6 week, biol rep 2

description:
Library name: Rat B Control
Column name in TPM_allSamples.tsv is d15493.B.cont


title: Rat A Surgical side 6 week, biol rep 1

description:
Library name: Rat A Surgery
Column name in TPM_allSamples.tsv is d15492.A.surg


title: Rat OPCs, Bavisant, day 5 [Bav_10-P13]

city: Paris

first: Nadjet

last: Gacem

address: 47 BD de l'Hôpital, Hôpital de la Pitié Salpêtrière

institute: Paris Brain Institute

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.4) was used for mapping on rn6 reference genome and quantification with gencode v103 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Supplementary files format and content: rn6
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: Rat OPCs, Bavisant, day 5

growth_protocol: Purified rat OPCS were cultured in DMEM-F12, 1% penicillin-streptomycin, 1% laminin, Biotin, 2% B27 and N1 mix (differentiation medium). Cells were incubated at 37°C (5% CO2) for 5 days in the presence or absence of Bavisant at 1mM or 10 µM. The medium was changed every 2 days.

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen).
mRNA library preparation was perfromed following manufacturer’s recommendations (Illumina Stranded mRNA Prep Kit from ILLUMINA).
Final samples pooled libraries were sequenced on Nextseq 500 ILLUMINA with HighOutPut cartridge (2x400Millions of 75 bases reads), corresponding to 2x40Millions of reads per sample after demultiplexing.

treatment_protocol: Cells were cultured in differentiation medium in the presence or absence of Bavisant at 1 mM and 10µM, respectively

value: Brain

value: OPCs


title: Rat OPCs, Bavisant, day 5 [Bav_10-P11]


title: Rat OPCs, Bavisant, day 5 [Bav_10-P14]


title: Rat OPCs, Bavisant, day 5 [Bav_1-P14]


title: Rat OPCs, Bavisant, day 5 [Bav_1-P11]


title: Rat OPCs, Basal, day 5 [Ctl-P14]

source_name: Rat OPCs, Basal, day 5

value: Basal


title: eff-1 P37Stop L1 C. elegans Larva rep2 sample 3

city: Laramie

first: Owen

last: Funk

address: 1000 E. University Ave

institute: University of Wyoming

description: Library name: P37Stop_3

data_processing:
Low-quality reads were filtered using fastp.
Reads were aligned to the ce11 reference genome using STAR.
Duplicate reads were removed using Picard.
Gene counts were collected using htseq.
Differential expression analysis was performed using DESeq2
Assembly: ce11
Supplementary files format and content: gene counts csv file

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Trizol reragent extraction
TruSeq Library Prep Kit

value: whole worm

tag: batch


title: Rat OPCs, Bavisant, day 5 [Bav_1-P13]


title: eff-1 P37Stop L1 C. elegans Larva rep2 sample 1

description: Library name: P37Stop_1


title: sham rep2


title: Rat OPCs, Basal, day 5 [Ctl-P13]


title: L1 C. elegans Larva rep2 sample 1

description: Library name: WT_Rep2_1


title: Rat OPCs, Basal, day 5 [Ctl-P11]


title: eff-1 P37Stop L1 C. elegans Larva rep2 sample 2

description: Library name: P37Stop_2


title: L1 C. elegans Larva rep2 sample 3

description: Library name: WT_Rep2_3


title: eff-1 P183L L1 C. elegans Larva rep1 sample 2

description: Library name: P183L_2

value: eff-1 P183L


title: L1 C. elegans Larva rep2 sample 2

description: Library name: WT_Rep2_2


title: eff-1 P183L L1 C. elegans Larva rep1 sample 1

description: Library name: P183L_1


title: eff-1 P183L L1 C. elegans Larva rep1 sample 3

description: Library name: P183L_3


title: eff-1 S441L L1 C. elegans Larva rep1 sample 2

description: Library name: S441L_2

value: eff-1 S441L


title: L1 C. elegans Larva rep1 sample 3

description: Library name: WT_Rep1_3

value: WT


title: eff-1 S441L L1 C. elegans Larva rep1 sample 1

description: Library name: S441L_1


title: L1 C. elegans Larva rep1 sample 2

description: Library name: WT_Rep1_2


title: L1 C. elegans Larva rep1 sample 1

description: Library name: WT_Rep1_1


title: gyf1 gyf2-2-1

city: Weifang

first: Yingtang

last: Ma

address: No. 699 Binhu Road, Xiashan Ecological Economic Development Zone

institute: Peking University Institute of Advanced Agricultural Sciences

description: Library name: sample 13

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 100 mg samples of 1-week-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: whole seedlings

value: gyf1 gyf2-2 mutant

value: no treatment


title: gyf1 gyf2-1-1

description: Library name: sample 10

value: gyf1 gyf2-1 mutant


title: gyf1 gyf2-2-3

description: Library name: sample 15


title: gyf2-2

description: Library name: sample 8

value: gyf2 mutant


title: gyf2-3

description: Library name: sample 9


title: gyf1 gyf2-1-3

description: Library name: sample 12


title: gyf1 gyf2-2-2

description: Library name: sample 14


title: gyf2-1

description: Library name: sample 7


title: gyf1-3

description: Library name: sample 6

value: gyf1 mutant


title: gyf1-2

description: Library name: sample 5


title: gyf1-1

description: Library name: sample 4


title: WT-3

description: Library name: sample 3

value: wild type


title: WT-1

description: Library name: sample 1


title: WT-2

description: Library name: sample 2


title: eff-1 S441L L1 C. elegans Larva rep1 sample 3

description: Library name: S441L_3


title: Eleveted CO2_replicate2

city: Antwerp

first: Hamada

last: AbdElgawad

address: Groenenborgerlaan 171

country: Belgium

institute: Antwerp University

data_processing:
CLC Genomics Workbench v.6
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 Arabidopsis thaliana Col-0 TAIR10) sequence database http://www.arabidopsis.org/ as the reference genome using default seeting
Read count extraction and normalization were performed using CLC genomic benchwork
The expression values were normalized by scaling to corresponding controls, and the significance of the effect of treatments was determined using Baggerley’s test (Baggerly, Deng, Morris, & Aldaz, 2003).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Leaves

growth_protocol: Plants were grown in a growth cabinet with contrasting CO2 levels, i.e., 1) ambient CO2 (375±9 ppm; aCO2); 2) aCO2 + drought 40% (Soil Water Content, SWC; D); 3) elevated CO2 (eCO2) (633±16 ppm); 4) aCO2 + drought stress (40% SWC; DCO2). Light levels were 150 μmol PAR m−2 s−1, day/night photoperiod was 16/8 h, air temperature 21/18 oC, and humidity 60/70%.

extract_protocol:
Total RNA was extracted from frozen rosettes harvested at 21 DAS by using the RNeasy Plant Mini Kit; (Qiagen, Germany). 2.5 ug of total RNA was used for the construction of sequencing libraries.
Library preparation was performed using the TruSeq® Stranded mRNA sample preparation 96 rcx kit, Illumina™) following the low sample protocol according to Illumina™ guidelines

treatment_protocol: Plants were in a growth cabinet with contrasting CO2 levels, i.e., 1) ambient CO2 (375±9 ppm; aCO2); 2) aCO2 + drought 40% (Soil Water Content, SWC; D); 3) elevated CO2 (eCO2) (633±16 ppm); 4) aCO2 + drought stress (40% SWC; DCO2).

value: Leaves

value: Eleveted CO2

value: 28 days after sowing


title: Ambient CO2 + Drought stress_replicate3

value: Drought stress

value: 26 days after sowing


title: Eleveted CO2 + Drought stress_replicate 3

value: Eleveted CO2 + Drought stress

value: 32 days after sowing


title: Eleveted CO2 + Drought stress_replicate1

value: 30 days after sowing


title: Eleveted CO2_replicate3

value: 29 days after sowing


title: Eleveted CO2 + Drought stress_replicate2

value: WT

value: 31 days after sowing


title: Eleveted CO2_replicate1

value: 27 days after sowing


title: Ambient CO2_replicate2

value: Control

value: 22 days after sowing


title: MZtriple_5.3hpf_r2_Hi-C

first: Aleksandra

last: Galitsyna

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

description:
Triple_mutant_5.3hpf_r2_Hi-C
TR.1000.mcool

library_source: genomic

data_processing:
Hi-C data was mapped with distiller v 0.0.3 with default parameters to genome assembly danRer11 with canonical chromosomes.
Minimal data resolution was set to 1000 and MAPQ filter 30 applied.
Replicates were merged by summation of .cool files per replicate.
Genome_build: danRer11
Supplementary_files_format_and_content: .mcool

molecule: genomic DNA

organism: Danio rerio

source_name: whole embryo

growth_protocol: The fish embryos were obtained by natural matings. Embryos were collected within 15 minutes and incubated at 28.5°C until the indicated stage (hpf).

extract_protocol:
1000-3000 embryos were enzymatically dechorionated with Pronase E (Sigma, 240µg/ml ) in 25 ml 0.5x Danieau’s medium (29 mM NaCl, 350 µM KCl, 200 µM MgSO4, 300 µM Ca(NO3)2, 2.5 µM HEPES buffer, pH7.6),  in 250 ml  glass beaker. Pronase E was stopped by adding 1 ml 1%BSA. The embryos were washed 5 times in 0.5x Danieaus, to get rid of the chorions.  400-600 Embryos were transferred   in 2 ml eppendorf tubes filled with 1640 µl 0.5x Danieaus medium with PIC (protease inhibitor cocktail EDTA-free, Roche) and fixed immediately for 10 minutes by adding 110 µl of 16% methanol-free formaldehyde (Thermo Scientific #28906). At the beginning of the fixation, the embryos were homogenized with 10 strokes of yellow pipet tip, then put on a rotating wheel. The reaction was quenched with by the addition of 1M glycine (Sigma-Aldrich), to a final concentration of 125 mM. Cells were pelleted by centrifugation (5,000 ´ g, 5 min, 4 °C), and washed 3x in ice-cold PBST (PBS + 0.1% Tween 20) +PIC. The pellet was resuspended in 1 ml cell lysis buffer (10mM Tris-HCl (pH7.5)  10mM NaCl, 0.5% NP-40, PIC) and kept on ice for 1 min. The nuclei were pelleted by centrifugation and resuspended in 1 ml PBST. 10 µl of the resuspended nuclei were stained by mixing with 10µl Sytox Green (12,5 µm), and the nuclei were scored in Neubauer chamber under the microscope equipped with epifluorescence. The rest of the nuclei were pelleted, snap-frozen in liquid nitrogen, and stored at -80°C.  A total of 5-10 million nuclei was used for further processing.  Nuclei were lysed in 1.5 ml isotonic buffer [50 mM Tris-HCl pH 8.0 (Sigma-Aldrich), 150 mM NaCl (Sigma-Aldrich), 0.5% (v/v) NP-40 substitute (Fluka), 1% (v/v) Triton-X100 (Sigma-Aldrich), 1× Halt™ Protease Inhibitor Cocktail (Thermo Scientific)], on ice for 15 min. Nuclei  were pelleted by centrifugation at 2,500 ´ g for 5 min, resuspended in 100 ml 1× DpnII buffer (New England Biolabs), and pelleted again. The pellet was resuspended in 200 ml 0.3% SDS (Sigma-Aldrich) in 1.1× DpnII buffer (New England Biolabs) and incubated at 37°C for 1 h. Then, 330 ml 1.1× DpnII buffer and 53 ml 20% Triton X-100 were added, and the suspension was incubated at 37°C for 1 h. Next, 600 U DpnII enzyme (New England Biolabs) were added, and the chromatin was digested overnight (14-16 h), at 37°C, with shaking (1,400 rpm). In the morning, 200 U DpnII enzyme was added, and the cells were incubated for 2 h. DpnII was then inactivated by incubation at 65°C for 20 min. The nuclei were harvested for 10 min at 5,000 ´ g, washed with 100 ml 1× NEBuffer 2 (New England Biolabs), and resuspended in 125 ml 1.2× NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 ml biotin fill-in mixture [0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (New England Biolabs)]. The samples were incubated at 37°C for 75 min, with shaking (1,400 rpm). Nuclei were pelleted by centrifugation at 3,000 ´ g for 5 minutes, resuspended in 300 ml 1× T4 DNA ligase buffer (Thermo Scientific), and pelleted again. The pellet was resuspended in 300 ml 1× T4 DNA ligase buffer, and 75 U T4 DNA ligase (Thermo Scientific) was added. Chromatin fragments were ligated at 20°C for 6 h. The cross-links were reversed by overnight incubation at 65°C in the presence of proteinase K (100 μg/ml) (Sigma-Aldrich). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction, followed by ethanol precipitation [glycogen (Thermo Scientific) at a concentration of 20 μg/ml was used as co-precipitator]. After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl, pH 8.0. To remove residual RNA, samples were treated with 50 mg RNase A (Thermo Scientific) for 45 min at 37°C. To remove residual salts and DTT, the DNA was purified using Agencourt AMPure XP beads (Beckman Coulter).
Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U T4 DNA polymerase (New England Biolabs) in NEBuffer 2, supplemented with 0.025 mM dATP and 0.025 mM dGTP, at 20°C for 4 h. Next, the DNA was purified using Agencourt AMPure XP beads. The DNA was then dissolved in 500 ml sonication buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp, using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified), using AMICON Ultra Centrifugal Filter Units (Merck), to a total volume of approximately 50 ml. The DNA ends were repaired by adding 62.5 ml MQ water, 14 ml 10× T4 DNA ligase reaction buffer, 3.5 ml 10 mM dNTP mix (Thermo Scientific), 5 ml 3 U/ml T4 DNA polymerase (New England Biolabs), 5 ml 10 U/ml T4 polynucleotide kinase (New England Biolabs), and 1 ml 5 U/ml Klenow DNA polymerase (New England Biolabs) and incubating at 20°C for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 ml 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 ml 10× NEBuffer 2, 1.2 ml 10 mM dATP, 1 ml MQ water and 3.6 ml 5 U/ml Klenow (exo-) (New England Biolabs). The reactions were performed for 30 min at 37°C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65°C for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 200 ml 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 ml MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads attached to captured ligation junctions were resuspended in 50 ml adapter ligation mixture, composed of 41.5 ml MQ water, 5 ml 10× T4 DNA ligase reaction buffer (Thermo Scientific), 2.5 ml Illumina TruSeq adapters and 1 ml 5 U/ml T4 DNA ligase (Thermo Scientific). Adapter ligation was performed at 22°C, for 2.5 h, and the beads were washed twice with 100 ml TWB (5 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20 (Sigma-Aldrich)), once with 100 ml 1× binding buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 2 M NaCl), and once with 100 ml CWB (10 mM Tris-HCl, pH 8.0 and 50 mM NaCl), and then resuspended in 20 ml MQ water. Test PCR reactions containing 4 ml streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles necessary to generate sufficient PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98°C, followed by 6, 9, 12, 15, and 18 cycles of 20 s at 98°C, 15 s at 65°C, and 20 s at 72°C. The PCR reactions were separated on a 2% agarose gel supplemented with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 9-12 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified using Agencourt AMPure XP beads.

treatment_protocol: no

tag: developmental stage

value: blastula, 50percent-epiboly, 5.3 hpf

tag: biological replicate


title: gyf1 gyf2-1-2

description: Library name: sample 11

tag: tissue

value: whole seedlings

value: gyf1 gyf2-1 mutant

value: no treatment


title: MZtriple_5.3hpf_r1_Hi-C

description:
Triple_mutant_5.3hpf_r1_Hi-C
TR.1000.mcool

tag: genotype


title: Ambient CO2_replicate3

tag: cell type

value: Leaves

tag: treatment

value: 23 days after sowing


title: Ambient CO2 + Drought stress_replicate2

value: Drought stress

value: 25 days after sowing


title: Ambient CO2_replicate1

value: 21 days after sowing


title: MZsox19b_5.3hpf_r2_Hi-C

description:
Sox19b_mutant_5.3hpf_r2_Hi-C
MZsox19b_5.3.1000.mcool


title: MZspgsox19b_5.3hpf_r2_Hi-C

description:
Pou5f3_Sox19b_double_mutant_5.3hpf_r2_Hi-C
PS.1000.mcool


title: MZnanogsox19b_5.3hpf_r2_Hi-C

description:
Sox19b_Nanog_double_mutant_5.3hpf_r2_Hi-C
SN.1000.mcool


title: MZnanogspg_5.3hpf_r1_Hi-C

description:
Nanog_Pou5f3_double_mutant_5.3hpf_r1_Hi-C
NP.1000.mcool


title: MZspg_5.3hpf _r2_Hi-C

description:
Pou5f3_mutant_5.3hpf _r2_Hi-C
MZspg_5.3.1000.mcool


title: MZspg_5.3hpf _r1_Hi-C

description:
Pou5f3_mutant_5.3hpf _r1_Hi-C
MZspg_5.3.1000.mcool


title: MZnanogspg_5.3hpf_r2_Hi-C

description:
Nanog_Pou5f3_double_mutant_5.3hpf_r2_Hi-C
NP.1000.mcool


title: MZspgsox19b_5.3hpf_r1_Hi-C

description:
Pou5f3_Sox19b_double_mutant_5.3hpf_r1_Hi-C
PS.1000.mcool


title: MZspg_ 2.75hpf _r2_Hi-C

description:
Pou5f3_mutant_ 2.75hpf _r2_Hi-C
MZspg_2.75.1000.mcool

value: blastula, 512-cell, 2.75 hpf


title: MZnanog_5.3hpf _r1_Hi-C

description:
Nanog_mutant_5.3hpf _r1_Hi-C
MZnanog_5.3.1000.mcool


title: MZspg_ 2.75hpf _r1_Hi-C

description:
Pou5f3_mutant_ 2.75hpf _r1_Hi-C
MZspg_2.75.1000.mcool


title: Ambient CO2 + Drought stress_replicate1

value: 24 days after sowing


title: MZnanog_5.3hpf _r2_Hi-C

description:
Nanog_mutant_5.3hpf _r2_Hi-C
MZnanog_5.3.1000.mcool


title: MZnanog_ 2.75hpf _r2_Hi-C

description:
Nanog_mutant_ 2.75hpf _r2_Hi-C
MZnanog_2.75.1000.mcool


title: MZnanog_ 2.75hpf _r1_Hi-C

description:
Nanog_mutant_ 2.75hpf _r1_Hi-C
MZnanog_2.75.1000.mcool


title: WT_25hpf_r2_Hi-C

description:
wild-type_25hpf_r2_Hi-C
Wild-Type_25.1000.mcool

value: pharyngula, prim-6, 25 hpf

value: wild-type AB/TL strain


title: WT_ 5.3hpf _r4_Hi-C

description:
wild-type_ 5.3hpf _r4_Hi-C
WT.1000.mcool


title: WT_11hpf_r1_Hi-C

description:
wild-type_11hpf_r1_Hi-C
Wild-Type_11.1000.mcool

value: segmentation, 3-somite, 11 hpf


title: WT_ 5.3hpf _r3_Hi-C

description:
wild-type_ 5.3hpf _r3_Hi-C
WT.1000.mcool


title: WT_ 5.3hpf _r2_Hi-C

description:
wild-type_ 5.3hpf _r2_Hi-C
Wild-Type_5.3.1000.mcool


title: WT_sperm_r2_Hi-C

description:
wild-type_sperm_r2_Hi-C
sperm.1000.mcool

source_name: sperm

value: adult


title: WT_ 2.75hpf _r1_Hi-C

description:
wild-type_ 2.75hpf _r1_Hi-C
Wild-Type_2.75.1000.mcool


title: WT_sperm_r1_Hi-C

description:
wild-type_sperm_r1_Hi-C
sperm.1000.mcool


title: WT_25hpf_r1_Hi-C

description:
wild-type_25hpf_r1_Hi-C
Wild-Type_25.1000.mcool


title: actin KD, 24 h, replicate 3

city: Singapore

first: Fengjun

address: S1A, #06-04, 14 Sicence Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

data_processing:
Reads were alignment to the 11 megabase chromosomes of T. brucei TREU 927 reference genome with Bowtie2 version 2.4.1 (local sensitive mode) using default parameters
Read counts for the annotated genes were extracted using SAMTools pileup and RPM values were calculated.
Assembly: Reads were alignment to the 11 megabase chromosomes of T. brucei TREU 927 reference genome with Bowtie2 version 2.4.1 (local sensitive mode) using default parameters
Supplementary files format and content: CSV files contains raw counts for each sample
Supplementary files format and content: CSV files contains raw counts for each sample

organism: Trypanosoma brucei

source_name: Lister 427 (BSF)

growth_protocol: BSFcells  were cultured in HMI-9 medium supplemented with 10% FBS at 37 ºC with 5% CO2. PCF cells were cultured in Cunningham medium supplemented with 10% FBS at 27  ºC.

extract_protocol:
The total RNA was extracted using Rneasy mini plus kit from Qiagen. On column Dnase I treatment was performed.
The library was constructed in Duke-NUS Genome Biology Facility (DGBF), Singapore.

treatment_protocol: RNAi was induced with 10 µg/ml tetracycline. In vitro differentiation was perfomed by: 1. wash the BSF cells with Cunningham medium; 2. resuspended cells in Cunningham medium at a density of 3-5 x 1000000 cells/ml; 3. add 6 mM CCA; 4. transfer to 27 ºC.

value: Lister 427 (BSF)

value: protozoan parasite

value: actin KD

value: no


title: MZnanogsox19b_5.3hpf_r1_Hi-C

description:
Sox19b_Nanog_double_mutant_5.3hpf_r1_Hi-C
SN.1000.mcool

value: blastula, 50percent-epiboly, 5.3 hpf


title: WT_ 2.75hpf _r2_Hi-C

description:
wild-type_ 2.75hpf _r2_Hi-C
Wild-Type_2.75.1000.mcool


title: WT_ 5.3hpf _r1_Hi-C

description:
wild-type_ 5.3hpf _r1_Hi-C
Wild-Type_5.3.1000.mcool


title: MZsox19b_5.3hpf_r1_Hi-C

description:
Sox19b_mutant_5.3hpf_r1_Hi-C
MZsox19b_5.3.1000.mcool


title: actin KD, 24 h, replicate 2


title: actin KD, 24 h, replicate 1


title: Rab2B KD, 20 h, replicate 2

value: Rab2B KD


title: Rab2B KD, 20 h, replicate 1


title: new PCF replicate 2

source_name: Lister 427 (PCF)

value: Lister 427 (PCF)

value: Rab2B KD, differentiated to PCF

value: in vitro differentiation


title: new PCF replicate 1


title: BSF 427 WT replicate 2

value: WT


title: BSF 427 WT replicate 1


title: SK-N-BE, siTRMT6，Input-2

city: shenzhen

first: Xin

middle: xin

last: Zhang

state: china/guangdong

address: No.7 pengfei road Dapend

department: agricultural genomics institute at shenzhen

institute: chinese academy of agricultural science

description: Library name: siTRMT6_2-Input-2

data_processing:
Library sequencing was performed using illumina Novaseq™ 6000 with 150-bp paired-end. Paired-end data was quality controlled by fastQC (version 0.11.3). Reads uniquely aligned to the reference genome (STAR) were used to call m1A peak using exomePeak
Assembly: hg38
Supplementary files format and content: bed

source_name: SK-N-AS

extract_protocol:
transfection siRNA target TRMT6 to redece its expression
m1A-map-seq was performed as following. In brief, Dynabeads Oligo (dT) purified mRNA was fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB, USA) and immunoprecipitated using m1A antibody (MLB). The immunoprecipitated m1A RNA fragments were extracted with Trizol reagent (Thermo Fisher, USA). Then, input sample without immunoprecipitation and m1A IP RNA fragments respectively generated libraries.

value: SK-N-AS

value: silence TRMT6


title: WT_11hpf_r2_Hi-C

description:
wild-type_11hpf_r2_Hi-C
Wild-Type_11.1000.mcool


title: SK-N-BE, siTRMT6，m1A-1

description: Library name: siTRMT6_1-M1A-1


title: SK-N-BE, control，m1A-2

description: Library name: NC_2-M1A-2

value: control


title: SK-N-BE, siTRMT6，Input-1

description: Library name: siTRMT6_1-Input-1


title: SK-N-BE, control，Input-2

description: Library name: NC_2-Input-2


title: SK-N-BE, control，m1A-1

description: Library name: NC_1_M1A-1


title: SK-N-BE, control，Input-1

description: Library name: NC_1-Input-1


title: PS5X mice (two pooled samples), rep 1

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description: Library name: PS5X_1

data_processing:
Adapter sequences were removed by matching them to a reference with a maximum mismatch of 2, and the clipping thresholds were set for seed and palindrome to 30 and 10, respectively. Reads were then trimmed using a sliding window of 4 base pairs, where trimming occurred if the average quality score within the window fell below 30. Bases at the leading and trailing ends of the reads were removed if their quality score was below 15.
Reads shorter than 30 bases after trimming were discarded. The trimmed reads were then pseudoaligned to the GRCh38 reference genome with Gencode v29 annotations using Kallisto 0.48.0 to quantify transcript abundances.
Assembly: Human GRCh38 reference genome
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for all FASTQ files.

extract_protocol:
half brains were immediately dissected, the cerebellum removed, and the tissue stored brieﬂy in RPMI. Tissue dissociation was then performed using a Dounce homogenizer. Dissociated cell pellets were treated with Mouse cell removal beads (Miltenyi) to remove all mouse cells. Samples were then separated using LS columns and the Midi MACs separator (Miltenyi). Myelin and debris were removed by resuspending the pellet in 8mL 30% Percoll, overlaid with 2mL of 1X DPBS, Purified human cells were then pelleted via centrifugation (10 min, 400xg, 4°C) and dead/apoptotic cells were removed using the EasySep Dead Cell Removal (Annexin V) kit (Miltenyi; Cat. # 17899). Cell pellets were resuspended in 70uL of Dead Cell Removal (DCR) buffer (2% BSA and 1mM CaCl2 in PBS) followed by the addition of 5uL of the DCR Cocktail and 5uL of the Biotin Selection Cocktail. Samples were then incubated at room temperature for 3 min. After incubation, 10mL of DCR beads were added immediately followed by 2.4mL of DCR buffer and incubated at RT for 10 minutes on the EasyEights EasySep magnet (StemCell Technologies; Cat. #18103). Keeping the sample on the magnet, the supernatant was collected and pelleted by centrifugation (10 min, 400xg, 4°C). Cells were then counted on a hemocytometer and resuspended at ~1,000 total cells per microliter in FACS buffer. High quality and low-debris samples were then pooled to result in 1-2 scRNA-seq samples per genotype.
scRNA-seq library preparation was performed according to the 10X Genomics Chromium Single Cell 3’ Reagents kit v3 user guide except that sample volumes containing 25,000 cells are loaded onto the 10X Genomics flow cell to capture ~10,000 total cells. Raw bulk RNA-seq data was initially assessed for quality using FastQC 0.11.9, and results summarized with MultiQC 1.10.1. Data then underwent quality trimming and adapter removal using Trimmomatic 0.39.

value: transplanted iPSC-Microglia


title: PS19 mice (two pooled samples), rep 1

description: Library name: PS19_1


title: PS5X mice (two pooled samples), rep 2

description: Library name: PS5X_2


title: 5X mice (two pooled samples), rep 2

description: Library name: 5X_2


title: WT mice (two pooled samples), rep 1

description: Library name: WT_1


title: WT mice (two pooled samples), rep 2

description: Library name: WT_2


title: HGPS viECs, 0031D, Flow, 2

city: Durham

first: Crystal

last: Kennedy

state: North Carolina

address: 101 Science Drive

department: Genetics and Genomics

institute: Duke University

description: Library name: Sample24

data_processing:
Fastq files were processed with a bash script to trim adapters and low-quality reads using TrimGalore!, check quality of files using FastQC, align to the human genome hg38 and quantify read counts using STAR software. Read count data was processed using DESeq2 in R.
Assembly: hg38
Supplementary files format and content: Procesed files are tab delimited .txt files with raw counts per gene ID.

extract_protocol:
RNA isolation was performed using the Qiagen RNEasy kit following manufacturer protocols.
Library construction was performed using the Roche Kapa Stranded RNA-seq kit following manufacturer protocols.

value: 2D iPSC-derived endothelial cells

tag: group

value: HGPS

value: flow


title: HGPS viECs, 0031D, Static, 2

description: Library name: Sample23

tag: cell line

value: static


title: HGPS viECs, 0031D, Flow, 1

description: Library name: Sample22


title: HGPS viECs, 0031D, Static, 1

description: Library name: Sample21


title: HGPS viECs, 167CL2, Static, 2

description: Library name: Sample19


title: HGPS viECs, 167CL2, Flow, 2

description: Library name: Sample20


title: SK-N-BE, siTRMT6，m1A-2

description: Library name: siTRMT6_2-M1A-2


title: Rab2B KD, 20 h, replicate 3

value: Lister 427 (BSF)

value: protozoan parasite


title: Healthy viECs, 0901B, Flow, 2

description: Library name: Sample16

value: Healthy


title: HGPS viECs, 167CL2, Static, 1

description: Library name: Sample17


title: Healthy viECs, 0901B, Static, 2

description: Library name: Sample15


title: HGPS viECs, 167CL2, Flow, 1

description: Library name: Sample18


title: Healthy viECs, 168CL3, Static, 2

description: Library name: Sample11


title: Healthy viECs, 168CL3, Flow, 1

description: Library name: Sample10


title: Healthy viECs, 168CL2, Flow, 3

description: Library name: Sample6


title: PS19 mice (two pooled samples), rep 2

description: Library name: PS19_2


title: Healthy viECs, 168CL2, Flow, 4

description: Library name: Sample8


title: Healthy viECs, 0901B, Static, 1

description: Library name: Sample13


title: Healthy viECs, 168CL3, Flow, 2

description: Library name: Sample12


title: 5X mice (two pooled samples), rep 1

description: Library name: 5X_1


title: Healthy viECs, 168CL3, Static, 1

description: Library name: Sample9


title: Healthy viECs, 168CL2, Flow, 1

description: Library name: Sample2


title: Healthy viECs, 168CL2, Static 2

description: Library name: Sample3


title: Healthy viECs, 168CL2, Flow, 2

description: Library name: Sample4


title: Healthy viECs, 168CL2, Static, 1

description: Library name: Sample1


title: Healthy viECs, 0901B, Flow, 1

description: Library name: Sample14


title: parental_rep3

city: Zürich

first: Valdemar

middle: Jacob Sven-Åke

last: Priebe

address: Lengghalde 5

country: Switzerland

institute: Kindersptal Zürich/University of Zurich

description: Library name: Sample9

data_processing:
Nextflow 23.04.4 nf-core/rnaseq 3.12.0 pipeline
Sequenced reads were trimmed for adapter sequences/low-quality reads with trimmgalore 0.6.7 (parameters --phred33 --length 30 -j 4).
Trimed sequences were aligned using STAR aligment 2.7.9a (parameters --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterMMp 0.1 0.1 --clip3pAdapterSeq AAAAAAAA AAAAAAAA)
Read count quantification and normalization was done with Salmon 1.10.1.
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set
Supplementary files format and content: Tab-separated values file includes counts for each sample
Supplementary files format and content: Tab-separated values file includes TPM values for each sample

growth_protocol: Cell lines were grown in RPMI 1640 Media (GIBCO) supplemented with 10% fetal bovine serum (FBS), 1% glutamine (GIBCO), penicillin (100U/mL) and streptomycin (100 μg/mL) at 37°C and 5% CO2. Mycoplasma tests were routinely performed.

extract_protocol:
Total RNA was extracted  by harvesting cells in TRIzol and using the Direct-zol RNA Miniprep Kit from Zymo Research.
RNA libraries for RNA-seq were generated usign lllumina Truseq mRNA Kit according to manufacturere's protocols.

treatment_protocol: HAL-01 cells stably expressing Cas9GFP, were  introduced with sgRNA targeting the wild-type TCF3. 697 cells were transduced with shSCR.

value: Leukemia cell line

value: Cas9GFP, Ctr_SCR


title: parental_rep2

description: Library name: Sample8


title: parental_rep1

description: Library name: Sample7


title: X697_rep3

description: Library name: Sample3

value: shSCR


title: TCF3_KO_rep3

description: Library name: Sample6

value: Cas9GFP, wtTCF3 KO


title: TCF3_KO_rep1

description: Library name: Sample4


title: SH-SY5Y cells, ρ+, sample 10

city: Fairway

first: Russell

middle: H

last: Swerdlow

state: KS

address: 4350 Shawnee Mission Parkway

institute: University of Kansas Alzheimer's Disease Center

description:
Library name: SY5Y-WT-10_S34
SY5Y-WT-10

data_processing:
The quality of the raw FastQ files were first assessed using the FastQC pipeline.  Reads were mapped, and transcript abundance was quantified at the gene level using RNA-seq by Expectation Maximization (RSEM) with the bowtie2 aligner and the human genome assembly hg38.
Assembly: hg38
Supplementary files format and content: counts.txt is a matrix of genes x samples that contains the quantified counts by RSEM.

growth_protocol: SH-SY5Y and NTERA‑2/NT2 (NT2) mtDNA-depleted (ρ0) cell lines were generated by exposing the parent (ρ+) lines to ethidium bromide for prolonged durations before transferring them to media that did not contain ethidium bromide. For this study SH-SY5Y ρ0 and ρ+ cells were maintained in DMEM containing 25mM glucose (Gibco #11965) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 100 μg/mL sodium pyruvate, and 50 μg/mL uridine. The NT2 ρ0 and ρ+ cells were maintained in DMEM containing 25 mM glucose (Gibco #11965) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 200 μg/mL sodium pyruvate, and 150 μg/mL uridine. Cells were kept in a 5% CO2 humidified incubator at 37℃, with medium exchanges performed every other day for cultures below 50% confluence and daily for those above 50% confluence.

extract_protocol:
RNA isolations from our ρ0 and ρ+ cell lines were performed using a Qiagen miRNeasy Mini kit (217004) with on column DNase treatment using a Qiagen RNase-Free DNase Set (79254).
The stranded RNA-seq was performed using an Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center Genomics Core (Kansas City, KS). Quality control of the total RNA submissions was completed using an Agilent TapeStation 4200 using an RNA ScreenTape Assay kit (Agilent Technologies 5067-5576). Total RNA (1 ug) was used to initiate the library preparation protocol. The total RNA fraction was processed by oligo dT bead capture of mRNA, fragmentation of enriched mRNA, reverse transcription into cDNA, end repair of cDNA, ligation with the appropriate Unique Dual Index (UDI) adaptors, and strand selection and library amplification by PCR using a Universal Plus mRNA-seq with NuQuant library preparation kit (Tecan Genomics 0520-A01). Library validation was performed using a D1000 ScreenTape Assay kit (Agilent Technologies 5067-5582) on an Agilent TapeStation 4200. Concentration of each library was determined with the NuQuant module of the library prep kit using a Qubit 4 Fluorometer (ThermoFisher/Invitrogen), Libraries were normalized to 4 nM concentration and pooled. The multiplexed pool was quantitated, in triplicate, using a Roche Lightcycler96 with FastStart Essential DNA Green Master (Roche 06402712001) and KAPA Library Quant (Illumina) DNA Standards 1-6 (KAPA Biosystems KK4903). Using the qPCR results, the RNA-Seq library pool was adjusted to 1.9 nM for multiplexed sequencing. Pooled libraries were denatured with 0.2 N NaOH (0.04 N final concentration) and neutralized with 400 mM Tris-HCl pH 8.0. A dilution of the pooled libraries to 380 pM was performed in the sample tube, on instrument, followed by onboard clonal clustering of the patterned flow cell using a NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycle) (Illumina 20028318). A 2x101 cycle sequencing profile with dual index reads was completed using the following sequence profile: Read 1 – 101 cycles x Index Read 1 – 8 cycles x Index Read 2 – 8 cycles x Read 2 – 101 cycles.

value: human neuroblastoma cell line


title: X697_rep1

description: Library name: Sample1


title: Healthy viECs, 168CL2, Static, 4

description: Library name: Sample7


title: SH-SY5Y cells, ρ+, sample 9

description:
Library name: SY5Y-WT-9_S33
SY5Y-WT-9

value: WT


title: SH-SY5Y cells, ρ+, sample 7

description:
Library name: SY5Y-WT-7_S31
SY5Y-WT-7


title: Healthy viECs, 168CL2, Static 3

description: Library name: Sample5


title: SH-SY5Y cells, ρ+, sample 8

description:
Library name: SY5Y-WT-8_S32
SY5Y-WT-8


title: SH-SY5Y cells, ρ+, sample 5

description:
Library name: SY5Y-WT-5_S29
SY5Y-WT-5


title: SH-SY5Y cells, ρ+, sample 3

description:
Library name: SY5Y-WT-3_S27
SY5Y-WT-3


title: SH-SY5Y cells, ρ+, sample 4

description:
Library name: SY5Y-WT-4_S28
SY5Y-WT-4


title: SH-SY5Y cells, ρ+, sample 6

description:
Library name: SY5Y-WT-6_S30
SY5Y-WT-6


title: SH-SY5Y cells, ρ0, sample 9

description:
Library name: SY5Y-p0-9_S43
SY5Y-p0-9

value: mtDNA-depleted


title: SH-SY5Y cells, ρ0, sample 10

description:
Library name: SY5Y-p0-10_S44
SY5Y-p0-10


title: SH-SY5Y cells, ρ0, sample 7

description:
Library name: SY5Y-p0-7_S41
SY5Y-p0-7


title: SH-SY5Y cells, ρ0, sample 8

description:
Library name: SY5Y-p0-8_S42
SY5Y-p0-8


title: SH-SY5Y cells, ρ0, sample 5

description:
Library name: SY5Y-p0-5_S39
SY5Y-p0-5


title: SH-SY5Y cells, ρ0, sample 3

description:
Library name: SY5Y-p0-3_S37
SY5Y-p0-3


title: NT2 cells, ρ+, sample 10

description:
Library name: NT2-WT-10_S54
NT2-WT-10

value: human embryonal carcinoma cell line


title: TCF3_KO_rep2

description: Library name: Sample5


title: SH-SY5Y cells, ρ0, sample 2

description:
Library name: SY5Y-p0-2_S36
SY5Y-p0-2


title: NT2 cells, ρ+, sample 8

description:
Library name: NT2-WT-8_S52
NT2-WT-8


title: X697_rep2

description: Library name: Sample2


title: NT2 cells, ρ+, sample 7

description:
Library name: NT2-WT-7_S51
NT2-WT-7


title: SH-SY5Y cells, ρ+, sample 1

description:
Library name: SY5Y-WT-1_S25
SY5Y-WT-1


title: NT2 cells, ρ+, sample 5

description:
Library name: NT2-WT-5_S49
NT2-WT-5


title: NT2 cells, ρ+, sample 3

description:
Library name: NT2-WT-3_S47
NT2-WT-3


title: NT2 cells, ρ0, sample 10

description:
Library name: NT2-p0-10_S64
NT2-p0-10


title: NT2 cells, ρ+, sample 9

description:
Library name: NT2-WT-9_S53
NT2-WT-9


title: NT2 cells, ρ0, sample 8

description:
Library name: NT2-p0-8_S62
NT2-p0-8


title: NT2 cells, ρ0, sample 3

description:
Library name: NT2-p0-3_S57
NT2-p0-3


title: NT2 cells, ρ+, sample 2

description:
Library name: NT2-WT-2_S46
NT2-WT-2


title: NT2 cells, ρ+, sample 1

description:
Library name: NT2-WT-1_S45
NT2-WT-1


title: NT2 cells, ρ0, sample 7

description:
Library name: NT2-p0-7_S61
NT2-p0-7


title: NT2 cells, ρ0, sample 2

description:
Library name: NT2-p0-2_S56
NT2-p0-2


title: NT2 cells, ρ+, sample 6

description:
Library name: NT2-WT-6_S50
NT2-WT-6


title: SH-SY5Y cells, ρ0, sample 4

description:
Library name: SY5Y-p0-4_S38
SY5Y-p0-4


title: NT2 cells, ρ0, sample 9

description:
Library name: NT2-p0-9_S63
NT2-p0-9


title: SH-SY5Y cells, ρ0, sample 6

description:
Library name: SY5Y-p0-6_S40
SY5Y-p0-6


title: NT2 cells, ρ+, sample 4

description:
Library name: NT2-WT-4_S48
NT2-WT-4


title: NT2 cells, ρ0, sample 6

description:
Library name: NT2-p0-6_S60
NT2-p0-6


title: NT2 cells, ρ0, sample 1

description:
Library name: NT2-p0-1_S55
NT2-p0-1


title: RNA-seq of MDA-MB-231 shARMCX3 replicate 1

city: 成都

first: jiandong

last: wang

state: 四川

address: 新都大道

department: 生命科学学院

institute: 成都医学院

description:
Library name: MDA231 shARMCX3 1
MDA-MB-231 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 1. RNA-seq to assess transcriptomic changes.

data_processing:
Raw reads were subjected to quality control using FastQC (v0.11.9). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39).
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters.
Gene-level read counts were quantified using featureCounts (Subread v2.0.1).
FPKM values were calculated and differential expression analysis was performed using DESeq2 (v1.30.1) in R.
Assembly: GRCh38 (hg38), GENCODE v38 annotation
Supplementary files format and content: fpkm, gene-level raw read counts

growth_protocol: MCF-7 and MDA-MB-231 breast cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA quality and integrity were assessed using Agilent 2100 Bioanalyzer.the Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.l
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s protocol. Libraries were quantified by Qubit and sequenced on the Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: Cells were transduced with lentiviral particles carrying ARMCX3-targeting shRNA or non-targeting control shRNA. Stable knockdown was selected with puromycin.

value: breast cancer cell line

value: ARMCX3 knockdown


title: RNA-seq of MDA-MB-231 shARMCX3 replicate 3

description:
Library name: MDA231 shARMCX3 3
MDA-MB-231 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 3. RNA-seq to assess transcriptomic changes.


title: NT2 cells, ρ0, sample 4

description:
Library name: NT2-p0-4_S58
NT2-p0-4


title: SH-SY5Y cells, ρ0, sample 1

description:
Library name: SY5Y-p0-1_S35
SY5Y-p0-1


title: RNA-seq of MCF-7 shARMCX3 replicate 3

description:
Library name: MCF7 shARMCX3 3
MCF-7 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 3. RNA-seq to assess transcriptomic changes.


title: RNA-seq of MDA-MB-231 negative control replicate 3

description:
Library name: MDA231 NC 3
MDA-MB-231 breast cancer cell line, negative control, replicate 3. RNA-seq to profile gene expression.

value: NC

value: negative control


title: NT2 cells, ρ0, sample 5

description:
Library name: NT2-p0-5_S59
NT2-p0-5


title: RNA-seq of MCF-7 shARMCX3 replicate 2

description:
Library name: MCF7_shARMCX3_2
MCF-7 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 2. RNA-seq to assess transcriptomic changes.


title: RNA-seq of MDA-MB-231 shARMCX3 replicate 2

description:
Library name: MDA231 shARMCX3 2
MDA-MB-231 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 2. RNA-seq to assess transcriptomic changes.


title: RNA-seq of MCF-7 shARMCX3 replicate 1

description:
Library name: MCF7 shARMCX3 1
MCF-7 breast cancer cell line, ARMCX3 knockdown (shRNA), replicate 1. RNA-seq to assess transcriptomic changes.


title: RNA-seq of MCF-7 negative control replicate 3

description:
Library name: MCF7 NC 3
MCF-7 breast cancer cell line, negative control, replicate 3. RNA-seq to profile gene expression.


title: RNA-seq of MCF-7 negative control replicate 2

description:
Library name: MCF7 NC 2
MCF-7 breast cancer cell line, negative control, replicate 2. RNA-seq to profile gene expression.


title: RNA-seq of MCF-7 negative control replicate 1

description:
Library name: MCF7 NC 1
MCF-7 breast cancer cell line, negative control, replicate 1. RNA-seq to profile gene expression.


title: Naive B cells of CBL deficient Patient 3 after 24 hours culture without stimulation

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

description:
Library name: CBL_MB016036_NaiveB_NS_24h
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_CBL.BAM.CBL_MB016036_NaiveB_NS_24h

data_processing:
The FASTQ files generated were first inspected by fastqc to check sequencing quality. Sequences were aligned with the GENCODE reference genome (GRCh37.p13 and GRCm38.p6 for human and mouse, respectively) with STAR aligner v2.6. Gene-level features were quantified with featureCounts v1.6.0. Geneset enrichment analysis (GSEA) was conducted with the fgsea package by projecting genes ranked by their fold-changes in expression with effect-size shrinkage onto the Hallmark genesets retrieved from the MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/). Several of the healthy pediatric donor datasets are already published (68) and accessible on the NCBI Sequence Read Archive (accession no. PRJNA1141130).
Assembly: HgCH38
Supplementary files format and content: .csv Read counts per gene

source_name: Blood

extract_protocol:
RNA was extracted with the RNeasy Plus Micro Kit (Qiagen) from sorted naïve B cells (2 × 104 cells) sorted from the PBMCs of CBL LOH patients, and age-matched healthy children.
Full-length cDNA was generated from 1 ng total RNA with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888), and 1 ng cDNA was then used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024). Libraries with unique barcodes were pooled at equal molar ratios and sequenced on an Illumina NovaSeq 6000 sequencer with V1.5 reagents and NovaSeq Control Software V1.7.0 to generate 100 bp paired-end reads, according to the manufacturer’s protocol.

value: Blood

value: Naive B cells

value: CBL Y371C Hom

value: unstimulated for 24h


title: Naive B cells of CBL deficient Patient 2 after 24 hours culture without stimulation

description:
Library name: CBL_MB016035_NaiveB_NS_24h
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_CBL.BAM.CBL_MB016035_NaiveB_NS_24h


title: Naive B cells of CBL deficient Patient 2 after 24 hours culture with CD40L and IL21

description:
Library name: CBL_MB016035_NaiveB_CD40LIL21_24h
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_CBL.BAM.CBL_MB016035_NaiveB_CD40LIL21_24h

value: CD40L + IL21


title: Naive B cells of CBL deficient Patient 3 at baseline

description:
Library name: CBL_MB016036_NaiveB_Base
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_Base.Result.BAM.CBL_MB016036_NaiveB_Base


title: SH-SY5Y cells, ρ+, sample 2

description:
Library name: SY5Y-WT-2_S26
SY5Y-WT-2


title: NHP2_DOX, in vitro overexpression of Nhp2 in NCC

city: Vienna

first: Irina

last: Poverennaya

address: Spitalgasse 4

country: Austria

institute: Medical University of Vienna

description: Library name: NHP2_DOX

data_processing:
Raw sequencing data were processed using CellRanger (v8.0.1)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files (output of CellRanger)

source_name: hiPSCs STAN line

growth_protocol: hiPSCs STAN line (WiCell #STAN061i-164-1) were cultured on Matrigel-coated plates (Corning #354277; Sarstedt #83.3920) in mTESRplus medium (STEMCELL Technologies #100-0276). The STAN tTS/rtTA-Bsd line was generated at passage 27 by lentiviral transduction with pLV[Exp]-Bsd-EF1A>tTS/rtTA(ns):T2A:EGFP (VectorBuilder #VB220929-1208sva, MOI 50, 5 µg/mL Polybrene) and selected with 10 µg/mL blasticidin (Sigma #SBR00022) for 10 days. At passage 30, cells were further transduced with TRE-driven lentiviral vectors encoding EMG1, NHP2, or TSR3 (VectorBuilder IDs VB240408-1194zuq, VB240408-1195ftw, VB240408-1191wdj) and maintained under puromycin (1 µg/mL; Sigma #P9620-10ML) and blasticidin (10 µg/mL).

extract_protocol:
Prior to sequencing, cells were FACS-sorted for EGFP+ populations to ensure enrichment of transfected cells
Library was performed according to the manufacter's instructions (10X Single Cell 3' v3 protocol)

treatment_protocol: Cells were differentiated into neural crest cells using the STEMdiff™ Neural Crest Differentiation Kit (STEMCELL #08610). Overexpression of EMG1, NHP2, or TSR3 was induced by adding doxycycline hyclate (1 µg/mL; Sigma #D5207-5G) from day 1 of differentiation. Cells were harvested on day 6 (day 0 = seeding).

value: hiPSCs STAN line

value: neural crest


title: RNA-seq of MDA-MB-231 negative control replicate 1

description:
Library name: MDA231 NC 1
MDA-MB-231 breast cancer cell line, negative control, replicate 1. RNA-seq to profile gene expression.


title: EMG1_DOX, in vitro overexpression of Emg1 in NCC

description: Library name: EMG1_DOX


title: Akata cells, PIAS1 replicate 1 (ChIP)

city: Pittsburgh

first: Febri

last: Sugiokto

state: Pennsylvania

address: 5117 Centre Avenue

institute: University of Pittsburgh

description: Library name: Akata replicate 1 (ChIP)

data_processing:
ChIP-Seq FASTQ files were processed and analyzed using the GALAXY web server. Initially, raw reads were assessed for quality using FastQC, and low-quality sequences were trimmed accordingly. High-quality reads were then aligned to the human reference genome and the EBV Akata strain (GenBank: KC207813) using Bowtie2. Peak calling was performed with MACS2, using input DNA as a control to identify significant enrichment regions
Assembly: EBV Akata strain (GenBank: KC207813)
Supplementary files format and content: Bigwig

source_name: Akata EBV+

growth_protocol: Cells were grown in RPMI with 10% FBS in 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and ChIP-derived DNA was further sheared to an average fragment size of ~200 bp using a Covaris system
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: Akata EBV+

value: B-cell lymphoma

tag: chip antibody

value: PIAS1 (Abcam #ab77231)


title: Naive B cells of CBL deficient Patient 1 at baseline

description:
Library name: CBL_MB016034_NaiveB_Base
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_Base.Result.BAM.CBL_MB016034_NaiveB_Base


title: PS-NP-treated liver organoid (0 µg/mL)

city: Chuncheon-si

first: Kim

last: Wijin

address: Kangwondaehak-gil

country: South Korea

institute: kangwon national university

description: Library name: MH_0

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform.
Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Homo sapiens (GRCh38) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw read count and Normalized values for each Sample

source_name: iPSC

growth_protocol: hiPSCs were cultured on Matrigel™-coated (Corning, NY, USA) dishes in Essential 8™ Medium (Thermo Fisher Scientific, Waltham, MA, USA). The medium was replaced daily.

extract_protocol:
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).
The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

treatment_protocol: A multistep differentiation protocol was used to generate liver organoids from undifferentiated hiPSCs. First, single-cell-dissociated hiPSCs were seeded at 1 × 10⁴ cells per well in round-bottom, ultra-low attachment 96-well plates (Corning, NY, USA) and cultured for 24 hours in Essential 8™ medium containing 10 µM Y-27632 ROCK inhibitor (Sigma-Aldrich, St. Louis, MO, USA) at 37℃ in a humidified 5% CO2 incubator, to allow spheroid formation. To induce definitive endoderm differentiation, Essential 8™ medium was replaced with RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 100 ng/mL Activin A (PeproTech, Rocky Hill, NJ, USA), 2.0% B27 supplement (Thermo Fisher Scientific), 3 µM CHIR99021 (Sigma-Aldrich), and Primocin™ (InvivoGen, San Diego, CA, USA). Thereafter, the medium was replaced with RPMI-1640 containing 2% B27, 20 ng/mL BMP4 (R&D Systems, Minneapolis, MN, USA), 5 ng/mL bFGF (PeproTech, Rocky Hill, NJ, USA), 0.5% DMSO (Sigma-Aldrich) and Primocin™ to drive hepatic endoderm differentiation over five days. Finally, spheroids were matured into liver organoids by culturing for 14 days in Hepatocyte Culture Medium (Lonza, Basel, Switzerland) supplemented with 20 ng/mL Oncostatin M and 20 ng/mL HGF (both PeproTech), under the same conditions (37°C, 5 % CO₂).

value: iPSC


title: MSKPCA3_shKMT2D_GDC0941_rep3

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

institute: johns hopkins university

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep3

data_processing:
Adaptor sequences were removed using Trimmomatic v0.39 and aligned to the hg38 human genome using STAR2.6.0. The reads that are uniquely mapped are counted using HTSeq0.9.1. The reads per kilobase per million (RPKM) was calculated for each gene and normalized to obtain gene expression levels.
Differential expression analysis of shKMT2D versus control was performed using DESeq2. Heatmaps of shKMT2D and control samples were then generated using the ComplexHeatmap package in R.
Assembly: hg38
Supplementary files format and content: fastq

source_name: Prostate

growth_protocol: MSKPCA3 organoids were grown as per established protocols (Gao et al. Science 2014)

extract_protocol:
Qiagen RNeasy Mini Kit
NEBNext Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: Organoids were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 1µM GDC0941 for 24 hours, before processing for RNA-Seq

value: Prostate

value: MSKPCA3 organoid

value: prostate cancer

value: Doxycycline, GDC0941


title: Naive B cells of CBL deficient Patient 3 after 24 hours culture with CD40L and IL21

description:
Library name: CBL_MB016036_NaiveB_CD40LIL21_24h
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_CBL.BAM.CBL_MB016036_NaiveB_CD40LIL21_24h


title: Akata cells (Input)

description: Library name: Akata (Input)


title: Akata cells, PIAS1 replicate 2 (ChIP)

description: Library name: Akata replicate 2 (ChIP)


title: MSKPCA3_control_GDC0941_rep2

description: Library name: MSKPCA3_control_GDC0941_rep2

value: DMSO, GDC0941


title: RNA-seq of MDA-MB-231 negative control replicate 2

description:
Library name: MDA231 NC 2
MDA-MB-231 breast cancer cell line, negative control, replicate 2. RNA-seq to profile gene expression.

value: breast cancer cell line

value: NC

value: negative control


title: Naive B cells of CBL deficient Patient 2 at baseline

description:
Library name: CBL_MB016035_NaiveB_Base
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_Base.Result.BAM.CBL_MB016035_NaiveB_Base

value: Blood

value: Naive B cells

value: CBL Y371C Hom


title: MSKPCA3_shKMT2D_GDC0941_rep2

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep2


title: MSKPCA3_control_GDC0941_rep1

description: Library name: MSKPCA3_control_GDC0941_rep1


title: iPSC only

description: Library name: iPSC


title: Naive B cells of individual MD029675 at baseline

description:
Library name: CBL_MB029675_NaiveB_Base
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_Base.Result.BAM.CBL_MB029675_NaiveB_Base

value: WT


title: Naive B cells of individual MD029674 at baseline

description:
Library name: CBL_MB029674_NaiveB_Base
SMART-Seq v4 Ultra Low Input RNA Kit
Batch34PD1_Base.Result.BAM.CBL_MB029674_NaiveB_Base

value: CBL Y371C het


title: MSKPCA3_shKMT2D_DMSO_rep2

description: Library name: MSKPCA3_shKMT2D_DMSO_rep2

value: Doxycycline, DMSO


title: MSKPCA3_shKMT2D_DMSO_rep1

description: Library name: MSKPCA3_shKMT2D_DMSO_rep1


title: MSKPCA3_control_GDC0941_rep3

description: Library name: MSKPCA3_control_GDC0941_rep3


title: MSKPCA3_shKMT2D_GDC0941_rep1

description: Library name: MSKPCA3_shKMT2D_GDC0941_rep1


title: LNCAP_shKMT2D_GDC0941_rep1

description: Library name: LNCAP_shKMT2D_GDC0941_rep1

growth_protocol: LNCaP cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin in plates coated with 0.01% poly L-lysine.

treatment_protocol: LNCaP cells were androgen deprived and cultured in DMSO or 1µg/ml doxycycline for 72h and treated with 10nM DHT, 1µM PI3K inhibitor GDC0941 or both for 24h, before processing for RNA-Seq.

value: LNCaP


title: LNCAP_shKMT2D_DMSO_rep2

description: Library name: LNCAP_shKMT2D_DMSO_rep2


title: TSR3_DOX, in vitro overexpression of Tsr3 in NCC

description: Library name: TSR3_DOX

value: hiPSCs STAN line

value: neural crest


title: PS-NP-treated liver organoid (10 µg/mL)

description: Library name: MH_10

value: iPSC


title: MSKPCA3_shKMT2D_DMSO_rep3

description: Library name: MSKPCA3_shKMT2D_DMSO_rep3

value: Prostate

value: MSKPCA3 organoid


title: MSKPCA3_control_DMSO_rep3

description: Library name: MSKPCA3_control_DMSO_rep3

value: prostate cancer

value: DMSO


title: MSKPCA3_control_DMSO_rep1

description: Library name: MSKPCA3_control_DMSO_rep1


title: LNCAP_control_GDC0941_rep1

description: Library name: LNCAP_control_GDC0941_rep1

value: DMSO, GDC0941


title: LNCAP_shKMT2D_DMSO_rep1

description: Library name: LNCAP_shKMT2D_DMSO_rep1


title: LNCAP_shKMT2D_GDC0941_rep2

description: Library name: LNCAP_shKMT2D_GDC0941_rep2

value: Doxycycline, GDC0941


title: LNCAP_shKMT2D_DHT_rep1

description: Library name: LNCAP_shKMT2D_DHT_rep1

value: Doxycycline, DHT


title: LNCAP_control_DMSO_rep1

description: Library name: LNCAP_control_DMSO_rep1


title: LNCAP_control_DHT_rep2

description: Library name: LNCAP_control_DHT_rep2

value: DMSO, DHT


title: MSKPCA3_control_DMSO_rep2

description: Library name: MSKPCA3_control_DMSO_rep2


title: LNCAP_control_DHT+GDC0941_rep1

description: Library name: LNCAP_control_DHT+GDC0941_rep1

value: DMSO, DHT+GDC0941


title: LNCAP_shKMT2D_DHT+GDC0941_rep2

description: Library name: LNCAP_shKMT2D_DHT+GDC0941_rep2

value: Doxycycline, DHT+GDC0943


title: LNCAP_shKMT2D_DHT_rep2

description: Library name: LNCAP_shKMT2D_DHT_rep2


title: LNCAP_control_DHT_rep1

description: Library name: LNCAP_control_DHT_rep1


title: LNCAP_shKMT2D_DHT+GDC0941_rep1

description: Library name: LNCAP_shKMT2D_DHT+GDC0941_rep1

value: Doxycycline, DHT+GDC0941


title: LNCAP_control_DMSO_rep2

description: Library name: LNCAP_control_DMSO_rep2


title: HG-M

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

description: Library name: step3_6q_3

data_processing:
10X Genomic
genome build: GRCh38
Supplementary files format and content: mtx, barcodes, features

source_name: retina

extract_protocol:
Macular and peripheral explants were dissociated into single cells following light treatment using Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.Then The single-cell suspension was combined with barcoded gel beads in a microfluidic chip and run on the Chromium Controller (10X Genomics) to create gel bead-in-emulsion (GEMs) droplets (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268, 10×Genomics). The GEMs were incubated, enabling mRNA reverse transcription into cDNA.
The barcoded cDNA was then amplified using PCR to construct a library according to users guide of Chromium Single Cell 3ʹ Reagent Kits v3

treatment_protocol: Macular and peripheral explants were dissociated into single cells following light  treatment. In brief,We employed a custom-built light exposure system situated within the tissue culture incubator to induce light stress in retinal explants.Light stress was accomplished by subjecting explants to intense light at 32k lux, while the control group were exposed to 5k lux light. Retinal explant tissues were placed on 12-well plate transwell inserts (#3460, Corning) with neurobasal medium (#21103049, Gibco), 2% B27 (#17504044, Gibco), 1% N2 (#17502048, Gibco), 1% fetal bovine serum (FBS, #F9423, Sigma‐Aldrich), 1% GlutaMax (#35050, Gibco), 1%ITS (#51500056, Gibco) and 1% penicillin-streptomycin (P/S, #P4333, Sigma‐Aldrich). Macular and peripheral neural retinal explants were exposed to light exposure for 4 hr.Single cell dissociation was achieved using the Papain Dissociation System (Worthington Biochem, NJ, USA) according to the manufacturer’s protocol.

value: retina


title: LNCAP_control_GDC0941_rep2

description: Library name: LNCAP_control_GDC0941_rep2