title: A1_PBS

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

description:
Library name: A1_PBS
Lung single-cell suspensions freshly isolated from PBS-treated mice

data_processing:
Libraries were sequenced on an Illumina NovaSeq S2 platform (50 bp paired-end, 100-cycle run). FASTQ files were generated and processed using 10x Genomics Cell Ranger ATAC (v2.1.0), with reads aligned to the mm10 reference genome. Approximately 8,000 nuclei were recovered per sample. Cells with fewer than 1,000 unique fragments or transcription start site (TSS) enrichment scores <5 were excluded. Fragment files were converted to a binarized cell-by-window matrix, retaining the top 20,000 most accessible peaks. Dimensionality reduction was performed using Latent Semantic Indexing (LSI), including TF-IDF transformation and singular value decomposition (SVD), followed by clustering with the Seurat R package (v3.1.4).
Assembly: Mouse (mm10) 2020-A-2.0.0

source_name: Lung

extract_protocol:
Lung single-cell suspensions freshly isolated from PBS- or SCV2-infected mice at 28 d.p.i. were processed for ATAC library construction using the Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics), following the manufacturer’s protocol
Lung single-cell suspensions freshly isolated from PBS- or SCV2-infected mice at 28 d.p.i. were processed for ATAC library construction using the Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics), following the manufacturer’s protocol

value: Lung

value: tissue


title: Wild plant control group 1

status: Public on Jan 27 2026

type: SRA

city: Changchun

first: Bo

last: Xu

address: 5268 Renmin Street

department: College of Forestry and Grassland Science

country: China

institute: Jilin Agricultural University

description:
Library name: WT_1
Column name in gene_count.xls:WT-1

library_source: transcriptomic

data_processing:
Clean reads obtained after quality filtering were aligned to the M.sativa reference genome (Zhongmu No. 4) using HISAT2 (v2.2.1)(Long et al. 2022). Transcript assembly and gene expression quantification were performed based on the reference genome annotation. Differentially expressed genes were identified using DESeq2, with genes showing an adjusted P value < 0.05 considered significantly differentially expressed.
Assembly: M.sativa reference genome (Zhongmu No. 4)
Supplementary files format and content: Excel read count of genes for each sample

molecule: polyA RNA

organism: Medicago sativa

source_name: flowers

extract_protocol:
Transcriptome sequencing was performed by Wuhan MetWare Biotechnology Co., Ltd. using a standard plant mRNA-seq workflow. Anther samples from wild-type (WT) plants and two atp8 overexpression lines (atp8-OE1 and atp8-OE2) were collected, with three independent biological replicates per genotype. Total RNA was extracted following standard protocols, and RNA quality was assessed prior to library construction.
RNA sequencing was conducted by Illumina platforms based on sequencing-by-synthesis (SBS) technology.

tag: tissue

value: flowers


title: A2_SCV2

country: USA

description:
Library name: A2_SCV2
Lung single-cell suspensions freshly isolated from SCV2-infected mice at 28 d.p.i.

library_source: genomic single cell

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type


title: HSkM cells, wt, siDP427/UTRN, biol rep 2

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description:
Library name: HSkM D12 wt siDP427/UTRN_rep 2
Column name in All_samples_raw_counts.csv; HSkM_D427U_2_htseq

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parametr quality q 25, minimal read lenght m 20)
Trimmed sequence reads were mapped to GRCh38.p14 using Hisat2 (–rna-strandness FR)
Read count extraction and normalization were performed using Htseq
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: HSkM

growth_protocol: HSkM cells were maintained in Nutrient Mixture F-10 Ham medium supplement with 20% fetal bovine serum (FBS), 10 ug/ul epidermal growth factor (EGF), 1 mg/ul dexamethasone, and 1% antibiotics. Differentiation of HSkM cells were maintained in DMEM-HA with 2% horse serum and 1% antibiotics. All cells were grown at 37 °C in a humidified incubator containing 5% CO2

extract_protocol:
RNA was extracted using the Total RNA Zol-Out™(A&A Biotechnology) kit and RNA Clean & Concentrator™-5 with DNase I (ZYMO Research). 1000 ng/ul of total RNA was used for rRNA depletion. 2 ng/ul depleted RNA was used for the construcion of sequencing librabies.
RNA libraries for RNA-seq were prepared using RiboCop rRNA Depletion Kit V2 (Lexogen) and RNA-Seq V2 Library Prep Kit with UDIs (Lexogen) following the Long Insert Sizes (RTL) manufacturer's protocols.

treatment_protocol: HSkM cells were transfected with DMD, DP427 and UTRN siRNA using Silence Select siRNA (Thermo Fisher) and Lipofectamine RNAiMAX Transfection Reagent, following the manufacturer's protocol. The final concentration of each siRNA was 25 nM. In the case of double siRNA transfection, the final concentration of the negative control siRNA was 50 nM.

value: HSkM

value: human skeletal myoblasts

tag: genotype

value: wild-type

tag: treatment

value: differentiation, siDP427/UTRN

tag: time

value: Day 12


title: CVST_Ligation_4_PBA_3

city: fuzhou

first: jianbin

last: ying

address: No. 156, North Section of West Second Ring Road, Gulou District

institute: Fuzong Clinical Medical College of Fujian Medical University

description: Library name: mousebrain_09

data_processing:
Raw fastq files were deposited in SRA under PRJNA1402278.  Adaptor and low-quality reads were trimmed using fastp with default parameters.  Clean reads were aligned to the mouse reference genome (mm10/GRCm38) using HISAT2 in orientation mode.  Transcripts were assembled with StringTie and gene-level abundance was quantified as TPM using RSEM.  All software was run according to the author-recommended settings.
Assembly: mm10/GRCm38
Supplementary files format and content: Paired-end reads 1 (fastq)
Supplementary files format and content: Paired-end reads 2 (fastq)

source_name: brain

extract_protocol:
RNA was harvested using the TRIzol reagent (Invitrogen, USA). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  NovaSeg Reagent Kits (Majorbio, China) on the NovaSeq X Plus platform (PE150) following manufacturer's protocols.

value: brain


title: T cells from donor D1007, untreated (N), TCR

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

description:
Library name: D1007-N-TCR
10X Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger-multi software (v7.1.0 ) for CITEseq (5' RNA, FB and TCR) or Cell-Ranger ATAC software (v2.1.0)
Assembly: scRNAseq (GRCh38-2020-A) scTCRseq(GRCh38-alts-ensembl-7.1.0) scATACseq (GRCh38-r107)
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv.gz
Supplementary files format and content: CellRanger-ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz

molecule: other

source_name: T cells from a healthy donor

extract_protocol:
Tumor specimens were dissociated by a gentleMACS dissociator (Miltenyi Biotec) and cryopreserved. After thawing, CD3+ live cells were sorted by FACS and subjected to scATACseq sample preparation. PBL samples from the same patients were also sorted for live cells for scATACseq sample preparation.
Libraries were prepared according to manufactures' instruction (single-cell 5' immune profiling and single-cell ATAC) (10X Genomics)

treatment_protocol: PBMCs from healthy donors were stimulated with CD3/CD28 beads from day 0 to day 10, followed by 5-FU or cisplatin treatment from day 3 to day 7. The stimulation and treatment were repeated for a total of 3 cycles.

value: T cells from a healthy donor

value: T cells

value: unstimulated


title: CVST_Ligation_1

description: Library name: mousebrain_04


title: HSkM cells, wt, siDP427, biol rep 3

description:
Library name: HSkM D12 wt siDP427_rep 3
Column name in All_samples_raw_counts.csv; HSkM_D427_3_htseq

value: differentiation, siDP427


title: CVST_Ligation_2

description: Library name: mousebrain_05


title: HSkM cells, wt, siDP427/UTRN, biol rep 1

description:
Library name: HSkM D12 wt siDP427/UTRN_rep 1
Column name in All_samples_raw_counts.csv; HSkM_D427U_1_htseq


title: CVST_Ligation_3

description: Library name: mousebrain_06


title: HSkM cells, wt, siDMD, biol rep 3

description:
Library name: HSkM D12 wt siDMD_rep 3
Column name in All_samples_raw_counts.csv; HSkM_siD_3_htseq

value: differentiation, siDMD


title: HSkM cells, wt, siDP427/UTRN, biol rep 3

description:
Library name: HSkM D12 wt siDP427/UTRN_rep 3
Column name in All_samples_raw_counts.csv; HSkM_D427U_3_htseq


title: HSkM cells, wt, siDP427, biol rep 2

description:
Library name: HSkM D12 wt siDP427_rep 2
Column name in All_samples_raw_counts.csv; HSkM_D427_2_htseq


title: CVST_Ligation_4_PBA_1

description: Library name: mousebrain_07


title: T cells from donor D2008, untreated (N), TCR

description:
Library name: D2008-N-TCR
10X Genomics


title: T cells from donor D1007, 5-FU-treated, TCR

description:
Library name: D1007-5FU-TCR
10X Genomics


title: HSkM cells, wt, siDP427, biol rep 1

description:
Library name: HSkM D12 wt siDP427_rep 1
Column name in All_samples_raw_counts.csv; HSkM_D427_1_htseq


title: CVST_Ligation_4_PBA_2

description: Library name: mousebrain_08


title: CVST_1

description: Library name: mousebrain_01


title: CVST_2

description: Library name: mousebrain_02


title: CVST_3

description: Library name: mousebrain_03


title: T cells from donor D1007, untreated (N), GEX

description:
Library name: D1007-N-GEX
10X Genomics

library_source: transcriptomic single cell


title: 72h-3

city: Suzhou

first: Xiaoli

last: Pan

state: Jiangsu

address: No. 100, Chongwen Road.

institute: Suzhou institude of systems medicine

description: Library name: 72h-3

data_processing:
The raw read counts were extracted and then normalized by their library size factors and read and gene lengths using edgeR (v.3.36.0)73, which was then used to calculate differential genes. Detailed information on trimming, alignment and quantification can be found as previously reported74 and further details are available at https://github.com/danielgchen/FH_bulk-RNA-seq_pipeline. In brief, data were trimmed using cutadapt (v.2.9)75, quality checked before and after trimming using FastQC (v.0.11.9), and then mapped and quantified using STAR (v.2.7.7a)76. The pathway enrichment analysis of differentially expressed genes was conducted using clusterProfiler (v.4.12.0)77. GSEA was performed with GSEA (v.4.1.0)68; log2 fold changes were calculated with a 1 × 10−2 pseudo-count to account for zero-count genes and avoid infinite values.
Assembly: GRCm39
Supplementary files format and content: .xlsx

source_name: Spleen

extract_protocol:
Total RNA from the iso-lated transferred OT-I T cells was extracted using the RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s instructions and stored at −80 °C for RNA-seq.
RNA-seq

value: Spleen

value: Primary

value: CD8+ T cell


title: HSkM cells, wt, siDMD, biol rep 1

description:
Library name: HSkM D12 wt siDMD_rep 1
Column name in All_samples_raw_counts.csv; HSkM_siD_1_htseq


title: HSkM cells, wt, siDMD, biol rep 2

description:
Library name: HSkM D12 wt siDMD_rep 2
Column name in All_samples_raw_counts.csv; HSkM_siD_2_htseq


title: 72h-2

description: Library name: 72h-2


title: PROseq_THZ531_2h_R1

city: Boston

first: Apoorva

last: Baluapuri

state: MA

address: 45 Shattuck St.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: Library name: PROseq_THZ531_2h_R1

data_processing:
FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the mm10 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
Data was normalized to spike-in reads and adjusted to account for variability in sequencing and spike batch.
Assembly: hg38
Supplementary files format and content: bedGraphs representing spike-normalized read coverage
Library strategy: PRO-Seq

molecule: nuclear RNA

source_name: breast cancer

growth_protocol: HCC1954 cells grown in standard growth media

extract_protocol:
Cells were permeabilized as in Mimoso et al. 2024; run-ons were performed with biotinylated NTPs and then purified
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

value: breast cancer


title: 48h-2

description: Library name: 48h-2


title: 72h-1

description: Library name: 72h-1


title: 24h-1

description: Library name: 24h-1


title: HUVEC exposed to PMA-differentiated U937 for 8 h,A

city: Tübingen

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

country: Germany

institute: University of Tübingen

description:
Library name: Sample 17
UI8A

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM (fragments per kilobase of transcript per million mapped reads) in group ≥ 0.5. FPKM is equal to the number of fragments that map a certain gene or transcipt times a million divided by the length of the gene in Kb and the fragmnets number that map to all genes/transcripts.
Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Assembly: GRCh37
Supplementary files format and content: Expression_Gene.xlsx file contains in column A the Track_id which is the database name in gene level, in column B the name of the gene, in column C its locus, in column D the strand of the gene, in column E the gene type and in colunms F through U the FPKM of each gene for each one of the samples. Likewise, Expression_Transcript.xlsx file contains in column A the Track_id which is the database name in transcript level, in column B the name of the transcript, in column C the ENSEMBL gene id of the transcript, in column D the name of the gene, in column E the locus, in column F the strand, in column F the biological type of the transcript and in colunms H through W the FPKM of trasncript in samples. Differentially_Expressed_Genes.xlsx and Differentially_Expressed_Transcripts.xlsx show differentially expressed genes or transcripts when comparisons between different groups os samples are performed. Different groups compared are shown in different sheets within the xlsx file.

source_name: umbilical vein

growth_protocol: Primary human umbilical vein endothelial cells (HUVEC) were purchased from Tebubio (C2517A) at P0 and cultured in tissue culture-treated flasks (Sarstedt 833.912.002) in 500 mL of Endothelial Cell Growth Basal Medium-2 (EBM™-2), supplemented with EGMTM-2 BulletKitTM Medium (Lonza, MEDIUM CC-3156 and Kit CC-4176) up until P9.  RFP expressing HUVEC were purchased from Pelobiotech at P3 and were cultured in cell culture flasks (Sarstedt 833.912.002) coated with Quick Coating Solution (cAP-01) in Endothelial Basal Medium (EBM, cAP-03) containing 5% fetal bovine serum (FBS). Cells of passages 3-12 were only used. U937 pro-monocytic human cells (cell line, generous gift from the Theriot Lab, University of Washington) were kept in suspension cell tissue culture flasks (Sarstedt 83.3911.502) in RPMI 1640 medium, HEPES (Gibco) supplemented with 10% FBS and antibiotic-antimycotic solution (Thermofisher, 15240062) at a density of 2-10 x105 cells/mL. The Listeria monocytogenes (LM) strains used in this study are JAT606 (Species: LM 1043S, Genotype/Description: Constitutive GFP expression). GFP expressing Listeria monocytogenes (LM) strain JAT606 was streaked from a glycerol stock on a BHI agar plate (10006334, Fisher) containing 7.5ng/mL chloramphenicol (15353771, Fisher Scientific) and 100ng/mL streptomycin (15424871, Fisher Scientific), and incubated for 3 days at 37°C. The evening before infection a single colony was picked and incubated at room temperature overnight in BHI (53286, Sigma) supplemented with 7.5ng/mL chloramphenicol and 100ng/ml streptomycin.

extract_protocol:
Cells were harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by Arraystar Inc.
The total RNA was depleted of rRNAs by Arraystar rRNA Removal Kit. We used Illumina kits for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Finally, the prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method. The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using NovaSeq 6000 S4 Reagent Kit (300 cycles). Sequencing was carried out using the Illumina NovaSeq 6000 according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: U937 monocyte-like cells were differentiated to macrophage-like cells prior to infection by addition of 500ng/mL PMA (Sigma, P1585-1MG) in RPMI 1640 medium, HEPES (Gibco) supplemented with 10% FBS (referred to as RPMI from now on) and antibiotic-antimycotic solution. The cells were incubated for 48h at 37°C and 5% CO2. GFP expressing Listeria monocytogenes (LM) strain JAT606 was streaked from a glycerol stock on a BHI agar plate (10006334, Fisher) containing 7.5ng/mL chloramphenicol (15353771, Fisher Scientific) and 100ng/mL streptomycin (15424871, Fisher Scientific), and incubated for 3 days at 37°C. The evening before infection a single colony was picked and incubated at room temperature overnight in BHI (53286, Sigma) supplemented with 7.5ng/mL chloramphenicol and 100ng/ml streptomycin. The day before infection also, human umbilican vein endothelial cells (HUVEC) were seeded on collagen I coated glass bottoms of 24-well plates (cat. # P24-1.5H-N, Cellvis) at a concentration of 2.5∗10^5 cells/well for 24 h until they form a confluent monolayer. The next morning the liquid cultures that had an optical density (OD) of approximately 1-2, were centrifuged at 2000g for 5 min at room temperature. The pellet was washed 1x with PBS (10010023, Thermofisher) and 5x the original volume of RPMI and added to the differentiated U937 cells (12 mL per T175 flask). U937 were incubated for 40 min at 37°C. Afterwards, the bacterial suspension was removed, cells were washed 1x with PBS and resuspended in RPMI supplemented with 20 µg/mL gentamycin (15820243, Fisher). U937 cells were incubated for 2.5-3.5 h. Prior to flow sorting, cells were washed 1x with PBS, detached using 0.25% trypsin EDTA (25200056, Thermofischer), and suspended in Leibovitz's L-15 CO2 independent medium (21083027, Thermofisher) during flow sorting with the multi-application cell sorter MA 900 (Sony Biotechnology). GFP positive (i.e., bacteria postiive) U937 were collected to then be exposed to HUVEC in monolayer at a concentration of 2.5∗10^4 cells/well. Additional conditions tested were uninfected PMA-differentiated U937  added at same numbers to HUVEC monolayers, and also unexposed HUVEC in monolayer (no U937 addition). Samples were incubated with or without (infected) U937 for additional 8 or 24 h. Samples were washed throoughly to remove U937 and then lyzed for RNA extraction. Considering the 10 fold higher number of HUVEC compared to U937 and the washes performed prior to lyzing, it can be assumed that the RNA analyzed is mostly originating from HUVEC. To unambigusouly confirm that one would have to perform single cell RNA sequnecing.

value: umbilical vein

value: primary cells, HUVEC

value: WT


title: HUVEC exposed to PMA-differentiated U937 for 8 h, C

description:
Library name: Sample 19
UI8C

value: human umbilical vein endothelial cells (HUVEC)


title: Naive3

description: Library name: Naive3


title: HUVEC exposed to PMA-differentiated U937 for 24 h, B

description:
Library name: Sample 22
UI24B


title: 48h-3

description: Library name: 48h-3


title: HUVEC exposed to PMA-differentiated U937 for 8 h, B

description:
Library name: Sample 18
UI8B


title: PROseq_THZ531_2h_R2

description: Library name: PROseq_THZ531_2h_R2


title: 48h-1

description: Library name: 48h-1


title: PROseq_DMSO_2h_R1

description: Library name: PROseq_DMSO_2h_R1

value: DMSO, 2h


title: WT_14_somites_embryo2

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

description: Library name: RNA-Seq 23

data_processing:
ChIP-Rx: Chromosome names for the mouse genome were modified with the prefix ‘mm10_’ and a metagenome was created by concatenating the mouse and human (spikein) reference genomes (mm10 and hg38, respectively) before indexing with Bowtie2 73. Reads were aligned to the metagenome using Bowtie2 with default parameters. Non-unique read alignments were filtered out using SAMtools to exclude those with an alignment quality of <2. The mm10_ prefix appended to chromosome names was used to separate reads as aligned to the reference mouse or spike-in human genomes. SAMtools was used to convert SAM files to BAM files and to remove duplicate aligned reads. Spike-in normalization factors were calculated for each ChIP dataset using the formula for normalized reference-adjusted reads per million (RRPM) (1 per million spike-in reads). BigWig files were generated using the bamCoverage tool from the deepTools suite (version 3.3.0) with a bin size of 10 and data were subsequently visualized as ChIP-Rx normalized tracks using the IGV genome browser. RNA-seq: All fastq files were trimmed using Trim Galore (version 0.5.0), then transcripts were quantified using Salmon (version 1.5.2) using a mouse reference genome (mm10) indexed with Bowtie2. Gene-level count matrices for differential expression analysis were generated from the Salmon transcript quantification output files (quant.sf files), with experimental groups (i.e. genotype and somite number) annotated using a csv annotation table. Transcripts were mapped to genes using the TxDb.Mmusculus.UCSC.mm10.knownGene annotation package. Transcript-level abundance estimates were then summarised to the gene level with tximport, and passed to the DESeq function from DESeq2 (version1.46.0). A regularised log transformation was then performed to the resulting object using the rlog function. To calculate changes in gene expression for multiple contrasts in a single plot, embryos were partitioned into pairs of groups (i.e. group A and group B), chosen from the condition label in the annotation table according to the genotype and somite number. For each specified contrast, the change in expression for a given gene was calculated as the difference between the mean rlog expression in group B and the mean rlog expression in group A (i.e. mean(rlog(group B)) - mean(rlog(group A)). The resulting matrix was visualized using the pheatmap package (version 1.0.12).
Assembly: mm10 and hg38
Supplementary files format and content: bigWig
Supplementary files format and content: quant.sf files generated by Salmon

source_name: mouse embryonic tailbud

growth_protocol: Bruce-4 mouse embryonic stem cells were cultured at 37 °C with 5% CO2 in DMEM growth medium, supplemented with 15% FBS (Scientifix FBSAU-2007A), 1% penicillin-streptomycin (Thermo Scientific 15140122), MEM Non-Essential Amino Acids Solution (Thermo Scientific 11140050), Glutamax™ Supplement (Thermo Scientific 35050061), 0.1 mM 2-Mercaptoethanol (Merck M3148) and 1:1000 homemade LIF. The cells were grown on gelatinised plates, passed every 2-3 days, and the media was replaced daily. Bruce-4 cells (derived from C57BL/6J-Thy1.1 strain, kindly gifted to Monash Genome Modification Platform by Colin Stewart) were authenticated by ATCC using short tandem repeat (STR) analysis. Cells were tested periodically for mycoplasma contamination using PCR.

extract_protocol:
ChIP-RX: Cells were collected by replacing the culture media with trypsin for <5 minutes, then resuspending the detached cells in growth media and centrifuging for 5 minutes at 300 g. The cells were first washed once in PBS, then crosslinked for 10 minutes at room temperature in PBS with 1% (v/v) formaldehyde. The formaldehyde was quenched by adding glycine to a final concentration of 0.125 M, and was then washed twice in PBS. Cell pellets containing an equal number of cells in each sample were snap frozen with liquid nitrogen and stored at -80°C. The cell pellets were thawed on ice and lysed in lysis buffer (100 mM NaCl, 0.5% (v/v) SDS, 5 mM EDTA, 50 mM Tris-HCl pH 8 and 1X protease inhibitor cocktail (Sigma #4693132001)) on ice, then centrifuged for 6 minutes at 300 g. The resulting chromatin pellet was resuspended in ChIP buffer (a 2:1 ratio of lysis buffer and dilution buffer (100 mM NaCl, 5% (v/v) Triton X-100, 5mM EDTA, 100mM Tris-HCl pH 8.5 and 1X protease inhibitor cocktail (Sigma #4693132001))). For every 1x107 cells, chromatin from 5x106 cross-linked NTERA-2 cells were added. All samples were then sonicated at 4°C in a Bioruptor set to high, with 30 cycles of 30 s on and 30 s off. The sonicated samples were diluted to 1x107 cells per mL, and 1mL per antibody was used for ChIP, with 1% kept as input. Antibodies were added to each sample as specified and incubated overnight at 4 °C rotating at low speed. After the antibody incubation, the lysate was centrifuged at max speed for 30 minutes at 4 °C. The pellet was discarded and 40 µL of Dynabeads Protein G (Thermo #10003D), washed 5 times in ChIP buffer, were added to the supernatant of each sample and incubated for 2-4 hours at 4°C rotating at low speed. The beads were then washed 3 times in mixed micelle buffer (150 mM NaCl, 20 mM Tris-HCl pH 8, 5 mM EDTA, 5.2% (w/v) sucrose and 1% (v/v) Triton X-100), twice in buffer 500 (0.1% (w/v) sodium deoxycholate, 1 mM EDTA, 50 mM HEPES pH 7.5 and 1% (v/v) Triton X-100), twice in LiCl/detergent wash buffer (0.5% (w/v) sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% (v/v) NP-40, 10 mM Tris-HCl pH 8) and once in TE (10 mM Tris-HCl pH 8 and 1 mM EDTA). The beads were then resuspended in 100 µL elution buffer (1% (v/v) SDS and100 mM NaHCO3) and incubated at 65°C for 1 hour with shaking. The eluate was removed from the beads, and 10 µL of the input was combined with 90 µL of elution buffer, then all samples were reverse-crosslinked by shaking at 65 °C overnight. 1 µL of RNase A (Thermo #EN0531) was then added to all samples and incubated shaking at 37 °C for 1 hour, followed by 1 µL of Proteinase K (NEB #P8107S) with 2 hours of shaking at 55 °C. DNA was purified from these samples using the Qiagen MinElute PCR purification kit (Qiagen #28006) according to the instructions of the manufacturer. The purified DNA was dried overnight at room temperature in a biosafety hood before shipment to Azenta for Illumina sequencing with 20 million paired-end reads of 150bp per library. The antibodies used for ChIP included: anti-SUZ12 (Cell Signalling 3737, 5 µL), anti-H3K27me3 (Cell Signalling 35861SF, 3 µL) anti-Jarid2 (Cell Signalling 13594S, 5 µL), and anti-MTF2 (Proteintech 16208-1-AP, 5 µL). RNA-Seq: Mice heterozygous for the JARID2 K116R mutation were time-mated, embryos harvested at approximately embryonic day 9.5, and the yolk sac was genotyped by Transnetyx using real-time PCR. Given JARID2 K116R mutant embryos exhibited a small temporal developmental delay compared to their littermate wildtype embryos, control embryos were generated from a wild type intercross that were collected approximately 0.5 days earlier (E9.0, i.e. 12 to 14 somites). This was done to ensure that mutant and wild-type embryos were assayed at the same somite stage of development, allowing a direct comparison of Hox gene expression levels which are known to be highly dynamic in the tailbud at these stages of development [REF: PMID: 35017475] . Embryos were dissected out of uterine horns in cold PBS. Immediately after harvesting each embryo, the tailbud tissue was removed, placed in 350μL lysis buffer (buffer RLT) from an RNeasy mini kit (Qiagen 74106), then snap frozen in dry ice and stored at -80°C. The remainder of the embryo was fixed overnight in PBS with 4% PFA at 4°C with rocking. After fixing, the embryos were washed in PBT (PBS with 1% Tween-20) then dehydrated by transferring through a series of PBT-methanol solutions, each containing a higher concentration of methanol (25%, 50%, 75%, 100% methanol) for 5 minutes each, then frozen in 100% methanol until further processing. In-situ hybridisation was used to stain the somites in the fixed embryos, using an RNA probe against Uncx4.1. After staining, the number of somites were counted and recorded for each embryo. The solution containing the tailbud tissue was passed through a Qiashredder column (Qiagen 79654), and RNA then was extracted and purified using the RNeasy mini kit according to the manufacturers instructions, including DNase digestion. The purified RNA was dried overnight at room temperature in a biosafety hood before shipment to Azenta. Library preparation and Illumina sequencing with SMRT-based library preparation and 30 million paired-end reads of 150bp per library was performed by Azenta for all samples.
All libraries were constructed by Azenta. In brief, the starting material was DNA (100 - 1000ng) that passed quality control. DNA underwent end repair, dA-tailing, adapter ligation and purification. The purified DNA underwent size selection before PCR amplification for library construction. The preliminary quantification and dilution of the library was performed using Qubit3.0, and then Agilent 2100 was used to determine the insert size and nucleic acid concentration of the resulting library sample. The effective concentration of each sample library in the library mixture was determined by qPCR before sequencing to ensure the accuracy of the sample concentration and the reliability of the sequencing data.

value: mouse embryonic tailbud


title: 24h-3

description: Library name: 24h-3


title: Naive2

description: Library name: Naive2


title: PROseq_DMSO_2h_R2

description: Library name: PROseq_DMSO_2h_R2


title: WT_14_somites_embryo3

description: Library name: RNA-Seq 24


title: Naive1

description: Library name: Naive1


title: 24h-2

description: Library name: 24h-2


title: HUVEC exposed to PMA-differentiated U937 for 8 h, D

description:
Library name: Sample 20
UI8D


title: HUVEC exposed to no U937 for 24 h, D

description:
Library name: Sample 16
UE24D

value: no treatement (i.e., no U937 exposure) for 24 h


title: HUVEC exposed to no U937 for 24 h, B

description:
Library name: Sample 14
UE24B


title: HUVEC exposed to PMA-differentiated U937 for 24 h, A

description:
Library name: Sample 21
UI24A


title: WT_14_somites_embryo4

description: Library name: RNA-Seq 25


title: HUVEC exposed to no U937 for 24 h, C

description:
Library name: Sample 15
UE24C


title: MUT_14_somites_embryo2

description: Library name: RNA-Seq 27

value: MUT


title: MUT_14_somites_embryo1

description: Library name: RNA-Seq 26


title: HUVEC exposed to no U937 for 24 h, A

description:
Library name: Sample 13
UE24A


title: HUVEC exposed to PMA-differentiated U937 for 24 h, D

description:
Library name: Sample 24
UI24D


title: HUVEC exposed to PMA-differentiated U937 for 24 h, C

description:
Library name: Sample 23
UI24C


title: HUVEC exposed to no U937 for 8 h, C

description:
Library name: Sample 11
UE8C

value: no treatement (i.e., no U937 exposure) for 8 h


title: HUVEC exposed to no U937 for 8 h, D

description:
Library name: Sample 12
UE8D


title: WT_14_somites_embryo1

description: Library name: RNA-Seq 22


title: MUT_12_somites_embryo1

description: Library name: RNA-Seq 14


title: HUVEC exposed to no U937 for 8 h, A

description:
Library name: Sample 9
UE8A


title: HUVEC exposed to no U937 for 8 h, B

description:
Library name: Sample 10
UE8B


title: MUT_12_somites_embryo2

description: Library name: RNA-Seq 15


title: MUT_13_somites_embryo2

description: Library name: RNA-Seq 21


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 8 h, D

description:
Library name: Sample 4
I8D


city: Shanghai

first: Li

last: Zhixue

address: 320 Yueyang Road, Xuhui District

institute: CAS Center for Excellence in Molecular Cell Science

description: Library name: uSpyCLIP-seq of PTBP1 with 1,000 cells, rep2

data_processing:
Reads were trimmed using Trim-Galore (v.0.0.6) and the 10-nucleotides unique molecular identifier (UMI) at the 5′end of the reads were removed and used as the read identity for further deduplication.
The remaining reads were mapped to the human genome (v.hg38) using the STAR program (v.2.7.9a)53 with the parameter (--twopassMode Basic --outFilterMultimapNmax 1 –alignEndsType Extend5pofRead1).
PCR duplicates were collapsed into a single read using the de-duplication function of umitools (v.1.0.1)
The remaining usable reads were used for identification of clusters using the iCount program with 7-nt clustering window (v2.0.0).
Assembly: hg38
Supplementary files format and content: bed

source_name: Human embryonic kidney

growth_protocol: RBP-expressing Lenti-X 293T stable cell lines were maintained in DMEM supplemented with 10% Fetal Bovine Serum at 37℃ with 5% CO2.

extract_protocol:
The crosslinked cell pellets were resuspended with lysis buffer (50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, 1×Protease Inhibitor Cocktail) using 1 ml per 10 million cells and lysed on ice for 10 min. RNA was rationally fragmented using RNase I.
uSpyCLIP libraries were constructed using the uSpyCLIP method developed in-house

treatment_protocol: RBP-expressing Lenti-X 293T cells were rinsed with ice-cold PBS and irradiated on ice with UV-C light at 400 mJ/cm2 in a UV Crosslinker

value: Human embryonic kidney

value: Epithelial cell


title: WT_13_somites_embryo3

description: Library name: RNA-Seq 18


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 8 h, A

description:
Library name: Sample 1
I8A


title: MUT_13_somites_embryo1

description: Library name: RNA-Seq 20


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 8 h, B

description:
Library name: Sample 2
I8B


title: WT_13_somites_embryo1

description: Library name: RNA-Seq 16


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 24 h, C

description:
Library name: Sample 7
I24C


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 24 h, D

description:
Library name: Sample 8
I24D


title: MUT_16_somites_embryo5

description: Library name: RNA-Seq 9


title: WT_12_somites_embryo1

description: Library name: RNA-Seq 10


title: WT_13_somites_embryo4

description: Library name: RNA-Seq 19


title: dRfxCas13d-TP53g1-rep2

description: Library name: dRfxCas13d-TP53g1-rep2

data_processing:
Adapters were trimmed from the raw paired-end fastq reads using Trim-Galore (v.0.0.6) with the parameters –quality 20 --stringency=1 --length=35 --paired.
The remaining reads were mapped to the human genome (hg38) using the STAR program (v.2.7.9a).
Gene abundance was normalized as TPM (transcripts per million).
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

growth_protocol: Lenti-X 293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum at 37℃ with 5% CO2.

extract_protocol:
RNA was isolated by standard Trizol-chloroform extraction according to the manufacturer’s instructions
mRNA libraries were constructed using Smart-seq2 as previously described. Briefly, 10 ng of total RNA was reverse transcribed using ProtoScript II Reverse Transcriptase (NEB, M0368). After PCR pre-amplification, cDNA libraries were purified using Agencourt Ampure XP beads (Beckman Coulter, A63881) and 2 ng of purified cDNA was used for the next tagmentation reaction. The final amplified libraries were purified again by Agencourt Ampure XP beads and sequenced at 2×150 bp on Illumina NovaSeq 6000 platform.

treatment_protocol: Lenti-X 293T cells transfected with the indicated plasmids were treated with 10 ng/ml Doxycycline for the induction of dPspCas13 or dRfxCas13d protein.


title: MUT_16_somites_embryo3

description: Library name: RNA-Seq 7


title: WT_12_somites_embryo4

description: Library name: RNA-Seq 13


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 24 h, B

description:
Library name: Sample 6
I24B


title: MUT_16_somites_embryo4

description: Library name: RNA-Seq 8


title: WT_12_somites_embryo2

description: Library name: RNA-Seq 11


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 8 h, C

description:
Library name: Sample 3
I8C


title: MUT_16_somites_embryo2

description: Library name: RNA-Seq 6


title: WT_13_somites_embryo2

description: Library name: RNA-Seq 17


description: Library name: uSpyCLIP-seq of PTBP1 with 1,000 cells, rep1


title: dRfxCas13d-EZH2g2-rep2

description: Library name: dRfxCas13d-EZH2g2-rep2


title: WT_12_somites_embryo3

description: Library name: RNA-Seq 12


title: dRfxCas13d-TP53g1-rep1

description: Library name: dRfxCas13d-TP53g1-rep1


title: dRfxCas13d-TP53g1-rep3

description: Library name: dRfxCas13d-TP53g1-rep3


title: WT_16_somites_embryo3

description: Library name: RNA-Seq 3


title: dRfxCas13d-EZH2g1-rep3

description: Library name: dRfxCas13d-EZH2g1-rep3


title: HUVEC exposed to Listeria monocytogenes-infected PMA-differentiated U937 for 24 h, A

description:
Library name: Sample 5
I24A


title: dRfxCas13d-EZH2g2-rep1

description: Library name: dRfxCas13d-EZH2g2-rep1


title: Mus pahari spleen

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description: Library name: Spleen_pahari_RNA

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Hisat2 v2.0.5 with --no-softclip.
Reads with MAPQ < 2 were removed.
Raw read counts per gene were extracted using Seqmonk.
Assembly: mm10 (Mus musculus); GCF_900095145 (Mus pahari)
Supplementary files format and content: txt, table of raw counts

organism: Mus pahari

growth_protocol: TS conditioned medium (TS-CM) was prepared by incubating TS base medium (TS-BM; RMPI 1640 supplemented with 20% FBS, 1X antibiotic-antimycotic, 1 mM sodium pyruvate and 50 µM 2-mercaptoethanol) on confluent, mitomycin-treated primary mouse embryonic fibroblast (PMEF) feeders for 72 h, followed by filtration through a 0.45 µm PES membrane. Blastocysts from C57BL/6 mice were plated individually onto gelatin-coated wells containing mitomycin-treated PMEF feeders in medium consisting of 70% TS-CM and 30% TS-BM, supplemented with 50 ng/ml bFGF, 2 μg/ml heparin and 100 µM Y-27632 (ROCK inhibitor). Following hatching, once 3-4 layers of TSCs formed around the blastocyst, outgrowths were dissociated using 0.5% trypsin-EDTA. TSCs were passaged at sub-confluency until feeder cells were eliminated and subsequently cryopreserved in liquid nitrogen in freezing medium containing 90% culture medium and 10% DMSO. For regular passaging of established lines (B6 TSCs, GFP TSCs and Rs26 TSCs), medium with no ROCK inhibitor and reduced bFGF (25 ng/ml) and heparin (1 µg/ml) was used. Cells were kept in humidified atmosphere with 5% CO2 at 37 ˚C.

extract_protocol:
Total RNA was isolated using a commercial RNA extraction kit (Qiagen) and treated with DNase I (Ambion) to remove residual genomic DNA.
500 ng of total RNA was subjected to ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2. Strand-specific libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Rs26 KRAB sgIAP TSCs were treated with 8 µg/ml doxycycline hydrochloride to induce CRISPR interference.


title: WT_16_somites_embryo2

description: Library name: RNA-Seq 2


title: MUT_16_somites_embryo1

description: Library name: RNA-Seq 5


title: WT_16_somites_embryo4

description: Library name: RNA-Seq 4


title: Rep3_H3K27me3_wt

description: Library name: ChIP-Rx-seq 33

library_source: genomic

source_name: mESC

value: mESC


title: Rep3_H3K27me3_single_Jarid2_mut

description: Library name: ChIP-Rx-seq 32

value: Jarid2 single SOF mutant


title: dRfxCas13d-EZH2g1-rep1

description: Library name: dRfxCas13d-EZH2g1-rep1


title: Mus pahari liver

description: Library name: Liver_pahari_RNA

source_name: Liver

value: Liver


title: Mus pahari placenta, rep 2

description: Library name: Placenta_pahari_RNA-3

source_name: Placenta

value: Placenta


title: Mus pahari spleen IgG

description: Library name: IgG_spleen_pahari

data_processing:
Sequencing reads were trimmed using Trim_galore, with default settings.
Mapping was done with Bowtie2, with default settings.
Reads with MAPQ < 2 were removed.
Peak detection was performed using GoPeaks with -r set to the number of million reads mapped; -t 200 was used for H3K4me3 and H3K27ac, and -t 2000 -l 200 for the broader H3K4me1 signal.
Assembly: mm10 (Mus musculus); GCF_900095145 (Mus pahari)
Supplementary files format and content: bed, genomic coordinates of peaks
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed using either 50,000 cells or 5 mg of tissue per antibody. Cells were harvested fresh using TrypLE Express and centrifuged at 600 × g for 5 min at room temperature (RT). Placentas were homogenised in 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X protease inhibitor cocktail (PIC), 0.1% BSA) with a Dounce homogeniser using a tight pestle 30 times. Dounced tissue was transferred to a 1.5 ml tube and centrifuged at 600 × g for 5 min at RT. Pellet was resuspended in 500 µl ice-cold nuclei extraction buffer (20 mM HEPES pH 7.5, 10 mM KCl, 0.5 mM spermidine, 1% Triton X-100, 20% glycerol, 1X PIC) and incubated on ice for 10 minutes. Nuclei were pelleted by centrifugation at 1,300 × g for 5 min at 4 ˚C. Pelleted cells or nuclei were washed twice with 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC) by gentle pipetting. BioMagPlus Concanavalin A-coated magnetic beads (Generon) were activated by washing and resuspension in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂). Activated beads (10 µL per sample) were added to the cells and incubated for 10 min at RT. Bead-bound cells were isolated using a magnetic stand, the supernatant was removed, and cells were resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin, 2 mM EDTA, 0.1% BSA). Primary antibodies (H3K4me1 [Abcam ab8895], H3K4me3 [Active Motif 39060], H3K27ac [Abcam ab4729], or IgG [Santa Cruz sc-2027]) were added at a 1:100 dilution, and samples were incubated overnight at 4 °C on a nutator. Cells were incubated with secondary antibody (guinea pig anti-rabbit IgG [ABIN101961]) diluted 1:100 in 100 µl Dig-Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin) for 1 h at RT on a nutator. Cells were washed three times with 800 µl Dig-Wash buffer before incubation with Protein A-Tn5 transposase fusion protein (pA-Tn5), pre-loaded with Illumina Nextera adapters (kind gift from the Henikoff laboratory via the Madapura laboratory). pA-Tn5 was diluted 1:250 in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1X PIC, 0.05% digitonin), and 100 µl was added per sample followed by incubation for 1 h at RT on a nutator. Unbound pA-Tn5 was removed by three washes with 800 µL Dig-300 buffer. Cells were then resuspended in 300 µl tagmentation buffer (10 mM MgCl₂ in Dig-300 buffer) and incubated at 37 °C for 1 h on a nutator. Tagmentation was stopped by the addition of 10 µl 0.5 M EDTA, 3 µl 10% SDS, and 2.5 µl Proteinase K (20 mg/ml), followed by overnight incubation at 37 °C. DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1, v/v; Sigma-Aldrich) and Phase Lock Gel Heavy tubes (5 PRIME), followed by chloroform extraction and ethanol precipitation. DNA pellets were washed with 100% ethanol, air-dried, and resuspended in 30 µl TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) containing RNase A (1:400).
Libraries were amplified using 8 µl DNA per sample with NEBNext HiFi 2X PCR Master Mix, universal i5 primer, and uniquely indexed i7 primers (0.5 µM each). PCR conditions were 72 °C for 5 min, 98 °C for 30 s, followed by 12 cycles of 98 °C for 10 s and 63 °C for 10 s, with a final extension at 72 °C for 1 min. Libraries were purified using AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions.

value: Spleen

tag: antibody

value: IgG [Santa Cruz sc-2027]


title: Mus pahari placenta, rep 1

description: Library name: Placenta_pahari_RNA-2


title: Mus pahari kidney

description: Library name: Kidney_pahari_RNA

source_name: Kidney

value: Kidney


title: Mus pahari spleen H3K4me1

description: Library name: H3K4me1_spleen_pahari

value: H3K4me1 [Abcam ab8895]


title: Mus pahari kidney IgG

description: Library name: IgG_kidney_pahari


title: dRfxCas13d-gNT-rep1

description: Library name: dRfxCas13d-gNT-rep1


title: WT_16_somites_embryo1

description: Library name: RNA-Seq 1

value: WT


title: Mus pahari brain

description: Library name: Brain_pahari_RNA

source_name: Brain

value: Brain


title: dRfxCas13d-EZH2g1-rep2

description: Library name: dRfxCas13d-EZH2g1-rep2


title: Rep3_H3K27me3_mut

description: Library name: ChIP-Rx-seq 31

value: Pali1/Jarid2 SOF mutant


title: dRfxCas13d-gNT-rep2

description: Library name: dRfxCas13d-gNT-rep2


title: dRfxCas13d-gNT-rep3

description: Library name: dRfxCas13d-gNT-rep3


title: Mus pahari liver IgG

description: Library name: IgG_liver_pahari


title: Mus pahari spleen H3K27ac

description: Library name: H3K27ac_spleen_pahari

value: H3K27ac [Abcam ab4729]


title: Mus pahari liver H3K4me3

description: Library name: H3K4me3_liver_pahari

value: H3K4me3 [Active Motif 39060]


title: Mus pahari kidney H3K4me3

description: Library name: H3K4me3_kidney_pahari


title: Rep2_RING1Bmut

description: Library name: ChIP-Rx-seq 29


title: Mus pahari kidney H3K4me1

description: Library name: H3K4me1_kidney_pahari


title: Rep2_RING1Bwt

description: Library name: ChIP-Rx-seq 30


title: Mus pahari liver H3K27ac

description: Library name: H3K27ac_liver_pahari


title: Mus pahari liver H3K4me1

description: Library name: H3K4me1_liver_pahari


title: Rep2_H2AK119ub_mut

description: Library name: ChIP-Rx-seq 25


title: Mus pahari brain IgG

description: Library name: IgG_brain_pahari


title: dRfxCas13d-rep2

description: Library name: dRfxCas13d-rep2


title: dPspCas13b-TP53g1-rep3

description: Library name: dPspCas13b-TP53g1-rep3


title: dRfxCas13d-EZH2g2-rep3

description: Library name: dRfxCas13d-EZH2g2-rep3


title: dPspCas13b-TP53g1-rep2

description: Library name: dPspCas13b-TP53g1-rep2


title: Rep2_H2AK119ub_wt

description: Library name: ChIP-Rx-seq 26


title: dRfxCas13d-rep1

description: Library name: dRfxCas13d-rep1


title: Mus pahari placenta IgG, rep 3

description: Library name: IgG_placenta_pahari-3


title: Mus pahari placenta IgG, rep 2

description: Library name: IgG_placenta_pahari-2


title: dPspCas13b-TP53g1-rep1

description: Library name: dPspCas13b-TP53g1-rep1


title: Mus pahari spleen H3K4me3

description: Library name: H3K4me3_spleen_pahari


title: Mus pahari brain H3K4me3

description: Library name: H3K4me3_brain_pahari


title: Rep1_RING1Bwt

description: Library name: ChIP-Rx-seq 24


title: Rep2_H3K4me3mut

description: Library name: ChIP-Rx-seq 27


title: Mus pahari placenta IgG, rep 1

description: Library name: IgG_placenta_pahari-1


title: dPspCas13b-EZH2g2-rep3

description: Library name: dPspCas13b-EZH2g2-rep3


title: Rep2_H3K4me3wt

description: Library name: ChIP-Rx-seq 28


title: Rep1_H3K4me3mut

description: Library name: ChIP-Rx-seq 21


title: Mus pahari placenta H3K4me3, rep 3

description: Library name: H3K4me3_placenta_pahari-3


title: Mus pahari brain H3K4me1

description: Library name: H3K4me1_brain_pahari


title: Rep1_H3K4me3wt

description: Library name: ChIP-Rx-seq 22


title: dPspCas13b-EZH2g2-rep2

description: Library name: dPspCas13b-EZH2g2-rep2


title: Rep1_RING1Bmut

description: Library name: ChIP-Rx-seq 23


title: Mus pahari placenta H3K4me1, rep 2

description: Library name: H3K4me1_placenta_pahari-2


title: Mus pahari placenta H3K4me3, rep 2

description: Library name: H3K4me3_placenta_pahari-2


title: Mus pahari brain H3K27ac

description: Library name: H3K27ac_brain_pahari


title: dRfxCas13d-rep3

description: Library name: dRfxCas13d-rep3


title: dPspCas13b-EZH2g1-rep3

description: Library name: dPspCas13b-EZH2g1-rep3


title: Mus pahari placenta H3K27ac, rep 3

description: Library name: H3K27ac_placenta_pahari-3


title: Mus pahari placenta H3K4me1, rep 3

description: Library name: H3K4me1_placenta_pahari-3


title: Rep1_H2AK119ub_wt

description: Library name: ChIP-Rx-seq 20


title: Mus pahari placenta H3K27ac, rep 2

description: Library name: H3K27ac_placenta_pahari-2


title: dPspCas13b-EZH2g2-rep1

description: Library name: dPspCas13b-EZH2g2-rep1


title: Mus pahari placenta H3K4me1, rep 1

description: Library name: H3K4me1_placenta_pahari-1


title: dPspCas13b-EZH2g1-rep2

description: Library name: dPspCas13b-EZH2g1-rep2


title: Dam-ATF4 fusion, replicate 3

city: Cambridge

first: Stephen

middle: Peter

last: Burr

address: Mitochondrial Biology Unit, Keith Peters Building, Cambridge Biomedical Campus, Hills Road

department: Clinical Neurosciences

institute: University of Cambridge

description:
Library name: ATF4_Dam_fusion_rep3
Dam-fusion replicate 3

data_processing:
FASTQ were processed using damid-seq_pipeline (v1.5.3). Paired-end reads were aligned to the GRCm38/mm10 reference genome using Bowtie2 (v1.3.1), and mapped reads were assigned to GATC fragments. Signal intensities were computed in 300 bp bins using RPM (reads per million) normalization. Each of the 3 ATF4_Dam_fusion replicates was normalized against each of the 2 Dam_P2A_control replicates (as log2 RPM ratios), resulting in six pairwise comparisons. The normalized differential signals were saved as BedGraph files and converted to BigWig format using bedGraphToBigWig (v2.10) for visualisation.
Peak calling on each pairwise comparison was performed using MACS3 (v3.0.3) with the ATF4_Dam_fusion sample used as treatment and the Dam_P2A_control sample as control. Peaks were called in broad mode, with a fixed fragment size of 300 bp and no model estimation (--nomodel). The effective genome size was computed from the mm10 reference genome, and significance thresholds were set at p < 0.05 with an mfold range of 5 to 50. The initial peak calls from MACS3 were saved in BroadPeak format.
Following MACS3, for each of the three ATF4_Dam_fusion biological replicates, its respective peak sets (derived from its comparisons against control samples) were merged and de-duplicated based on signal strength. To identify highly reproducible peaks across these replicates, Irreproducible Discovery Rate (IDR) analysis was performed using the python IDR package (v2.0.3) on all pairwise combinations of the three merged ATF4_Dam_fusion sample peak sets. Peaks with an IDR score below 0.01 were retained. Finally, a multi-sample intersection of these IDR-passing peaks was performed using bedtools multiinter (v2.31.0) to generate a consensus peak set, representing regions consistently bound across replicates. The final consensus peak set was saved in BED format as the set of identified ATF4 binding regions.
The resulting peaks were annotated using HOMER (v5.1) annotatePeaks.pl and the results were stored as tsv files.
Assembly: GRCm38/mm10
Supplementary files format and content: *.bam: alignment files for mapped reads
Supplementary files format and content: *.bedgraph: damidseq_pipeline output containing log2 RPM ratios
Supplementary files format and content: *.broadPeak: MACS3 output containing called peaks
Supplementary files format and content: ATF4_IDR_filtered_peaks.bed: contains genomic coordinates of reproducible peaks
Supplementary files format and content: ATF4_IDR_filtered_peaks_annotated.tsv: contains gene annotation information for peaks
Supplementary files format and content: ATF4_target_genes.tsv: contains target genes identified with representative peaks
Library strategy: DamID-Seq

source_name: m.5024C>T SV40-immortalized MEF

growth_protocol: Primary m.5024C>T MEFs were isolated from individual E13.5 embryos from the m.5024C>T mouse line (Allele symbol: mt-Tam1Jbst, MGI ID: 5902095), bred on the C57BL/6 background, and immortalized by transfection with the SV40 large T antigen (pBSSVD2005, Addgene plasmid #21826), as described in (Burr et al., Cell 2023, DOI: 10.1016/j.cell.2023.01.034). m.5024C>T MEFs were maintained in DMEM-high glucose-pyruvate (Gibco, 41966-029) supplemented with 10% fetal bovine serum (Gibco, 16000-044) and 50 µg/mL uridine (Sigma, U3750) at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Genomic DNA was extracted from cells using a QiaAmp DNA Micro kit (Qiagen 56304) according to the manufacturer's instructions.
gDNA was fragmented using DpnI digestion overnight at 37°C, followed by dsAdR adaptor ligation using T4 DNA ligase for 2 h at 16°C, followed by ligase inactivation for 10 min at 65°C. Digestion using DpnII was then performed for 2 h at 37°C, followed by DpnII inactivation for 20 min at 65°C. The reaction mixture was subsequently purified using Seramag magnetic beads, followed by PCR amplification using the DreamTaq protocol. The processed DamID fragments (AlwI-digested and sonicated) were  purified using Seramag magnetic beads and  Illumina sequencing libraries were then constructed using NEBNext Ultra II DNA Library Prep Kit. After a further Seramag bead purification, the adaptor-ligated DNA was amplified for 6 cycles using NEBNext Ultra II Q5 Master Mix with i5 and i7 index primers to prepare the libraries.

treatment_protocol: m.5024C>T MEF cells were plated at 2 x 10^6 cells per well in 6-well plates in 2 mL of serum-free media immediately prior to transfection. All transient transfections were performed using Lipofectamine 2000 (Thermo, 11668027). Following the manufacturer's protocol, 1 µg of plasmid (either pCAG-mCherry-P2A-i4Dam-ATF4 or pCAG-mCherry-P2A-i4Dam as specified for each sample), prepared in dam-/dcm- competent E. coli NEB C2925H was added to each well in a 6-well plate. After 5 hours, the media was replaced with DMEM plus 10% FBS and 50 µg/mL uridine. Cells were harvested 48 hours post-transfection.

value: m.5024C>T SV40-immortalized MEF

value: Mouse Embryonic Fibroblast (MEF)

value: Genetic background:C57BL/6; Mitochondrial DNA mutation:m.5024C>T (Allele symbol:mt-Tam1Jbst)


title: Mus pahari placenta H3K27ac, rep 1

description: Library name: H3K27ac_placenta_pahari-1


title: dPspCas13b-EZH2g1-rep1

description: Library name: dPspCas13b-EZH2g1-rep1

value: Human embryonic kidney

value: Epithelial cell


title: hcc1143_IDB-002_0.08uM_rep2

city: SOUTH SAN FRANCISCO

first: Paige

middle: D

last: Diamond

state: California

address: 201 HASKINS WAY

institute: Interdict Bio

description: Library name: EXP025_D6

data_processing:
Raw ribosome profiling sequencing reads were first trimmed to remove adapter sequences using Cutadapt, discarding any reads shorter than 16 nucleotides. The trimmed reads were then mapped sequentially to rRNA, cytoplasmic and mitochondrial tRNA references, followed by alignment to mitochondrial mRNA, mitochondrial DNA, and various noncoding RNA references with Bowtie and Bowtie2. Next, any remaining reads were aligned to human mRNA (RefSeq MANE v1.3) and processed through RSEM for transcript quantification. RSEM quantifications of mRNA-aligned RFPs were used for all downstream analyses. Using the length of each ribosome footprint and the reading frame identified at the 5’ end of the ribosome-protected fragment, the A-site codon was inferred and subsequently used to determine the corresponding peptide sequence in the nascent polypeptide chain.
The position-weighted matrix analysis was performed by extracting amino acid identities from ribosome footprints and corresponding nascent peptide sequences from nascent chain position (-7 to 0). After filtering for coverage threshold (genes with > 0.1 read/codon) and normalizing to library size, log2 fold-change was calculated by comparing each treatment condition to DMSO for every residue at each position.
Assembly: H. sapiens genomic annotations were from GRCh38 and transcript annotations from NCBI RefSeq MANE v.1.3.
Supplementary files format and content: Position-weighted frequency matrix is included for amino acid positions -7 to 0. Identity and position columns correspond to amino acid residue and position within the nascent chain, respectively. All other column names correspond to library names and values correspond to frequency of that identity at that position.
Library strategy: Ribo-Seq

growth_protocol: HCC1143 breast cancer cells (ATCC) were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 1% GlutaMax (Gibco).

extract_protocol:
Cells were washed with ice-cold phosphate-buffered saline and lysed in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1mM DTT, 1% v/v Trizon X-100, 25 U/mL Turbo DNase I). Lysates were incubated on ice for 30 minutes to allow for DNase digestion and clarified by centrifugation at 20,000 × g for 30 minutes at 4 °C. Lysates were digested with 3.33 U/µg RNase I (Ambion) for 45 minutes at room temperature with gentle agitation. Resulting monosomes were isolated by sucrose cushion, using 450 µL 1M sucrose in polysome buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1mM DTT) for 400 µL of digested lysate material. Sucrose cushions were performed with MLA-130 rotor in an Optima Max-XP ultracentrifuge (Beckman Coulter) at 100,000 × g for 90 minutes at 4 °C. Pellet were resuspended in resuspension buffer (150 mM NaCl, 20 mM EDTA, 1% Triton X-100, 20 mM pH 7.5 Tris-HCl) and incubated at room temperature for at least 10 minutes. RNA was extracted using Direct-zol RNA miniprep kit (Zymo), according to manufacturer’s instructions. Ribosome footprint RNA size selection was performed as previously described (McGlincy & Ingolia 2017, Methods) with minor modifications, including the use of 10% TBE-urea gel (Biorad) and custom sizing markers (oIB188-190, 17nt-34nt). Following overnight gel extraction and ethanol precipitation, RNA was dephosphorylated with T4 PNK (NEB) at 37C for 1 hour.
Ribosome footprint cDNA libraries were subsequently constructed with Ordered Two-Template Relay kits (Karnateq) according to manufacturer’s recommendations (Ferguson et al. (2023), Nat. Methods). cDNA libraries were indexed and amplified with NEBNext Indexing Primers (NEB).

treatment_protocol: When cells reached 70-80% confluency, they were treated with anisomycin (ANS) or Interdictor for 60 minutes at noted concentrations.

value: epithelial cell

tag: batch


title: hcc1143_IDB-001_2.5uM_rep2

description: Library name: EXP025_H5


title: hcc1143_IDB-002_0.08uM_rep1

description: Library name: EXP025_C6


title: Dam-ATF4 fusion, replicate 2

description:
Library name: ATF4_Dam_fusion_rep2
Dam-fusion replicate 2


title: Rep1_H2AK119ub_mut

description: Library name: ChIP-Rx-seq 19

value: mESC


title: dPspCas13b-gNT-rep3

description: Library name: dPspCas13b-gNT-rep3


title: hcc1143_IDB-001_2.5uM_rep1

description: Library name: EXP025_F5


title: hcc1143_IDB-001_0.5uM_rep2

description: Library name: EXP025_E5


title: Dam-ATF4 fusion, replicate 1

description:
Library name: ATF4_Dam_fusion_rep1
Dam-fusion replicate 1


title: dPspCas13b-gNT-rep1

description: Library name: dPspCas13b-gNT-rep1


title: hcc1143_IDB-001_0.08uM_rep1

description: Library name: EXP025_B5


title: Dam-P2A control for ATF4 DamID, replicate1

description:
Library name: Dam_P2A_control_rep1
Dam-only replicate 1


title: A549 sh-IL11 3

city: suzhou

first: Gaomeng

last: Luo

address: 199 Renai Road, Industrial Park

institute: soochow university

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an Illumina Novaseq X Plus platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s  instructions.

value: Lung adenocarcinoma cells

value: IL11 knock down


title: A549 scr-shRNA 3

description: Library name: Sample 3


title: dPspCas13b-rep3

description: Library name: dPspCas13b-rep3


title: A549 sh-IL11 2

description: Library name: Sample 5


title: Multiome, MEF cells, GEX, biol rep 2

description:
Library name: MitoPerturbSeq_Replicate_2_RNAseq
GEX (3' mRNA) library: Read 1 file contains cell barcode & UMI, Read 2 file contains transcript
MitoPerturbSeq_Unintegrated_rna_raw_counts.tsv.gz
MitoPerturbSeq_Integrated_sct_log_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv

data_processing:
RNAseq & ATACseq fastq files were processed using the Cell Ranger ARC (v2.0.1) pipeline using a reference genome with nuclear mitochondrial DNA sequences (NUMTs) masked, as described by Caleb Lareau (https://github.com/caleblareau/mgatk/wiki/Increasing-coverage-from-10x-processing). Additional mtDNA ATAC reads from the ATAC hybridization/capture enrichment experiments were added to the ATACseq fastqs prior to running Cell Ranger ARC
A combined ATAC peaks .bed file was generated with MACS2 (v2.2.9.1) using the individual replicate Cell Ranger ATAC fragment files
Basic QC of RNAseq & ATACseq Cell Ranger outputs was performed in Seurat (v5.1.0), removing cells with < 1,000 or > 60,000 transcript counts, < 1,000 or > 10,000 detected genes, > 10% mitochondrial RNA content, > 30% ribosomal RNA content, < 1,000 or > 150,000 ATAC fragments, < 500 or > 55,000 ATAC accessible regions, > 2 nucleosome signal or < 1 transcription start site enrichment
Following basic QC filtering, RNAseq data was normalised using SCTransform and integrated using the canonical correlation analysis (CCA) method in Seurat. ATAC data was integrated using the reciprocal LSI (RLSI) method in Seurat
mtDNA variants and sequencing depth were analysed with the mgatk software package (v0.7.0, Lareau et al, 2020, https://doi.org/10.1038/s41587-020-0645-6) using the atac_possorted_bam.bam output from Cell Ranger ARC. Following mgatk analysis, per-cell per-base mtDNA sequence data was imported into Seurat and used to calculate variant heteroplasmy burden in each cell. Overall heteroplasmy burdens are reported in the integrated metadata file
gRNA transript reads were identified by aligning GEX fastq files to a custom reference genome containing the guide sequences flanked upstream & downstream by 85bp of the surrounding CROP-RFP plasmid backbone sequence with BWA (v0.7.17), the corresponding cell barcodes of aligned reads were then used to assign each cell with a unique gRNA. Cells with multiple guide alignments were assigned as 'multiple_guides', cells with no guide detected were termed 'unknown'. Guide assignments are reported in the integrated metadata file
Assembly: GRCm38 (mm10)
Supplementary files format and content: Cell Ranger output files RNAseq: Replicate_X_RNAseq_barcodes.tsv, Replicate_X_RNAseq_features.tsv.gz, Replicate_X_RNAseq_matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files ATACseq: Replicate_X_ATACseq_fragments.tsv.gz, Replicate_X_ATACseq_fragments.tsv.gz.tbi, Replicate_X_ATACseq_peaks.bed
Supplementary files format and content: Combined ATAC peaks file generated from Cell Ranger outputs with MACS2: Combined_ATACseq_peaks.bed
Supplementary files format and content: Combined Raw RNAseq counts matrix following intial Seurat QC: Unintegrated_rna_raw_counts.tsv.gz
Supplementary files format and content: Integrated SCT log-normalized RNAseq counts matrix: Integrated_sct_log_counts.tsv.gz
Supplementary files format and content: Integrated normalized ATACseq feature counts matrix: Integrated_ATACseq_normalized_feature_counts.tsv.gz
Supplementary files format and content: Combined mgatk mtdna base call counts: Combined_mgatk_counts.tsv.gz
Supplementary files format and content: Cell-level metadata for integrated QC filtered data: Integrated_metadata.tsv

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEFs were cultured in standard high glucose DMEM supplemented with 10% FBS & 50ug/ml uridine

extract_protocol:
CROP-RFP-positive cells were flow sorted, fixed in 0.1% formaldehyde for 5 minutes, permeabilized in 0.1% NP-40 for 5 minutes and resuspended in 10X Genomics Diluted Nuclei Buffer at 3x10e6 cells per ml. 5ul (15,000 cells) of fixed/permeabilized cells was input to the 10X library preparation step.
GEX & ATAC libraries were generated on the 10X Chromium Controller using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit according to the manufacturer's instructions
gRNA enrichment was performed on the GEX cDNA library using the TAPseq protocol (Schraivogel et al, 2020, https://doi.org/10.1038/s41592-020-0837-5)
mtDNA enrichment was performed on the ATAC library by hybridization enrichment with a bespoke panel of mtDNA probes (IDT) using the IDT xGen Hybridization and Wash Kit according to manufacturer's instructions

treatment_protocol: Transduction with CROP-RFP CRISPR library 10 days prior to extraction.

value: Mouse Embryonic Fibroblast

value: m.5024C>T Cas9-Blast

value: CROPseq CRISPR library


title: dPspCas13b-rep1

description: Library name: dPspCas13b-rep1


title: Multiome, MEF cells, ATAC, biol rep 2

description:
Library name: MitoPerturbSeq_Replicate_2_ATACseq
ATAC library, Read 1 & Read 3 files contain ATAC sequences, Read 2 file contains cell barcode
MitoPerturbSeq_Combined_ATACseq_peaks.bed
MitoPerturbSeq_Integrated_ATACseq_normalized_feature_counts.tsv.gz
MitoPerturbSeq_Combined_mgatk_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv


title: A549 scr-shRNA 2

description: Library name: Sample 2

value: WT


title: A549 scr-shRNA 1

description: Library name: Sample 1


title: Multiome, MEF cells, ATAC, biol rep 1

description:
Library name: MitoPerturbSeq_Replicate_1_ATACseq
ATAC library, Read 1 & Read 3 files contain ATAC sequences, Read 2 file contains cell barcode
MitoPerturbSeq_Combined_ATACseq_peaks.bed
MitoPerturbSeq_Integrated_ATACseq_normalized_feature_counts.tsv.gz
MitoPerturbSeq_Combined_mgatk_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv


title: hcc1143_IDB-001_0.5uM_rep1

description: Library name: EXP025_D5


title: dPspCas13b-rep2

description: Library name: dPspCas13b-rep2


title: Dam-P2A control for ATF4 DamID, replicate2

description:
Library name: Dam_P2A_control_rep2
Dam-only replicate 2


title: dPspCas13b-gNT-rep2

description: Library name: dPspCas13b-gNT-rep2


title: A549 sh-IL11 1

description: Library name: Sample 4


title: hcc1143_IDB-001_0.08uM_rep2

description: Library name: EXP025_C5


title: cll_12, IBR, timepoint 3, bcr library

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

description:
Library name: cll_12_relapse_bcr
10X Genomics

data_processing:
Cell barcode/gene matrices, TCRA/TCRB, and IGH/IGL CDR3 cell clonotypes were generated using CellRanger v3.1.0.
Assembly: GRCh38
Supplementary files format and content: cellular barcodes:  tab separated values; feature ids:  tab separated values; count matrices:  sparse matrix format

source_name: peripheral blood

extract_protocol:
PBMC were collected by density gradient centrifugation and cryopreserved.  Samples were thawed, counted and immediately processed for single cell capture using the 10X Genomics immune profiling platform.
Gene expression, TCR, and BCR libraries were made according to the manufacturer's instructions.

treatment_protocol: All patients were treated with ibrutinib

value: peripheral blood

tag: patient

tag: patient type

value: IBR

tag: timepoint

tag: library type

value: bcr


title: cll_12, IBR, timepoint 3, gex library

description:
Library name: cll_12_relapse_gex
10X Genomics

value: gex


title: cll_12, IBR, timepoint 3, tcr library

description:
Library name: cll_12_relapse_tcr
10X Genomics

value: tcr


title: Multiome, MEF cells, GEX, biol rep 1

description:
Library name: MitoPerturbSeq_Replicate_1_RNAseq
GEX (3' mRNA) library: Read 1 file contains cell barcode & UMI, Read 2 file contains transcript
MitoPerturbSeq_Unintegrated_rna_raw_counts.tsv.gz
MitoPerturbSeq_Integrated_sct_log_counts.tsv.gz
MitoPerturbSeq_Integrated_metadata.tsv


title: Control-rep3

description: Library name: Control-rep3

value: control


title: Control-rep2

description: Library name: Control-rep2


title: cll_12, IBR, timepoint 2, tcr library

description:
Library name: cll_12_btk_clone_tcr
10X Genomics


title: cll_12, IBR, timepoint 2, gex library

description:
Library name: cll_12_btk_clone_gex
10X Genomics


title: Rep2_Suz12mut

data_processing:
Chromosome names for the mouse genome were modified with the prefix ‘mm10_’ and a metagenome was created by concatenating the mouse and human (spikein) reference genomes (mm10 and hg38, respectively) before indexing with Bowtie2 73. Reads were aligned to the metagenome using Bowtie2 with default parameters. Non-unique read alignments were filtered out using SAMtools to exclude those with an alignment quality of <2. The mm10_ prefix appended to chromosome names was used to separate reads as aligned to the reference mouse or spike-in human genomes. SAMtools was used to convert SAM files to BAM files and to remove duplicate aligned reads. Spike-in normalization factors were calculated for each ChIP dataset using the formula for normalized reference-adjusted reads per million (RRPM) (1 per million spike-in reads). BigWig files were generated using the bamCoverage tool from the deepTools suite (version 3.3.0) with a bin size of 10 and data were subsequently visualized as ChIP-Rx normalized tracks using the IGV genome browser.
Assembly: mm10 and hg38
Supplementary files format and content: bigWig

extract_protocol:
After 48 hours, cells were collected by replacing the culture media with trypsin for <5 minutes, then resuspending the detached cells in growth media and centrifuging for 5 minutes at 300 g. The cells were first washed once in PBS, then crosslinked for 10 minutes at room temperature in PBS with 1% (v/v) formaldehyde. The formaldehyde was quenched by adding glycine to a final concentration of 0.125 M, and was then washed twice in PBS. Cell pellets containing an equal number of cells in each sample were snap frozen with liquid nitrogen and stored at -80°C. The cell pellets were thawed on ice and lysed in lysis buffer (100 mM NaCl, 0.5% (v/v) SDS, 5 mM EDTA, 50 mM Tris-HCl pH 8 and 1X protease inhibitor cocktail (Sigma #4693132001)) on ice, then centrifuged for 6 minutes at 300 g. The resulting chromatin pellet was resuspended in ChIP buffer (a 2:1 ratio of lysis buffer and dilution buffer (100 mM NaCl, 5% (v/v) Triton X-100, 5mM EDTA, 100mM Tris-HCl pH 8.5 and 1X protease inhibitor cocktail (Sigma #4693132001))). For every 1x107 cells, chromatin from 5x106 cross-linked NTERA-2 cells were added. All samples were then sonicated at 4°C in a Bioruptor set to high, with 30 cycles of 30 s on and 30 s off. The sonicated samples were diluted to 1x107 cells per mL, and 1mL per antibody was used for ChIP, with 1% kept as input. Antibodies were added to each sample as specified and incubated overnight at 4 °C rotating at low speed. After the antibody incubation, the lysate was centrifuged at max speed for 30 minutes at 4 °C. The pellet was discarded and 40 µL of Dynabeads Protein G (Thermo #10003D), washed 5 times in ChIP buffer, were added to the supernatant of each sample and incubated for 2-4 hours at 4°C rotating at low speed. The beads were then washed 3 times in mixed micelle buffer (150 mM NaCl, 20 mM Tris-HCl pH 8, 5 mM EDTA, 5.2% (w/v) sucrose and 1% (v/v) Triton X-100), twice in buffer 500 (0.1% (w/v) sodium deoxycholate, 1 mM EDTA, 50 mM HEPES pH 7.5 and 1% (v/v) Triton X-100), twice in LiCl/detergent wash buffer (0.5% (w/v) sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% (v/v) NP-40, 10 mM Tris-HCl pH 8) and once in TE (10 mM Tris-HCl pH 8 and 1 mM EDTA). The beads were then resuspended in 100 µL elution buffer (1% (v/v) SDS and100 mM NaHCO3) and incubated at 65°C for 1 hour with shaking. The eluate was removed from the beads, and 10 µL of the input was combined with 90 µL of elution buffer, then all samples were reverse-crosslinked by shaking at 65 °C overnight. 1 µL of RNase A (Thermo #EN0531) was then added to all samples and incubated shaking at 37 °C for 1 hour, followed by 1 µL of Proteinase K (NEB #P8107S) with 2 hours of shaking at 55 °C. DNA was purified from these samples using the Qiagen MinElute PCR purification kit (Qiagen #28006) according to the instructions of the manufacturer. The purified DNA was dried overnight at room temperature in a biosafety hood before shipment to Azenta for Illumina sequencing with 20 million paired-end reads of 150bp per library. The antibodies used for ChIP included: anti-SUZ12 (Cell Signalling 3737, 5 µL), anti-H3K27me3 (Cell Signalling 35861SF, 3 µL) anti-Jarid2 (Cell Signalling 13594S, 5 µL), and anti-MTF2 (Proteintech 16208-1-AP, 5 µL).
All libraries were constructed by Azenta. In brief, the starting material was DNA (100 - 1000ng) that passed quality control. DNA underwent end repair, dA-tailing, adapter ligation and purification. The purified DNA underwent size selection before PCR amplification for library construction. The preliminary quantification and dilution of the library was performed using Qubit3.0, and then Agilent 2100 was used to determine the insert size and nucleic acid concentration of the resulting library sample. The effective concentration of each sample library in the library mixture was determined by qPCR before sequencing to ensure the accuracy of the sample concentration and the reliability of the sequencing data.
ChIP-Seq (with spike-in normalisation)

tag: chip antibody

value: anti-SUZ12 (Cell Signalling 3737)

value: Pali1/Jarid2 SOF mutant


title: Control-rep1

description: Library name: Control-rep1

value: Human embryonic kidney

value: Epithelial cell


title: cll_12, IBR, timepoint 1, tcr library

description:
Library name: cll_12_baseline_tcr
10X Genomics


title: cll_12, IBR, timepoint 1, bcr library

description:
Library name: cll_12_baseline_bcr
10X Genomics


title: cll_12, IBR, timepoint 2, bcr library

description:
Library name: cll_12_btk_clone_bcr
10X Genomics


title: Rep2_Suz12wt

value: mESC


description: Library name: uSpyCLIP-seq of dRfxCas13d TP53g1, UV crosslinking, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d TP53g1, UV crosslinking, rep1


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT8, rep2

city: WEST LAFAYETTE

first: Weake

middle: Marie

last: Vikki

state: IN

address: 175 S University st

department: Biochemistry

institute: Purdue University

data_processing:
Raw fq.gz files are acquired from Novogene. The first 5bp from the 5' end of the forward read is cut using Cutadapt version 3.7 as suggested by Ovation SoLo RNAseq system kit. Trimmomatic version 0.39 is used to trim the paired-end reads with the following condition: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Trimmed reads are aligned to Drosophila melanogaster genome dm6 by hisat2 version 2.2.1 with the following seeting --rna-strandness FR. Samtools version 1.17 is used to convert sam files to bam files, and to sort, index bam files.
FeatureCounts function in Subread version 2.0.1 is used to count mapped reads using the following setting: -p -t exon ig gene_id
Assembly: dm6
Supplementary files format and content: Processed data files are txt files that contain quantification results of mapped reads for genes using featureCounts. Drosophila_melanogaster.BDGP6.46.111.gtf from Ensembl is used as a reference.

organism: Drosophila melanogaster

source_name: Photoreceptor cells

growth_protocol: Flies are raised in 12 hour light and 12 hour dark, 25 °C, 80% humidity incubators to Day 10 post-eclosion.

extract_protocol:
400 flies are decapitated by vortexing after being flash frozen in liquid nitrogen. Fly heads are separated using pre-chilled sieves of different sizes. The fly heads are then homogenized using glass homogenizer and the homogenate (cell debris and intact nuclei) are incubated with Anti-GFP-attached beads to enrich GFP-tagged photoreceptor nuclei.
Photoreceptor nuclear RNA are extracted using ZYMO Direct-zol RNA Microprep Kits (#R2061). cRNA library is prepared using Ovation® SoLo RNA-Seq System (#0502-32) that has Drosophila ribosomal RNA depletion built into the protocol.

treatment_protocol: KD F1 flies are generated by crossing Rh1-Gal4 flies and UAS-RNAi flies.

value: Photoreceptor cells

value: Trx KD

tag: Sex

value: Male


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g2, UV crosslinking, rep2


title: cll_11, IBR, timepoint 3, gex library

description:
Library name: cll_11_relapse_gex
10X Genomics


title: Rep2_Mtf2wt

value: anti-MTF2 (Proteintech 16208-1-AP)


description: Library name: uSpyCLIP-seq of dRfxCas13d TP53g1, UV crosslinking, rep2


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT8, rep3


title: cll_11, IBR, timepoint 1, tcr library

description:
Library name: cll_11_baseline_tcr
10X Genomics


title: Rep2_H3K27me3wt

value: anti-H3K27me3 (Cell Signalling 35861SF)


title: cll_11, IBR, timepoint 3, tcr library

description:
Library name: cll_11_relapse_tcr
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT4, rep2


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT8, rep1


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g2, UV crosslinking, rep3


title: cll_11, IBR, timepoint 3, bcr library

description:
Library name: cll_11_relapse_bcr
10X Genomics


title: Rep2_Jarid2mut

value: anti-Jarid2 (Cell Signalling 13594S)


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g1, UV crosslinking, rep2


title: Rep2_Jarid2wt

value: WT


title: cll_11, IBR, timepoint 2, gex library

description:
Library name: cll_11_btk_clone_gex
10X Genomics

value: peripheral blood

value: IBR


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT4, rep1


title: Rep2_Mtf2mut


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g1, UV crosslinking, rep3


title: cll_12, IBR, timepoint 1, gex library

description:
Library name: cll_12_baseline_gex
10X Genomics

value: gex


title: Rep1_Suz12mut


title: Rep1_Suz12wt


title: cll_11, IBR, timepoint 1, gex library

description:
Library name: cll_11_baseline_gex
10X Genomics


title: Rep2_inputwt


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT4, rep3


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT20, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g2, UV crosslinking, rep1


title: Rep2_H3K27me3mut


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT20, rep1


title: cll_11, IBR, timepoint 2, tcr library

description:
Library name: cll_11_btk_clone_tcr
10X Genomics

value: tcr


description: Library name: uSpyCLIP-seq of dRfxCas13d gNT, UV crosslinking, rep2


title: cll_10, IBR, timepoint 3, tcr library

description:
Library name: cll_10_relapse_tcr
10X Genomics


title: Rep1_Jarid2wt


description: Library name: uSpyCLIP-seq of dRfxCas13d gNT, UV crosslinking, rep1


title: Rep1_Mtf2mut


title: cll_10, IBR, timepoint 3, bcr library

description:
Library name: cll_10_relapse_bcr
10X Genomics

value: bcr


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT16, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d only, UV crosslinking, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d EZH2g1, UV crosslinking, rep1


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT16, rep2


title: cll_11, IBR, timepoint 1, bcr library

description:
Library name: cll_11_baseline_bcr
10X Genomics


title: Rep1_Jarid2mut


title: cll_11, IBR, timepoint 2, bcr library

description:
Library name: cll_11_btk_clone_bcr
10X Genomics


title: Rep1_inputwt


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT12, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d only, NonUV, rep3


title: Rep1_Mtf2wt


title: cll_10, IBR, timepoint 2, gex library

description:
Library name: cll_10_btk_clone_gex
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT20, rep2


title: cll_10, IBR, timepoint 1, tcr library

description:
Library name: cll_10_baseline_tcr
10X Genomics


title: Rep1_H3K27me3mut


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT12, rep1


description: Library name: uSpyCLIP-seq of dRfxCas13d only, UV crosslinking, rep1


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT16, rep1


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT0, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d gNT, UV crosslinking, rep3


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT0, rep2


description: Library name: uSpyCLIP-seq of dPspCas13b TP53g1, UV crosslinking, rep3


title: cll_9, IBR, timepoint 3, tcr library

description:
Library name: cll_9_relapse_tcr
10X Genomics


title: cll_10, IBR, timepoint 2, tcr library

description:
Library name: cll_10_btk_clone_tcr
10X Genomics


title: cll_10, IBR, timepoint 3, gex library

description:
Library name: cll_10_relapse_gex
10X Genomics


title: cll_10, IBR, timepoint 2, bcr library

description:
Library name: cll_10_btk_clone_bcr
10X Genomics


title: cll_10, IBR, timepoint 1, gex library

description:
Library name: cll_10_baseline_gex
10X Genomics


title: Mus pahari placenta H3K4me3, rep 1

description: Library name: H3K4me3_placenta_pahari-1

value: Placenta

value: H3K4me3 [Active Motif 39060]


title: CD4+ T cells, HTO

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
CellRanger v5.0.0 count
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger count output files: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz

molecule: protein

extract_protocol:
Spleen of unimmunized mice (KO and Ctrl) and day-4 SRBC-immunized mice (KO and Ctrl) were recovered. Splenic B and CD4+ T cells were magnetically isolated with Mouse B cell isolation kit and naive CD4+ T cells respectively (Miltenyi).
Library was performed according to the manufacter's instructions (single cell 5' V2 protocol, 10X genomics with feature barcode technology). Briefly, B and CD4+ T cells were resuspended in the master mix and loaded together with partioning oil and gel beads into the chip to generate the gel bead-in emulsion (GEM). The poly-A RNA from the lysate containing in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequance, unique molecular identifier (UMI) and the 10X barcode. The pooled bacoded cDNA was then cleaned up with Silane Dynabeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. In parallele, we performed cell surface protein/immune receptor mapping library (HTO) to multiplex B cells from control (Cre) and KO mice unimmunized (D0) or after 4 days (D4) SRBC immunization in the same library, and to multiplex T cells from control (Cre) and KO mice unimmunized (D0) or after 4 days (D4) SRBC immunization in a second library.

treatment_protocol: Il2rb KO and Ctrl mice were immuninized intraperitoneally with 4 x 10^9 Sheep red blood cells .

value: Spleen

value: primary cell

value: mixed sorted CD4+ T cells from KO and Ctrl mice

value: C57BL/6NRj CD19Cre/+ Il2rbfl/fl (Ctrl) or C57BL/6NRj CD19Cre/+ Il2rbfl/fl (KO)

value: SRBC i.p. immunisation

value: mixed sample (Day 0 and Day 4 post immunisation)

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag1, TotalSeq-C0302 anti-mouse Hashtag2, TotalSeq-C0303 anti-mouse Hashtag3, TotalSeq-C0304 anti-mouse Hashtag4


description: Library name: uSpyCLIP-seq of dPspCas13b TP53g1, UV crosslinking, rep1

value: Human embryonic kidney

value: Epithelial cell


description: Library name: uSpyCLIP-seq of dRfxCas13d only, NonUV, rep1


description: Library name: uSpyCLIP-seq of dRfxCas13d only, UV crosslinking, rep2


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g2, UV crosslinking, rep3


description: Library name: uSpyCLIP-seq of dRfxCas13d only, NonUV, rep2


title: Rep1_H3K27me3wt

value: mESC

value: anti-H3K27me3 (Cell Signalling 35861SF)

value: WT


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT8, rep3

value: Photoreceptor cells

value: Trr KD

value: Male


title: 807 aBCR IL5 IL2 J3

data_processing:
Quality of the sequence read was check with Fastqc program
Sequence reads were trimmed for adaptor sequence/low quality sequence using cutadapt
Trimmed sequence reads were mapped to GRCm39_ENSMUSG using Star program
Read counts extraction and normalization were performed using featureCounts program
Normalized counts were used to analyse differentially expressed genes using DEseq2 program
Assembly: GRCm39_ENSMUSG
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: spleen

growth_protocol: Murine B cells were isolated with Mouse B cell isolation kit (Miltenyi) and cultured in complet media (RPMI, 10% fetal bovin serum (FBS), 1X Non essential AA, 1mM Sodium pyruvate, 1X penicilline/stretomycine, 10mM HEPES pH=7, 50µM beta-mercaptoethanol) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cell pellets were extracted with Nucleospin RNA plus XS kit (Macherey-Nagel)
RNA were first enriched with Oligo(dT) beads and then fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR.

treatment_protocol: cells were treated 3 days with 8µg/mL of anti-BCR ((F(ab')2-Goat anti-Mouse IgM (Mu chain) Secondary Antibody, Functional Grade, ThermoFisher Scientific), 50U/mL of IL-5 (Stem cell) with or without 50U/mL IL-2 (Miltenyi)

value: spleen

value: B cells

value: C57BL/6NRj CD19Cre/+

value: in vitro stimulation during 3 days with aBCR IL5 + IL2


title: B cells, HTO

description: Hashtag-derived oligonucleotide (HTO)

value: Spleen

value: primary cell

value: mixed sorted B cells from KO and Ctrl mice

value: C57BL/6NRj CD19Cre/+ Il2rbfl/fl (Ctrl) or C57BL/6NRj CD19Cre/+ Il2rbfl/fl (KO)


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT12, rep2

value: Trx KD


title: cll_10, IBR, timepoint 1, bcr library

description:
Library name: cll_10_baseline_bcr
10X Genomics

value: peripheral blood

value: IBR

value: bcr


title: cll_9, IBR, timepoint 3, gex library

description:
Library name: cll_9_relapse_gex
10X Genomics

value: gex


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g2, UV crosslinking, rep2

value: Human embryonic kidney

value: Epithelial cell


title: CD4+ T cells, GEX

description: polyRNA

value: mixed sorted CD4+ T cells from KO and Ctrl mice

value: SRBC i.p. immunisation

value: mixed sample (Day 0 and Day 4 post immunisation)

value: mRNA


description: Library name: uSpyCLIP-seq of dPspCas13b TP53g1, UV crosslinking, rep2


title: cll_9, IBR, timepoint 2, tcr library

description:
Library name: cll_9_btk_clone_tcr
10X Genomics

value: tcr


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT4, rep3

value: Photoreceptor cells

value: Trr KD

value: Male


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g2, UV crosslinking, rep1


title: cll_9, IBR, timepoint 2, bcr library

description:
Library name: cll_9_btk_clone_bcr
10X Genomics


title: cll_9, IBR, timepoint 3, bcr library

description:
Library name: cll_9_relapse_bcr
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT8, rep1


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g1, UV crosslinking, rep3


title: B cells, GEX

description: polyRNA

value: Spleen

value: primary cell

value: mixed sorted B cells from KO and Ctrl mice


title: 807 aBCR IL5 J3

value: spleen

value: B cells

value: C57BL/6NRj CD19Cre/+

value: in vitro stimulation during 3 days with aBCR IL5


title: Photoreceptor nuclei, dsRNA targets at Trx, ZT0, rep1

value: Trx KD


title: cll_9, IBR, timepoint 2, gex library

description:
Library name: cll_9_btk_clone_gex
10X Genomics

value: peripheral blood

value: IBR

value: gex


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT4, rep2


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT8, rep2


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT20, rep3


title: cll_9, IBR, timepoint 1, bcr library

description:
Library name: cll_9_baseline_bcr
10X Genomics

value: bcr


title: cll_9, IBR, timepoint 1, gex library

description:
Library name: cll_9_baseline_gex
10X Genomics


title: 805 aBCR IL5 IL2 J3

value: in vitro stimulation during 3 days with aBCR IL5 + IL2


title: 805 aBCR IL5 J3


title: 732 aBCR IL5 IL2 J3


title: 732 aBCR IL5 J3


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT4, rep1


title: 750 aBCR IL5 IL2 J3


title: 750 aBCR IL5 J3


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g1, UV crosslinking, rep1

value: Human embryonic kidney

value: Epithelial cell


description: Library name: uSpyCLIP-seq of dPspCas13b EZH2g1, UV crosslinking, rep2


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT20, rep2

value: Photoreceptor cells

value: Trr KD


title: cll_9, IBR, timepoint 1, tcr library

description:
Library name: cll_9_baseline_tcr
10X Genomics

value: tcr


description: Library name: uSpyCLIP-seq of dPspCas13b only, UV crosslinking, rep3


title: 119 aBCR IL5 IL2 J3

value: primary cell

value: C57BL/6NRj CD19Cre/+ Il2rbfl/fl


title: cll_8, IBR, timepoint 3, bcr library

description:
Library name: cll_8_relapse_bcr
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT20, rep1

value: Male


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT16, rep3


title: cll_8, IBR, timepoint 3, tcr library

description:
Library name: cll_8_relapse_tcr
10X Genomics


description: Library name: uSpyCLIP-seq of dPspCas13b only, UV crosslinking, rep2


title: 118 aBCR IL5 IL2 J3

value: spleen

value: B cells


title: cll_8, IBR, timepoint 3, gex library

description:
Library name: cll_8_relapse_gex
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT16, rep2


description: Library name: uSpyCLIP-seq of dPspCas13b only, NonUV, rep2


description: Library name: uSpyCLIP-seq of dPspCas13b only, UV crosslinking, rep1


title: 119 aBCR IL5 J3

value: in vitro stimulation during 3 days with aBCR IL5


title: cll_8, IBR, timepoint 2, tcr library

description:
Library name: cll_8_btk_clone_tcr
10X Genomics


title: 118 aBCR IL5 J3


description: Library name: uSpyCLIP-seq of dPspCas13b only, NonUV, rep1


title: 117 aBCR IL5 IL2 J3


title: cll_8, IBR, timepoint 2, bcr library

description:
Library name: cll_8_btk_clone_bcr
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT16, rep1


title: cll_8, IBR, timepoint 2, gex library

description:
Library name: cll_8_btk_clone_gex
10X Genomics


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT12, rep3


title: uSpyCLIP-seq SpyCatcher2.0, 40ug

description: Library name: uSpyCLIP-seq SpyCatcher2.0, 40ug


title: 116 aBCR IL5 IL2 J3


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT0, rep3


title: 117 aBCR IL5 J3


description: Library name: uSpyCLIP-seq of dPspCas13b only, NonUV, rep3


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT12, rep2


title: cll_7, IBR, timepoint 3, tcr library

description:
Library name: cll_7_relapse_tcr
10X Genomics


title: cll_8, IBR, timepoint 1, gex library

description:
Library name: cll_8_baseline_gex
10X Genomics


title: Fasted3

city: Guangzhou

first: Yiming

last: Zhu

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
FastQC (v0.11.9) package was used to check the quality of raw data, and the Trim-Galore (v0.6.7) for trimming the adapter sequence and filter reads with low quality.
Paired-end sequencing reads were aligned to the mouse genome (GRCm38.primary_assembly.genome) using Spliced Transcripts Alignment to a Reference (STAR) 2.7.10a.
Package featureCounts v.2.0.1 was used to count the read numbers mapped of each gene.
Assembly: mouse genome(GRCm38.primary_assembly.genome)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA from 10,000 sorted PCs was extracted using the EZ-press RNA Purification Kit PLUS (EZB, B0004-PLUS-S).
Reverse transcription, PCR preamplification, and purification of PCR products were conducted using the Discover-sc WTA Kit V2 (Vazyme Biotech). The RNA-seq library was generated by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) using 10 ng amplified cDNAs as input following the manufacturer's protocols.

treatment_protocol: Mice were subjected to a prolonged fasting treatment (72 hours)  or had free access to food, respectively. Then 10,000 plasma cells (CD138high CD267high) in bone marrow of these mice were sorted using BD FACSAria Ⅲ.

value: Bone marrow

value: Plasma cells

tag: stain

value: Fasting


title: cll_8, IBR, timepoint 1, bcr library

description:
Library name: cll_8_baseline_bcr
10X Genomics

value: peripheral blood

value: IBR


title: Fasted2


description: Library name: uSpyCLIP-seq of RBFOX2 with 10,000,000 cells, rep1


title: 116 aBCR IL5 J3


title: cll_8, IBR, timepoint 1, tcr library

description:
Library name: cll_8_baseline_tcr
10X Genomics


title: cll_7, IBR, timepoint 3, bcr library

description:
Library name: cll_7_relapse_bcr
10X Genomics

value: bcr


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT0, rep1


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT8, rep3

value: Set1 KD


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT8, rep2


description: Library name: uSpyCLIP-seq of PTBP1 with 10,000 cells, rep1

value: Human embryonic kidney

value: Epithelial cell


title: cll_7, IBR, timepoint 3, gex library

description:
Library name: cll_7_relapse_gex
10X Genomics

value: gex


title: cll_7, IBR, timepoint 2, gex library

description:
Library name: cll_7_btk_clone_gex
10X Genomics


description: Library name: uSpyCLIP-seq of RBFOX2 with 10,000,000 cells, rep2


title: cll_7, IBR, timepoint 1, tcr library

description:
Library name: cll_7_baseline_tcr
10X Genomics

value: tcr


title: uSpyCLIP-seq SpyCatcher1.0, 40ug

description: Library name: uSpyCLIP-seq SpyCatcher1.0, 40ug


description: Library name: uSpyCLIP-seq of PTBP1 with 10,000 cells, rep2


title: Photoreceptor nuclei, dsRNA targets at Set1, ZT4, rep1

value: Photoreceptor cells


title: Photoreceptor nuclei, dsRNA targets at Trr, ZT0, rep2

value: Trr KD


title: uSpyCLIP-seq SpyCatcher2.0, 20ug

description: Library name: uSpyCLIP-seq SpyCatcher2.0, 20ug


title: KD2

treatment_protocol: Mice were provided with regular diet or ketoenic diet for three weeks, respectively. Then 10,000 plasma cells(CD138high CD267high) in bone marrow of these mice were sorted using BD FACSAria Ⅲ.

value: not applicable

value: ketogenic diet