title: scRNA-seq of HoxB Del(i9-13)/+ 144h gastruloid

data_processing:
Mapping, demultiplexing of cell barcode and quantification was performed using rna_STARsolov2.7.10b on the mm10 reference genome, and a modified gtf file based on Ensembl v102, with the parameters: --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'Gene Expression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000. Then DropletUtils v1.10.0 was used to remove barcodes which were not corresponding to cells (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
Assembly: mm10
Supplementary files format and content: RDS: R object with everything to redo the plots
Supplementary files format and content: tar.gz: output of STARsolo as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)

source_name: gastruloid

extract_protocol:
Gastruloids were collected, pooled in a 1.7 ml Eppendorf tube and washed twice in 1 ml of PBS. The number of gastruloids used in each condition was chosen to ensure that more than 300 000 cells were obtained. They were then dissociated in 100 µl of Accutase (Stempro) for 5 min at 37°C. Full dissociation was completed using mechanical dissociation and verified to ensure the absence of doublet cells. Cells were then resuspended in 200 µl of PBS and counted on a Countess 3 automated cell counter (Invitrogen). All centrifugations were done at 400g for 5 minutes. Samples were then analysed with the standard 10x genomics pipeline (Chemistry v3). After counting, dissociated cells were diluted in PBS BSA 0.04% (Millipore, A1595) to 1x106 cells/ml. Samples were then filtered using a 40 µm cell strainer (Flowmi, BAH136800040).
The pool of cells was counted and subjected to single cell RNA-seq following manufacturer’s recommendation, we aimed for a recovery of c.a. 6000 cells per sample. cDNA preparations were performed according to 10x Genomics recommendations, amplified for 10–12 cycles and verified on fragment analyser.

value: gastruloid

value: HoxB Del(i9-13)/+

tag: stage (h_after_aggregation)


title: BMDM_PBS_1

status: Public on Jul 18 2024

type: SRA

city: San Francisco

first: Robert

last: Raffai

state: California

address: 4150 Clement St

department: Surgery

country: USA

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Aligned with STAR v 2.7.5c
Assembly: GRCm38
Supplementary files format and content: gene by read counts table text file

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow cells were collected from male mice that are 6- to 12-week-old. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% GlutaMAX, and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA were collected using the Qiagen RNeasy Mini Kit.
Universal Plus mRNA-Seq library preparation kit

treatment_protocol:
Cells were treated with 25 ng/mL recombinant murine M-CSF every two days for six days total.
Upon differentiation into BMDM, cells were treated with 2 x 10^9 particles/mL of EKO-BMDM-exo, or WT-BMDM-exo, or PBS for 18 hours.

tag: tissue

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT

tag: treatment 1

value: Macrophage differentiation w/ M-CSF

tag: treatment 2

value: PBS


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 3

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
For data analysis, adapter and bad quality bases were removed from fastq files using cutadapt version 1.18  (Martin, 2011) (-q 30 -m 15 and sequences for -a and -A were adapted to the library).
Filtered reads were aligned on mm10 using STAR version 2.7.10a (Dobin et al, 2013) with the ENCODE parameters and a custom gtf (https://doi.org/10.5281/zenodo.7510406). Coverages were also obtained by STAR.
FPKM were computed with cufflinks version 2.2.1 (Roberts et al, 2011; Trapnell et al, 2010) using --max-bundle-length 10000000 --multi-read-correct --library-type "fr-firststrand" -b mm10.fa --no-effective-length-correction -M mm10_chrM.gtf.
Assembly: mm10
Supplementary files format and content: bw: normalized coverage on uniquely mapped reads
Supplementary files format and content: AllCufflinks_Simplified.txt.gz: table with all FPKM values (one row per ensembl id, one column per sample)
Supplementary files format and content: AllHTSeqCounts.txt.gz: table with all count values obtained with STAR (one row per ensembl id, one column per sample)

molecule: polyA RNA

extract_protocol:
Gastruloids were collected and RNA was extracted as in (Beccari et al, 2018).
Most of Llibraries were prepared with ISML kit from Illumina but two replicates of HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 at 120h were prepared with the TruSeq Stranded mRNA kit from Illumina.

tag: library

tag: stage (h_after_agregation)


title: TAK-1 CD4

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: T cell

growth_protocol: CS1-CAR T cells were thawed and cultured in RPMI medium with 10% FBS, 50U/ml IL2, and 0.5ng/ml rhIL15.

extract_protocol:
Total RNA of sorted cells were exacted using Qiagen miRNAeasy kit.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

treatment_protocol: CS1-CAR T cells were treated with DMSO (Vehicle, Veh) or 0.1µM TAK-981 (TAK) for 16 h, then CD4+ and CD8+ subsets of CS1 CAR T cells treated were purified by FACS sorting after staining with CD4 and CD8 antibodies. In co-culture experiment, CS1-CAR T cells were treated with vehicle (Veh) or TAK-981 (0.1µM, TAK) for 16 h. CAR T were spin down and washed off compound, then CAR T cells were cultured with MM1S-Luc cells at 1:1 ratio for 24 h. Cell mixtures were harvested then CD4+ and CD8+ CAR T cells were purified by FACS sorting after staining with CD4 and CD8. In both experiments, CS1 CAR T cells generated from two individual donors were used as biological replicates.

value: T cell

tag: treatment


title: BMDM_EKO_3

value: EKO-BMDM-exo


title: RNAseq of 78h WT gastruloids replicate3

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

data_processing:
Raw RNA-seq reads generated in this study were trimmed to remove Nextera adapters or bad quality bases (Cutadapt v4.043 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15). Mapping and counting were performed on filtered reads on the mouse genome mm10 with STAR version 2.7.8a44 with a custom gtf based on Ensembl version 10245 and ENCODE parameters. FPKM values were obtained by Cufflinks version 2.2.146,47 with options --no-effective-length-correction -b 'mm10.fa' --multiread-correct --library-type fr-firststrand --mask-file 'chrM_mm10.gtf' --max-bundle-length 10000000 --max-bundle-frags 1000000 (where chrM_mm10.gtf contains a transcript on each strand of the whole chrM). Uniquely mapped reads were filtered with bamFilter48 version 2.5.1. Coverages were computed with BEDTools49 version 2.30.0 for each strand using the '-scale' parameter to normalize to million uniquely mapped reads. Average between duplicates was performed with bigwigAverage v3.5.4 from deepTools50. All samples were of good quality and none were excluded from the analysis. Genes were called differentially expressed when they had both abs(log2fc) > 1 and padj < 0.05
All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: repX_both_strands.bw: normalized coverage (to million of uniquely mapped reads) with both strands combined
Supplementary files format and content: repX_negative_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on negative strand
Supplementary files format and content: repX_positive_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on positive strand
Supplementary files format and content: .bw: average of normalized coverage of the two or three replicates (96h_WT is the average of rep1, rep2 and rep3 while 96h_Snai1WT is the average of 96h_WT_rep4 and rep5)
Supplementary files format and content: tablesX.tar.gz: archive with two tables: AllCufflinks_Simplified.txt.gz: single table with all FPKM values from cufflinks and AllHTSeqCounts.txt.gz: single table with all counts from STAR
Supplementary files format and content: DESeq2_summary.txt: tabular separated text file where each row is a gene and columns indicates log2FC, padj and weather it was significant in each of the analysis
Supplementary files format and content: DESeq2_summary_long.txt: tabular separated text file where each row is a gene in a DESeq2 comparison. This format is more compatible with ggplot2.

source_name: Gastruloids

extract_protocol:
Gastruloids were collected and pooled in a 2-ml Eppendorf tube at the indicated timepoints. After medium removal, gastruloids were washed once with PBS, pelleted and stored at −80 °C until RNA extraction. RNeasy Mini kit (Qiagen) with on-column DNase digestion was used for RNA extraction following manufacturer’s instructions. RNA quality was assessed on a Tapestation TS4200, all RNA samples showed quality number (RIN) above 9.5.
RNA-seq library preparation with Poly-A selection was performed with 1000 ng (for time course analysis) or 500 ng (for mutant gastruloid analysis) of RNA using the Illumina stranded mRNA ligation and following the manufacturer’s protocol 1000000124518 v01. Library quality was assessed with a Libraries were quantified by qubit DNA HS and profile analysis was done on TapeStation TS4200. Libraries were sequenced on HiSeq 4000 Illumina, with paired end 75 bp reads.

value: Gastruloids

tag: replicate

tag: Stage

tag: background


title: Veh-2 CD4

value: vehicle


title: BMDM_EKO_2


title: RNAseq of 78h WT gastruloids replicate2


title: coVeh-1 CD4

value: vehicle, co-culture with MM1S for 24h


title: A: GE-0112 VS GE-0117

type: RNA

city: Elche

first: Víctor M.

last: Barberá

state: Not US or Canada

address: Camí de l'Almazara, 11

department: Laboratorio de Genética Molecular

country: Spain

institute: Hospital General Universitario de Elche

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5)

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: Untreated glioblastoma multiforme specimen 1

label_protocol: Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling (version 6.5)

growth_protocol: The samples were not cultured or treated in cell culture, they were processed directly from the surgical resection specimen of the tumor.

extract_protocol: Total RNA isolation from human GBM biopsies was performed using the RNAqueous-Micro Kit (Ambion), following the manufacturer’s instructions. Normal human brain RNA was purchased from BioChain

tag: age

tag: Sex

value: Male

source_name: Untreated glioblastoma multiforme specimen 5

value: Female


title: BMDM_EKO_1


title: Veh-1 CD4


title: RNAseq of 78h WT gastruloids replicate1


title: RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 2


title: CTCF ChIPmentation of wild-type gastruloids at 96h

library_source: genomic

data_processing:
Adapter and bad quality bases were removed from fastq files using cutadapt version 4.1 (Martin, 2011) (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC  -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15).
Filtered reads were aligned on the in silico mutant genome using bowite2 version 2.4.5 with default parameters (Martin, 2011).
No filtering for mutlimap reads was performed as sequences are duplicated between both alleles of chromosome 11.
Coverage was computed with macs2 version 2.2.7.1 (Zhang et al, 2008) (--call-summits --format BAMPE -B) removing PCR duplicates and then normalized to the million fragments after filtering used by macs2.
Assembly: mm10_HoxB_deli9-13insCBS5-10_del
Supplementary files format and content: *bw = coverage normalized to million mapped fragments
Supplementary files format and content: *narrowPeak.gz = peak obtained by macs2
Library strategy: ChIPmentation

molecule: genomic DNA

source_name: gastruloids

extract_protocol:
Collected gastruloids were pooled in a 15 ml falcon tube, washed with PBS and resuspended in 1 ml PBS containing 1% formaldehyde for fixation during 10 min at room temperature. The crosslink reaction was stopped by adding a glycine solution to a final concentration of 0.125 M. Fixed gastruloids were pelleted and stored at -80°C until further use.
ChIPmentation experiments were performed according to the protocol described in (Rodriguez-Carballo et al., 2017) and (Darbellay et al., 2019), and adapted for gastruloids. Samples were resuspended in a sonication buffer (Tris HCl pH=8.0 50 mM; EDTA 10 mM; SDS 0.25% and protease inhibitors) and sonicated in a Covaris E220 device for 14 min (duty cycle 2%, peak incident power 105 W) to obtain an average chromatin fragment size of 300-500 bp. A dilution buffer (HEPES pH=7.3 20 mM; EDTA 1 mM; NP40 0.1%; NaCl 150 mM and protease inhibitors) was added to the sonicated chromatin and incubated with the antibody-bead complex (Pierce Protein A/G Magnetic Beads, Thermo Scientific) overnight at 4°C. Sequential washes were then performed twice with RIPA buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 140 mM and protease inhibitors), RIPA High salt buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 500 mM and protease inhibitors), LiCl buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; LiCl 250 mM; Sodium Deoxycholate 0.5%; NP40 0.5% and protease inhibitors) and Tris HCl buffer (pH=8.0 10mM and protease inhibitors).  DNA fragments bound to the antibody-bead complex  (CTCF (61311, Active Motif), RAD21 (ab992, Abcam) were tegmented using the Nextera Tegmentation kit. Beads were resuspended in the tegmentation buffer and incubated at 37° for 2 min with 1 µl of the Tn5 transposase. Fragment were then eluted and purified as described previously, and amplified using Nextera primers. Final DNA libraries were purified and size selected using AMPure XP magnetic beads (Beckman Coulter), and a fragment analysis was performed before sequencing.

value: gastruloids

tag: antibody

value: CTCF (61311, Active Motif)

value: wild-type

tag: stage (in_hours_after_aggregation)


title: RNAseq of 84h WT gastruloids replicate2


title: CTCF ChIPmentation of HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS7-10) gastruloids at 96h


title: RNAseq of 84h WT gastruloids replicate1


title: RNAseq of 72h WT gastruloids replicate2


title: Mycosis fungoides, individual 41, rep1

city: Tampere

first: Henry

middle: Juho

last: Barton

state: Pirkanmaa

address: Hämeenkatu 14 C 33

country: Finland

institute: Genevia Technologies Oy

data_processing:
Lexogen Quantseq 2.3.6 FWD UMI pipeline
Assembly: human GRCh38
Supplementary files format and content: Sample specific per gene read counts

source_name: Skin (FFPE tissue blocks)

extract_protocol:
Microdissection was performed for 8–15 paraffin-embedded slide–sections sequentially sliced with a thickness of 5 µm and installed on polyethylene terephthalate slides (Leica AS LMD; Leica Microsystems Ltd., Wetzlar, Germany). The paraffin was removed by dipping the samples twice in xylene for 10 min, and thereafter the sections were stained with hematoxylin for 10 min. CD3 antibody-stained slides (NCL-L-CD3-565) were used to differentiate between lymphocytic and epithelial cells (Supplementary Figure 6). Laser capture microdissection (LCM) using a ZEISS PALM MicroBeam Microdissection System (CarlZeiss Microscopy GmbH, Oberkochen, Germany) and adhesive collection caps with a minimum microdissected lymphocytic cell area of 5 × 106 µm2 was conducted for each sample according to the recommendations of the Quiagen RNA extraction manuals. Following microdissection, the samples were stored in collection vessels containing appropriate volumes of Deparaffinization Solution (#19093, Qiagen GmbH, Hilden, Germany), and the RNA was extracted using a MiRNeasy FFPE extraction kit (#217504, Qiagen GmbH, Hilden, Germany), according to the manufacturer’s instructions. After adding the proteinase K solution, the samples were incubated overnight at 56 ◦C with gentle shaking to obtain a better yield of RNA.
The quality and quantity of the extracted RNA samples were analyzed using a LabChip GX Touch HT RNA Assay Reagent Kit (PerkinElmer, Waltham, MA, USA), and a Qubit RNA BR Kit (Thermo Fisher Scientific, Waltham, MA, USA) was used for the genomic DNA contamination measurements. Dual-indexed mRNA libraries were prepared from 150 ng of total RNA using the QuantSeq 3’ mRNA–Seq Library Prep Kit FWD (Lexogen GmbH, Vienna, Austria) according to user guide version 015UG009V0251. During second strand synthesis, 6 bp Unique Molecular Identifiers (UMI) were introduced with the UMI Second Strand Synthesis Module (Lexogen Gmbh, Vienna, Austria) for the detection and removal of PCR duplicates. Library quality was measured using a LabChip GX Touch HT DNA High Sensitivity Reagent Kit (PerkinElmer, Waltham, MA, USA). Sequencing was performed using the NovaSeq 6000 System (Illumina, San Diego, CA USA) with a read length of 2 × 101 bp and a target coverage of 10 M reads per library.

value: Skin (FFPE tissue blocks)

value: female

tag: clustering group

tag: time point

value: diagnostic


title: RNAseq of 72h WT gastruloids replicate3

tag: tissue


title: Mycosis fungoides, individual 40, rep 2

value: male


title: RNAseq of 90h WT gastruloids replicate2

value: WT


title: CTCF ChIPmentation of HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids at 96h

value: HoxB Del/Del(i9-13):Ins(CBS5-10)


title: Mycosis fungoides, individual 40, rep 1

value: filtered

value: followup


title: RNAseq of 72h WT gastruloids replicate1


title: CTCF CUT&RUN of HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10):Del(CBS7-10) mESC

data_processing:
Adapter and bad quality bases were removed from fastq files using cutadapt version 4.1 (Martin, 2011)(-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-q 30 -m 15).
Filtered reads were aligned on the in silico mutant genome using bowtie2 version 2.4.5 (Langmead & Salzberg, 2012)with adapted parameters (--very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000).
No filtering for mutlimap reads was performed as sequences are duplicated between both alleles of chromosome 11.
PCR duplicates were removed with Picard MarkDuplicates version 2.27.4 (Broad Institute).
Filtered BAM file was converted to BED with BEDTools version 2.30.0 (Quinlan & Hall, 2010).
Coverage was computed with macs2 version 2.2.7.1 (Zhang et al, 2008) (--nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B) and then normalized to the million reads in peaks.
Assembly: mm10_HoxB_deli9-13insCBS5-10_del
Supplementary files format and content: *bw = coverage normalized to million reads in peaks
Supplementary files format and content: *narrowPeak.gz = peak obtained by macs2
Library strategy: CUT&RUN

source_name: mESC

extract_protocol:
Each ESC per genotype were washed into fresh PBS before dissociation. The dissociation was performed in 0.5mL StemPro Accutase (Gibco A1110501), 5min at 37°C. Cells were resuspended into 2mL of ESC media and span at 300g for 2min.
Then, 0.5x106 cells were processed according to the CUT&RUN protocol55. First, cells were resuspended into 1mL of Wash Buffer (WB: 20mM HEPES-KOH pH7.5, 150 mM NaCl, 0.5mM Spermidin (Sigma S2626)) and bound to Concanavalin A-coated beads (BioMagPlus 86057) into Digitonin Wash Buffer (DWB) using a ﬁnal concentration of 0.02% digitonin (Apollo APOBID3301) into WB. Second, cells were incubated with 0.5µg/100μl of anti-CTCF antibody (Active Motif 61311) in DWB at 4°C for 2hr. The pA-MNase was produce by the Protein Production and Structure Core Facility at EPFL and added at 0.5 μl/100 μl in Digitonin Wash Buffer for 1hr at 4°C. Third, cells were digested in Low Calcium Buffer (100mM CaCl2 into DWB). Reaction was stopped using cold 2X STOP Buffer (340mM NaCl, 4mM EGTA, 20mM EDTA, 0.02% Digitonin, 50µg RNase A (10mg/mL), 50µG Glycogen (5mg/mL)) for 5min. Finally, targeted chromatin was released for 30 min at 37 °C, then precipitated into 70% EtOH and stored at -20°C until sequencing libraries generation. Sequencing libraries were prepared with KAPA HyperPrep reagents (07962347001) with 2.5µl of adapters at 0.3µM and ligated for 1 h at 20 °C. Then, DNA was cleaned and size selected using 1:1 ratio of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. The DNA was ampliﬁed for 16 cycles. Post-ampliﬁed DNA was cleaned and size selected using 1:1 ratio followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5 M NaCl.

tag: cell line

value: mESC


title: Mycosis fungoides, individual 39, rep1


title: RNAseq of 66h WT gastruloids replicate3

value: Gastruloids

tag: genotype


title: CTCF CUT&RUN of HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) mESC


title: RNAseq of 66h WT gastruloids replicate1


title: MDWD8

city: Manchester

first: Hannah

middle: L

last: Morgan

address: Oxford Road

country: United Kingdom

institute: University of Manchester

data_processing:
Raw reads were trimmed of Illumina adapters and low quality (Q <20) nucleotides using TrimGalore (v 0.6.7). Reads shorter than 15 bp were discarded.
Trimmed reads were aligned to the Mus musculus reference genome GRCm39 using HISAT2 (v 2.2.1).
StringTie (v 2.2.1) was used to assemble genes and calculate gene abundance. Differential expression analysis was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-deliminated txt file with normalised counts for each samples

source_name: Liver

extract_protocol:
Total RNA was isolated from snap-frozen (liquid nitrogen) samples of maternal liver at late gestation using the RNeasy Mini plus kit (Qiagen, UK), in accordance with the manufacturer’s instructions. RNA was treated with QIAseq FastSelect -rRNA HMR, to prevent any rRNA present from being converted into the sequencing library
Stranded RNA-seq libraries were prepared from 500 ng of total RNA per sample, using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (NEB; E7760) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Pairs) (NEBNext; E6440). Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distributions were analysed using the Agilent 4200 TapeStation and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Libraries were pooled in equimolar amounts and final library quantification was performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824). The library pool was sequenced on the Illlumina NextSeq500 over three NextSeq500 High Output 150 cycle kits (Illumina; 20024907), to generate over 40 million pairs of 75-bp paired-end reads per sample.

value: Liver

tag: diet

value: MDWD


title: MDWD6


title: RAD21 ChIPmentation of HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids at 96h

value: RAD21 (ab992, Abcam)


title: Mycosis fungoides, individual 36, rep1


title: RNAseq of 60h WT gastruloids replicate2


title: Mycosis fungoides, individual 38, rep1


title: Mycosis fungoides, individual 42, rep1


title: Mycosis fungoides, individual 37, rep1


title: RNAseq of 60h WT gastruloids replicate3


title: MDWD4


title: HTO-derived cDNA

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

library_source: other

data_processing:
Gene expression reads were aligned against the GRCh38 reference genome, and feature barcodes against TotalSeqTM-A sequences. Feature barcode demultiplexing was performed using the demultiplexing workflow from cumulus (version 0.14.0) which uses DemuxEM. Cells identified as doublets by DemuxEM were excluded from analysis. We further removed cells with less than 500 detected genes, as well as cells where more than 20 % transcript counts derived from mitochondrial-encoded genes. Because high UMI counts might indicate doublets, we excluded cells with more than 6000 UMI counts
The computational analysis for the filtered and quality-controlled cells was largely performed using the python package Scanpy using standard protocols. Briefly, count matrices were merged, normalized and logarithmized before selecting the top 2000 highly variable genes per donor with a mean expression between 0.01 and 5. Harmony was used to integrate the datasets by donor, and this new projection used to calculate the neighborhood graph and UMAP embedding. We sequenced a total of 248,262 raw cells, and 176,564 high quality cells were retained for further analysis after standard quality control.
Assembly: hg38
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: blood derived

extract_protocol: Libraries were prepared following the Chromium Single Cell 3′ Library and Gel Bead Kit v2, following the manufacturer’s manual (CG00052 Chromium Single Cell 3′ Reagent Kits v2 User Guide RevA; 10X Genomics). HTO library was prepared according to published guidelines. Libraries were profiled by a Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using the Kapa Library Quantification Kit (Kapa Biosystems). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer’s sequencing specification (10X Genomics).

value: blood derived

tag: cell type

value: monocyte-derived macrophages

tag: library type

value: HTO


title: MDWD3


title: MDWD2


title: Mycosis fungoides, individual 34, rep1


title: mRNA-derived cDNA

description: Cell x Gene matrix including annotations

value: mRNA


title: H: GE-0123 VS GE-0135

source_name: Untreated glioblastoma multiforme specimen 2

treatment_protocol: The samples were not cultured or treated in cell culture, they were processed directly from the surgical resection specimen of the tumor.

value: Male

source_name: Untreated glioblastoma multiforme specimen 3

value: Female


title: Mycosis fungoides, individual 35, rep1

value: Skin (FFPE tissue blocks)

value: female


title: RNAseq of 60h WT gastruloids replicate1

value: WT


title: RNAseq of 54h WT gastruloids replicate3


title: Mycosis fungoides, individual 33, rep1

value: diagnostic


title: MDWD1


title: RNAseq of 54h WT gastruloids replicate2


title: Mycosis fungoides, individual 32, rep1

value: male


title: WD8

value: WD


title: RNAseq of 54h WT gastruloids replicate1


title: OFO1005V2

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using featureCounts from the SubRead package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: iPSC-derived forebrain organoids

growth_protocol: We generated 3-D iPSC-derived forebrain organoids. Briefly, pre-patterned floating embryonic bodies (EBs) formed from intact iPSC colonies were embedded in matrigel and cultured with 1x N2, 1x NEAA and 1x Glutamax (Invitrogen, Grand Island, NY), 1 μM SB431542, and 1 μM CHIR99021 (Selleckchem, Carlsbad, CA) for 7 days. On day 14, organoids were mechanically dissociated from the matrigel and cultured in a bioreactor (16). Culture medium from days 14-70 consisted of DMEM/F12 medium supplemented with 1x N2, 1x B27, 1x NEAA and 1x Glutamax, 1x 2-metabptoethanol, 100x penicillin-streptomycin solution, and 2.5 μg/ml insulin (Sigma-Aldrich, St Louis, MO). The medium was changed every other day. From day 70 onward, supplementing media with 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech, Rocky Hill, NJ), 0.2 mM L-Ascorbic Acid, and 0.5 mM cAMP (Sigma-Aldrich, St Louis, MO) was used.

extract_protocol: Drug treatment was conducted at 83-90 days of forebrain organoid differentiation and at 28-34 days of forebrain neuron differentiation. The concentrations of oxycodone (50 µg/L) and buprenorphine (2 ng/mL) used to perform these experiments were selected to fall within the range of blood drug concentrations in patients taking standard clinical doses of these two drugs. 3-D iPSC-derived brain organoids were cultured in the bioreactors with the drugs for seven days, and the medium was changed daily.

value: iPSC-derived forebrain organoids

tag: disease

value: opioid use disorder

value: PBS


title: Mycosis fungoides, individual 19, rep 2

value: followup


title: OFO1005O1

tag: treatment

value: oxycodone


title: RNAseq of 48h WT gastruloids replicate2

value: Gastruloids

tag: replicate


title: Mycosis fungoides, individual 31, rep1


title: WD6

value: Liver


title: WD7


title: RNAseq of 48h WT gastruloids replicate1

tag: Stage


title: OFO1005B2

value: buprenorphine


title: Mycosis fungoides, individual 29, rep1


title: Mycosis fungoides, individual 28, rep1


title: Right kidney, Unilateral nephrectomised, 72h, rep6, RNAseq

city: Bedford Park

first: Jonathan

last: Gleadle

state: SA

address: 3D226 Renal Lab, Flinders Medical Centre, Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description:
RNASeq-18
RNASeq-18

data_processing:
RNA-seq raw data in FASTQ format from individual libraries were uploaded to Deep Thought High Performance Compute Server, hosted by Flinders University for processing. FastQC (v0.11.8) was used for checking the quality of the FASTQ file. After inspection of data quality, low quality bases and Illumina Truseq adapters were then removed using AdapterRemoval version 2.3.2 with parameters --trimns --minquality 30 --minlength 50.  Quantification of transcript expression in RNA-seq data was conducted using Salmon version 1.5.0 using parameters -libType A --seqBias --numBootstraps 50 –validate Mappings. First, a decoy-aware transcriptome index was built using transcript sequences and primary assembly genome sequences from GENCODE Mouse Release M27. RNA-seq reads were then pseudoaligned to the transcriptome index and output was generated in a sub-directory containing a simple TSV format file listing the name of each transcript, its length, effective length, and its abundance in terms of Transcripts Per Million (TPM) as well as estimated number of reads originating from each transcript. After the quantification, transcript counts from Salmon output were imported into R statistical software environment version 4.10 (R Core Team, 2020)  and the bootstrap samples were used to estimate the mapping uncertainty for each transcript. Transcripts were then associated with gene IDs for gene-level summarization for downstream analysis.
GRCm39
csv files; meta data and information for each samples.
csv files; raw gene-level counts from summarisation of transcript with the same gene id for each samples.

source_name: cross sectional sample

extract_protocol:
Kidney cross-section were freshly harvested at various timepoints after sham surgery or nephrectomy and tissue samples were flash frozen in liquid nitrogen. Samples were stored at -80°C until extraction. Prior to extraction the frozen kidney samples were immersed overnight at -20°C in RNAlater -ICE (Thermo Fisher AM7030) as per the manufacturer’s instructions to transition the tissue to a state that was more amenable to pestle homogenisation. Total RNA was isolated from the kidney samples using the mirVana isolation kit (AM1561) as per the manufacturer’s instructions except that Trizol reagent was used instead of phenol. RNA was eluted in 35µl of elution buffer. The LabChip GX Nucleic Acid Analyser (Perkin Elmer) and the Qubit RNA HS (Thermo Fisher Q32852) were used according to the manufacturer’s instructions to quantify the RNA.
Library preparation was performed using the Illumina TruSeq Stranded mRNA library preparation kit. Briefly, poly-A containing mRNA molecules were purified, fragmented, and converted to strand specific cDNA. This was followed by second strand cDNA synthesis, adapter ligation and PCR amplification. Resulting libraries were quality controlled using the Qubit 2.0 (Thermo Fisher Scientific) for quantitation and the LabChip GX Touch 24 (Perkin Elmer) for quality assessment. Individual libraries were combined into a final equimolar pool and then sequenced using 150bp paired end runs on the NovaSeq  system (Illumina).

value: Right kidney

value: cross sectional sample

tag: strain

value: Unilateral nephrectomy

tag: time post_surgery

tag: gender

tag: mouse id

tag: batch

value: 8-12 weeks

tag: library kit

tag: bp size


title: WD5

tag: tissue


title: WD2


title: Mycosis fungoides, individual 30, rep1

value: Skin (FFPE tissue blocks)

tag: Sex

tag: clustering group

tag: time point


title: RNAseq of 48h WT gastruloids replicate3

tag: genotype

value: WT

tag: background


title: Right kidney, Unilateral nephrectomised, 72h, rep5, RNAseq

description:
RNASeq-17
RNASeq-17

value: Male

tag: age

value: Illumina TruSeq Stranded mRNA library preparation kit


title: OFO1004V2

tag: cell type

tag: disease

tag: treatment


title: OFO1005B1


title: Mycosis fungoides, individual 22, rep 3

value: male

value: filtered


title: MDL8

tag: diet

value: MDL


title: OFO1005V1

value: iPSC-derived forebrain organoids

value: opioid use disorder

value: PBS


title: Right kidney, Unilateral nephrectomised, 72h, rep4, RNAseq

description:
RNASeq-16
RNASeq-16

tag: strain

tag: time post_surgery


title: OFO1004V1


title: Mycosis fungoides, individual 27, rep1

value: female

value: followup


title: MDL7

value: Liver


title: Right kidney, Unilateral nephrectomised, 72h, rep3, RNAseq

description:
RNASeq-15
RNASeq-15

value: Right kidney

tag: gender

tag: mouse id


title: WD4

value: WD


title: OFO1004O2

value: oxycodone


title: Mycosis fungoides, individual 26, rep1


title: MDL6


title: Right kidney, Unilateral nephrectomised, 72h, rep2, RNAseq

description:
RNASeq-14
RNASeq-14

value: cross sectional sample

value: Unilateral nephrectomy

tag: batch

value: 8-12 weeks

tag: library kit


title: MDL4

tag: tissue


title: Mycosis fungoides, individual 9, rep 2

value: Skin (FFPE tissue blocks)

tag: Sex


title: OFO1004B2

value: buprenorphine


title: Right kidney, Unilateral nephrectomised, 48h, rep6, RNAseq

description:
RNASeq-6
RNASeq-6

value: Male

value: Illumina TruSeq Stranded mRNA library preparation kit

tag: bp size


title: Mycosis fungoides, individual 22, rep 2

tag: clustering group

value: filtered

tag: time point


title: MDL3

tag: genotype

value: MDL


title: OFO1004B1

value: iPSC-derived forebrain organoids

value: opioid use disorder


title: Right kidney, Unilateral nephrectomised, 72h, rep1, RNAseq

description:
RNASeq-13
RNASeq-13

tag: age


title: Mycosis fungoides, individual 25, rep1

value: male

value: diagnostic


title: MDL1

value: Liver


title: Right kidney, Unilateral nephrectomised, 48h, rep5, RNAseq

description:
RNASeq-5
RNASeq-5

value: Right kidney


title: LPD10


title: OFO1003V1

tag: cell type

value: PBS


title: Mycosis fungoides, individual 24, rep1

value: female


title: Right kidney, Unilateral nephrectomised, 48h, rep4, RNAseq

description:
RNASeq-4
RNASeq-4

value: cross sectional sample


title: LPD9

value: LPD


title: Mycosis fungoides, individual 23, rep1


title: Right kidney, Unilateral nephrectomised, 48h, rep3, RNAseq

description:
RNASeq-3
RNASeq-3

value: Unilateral nephrectomy

value: 8-12 weeks


title: Mycosis fungoides, individual 22, rep 1

value: Skin (FFPE tissue blocks)

value: followup


title: OFO1003O2

tag: disease

value: oxycodone


title: LPD8


title: OFO1003O1

tag: treatment


title: coVeh-1 CD8

value: T cell

value: vehicle, co-culture with MM1S for 24h


title: LPD6

tag: diet


title: Mycosis fungoides, individual 21, rep1


title: Right kidney, Unilateral nephrectomised, 48h, rep1, RNAseq

description:
RNASeq-1
RNASeq-1

tag: strain

value: Male

value: Illumina TruSeq Stranded mRNA library preparation kit


title: OFO1003B2

value: iPSC-derived forebrain organoids

value: opioid use disorder

value: buprenorphine


title: Right kidney, Unilateral nephrectomised, 24h, rep6, RNAseq

description:
RNASeq-34
RNASeq-34

value: Right kidney

tag: time post_surgery


title: Mycosis fungoides, individual 19, rep 1

value: male

value: filtered


title: OFO1003B1


title: Mycosis fungoides, individual 20, rep1


title: OFO1003V2

value: PBS


title: OFO1005O2


title: LPD4

value: Liver

value: LPD


title: LPD3


title: Right kidney, Unilateral nephrectomised, 24h, rep5, RNAseq

description:
RNASeq-33
RNASeq-33

value: cross sectional sample

value: Unilateral nephrectomy

tag: gender

value: 8-12 weeks


title: NAA-Input_rep2

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

country: China

institute: Hunan university

description:
m6A-seq NAA treated Input replicate 2
WT.NAA.IP.input.subtract.bw

data_processing:
Adapters were removed from reads with the AdapterRemoval tool.
Reads were then mapped against the Arabidopsis (TAIR10) with STAR (v 2.5.3a).
Peak calling was done with MACS2. The overlap of peaks from two biological replicates were used to generate the final peak list.
Reads Per Kilobase per Million mapped reads (RPKM) were calculated in R. In short, the number of reads falling in the each gene were counted and normalized by the length of genes and by the size of the library.
Genome_build: tir10
Supplementary_files_format_and_content: m6A-seq:  peak .txt files
Supplementary_files_format_and_content: m6A-seq:  bigwig files were generated using bedGraphToBigWig; Scores represent Reads Per 10 Million mapped reads (RP10M); Scores of Input were subtracted from that of IP.
Supplementary_files_format_and_content: RNA-seq: comma separated text file includes RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 15-day-old seedlings

growth_protocol: All plants were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. PolyA mRNA was isolated by oligodT beads and further fragmented. The m6A containing RNA was isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. m6A-seq libraries were prepared according to Shen, L. et al., Developmental Cell, 2016. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Novaseq 6000 platform as single-end 150 bp reads at the OE Biotech (Shanghai, China) following the vendor's recommended protocol.

treatment_protocol: 15-day-old seedlings were treated with mock or 50 µM NAA for 3 h.

tag: rip antibody

value: treated with 50 µM NAA for 3 h

value: wild type


title: CD9

value: CD


title: Mycosis fungoides, individual 18, rep1

value: Skin (FFPE tissue blocks)

value: diagnostic


title: NAA-Input_rep1

description:
m6A-seq NAA treated Input replicate 1
WT.NAA.IP.input.subtract.bw


title: OFO1004O1

value: iPSC-derived forebrain organoids

value: oxycodone


title: Mycosis fungoides, individual 17, rep1


title: Right kidney, Unilateral nephrectomised, 24h, rep4, RNAseq

description:
RNASeq-32
RNASeq-32

value: Male

tag: mouse id

tag: batch

value: Illumina TruSeq Stranded mRNA library preparation kit


title: Right kidney, Unilateral nephrectomised, 24h, rep3, RNAseq

description:
RNASeq-31
RNASeq-31

tag: tissue

value: Right kidney

tag: library kit


title: Right kidney, Unilateral nephrectomised, 48h, rep2, RNAseq

description:
RNASeq-2
RNASeq-2

tag: bp size


title: Right kidney, Unilateral nephrectomised, 24h, rep2, RNAseq

description:
RNASeq-30
RNASeq-30


title: CD6


title: Mycosis fungoides, individual 16, rep1

tag: Sex

value: male

tag: clustering group


title: CD5

tag: genotype


title: NAA-m6A_rep1

description:
m6A-seq NAA treated IP replicate 1
NAA.IP.b1_peaks.txt
WT.NAA.IP.input.subtract.bw

value: m6A (Synaptic Systems, 202003)


title: Mycosis fungoides, individual 15, rep1

value: female

tag: time point


title: Right kidney, Unilateral nephrectomised, 24h, rep1, RNAseq

description:
RNASeq-29
RNASeq-29

tag: age


title: mock-Input_rep2

description:
m6A-seq mock treated Input replicate 2
WT.IP.input.subtract.bw

value: treated with mock for 3 h


title: Right kidney, Sham operated, 72h, rep6, RNAseq

description:
RNASeq-24
RNASeq-24

value: cross sectional sample

value: Sham operation


title: Mycosis fungoides, individual 13, rep1

value: followup


title: mock-Input_rep1

description:
m6A-seq mock treated Input replicate 1
WT.IP.input.subtract.bw


title: CD4

value: Liver


title: NAA-m6A_rep2

description:
m6A-seq NAA treated IP replicate 2
NAA.IP.b2_peaks.txt
WT.NAA.IP.input.subtract.bw

value: treated with 50 µM NAA for 3 h

value: wild type


title: CD1

value: CD


title: Right kidney, Sham operated, 72h, rep5, RNAseq

description:
RNASeq-23
RNASeq-23

value: 8-12 weeks


title: mock-m6A_rep2

description:
m6A-seq mock treated IP replicate 2
IP.b2_peaks.txt
WT.IP.input.subtract.bw


title: CD7


title: scRNA-seq on WT gastruloids at 144h replicate 1

library_source: transcriptomic single cell

data_processing:
Gene expression librairies were analysed similarly for standard 10x and CellPlex samples to generate the cell-gene expression matrices. For both Mapping, demultiplexing of cell barcode and quantification was performed using rna_STARsolov2.7.10b on the mm10 reference genome, and a modified gtf file based on Ensembl v102, with the parameters: --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'Gene Expression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000. Then DropletUtils v1.10.0 was used to remove barcodes which were not corresponding to cells (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01). Cell multiplexing oligo (CMO) librairies which identify the sample of origin in multiplexed experiments were quantified using CITE-seq-Count v1.4.455 --cell_barcode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 --bc_collapsing_dist 1 --umi_collapsing_dist 2 --expected_cells 24000 --whitelist '3M-february-2018.txt' --max-error 2.
Individual 10x gene expression librairies, were analysed using Seurat v4.3. We first filtered out barcodes with less than 200 identified gene and genes identified in less than three cells. For CMO libraries, the demultiplexing by barcode was done in R using counts from CITE-seq-Counts. Cell barcodes with less than 5 CMO UMI and absent in the seurat object were discarded. Then sample attribution was performed using demuxmix using the total number of UMI per cell. Cells which were not classified by demuxmix as singlet (negative, unsure, doublet) were excluded from the analysis.
Low quality cells and potential doublets were removed by computing the mean UMI content and the percentage of mitochondrial genes and filtering out barcodes with less than 0.4 times the mean UMI or more than 2.5 times the mean UMI. Only barcodes between 0.05 and 8 percent of mitochondrial UMI were kept. Matrices were normalised and the cell cycle score (using the 2019 updated gene list from Seurat) from these filtered libraries were computed. Then we merged the different samples using the merge command by Seurat. The combined Seurat object was then normalised, 2000 variable features were identified and the data was scaled and regressed by cell cycle score, and percentage of mitochondrial reads. Principal component were then computed using variable genes falling within the 5th and 80th percentile of expression to limit batch effect as performed here. UMAP and k-nearest neighbors were then computed using 30 principal components. The resolution to cluster the data was chosen by ensuring that no cluster was missed, and that no duplicated clusters were found. Cluster annotation was performed manually. Marker identification was done using a maximum of 400 cells per identity to limit the impact of widely variable cluster sizes in the ability to identify markers, these also required a difference of 20% in the proportion of expressing cells and a logFC >0.5.
For RNA velocity analysis, Velocyto v0.17.1759 was used with the run10x command on the BAM files generated by STARsolo. Then, velocyto.R v0.6 was used to identify the velocity using the RunVelocity function with the settings: spliced.average = 0.2, unspliced.average = 0.02, deltaT = 1, kCells = 20, fit.quantile = 0.02. RNA velocity was then displayed on the UMAP embedding with the show.velocity.on.embedding.cor function with the setting: n = 300, scale='sqrt', cell.colors = ac(subset.seurat$FateColor, alpha=0.5), cex=0.8, arrow.scale = 5, show.grid.flow=TRUE, min.grid.cell.mass = 0.5, grid.n=40, arrow.lwd = 1, do.par = F, cell.border.alpha = 0.
Scoring of cells based on this list of genes up- /down-regulated in Snai1-/- was performed with the addModuleScore by Seurat. All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: loom: output of velocyto (quantification of spliced and unspliced)
Supplementary files format and content: tar.gz: output of STARsolo or CITE-seq-Counts (translated) as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)
Supplementary files format and content: RDS: R object with everything to redo the plots
Supplementary files format and content: CMO.Samples.csv: comma separated text file with for each Library (first column), the different samples (second column), with their barcodes (third column). A sample to NA indicates that it has not been used into this study

extract_protocol:
Gastruloids were collected, pooled in a 1.7 ml Eppendorf tube and washed twice in 1 ml of PBS. The number of gastruloids used in each condition was chosen to ensure that more than 300 000 cells were obtained. They were then dissociated in 100 µl of Accutase (Stempro) for 5 min at 37°C. Full dissociation was completed using mechanical dissociation and verified to ensure the absence of doublet cells. Cells were then resuspended in 200 µl of PBS and counted on a Countess 3 automated cell counter (Invitrogen). All centrifugations were done at 400g for 5 minutes. Some samples were then analysed with the standard 10x genomics pipeline (Chemistry v3 and v3.1), while others also included a CellPlex procedure to multiplex samples (see Supplementary Table 6 for list of samples and the method used). For the sample treated with the normal 10x procedure, after counting, dissociated cells were diluted in PBS BSA 0.04% (Millipore, A1595) to 1x106 cells/ml. For samples treated with the CellPlex multiplexing approach, cells were pelleted and incubated for 5 minutes in 50 µl of cell multiplexing oligos (3' CellPlex Kit Set A, PN-1000261) at room temperature. They were then washed three times with 1ml of PBS 1% BSA and finally they were resuspended in 110 µl of PBS 1% BSA and counted. The multiplexed samples were then pooled in equal proportions for each targeted sample. Both CellPlex and standard 10x Genomics sample were then filtered using a 40 µm cell strainer (Flowmi, BAH136800040).
The pool of cells was counted and subjected to single cell RNA-seq following manufacturer’s recommendation similarly as non-CellPlex samples (protocol CG000388 Rev A). For standard 10x samples, we aimed for a recovery of c.a. 6000 cells per sample while for multiplexed single cell RNA-seq we aimed for a recovery of maximum 24 000 cells as more doublet can be resolved with this method. cDNA preparations were performed according to 10x Genomics recommendations, amplified for 10–12 cycles and verified on fragment analyser. Both cell multiplexing oligo, and gene expression libraries were sequenced on a HiSeq 4000 (ref 15065681 v03) or a Novaseq (Illumina protocol #1000000106351 v03) with the cbot2 chemistry.

value: Gastruloids

tag: Stage

value: WT

tag: multiplexing

tag: 10x well

tag: background


title: mock-m6A_rep1

description:
m6A-seq mock treated IP replicate 1
IP.b1_peaks.txt
WT.IP.input.subtract.bw

tag: treatment


title: Mycosis fungoides, individual 12, rep1

value: Skin (FFPE tissue blocks)

value: diagnostic


title: Right kidney, Sham operated, 72h, rep4, RNAseq

description:
RNASeq-22
RNASeq-22

value: Right kidney

tag: strain

tag: time post_surgery

tag: gender

value: Male

value: Illumina TruSeq Stranded mRNA library preparation kit


title: Mycosis fungoides, individual 10, rep1

value: male


title: Right kidney, Sham operated, 72h, rep3, RNAseq

description:
RNASeq-21
RNASeq-21

tag: mouse id

tag: batch


title: Mycosis fungoides, individual 14, rep1

tag: tissue


title: Right kidney, Sham operated, 72h, rep2, RNAseq

description:
RNASeq-20
RNASeq-20

tag: library kit

tag: bp size


title: MI rat,sc-RNA seq

city: Hangzhou

first: Jinying

state: --- Select One ---

address: No. 866 Yuhangtang Road, Zijingang Campus, Zhejiang University

institute: zhejiang university

description: 10x Genomics

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Tissue collection and CD45+ cells isolation Left ventricles of hearts from the MI and PUR-hAESC groups were collected and minced into fine pieces (including the infarcted and peri-infarcted regions). Tissues were enzymatically digested with collagenase A and elastase at 37°C rotationally. After dissociation, cell suspensions were passed through a 30 µm cell strainer, followed by red blood cell lysis. For sorting of all the immune cells (CD45+), the digested suspensions were stained with Propidium Iodide  and FITC anti- rat CD45 antibody , and sorted on a FACS Aria III (BD Biosciences, Franklin Lakes, NJ) with a 100 µm nozzle.
CD45+ cells were sorted using FACS from single-cell suspensions of hearts of MI- or PUR-hAESC-operated rats 1 week after surgery. After washing and resuspending in 0.5mL cold PBS, purified CD45+ cells were processed in the Chromium single cell gene expression platform (10x Genomics). Briefly, Single Cell 3′ Reagent Kit v2 was used to generate droplets encapsulating single cell and barcoded beads. Following capture and lysis, reverse transcription was performed in a thermal cycler (ProFlex PCR). cDNA was synthesized and amplified for 14 cycles. The amplified-cDNA was fragmented, ligated with adapter and sample index, and selected with SPRI beads (Beckman). Sequencing was performed on the NovaSeq 6000 Illumina sequencing platform. Bioinformatic analysis was performed using the OmicStudio tools at https://www.omicstudio.cn/tool.
scANS-seq

value: heart

tag: cell type

value: wt

value: MI


title: MI+PUR-AEC ,sc-RNA seq

description: 10x Genomics

data_processing: Sequencing was performed on the NovaSeq 6000 Illumina sequencing platform. Bioinformatic analysis was performed using the OmicStudio tools at https://www.omicstudio.cn/tool.

tag: genotype

value: MI+PUR-hAESC


title: Right kidney, Sham operated, 72h, rep1, RNAseq

description:
RNASeq-19
RNASeq-19

value: cross sectional sample

value: Sham operation


title: scRNA-seq on WT anterior gastruloids at 120h replicate 1


title: Mycosis fungoides, individual 1, rep 2

tag: Sex

value: female

tag: clustering group

value: filtered

tag: time point

value: followup


title: Mycosis fungoides, individual 9, rep 1


title: Right kidney, Sham operated, 48h, rep6, RNAseq

description:
RNASeq-12
RNASeq-12

tag: age

value: 8-12 weeks


title: ATAC-seq on WT gastruloids at 120h replicate 3

data_processing:
Raw ATAC-seq reads were trimmed to remove Nextera adapters or bad quality bases (Cutadapt v4.043 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15). Mapping was performed on filtered reads on the mouse genome mm10 with Bowtie2 version 2.5.044 (--very-sensitive 2). Resulting Bam files were sorted using samtools. Reads mapping to the mitochondrial chromosome or unconcordantly were discarded with bamFilter v2.5.248. Duplicates were removed with picard MarkDuplicates version 2.18.2. BAM was converted to BED with BEDTools version 2.30.0 in order to use both mates to call peaks. Peaks were called using macs2_callpeak v2.2.7.1. with the options (--gsize '1870000000' --call-summits --keep-dup 'all' --nomodel --extsize '200' --shift '-100' --bdg). Coverages were converted to bigwig and normalied to the number of million reads mapped less than 500bp from a peak summit. Normalised coverages from wild-type replicates 1 and 2 were averaged with bigwigAverage version 3.5.4 from deepTools as well as the coverages from the two KO clones at 72 and 96h. In order to build a comprehensive confident list of peaks from the wild-type time course, at each time point the following strategy was adopted. The BED with the largest number of reads was downsampled to match the number of reads of the other replicate. Peaks were called using a merged of equally sized BED. Only peaks whose summit was overlapping a peak in each of both replicates were kept. The four lists of confident peaks (one per time point) were concatenated and merged with BEDTools version 2.30.0. The number of reads falling into this comprehensive confident list were quantified with deeptools multiBamSummary version 3.5.150. DESeq2 was used to compare the wild-type duplicates of 72h with the wild-type duplicates of 96h to determine the loci with a significant change in accessibility (abs(log2FC) > 1 an adjusted p-value < 0.05).  All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: .narrowPeak.gz: narrowPeak from MACS2
Supplementary files format and content: _repX.bw: coverage from MACS2 normalized to million reads in peaks
Supplementary files format and content: .bw: average of normalized coverage of the two first replicates
Supplementary files format and content: WT.narrowPeak.gz: consensus, confident peaks from two first replicates

molecule: other

extract_protocol:
Assay for Transposase Accessible Chromatin was performed as described in Corces et al. 2017. Gastruloids were collected, pooled in a 1.7 ml Eppendorf tube and washed twice in 1 ml of PBS. They were then dissociated in 100 µl of Accutase (Stempro) for 5 min at 37°C. Full dissociation was completed by mechanical dissociation and verified to ensure proper dissociation. Dissociated cells were then washed in 500 µl of PBS (centrifugation 5 minutes at 4°C at 400g) and resuspended in 200 µl of resuspension buffer RSB (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2). 50 000 cells were extracted, pelleted (centrifugation 5 minutes at 4°C at 400g) and incubated 3 minutes on ice in cold lysis buffer (RSB, 0.1% NP40, 0.1% Tween-20, 0.01% Digitonin). Nuclei were then washed in 1 ml of lysis washout buffer (RSB, 0.1% Tween-20) and pelleted at 500g for 10 minutes at 4°C. Pelleted nuclei were resuspended in 50ul of cold transposition buffer (25 ulTD Buffer, 2,5ul  Tn5 (Illumina, 20034197), 20% PBS, 0.01% Digitonin, 0.1% Tween-20, 10% water) and incubated 30 minutes at 37°C. For the samples : 48h_WT_rep1, 48h_WT_rep2, 72h_WT_rep1, 72h_WT_rep2, 96h_WT_rep1, 96h_WT_rep2, 120h_WT_rep1, 120h_WT_rep2, after dissociation, the Buenrostro et al. 2013 version of the ATAC protocol was used. Briefly, following accutase dissociation, 50 000 cells were resuspended in ice cold Lysis buffer (10 mM Tris-Cl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40). Samples were then  centrifuge at 4°C for 10 minutes, and supernatant was removed. Tagmentation was  performed by resuspending the pellet in  in 50 ul of tagmentation mix (25 ul TD buffer, 2,5 ul Tn5, 22.5 ul H2O), then all samples underwent the same procedure for library preparation, quality control and analysis
Each reaction was purified using the Qiagen MinElute PCR purification kit. The reaction was then amplified by PCR using the NEBNext Master Mix and Nextera primers.

value: Gastruloids

tag: Stage

value: WT

tag: replicate


title: ATAC-seq on Snai1KO gastruloids at 120h clone 1

value: Snai1 KO

tag: clone

tag: background


title: SD3 cells, SCID mouse brain, rep 3

city: Boston

first: Vivian

middle: K

last: Lee

state: Massachusetts

address: 60 Fenwood rd, 5016E

institute: Brigham and Womens Hospital, Harvard Medical School

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
12-SD3_invivo

data_processing:
Raw sequence reads from samples were mapped to the human genome (hg38) using HISAT2
Counts of reads mapping to genes were obtained using HTSeq-count software against Ensembl v90 annotation
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM counts for each sample

source_name: patient-derived GBM cell line

growth_protocol: SD2 and SD3 Glioblastoma cells were maintained in NeuroCult NS-A proliferation medium for human cells (Stemcell Technologies) with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen), with ~50-150 ng of RNA input per replicate sample.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: SD2 and SD3 Glioblastoma cells were cultured in vitro or grown in vivo using intracranial transplant models.

value: patient-derived GBM cell line

tag: cell line

value: Glioblastoma

tag: treatment

value: in vivo intracranial transplant


title: scRNA-seq on WT posterior gastruloids at 120h replicate 1

tag: multiplexing

tag: 10x well


title: ATAC-seq on Snai1KO gastruloids at 96h clone 2

tag: tissue


title: Mycosis fungoides, individual 8, rep1

value: Skin (FFPE tissue blocks)

value: male

value: diagnostic


title: SD3 cells, SCID mouse brain, rep 2

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
11-SD3_invivo


title: SD3 cells, SCID mouse brain, rep 1

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
10-SD3_invivo


title: SD3 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 3

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
9-SD3_3D_GAPE

value: in vitro culture


title: ATAC-seq on Snai1KO gastruloids at 96h clone 1


title: Mycosis fungoides, individual 11, rep1


title: Right kidney, Sham operated, 48h, rep5, RNAseq

description:
RNASeq-11
RNASeq-11

value: Right kidney

tag: strain

tag: time post_surgery

tag: gender

value: Male

tag: mouse id

tag: batch

tag: library kit

value: Illumina TruSeq Stranded mRNA library preparation kit


title: Mycosis fungoides, individual 7, rep1

tag: Sex

tag: clustering group

tag: time point


title: ATAC-seq on Snai1KO gastruloids at 72h clone 2

tag: Stage

tag: genotype

tag: replicate


title: ATAC-seq on WT gastruloids at 96h replicate 3

tag: background


title: Right kidney, Sham operated, 48h, rep2, RNAseq

description:
RNASeq-8
RNASeq-8

value: cross sectional sample

tag: treatment

value: Sham operation

tag: age

tag: bp size


title: Mycosis fungoides, individual 4, rep1

tag: tissue


title: Right kidney, Sham operated, 48h, rep4, RNAseq

description:
RNASeq-10
RNASeq-10

tag: strain


title: Mycosis fungoides, individual 6, rep1

value: followup


title: Right kidney, Sham operated, 48h, rep3, RNAseq

description:
RNASeq-9
RNASeq-9

tag: time post_surgery

value: 8-12 weeks


title: SD3 cells, 3D in vitro, rep 2

description:
cells cultured in 3D hydrogel
5-SD3_3D_G

tag: cell line

tag: cell type


title: SD3 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 2

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
8-SD3_3D_GAPE


title: Right kidney, Sham operated, 48h, rep1, RNAseq

description:
RNASeq-7
RNASeq-7

tag: gender

tag: mouse id

tag: batch


title: Mycosis fungoides, individual 5, rep1

tag: Sex

tag: clustering group


title: ATAC-seq on WT gastruloids at 120h replicate 2

value: Gastruloids

tag: Stage


title: SD3 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 1

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
7-SD3_3D_GAPE

tag: genotype

value: WT


title: SD3 cells, 3D in vitro, rep 3

description:
cells cultured in 3D hydrogel
6-SD3_3D_G


title: Mycosis fungoides, individual 3, rep1

tag: time point


title: SD3 cells, 3D in vitro, rep 1

description:
cells cultured in 3D hydrogel
4-SD3_3D_G


title: ATAC-seq on WT gastruloids at 72h replicate 3

tag: replicate

tag: background


title: Right kidney, Sham operated, 24h, rep5, RNAseq

description:
RNASeq-39
RNASeq-39

tag: treatment

tag: age

tag: library kit


title: Right kidney, Sham operated, 24h, rep4, RNAseq

description:
RNASeq-38
RNASeq-38

tag: tissue

tag: strain

tag: bp size


title: ATAC-seq on Snai1KO gastruloids at 72h clone 1

value: Snai1 KO

tag: clone


title: LuCaP35CR, LX1_4

city: Sacramento

first: Allen

middle: C

last: Gao

address: 4645 2nd Ave, Research III Bldg

department: Urologic Research

institute: University of California Davis

data_processing:
RNA-Seq data was analyzed using a Spliced Transcripts Alignment to a Reference (STAR)-Partek E/M quantify to annotation model pipeline. Raw sequence reads (FASTQ format) were mapped with the STAR aligner to the reference human genome index (GRCh38/hg38, GENCODE release 43) and quantified with the Partek E/M quantify to annotation model.
Processed data are gene-level read counts generated from the output of STAR alignment and subsequent quantification with the Partek E/M quantify to annotation model  for each sample.
Assembly: Assembly: GRCh38/hg38, GENCODE release 43
Supplementary files format and content: tab-delimited text file "RNAseq_matrix_MDVR" consisting of a data matrix for all samples.
Supplementary files format and content: tab-delimited text file "RNAseq_matrix_LuCaP" consisting of a data matrix for all samples.

source_name: prostatic adenocarcinoma

extract_protocol:
Total cellular RNA was isolated from the prostate cancer cell lines using the TRIzol Reagent (ThermoFisher Scientific).
cDNA

value: prostatic adenocarcinoma

tag: cell line

tag: cell type

value: prostate cancer patient-derived xenograft


title: ATAC-seq on WT gastruloids at 120h replicate 1


title: Right kidney, Sham operated, 24h, rep3, RNAseq

description:
RNASeq-37
RNASeq-37

tag: time post_surgery

tag: gender

tag: mouse id

tag: batch


title: SD3 cells, 2D in vitro, rep 3

description:
cells cultured on 2D cell culture plastic
3-SD3_2D_G

value: patient-derived GBM cell line

value: Glioblastoma

tag: genotype


title: Mycosis fungoides, individual 1, rep 1

value: Skin (FFPE tissue blocks)

tag: Sex

value: female

tag: clustering group

tag: time point


title: Right kidney, Sham operated, 24h, rep6, RNAseq

description:
RNASeq-40
RNASeq-40

tag: treatment


title: SD3 cells, 2D in vitro, rep 2

description:
cells cultured on 2D cell culture plastic
2-SD3_2D_G

value: in vitro culture


title: ATAC-seq on WT gastruloids at 96h replicate 2

tag: Stage

tag: replicate

tag: background


title: Mycosis fungoides, individual 2, rep1

tag: tissue

value: male


title: ATAC-seq on WT gastruloids at 96h replicate 1


title: LuCaP35CR, LX1_3


title: Right kidney, Sham operated, 24h, rep2, RNAseq

description:
RNASeq-36
RNASeq-36

value: Right kidney

tag: strain

value: Male

tag: age

tag: library kit

tag: bp size


title: SD3 cells, 2D in vitro, rep 1

description:
cells cultured on 2D cell culture plastic
1-SD3_2D_G

tag: cell line

tag: cell type


title: ATAC-seq on WT gastruloids at 72h replicate 1


title: Right kidney, Sham operated, 24h, rep1, RNAseq

description:
RNASeq-35
RNASeq-35

value: cross sectional sample

tag: time post_surgery

tag: gender

tag: mouse id

value: Illumina TruSeq Stranded mRNA library preparation kit


title: LuCaP35CR, LX1_1

tag: genotype


title: SD2 cells, SCID mouse brain, rep 2

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
11-SD2_invivo

value: in vivo intracranial transplant


title: ATAC-seq on WT gastruloids at 48h replicate 2


title: WT4

city: Xiamen

first: Shuqin

state: Fujian Province

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

data_processing:
Clean reads were obtained by removing reads containing adapter, N base and low quality from raw data.
Paired-end clean reads were aligned to the reference genome (mm10) using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: colon

extract_protocol:
Tregs (CD45+CD3+CD4+CD25+GFP+) were sort-purified from Apc Min/+ Foxp3 DTR colon tumor or Foxp3 DTR mice.
Sorted cells were used to prepare RNA sequencing libraries using the TruePrep® DNA Library Prep Kit V2 for Illumina following manufacturer's protocols..

value: colon

value: regulatory T cell

tag: Sex

value: 16 weeks old


title: ATAC-seq on WT gastruloids at 72h replicate 2

source_name: Gastruloids

value: Gastruloids

value: WT


title: WT5


title: WT3


title: LuCaP35CR, Vehicle2

value: prostatic adenocarcinoma

value: prostate cancer patient-derived xenograft

value: Vehicle


title: SD2 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 3

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
9-SD2_3D_GAPE

value: patient-derived GBM cell line

value: Glioblastoma


title: LuCaP35CR, LX1_2


title: WT2


title: ATAC-seq on WT gastruloids at 48h replicate 1


title: C4-2B MDVR cells, LX1

source_name: Human prostate cancer cell line

value: Human prostate cancer cell line

value: C4-2B MDVR

value: prostate cancer cells


title: LuCaP35CR, Vehicle1


title: SD2 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 2

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
8-SD2_3D_GAPE

value: in vitro culture


title: WT1

value: male


title: Sperm_MDWD_Male12 [MDWD12]

data_processing:
Raw reads were trimmed of Illumina adapters and low quality (Q<20) nucleotides using TrimGalore (v 0.6.7) [1]. Reads shorter than 15 bp were discarded.
Trimmed reads were aligned to Mus musculus reference genome GRCm39 using HISAT2 (v 2.2.1) [2]. StringTie (v 2.2.1) [3] was used to assemble genes and calculate gene abundance
Differential expression analysis was performed using DESeq2.
Spearman correlation method was used to calculate the distance between samples as the method measures similarities in features even if the observed values may be far apart, and can mitigate the possible impact of outliers
Assembly: GRCm39
Supplementary files format and content: tab-deliminated txt file with normalised counts for each samples

source_name: Sperm

extract_protocol:
RNA was extracted from total sperm (approx. 4x10^6 to 8x10^6 cells per sample) using miRNeasy micro Qiagen kit with Qiazol homogenisation on TissueLyser.
Stranded RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (NEB; E7760) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Pairs) (NEBNext; E6440). Prior to library preparation, total RNA was treated with QIAseq FastSelect -rRNA HMR, to prevent any rRNA present from being converted into sequencing library. Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distributions were analysed using the Agilent 4200 TapeStation and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Libraries were pooled in equimolar amounts and final library quantification was performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824). The library pool was sequenced on the Illlumina NextSeq500 over three NextSeq500 High Output 150 cycle kits (Illumina; 20024907), to generate over 40 million pairs of 75-bp paired-end reads per sample.

value: Sperm

value: Western diet + methyl-donor supplement fed males


title: SD2 cells, SCID mouse brain, rep 3

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
12-SD2_invivo

value: in vivo intracranial transplant


title: C4-2B MDVR cells, LX5


title: SD2 cells, 3D in vitro, rep 3

description:
cells cultured in 3D hydrogel
6-SD2_3D_G


title: RNAseq of 66h WT gastruloids replicate2

data_processing:
Raw RNA-seq reads generated in this study were trimmed to remove Nextera adapters or bad quality bases (Cutadapt v4.043 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15). Mapping and counting were performed on filtered reads on the mouse genome mm10 with STAR version 2.7.8a44 with a custom gtf based on Ensembl version 10245 and ENCODE parameters. FPKM values were obtained by Cufflinks version 2.2.146,47 with options --no-effective-length-correction -b 'mm10.fa' --multiread-correct --library-type fr-firststrand --mask-file 'chrM_mm10.gtf' --max-bundle-length 10000000 --max-bundle-frags 1000000 (where chrM_mm10.gtf contains a transcript on each strand of the whole chrM). Uniquely mapped reads were filtered with bamFilter48 version 2.5.1. Coverages were computed with BEDTools49 version 2.30.0 for each strand using the '-scale' parameter to normalize to million uniquely mapped reads. Average between duplicates was performed with bigwigAverage v3.5.4 from deepTools50. All samples were of good quality and none were excluded from the analysis. Genes were called differentially expressed when they had both abs(log2fc) > 1 and padj < 0.05
All the code required to reproduce the analysis is available here (https://github.com/MayranA/allScriptsFromMayranEtAl2023)
Assembly: mm10
Supplementary files format and content: repX_both_strands.bw: normalized coverage (to million of uniquely mapped reads) with both strands combined
Supplementary files format and content: repX_negative_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on negative strand
Supplementary files format and content: repX_positive_strand.bw: normalized coverage (to million of uniquely mapped reads) with coverage on positive strand
Supplementary files format and content: .bw: average of normalized coverage of the two or three replicates (96h_WT is the average of rep1, rep2 and rep3 while 96h_Snai1WT is the average of 96h_WT_rep4 and rep5)
Supplementary files format and content: tablesX.tar.gz: archive with two tables: AllCufflinks_Simplified.txt.gz: single table with all FPKM values from cufflinks and AllHTSeqCounts.txt.gz: single table with all counts from STAR
Supplementary files format and content: DESeq2_summary.txt: tabular separated text file where each row is a gene and columns indicates log2FC, padj and weather it was significant in each of the analysis
Supplementary files format and content: DESeq2_summary_long.txt: tabular separated text file where each row is a gene in a DESeq2 comparison. This format is more compatible with ggplot2.

extract_protocol:
Gastruloids were collected and pooled in a 2-ml Eppendorf tube at the indicated timepoints. After medium removal, gastruloids were washed once with PBS, pelleted and stored at −80 °C until RNA extraction. RNeasy Mini kit (Qiagen) with on-column DNase digestion was used for RNA extraction following manufacturer’s instructions. RNA quality was assessed on a Tapestation TS4200, all RNA samples showed quality number (RIN) above 9.5.
RNA-seq library preparation with Poly-A selection was performed with 1000 ng (for time course analysis) or 500 ng (for mutant gastruloid analysis) of RNA using the Illumina stranded mRNA ligation and following the manufacturer’s protocol 1000000124518 v01. Library quality was assessed with a Libraries were quantified by qubit DNA HS and profile analysis was done on TapeStation TS4200. Libraries were sequenced on HiSeq 4000 Illumina, with paired end 75 bp reads.


title: C4-2B MDVR cells, DMSO

value: DMSO


title: SD2 cells, 3D in vitro with astrocytes, pericytes, and endothelial cells, rep 1

description:
cells cultured in 3D GBM model: GSCs, astrocytes, pericytes, endothelial cells
7-SD2_3D_GAPE


title: Tumor5

value: colon

value: regulatory T cell

value: Apc Min/+

value: 16 weeks old


title: Group D, replicate 4, snRNAseq

city: Beijing

first: Jiangping

last: Song

address: 167A Beilishi Road, Xi Cheng District

institute: Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: 10x Genomics

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (Version 6.1.2) pipeline coupled with human reference version GRCh38. Contamination in individual cells was estimated and removed by DecontX (celda package, Version 1.10.0). The output gene expression matrices were analyzed by R software (Version 4.1.2) with the Seurat package (Version 4.1.1). In brief, low-quality cells were removed if they met the following criteria: 1) < 200 genes; 2) expressed gene counts < 3; After the removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function.
Assembly: Human GRCh38-2020-A
Supplementary files format and content: TSV
Supplementary files format and content: mtx

source_name: Heart (left ventricle)

extract_protocol:
After being removed from the -80°C refrigerator, the heart samples were dissected in 4°C PBS buffer (#C10010500BT, Gibco, USA). The tissue fragments were resuspended in 30ml lysis buffer. The suspension fluid was homogenized in the Dounce tissue grinder set (Pestle B). The supernatant was filtered through 100μm and 70μm filters. After centrifugation (700rcf, 10 min, 4°C), the supernatant was discarded and the pellet was resuspended using 20 ml preservation buffer. After recentrifugation (13000rpm, 1h, 4°C), the supernatant was discarded, and the pellet was resuspended using PBS buffer. The nuclei suspension was mixed with trypan blue (1:1) and counted by using the hemocytometer.
The processing of libraries was performed according to the manufacturer’s instructions. The snRNA-seq libraries were prepared using the ChromiumTM Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit, version 3.1, 16 reactions (10X Genomics) and sequenced using the NoveSeq 6000 (Illumina, USA).

value: Heart (left ventricle)

tag: disease state

value: Dilated Cardiomyopathy (end-stage)

value: Without DCM-related gene mutation


title: Sperm_MDWD_Male14 [MDWD14]

tag: treatment


title: SD2 cells, SCID mouse brain, rep 1

description:
cells in SCID mouse brain for 7 weeks , HLA+ sorted
10-SD2_invivo

value: patient-derived GBM cell line

value: Glioblastoma

value: WT


title: SD2 cells, 3D in vitro, rep 1

description:
cells cultured in 3D hydrogel
4-SD2_3D_G


title: Tumor3


title: Tumor2


title: Sperm_MDWD_Male16 [MDWD16]


title: Tumor4


title: SD2 cells, 2D in vitro, rep 3

description:
cells cultured on 2D cell culture plastic
3-SD2_2D_G


title: Group D, replicate 1, snRNAseq

description: 10x Genomics


title: SD2 cells, 3D in vitro, rep 2

description:
cells cultured in 3D hydrogel
5-SD2_3D_G


title: Group D, replicate 3, snRNAseq

description: 10x Genomics

value: female


title: Sperm_MDWD_Male10 [MDWD10]


title: Group D, replicate 2, snRNAseq

description: 10x Genomics


title: CD4-Cre ICOS KO

city: Montreal

first: Woong-Kyung

last: Suh

state: Quebec

address: 110 avenue des Pins

country: Canada

institute: IRCM

data_processing:
Analysis of the single-cell RNA sequencing data was carried out using Seurat v3.0. For the single cell expression matrix analysis, cells with more than 10 % mitochondrial RNA contamination, corresponding to dead cells, were filtered out of the dataset. Cells with less than 200 and more than 6000 unique genes expressed were also eliminated, as they correspond to empty droplets and multiplets. The data was then log normalized, and following the identification of the most differentially expressed genes within the samples, the data was scaled. Linear dimensional reduction was subsequently performed using the Principal Component Analysis (PCA) approach based on the 2000 most variable features. The first 40 most important components produced by the PCA analysis were selected, and a Shared Nearest Neighbour (SNN) graph was constructed. Modularity Optimizer version 1.3.0 was used to identify 19 clusters in the CD4cre dataset, and 20 clusters in the Foxp3cre dataset. The Uniform Manifold Approximation and Projection (UMAP) method was used to visualize the cells on a two-dimensional space. T cell clusters were identified and separately clustered, generating 13 clusters in the Foxp3cre dataset and 15 clusters in the CD4cre dataset. For the analysis of CD8+ T cells, clusters corresponding to CD8+ T cells were identified based on Cd8a expression and separately clustered, generating 6 clusters in both Foxp3cre and CD4cre datasets. For the analysis of Treg cells in the Foxp3cre dataset, CD4+ T cells were identified based on Foxp3 expression and separately clustered, generating 6 clusters. Analysis of gene expression patterns were then performed using the Seurat functions FeaturePlot, DoHeatmap, and VlnPlot. We then performed RNA velocity analysis on a subset of CD8+ T cell clusters expressing either Tbx21 or Eomes. We used velocyto (version 0.17.17) to calculate splicing rates, scVelo (version 0.2.4) to draw RNA velocities on the UMAP space, and CellRank (version 1.5.1) to predict terminal states.
Assembly: mm10
Supplementary files format and content: Seurat Object Rdata

source_name: Lung, B16-OVA tumor

extract_protocol:
10 mL of collagenase solution containing 300 U/mL collagenase type II (Worthington Biochemical) and 10 mg/mL DNAse I (MilliporeSigma) was added to each lung and digested for 50 minutes at 37 °C with 300 rpm horizontal shaking. Lung digests were then filtered through 40 μM cell strainers, and red blood cells were depleted. Cells were filtered once more through 70 μM cell strainers
Libraries were generated at the Institut de Recherches Cliniques de Montréal Molecular Biology and Functional Genomics Core facility using the following components from 10x Genomics: Chromium Next GEM Chip G Single Cell kit, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1, Chromium i7 Multiplex kit. Sequencing was performed by Genome Québec using a NovaSeq 6000 (Illumina).

value: Lung, B16-OVA tumor

value: CD4, CD8 T cells

value: CD4-cre ICOS f/f


title: Sperm_WD_Male14 [WD14]

value: Sperm

value: Western diet fed males


title: Sperm_WD_Male12 [WD12]


title: Group C, replicate 2, snRNAseq

description: 10x Genomics

value: male


title: Sperm_MDWD_Male9 [MDWD9]

value: Western diet + methyl-donor supplement fed males


title: VAV05_3d

city: Ulju-gun

first: Wonhyo

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

country: South Korea

institute: UNIST

data_processing:
Raw fastq file is trimmed by skewer to get eliminate adaptor sequence of TN5
trimmed fastq file is aligned on Hg19 reference genome by bowtie 2 software
Homer software constructed Tag directories based on aligned bam files
Homer software transformed Tag directories to bedgraph
Assembly: hg19
Supplementary files format and content: bedgraph.gz

source_name: Peripheral Blood

extract_protocol:
To prepare nuclei, we spun 50,000 cells at 500 × g for 5 min, washed the cells with 50 mL of cold 1× PBS, and then centrifuged them at 500 × g for 5 min. Cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 min in a refrigerated centrifuge. Immediately following nuclei preparation, the pellet was resuspended in transposase reaction mix (Illumina). The transposition reaction was carried out for 30 min at 37°C.
ATAC-seq library was constructed by using illumina Tag DNA Enzyme & Buffer kit.

value: Peripheral Blood

value: Cd14+ Monocyte


title: Sperm_WD_Male10 [WD10]


title: Tumor1

value: colon

value: regulatory T cell

value: Apc Min/+

value: 16 weeks old


title: Sperm_WD_Male13 [WD13]


title: Group C, replicate 3, snRNAseq

description: 10x Genomics

value: Heart (left ventricle)

value: Dilated Cardiomyopathy (end-stage)

value: Without DCM-related gene mutation


title: Sperm_WD_Male11 [WD11]


title: SD2 cells, 2D in vitro, rep 2

description:
cells cultured on 2D cell culture plastic
2-SD2_2D_G

value: patient-derived GBM cell line

value: Glioblastoma

value: WT

value: in vitro culture


title: VAV05_1d


title: CD4-cre ICOS WT

value: Lung, B16-OVA tumor

value: CD4, CD8 T cells

value: CD4-cre ICOS +/+


title: Group C, replicate 1, snRNAseq

description: 10x Genomics

value: male


title: FYC ICOS KO

description: Treg, CD4, CD8 T cells

value: ICOS f/f


title: Group C, replicate 4, snRNAseq

description: 10x Genomics


title: Group B, replicate 3, snRNAseq

description: 10x Genomics


title: FYC ICOS WT

description: Treg, CD4, CD8 T cells

value: ICOS +/+


title: CysK2_KO+CHP 2

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
Illumina adapters and low-quality reads were removed from raw sequencing reads using cutadapt Martin . Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the Mycobacterium tuberculosis H37RV, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, using hisat2 with default parameters  . Uniquely aligned reads were counted using featureCounts of Subread package . There were 4008 genes in the gtf file, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, for which we had count information. Genes with total read count less than 10 across all the samples were removed, and the rest were used for further analysis. Differential gene expression analysis was performed using DESeq2 . Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Assembly: Mycobacterium tuberculosis H37Rv
Supplementary files format and content: tab-delimited text files includes count data for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis H37Rv genetic deletion mutant of cysK2

growth_protocol: Mtb strains were grown in Middlebrook 7H9 liquid medium (BD Biosciences) supplemented with 10% ADC (albumin, dextrose, NaCl, catalase), 0.2% glycerol and 0.05% Tween-80.  For oxidative stress-related experiments, 7H9 medium was supplemented with ADS (ADC without catalase). H37Rv was either left untreated, or treated with 50 micromolar of CHP for 6 h for oxidative stress, resuspended in PBS for 7 days for starvation, 0.1% SDS for surfactant stress for 3 h, resuspended in pH 5.5 media for acidic stress for 2 days or were treated with sodium nitrate in pH 5.5 for 2 days for nitrosative stress. Comparative gene expression profiling analysis of RNA-seq data for H37Rv, RvDcysM, RvDcysK2 with and without oxidative stress. H37Rv, RvDcysM, , RvDcysK2 were either left untreated or treated with 50 micromolar CHP for 6 hours.

extract_protocol: Total RNA was isolated from two-three biological replicates of indicated Mtb strains, and their concentrations were checked by Qubit (ThermoFischer Scientific) followed by quality assessment through Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit). All samples were processed at the same time and same set of control (Rv) triplicates were used for the comparative analysis. Samples with RIN values > 7 were processed for RNA sequencing at CSIR-Centre for Cellular and Molecular Biology, India, using the Illumina NovaSeq 6000 Platform with a read length of 100 bp, generating 20 million paired-end reads per sample.

value: 50 micromolar CHP

tag: time

value: 6 hours


title: VAV05_12d

value: Peripheral Blood

value: Cd14+ Monocyte


title: SD2 cells, 2D in vitro, rep 1

description:
cells cultured on 2D cell culture plastic
1-SD2_2D_G


title: Sperm_MDL_Male15 [MDL15]

value: Sperm

value: Western diet fed males


title: VAV04_3d


title: CysK2_KO+CHP 3

value: Mycobacterium tuberculosis H37Rv genetic deletion mutant of cysK2


title: Group B, replicate 4, snRNAseq

description: 10x Genomics

value: Heart (left ventricle)

value: Dilated Cardiomyopathy (end-stage)

value: Without DCM-related gene mutation


title: VAV05_0d


title: VAV04_1d


title: Sperm_MDL_Male11 [MDL11]

value: Low-protein diet + methyl-donor supplement fed males


title: Sperm_MDL_Male9 [MDL9]


title: CysK2_KO 3

value: Untreated


title: VAV04_0d


title: Sperm_LPD_Male15 [LPD15]


title: Sperm_MDL_Male10 [MDL10]


title: CysK2_KO 1


title: Group B, replicate 2, snRNAseq

description: 10x Genomics

value: female


title: CysK2_KO+CHP 1


title: Group A, replicate 4, snRNAseq

description: 10x Genomics


title: VAV04_12d


title: Group B, replicate 1, snRNAseq

description: 10x Genomics


title: Group A, replicate 3, snRNAseq

description: 10x Genomics


title: VAV03_3d


title: Sperm_LPD_Male13 [LPD13]

value: Low-protein diet fed males


title: CysK2_KO 2


title: Group A, replicate 2, snRNAseq

description: 10x Genomics

value: male


title: CysM_KO+CHP 1

source_name: Mycobacterium tuberculosis H37Rv genetic deletion mutant of cysM


title: VAV03_12d


title: VAV03_1d


title: VAV03_0d


title: CysM_KO 2

value: Mycobacterium tuberculosis H37Rv genetic deletion mutant of cysM


title: Sperm_LPD_Male12 [LPD12]


title: CysM_KO+CHP 2


title: Group A, replicate 1, snRNAseq

description: 10x Genomics


title: Sperm_LPD_Male11 [LPD11]


title: CD5 KO CART19 GEX

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd.

institute: University of Pennsylvania

description:
cd5ko_barcodes.tsv.gz
cd5ko_features.tsv.gz
cd5ko_matrix.mtx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary T cell

extract_protocol: Primary human CAR T cells were generated and injected into NSG mice engrafted with CD19+ DLBCL cell line OCI-Ly18. 16 days post-CAR T injection, primary human T cells were collected from the peripheral blood by FACS sorting

value: Primary T cell

value: KO

value: electroporated with RNP complex


title: Sperm_NPD_Male15 [NPD15]


title: Sperm_LPD_Male10 [LPD10]


title: CD5 KO CART19 BC


title: VAV02_3d

value: Peripheral Blood


title: VAV02_1d

value: Cd14+ Monocyte


title: Sperm_NPD_Male12 [NPD12]

value: Sperm

value: Control (normal protein diet fed males)


title: CysM_KO 1


title: Mock KO CART19 GEX

description:
mockko_barcodes.tsv.gz
mockko_features.tsv.gz
mockko_matrix.mtx

value: WT

value: electroporated without RNP complex


title: shTIRR-IR-rep-3

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

institute: University of Oxford

data_processing:
Sequence reads were trimmed for adaptor sequence using Cutadapt
Sequencing data was aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a)
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92
Genes with low counts across most libraries, Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were removed
Assembly: GRCh38
Supplementary files format and content: txt file containing read counts per gene for each sample

source_name: Hela

growth_protocol: Stably integrated inducible shRNA Hela cells, expressing shRNA for TIRR or GFP as a control, were cultured in DMEM containing 1% L-glutamine, and 10% FBS at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted by scrapping from plates using RNA lysis reagent from the Monarch Total RNA Miniprep Kit. RNA was eluted in water and quantified using an Implen NanoPhotometer N60.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DoDouble strand breaks were induced using Ionising Radiation (IR) using a Gravatom or by Etoposide - Eto (5-10μM). TIRR knockdown was induced using doxycycline for 48 hours, before inducing damage using IR (10Gy) or Eto (5-10μM). RNA was collected before andafter DNA damage,inducedby IR and followed by 1 hour incubation,or by Eto incubation for 2 hours.

value: Hela

value: shTIRR

value: IR


title: Starvation 2

source_name: Mycobacterium tuberculosis H37Rv

value: Mycobacterium tuberculosis H37Rv

value: PBS

value: 7 days


title: VAV02_0d


title: shTIRR-IR-rep-2


title: Sperm_NPD_Male14 [NPD14]


title: VAV02_12d


title: SDS 3

value: SDS

value: 0.1percent sodium dodecyl sulfate

value: 3 h


title: Mock KO CART19 BC

value: Primary T cell


title: Starvation 1


title: Sperm_NPD_Male10 [NPD10]


title: SDS 2


title: PTCL_SAHA_54

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

data_processing:
Raw data was processed by the 10X Genomics software Cell Ranger (version 3.0.2) and the reads aligned to the mouse reference genome (mm10, v1.2.0). Default parameters were used to retain valid barcodes and unique molecular identifiers (UMIs).
Further analyses were performed in R using the package Seurat (v3.1.3). All samples were loaded in R separately, and Seurat objects were created retaining genes expressed in at least 3 cells, and cells expressing at least 50 genes. After assessing the distributions of the number of genes and percentage of mitochondrial genes (percent.mito) by UMI counts per sample, we determined filtering cutoffs equal for all samples. In particular, we filtered out cells having a number of genes < 500 and percent.mito > 50%.
Normalization was performed using the Seurat function NormalizeData (method = “LogNormalize”, scale.factor = 10,000). Finally, highly variable genes (n = 2,000) were calculated with the selection method “vst”.
To integrate samples from different conditions, we applied Seurat v3 integration method. Each sample was considered as one batch.
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix (UMI counts) for each sample and each gene. Files provided in tab-delimited format. Supplementary file contains all four digital gene expression matrices.

source_name: Spleen

extract_protocol:
Spleens were isolated and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. Vital cells were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp).

treatment_protocol: Mice were treated with SAHA, applied intraperitoneally 3 times/week for 3 weeks (50 mg/kg), or vehicle

tag: age (weeks)

value: SAHA treated

value: male


title: shTIRR-ETO-rep-3

value: ETO


title: Starvation 3


title: VAV01_3d

value: Peripheral Blood

value: Cd14+ Monocyte


title: VAV01_1d


title: SDS 1


title: VAV01_12d


title: shTIRR-ETO-rep-2


title: Ph5.5 3

value: NitroNeg

value: pH 5.5 media

value: 2 days


title: VAV01_0d


title: Sperm_NPD_Male11 [NPD11]

value: Sperm

value: Control (normal protein diet fed males)


title: CD4Smarcb1_9

value: control


title: shTIRR-control-rep-3

value: Hela

value: shTIRR


title: Ph5.5 2

value: Mycobacterium tuberculosis H37Rv


title: shTIRR-ETO-rep-1


title: 15__SAHA_n3

data_processing:
Raw FASTQ files were obtained and, after explorative quality control with FastQC (v0.11.8) and MultiQC (v1.7), we used Salmon (v0.14.1) for pseudo-alignment and quantification of the samples to the mouse transcriptome (downloaded from Ensembl, release 94). Default parameters were used.
Further analyses were performed in R. We employed the Bioconductor package tximport (v1.10.1) to summarize transcript-level estimates computed by Salmon for a gene-level analysis.
To find differentially expressed genes, we used the package DESeq2 (v1.22.2) and tested for SMARCB1 re-expression versus control conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_gene_counts_matrix.txt contains tab-separated raw counts for each gene and each sample

source_name: T15 cell line - treated

growth_protocol: All cells were maintained at 37°C and 5% CO2 in  RPMI 1640 medium with 10% FBS, 1% HEPES 1M, 1% penicillin/streptomycin (10,000 U/ml), sodium pyruvate (100 nM), l-glutamine (200 nM) and 0.1% β-mercaptoethanol (50 nM; all from Gibco).

extract_protocol:
Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's guidelines.

treatment_protocol: For T15-Smarcb1 re-expression, T15 cells were lentivirally transduced with a control (Smarcb1-) or Smarcb1 expression plasmid pInd20. After antibiotic selection (G418) and Doxycyclin induction (0.5 µg/µl) (72 h) total RNA was extracted and sequenced. For T15-SAHA: T15 cells were treated with SAHA (1 µM final concentration) or vehicle twice in 72 h. Afterwards, RNA was isolated and sequenced.

tag: treatment group

value: SAHA


title: shTIRR-IR-rep-1

value: IR


title: OE- 15DAF_Re3

city: Shanghai

first: Ma

last: Bin

state: Shanghai

address: Fenglin 300 Road, Shanghai, China

institute: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Assembly: RGAP_V7.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: rice leaves

growth_protocol: All rice plants were normally grown in paddy field.

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini Kit (Cat 74904, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: flag leaf at grain filling stage

value: overexpression

tag: ture name


title: OE- 15DAF_Re2


title: CD4Smarcb1_20

value: male


title: shGFP-IR-rep-3

value: shGFP


title: 09__ctrl_n3

source_name: T15 cell line

value: Control


title: Nitrostative 1

value: NitroPos

value: Sodium nitrate in acidified media (pH 5.5)


title: 08__ctrl_n2


title: Ko1- 15DAF_Re3

value: mutant


title: Nitrostative 3

value: 2 days


title: 14__SAHA_n2


title: OE- 15DAF_Re1


title: Ph5.5 1

value: NitroNeg

value: pH 5.5 media


title: 07__ctrl_n1


title: PTCL_SAHA_49

value: SAHA treated


title: Ko1- 15DAF_Re2


title: Nitrostative 2


title: shGFP-ETO-rep-2

value: Hela

value: ETO


title: 13__SAHA_n1


title: WT- 15DAF_Re2

value: wild type

value: WT


title: Sperm_MDL_Male14 [MDL14]

city: Manchester

first: Hannah

address: Oxford Road

value: Sperm

value: Low-protein diet + methyl-donor supplement fed males


title: Oxidative 1

value: Mycobacterium tuberculosis H37Rv

value: RvCHP

value: 50 micromolar CHP

value: 6 h


title: WT- 15DAF_Re1

value: flag leaf at grain filling stage


title: Control 3

value: Control

value: Untreated


title: Oxidative 3


title: WT- 15DAF_Re3


title: Ko1- 15DAF_Re1

value: mutant


title: shTIRR-control-rep-2

value: shTIRR

value: control


title: shGFP-ETO-rep-1

value: shGFP


title: Control 2


title: shTIRR-control-rep-1

value: Hela


title: shGFP-ETO-rep-3

value: ETO


title: Oxidative 2


title: shGFP-control-rep-3