title: PBMC_V3_Day17_rep5

description: Gene expression (mice PBMC) at Day 17 after 3 vaccine doses (500 attenuated cercariae)

source_name: PBMC, V3, Day17, rep5


title: Pt18_T2, scRNAseq

status: Public on Jan 05 2024

type: SRA

city: Guangzhou

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

country: China

institute: Sun Yat-sen University First Affiliated Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: liver metastasis

extract_protocol:
Tissue samples were processed with mechanical chopping with blades, followed by Tumor Dissociation Kit (Miltenyi Biotec) and DNaseI (DN25-100MG, Sigma Aldrich) digestion in medium (RPMI1640 with 5% FBS) for 30 min at 37°C. The cell suspension was passed through a 70-um filter (Miiltenyi Biotec), followed by 1×RBC lysis buffer (eBioscience) treatment.
Single cells were processed with the GemCode Single Cell Platform using the Gemcode Gel Bead, Chip and Libraray Kits (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol with modifications. Briefly, samples were processed using kits pertaining to the Chromium 5' immune profling v2 barcoding chemistry of 10x Genomics. Libraries were constructed according to the standard 10x Genomics protocol (Single Cell 5’Reagent Kits v5.2 User Guide) with modifications and performed the paired-end 2×150bp (PE150) sequencing on Novaseq 6000 (llumina, San Diego, CA).

tag: tissue

value: liver metastasis


title: Pt17_T1, scRNAseq

description: 10x Genomics

source_name: primary tumor

value: primary tumor


title: PBMC_VC_Day17_rep4

type: RNA

city: Salvador

first: Almiro

middle: Pires

last: Neto

state: Bahia

address: Waldemar Falcão Street

department: Immunology

country: Brazil

institute: Gonçalo Muniz Institute

description: Gene expression (mice PBMC) at Day 17 after infection (500 normal cercariae)

hyb_protocol: Sample hybridizations were performed on Agilent slides for 16 h at 65°C. After gentle washing in accordance with Agilent’s protocol, microarrays were scanned on a C scanner (Agilent)

scan_protocol: Slides were scanned immediately after washing on a Agilent G2565CA DNA Microarray Scanner using one color scan setting for SurePrint G3 Mouse GE 8x60K array slides

data_processing: Agilent Feature Extraction software (v10.7) was used to read and process microarray image files. The software determined feature intensities and background, rejected outliers, and generated validated data files for further analyses. Each array was validated via the analysis of additive error, spatial distribution of outliers in the array, a histogram of signal plots, background sub-signal value and linear range spike-in statistics.

organism: Mus musculus

source_name: PBMC, VC, Day17, rep4

label_protocol: To produce Cy3-labeled cRNA, total RNA was amplified and labeled using an Agilent Low Input Quick Amplification Labeling Kit in strict accordance with manufacturer instructions. Briefly, 100 ng of template RNA was used for cDNA synthesis, and T7 RNA polymerase was then used for cRNA amplification and Cy3 labeling. After purification, yield and dye incorporation was measured using a Nanodrop spectrophotometer (Thermo Scientific).

extract_protocol: Total RNA was extracted using TRizol® Reagent (Ambion RNA, Life Technologies), with a precipitation step incorporating glycogen (5mg/mL, Ambion, USA) plus 3M sodium acetate (Ambion, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 mice were distributed into five groups: control (C), non-treated animals; vaccinated once (V1) with 500 attenuated cercariae and challenged with 120 normal cercariae; vaccinated three times (V3) with 500 attenuated cercariae (4-week intervals) and challenged with 120 normal cercariae; only challenged with 120 normal cercariae (Chc); and  infected with 500 normal cercariae (Inf) in parallel with the 1V group. Blood was drawn from the same groups of mice in a time-course manner at Days 7 and 17 after imunization/infection, and Day 7 post-challenge and the PBMC was purified.

value: Peripheral blood mononuclear cells

tag: gender

value: Female


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 47

first: Jinyi

last: Wu

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou Laboratory

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-47

data_processing:
For bulk RNA-seq data, raw reads of fastq format from this study were first processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw reads. Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. For single cell RNA-seq data, data of day 6 blastoids was pre-processed through Trimmomatic software to remove adapters and to drop low quality reads or short reads below 26 bps. Other single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq and scRNAseq (Smartseq2) count table: gene by cell expression matrix generated with STAR; scRNAseq (10X) count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: blastoids

extract_protocol:
For bulk RNA-seq, total RNAs were collected and isolated from cells using RNAiso Plus (Takara). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina following manufacturer’s recommendations. For scRNA-seq, CI-hnESCs and day 2 aggregates were dissociated and sorted by flow cytometer for Smart-seq2 library construction and the libraries were sequenced on MGISEQ2000 (MGI Tech) platform to generate 100-bp paired-end reads. Day 3, day6 blastoids and the blastoids upon removing MEK/BRAF inhibition from Aggrewell were manually picked and polled with a mouth pipette, washed once with DPBS and then dissociated with 0.25% trypsin-EDTA (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Attached cultured bE14 blastoids were first rinsed once with DPBS and then treated with cold DPBS and incubated in 4°C for 10-20min to allow breaking of the matrix. When the samples became mobile under a microscope upon gentle shaking, the bE14 blastoids were transferred to a clean tube using a cut-tip and dissociated with 0.25% trypsin-EDTA at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: pluripotent stem cell

value: blastoids


title: Pt16_Z1, scRNAseq

description: 10x Genomics

source_name: liver adjacent tissue

value: liver adjacent tissue


title: Pt17_T2, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 48

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-48


title: Pt16_T1, scRNAseq

description: 10x Genomics


title: Pt15_Z1, scRNAseq

description: 10x Genomics

source_name: colon adjacent tissue

value: colon adjacent tissue


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 46

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-46


title: Pt15_T2, scRNAseq

description: 10x Genomics


title: Pt15_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 45

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-45


title: Pt13_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 44

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-44


title: PBMC_V3_Day17_rep4

source_name: PBMC, V3, Day17, rep4


title: PBMC_V3_Day17_rep3

source_name: PBMC, V3, Day17, rep3


title: Pt13_Z1, scRNAseq

description: 10x Genomics


title: Pt10_T2, scRNAseq

description: 10x Genomics


title: Pt11_T2, scRNAseq

description: 10x Genomics


title: PBMC_V1_Day17_rep4

description: Gene expression (mice PBMC) at Day 17 after 1 vaccine dose (500 attenuated cercariae)

source_name: PBMC, V1, Day17, rep4


title: PBMC_V3_Day17_rep1

source_name: PBMC, V3, Day17, rep1


title: PBMC_V3_Day17_rep2

source_name: PBMC, V3, Day17, rep2


title: 293T, WT, 4

city: Poznan

first: Zbigniew

last: Warkocki

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

library_source: transcriptomic

data_processing:
From 3'RACE-Seq raw reads, adapters were removed with cutadapt (v4.0) and sequences shorter than 20 nt were discarded. Low-quality nucleotides from 3’ end of reads were removed using ConDeTri (v2.3) with the following settings hq=37, ml=1, mh=5 and minlen=40.
For further analyses only reads containing a unique molecular identifier (UMI) in length 15 nt and delimiter (GTCAG) on 5’ end of read R2 were kept.
UMI and delimiter sequences were removed from read sequences and moved to the read name with the extract mode of UMI-tools (v1.1.2).
Reads were mapped to reference using STAR (v2.7.9a) with soft-clipping allowed (with the following settings outFilterMatchNmin 20, outFilterScoreMinOverLread 0.1 and outFilterMatchNminOverLread 0.1). Mapped reads were deduplicated with UMIcollapse.
For pair of reads in which both reads mapped non-templated tails and their nucleotide compositions were retrieved from the sam file from the soft-clipped fragments of read R2 using the previously published script (get_softclipped_reads_from_sam.pl) [Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022)]. For pair of reads in which only R1 mapped due to presence of long homopolymeric sequence in the read R2 length sequence of tails were extracted directly from the read R2.
Statistical analyses were performed in R (v4.2). In these analyses were included reads with no tails and those with the following composition: tails containing only A (A tails), only U (U tails), A with U on their 3’ (AU tails). In AU tails were allowed tails with U between A but not at the beginning of the tail. All operations on bam and sam files were performed with samtools (v1.13).
Assembly: LINE-1 sequence
Supplementary files format and content: tails_LINE1_3KOs.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_LINE1_PA1cells.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_LINE1_293Tcells.txt; tab-delimited text file containing tails sequences and lengths
Library strategy: 3' RACE-seq to assess non-templated 3' ends

extract_protocol:
RNA was isolated by using extraction with TRI (Chomczynski and Sacchi, 1987), followed by extraction with chloroform. After precipitation samples were dilluted in TNES with 20ng/µl proteinase K (USB), incubated at 37C for ~15mins, and purified again by phenol/chloroform/isoamly alc. (PCIA), followed by chloroform extractions, and precipitated with isopropanol in the presence of 100mM NaOAc 5.2. Nucleic acids were centrifuged and treated with TURBO DNAse in 0,5x buffer in 100µl for 15mins, followed by another round of extractions with PCIA, chlorofom, and precipitation. Such RNA was measured (for all A260/280 >1,85, A260/230 >2), analyzed for quality by electrophoresis in agarose gels, staining and photographing followed by quantitation of 28S RNA to 18S rRNA ratios. Good quality RNA was used for 3' RACE-seq library preparations, RT-qPCR, and Northern blots (all with same preparations of RNA). Endogenous L1 were amplified by nested PCR to prepare libraries for Illumina 100+100 paired-end sequencing
For the 12 home-made 293T cell lines (this paper) including the wild-type and the XRN1 KO each biological replicate was a single technical replicate (one index per cell line). For the PA-1 cells, 2 sets of RNAi-induced knock-downs were prepared and analyzed: including control kd, XRN1 kd, DCP2 kd, and DIS3L2 kd (only 1 set). Set 1 = 1 transfection with siRNA, 48h between transfection and harvest for RNA, 3 biological replicates for each condition, each a different siRNA, but for DIS3L2 for which only 1 siRNA was transfected into 3 independent wells of a multiwell plate. Set 2 = 2 transfections with siRNA, 1st transfection (siRNA silencer select for each of two duplicates for each condition), 72h, 2nd transfection (same siRNA), 54h, harvest; each well was considered as an independednt biological replicate. Each biological replicate were performed and marked with a different index. For all libraries after index installation during RT, libraries from a single conditions were pooled (e.g. WT or XRN1 KO), and PCR1 and PCR2 were performed on pools of each of the conditions (e.g. 6 indexes for 293T Wt were RT separately, but amplified in a common pool). Libraries were prepared as described in (10.1016/j.cell.2018.07.022) with modifications. Briefly, 2µg total RNA after DNase treatment were ligated with 100pmole RA3_15N 5’ preadenylated adapter comprising a 15-nucleotide unique molecular identifier (UMI) in 20µl of 1x enzyme-supplied buffer, 15% PEG 8000 by T4 RNA ligase 2 truncated (NEB, M0242) for 18h at 18˚C. Nucleic acids of each reaction were purified using 20µl Ampure XP magnetic beads, eluted in and used for reverse transcription in 20µl with 100pmoles RPI primer (containing an 6-nucleotide index) using Superscript III (ThermoScientific) enzyme according to the manufacturer’s protocol (2mins at 50˚C, 30mins at 45˚C, 15mins at 85˚C), followed by purification on 1,25 volume of Ampure XP magnetic beads. Nested PCR was performed with PrimeSTAR GLX polymerase (TaKaRa, R050B) since it proofed best at elongating long poly(A) tracts (as compared to Phusion of ThermoScientific and Q5 polymerases of NEB; not shown). First round PCR were performed in 25µl with an equivalent of 500ng input total RNA (input to RT step) per reaction. Primers at 0,35µM were 3UNP1f for L1, universal reverse primer, RP_uni, was added at 0,4µM. Reactions were carried out: 98˚C 2mins, [98˚C 12sec, 52˚C 15sec, 70˚C 40sec]x30 (set 1 PA-1)/33 (set 2 PA-1 & 293T), 68˚C 1min, 1/10 of each reaction was used without purification as template for second round PCR in 50µl (set 1) or 2x50µl (total 100µl; set 2 & 293T) with 0,36µM transcript-specific forward primer: L-1rep_NGS1, and 0,4µM universal reverse primer RP_uni. PCRs were carried out: 98˚C 2mins, [98˚C 12sec, 55˚C 15sec, 70˚C 30sec]x30 (set 1 PA-1)/33 (set 2 PA-1 & 293T), 70˚C 1min. The reactions of set 1 PA-1 (48h RNAi) were purified on 1,3 volume Ampure XP magnetic beads, and eluted. The reactions of set 2 PA-1 (126h) and 293T: duplicate 50µl were pooled and precipitated, separated on 5% non-denaturing PAA in 1x TBE for 45min @ 500V, stained with SYBR Gold (Thermo Fisher Scientific) 1:2000 in 1x TBE, cut within a range from 180 to 500bp (as assessed by comparison with migration ladders), eluted in 1x TNES (10mM Tris 8.0/100mM NaCl/2mM EDTA/0,1% SDS), precipitated with 1,2vol isopropanol in the presence of 1µl glycoblue co-precipitant and 100mM NaOAc 5,2, sedimented overnight, washed 2x with 70% ethanol, air-dried and suspended in 14µl. Set 1 libraries were measured and diluted to ~5ng/µl, set 2 & 293T libraries were analysed by electrophoresis in agarose gels. All libraries were analysed on TapeStation (Agilent). The set 2 and 293T were 'overamplified' as suggested by smearing in PAA and on Tapestation but not in agarose gels. On the other hand performing less cycles did not yield any interpretable signal on the gels and preculded size-based separation on PAA gels, which was performed to exclude libraries of sizes of lenghts matching just forward and reverse primers (160bp). Before running on Illumina Novaseq libraries were quantitated by qPCR to adjust the number of reads to ~3-5 MRds for each transcript for each biological/technical replicate (each index).

tag: cell line

tag: genotype

value: WT


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 43

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-43


title: Pt11_T1, scRNAseq

description: 10x Genomics


title: Pt10_T1, scRNAseq

description: 10x Genomics


title: PBMC_V1_Day17_rep3

source_name: PBMC, V1, Day17, rep3


title: Pt09_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 42

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-42


title: PBMC_V1_Day17_rep2

source_name: PBMC, V1, Day17, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 41

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-41


title: Pt08_T3, scRNAseq

description: 10x Genomics


title: Pt08_T4, scRNAseq

description: 10x Genomics


title: Pt08_T2, scRNAseq

description: 10x Genomics


title: Pt07_T1, scRNAseq

description: 10x Genomics


title: PBMC_V1_Day17_rep1

source_name: PBMC, V1, Day17, rep1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 40

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-40


title: PBMC_VC_Day7_rep4

description: Gene expression (mice PBMC) at Day 7 after infection (500 normal cercariae)

source_name: PBMC, VC, Day7, rep4


title: PBMC_VC_Day7_rep3

source_name: PBMC, VC, Day7, rep3


title: Pt06_T2, scRNAseq

description: 10x Genomics


title: Pt07_T2, scRNAseq

description: 10x Genomics


title: Pt06_T3, scRNAseq

description: 10x Genomics


title: Pt06_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 38

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-38


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 37

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-37


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 36

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-36


title: PBMC_VC_Day7_rep1

source_name: PBMC, VC, Day7, rep1


title: Pt05_T2, scRNAseq

description: 10x Genomics

source_name: liver metastasis


title: PBMC_V3_Day7_rep5

description: Gene expression (mice PBMC) at Day 7 after 3 vaccine doses (500 attenuated cercariae)

source_name: PBMC, V3, Day7, rep5


title: Pt05_T3, scRNAseq

description: 10x Genomics


title: Pt05_T1, scRNAseq

description: 10x Genomics

source_name: primary tumor


title: Pt04_T2, scRNAseq

description: 10x Genomics


title: Pt08_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 35

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-35

source_name: blastoids


title: Pt03_T2, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 34

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-34


title: Pt17_Z1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 39

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-39


title: PBMC_V3_Day7_rep4

source_name: PBMC, V3, Day7, rep4


title: PBMC_V3_Day7_rep3

source_name: PBMC, V3, Day7, rep3


title: Pt03_T1, scRNAseq

description: 10x Genomics


title: Pt02_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 33

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-33


title: Pt01_T2, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 32

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-32


title: Day 5 - CD8 - T cells replicate 2

city: Gif-sur-Yvette

first: Adèle

last: Mangelinck

state: Essonne

address: 22 route 128 - rue Francis Perrin

country: France

institute: Servier

description:
10x Genomics
CD8_MLR_kinetics_counts.csv
CD8_MLR_kinetics_metadata.csv

data_processing:
Cell Ranger (v6.0.1, 10x Genomics Inc) was applied for demultiplexing, reads mapping against the GRCh38 human reference genome, and UMI counting.
Seurat package (v4.2.1) was used to generate Seurat objects. Only genes detected in at least 3 cells were kept. Cells with fewer than 200 genes detected or >15% mitochondrial UMI counts were filtered out. Samples were merged in a CD4 and a CD8 objects according to their T cells types then count data normalization and scaling was performed using Seurat with default parameters. The 2000 most highly variable genes were used for Principal Component Analysis (PCA). Harmony (v0.1.1) was applied for batch effect correction then Uniform Manifold Approximation and Projection (UMAP) and clustering using the Louvain algorithm were performed on the harmony reduction. Non-T or -MoDC clusters were removed for further analysis.
Assembly: GRCh38
Supplementary files format and content: Comma-separated counts and metadata files

source_name: PBMC

extract_protocol:
On each timepoint, cells suspensions in culture medium were recovered, washed once with 0.04% BSA in 1X PBS and processed through 10x Cell Multiplexing Oligo Labeling protocol (10x Genomics, USA) according to the manufacturer’s instructions. ~1,500 cells/µl pooled cell suspensions were prepared with equal number of cells per sample, one for MLR samples and one for T cells samples on each timepoint.
Libraries were prepared using the 10x Chromium Single-Cell 3’ v3.1 protocol with Feature Barcode (10x Genomics, USA), according to the manufacturer’s instructions.

value: PBMC


title: PBMC_VC_Day7_rep2

source_name: PBMC, VC, Day7, rep2


title: Day 5 - CD8 - T cells replicate 1


title: Pt01_T1, scRNAseq

description: 10x Genomics


title: Day 1 - CD8 - T cells replicate 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 30

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-30


title: Pt02_T2, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 29

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-29


title: Pt04_T1, scRNAseq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 31

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-31


title: Day 5 - CD8 - MLR replicate 2


title: Day 5 - CD8 - MLR replicate 1


title: PBMC_V3_Day7_rep2

source_name: PBMC, V3, Day7, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 28

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-28


title: PBMC_V1_Day7_rep4

description: Gene expression (mice PBMC) at Day 7 after 1 vaccine dose (500 attenuated cercariae)

source_name: PBMC, V1, Day7, rep4


title: Day 6 - CD8 - MLR replicate 2


title: Day 2 - CD8 - MLR replicate 2


title: D20 TGF-b Replicate 3

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

data_processing:
Low quality bases were trimmed from pre-aligned reads, then aligned to hg19 reference genome using STAR v2.7, followed by quantification using salmon v1.4.
The normalised gene level expression data was further used to plot our signature of 101 genes across different EMT timepoints (day1-day20)
Assembly: hg19
Supplementary files format and content: Normalised count matrix

source_name: Not applicable

growth_protocol: Cells were seeded at the same starting density (200K per well)

extract_protocol:
RNA was extracted using Trizol, isolated using chloroform, precipitated using isopropanol and the RNA pellet washed with ethanol before re-suspension in DEPC water
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were with TGFβ induction at day1, day4, day7, day10, day15 and day20

value: Not applicable

value: HMLE

value: Human mammary epithelialcells(HMLE)

value: D20 TGF-b

tag: treatment


title: PBMC_V1_Day7_rep3

source_name: PBMC, V1, Day7, rep3


title: D20 TGF-b Replicate 2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 27

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-27


title: Day 2 - CD8 - MLR replicate 1


title: Day 1 - CD8 - MLR replicate 2


title: D20 TGF-b Replicate 1


title: PBMC_V3_Day7_rep1

source_name: PBMC, V3, Day7, rep1


title: PBMC_V1_Day7_rep2

source_name: PBMC, V1, Day7, rep2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 26

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-26


title: Day 5 - CD4 - T cells replicate 1

description:
10x Genomics
CD4_MLR_kinetics_counts.csv
CD4_MLR_kinetics_metadata.csv


title: Day 5 - CD4 - T cells replicate 2


title: Day 1 - CD4 - T cells replicate 1


title: PBMC_V1_Day7_rep1

source_name: PBMC, V1, Day7, rep1


title: Day 1 - CD8 - MLR replicate 1


title: D15 TGF-b Replicate 3

value: D15 TGF-b


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 25

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-25


title: Day 6 - CD4 - MLR replicate 2


title: Day 1 - CD4 - T cells replicate 2


title: D15 TGF-b Replicate 2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 24

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-24


title: Day 6 - CD4 - MLR replicate 1


title: D15 TGF-b Replicate 1


title: D10 TGF-b Replicate 3

value: D10 TGF-b


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 23

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-23


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 21

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-21


title: Day 2 - CD4 - MLR replicate 2


title: Day 5 - CD4 - MLR replicate 1


title: D10 TGF-b Replicate 2


title: D10 TGF-b Replicate 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 22

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-22


title: Day 1 - CD4 - MLR replicate 1


title: D7 TGF-b Replicate 3

value: D7 TGF-b


title: Day 1 - CD4 - MLR replicate 2


title: VMT_MDAMB231

city: Irvine

first: Christopher

middle: J

last: Hatch

state: CA

address: 2400 Biological Sciences III

country: USA

institute: University of California, Irvine

data_processing:
FASTQ files for each library were aligned to an indexed GRCh38 reference genome using Cell Ranger (10X genomics)
Count matrices were imported into R and analyzed using the standard Seurat SCT pipeline
Assembly: GRCh38

source_name: Endothelial colony-forming cell-derived endothelial cells + primary human normal breast stromal cells + MDA-MB-231 TNBC cells

extract_protocol:
Media was aspirated from each well and the high- throughput plates were inverted so that the device layer was facing up. The bottom membrane was gently peeled off the device to expose the tissue chambers. Devices were first washed with 500 µL of HBSS. To each device unit, 100 µL of TrypLE was added and allowed to sit as a bubble on top of the device while the plate was put back in the 37 ◦C incubator for 5 minutes. After digestion, a P200 pipet was used to pipet up and down across the tissue chambers to collect the tissues in the TrypLE. The pipet tip was moved back and forth across each device to ensure full removal of the tissue and collected into a 15 mL conical with EGM2 to neutralize the TrypLE. For full removal of remaining cells from the tissue chamber, 500 µL of EGM2 was added to each device unit and washed with the P200. Digestion solution containing the dislodged tissues was centrifuged at 300xg for 5 minutes at 4 ◦C to pellet single cells and whole tissues. Media was carefully aspirated and a solution of 1 mg/mL (200 U/mL) collagenase III in HBSS was added to the undigested tissues. After gentle pipetting, the solution was allowed to sit for 2 minutes at room temperature before pipetting gently again to dissociate the gel. Digestion mix was washed with 10 mL of EGM2 and centrifuged at 300xg for 5 minutes at 4 ◦C. Cells were resuspended into 1X DPBS with 1% human serum albumin and passed through a pre-wetted 70 µm filter by spinning at 200xg for 1 minute. Cells were counted and volume was adjusted so that total cells were at a concentration of 1000 cell per uL.
Cellular suspensions were loaded onto a Chromium Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsion (GEMs). GEMs were processed to generate cDNA libraries by using 10X Genomics v2 chemistry according to the Chromium Single Cell 3’ Reagents kits v2 user guide: CG00052 Rev B. Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay kit (Life Technologies Q32851), high-sensitivity DNA chips (Agilent 5067-4626) and KAPA qPCR (Kapa Biosystems KK4824). Libraries were sequenced on an Illumina NovaSeq6000 to achieve an average of 50,000 reads per cell.

tag: time

value: Day 7


title: D7 TGF-b Replicate 2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 19

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-19


title: VMT_HCC1599

source_name: Endothelial colony-forming cell-derived endothelial cells + primary human normal breast stromal cells + HCC1599 TNBC cells


title: VMO_MDAMB231

source_name: Endothelial colony-forming cell-derived endothelial cells + primary human normal breast stromal cells


title: D7 TGF-b Replicate 1


title: BT20 Jagged1 8h #5

city: Stockholm

first: Eike-Benjamin

last: Braune

address: Nobels väg 6

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Data have initially been processed and quality checked at SciLife laboraoties, Sweden following the nf-core/rnaseq (Ewels et al., 2020. Nat Biotechnol. doi: 10.1038/s41587-020-0439-x.doi: 10.1038/s41587-020-0439-x)
Reads were aligned using STAR (Spliced Transcripts Alignment to a Reference)
Gene and transcript counts were generated using the mentioned rna-seq pipeline
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: salmon merged gene counts (generated with pipeline described above)

growth_protocol: The breast cancer cell lines (BT-20, HCC70, HCC1187, HCC1599, MDA-MB-468, MDA-MB-436) used for establishing the Notch transcriptomic signature were purchased fresh from the American Type Culture Collection (ATCC) and maintained in RPMI 1640 medium (ATCC’s modification, cat #A1049101, Thermo Fisher Scientific) with 10% fetal bovine serum (FBS, heat inactivated, cat #A3840402, Thermo Fisher Scientific) and 1% penicillin-streptomycin (cat #15140-122, Thermo Fisher Scientific). The 19 breast cancer cell lines used to generate an independent validation data set were maintained as described (Brunner et al., 2020). Accutase (cat # A6964-100ML, Sigma-Aldrich) was used to detach the cells prior to seeding on coated plates and during maintenance. All cell lines were cultivated with 5% CO2 at 37°C.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen)
Illumina TruSeq Stranded mRNA

treatment_protocol: Activation of Notch signaling in the cell lines used for validation of the signature was achieved as previously described (Sahlgren et al., 2008) with minor modifications: 1µg rat Jagged1-Fc (cat #599-JG, R&D systems) or ChromPure Human IgG, Fc (cat #009-000-008, Jackson ImmunoResearch) was used instead of 2 µg. Blockage of Notch signaling was in both cases achieved by adding 10 µM DAPT (InSolution™ γ-Secretase Inhibitor IX, cat #565784, MerckMillipore) directly to the cell culture medium and cells were incubated with DAPT for 8h and 72h. Non-GSI treated cells (Fc control, Jagged1-Fc) were treated with equimolar volumes of carrier control (DMSO, cat #D8418-50ML, Sigma-Aldrich). Transcriptimes were harvested after 8h and 72h of treatment. Activation of Notch signaling in the cell lines used to establish a Notch transcriptomic signature was performed as described above with minor modifications: Tissue culture treated plates were incubated over night at 4°C or for 1h at room temperature with 5µg/ml Protein G (cat #21193, Thermo Fisher Scientific) in PBS. Non-specific binding was blocked by incubating coated plates with 1x blocking buffer (Thermo Fisher Scientific, cat #37525) and plates were incubated with immobilized ligand or Fc control for 1.5h at room-temperature. Blockage of Notch signaling was in both cases achieved by adding 10 µM DAPT (InSolution™ γ-Secretase Inhibitor IX, cat #565784, MerckMillipore) directly to the cell culture medium and cells were incubated with DAPT for 8h and 72h. Non-GSI treated cells (Fc control, Jagged1-Fc) were treated with equimolar volumes of carrier control (DMSO, cat #D8418-50ML, Sigma-Aldrich).

value: breast cancer

tag: treatment time

tag: biological replicate

value: JAG1  (ligand)

tag: mreads


title: Day 6 - CD8 - MLR replicate 1


title: VMO_HCC1599

value: Endothelial colony-forming cell-derived endothelial cells + primary human normal breast stromal cells


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 17

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-17

value: pluripotent stem cell


title: D4 TGF-b Replicate 3

value: D4 TGF-b


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 18

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-18

value: blastoids


title: BT20 FC 8h #5

value: FC


title: Day 5 - CD4 - MLR replicate 2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 16

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-16


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 20

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-20


title: BT20 FC 8h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 15

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-15


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 14

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-14


title: BT20 DAPT 72h #4

value: DAPT (GSI)


title: D4 TGF-b Replicate 2


title: D1 TGF-b Replicate 3

value: D1 TGF-b


title: D4 TGF-b Replicate 1

value: Not applicable


title: Day 2 - CD4 - MLR replicate 1

value: PBMC


title: BT20 FC 72h #4


title: HCC1599 DAPT 8h #4


title: BT20 DAPT 8h #5


title: HCC1599 FC 8h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 12

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-12


title: HCC1599 Jagged1 72h #4


title: Untreated Replicate 3

value: HMLE

value: Human mammary epithelialcells(HMLE)

value: Untreated


title: HCC1599 FC 72h #4


title: BT20 Jagged1 8h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 11

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-11


title: BT20 DAPT 8h #4


title: BT20 Jagged1 72h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 10

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-10


title: HCC1187 DAPT 8h #6


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 9

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-9


title: Untreated Replicate 1


title: HCC1599 DAPT72h #4


title: HCC1187 Jagged1 8h #6


title: Untreated Replicate 2


title: HCC1187 Jagged1 8h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 13

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-13


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 8

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-8


title: HCC1187 DAPT 8h #4


title: HCC1599 Jagged1 8h #4


title: D1 TGF-b Replicate 1


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 7

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-7


title: HCC1187 Jagged1 72h #6


title: HCC1187 FC 72h #6


title: D1 TGF-b Replicate 2


title: HCC1187 FC 8h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 6

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-6


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 5

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-5


title: HCC1187 DAPT 72h #6


title: HCC1187 DAPT 72h #4


title: HCC1187 FC 72h #4


title: BT20 Jagged1 72h #3


title: HCC1187 Jagged1 72h #4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 4

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-4


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 3

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-3


title: BT20 DAPT 72h #2


title: BT20 Jagged1 72h #2


title: MDAMB436 Jagged1 72h #3


title: BT20 DAPT 72h #3


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 2

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-2


title: HCC1187 FC 8h #6


title: Control_rep2

city: Shanghai

first: Ji

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
BBMAP used for triming reads. It can binning reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
DEseq2 used to analyze the difference expression of mRNA
Genome_build: mm9
Supplementary_files_format_and_content: txt file include gene counts for each Sample

source_name: Female germline stem cell

extract_protocol:
Total RNA was extracted from FGSCs using Trizol reagent (Life Technologies, CA). Next, 1000 ng of the digested RNA was used for the VAHTSTM mRNA-seqv2 Library Prep kit for Illumina1, and sequencing libraries were created according to the manufacturer's protocol.
The extracted further treated with DNase to remove genomic DNA contamination. Isolation of mRNA was performed using the Oligotex mRNA Mini Kit (Qiagen GmbH, Hilden, Germany) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: Female germline stem cell

tag: passages

tag: strain

value: control


title: MDAMB436 Jagged1 72h #2


title: BT20 FC 72h #2


title: scRNA-seq (Smartseq2) of D2 Spontaneous Blastoids - cell 1

description:
SpontaneousBlastoid_D0andD2_count.csv
day2-blastoids-1


title: Control_rep1


title: MDAMB436 Jagged1 72h #1


title: MDAMB436 DAPT 72h #3


title: SPD_rep2

value: SPD


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 83

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-83

source_name: TJ 1# CI-hnESC

value: TJ 1# CI-hnESC


title: MDAMB436 DAPT 72h #2

value: breast cancer


title: MDAMB436 FC 72h #3


title: MDAMB436 DAPT 72h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 82

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-82


title: SPD_rep1


title: MDAMB436 FC 72h #2


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 7, repeat 2

city: Oxford

first: Elizabeth

last: Brown

address: Roosevelt Drive

department: Centre for Medicines Discovery

country: United Kingdom

institute: University of Oxford

data_processing:
trimmed reads were pseudoaligned to the human transcriptome (hg38) with kallisto
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: CNS

growth_protocol: Cells were cultured as described in (Mohammad, 2017, doi: 10.1038/nm.4293)

extract_protocol:
Total cellular RNA was harvested with the RNeasy Mini Kit (Qiagen, 74104), including on-column DNase digestion with RNase-free DNase (Qiagen, 79256). RNA quality was assessed with an Agilent Tapestation 4150 (all samples had a RNA integrity number of >9.9).
cDNA libraries were synthesised from 200 ng RNA using an NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB #E7760) according to manufacturer’s instructions.

treatment_protocol: treated +/- LLY-283 GI(40) single dose

value: CNS

value: Diffuse midline glioma cells

value: H3F3A K27M; ACVR1 R206H; PIK3CA MIS


title: MDAMB436 FC 72h #1


title: HCC1599 Jagged1 72h #2

value: JAG1  (ligand)


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 81

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-81

value: pluripotent stem cell


title: HSJD-DIPG-007 cells, vehicle treatment, day 7, repeat 2

value: Vehicle


title: HCC1599 Jagged1 72h #3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 80

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-80


title: HSJD-DIPG-007 cells, vehicle treatment, day 7, repeat 1


title: HCC1599 DAPT 72h #2

value: DAPT (GSI)


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 5, repeat 3


title: HCC1599 DAPT 72h #3


title: HCC1599 FC 72h #3

value: FC


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 79

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-79


title: HCC1599 FC 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 84

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-84


title: HCC70 Jagged1 72h #3


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 5, repeat 2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 78

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-78


title: HCC70 Jagged1 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 77

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-77


title: HCC70 Jagged1 72h #1


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 5, repeat 1


title: HCC70 DAPT 72h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 75

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-75


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 3, repeat 1


title: HCC70 FC 72h #3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 76

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-76


title: HSJD-DIPG-007 cells, vehicle treatment, day 3, repeat 1


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 2, repeat 1


title: HCC70 FC 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 73

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-73


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 74

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-74


title: MDAMB468 Jagged1 72h #3


title: MDAMB468 DAPT 72h #3


title: MDAMB468 Jagged1 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 72

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-72


title: MDAMB468 DAPT 72h #2


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 1, repeat 1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 71

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-71


title: MDAMB468 DAPT 72h #1


title: HSJD-DIPG-007 cells, vehicle treatment, day 1, repeat 1


title: MDAMB468 FC 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 70

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-70


title: MDAMB468 Jagged1 72h #1


title: HSJD-DIPG-007 cells, vehicle treatment, day 2, repeat 1


title: MDAMB468 FC 72h #1


title: HCC70 DAPT 72h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 69

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-69


title: HCC70 FC 72h #1


title: HCC70 DAPT 72h #3


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 0, repeat 3


title: HCC1187 FC 72h #1


title: MDAMB468 FC 72h #3


title: HCC1187 Jagged1 72h #1


title: Day 1 - CD8 - T cells replicate 2

description:
10x Genomics
CD8_MLR_kinetics_counts.csv
CD8_MLR_kinetics_metadata.csv

value: PBMC


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 67

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-67


title: BT20 DAPT 8h #3


title: MDAMB436 Jagged1 8h #3


title: MDAMB436 Jagged1 8h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 65

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-65


title: HSJD-DIPG-007 cells, vehicle treatment, day 0, repeat 3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 66

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-66


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 0, repeat 1


title: BT20 Jagged1 8h #3


title: HSJD-DIPG-007 cells, vehicle treatment, day 0, repeat 2


title: MDAMB436 Jagged1 8h #1


title: MDAMB436 DAPT 8h #3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 64

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-64


title: HSJD-DIPG-007 cells, vehicle treatment, day 0, repeat 1


title: MDAMB436 DAPT 8h #1


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 0, repeat 2


title: MDAMB436 DAPT 8h #2


title: HCC1187 DAPT 72h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 68

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-68


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 63

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-63


title: MDAMB436 FC 8h #3


title: HSJD-DIPG-007 cells, vehicle treatment, day 5, repeat 2


title: MDAMB436 FC 8h #2


title: HSJD-DIPG-007 cells, vehicle treatment, day 5, repeat 1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 62

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-62


title: MDAMB436 FC 8h #1


title: HCC1599 Jagged1 8h #3


title: HSJD-DIPG-007 cells, vehicle treatment, day 5, repeat 3


title: HCC1599 Jagged1 8h #1


title: BT20 FC 8h #3


title: HCC1599 DAPT 8h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 60

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-60


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 10, repeat 1


title: HCC1599 FC 8h #3


title: HSJD-DIPG-007 cells, vehicle treatment, day 10, repeat 1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 58

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-58


title: HCC1599 FC 8h #1

value: JAG1 + DAPT


title: HCC70 Jagged1 8h #3


title: HSJD-DIPG-007 cells, LLY-283 treatment, day 7, repeat 1


title: HCC70 Jagged1 8h #1


title: NG-8304_Dscam1_lib80429_all

city: Birmingham

first: David

middle: William John

last: McQuarrie

address: School of Biosciences

institute: University of Birmingham

data_processing:
Reads were mapped using STAR version 272B the following parameters: --alignIntronMin 20   --alignIntronMax 200000   --alignMatesGapMax 200000   --twopassMode Basic
An in-house script was used to demultiplex the reads, described in Ustaoglu et al., 2023.
Assembly: Amel_HAv3.1
Supplementary files format and content: Exel: Exon 4, 6, and 10 decomplexed reads

organism: Apis mellifera

source_name: Central brain

extract_protocol:
Total RNA was extracted from honey bee central brains and reverese transcribed as per Ustaoglu et al., 2023. Amplicons for Dscam variable clusters (exon4, exon 6 and exon 10) were then PCR amplified and Illumina sequenced.
Libraries from indexed PCR amplicons were prepared by GATC as per Ustaoglu et al., 2023.
Amplicon-seq. Amplicons as per primers in Ustaoglu et al 2023: bee exons 3-5 (bee 5) and 9-10 (bee 6) are unique primers. Exon 6 was indexed in the 5' primer for unpaired control (CGTCTAAT. bees 7-9), fast learners (CCATGAGT, bees 10-12) and slow learners (GTCATTATG, bees 13-15). The same indexes in the return primer were used for different individuals.

value: Central brain

value: Wild type

value: Associative olfactory conditioning


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 56

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-56


title: HCC70 DAPT 8h #1


title: HCC70 FC 8h #3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 57

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-57


title: HCC70 DAPT 8h #2


title: t821-2_LSCs

city: Nottingham

first: Sophie

middle: G

last: Kellaway

department: School of Medicine

institute: University of Nottingham

data_processing:
Raw paired-end reads were processed with Trimmomatic v0.39 to remove sequencing adaptors and low-quality sequences. The processes reads were then aligned to the human genome (version hg38) using Hisat2 v2.2.1 with default parameters.
Gene expression from sorted LSC and blast experiments were calculated as fragments per kilobase of transcript per million mapped reads (FPKM) using Stringtie v2.1.3 with default parameters and gene models from Ensembl as the reference transcriptome. Only protein-coding genes that were expressed with an FPKM value > 1 in either the LSC or blast samples were retained for further analysis. FPKM values were normalized using upper-quartile normalization and further log2-transformed with a pseudocount of 1 added before transformation. A gene was considered to be either LSC or blast specific if it had a fold-change > 1 between cell types.
Counts from all other RNA-Seq experiments were obtained using featureCounts from the Subread package v2.0.1 using the options -p -B -s2 and gene models from refSeq as the reference transcriptome. Only genes with at least 50 counts in at least one sample were retained for further analysis. Counts were normalized using the edgeR package in R v4.1.0, and differential gene expression analysis was then carried out using limma-voom. For experments where replicates were available, a gene was considered to be differentially expressed if it had a fold-change of at least 2 and a Benjamini-Hochberg adjusted p-value < 0.1. In cases where no replicates were possible, only a 2-fold-change was used.
Assembly: hg38

source_name: CD34+CD38- leukemic stem cells

extract_protocol:
RNA was isolated using the Nucleospin RNA kit (Macherey-Nagel) for Kasumi-1, or RNeasy Plus micro kit (Qiagen) for patient/PDX cells
RNA libraries were generated using TruSeq stranded total RNA library prep kit with ribo-zero for Kasumi-1, or NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) for primary cells, per the manufacturer’s instructions
Libraries were sequenced on an Illumina NextSeq 550 run in paired end mode for 150 cycles

value: CD34+CD38- leukemic stem cells


title: HCC70 DAPT 8h #3


title: t821-2_blasts

source_name: CD34+CD38+ leukemic blasts

value: CD34+CD38+ leukemic blasts


title: HCC70 FC 8h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 61

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-61

value: TJ 1# CI-hnESC


title: t821-1_LSCs


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 55

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-55


title: HCC70 FC 8h #1

value: breast cancer


title: MDAMB468 Jagged1 8h #3


title: MDAMB468 Jagged1 8h #2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 54

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-54


title: t821-1_blasts


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 53

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-53


title: MDAMB468 Jagged1 8h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 59

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-59


title: MDAMB468 DAPT 8h #3


title: HCC70 Jagged1 8h #2


title: PDX_EV

source_name: patient derived xenograft CD34+ leukemic blasts

value: dnFOS uninduced


title: MDAMB468 DAPT 8h #2


title: MDAMB468 DAPT 8h #1


title: PDX_dnFOS

value: patient derived xenograft CD34+ leukemic blasts

value: dnFOS induced


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 52

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-52


title: MDAMB468 FC 8h #3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 51

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-51


title: HCC1187 DAPT 8h #1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 50

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-50


title: MDAMB468 FC 8h #1


title: MDAMB468 FC 8h #2


title: PBSC_EV

source_name: CD34+ peripheral blood stem cells

value: CD34+ peripheral blood stem cells


title: HCC1187 Jagged1 8h #1

value: JAG1  (ligand)


title: PBSC_dnFOS


title: 2388784_Cee2-2

city: Memphis

first: Beisi

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Paired-end sequencing was performed using Novaseq Illumina sequencer with read length capacity of 100 bps.
The read alignment to the human reference genome(hg38) was performed using STAR (version 2.7).
Gene level quantification was determined using RSEM (version 1.3.1).
Assembly: hg38

growth_protocol: MEG-01 cells were cultured in Roswell Park Memorial Institute (RPMI, Gibco) media supplemented with 10% fetal bovine serum (FBS) and 2mM glutamine in a humidified incubated at 37°C supplied with 5% CO2.

extract_protocol:
RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina PN 20020595). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: MEG-01 cells were differetiated with Phorbol 12-myristate 13-acetate (PMA, 100 nM) with or without Ceefourin 2 (20 µM) for 48 hours.

value: Human megakaryoblast cell line

value: Ceefourin 2 (48hrs)


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 49

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-49

value: pluripotent stem cell


title: HCC1187 FC 8h #1

value: FC


title: 2388782_PMA_cee2-2

value: PMA+Ceefourin 2 (48hrs)


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 48

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-48


title: Kasumi_dnFOS_Rep2


title: Kasumi_dnFOS_Rep1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 47

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-47


title: Kasumi_CTRL_Rep2


title: 2388783_Cee2-1


title: 2388781_PMA_cee2-1


title: Kasumi_CTRL_Rep1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 46

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-46


title: 2388779_PMA-1

value: PMA (48hrs)


title: 2388780_PMA-2


title: 2388778_UT-2

value: Untreated


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 45

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-45


title: 2388777_UT-1


title: Kasumi_dnFOS

library_source: genomic

data_processing:
DNaseI sequencing reads were processed with Trimmomatic v0.39 to remove sequencing adaptors and low-quality reads. Trimmed reads were aligned to the human genome (version hg38) using Bowtie2 v2.3.5.1 using the setting --very-sensitive-local. PCR duplicates were removed using the MarkDuplicates function in Picard 2.21.1. Peaks were called using MACS2 v2.2.7.1 using the settings -q 0.0005 -B --trackline --nomodel --shift -100 --extsize 200.
Assembly: hg38
Supplementary files format and content: BedGraph pileups produced by MACS2
Library strategy: DNase1-seq

molecule: genomic DNA

extract_protocol:
DNaseI digestions were performed as in (Bert AG et al., MCB, 2007). Cells were permeabilized in DNaseI resuspension buffer (60mM KCl, 10 mM Tris pH7.4, 15 mM NaCl, 5 mM MgCl2 and 300 mM sucrose) and then DNaseI diluted in dilution buffer (60mM KCl, 0.4% NP40, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH 7.4 and 2mM CaCl2 was added and incubated at 22°C for exactly 3 minutes. The digestion was terminated by adding cell lysis buffer (300 mM Sodium Acetate, 10 mM EDTA pH 7.4, 1% SDS and 1 mg/ml proteinase K). DNA was purified using phenol-chloroform extraction.
Library preparation was performed using the KAPA HyperPrep kit (Roche) on extracted DNA with size selection for 200-300 bp fragments
Libraries were sequenced on an Illumina NextSeq 550 run in single end mode for 75 cycles


title: Kasumi_CTRL


title: MGI3779_C1

city: St. Louis

first: Benjamin

last: Humphreys

state: Missouri

address: 4523 Clayton Ave,

department: Nephrology

institute: Washington University School of Medicine in St. Louis

description: Spaital Data FFPE Sections

data_processing:
Samples run through SpaceRanger Analysis pipeline to perform sample demultiplexing, image alignment, barcode processing, and gene counting.
Assembly: Human Genome
Supplementary files format and content: High Resolution Images and CSV Files

source_name: Female Kidney Cortex AKI

extract_protocol:
5um Tissue sections placed on Visium slides for probe binding and mRNA extraction using Visium V1.0 chemistry
Visium FFPE V1.0 Transcriptome Probe panels amplified using manufacturing protocol
Double ended amplification of Transcriptome probe panels covering a spatial barcode and UMI regions of tissue specific spots

value: Female Kidney Cortex AKI

value: female

tag: disease

value: AKI


title: MGI3779_A1

description: Spaital Data FFPE Sections

source_name: Male Kidney Cortex CKD

value: Male Kidney Cortex CKD

value: male

value: CKD


title: RUNX1_dnFOS

data_processing:
ChIP-sequencing reads were processed with Trimmomatic v0.39 to remove sequencing adaptors and low quality reads. Trimmed reads were aligned to the human genome (version hg38) using Bowtie2 v2.3.5.1 using the setting --very-sensitive-local. PCR duplicates were removed using the MarkDuplicates function Picard v2.21.1. Peaks were called using MACS2 using the settings -q 0.01 -B --trackline.
Assembly: hg38
Supplementary files format and content: BedGraph pileups produced by MACS2

extract_protocol:
Between 2 and 20 x106 cells (number is antibody dependent) were crosslinked following 72 hours of dnFOS induction with doxycycline, using 1% formaldehyde for 10 minutes at room temperature. For GATA2 and FOS cells were double crosslinked, by adding 415 µg/ml Di(N-succinimidyl) glutarate for 45 minutes prior to formaldehyde crosslinking. Cells were lysed and nuclei extracted using lysis buffer (10 mM HEPES pH 8.0, 10 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.25% Triton X-100, protease inhibitor cocktail (PIC) 1:100) followed by nuclear lysis buffer (10 mM HEPES pH 8.0, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.01% Triton X-100, 200mM NaCl, PIC 1:100). Nuclei were sheared to around 100-600 bp in sonication buffer (25 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.25% SDS, PIC 1:100), using a Picoruptor (Diagenode) for between 4 and 16 cycles of 30s on/30s off (cycle number dependent on  cell number and crosslinking). Sheared chromatin was diluted in IP buffer (25 mM Tris 1M pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 7.5% Glycerol, PIC 1:1000). Dyanbeads protein G were pre-incubated with antibodies against FOS, CEBPA, RUNX1, RUNX1-ETO, PU.1 GATA2, H3K27ac, H3K9acS10P or H3K4me3 for 2 hours at 4°, then added to the chromatin. Chromatin and antibody-beads mixture were incubated for between 4 and 18 hours (antibody dependent) at 4°. Beads were then washed sequentially: once with buffer 1 (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), twice with buffer 2 (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), once with buffer 3 (10 mM Tris pH 8.0, 250 mM LiCl, EDTA pH 8.0, 0.5% NP-40, 0.5% Sodium deoxycholate), twice with buffer 4 (10 mM Tris pH 8.0, 50 mM NaCl, 1 mM EDTA pH 8.0). Enriched DNA was eluted from the beads with 100 mM sodium bicarbonate and 1% SDS. Crosslinks were reversed with 25 µg Proteinase K for 16 hours at 65°C and DNA was purified using AmpureXP beads (Beckman Coulter). Enrichment was confirmed using qRT-PCR with known positive and negative binding sites for each protein target
Library preparation was performed using the KAPA HyperPrep kit (Roche) on extracted DNA with size selection for 200-500 bp fragments
Libraries were sequenced on an Illumina NextSeq 550 run in single end mode for 75 cycles

tag: antibody

value: RUNX1 (Abcam Cat# ab23980, RRID:AB_2184205)


title: MGI3535_D1

description: Spaital Data FFPE Sections

source_name: Female Kidney Cortex Healthy

value: Female Kidney Cortex Healthy

value: healthy


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 42

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-42

value: TJ 1# CI-hnESC


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 43

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-43


title: MGI3535_C1

description: Spaital Data FFPE Sections

source_name: Male Kidney Cortex Healthy

value: Male Kidney Cortex Healthy


title: MGI3779_B1

description: Spaital Data FFPE Sections


title: MGI3535_B1

description: Spaital Data FFPE Sections


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 41

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-41


title: Control, AJDV174, Multiome ATAC

city: Philadelphia

first: Parker

last: Wilson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description:
genomic DNA
10x Genomics Single Cell Multiome ATAC + Gene Expression

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellranger-atac v2.1 or cellranger-arc v2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For snATACseq: A target of 10,000 nuclei were loaded onto each lane. Sample index PCR was performed at 12 cycles. Libraries were sequenced on an Illumina Novaseq instrument, demultiplexed with bcl2fastq, and counted with cellranger-atac v2.0 (10X Genomics) using the refdata-cellranger-arc-GRCh38-2020-A-2.0.0 reference.
For single nucleus multiomes: A target of 10,000 nuclei were loaded onto each lane. Sample index PCR was performed at 12 cycles. Libraries were sequenced on an Illumina Novaseq instrument, demultiplexed with bcl2fastq, and counted with cellranger-atac v2.0 (10X Genomics) using the refdata-cellranger-arc-GRCh38-2020-A-2.0.0 reference.
Assembly: GRCh38
Supplementary files format and content: fragment files, filtered  barcode matrices, and single cell metrics files

source_name: Kidney cortex

extract_protocol:
For single nucleus multiomes, samples were cut into < 2 mm pieces and homogenized using a Dounce homogenizer with the loose head pestle (885302-0002; Kimble Chase) in 2 ml of Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) with protease inhibitor (5892791001; Roche) at 4°C. Samples were then filtered through a 200μm cell strainer (43-50200; pluriSelect) and homogenized in a Dounce homogenizer with the tight head pestle. Samples were incubated on ice for 5 minutes in 4 ml of EZ Lysis buffer, then filtered through a 40μm cell strainer (43-50040; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The resuspended pellet was then washed with 4ml of lysis buffer and incubated for 5 minutes at 4°C. The sample was centrifuged again and resuspended in Diluted Nuclei Buffer (PN-2000153; 10X Genomics) and filtered through a 5μm cell strainer (43-50005; pluriSelect). After counting, nuclei suspensions were diluted as needed to target 10,000 nuclei per lane and loaded into a thermal cycler to begin the transposition reaction. The manufacturer’s protocol was followed for the completion of library preparation. For snATAC-seq, samples were chopped into < 2 mm pieces, homogenized with a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) with protease inhibitor (5892791001; Roche) and incubated on ice for 5 min. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500 × g for 5 min at 4 °C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 min. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10 × Genomics, PN-2000153). The suspension was then filtered through a 5-μm cell strainer (43-50005-03, pluriSelect) and counted. After counting, nuclei suspensions were diluted to target 10,000 nuclei per lane and loaded into a thermal cycler to begin the transposition reaction. The manufacturer’s protocol was followed for the completion of library preparation.
Libraries were generated according to the manufacter’s instructions for either single cell multiome ATAC + gene expression OR single cell ATAC.
single cell multiome ATAC + gene expression OR single cell ATAC sequencing

value: Kidney cells

value: Kidney cortex

value: Male

tag: age


title: RUNX1_CTRL

value: dnFOS uninduced


title: MGI3535_A1

description: Spaital Data FFPE Sections


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 39

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-39

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 40

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-40


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 4

city: Atlanta

first: Timothy

last: Gershon

state: Georgia

address: 201 Dowman Dr

institute: Emory University

data_processing:
Raw sequence data were processed in a Linux environment using Drop-seq Tools V1.13. (https://github.com/broadinstitute/Drop-seq/releases) to generate a digital expression (DGE) matrix
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code:https://github.com/malawsky/Gershon_single-cell
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: digital expression matrix

source_name: medulloblastoma tumor

extract_protocol:
Brains were cut in half sagittally and one half was drop-fixed in 4% paraformaldehyde for IHC, and tumor from, the other half cerebellum was collected for Drop-Seq. Cells from the tumor were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18.
Drop-Seq 3' biased cell-indexed cDNA libraries were prepared according to the Drop-seq protocol V3.1 (ref.32), with full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL. to high-throughput sequencing facility that does their own QC before running samples. cDNA libraries were prepared for sequencing using standard Illumina protocols (Multiplexed samples using nextera indexes so that libraries could be pooled)

value: medulloblastoma tumor

value: heterogeneous

value: Math1-Cre/SmoM2/Bcl2l1 f/+


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 5


title: PU1_dnFOS

value: dnFOS induced

value: PU1 (Santa Cruz Cat# sc-352, RRID:AB_632289)


title: H3K9acS10P_shRE

value: shRUNX1-ETO induced

value: H3K9acS10P (Abcam Cat# ab12181, RRID:AB_298913)


title: PU1_CTRL


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 44

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-44


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 3


title: Control, AJDV174, Multiome RNA

description:
nuclear RNA
10x Genomics Single Cell Multiome ATAC + Gene Expression


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 37

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-37


title: MGI3779_D1

description: Spaital Data FFPE Sections

value: Male Kidney Cortex CKD

value: male

value: CKD


title: Control, AJDL105, Multiome ATAC

value: Female


title: H3K9acS10P_CTRL

value: shRUNX1-ETO uninduced


title: Control, AJDL105, Multiome RNA

value: Kidney cells


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 7


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 36

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-36

value: TJ 1# CI-hnESC


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 35

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-35


title: Control, AIL5160, Multiome ATAC

value: Kidney cortex


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 9

value: Math1-Cre/SmoM2/Bcl2l1 f/f


title: H3K4me3_CTRL

value: dnFOS uninduced

value: H3K4me3 (Millipore Cat# 04-745, RRID:AB_1163444)


title: Control, AIL5160, Multiome RNA


title: Math1-Cre/SmoM2/Bcl2l1 f/f 2

value: medulloblastoma tumor

value: heterogeneous


title: H3K27me3_CTRL


title: H3K27me3_dnFOS

value: dnFOS induced


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 38

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-38

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 34

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-34


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 33

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-33


title: Control, AIIM164, Multiome ATAC


title: Math1-Cre/SmoM2/Bcl2l1 f/f 1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 32

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-32


title: H3K27ac_dnFOS

value: H3K27ac (Abcam Cat# ab4729, RRID:AB_2118291)


title: Chronic Kidney Disease, 091422Nx, Multiome ATAC

value: Male


title: Math1-Cre/SmoM2/Bcl2l1 f/f 15


title: H3K27ac_CTRL


title: Math1-Cre/SmoM2/Bcl2l1 f/+ 8

value: Math1-Cre/SmoM2/Bcl2l1 f/+


title: Chronic Kidney Disease, 091422Nx, Multiome RNA


title: H3K4me3_dnFOS


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 31

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-31


title: GATA2_dnFOS


title: Math1-Cre/SmoM2/Bcl2l1 f/f 14


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 30

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-30


title: Chronic Kidney Disease, 090922Nx, Multiome ATAC


title: GATA2_CTRL


title: LPS + HS 2

first: Thirumala-Devi

last: Kanneganti

state: TN

institute: St. Jude Children's Research Hospital

data_processing:
Next-generation sequencing (NGS) of the PCR-amplified, barcoded gRNAs was performed to quantitatively identify gRNAs that were enriched in the surviving pool of cells. Because the presence of a gRNA should delete the corresponding gene in that cell, enriched gRNAs were expected to represent genes where deletion rescues the cells from LPS plus HS-mediated cell death, suggesting they are positive regulators of the cell death. Using the MAGeCK pipeline, the log2fold change was estimated with significance levels for the genes in the CRISPR screen. The genes with positive fold change were expected to be important for cell death.
Assembly: Barcoded sequences were mapped to the mouse Brie CRISPR KO library, a gift from David Root and John Doench (Addgene #73632 and #73633).
Supplementary files format and content: The .txt processed data file contains raw read counts for each sample.
Library strategy: NGS of the PCR-amplified, barcoded gRNAs

source_name: iBMDMs

growth_protocol: Immortalized BMDMs (iBMDMs) were cultured in DMEM (Gibco, 11995073) supplemented with 10% HI-FBS.

extract_protocol:
Total genomic DNA was isolated using NucleoSpin® Blood kits (Takara Bio Inc., USA; 740954 and 740950) and the concentrations of the isolated gDNA samples were measured using NanoDrop (Thermo Fisher Scientific, USA).
The Mouse Brie CRISPR KO library carrying four gRNAs for each gene to cover the entire genome was a gift from David Root and John Doench (Addgene #73632 and #73633). The plasmid library was amplified and validated in the Center for Advanced Genome Engineering (CAGE) at St. Jude as described in the Broad GPP protocol, the only exception being the use of Endura DUOs electrocompetent E. coli cells. The St. Jude Hartwell Center Genome Sequencing Facility provided all NGS sequencing. Single end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina). Validation to check gRNA presence and representation was performed using calc_auc_v1.1.py (https://github.com/mhegde/) and count_spacers.py84. Viral particles were produced by the St. Jude Vector Development and Production laboratory using co-transfection of the lentiviral packaging plasmids along with the Brie library in the 293T cells. CRISPR KO screens were analyzed using Mageck-Vispr v0.5.7.

treatment_protocol: Two replicates of an adequate number of cells were used as control to obtain a representation (screen depth) of > 500 cells for each sgRNA of the library, and a similar number of cells from the same batch of virus preparation were stimulated with LPS priming for 2 h, then incubated at 43 °C for 1 h to induce HS. After 24 h, the media was removed, and cells in the unstimulated and stimulated conditions were washed with PBS to remove the non-adherent dead cells, leaving only the adherent surviving cells for downstream analyses.

value: iBMDMs

value: WT

value: LPS + HS


title: FOS_shRE_shRE

value: shRUNX1-ETO induced

value: cFOS (Invitrogen Cat# MA5-15055, RRID:AB_10984728)


title: LPS + HS 1


title: Control, AIIM164, Multiome RNA

value: Kidney cells

value: Female


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 29

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-29

data_processing:
For bulk RNA-seq data, raw reads of fastq format from this study were first processed through in-house perl scripts to obtain clean reads by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw reads. Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. For single cell RNA-seq data, data of day 6 blastoids was pre-processed through Trimmomatic software to remove adapters and to drop low quality reads or short reads below 26 bps. Other single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq and scRNAseq (Smartseq2) count table: gene by cell expression matrix generated with STAR; scRNAseq (10X) count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
For bulk RNA-seq, total RNAs were collected and isolated from cells using RNAiso Plus (Takara). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina following manufacturer’s recommendations. For scRNA-seq, CI-hnESCs and day 2 aggregates were dissociated and sorted by flow cytometer for Smart-seq2 library construction and the libraries were sequenced on MGISEQ2000 (MGI Tech) platform to generate 100-bp paired-end reads. Day 3, day6 blastoids and the blastoids upon removing MEK/BRAF inhibition from Aggrewell were manually picked and polled with a mouth pipette, washed once with DPBS and then dissociated with 0.25% trypsin-EDTA (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Attached cultured bE14 blastoids were first rinsed once with DPBS and then treated with cold DPBS and incubated in 4°C for 10-20min to allow breaking of the matrix. When the samples became mobile under a microscope upon gentle shaking, the bE14 blastoids were transferred to a clean tube using a cut-tip and dissociated with 0.25% trypsin-EDTA at 37 °C in 20%O2 and 5% CO2 incubator for 30 min. Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TJ 1# CI-hnESC


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 28

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-28


title: Chronic Kidney Disease, 090922Nx, Multiome RNA

value: Kidney cortex


title: Math1-Cre/SmoM2/Bcl2l1 f/f 19

value: Math1-Cre/SmoM2/Bcl2l1 f/f


title: FOS_shRE_CTRL

value: shRUNX1-ETO uninduced


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 27

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-27


title: Chronic Kidney Disease, CKD_5, snATACseq

description:
genomic DNA
10x Genomics Single Cell ATAC v1


title: Untreated 2


title: Untreated 1


title: FOS_minusBEV

value: Control


title: FOS_plusBEV

value: Bevacizumab


title: Chronic Kidney Disease, CKD_4, snATACseq


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 25

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-25

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 26

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-26


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 24

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-24


title: Chronic Kidney Disease, CKD_2, snATACseq


title: FOS_dnFOS_plusdnFOS

value: dnFOS induced


title: FOS_dnFOS_CTRL

value: dnFOS uninduced


title: activated Fgl2 KO OT-I 4

first: Kelsey

last: Bennion

address: 201 Dowman Drive

department: Surgery

description: Naive FGL2KO OT-I 4

data_processing:
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count. Raw counts were analyzed in R using the DESeq2 and clusterProfiler packages from Bioconductor. Genes with a CPM <1 in any of the samples were excluded.
Differentially expressed gene analyses were performed and differentially expressed genes were processed through GSEA.HALLMARK gene sets and C7 immunological signature gene sets from the Mouse Molecular Signatures Database (MSigDB) were used.
Specifically, "HALLMARK_APOPTOSIS” and “GSE41867_MEMORY_VS_EXHAUSTED_CD8_TCELL_DAY30_LCMV_UP” are shown.
A p-value < 0.05 adjusted with the Benjamini-Hochberg correction was considered significant. Adjusted p-value and enrichment scores are shown.
complete
Assembly: Alignment was performed using STAR version 2.9.7a and transcripts were annotated using GRCm38_102.
Supplementary files format and content: Tab delimited text file contains raw counts for all samples.

source_name: spleen

growth_protocol: B16-OVA cells were passaged 2x prior to injection at 3e5 cells/mouse on day 0 into mice. OT-I mice were sacrificed on day -1, cell count was determined via flow cytometry and injected at 1e6 cells/mouse

extract_protocol:
On day 14 post B16-OVA challenge, mice were sacrificed and spleens were harvested and homogenized. After homogenization, cells were stained and sorted on CD3, CD8, and Thy1.1 on an Aria cell sorter prior to RNA extraction. ~10,000 CD3+CD8+Thy1.1+ cells were sorted, lysed, and then extracted using the RNAeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a Fragment Analyzer (Agilent) and then 1 ng of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

treatment_protocol: not applicable

value: spleen

value: MHC Class I restricted CD8 T cell

value: Fgl2 KO

value: activated


title: activated Fgl2 KO OT-I 3

description: Naive FGL2KO OT-I 3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 23

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-23


title: Chronic Kidney Disease, CKD_1, snATACseq


title: ETO_dnFOS

value: RUNX1-ETO (Diagenode Cat# C15310197, RRID:AB_2891230)


title: DCP2 XRN1 KO, Slavoff

data_processing:
From 3'RACE-Seq raw reads, adapters were removed with cutadapt (v4.0) and sequences shorter than 20 nt were discarded. Low-quality nucleotides from 3’ end of reads were removed using ConDeTri (v2.3) with the following settings hq=37, ml=1, mh=5 and minlen=40.
Specific amplicons were selected based on a sequence of forward primers with bbduk from BBTools. For further analyses only reads containing a unique molecular identifier (UMI) in length 15 nt and delimiter (GTCAG) on 5’ end of read R2 were kept.
UMI and delimiter sequences were removed from read sequences and moved to the read name with the extract mode of UMI-tools (v1.1.2). As references for control transcripts (GAPDH, ACTB, PABPC4) were used gene sequences provided by the Ensembl database (GRCh38).
Reads were mapped to reference using STAR (v2.7.9a) with soft-clipping allowed (with the following settings outFilterMatchNmin 20, outFilterScoreMinOverLread 0.1 and outFilterMatchNminOverLread 0.1). Mapped reads were deduplicated with UMIcollapse.
For pair of reads in which both reads mapped non-templated tails and their nucleotide compositions were retrieved from the sam file from the soft-clipped fragments of read R2 using the previously published script (get_softclipped_reads_from_sam.pl) [Warkocki et al., 2018 (https://doi.org/10.1016/j.cell.2018.07.022)]. For pair of reads in which only R1 mapped due to presence of long homopolymeric sequence in the read R2 length sequence of tails were extracted directly from the read R2.
Statistical analyses were performed in R (v4.2). In these analyses were included reads with no tails and those with the following composition: tails containing only A (A tails), only U (U tails), A with U on their 3’ (AU tails). In AU tails were allowed tails with U between A but not at the beginning of the tail. All operations on bam and sam files were performed with samtools (v1.13).
Assembly: Gene sequences of GAPDH, ACTB and PABPC4 from GRCh38 and LINE-1 sequence from the L1.3 nomarker L1 reporter plasmid
Supplementary files format and content: tails_X1KO.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: tails_X1D2KO.txt; tab-delimited text file containing tails sequences and lengths
Supplementary files format and content: spikein.txt; tab-delimited text file containing tails lengths of Spikes-IN
Library strategy: 3' RACE-seq to assess non-templated 3' ends

growth_protocol: 293T cells were grown in DMEM (Gibco ref no. 41966052) supplemented with 9% FBS (Gibco ref no. 10270106), and penicillin/streptomycin at 1x concnetration (Merck ref. no. P4458) at 37C in an atmosphere supplemented to 5% CO2 in a humidified incubator

extract_protocol:
~42-48hrs post-transfection total RNA was extracted using home-made Trizol reagent (according to Chomczynski and Sacchi, 1987, 10.1016/0003-2697(87)90021-2), 1ml trizol was used per 1 well, following precipitation RNA was repurified following treatment with proteinase K at 20ng per microliter in a Tris-buffered 1% SDS solution with 2mM EDTA and 100mM NaCl, purified by phenol-chloroform extraction, then samples  were deprived of DNA by treatment with Tubro DNase (Ambion) and again purified by phenol-chloroform extraction
For the 12 home-made 293T cell lines (this paper) including the wild-type and the XRN1 KO each biological replicate was a single technical replicate (one index per cell line). For the 4 acquired cell lines (10.1021/acs.biochem.0c00069) three technical replicates (starting at the RT step) of each biological replicate were performed and marked with a different index. Synthetic spike-ins had defined index sequences see Supplementary Table 1. Libraries were prepared as described in (10.1016/j.cell.2018.07.022) with modifications. Briefly, 2µg total RNA after DNase treatment were ligated with 100pmole RA3_15N 5’ preadenylated adapter comprising a 15-nucleotide unique molecular identifier (UMI) in 20µl of 1x enzyme-supplied buffer, 15% PEG 8000 by T4 RNA ligase 2 truncated (NEB, M0242) for 18h at 18˚C. Nucleic acids of each reaction were purified using 20µl Ampure XP magnetic beads, eluted in and used for reverse transcription in 20µl with 100pmoles RPI primer (containing an 6-nucleotide index) using Superscript III (ThermoScientific) enzyme according to the manufacturer’s protocol (2mins at 50˚C, 30mins at 45˚C, 15mins at 85˚C), followed by purification on 1,25 volume of Ampure XP magnetic beads. Nested PCR was performed with PrimeSTAR GLX polymerase (TaKaRa, R050B) since it proofed best at elongating long poly(A) tracts (as compared to Phusion of ThermoScientific and Q5 polymerases of NEB; not shown). First round PCR were performed in 25µl with an equivalent of 500ng input total RNA (input to RT step) per reaction. Primers at 0,35µM were either of: 3UNP1f, GAPDH_3R0, PABPC4_3R0 for L1, GAPDH, and PABPC4 respectively, universal reverse primer, RP_uni, was added at 0,4µM. Reactions were carried out: 98˚C 2mins, [98˚C 12sec, 52˚C 15sec, 70˚C 40sec]x21, 68˚C 1min, 1/5 of each reaction was used without purification as template for second round PCR with 0,36µM transcript-specific forward primer: L1_NGS4, or GAPDH_NGS, or PABPC4_NGS, and 0,4µM universal reverse primer RP_uni. PCRs were carried out: 98˚C 2mins, [98˚C 12sec, 55˚C 15sec, 70˚C 30sec]x21, 70˚C 1min. The reactions were purified on 1,3 volume Ampure XP magnetic beads, eluted, measured and diluted to ~5ng/µl, and analysed on TapeStation (Agilent). Before running on Illumina Novaseq libraries were quantitated by qPCR to adjust the number of reads to ~3-5 MRds for each transcript for each biological/technical replicate (each index).

treatment_protocol: ~200,000 to 350,000 cells were transfected in wells of a 6-well plate with 1microgram of L1.3 nomarker L1 reporter plasmid using Lipofectamine 2000, 5microliters per well.


title: activated Fgl2 KO OT-I 2

description: Naive FGL2KO OT-I 2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 19

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-19


title: DCP2 KO, Slavoff


title: ETO_CTRL


title: unchallenged_Fgl2 KO OT-I 1

description: FGL2KO OT-I 1

value: unchallenged


title: XRN1 KO, Slavoff


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 20

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-20


title: WT, 293T parental (Yale)


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 21

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-21


title: unchallenged_Fgl2 KO OT-I 2

description: FGL2KO OT-I 2


title: WT, 293T parental (EDI/Waw)


title: Chronic Kidney Disease, CKD_3, snATACseq

value: Kidney cells

value: Male


title: Kas_shRE_Ctrl

data_processing:
ATAC sequencing reads were processed with Trimmomatic v0.39 to remove sequencing adaptors and low-quality reads. Trimmed reads were aligned to the human genome (version hg38) using Bowtie2 v2.3.5.1 using the setting --very-sensitive-local. PCR duplicates were removed using the MarkDuplicates function in Picard 2.21.1. Peaks were called using MACS2 v2.2.7.1 using the settings -q 0.0005 -B --trackline --nomodel --shift -100 --extsize 200.
Assembly: hg38
Supplementary files format and content: BedGraph pileups produced by MACS2

extract_protocol:
Omni ATAC-seq was performed as in (Corces et al., 2017). Briefly, cells were washed in ATAC resuspension buffer (RSB) (10 mM Tris-HCl pH7.5, 10 mM NaCl and 3 mM MgCl2) and then lysed for 3 minutes on ice in RSB buffer with 0.1% NP-40, 0.1% Tween-20. Then the cells were washed with 1 ml of ATAC wash buffer consisting of RSB with 0.1% Tween-20. Nuclei were resuspended in ATAC transposition buffer consisting of 25μl TD buffer and a concentration of Tn5 transposase enzyme (Illumina) related to the number of input cells up to 2.5 μl, 16.5 μl PBS, 5 μl water, 0.1% tween-20 and 0.01% digitonin and then incubated on a thermomixer at 37°C for 30 minutes.
The transposed DNA was then amplified by PCR amplification up to ¼ of maximum amplification, as assessed by a qPCR side reaction
Libraries were sequenced on an Illumina NextSeq 550 run in single end mode for 75 cycles


title: CEBPA_dnFOS

value: CEBPA (Santa Cruz Cat# sc-61X, RRID:AB_631233)


title: unchallenged_Fgl2 KO OT-I 3

description: FGL2KO OT-I 3


title: WT, B17


title: CEBPA_CTRL


title: activated WT OT-I 4

description: Naive WT OT-I 4

value: WT


title: WT, B11


title: activated WT OT-I 2

description: Naive WT OT-I 2


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 18

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-18

value: TJ 1# CI-hnESC


title: activated WT OT-I 3

description: Naive WT OT-I 3


title: Kas_shRE_Dox

value: shRUNX1-ETO induced


title: WT, B7


title: unchallenged_Fgl2 KO OT-I 4

description: FGL2KO OT-I 4


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 22

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-22


title: activated Fgl2 KO OT-I 1

description: Naive FGL2KO OT-I 1


title: t821-2_LSCs

value: CD34+CD38- leukemic stem cells


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 15

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-15


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 14

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-14


title: activated WT OT-I 1

description: Naive WT OT-I 1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 16

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-16


title: t821-1_LSCs


title: WT, B5


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 13

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-13


title: unchallenged_WT OT-I 4

description: WT OT-I 4


title: t821-1_blasts

value: CD34+CD38+ leukemic blasts


title: WT, B1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 12

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-12

value: pluripotent stem cell


title: PDX_dnFOS

value: patient derived xenograft CD34+ leukemic blasts

value: Dominant negative FOS


title: unchallenged_WT OT-I 3

description: WT OT-I 3

value: spleen


title: PDX_EV

value: Empty vector control


title: t821-2_blasts


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 11

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-11


title: XRN1 KO, B9


title: unchallenged_WT OT-I 1

description: WT OT-I 1

value: MHC Class I restricted CD8 T cell


title: Stage 13-16 Embryos, Replicate 2, scRNA-seq

city: Baltimore

first: Da

last: Peng

state: Maryland

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

data_processing:
Alignment and gene quantification were done using CellRanger (version 6.1.2).
Biological replicates were combined using Seurat and underwent bacth correction using Harmony.
Assembly: dmel r6.33
Supplementary files format and content: raw counts matrix
Supplementary files format and content: seurat object with both biological replicates

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
Embryos were collected and aged to appropriate stages on apple juice caps seeded with yeast paste. Embryos were harvested in collection baskets, soaked in 50% bleach for 3 minutes to remove the outer chorion, then rinsed thoroughly and transferred to Dounce homogenizers containing 1 ml ice-cold 1X PBS. Embryos were disrupted using 20 strokes (up and down) of the loose “B” pestle. The material was then transferred to a 1.5 ml microfuge tube and pelleted by a3minute spin in atabletop centrifuge set at4000 RPM at 4°C. Supernatant was removed and material was resuspended in 1 ml fresh ice-cold 1X PBS, then passaged 20 times through a 22 gauge needle, and 4X through a 23 gauge needle.The cell suspension is then passed through a 40μm cell strainer into a 1.5 mL microcentrifuge tube.Cells were pelletedby a 3 minute spin in a tabletop centrifuge set at 6000 RPM at4°C, then resuspended in 100μL1X ice cold PBS and immediately brought to the sequencing center for viability counts and library preparation for 10X Genomics sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: whole embryo

value: OregonR

tag: developmental stage

value: stage 13-16


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 10

first: Jinyi

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-10


title: XRN1 KO, B8

first: Zbigniew


title: Stage 13-16 Embryos, Replicate 1, scRNA-seq


title: 2298891_C4KOBMCD41NO3

last: Xu

data_processing:
Paired-end sequencing was performed using Novaseq Illumina sequencer with read length capacity of 100 bps.
The read alignment to the human reference genome(mm10) was performed using STAR (version 2.7).
Gene level quantification was determined using RSEM (version 1.3.1).
Assembly: mm10

source_name: megakaryocytes

value: megakaryocytes


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 9

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-9

source_name: TJ 1# CI-hnESC


title: XRN1 KO, B6


title: 2298889_C4KOBMCD41NO1


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 8

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-8


title: 2298890_C4KOBMCD41NO2


title: XRN1 KO, B15


title: unchallenged_WT OT-I 2

description: WT OT-I 2

value: unchallenged


title: Stage 10-12 Embryos, Replicate 1, scRNA-seq

value: stage 10-12


title: XRN1 KO, B3


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 7

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-7


title: 2298888_WTBMCD41NO3

value: WT


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 6

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-6

value: TJ 1# CI-hnESC


title: 2298887_WTBMCD41NO2


title: Stage 10-12 Embryos, Replicate 2, scRNA-seq


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 5

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-5


title: XRN1 KO, B10


title: t821-2

data_processing:
Reads from single-cell RNA-Seq experiments were aligned to the human genome (version hg38) and quantified using the count function in CellRanger v3.1.0 from 10x Genomics and using gene models from Ensembl as the reference transcriptome.
Unique Molecular Identifier (UMI) count data was filtered for low quality cells by removing cells with less than 500 and more than 5000 detectable genes. Cells that had more than 20% of UMIs aligned to mitochondrial transcripts were also excluded from further analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated table of cell barcodes with inferred cell-cycle stage, cell-type and cluster assignments
Supplementary files format and content: HDF5 filtered feature barcode matrix file generated using CellRanger Count

source_name: CD34+CD38+ Leukemic blasts and CD34+CD38- Leukemic stem cells (pooled)

extract_protocol: Library generation for scRNA-Seq was performed by the genomics Birmingham sequencing facility using the Chromium Single Cell 3' library and gel bead kit v3 (10x Genomics). Libraries were pair-end sequenced on an Illumina NovaSeq 6000 using the cycle parameters recommended by 10x Genomics


title: Responding_Tumors, scRNA-seq

city: Haifa

middle: Jon

last: Cooper

address: 1 Efron St.

country: Israel

institute: Technion – Israel Institute of Technology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor (4T1 Breast Cancer)

extract_protocol:
The evaluation of GR1+ myeloid cells in responsive and non-responsive tumors was performed by a single-cell RNA sequencing (scRNA-seq). Briefly, 4T1P and 4T1M tumors were prepared as single cell suspensions. Subsequently, GR1+ cells were isolated by positive isolation (EasySep Mouse PE, Biolegend). The cells were than washed in PBS with 0.04% BSA and resuspended in 1000 cells/µL PBS.
RNA was extracted and immediately was acquired by the 10X Genomics single cell sequencing system, as per manufacture’s instruction.

value: Tumor (4T1 Breast Cancer)

value: BALB/c

value: 6-8 weeks old


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 4

city: Guangzhou

last: Wu

institute: Guangzhou Laboratory

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-4

value: pluripotent stem cell


title: t821-1

value: CD34+CD38+ Leukemic blasts and CD34+CD38- Leukemic stem cells (pooled)


title: Non-responding_Tumors, scRNA-seq

description: 10x Genomics


title: scRNA-seq (Smartseq2) of D0 Spontaneous Blastoids - cell 17

description:
SpontaneousBlastoid_D0andD2_count.csv
day0-blastoids-17


title: 2298886_WTBMCD41NO1