title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_wt

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

institute: CRG

description: Library name: Sample 56

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: S288C
Supplementary files format and content: MS Excel format; contains Dimsum fitness estimates, inferred growth rates and their corresponding errors for all libraries; see README tab for a description of all columns

organism: Saccharomyces cerevisiae

growth_protocol: For each library and assay (abundancePCA and bindingPCA) each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, saturated cells were diluted again to OD600nm = 0.05 in SC -URA/MET/ADE media and allowed to grow 5 generations until OD600nm = 1.6 at 30ºC and 200rpm. A fraction of the culture was then used to inoculate 400mL of competition media containing methotrexate at a starting OD600nm = 0.05, and the rest was harvested and pellets frozen and stored as INPUT.  Cells in competition media were allowed to grow for 5 generations, collected and frozen and stored as OUTPUT.

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 2 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 2 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.2 mL of NaOAc 3M and 4.4 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC at least for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (50 µL of QIAEX II beads, QIAGEN). The samples were washed twice with PE buffer and eluted twice by 125 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples in libraries 1-3 and containing a different barcode index in library 4. The reverse primer (3’ P7 Illumina adapter) differed by the barcode index  to be subsequently pooled together and demultiplex them after deep sequencing. All samples were pooled in an equimolar ratio and gel purified using the QIAEX II Gel Extraction Kit. The purified amplicon library pools were subjected to Illumina 150bp paired-end Nextseq500 (libraries 1-3) or Nextseq2000 (library 4) sequencing at the CRG Genomics Core Facility.


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_output_bio_rep_3

status: Public on Jul 25 2025

type: SRA

city: Barcelona

country: Spain

description: Library name: Sample 55

library_source: genomic

molecule: genomic DNA

tag: cell line


title: experiment3_0d_rep3

city: Hang Zhou

first: Wenya

last: Zhang

address: No. 600 Dunyu Road

country: China

institute: Westlake University

description:
Library name: Sample 32
column name in raw_counts_U_PA.xlsx: POS_3

library_source: transcriptomic

data_processing:
kallisto 0.46.2. R 4.0.5 and tximport 1.18.0 were used for alignment
Assembly: GCA_000572305.1 S. mediterranea reference transcriptome (smed_20140614)
Supplementary files format and content: csv files incude raw counts for each sample

molecule: total RNA

organism: Schmidtea mediterranea

source_name: planarian SiRNeoblast

growth_protocol: The culture medium, comprising KnockOut DMEM (ThermoFisher, 10829018), 100× non-essential amino acid solution (Gibco, 11140050), 100× vitamin solution (Gibco, 11120052), 100× sodium pyruvate (Gibco, 11360070), 100× Pen/Strep (Gibco, 15070063), and 20% heat-inactivated FBS (Sigma, F8318). 22℃, 5% CO2

extract_protocol:
2× lysis buffer (Plastech, XR2301) supplemented with RNase inhibitor (Vazyme, R301).
Reverse transcription was performed using 1M Betaine and LNA-modified TSO (template switching oligo). PCR amplification was performed with KAPA HiFi HotStart polymerase (Roche, KK2601) and ISPCR primers. The resulting PCR products were purified with AMPure XP bead (Beckman, A63881). Tagmentation was performed with Tn5 transposase (Vazyme, TD501), followed by indexing PCR with dual barcodes (i5/i7).

treatment_protocol: experiment1,  SiRNeoblasts were cultured on the flat substrate; experiment2,  SiRNeoblasts were cultured in the aggrewell plate or flat plate conditions for 1 day; experiment3, SiRNeoblasts were cultured in U-bottom plate or 100Pa PA gel or flat plate conditions for 1 day/2 days/3 days; experiment4, SiRNeoblasts were cultured in HFF1 feeder or MEF feeder or flat plate conditions for 1 day/3 days; experiment5, SiRNeoblasts were cultured in U-bottom plate-extract or U-bottom plate+extract  or flat -extract conditions for 1 day/3 days/7 days.

tag: cell type

value: planarian SiRNeoblast

tag: genotype

value: WT

tag: treatment

value: non cultured cells

tag: batch


title: SPC Mut4 AT2 CD44 pos

city: Philadelphia

first: Jeremy

last: Katzen

state: PA

address: 3450 Hamilton Walk, Stemmler Hall 216

country: USA

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
Bowtie2
Assembly: mm10
Supplementary files format and content: tab seperated files

organism: Mus musculus

source_name: Lung

extract_protocol:
Lungs were harvested from control and Sftpc mutant lungs, single cells suspension was prepared by mehcanical and enzymatic digetsion.  CD45+ and CD31+ cells were depleted using biotinylated antibodies followed by surface staining with antibody mix to identify CD44+ and CD44- AT2s. AT2 cells were identified as CD45-CD31-Epcam+CD104-CD200hi and then CD44+ or CD44-.. Dead cells were excluded by Dapi staining.
Libraries were prepared using Illumina stranded total RNA with Ribo-zero Plus kit accordine to manufacture instructions

tag: tissue

value: Lung

value: SP-C Mutant

value: OG TMX


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_output_bio_rep_2

description: Library name: Sample 54


title: SPC Mut3 AT2 CD44 pos


title: experiment3_0d_rep1

description:
Library name: Sample 30
column name in raw_counts_U_PA.xlsx: POS_1


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_output_bio_rep_1

description: Library name: Sample 53


title: experiment3_100Pa PA 3d_rep2

description:
Library name: Sample 29
column name in raw_counts_U_PA.xlsx: PA_3d_3

value: cells cultured 100Pa PAgel for 3d


title: experiment4_MEF 3d_rep2

description:
Library name: Sample 55
column name in feeder experiments counts.xlsx: 064-MEF3d-2

value: cells cultured on MEF feeder for 3d


title: experiment3_100Pa PA 3d_rep1

description:
Library name: Sample 28
column name in raw_counts_U_PA.xlsx: PA_3d_1


title: SPC Mut2 AT2 CD44 pos


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_input_bio_rep_3

description: Library name: Sample 52


title: experiment3_U 1d_rep1

description:
Library name: Sample 33
column name in raw_counts_U_PA.xlsx: U_1d_1

value: cells cultured in U plate for 1d


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_input_bio_rep_2

description: Library name: Sample 51


title: experiment3_100Pa PA 2d_rep1

description:
Library name: Sample 25
column name in raw_counts_U_PA.xlsx: PA_2d_1

value: cells cultured 100Pa PAgel for 2d


title: SPC Mut4 AT2 CD44 neg


title: SPC Mut1 AT2 CD44 pos


title: experiment3_100Pa PA 1d_rep3

description:
Library name: Sample 24
column name in raw_counts_U_PA.xlsx: PA_1d_3

value: cells cultured 100Pa PAgel for 1d


title: experiment3_100Pa PA 1d_rep1

description:
Library name: Sample 22
column name in raw_counts_U_PA.xlsx: PA1d_1


title: SPC Mut3 AT2 CD44 neg


title: experiment3_0d_rep2

description:
Library name: Sample 31
column name in raw_counts_U_PA.xlsx: POS_2


title: experiment3_100Pa PA 2d_rep2

description:
Library name: Sample 26
column name in raw_counts_U_PA.xlsx: PA_2d_2


title: libraryPDZ3_NC_bPCA_G05_DC_Na3_a2_input_bio_rep_1

description: Library name: Sample 50


title: experiment3_100Pa PA 2d_rep3

description:
Library name: Sample 27
column name in raw_counts_U_PA.xlsx: PA_2d_3


title: SPC Mut2 AT2 CD44 neg


title: experiment3_flat 3d_rep2

description:
Library name: Sample 20
column name in raw_counts_U_PA.xlsx: flat_3d_3

value: cells cultured in flat plate for 3d


title: experiment3_flat 3d_rep1

description:
Library name: Sample 19
column name in raw_counts_U_PA.xlsx: flat_3d_2


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_wt

description: Library name: Sample 49


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_output_bio_rep_3

description: Library name: Sample 48


title: SPC Mut1 AT2 CD44 neg


title: experiment3_flat 2d_rep3

description:
Library name: Sample 18
column name in raw_counts_U_PA.xlsx: flat_2d_3

value: cells cultured in flat plate for 2d


title: experiment3_flat 2d_rep2

description:
Library name: Sample 17
column name in raw_counts_U_PA.xlsx: flat_2d_2


title: experiment3_100Pa PA 1d_rep2

description:
Library name: Sample 23
column name in raw_counts_U_PA.xlsx: PA_1d_2


title: experiment3_flat 2d_rep1

description:
Library name: Sample 16
column name in raw_counts_U_PA.xlsx: flat_2d_1


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_output_bio_rep_2

description: Library name: Sample 47


title: WT4 AT2 CD44 pos

value: SP-C WT


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_output_bio_rep_1

description: Library name: Sample 46


title: experiment3_flat 3d_rep3

description:
Library name: Sample 21
column name in raw_counts_U_PA.xlsx: flat_3d_4


title: experiment3_flat 1d_rep3

description:
Library name: Sample 15
column name in raw_counts_U_PA.xlsx: flat_1d_3

value: cells cultured in flat plate for 1d


title: experiment3_flat 1d_rep2

description:
Library name: Sample 14
column name in raw_counts_U_PA.xlsx: flat_1d_2


title: WT3 AT2 CD44 pos


title: experiment3_flat 1d_rep1

description:
Library name: Sample 13
column name in raw_counts_U_PA.xlsx: flat_1d_1


title: WT2 AT2 CD44 pos


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_input_bio_rep_3

description: Library name: Sample 45


title: experiment2_flat 1d_rep1

description:
Library name: Sample 10
column name in raw_counts_aggrewell.xlsx: 064-F1


title: WT1 AT2 CD44 pos


title: experiment2_flat 1d_rep2

description:
Library name: Sample 11
column name in raw_counts_aggrewell.xlsx: 064-F2


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_input_bio_rep_1

description: Library name: Sample 43


title: libraryPDZ3_NC_aPCA_G05_DC_Na3_a1_input_bio_rep_2

description: Library name: Sample 44


title: WT4 AT2 CD44 neg


title: experiment2_aggrewell 1d_rep1

description:
Library name: Sample 7
column name in raw_counts_aggrewell.xlsx: 064-A1

value: cells cultured in aggrewell


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_wt

description: Library name: Sample 42


title: WT3 AT2 CD44 neg


title: experiment2_flat 1d_rep3

description:
Library name: Sample 12
column name in raw_counts_aggrewell.xlsx: 064-F3


title: experiment1_non-aggregating_2d_rep3

description:
Library name: Sample 6
column name in raw_counts.xlsx: 064-TS3

value: cells outside aggregates


title: experiment1_non-aggregating_2d_rep2

description:
Library name: Sample 5
column name in raw_counts.xlsx: 064-TS2

value: planarian SiRNeoblast


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_output_bio_rep_3

description: Library name: Sample 41


title: WT2 AT2 CD44 neg


title: experiment1_non-aggregating_2d_rep1

description:
Library name: Sample 4
column name in raw_counts.xlsx: 064-TS1

value: WT


title: experiment1_aggregates 2d_rep3

description:
Library name: Sample 3
column name in raw_counts.xlsx: 064-TA3

value: cells in aggregates


title: experiment2_aggrewell 1d_rep3

description:
Library name: Sample 9
column name in raw_counts_aggrewell.xlsx: 064-A3


title: experiment1_aggregates 2d_rep2

description:
Library name: Sample 2
column name in raw_counts.xlsx: 064-TA2


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_output_bio_rep_2

description: Library name: Sample 40


title: experiment1_aggregates 2d_rep1

description:
Library name: Sample 1
column name in raw_counts.xlsx: 064-TA1


title: experiment2_aggrewell 1d_rep2

description:
Library name: Sample 8
column name in raw_counts_aggrewell.xlsx: 064-A2


title: Sftpc_C121G_2

library_source: transcriptomic single cell

data_processing:
Fastq files were aligned to the mm10 reference genome using STARSolo
Downstream processing was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: Seurat processed h5 files

extract_protocol:
A single cell suspension was prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads followed by EPCAM+ cell enrichment using EPCAM microbeads. CD45-/CD31-/EPCAM- cells were considered lung mesenchymal cells. EPCAM+ and mesenchymal cells were prepared in 50/50 concentration for sequencing.
Libraries were prepared using Illumina stranded total RNA with Ribo-zero Plus kit accordine to manufacture instructions

value: Lung

value: EPCAM+/Mesenchyme


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_output_bio_rep_1

description: Library name: Sample 39


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_input_bio_rep_3

description: Library name: Sample 38


title: Sftpc_C121G_1

value: OG TMX


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_input_bio_rep_2

description: Library name: Sample 37


title: AC16, expressing PCBP1::Halo and PCBP2::Halo, rep 3

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

description: Library name: D_3

data_processing:
Reads were aligned to reference genome using STAR v.2.7.11a with --sjdbOverhang 149
Transcripts were assembled using StringTie v.2.1.1 with -e
Assembly: GENCODE v47/GRCh38.p14
Supplementary files format and content: csv file containing StringTie output gene counts for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human AC16 cells were expanded and maintained in 6-well TC plates in DMEM/F12 supplemented with 10% fetal bovine serum at 37 degC and 5% CO2.

extract_protocol:
Cells were lysed with Trizol (Cat# 15596018, Invitrogen) 48 hours post-transfection. Lysates were centrifuged at 13500 × g for 5 minutes and RNA extraction was performed using Direct-zol RNA Kit (Cat# R2050, Zymo
PolyA enrichment, library construction, and short-read sequencing were carried out at Novogene USA. Sequencing was performed in paired-end mode with a read length of 150 base pairs and depth of ~20 G per sample on an Illumina NovaSeq platform.

treatment_protocol: Cells were transfected with human PCBP1::Halo in pcDNA3.1 plasmid, PCBP2::Halo plasmid, or both at a concentration of 1 mg of each plasmid in 2 mL media using Lipofectamine 2000 (Cat# 11668019, Invitrogen) transfection reagent. Untransfected cells served as control

value: Cardiomyocyte fibroblast hybrid

value: PCBP1::Halo PCBP2::Halo


title: AC16, untransfected control, rep 3

description: Library name: U_3

value: Untransfected


title: AC16, untransfected control, rep 2

description: Library name: U_2


title: AC16, expressing PCBP1::Halo and PCBP2::Halo, rep 2

description: Library name: D_2


title: Sftpc_WT_2

value: SP-C Mutant


title: AC16, untransfected control, rep 1

description: Library name: U_1


title: experiment4_flat 1d_rep3

description:
Library name: Sample 41
column name in feeder experiments counts.xlsx: 064-flat1d-3


title: AC16, expressing PCBP1::Halo and PCBP2::Halo, rep 1

description: Library name: D_1


title: WT1 AT2 CD44 neg


title: libraryPDZ3_C_bPCA_G05_DC_a3_a2_input_bio_rep_1

description: Library name: Sample 36


title: AC16, expressing PCBP2::Halo, rep 3

description: Library name: B_3


title: AC16, expressing PCBP2::Halo, rep 2

description: Library name: B_2


title: AC16, expressing PCBP2::Halo, rep 1

description: Library name: B_1


title: AC16, expressing PCBP1::Halo, rep 3

description: Library name: A_3


title: Day 3 blastoids normoxia 2

city: Stanford

first: Laura

last: Amaya

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
Demultiplexed scRNA-seq fastq files were pre-processed using the Cell Ranger count pipeline (version 6.1.2) from 10x Genomics. Subsequent processing and filtering of scRNA-seq data were conducted using Seurat (v.3.0) with the following criteria: number of unique molecular identifiers (nUMI) ≥ 500, number of genes ≥ 250, and mitochondrial gene ratio < 0.20. The filtered data were then integrated, batch-effect-corrected, clustered, and analyzed using the standard dataset integration and analysis workflow in Seurat.
Assembly: mm10
Supplementary files format and content: filtered feature-barcode matrices, feature and barcode sequences corresponding to row and column indices respectively.

source_name: blastoids

growth_protocol: Natural embryos and blastoids were cultured on ibidi-u plates in IVC1 media as previously described (Bedzhov et al., 2014). In brief, mural trophectoderm was cut away from the embryos or blastoids and the remaining structures was placed in IVC1 media. Ibidi-u plates were then placed in 37oC incubator in normoxic conditions (20% O2 or 5% CO2).  Media was changed daily.   IVC1 consisted of the following: Advanced DMEM/F12 (12634-010, Thermo Fischer Scientific) supplemented with 20% (vol/vol) heat-inactivated FBS, 1% GlutaMAX, penicillin (25 units/ml)/Streptomycin (25 μg/ml), 1X ITS-X (10 mg/L insulin, 5.5 mg/L transferrin, 0.0067 mg/L sodium selenite, 2 mg/L etholamine; 51500-056, Thermo Fisher Scientific), 8 nM β-estradiol (E8875, Sigma-Aldrich), 200 ng/ml progesterone (P0130, Sigma-Aldrich), 25 μM N-acetyl-L-cysteine (A7250, Sigma-Aldrich).

extract_protocol:
Natural embryos were recovered as described above. Using a 96-well plate, embryos were washed twice in DEPC treated PBS, and then moved to dissociation mix: Ebioscience Accumax Cell Aggregate Dissociation Medium (00-4666-56, Thermo Scientific) supplemented with 1:1000 DNase to remove aberrant DNA released from lysed cells. Embryos were left in dissociation media at room temperature for 25-60 minutes with trituration by mouth pipetting and glass capillaries every 10 minutes. The dissociation reaction was quenched using equal parts FC media. Cells were passed through a 20 µM filter and spun down at 450 rcf. Cells were then resuspended in 0.04% BSA-PBS according to the 10X Chromium Next GEM single cell 3’ Kit v3.1 user guide.
Chromium scRNA-seq workflow

value: blastoids

value: day 4

tag: replicate

value: replica 2

value: normoxia


title: AC16, expressing PCBP1::Halo, rep 2

description: Library name: A_2


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_wt

description: Library name: Sample 35


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_output_bio_rep_3

description: Library name: Sample 34


title: Day 3 blastoids normoxia 1

value: day 3

value: replica 1


title: AC16, expressing PCBP1::Halo, rep 1

description: Library name: A_1


title: Day 3 blastoids hypoxia 2

value: hypoxia


title: NCI-H660 Input

city: Maywood

first: Steven

last: Kregel

state: IL

address: 2160 S. First Avenue

department: Cancer Biology

institute: Loyola University Chicago

description:
Library name: H660_p19, Input
bigWig file

data_processing:
Peaks were called using MACS2 and aligned to the human genome assembly GRCh38.p14. ChIP-seq data quality was assessed using FastQC (v0.12.1).
Assembly: GRCh38.p14
Supplementary files format and content: bigWig, BED (for all except inputs)

source_name: cell line

growth_protocol: CWR-R1 and NCI-H660 cells were plated at a density of 4.1 million cells per IP in 15cm3 dishes incubated at 37 ͦ C (5% CO2) for 24 hours.

extract_protocol:
Following fixation and quenching, we performed chromatin immunoprecipitation, size selection, and purification using the Diagenode iDeal ChIP kit for Transcription Factors (Diagenode, Cat: C01010055) according to manufacturer’s protocol.
Library preparation and sequencing was performed at the University of Illinois Urbana-Champaign (UIUC) Roy J. Carver Biotechnology Center using the Ovation® Ultralow System V2 DNA-Seq Library Preparation Kit (Tecan, Cat: 402666). The libraries were pooled; quantitated by qPCR and sequenced on one 25B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits (reads were 150bp in length). Fastq files were generated and demultiplexed with the bcl-convert v4.1.7 Conversion Software (Illumina).

treatment_protocol: The first grouping of CWR-R1 cells in 10% FBS RPMI (ATCC modification) were treated for 24 hours with either DMSO (Vehicle) or 20uM enzalutamide. In addition, another group of CWR-R1 cells were deprived of androgens for 21 hours in 10% CSS RPMI followed by subsequent treatment for 3 hours with either sterile-filtered ethanol (EtOH - Vehicle) or 1nM R1881. Both CWR-R1 and NCI-H660 cells were fixed in 1% w/v formaldehyde (ThermoFisher, Cat: ICN19404780) for 8 minutes followed by quenching in 125mM glycine (ThermoFisher, Cat: A13816.36) for 5 minutes shaking at room temperature.

value: cell line

value: NEPC


title: D: CD22 CAR+SLP-76 overexpression unstimulated

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Raw Novaseq BCLs were demultiplexed with cellranger mkfastq v7.0.2
Sequencing reads were aligned to the human hg38 reference genome with CellRanger v7.0.2
Cell x gene counts matrices in h5 format were produced using the default parameters in CellRanger count
Assembly: hg38
Supplementary files format and content: Gene expression counts matrices (h5) from CellRanger pipeline

source_name: T cell

growth_protocol: At day 0, PBMCs or isolated T cells were thawed and activated with Human T-Activator αCD3/CD28 Dynabeads (Gibco) at a 3:1 bead to cell ratio, in AIM-V media (Gibco) supplemented with 5% FBS, 10 mM HEPES, 1X penicillin-streptomycin-glutamine solution (Gibco) and 100 U/mL recombinant human IL-2 (Peprotech). Retroviral transduction was performed on days three and four post-activation. Twelve-well non-tissue culture treated plates were coated with RetroNectin (Takara Bio) and blocked with 2% BSA prior to incubation and centrifugation with the retroviral supernatant for at least two hours at 32 °C at 3,200 rpm. The co-expression of CAR and proximal signaling molecules was achieved by co-administration of two separate viral vectors. The supernatant was then removed and 0.5x106 T cells were added to each well in 1 mL of complete AIM-V media. Dynabeads were removed on day five post-activation by magnetic separation and the T cells were maintained in culture in complete AIM-V at a density of 0.3x106/ml until day 10-14, with media changes every 2-3 days.

extract_protocol: 10x Genomics NextGEM 5' scRNA-seq

treatment_protocol: Cells were restimulated and the profiled after 0hr, 5hr, or 24hr to study heterogenity in CAR response as a function of MT-SLP-76

value: T cell

value: CD22 targeted CAR T

value: unstim


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_output_bio_rep_1

description: Library name: Sample 32


title: NCI-H660 FOXA1 ChIP

description:
Library name: H660_p19_FOXA1_IP, ChIP
bigWig and BED files


title: NCI-H660 SOX2 ChIP

description:
Library name: H660_p19_SOX2_IP, ChIP
bigWig and BED files


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_output_bio_rep_2

description: Library name: Sample 33


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_input_bio_rep_3

description: Library name: Sample 31


title: Day 3 blastoids hypoxia 1


title: Sftpc_WT_1

value: Lung

value: EPCAM+/Mesenchyme

value: OG TMX


title: CWR-R1 SOX2 ChIP (EtOH)

description:
Library name: CWR_R1_p63_SOX2_IP_CSS_EtOH, ChIP
bigWig and BED files

value: prostate adenocracinoma

value: EtOH


title: CWR-R1 SOX2 ChIP (Enza)

description:
Library name: CWR_R1_p63_SOX2_IP_20_M_Enza, ChIP
bigWig and BED files

value: 20 uM Enzalutamide


title: Graft_GC+PTH

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

data_processing:
Barcoded samples were demultiplexed, aligned to the mouse genome, and UMI-collapsed with the Cellranger toolkit with standard settings  (version 7.1.0, 10X Genomics Inc)
Assembly: GRCm39.104
Supplementary files format and content: .h5 feature matrix
Supplementary files format and content: .h5 feature matrix

source_name: Graft tissue

growth_protocol: None. Freshly purified primary cells were used.

extract_protocol:
Target tissue was mechanically and enzymatically digested, stained for flow cytometric isolation and purified via FACS.
According to 10X Genomics manufacturer instructions
10X Genomics

treatment_protocol: There were four treatment groups of mice receiving subcutaneous release pellets of: (1) Placebo (Control), (2) Methylprednisolone (GC), (3) Methylprednisolone removal (GC removal), (4) Methylprednisolone (GC) + hPTH 1-34 (GC+PTH).

value: Graft tissue

value: tissue

value: GC+PTH


title: CWR-R1 SOX2 ChIP (DMSO)

description:
Library name: CWR_R1_p63_SOX2_IP_Veh_DMSO, ChIP
bigWig and BED files

value: DMSO


title: CWR-R1 FOXA1 ChIP (R1881)

description:
Library name: CWR_R1_p63_FOXA1_IP_CSS_1nM_R1881, ChIP
bigWig and BED files


title: CWR-R1 SOX2 ChIP (R1881)

description:
Library name: CWR_R1_p63_SOX2_IP_CSS_1nM_R1881, ChIP
bigWig and BED files


title: CWR-R1 FOXA1 ChIP (EtOH)

description:
Library name: CWR_R1_p63_FOXA1_IP_CSS_EtOH, ChIP
bigWig and BED files


title: CWR-R1 FOXA1 ChIP (Enza)

description:
Library name: CWR_R1_p63_FOXA1_IP_20_M_Enza, ChIP
bigWig and BED files


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_input_bio_rep_1

description: Library name: Sample 29


title: Graft_GC

value: GC


title: libraryPDZ3_C_aPCA_G05_DC_a3_a1_input_bio_rep_2

description: Library name: Sample 30


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_wt

description: Library name: Sample 28


title: CWR-R1 FOXA1ChIP (DMSO)

description:
Library name: CWR_R1_p63_FOXA1_IP_Veh_DMSO, ChIP
bigWig and BED files


title: Graft_Placebo

value: Placebo


title: CWR-R1 AR ChIP (R1881)

description:
Library name: CWR_R1_p63_AR_IP_CSS_1nM_R1881, ChIP
bigWig and BED files

value: cell line


title: Day 2 blastoids hypoxia

value: blastoids

value: day 2

value: replica 1

value: hypoxia


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_output_bio_rep_3

description: Library name: Sample 27


title: Femur_GC+PTH

source_name: Femur bone

value: Femur bone


title: Femur_GCremoval

value: GCremoval


title: E: CD22 CAR+SLP-76 24h stimulation

value: T cell

value: CD22 targeted CAR T


title: CWR-R1 Input (R1881)

description:
Library name: CWR_R1_p63_CSS_1nM_R1881, Input
bigWig file

value: prostate adenocracinoma


title: CWR-R1 AR ChIP (Enza)

description:
Library name: CWR_R1_p63_AR_IP_20_M_Enza, ChIP
bigWig and BED files

value: 20 uM Enzalutamide


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_output_bio_rep_1

description: Library name: Sample 25


title: CWR-R1 AR ChIP (DMSO)

description:
Library name: CWR_R1_p63_AR_IP_Veh_DMSO, ChIP
bigWig and BED files


title: CWR-R1 Input (EtOH)

description:
Library name: CWR_R1_p63_CSS_EtOH, Input
bigWig file

value: EtOH


title: Femur_GC

value: tissue


title: CWR-R1 Input (Enza)

description:
Library name: CWR_R1_p63_20_M_Enza, Input
bigWig file


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_input_bio_rep_3

description: Library name: Sample 24


title: Femur_Placebo


title: CWR-R1 Input (DMSO)

description:
Library name: CWR_R1_p63_Veh_DMSO, Input
bigWig file


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_input_bio_rep_2

description: Library name: Sample 23


title: IMR90, pSmad1/5/9, CUT&Tag, Enalapril treatment, rep2

city: Beijing

first: Haochen

last: Wang

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

data_processing:
Raw CUT&Tag data was trimmed using Trim Galore (version 0.6.10) software and the clean reads were mapped to the human reference genome hg38 using Bowtie2 (version 2.5.1) software with the following parameters “--very-sensitive --no-mixed --no-discordant -I 10 -X 1000”. The sam files were transformed to bam files through SAMtools (version 1.17) software. The CUT&Tag peaks were performed using the MACS2 (version 2.2.8) with the default parameters.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag kit (Vazyme, TD903)  was used to extract DNA.
TruePrep Index Kit V2 (TD903) for Illumina was used to construct library.

value: primary human embryonic lung fibroblasts

tag: antibody

value: WT

value: Enalapril treatment


title: Pancreas islet, aged, sample2, scRNA-seq

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

description: 10x Genomics

data_processing:
The demutipelexing, barcoded processing and gene counting  were made using the Cell Ranger (version 6.1.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreas islet

extract_protocol: The mice were sacrificed, and the abdominal cavity was opened. And 1-5 ml of cold 0.5 mg/ml collagenase solution was injected into the pancreas from the common bile duct using a syringe. The pancreases were incubated with 5 ml of cold 0.5 mg/ml collagenase solution at 37  C for 3 min. The digested product was filtered through a 0.25 mm nylon filter into a new 50 ml centrifuge tube, and were centrifuged at 200 x g for 1 min, and the supernatant was discarded. Islets were removed with a 200   L pipette and the islets were resuspended in 0.25% trypsin EDTA solution and incubated at 37  C for 5 min. Digestion was stopped by adding 0.4 volumes of cold fetal bovine serum (FBS) and Cells were resuspended in Hanks buffer (pH 7.4) containing 1% FBS. Then, the hypothalamus, pituitary gland, pineal gland, thyroid gland and adrenal gland were subsequently removed from the brain, thoracic cavity or abdominal cavity of each mouse. All tissue except hypothalamus were cut into small pieces using surgical scissors and were incubated with collagenase (0.5% in HBSS) at 37  C for 5-15 min(depends on the type of tissue) until they were dissociated into a single-cell suspension. The digested product was filtered through a 40   m nylon filter into a new 50 ml centrifuge tube, and wished with cold PBS. Then cells were resuspended in Hanks buffer (pH 7.4) containing 1% FBS. Hypothalamus were process into single nuclear suspension by using nuclear separation kit. Library was proformed according to the manufacter's instruction(single cell 3' v3.1 protocol, 10X Genomics). Briefly, prepare single cell master mix, load chromium next GEM chip G, run the chromium controller, transfer GEMs, GEM-RT incubation, post GEM-RT cleanup   Dynabeads, cDNA amplification, cDNA cleanup   SPRIselect and cDNA QC & quantification.

value: Pancreas islet

tag: age

value: 24 months old

tag: replicates

tag: sequencing type

value: scRNA-seq

tag: strain

value: SPF C57BL/6 mice


title: experiment4_HFF1 1d_rep2

description:
Library name: Sample 46
column name in feeder experiments counts.xlsx: 064-HFF11d-2

value: planarian SiRNeoblast

value: cells cultured on HFF1 feeder for 1d


title: IMR90, pSmad1/5/9, CUT&Tag, Enalapril treatment, rep1


title: CWR-R1 AR ChIP (EtOH)

description:
Library name: CWR_R1_p63_AR_IP_CSS_EtOH, ChIP
bigWig and BED files

value: cell line


title: IMR90 cell, shID, rep2

data_processing:
FastQC (version 0.11.5) software was first used for data quality control. Raw paired-end sequencing reads were trimmed by Trim Galore (version 0.6.10) software to remove adapter sequences and low quality reads. The high quality RNA-seq reads were mapped to the hg38/mm10 genome by using HISAT2 (version 2.2.1) software. SAMtools (version 1.17) software was then used to convert the generated sam files to bam files. To qualify gene expression, the number of reads mapped to each gene was counted using featureCounts (version 2.0.1) software.
Assembly: hg38/mm10
Supplementary files format and content: CSV files include raw counts of each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the instructions.
The extracted total RNA was then sent to Novogene for subsequent cDNA library construction.

value: ID knock down

value: shID treatment


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_input_bio_rep_1

description: Library name: Sample 22


title: libraryPDZ3_N_bPCA_G05_DC_N_a2_output_bio_rep_2

description: Library name: Sample 26


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_wt

description: Library name: Sample 21


title: IMR90 cell, shID Control, rep2

value: Control


title: Pancreas islet, young, sample2, scRNA-seq

description: 10x Genomics

value: 6 months old


title: Pancreas islet, aged, sample1, scRNA-seq

description: 10x Genomics


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_output_bio_rep_3

description: Library name: Sample 20


title: IMR90 cell, shID, rep1


title: IMR90 cell, shID Control, rep1


title: IMR90 cell, LDN treatment, rep2

value: LDN treatment


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_output_bio_rep_2

description: Library name: Sample 19


title: Pancreas islet, young, sample1, scRNA-seq

description: 10x Genomics


title: Adrenal gland, aged, sample2, scRNA-seq

description: 10x Genomics

source_name: Adrenal gland

value: Adrenal gland


title: IMR90 cell, Enaparil and LDN treatment, rep2

description: Enap-LDN-y

value: Enaparil and LDN treatment


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_output_bio_rep_1

description: Library name: Sample 18


title: Adrenal gland, young, sample2, scRNA-seq

description: 10x Genomics


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_input_bio_rep_3

description: Library name: Sample 17


title: IMR90 cell, CT, rep1

value: primary human embryonic lung fibroblasts


title: IMR90 cell, Enaparil and LDN treatment, rep1

description: Enap-LDN-x

value: WT


title: IMR90 cell, LDN treatment, rep1


title: IMR90 cells, 40 μM enalapril treatment, rep2

value: 40 μM enalapril treatment


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_input_bio_rep_2

description: Library name: Sample 16


title: IMR90 cells, 40 μM enalapril treatment, rep1


title: IMR90 cells, 20 μM enalapril treatment, rep2

value: 20 μM enalapril treatment


title: IMR90, pSmad1/5/9, CUT&Tag, Control, rep2


title: Adrenal gland, young, sample1, scRNA-seq

description: 10x Genomics


title: libraryPDZ3_N_aPCA_G05_DC_N_a1_input_bio_rep_1

description: Library name: Sample 15


title: IMR90 cells, 20 μM enalapril treatment, rep1


title: IMR90 cells, 10 μM enalapril treatment, rep2

value: 10 μM enalapril treatment


title: Thyroid gland, aged, sample2, scRNA-seq

description: 10x Genomics

source_name: Thyroid gland

value: Thyroid gland

value: 24 months old

value: scRNA-seq


title: libraryPDZ3_bPCA_G05_DC_a2_wt

description: Library name: Sample 14


title: IMR90 cells, 10 μM enalapril treatment, rep1


title: IMR90 cell, CT, rep2


title: IMR90 cells, 5 μM enalapril treatment, rep2

value: 5 μM enalapril treatment


title: Thyroid gland, young, sample2, scRNA-seq

description: 10x Genomics

value: SPF C57BL/6 mice


title: IMR90 cell, Control, rep2


title: libraryPDZ3_bPCA_G05_DC_a2_output_bio_rep_3

description: Library name: Sample 13


title: Thyroid gland, aged, sample1, scRNA-seq

description: 10x Genomics


title: Adrenal gland, aged, sample1, scRNA-seq

description: 10x Genomics


title: IMR90 cell, Control, rep1


title: libraryPDZ3_bPCA_G05_DC_a2_output_bio_rep_2

description: Library name: Sample 12


title: Teff, ex vivo, Day 7 post-immunization, biol rep 2

city: Boston

first: Xudong

last: Li

state: MA

address: 150 Harrison Avenue, Jaharis 523a, M&V 702 Building

department: Immunology

institute: Tufts University

description:
Library name: e_2_Teff
Column name in Normalized_Counts.csv: e_2_Teff

data_processing:
Analysis was performed on Galaxy Server.
Sequence reads were trimmed for adaptor sequences and low quality using Trimmomatic, default settings.
Sequence reads were aligned to mm39 using HISAT2, default settings.
Sequence reads were counted using FeatureCounts, default settings.
Differential gene expression analysis was performed with DESeq2, default settings.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv file contains normalized counts for each sample

source_name: Spleen and draining lymph node

extract_protocol:
RNA was extracted using the phenol/chlorophorm method.
Library was prepared using the Illumina Stranded mRNA Prep Kit following manufacturer protocol.

treatment_protocol: ER-Tregs were transferred into reciepient mice and mice were immunized with CFA/MOG. ER-Tregs, endogenous Tregs, and endogenous Teff were sort purified 7 days later directly into TRIzol for RNA extraction.

value: Spleen and draining lymph node

value: Primary T cells

value: Endogenous Teff

value: CFA/MOG immunization


title: libraryPDZ3_bPCA_G05_DC_a2_output_bio_rep_1

description: Library name: Sample 11


title: libraryPDZ3_bPCA_G05_DC_a2_input_bio_rep_3

description: Library name: Sample 10


title: Pineal gland, aged, sample2, scRNA-seq

description: 10x Genomics

source_name: Pineal gland

value: Pineal gland


title: nTregs, ex vivo, Day 7 post-immunization, biol rep 2

description:
Library name: e_2_nTr
Column name in Normalized_Counts.csv: e_2_nTr

value: Endogenous Tregs


title: Thyroid gland, young, sample1, scRNA-seq

description: 10x Genomics

value: 6 months old


title: nTregs, ex vivo, Day 7 post-immunization, biol rep 1

description:
Library name: e_1_nTr
Column name in Normalized_Counts.csv: e_1_nTr


title: IMR90 cells, 5 μM enalapril treatment, rep1

value: primary human embryonic lung fibroblasts


title: Pineal gland, young, sample2, scRNA-seq

description: 10x Genomics


title: ER-Tregs, ex vivo, Day 7 post-immunization, biol rep 1

description:
Library name: e_1_erTr
Column name in Normalized_Counts.csv: e_1_erTr

value: ER-Tregs

value: WT


title: libraryPDZ3_bPCA_G05_DC_a2_input_bio_rep_2

description: Library name: Sample 9


title: Pineal gland, aged, sample1, scRNA-seq

description: 10x Genomics


title: libraryPDZ3_bPCA_G05_DC_a2_input_bio_rep_1

description: Library name: Sample 8


title: Pineal gland, young, sample1, scRNA-seq

description: 10x Genomics


title: PrEC SOX2 ChIP

description:
Library name: PrEC_SOX2_IP, ChIP
bigWig and BED files

value: cell line

value: PrEC

value: primary prostate basal epithelial cells


title: Pituitary, aged, sample2, scRNA-seq

description: 10x Genomics

source_name: Pituitary

value: Pituitary gland

value: 24 months old


title: p.Glu50fs*3 + H20 (last 14 days) replicate 4

city: Cambridge

first: Li-Huei

last: Tsai

address: 77 Massachusetts Avenue

institute: MIT

description:
Library name: D24-18576
Column name in counts.txt: D24-18576

data_processing:
Sequencing data were processed using the BMC/BCC pipeline version 1.8 (updated 06/06/2023). Further details of the pipeline are available at: https://openwetware.org/wiki/BioMicroCenter:Software#BMC-BCC_Pipeline by the MIT BioMicro Center. Fastq files were subsequently processed in-house using STAR and featureCounts. Human reference genome (GRCh38.p14, GENCODE release 47) and annotation files were downloaded from GENCODE and indexed using STAR. Sequencing reads were trimmed using Trim Galore with Nextera-specific settings and a stringency of 3, requiring a minimum overlap of 3 bases with adapter sequences for trimming. Trimmed reads were then mapped to the indexed human genome using STAR, with paired-end reads processed concurrently. Gene-level counts were generated using featureCounts with settings optimized for paired-end data: counting only read pairs with both ends aligned (-B), excluding pairs mapping to different chromosomes or strands (-C), and counting fragments rather than individual reads (-p). Counts were summarized at the exon level, and grouped by gene identifier.
Assembly: GRCh38.p14, GENCODE release 47
Supplementary files format and content: The featureCounts output is provided as the counts.txt file.

source_name: Isogenic cell line

growth_protocol: We differentiated isogenic iPSCs into neurons (iNs) via lentiviral delivery of a doxycyclineinducible NGN2 expression cassette as previously described in https://doi.org/10.1016/j.ymeth.2015.11.019.

extract_protocol:
Total RNA was extracted from induced neurons using the RNeasy Mini Kit (Qiagen), and RNA quality was assessed using a 5300 Fragment Analyzer (Agilent). Only samples with an RNA Quality Number (RQN) greater than 9.5 were selected for library preparation.
Full-length cDNA was synthesized using the SMART-seq v4 kit (Takara Bio), and sequencing-ready libraries were subsequently prepared using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were sequenced as 75 bp + 75 bp paired-end reads with dual 8-nucleotide indexes on an Element AVITI sequencing platform (Element Biosciences) at the MIT BioMicro Center.

treatment_protocol: iPSC-derived neurons were treated with cytidine 5’-diphosphocholine (CDP-choline; Millipore Sigma 30290) to final concentrations of 100 µM beginning at day 14 and repeated with each media change until 28 days matured.

value: Isogenic cell line

value: iPSC-derivded induced neurons

value: + H20 (last 14 days)

value: Day 28


title: ER-Tregs, ex vivo, Day 7 post-immunization, biol rep 2

description:
Library name: e_2_erTr
Column name in Normalized_Counts.csv: e_2_erTr

value: Spleen and draining lymph node

value: Primary T cells


title: PrEC Input

description:
Library name: PrEC, Input
bigWig file


title: NCCIT SOX2 ChIP

description:
Library name: NCCIT_SOX2_IP, ChIP
bigWig and BED files

value: NCCIT

value: embryonal carcinoma


title: Pituitary, young, sample2, scRNA-seq

description: 10x Genomics

value: 6 months old

value: scRNA-seq

value: SPF C57BL/6 mice


title: Teff, ex vivo, Day 7 post-immunization, biol rep 1

description:
Library name: e_1_Teff
Column name in Normalized_Counts.csv: e_1_Teff

value: Endogenous Teff

value: WT

value: CFA/MOG immunization


title: p.Glu50fs*3 + H20 (last 14 days) replicate 2

description:
Library name: D24-18574
Column name in counts.txt: D24-18574


title: p.Glu50fs*3 + H20 (last 14 days) replicate 1

description:
Library name: D24-18572
Column name in counts.txt: D24-18572


title: NCCIT Input

description:
Library name: NCCIT, Input
bigWig file

value: cell line


title: Pituitary, young, sample1, scRNA-seq

description: 10x Genomics

value: Pituitary gland


title: p.Glu50fs*3 + H20 (last 14 days) replicate 0

description:
Library name: D24-18571
Column name in counts.txt: D24-18571


title: p.Tyr622* + CDP-choline (last 14 days)) replicate 4

description:
Library name: D24-18567
Column name in counts.txt: D24-18567

value: + CDP-choline (last 14 days))


title: p.Glu50fs*3 + H20 (last 14 days) replicate 3

description:
Library name: D24-18575
Column name in counts.txt: D24-18575

value: Isogenic cell line


title: Hypothalamus, young, sample2, snRNA-seq

description: 10x Genomics

source_name: Hypothalamus

value: Hypothalamus

value: snRNA-seq


title: SW48 GSK_WRN3

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.48, truncated to a single base, reads quantified in TA tracts both broken and not broken in drug.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file of genomic regions. Samples were imported into Seqmonk v1.48, truncated to a single base, reads quantified in TA tracts both broken and not broken in drug.
Library strategy: TrAEL-seq

extract_protocol:
½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: 1-2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE.

value: colorectal carcinoma

tag: fixation

value: unfixed


title: Pituitary, aged, sample1, scRNA-seq

description: 10x Genomics

value: 24 months old


title: Hypothalamus, aged, sample1, snRNA-seq

description: 10x Genomics


title: p.Tyr622* + CDP-choline (last 14 days)) replicate 3

description:
Library name: D24-18566
Column name in counts.txt: D24-18566

value: iPSC-derivded induced neurons

value: Day 28


title: SW48 smarcal HRO761

value: smarcal HRO761


title: p.Tyr622* + CDP-choline (last 14 days)) replicate 2

description:
Library name: D24-18565
Column name in counts.txt: D24-18565


title: Hypothalamus, young, sample1, snRNA-seq

description: 10x Genomics

value: 6 months old


title: LIF14

city: Sao Paulo

first: Marilene

middle: Hohmuth

last: Lopes

state: Sao Paulo

address: Av Prof Lineu Prestes, 1524, room 431

department: Cell and Developmental Biology

country: Brazil

institute: University of Sao Paulo

description: Library name: P02004

data_processing:
sequencing reads QA
adapters removal
Reads base correction and filtering
Reads mapping and counting
sample outliers removal                                          Normalization                                                                         Batch  effect correction                                                 Differential expression calculation
Assembly: GRC38 Ensemble release 100
Supplementary files format and content: A comma-separated values (CSV) file containing normalized gene counts, with genes in rows and samples in columns.

source_name: blastocyst-ICM

growth_protocol: Mouse embryonic stem cells (mESCs) were derived from genetically-modified mice expressing different levels of STIP1 (Beraldo et al., 2013; Lackie et al., 2020a; b, 2022). Cells were grown in Glasgow Minimal Essential Medium (GMEM, Sigma) supplemented with 20% fetal bovine serum (Gibco), 1X non-essential amino acids (Gibco), 1% L-glutamine (Sigma), 1% Sodium Pyruvate (Gibco), 2% Penicillin-Streptomycin (Gibco), 0.1mM β-mercaptoethanol (Sigma) and 1000U/mL of Leukemia Inhibitor Factor (LIF) (Millipore) on 0.1% gelatin (Millipore) coated flasks or plates.

extract_protocol:
Total RNA was extracted using RiboPure RNA Purification (Ambion) kit, following the manufacturer’s instructions. RNA concentration was quantified in BioTek Epoch (Agilent).
RNA-seq libraries were made by an outsourced service (Indegene) with the NextSeq 500/550 High Output Kit v2.5 (Illumina). Two biological replicates were used per group (samples coming from different mice within the same group). Sequencing depth ranged between 40-45 million reads per sample and reads length is of 76bp

treatment_protocol: culture conditions described above - no treatments

value: blastocyst-ICM

value: mouse embryonic stem cells

value: LIF


title: LIF17

description: Library name: P02006

value: STIP1+/- (HTKO)


title: LIF25

description: Library name: P02007


title: p.Tyr622* + CDP-choline (last 14 days)) replicate 1

description:
Library name: D24-18564
Column name in counts.txt: D24-18564


title: LIF16

description: Library name: P02005

value: WT


title: LIF20

description: Library name: P02010

value: TGA


title: LIF22

description: Library name: P02011


title: LIF09

description: Library name: P02008


title: SW48 smarcal

value: smarcal


title: Hypothalamus, aged, sample2, snRNA-seq

description: 10x Genomics

value: SPF C57BL/6 mice


title: SW48 HRO761


title: SW48 smarcal GSK_WRN3

value: smarcal GSK_WRN3


title: p.Tyr622* + CDP-choline (last 14 days)) replicate 0

description:
Library name: D24-18563
Column name in counts.txt: D24-18563

value: Isogenic cell line

value: + CDP-choline (last 14 days))


title: p.Tyr622* + H20 (last 14 days) replicate 4

description:
Library name: D24-18559
Column name in counts.txt: D24-18559

value: + H20 (last 14 days)


title: SW48

value: colorectal carcinoma

value: control

value: unfixed


title: mouse spleen, Enalapril, rep2

source_name: mouse spleen tissue

value: mouse spleen tissue

value: Enaparil treatment


title: mouse spleen, Enalapril, rep4


title: mouse spleen, Enalapril, rep3


title: PierA_Veh_rep1

city: San Francisco

first: Lin

last: Yuan

institute: UCSF

description:
Library name: PierA_Veh_1
Column name in RNAseq_gene_fpkm.csv: PierA_Veh1
RNAseq_gene_fpkm.csv

data_processing:
CRISPRi screen: processed using the MAGeCK-iNC bioinformatic pipeline developed by the Kampmann lab (Tian et al., 2019, availble at kampmannlab.ucsf.edu/mageck-inc); RNAseq: this step was outsourced to Novogene.
Assembly: CRISPRi screen: hCRISPRi_v2 (Horlbeck et al., 2016); RNAseq: GRCh38
Supplementary files format and content: CIRSPRi screen: .counts files contain the counts of each sgRNA where a separate file was generated for each biological replicates; RNAseq: .csv file contains the estimated gene expression FPKM of each biological replicates in separate columns of the same file.

extract_protocol:
CRISPRi screen: genomic DNA was extracted from 1-2 e8 cells/sample as described by Gilbert et al., 2014; RNAseq: RNA was extracted from 4e5 cells/sample. All RIN were over 8.
CRISPRi screen: Barcoded sgRNA were amplified and purified as described by Gilbert et al., 2014; RNAseq: cDNA libraries constructed from RNA. This step was outsourced to Novogene, and HISAT2 was used for mapping.

value: TRPV1, dCas9-KRAB

value: Pericidin A pretreated, Vehicle treated


title: Veh_Cap_rep2

description:
Library name: Veh_Cap_2
Column name in RNAseq_gene_fpkm.csv: Veh_Cap2
RNAseq_gene_fpkm.csv

value: Vehicle pretreated, Capsaicin treated


title: Veh_Cap_rep3

description:
Library name: Veh_Cap_3
Column name in RNAseq_gene_fpkm.csv: Veh_Cap3
RNAseq_gene_fpkm.csv


title: PierA_Cap_rep2

description:
Library name: PierA_Cap_2
Column name in RNAseq_gene_fpkm.csv: PierA_Cap2
RNAseq_gene_fpkm.csv

value: Pericidin A pretreated, Capsaicin treated


title: PierA_Veh_rep2

description:
Library name: PierA_Veh_2
Column name in RNAseq_gene_fpkm.csv: PierA_Veh2
RNAseq_gene_fpkm.csv


title: PierA_Veh_rep3

description:
Library name: PierA_Veh_3
Column name in RNAseq_gene_fpkm.csv: PierA_Veh3
RNAseq_gene_fpkm.csv


title: mouse spleen, Enalapril, rep1

value: WT


title: PierA_Cap_rep3

description:
Library name: PierA_Cap_3
Column name in RNAseq_gene_fpkm.csv: PierA_Cap3
RNAseq_gene_fpkm.csv


title: p.Tyr622* + H20 (last 14 days) replicate 3

description:
Library name: D24-18558
Column name in counts.txt: D24-18558

value: iPSC-derivded induced neurons

value: Day 28


title: PierA_Cap_rep1

description:
Library name: PierA_Cap_1
Column name in RNAseq_gene_fpkm.csv: PierA_Cap1
RNAseq_gene_fpkm.csv


title: IMR90, pSmad1/5/9, CUT&Tag, Control, rep1

value: primary human embryonic lung fibroblasts

value: Control


title: Veh_Cap_rep1

description:
Library name: Veh_Cap_1
Column name in RNAseq_gene_fpkm.csv: Veh_Cap1
RNAseq_gene_fpkm.csv


title: PedTALL_P15_D2_10x5_v2

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

description: scCITEseq, scTCRseq, scBCRseq (10x Genomics 5' v2)

data_processing:
Sequencing reads were demultiplexed and aligned to the GRCh38-3.0.0 reference genome using Cell Ranger 6.1.0.
Assembly: hg38
Supplementary files format and content: *metadata.tsv.gz: Metadata
Supplementary files format and content: *barcodes.tsv.gz: Raw cell barcodes.
Supplementary files format and content: *RNA_features.tsv.gz: Raw genes.
Supplementary files format and content: *RNA_matrix.mtx.gz: raw gene-barcode matrices.
Supplementary files format and content: *ADT_features.tsv.gz: Raw surface protein antibodies.
Supplementary files format and content: *ADT_matrix.mtx.gz: Raw surface protein antibody-barcode matrices.
Supplementary files format and content: *HTO_features.tsv.gz: Raw hashtag antibodies.
Supplementary files format and content: *HTO_matrix.mtx.gz: Raw hashtag antibody-barcode matrices.
Supplementary files format and content: *TCR_filtered_contig_annotation.tsv.gz: Filtered TCR contig sequences and annotations.
Supplementary files format and content: *BCR_filtered_contig_annotation.tsv.gz: Filtered BCR contig sequences and annotations.
Supplementary files format and content: Low_Input_RNAseq_invitro_Tcells_counts.txt: raw gene counts low-input RNA-seq in-vitro T-cells.
Supplementary files format and content: Low_Input_RNAseq_invitro_Tcells_meta.txt: metadata low-input RNA-seq in-vitro T-cells.

source_name: PB

extract_protocol:
Cryopreserved mononuclear cells from peripheral blood or bone marrow were thawed in prewarmed RPMI 1640 (Gibco) supplemented with 10% FBS (Gibco) and 2-Mercaptoethanol (Gibco) by a serial dilution according to protocol (10x Genomics). Mononuclear cells were pelleted by centrifugation (400g at 4C) and supernatant was discarded. After thawing, cells were kept on ice throughout the procedure until ready for loading onto the 10x Genomics Chromium Controller. Cell pellets were resuspended in 1% BSA in PBS and incubated with Human TruStain FcX Blocking Solution (Biolegend) for 10 mins on ice. After incubation, FITC-conjugated anti-human CD45 (Biolegend), PE-conjugated anti-human CD7 (Biolegend) were added and incubated for 30 mins on ice in the dark. In addition, samples were either stained with a custom anti-human Totalseq-C cocktail containing 204 CITE-seq antibodies (Biolegend) or with a hashtag antibody (Biolegend) to pool samples after sorting1 (Table S1). After incubation, cells were washed three times in 2.5ml PBS with 1% BSA at 400g for 5mins at 4°C. Finally, samples were resuspended in PBS with 1% BSA supplemented with 0.1uM DAPI for cell sorting.
Generation of the gene expression library, surface proteins library and the VDJ library was done according to the 10x Genomics Chromium Next GEM Single Cell V(D)J Reagent Kits with Feature Barcode technology for Cell Surface Protein v1.1 (21 samples) or v2 (9 samples) protocol. Transcriptome (5’), surface proteome and VDJ sequencing libraries were assessed by Agilent Tapestation and quantified using Qubit dsDNA before sequencing. 10x Genomics libraries were paired-end sequenced on a Nextseq500 with the following read configurations for the transcriptomic and feature barcoding libraries: 26-8-0-58 bp and for the immune repertoire libraries 26-8-0-134 bp.
scCITE-seq, scTCRseq and scBCRseq

value: PB

tag: disease state

value: Pediatric T-ALL

tag: disease stage

value: D2 (short-term treatment)

value: CD45+ immune cells and T-ALL cells


title: mouse spleen, Control, rep4


title: PedTALL_P15_Dx_10x5_v2

value: Diagnosis


title: p.Tyr622* + H20 (last 14 days) replicate 2

description:
Library name: D24-18557
Column name in counts.txt: D24-18557

value: Isogenic cell line

value: + H20 (last 14 days)


title: PedTALL_P14_D32_10x5_v2

value: D32 (remission)


title: mouse spleen, Control, rep3

value: mouse spleen tissue


title: p.Tyr622* + H20 (last 14 days) replicate 1

description:
Library name: D24-18556
Column name in counts.txt: D24-18556


title: Veh_Veh_rep2

description:
Library name: Veh_Veh_2
Column name in RNAseq_gene_fpkm.csv: Veh_Veh2
RNAseq_gene_fpkm.csv

value: TRPV1, dCas9-KRAB

value: Vehicle pretreated, Vehicle treated


title: mouse spleen, Control, rep2


title: PedTALL_P14_D2_10x5_v2


title: Veh_Veh_rep1

description:
Library name: Veh_Veh_1
Column name in RNAseq_gene_fpkm.csv: Veh_Veh1
RNAseq_gene_fpkm.csv


title: p.Tyr622* + H20 (last 14 days) replicate 0

description:
Library name: D24-18555
Column name in counts.txt: D24-18555


title: control + H20 (last 14 days) replicate 1

description:
Library name: D24-18554
Column name in counts.txt: D24-18554

value: control


title: CRISPRi_Cap_rep2

description: Library name: CRISPRi_Cap_2

data_processing:
CRISPRi screen: processed using the MAGeCK-iNC bioinformatic pipeline developed by the Kampmann lab (Tian et al., 2019, availble at kampmannlab.ucsf.edu/mageck-inc); RNAseq: this step was outsourced to Novogene.
Assembly: CRISPRi screen: hCRISPRi_v2 (Horlbeck et al., 2016); RNAseq: GRCh38
Supplementary files format and content: CIRSPRi screen: .counts files contain the counts of each sgRNA where a separate file was generated for each biological replicates; RNAseq: .csv file contains the estimated gene expression FPKM of each biological replicates in separate columns of the same file.
Library strategy: CRISPR Screen

value: Capsaicin

tag: time

value: Day 14


title: mouse spleen, Control, rep1

value: WT


title: Veh_Veh_rep3

description:
Library name: Veh_Veh_3
Column name in RNAseq_gene_fpkm.csv: Veh_Veh3
RNAseq_gene_fpkm.csv


title: mouse muscle, Enalapril, rep3

source_name: mouse muscle tissue

value: mouse muscle tissue

value: Enaparil treatment


title: CRISPRi_UT_rep2

description: Library name: CRISPRi_UT_2


title: CRISPRi_Cap_rep1

description: Library name: CRISPRi_Cap_1


title: PedTALL_P13_Dx_10x5_v2

value: PB


title: PedTALL_P13_D41_10x5_v2

value: Pediatric T-ALL

value: D41 (remission)


title: mouse muscle, Enalapril, rep4


title: PedTALL_P14_Dx_10x5_v2

value: CD45+ immune cells and T-ALL cells


title: mouse muscle, Enalapril, rep1


title: Karpas1106p, WT, 60 min, clone 26 biol rep 2

city: Vancouver

first: Gerben

last: Duns

state: BC

address: 675 West 10th Ave

department: Lymphoid Cancer Research

country: Canada

institute: BC Cancer

description: Library name: kar1106pcon26_60min_2

data_processing:
RNA-seq reads were aligned to the GRCh38 reference genome, and per-gene counts were generated using the STAR aligner.
Counts were normalized using the trimmed mean of M-values (TMM) method and scaled to log2-transformed counts per million (CPM)
Assembly: GRCh38
Supplementary files format and content: txt files include log2-transformed counts per million (CPM)

growth_protocol: The DOHH-2 and U-2940 cells were cultured in Roswell Park Memorial Institute-1640 medium (RPMI-1640) supplemented with 10% Fetal Bovine Serum (FBS) (Corning, catalog no. 35-077-CV). Karpas-1106p cells were cultured in RPMI-1640 supplemented with 20% FBS. All cell lines were maintained at 37°C in a 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat no. 74104) according to the manufacturer’s instructions. Briefly, cells were lysed in RLT buffer supplemented with β-mercaptoethanol, and homogenized by pipetting. The lysate was then mixed with ethanol and loaded onto a silica column. Following a series of wash steps, RNA was eluted in RNase-free water. RNA concentration and purity were assessed using a spectrophotometer.
200 ng of RNA was used to construct libraries using the Illumina Stranded mRNA Prep Ligation Kit (Illumina, catalog no. 20040534)

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells

value: Ephrin B2, 60 mins


title: PedTALL_P12_D33_10x5_v2

value: D33 (remission)


title: control + H20 (last 14 days) replicate 0

description:
Library name: D24-18553
Column name in counts.txt: D24-18553

value: Isogenic cell line

value: iPSC-derivded induced neurons

value: + H20 (last 14 days)

value: Day 28


title: mouse muscle, Enalapril, rep2


title: CRISPRi_T0_rep2

description: Library name: CRISPRi_T0_2

value: TRPV1, dCas9-KRAB

value: Day 0


title: CRISPRi_UT_rep1

description: Library name: CRISPRi_UT_1

value: Day 14


title: PedTALL_P13_D2_10x5_v2

value: D2 (short-term treatment)


title: Karpas1106p, WT, 30 min, clone 26 biol rep 2

description: Library name: kar1106pcon26_30min_2

value: Ephrin B2, 30 mins


title: Karpas1106p, WT, 30 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_30min_1


title: CRISPRi_T0_rep1

description: Library name: CRISPRi_T0_1


title: mouse muscle, Control, rep3

value: mouse muscle tissue

value: WT

value: Control


title: Karpas1106p, WT, 240 min, clone 26 biol rep 2

description: Library name: kar1106pcon26_240min_2

value: Ephrin B2, 240 mins


title: mouse muscle, Control, rep4


title: PedTALL_P12_Dx_10x5_v2

value: PB

value: Pediatric T-ALL

value: Diagnosis

value: CD45+ immune cells and T-ALL cells


title: Karpas1106p, WT, 60 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_60min_1

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells

value: Ephrin B2, 60 mins


title: H9c2_HPLM_without_Lactate_3

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: 161 x 150 cycle paired end sequence

data_processing:
NovaSeq 150x150 bp Sequencing:  Sequencing libraries were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP workflow (20043131).  Following transfer of the flowcell to an Illumina NovaSeq 6000 instrument, a 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).
Single base mismatch
XPRESSpipe v0.6.3 was used to process sequence files, with the following command: xpresspipe peRNAseq ... -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --sjdbOverhang 150 --quantification_method htseq --remove_rrna. See supplementary files for XPRESSpipe dependencies and settings used.
Assembly: Ensembl rattus_norvegicus release-104
Supplementary files format and content: Tab-delimited text file - sample counts

organism: Rattus norvegicus

growth_protocol: DMEM or HPLM in 10% FBS and 1% Penicillin-Streptavidin.

extract_protocol:
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.
Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: Grown for ~24 hours in the presence or absence of lactate.

value: Cardiomyoblast

value: HPLM -lactate


title: Karpas1106p, WT, 240 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_240min_1


title: mouse muscle, Control, rep2


title: H9c2_HPLM_without_Lactate_2

description: 160 x 150 cycle paired end sequence


title: Karpas1106p, WT, 120 min, clone 26 biol rep 2

description: Library name: kar1106pcon26_120min_2

value: Ephrin B2, 120 mins


title: PedTALL_P12_D5_10x5_v2

value: D5 (short-term treatment)


title: H9c2_HPLM_without_Lactate_1

description: 159 x 150 cycle paired end sequence


title: mouse muscle, Control, rep1


title: PedTALL_P11_Dx_10x5_v2


title: Karpas1106p, WT, 10 min, clone 26 biol rep 2

description: Library name: kar1106pcon26_10min_2

value: Ephrin B2, 10 mins


title: mouse liver, Enalapril, rep4

source_name: mouse liver tissue

value: mouse liver tissue

value: Enaparil treatment


title: PedTALL_P11_D4_10x5_v2

value: D4 (short-term treatment)


title: Karpas1106p, WT, 120 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_120min_1

source_name: cell line


title: H9c2_HPLM_2

description: 157 x 150 cycle paired end sequence

value: HPLM


title: Karpas1106p, WT, 10 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_10min_1


title: PedTALL_P10_D4_10x5_v1.1

description: scCITEseq, scTCRseq, scBCRseq (10x Genomics 5' v1.1)


title: H9c2_HPLM_1

description: 156 x 150 cycle paired end sequence


title: Karpas1106p, WT, 0 min, clone 26 biol rep 2

description: Library name: kar1106pcon26_0min_2


title: PedTALL_P10_D47_10x5_v1.1

value: D47 (remission)


title: mouse liver, Enalapril, rep3

value: WT


title: PedTALL_P10_Dx_10x5_v1.1

value: PB

value: Pediatric T-ALL


title: H9c2_HPLM_3

description: 158 x 150 cycle paired end sequence


title: mouse liver, Enalapril, rep2


title: mouse liver, Enalapril, rep1


title: H9c2_DMEM_Lactate_3

description: 155 x 150 cycle paired end sequence

value: DMEM +lactate


title: PedTALL_P9_D4_10x5_v1.1

value: CD45+ immune cells and T-ALL cells


title: mouse liver, Control, rep4

value: Control


title: PedTALL_P11_D32_10x5_v2

value: D32 (remission)


title: H9c2_DMEM_Lactate_2

description: 154 x 150 cycle paired end sequence

value: Cardiomyoblast


title: Karpas1106p, C99R, 60 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_60min_2

value: cell line

value: primary mediastinal B-cell lymphoma-derived cells

value: Ephrin B2, 60 mins


title: PedTALL_P9_Dx_10x5_v1.1

value: Diagnosis


title: mouse liver, Control, rep3

value: mouse liver tissue


title: H9c2_DMEM_Lactate_1

description: 153 x 150 cycle paired end sequence


title: Karpas1106p, C99R, 60 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_60min_1


title: PedTALL_P8_D32_10x5_v1.1


title: Karpas1106p, WT, 0 min, clone 26 biol rep 1

description: Library name: kar1106pcon26_0min_1


title: H9c2_DMEM_3

description: 152 x 150 cycle paired end sequence

value: DMEM


title: mouse liver, Control, rep2


title: PedTALL_P8_D6_10x5_v1.1

value: D6 (short-term treatment)


title: Karpas1106p, C99R, 30 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_30min_2

value: Ephrin B2, 30 mins


title: Karpas1106p, C99R, 30 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_30min_1


title: PedTALL_P8_Dx_10x5_v1.1


title: H9c2_DMEM_2

description: 151 x 150 cycle paired end sequence


title: H9c2_DMEM_1

description: 150 x 150 cycle paired end sequence


title: Karpas1106p, C99R, 240 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_240min_2

value: Ephrin B2, 240 mins


title: mouse kidney, Enalapril, rep4

source_name: mouse kidney tissue

value: mouse kidney tissue

value: WT

value: Enaparil treatment


title: mouse liver, Control, rep1


title: Karpas1106p, C99R, 240 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_240min_1


title: PedTALL_P7_Dx_10x5_v1.1

value: PB

value: Pediatric T-ALL


title: Tumor microenvironment sample 1 anti-PD-L1

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

institute: CNAG

data_processing:
Pre-processing was done with Cellranger v6.0.1 except for fibroblast data, v4.0.0
Assembly: Mm10
Supplementary files format and content: comma-separated files, count matrices
Supplementary files format and content: comma-separated files, TCR contig information
Supplementary files format and content: comma-separated files, hashing information

source_name: liver metastasis

growth_protocol: C57BL/6J mice, were purchased from Janvier Labs at six weeks of age, and injected at 7-8 weeks. Intrasplenic injections were used for liver colonization by the introduction of dissociated organoids (small 3-4 cell clusters) into the portal circulation.

extract_protocol:
Microdissected liver metastases were chopped with scalpels. Subsequent enzymatic digestion was performed with LiberaseTM (Roche, 5401119001), 10mg/ml DNase I (Roche, 10104159001) in DMEM (Invitrogen, 41966-029) for 90 min at 37 °C, in a shaking water bath. Digested tissue fragments were quenched, filtered through 70μm cell strainer and subsequently, washed with FACS Buffer (PBS with 1% BSA (Roche, 10735086001), 2mM EDTA (Sigma, E5134-500G), 0.05% NaN3 (Sigma, S2002-25G)).  Dead cells were stained with either LIVE/DEAD™ Fixable Dead Cell Stain Kit Yellow, Aqua (ThermoFisher, L34959 & L34957) or Zombie Violet™ Fixable Viability Kit (BioLegend, 423113) or DAPI (Sigma Aldrich, D9542). Samples were Fc-blocked with anti-CD16/32, and then cells were stained for the extracellular markers for 25 min at 4°C.
10x Genomics 3-prime v3.0 (TME and CAFs) and 5-prime v1.0 (T cells)

treatment_protocol: Galunisertib (also known as LY2157299) was synthesized in house and prepared as previously described (Tauriello et al, 2018). Galunisertib or vehicle control was administered by oral gavage in a 0.15 ml volume, twice per day, starting 12-15 days after cell injection for metastasis-initiation experiments, unless otherwise indicated. An 800 mg/kg dose per treatment was used for all experiments. For checkpoint immunotherapy or dual immunotherapy, we used rat anti-PD-L1 (10F.9G2; BioXCell BE0101) or rat anti-IgG2b (LTF-2; BioXCell BE0090) isotype-control antibodies.

value: liver metastasis

value: tumor microenvironment


title: PedTALL_P6_Dx_10x5_v1.1

value: CD45+ immune cells and T-ALL cells


title: mouse kidney, Enalapril, rep3


title: Karpas1106p, C99R, 120 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_120min_2

value: cell line

value: Ephrin B2, 120 mins


title: Tumor microenvironment sample 1 galunisertib

value: Galunisertib


title: PedTALL_P5_Dx_10x5_v1.1

source_name: BM

value: BM

value: Diagnosis


title: Tumor microenvironment sample 1 dual treatment

value: anti-PD-L1 + Galunisertib


title: mouse kidney, Enalapril, rep1


title: Karpas1106p, C99R, 120 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_120min_1

value: primary mediastinal B-cell lymphoma-derived cells


title: Tumor microenvironment sample 1 control

value: Control


title: PedTALL_P4_Dx_10x5_v1.1


title: mouse kidney, Control, rep4


title: Karpas1106p, C99R, 10 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_10min_2

value: Ephrin B2, 10 mins


title: PedTALL_P3_Dx_10x5_v1.1


title: mouse kidney, Control, rep3

value: mouse kidney tissue


title: DOHH2_rTA3-miniCMV_IRF4_C99-2

description: Library name: F111044

value: Diffuse Large B-Cell Lymphoma-derived cells


title: Karpas1106p, C99R, 0 min, clone 13 biol rep 2

description: Library name: kar1106pC99R13_0min_2


title: mouse kidney, Control, rep1

value: WT


title: Karpas1106p, C99R, 10 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_10min_1


title: PedTALL_P1_Dx_10x5_v1.1


title: Karpas1106p, C99R, 0 min, clone 13 biol rep 1

description: Library name: kar1106pC99R13_0min_1


title: DOHH2_rTA3-miniCMV_IRF4_WT-2

description: Library name: F111043


title: Normal_BM2_10x5_v1.1

value: Healthy donor

value: CD45+ immune cells


title: mouse heart, Enalapril, rep4

source_name: mouse heart tissue

value: mouse heart tissue

value: Enaparil treatment


title: DOHH2_rTA3-miniCMV_IRF4_C99-1

description: Library name: F111041


title: DOHH2_rTA3-miniCMV_IRF4_WT-1

description: Library name: F111040


title: mouse heart, Enalapril, rep3


title: CLN2-2_D200_4

city: Tuebingen

first: Kevin

last: Achberger

address: Oesterbergstrasse 3

country: Germany

institute: University Tübingen

description: Library name: 24022a016

data_processing:
The sequencing aimed to achieve a depth of approximately >20 million clusters per sample. Read quality of RNA-seq data in fastq files was assessed using ngs-bits (2023_11-253-gc83b16dc), to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification. Reads were aligned using STAR v2.7.10b (Dobin et al.,2013) to the GRCh38 and alignment quality was analyzed using ngs-bits and visually inspected in the Integrative Genome Viewer (v2.15.4). Normalized read counts for all genes were obtained using Subread (v2.0.4).
Assembly: GRCh38
Supplementary files format and content: tsv files for raw, tpm, cpm, fpkm

source_name: Retinal organoids

growth_protocol: ROs were differentiated from hiPSCs based on a previously described protocol by Zhong et al., 2014 with additional modifications  (Achberger et al., 2019)

extract_protocol:
RNA was extracted using the Qiagen MicroRNeasy Kit. The concentration of RNA was measured using the Qubit Fluorometric Quantitation and RNA Broad-Range Assay (Thermo Fisher Scientific, USA). RNA Integrity Number RIN was determined using the Fragment Analyzer 5300 and the Fragment Analyzer RNA kit (Agilent Technologies, USA) and presented a good integrity (RIN>7).
For library preparation, the mRNA fraction was enriched using polyA capture from 100ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Subsequently, libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext UDI UMI (NEB, USA) following the manufacturer’s instructions. To minimize technical batch effects, library preparations were performed using the liquid handler Biomek i7 (Beckman). The library molarity was determined by measuring the library size (approximately 400 bp) using the Fragment Analyzer 5300 and the Fragment Analyzer DNA HS NGS fragment kit (Agilent Technologies, USA) and the library concentration (>2 ng/µl) using Qubit Fluorometric Quantitation and dsDNA High sensitivity assay (Thermo Fisher Scientific, USA). The libraries were denaturated according to the manufacturer’s instructions, diluted to 150 pM and sequenced as paired-end 100bp reads on an Illumina NovaSeqX (Illumina, USA).

treatment_protocol: On day 0 of treatment, one RO was placed in each well of non-adherent 96-well plates in 80 µl BRDM with 10% FBS and 100 µM taurine (depending on the age of the ROs, the medium was additionally supplemented with RA, as mentioned above). AAVs were thawed in ice and added via a 50% medium change to obtain a genome copy number of 1.67x10^11 gc/well. On day 1, 20 µl of medium were added per well in order to have a final volume of 100 µl/well. The medium was changed twice per week by a 70% replacement. On day 7 the medium volume was increased to 150 µl/well and on day 35 the ROs were transferred to a 48-well plate with 300 µl culture medium. From day 49, the ROs were cultured in 500 µl/well. A. For the scRNA-seq analysis, the organoids were cultured for 70 days after treatment.

value: Retinal organoids

value: hIPSC-derived Retinal Organoids


title: CLN2-2_D200_3

description: Library name: 24022a015


title: mouse heart, Enalapril, rep2


title: DOHH2_rTA3-miniCMV_IRF4_Emp-1

description: Library name: F111039

value: cell line


title: CLN2-2_D200_2

description: Library name: 24022a014


title: libraryPDZ3_aPCA_G05_DC_a1_wt

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

institute: CRG

description: Library name: Sample 7

data_processing:
DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Assembly: S288C
Supplementary files format and content: MS Excel format; contains Dimsum fitness estimates, inferred growth rates and their corresponding errors for all libraries; see README tab for a description of all columns

extract_protocol:
Cell pellets (one for each experiment input/output replicate) were re-suspended in 2 mL of DNA extraction buffer, frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 2 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.2 mL of NaOAc 3M and 4.4 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC at least for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (50 µL of QIAEX II beads, QIAGEN). The samples were washed twice with PE buffer and eluted twice by 125 µL of 10 mM Tris-HCI buffer, pH 8.5. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
The sequencing libraries were constructed in two consecutive PCR reactions. The first PCR (PCR1) was designed to amplify the mutated protein of interest and to increase the nucleotide complexity of the first sequenced bases by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) was necessary to add the remainder of the Illumina adapter and demultiplexing indexes. PCR2 reactions were run for each sample independently using Hot Start High-Fidelity DNA Polymerase. In this second PCR the remaining parts of the Illumina adapters were added to the library amplicon. The forward primer (5’ P5 Illumina adapter) was the same for all samples in libraries 1-3 and containing a different barcode index in library 4. The reverse primer (3’ P7 Illumina adapter) differed by the barcode index  to be subsequently pooled together and demultiplex them after deep sequencing. All samples were pooled in an equimolar ratio and gel purified using the QIAEX II Gel Extraction Kit. The purified amplicon library pools were subjected to Illumina 150bp paired-end Nextseq500 (libraries 1-3) or Nextseq2000 (library 4) sequencing at the CRG Genomics Core Facility.


title: PedTALL_P2_Dx_10x5_v1.1

value: Pediatric T-ALL

value: CD45+ immune cells and T-ALL cells


title: CLN2-2_D200_1

description: Library name: 24022a013


title: mouse heart, Enalapril, rep1


title: MKN45, sgSETD1A

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Basecalls were performed using bcl2fastq.
Sequenced reads from RNA-seq experiments were aligned by using HISAT2.
FPKM was extracted using Cufflinks.
Assembly: hg19
Supplementary files format and content: tab-deliminated text file included TPM valuse for each sample

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptmycin. AGS cells were cultured in RPMI1640 containing additional 1% non-essential amino acid. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Doxycycline was prepared to a stock solution at a concentration of 1 mg/mL in PBS and used as 1:1000 dilution.

value: Human gastric cancer cell line

value: SETD1A knockout

value: Doxycycline 6 days


title: mouse kidney, Control, rep2

value: Control


title: Normal_PB1_10x5_v1.1

value: PB


title: mouse heart, Control, rep4


title: DOHH2_rTA3-miniCMV_IRF4_Emp-2

description: Library name: F111042


title: Normal_BM1_10x5_v1.1

value: BM


title: CLN2-1_D200_4

description: Library name: 24022a012


title: SNU719, sgSETD1A


title: libraryPDZ3_aPCA_G05_DC_a1_output_bio_rep_3

city: Barcelona

description: Library name: Sample 6


title: MKN45, sgEmpty

value: SETD1A wt


title: SNU719, sgEmpty


title: CLN2-1_D200_3

description: Library name: 24022a011


title: mouse heart, Control, rep1

value: WT


title: mouse heart, Control, rep3


title: Normal_PB2_10x5_v1.1

value: Healthy donor


title: libraryPDZ3_aPCA_G05_DC_a1_input_bio_rep_3

description: Library name: Sample 3


title: CLN2-1_D200_2

description: Library name: 24022a010


title: libraryPDZ3_aPCA_G05_DC_a1_output_bio_rep_1

description: Library name: Sample 4


title: mouse brain, Enalapril, rep4

source_name: mouse brain tissue

value: mouse brain tissue


title: CLN2-1_D200_1

description: Library name: 24022a009


title: AGS, sgSETD1A, H3K4me3, ChIP

data_processing:
Basecalls were performed using bcl2fastq.
Data were mapped to the University of California Santa Cruz human genome assembly (hg19) using Bowtie2 and duplicated reads were removed using Picard tools.
bigwig files were generated using HOMER software.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: AGS

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptmycin, 1% non-essential amino acid. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. For SETD1A, RNAP2, Ser2P and H3K36me3 ChIP, we fixed cells with 2 mM DSG for 30 min before formaldehyde fixation. After washing and cell lysis, nuclei pellets were sonicated by using Picoruptor (Diagenode)
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems).

value: AGS


title: libraryPDZ3_aPCA_G05_DC_a1_input_bio_rep_2

description: Library name: Sample 2


title: CTRL1_d200_4

description: Library name: 24022a008

value: CTRL


title: AGS, sgEmpty, H3K4me3, ChIP


title: libraryPDZ3_aPCA_G05_DC_a1_input_bio_rep_1

description: Library name: Sample 1


title: libraryPDZ3_aPCA_G05_DC_a1_output_bio_rep_2

description: Library name: Sample 5


title: mouse brain, Enalapril, rep3

value: Enaparil treatment


title: mouse heart, Control, rep2

value: mouse heart tissue


title: mouse brain, Enalapril, rep2


title: mouse brain, Enalapril, rep1


title: CTRL1_d200_2

description: Library name: 24022a006

value: Retinal organoids

value: hIPSC-derived Retinal Organoids


title: AGS, sgEmpty, H3K4me2, ChIP


title: Aged + Replacement + ICH, replicate 3, scRNA-seq

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
We performed alignment to this amended reference using BSCMatrix (http://www.bmkmanu.com/portfolio/tools) to obtained expression matrices, which employs the STAR sequence aligner
Assembly: GRCm38_release95
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The perihematomal brain tissues from aged ICH mice were dissociated enzymatically to obtain a single-cell suspension with the self-prepared hydrolysate or the hydrolysate kit (MACS Mouse Tumor Dissociation kit DS_130-096-730). Next, Hank’s Balanced Salt Solution with calcium and magnesium (Gibco, Germany) was added to stop the enzymatic reaction. A 70 and 40 μm strainer was used to filter the resulting cell suspension, followed by centrifuging at 300 × g, 4 °C for 10 min. Then, myelin was removed by centrifugation on a 22% Percoll gradient. Briefly, cells were suspended in 25 mL Percoll solution [18.9 mL gradient buffer containing 5.65 mM NaH2PO4H2O, 20 mM Na2HPO42 (H2O), 135 mM NaCl, 5 mM KCl, 10 mM glucose, 7.4 pH; 5.5 mL Percoll (GE Healthcare, Germany); 0.6 mL 1.5 M NaCl)], overlayered with 5 mL PBS and centrifuged for 20 min at 950 × g and 4 °C, without acceleration and brakes.
We prepared single cell suspensions from cultured cell lines and single cells were suspended in PBS containing 0.04% BSA. The cell suspension was loaded onto the BMKMANU C1000 Chip and ran the Droplet Generation Equipment to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer's protocol. The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100.

value: brain

value: neural cells and myeloid cells

value: 18 months old

value: Replacement + ICH


title: Aged + Replacement + ICH, replicate 2, scRNA-seq


title: CTRL1_d200_1

description: Library name: 24022a005


title: AGS, sgSETD1A, H3K4me1, ChIP

value: Human gastric cancer cell line

value: SETD1A knockout

value: Doxycycline 6 days


title: Aged + Replacement + ICH, replicate 1, scRNA-seq


title: mouse brain, Control, rep4

value: Control


title: CTRL2_d200_4

description: Library name: 24022a004


title: AGS, sgEmpty, H3K4me1, ChIP

value: SETD1A wt


title: mouse brain, Control, rep3

value: WT


title: CTRL2_d200_3

description: Library name: 24022a003


title: mouse brain, Control, rep2

value: mouse brain tissue


title: AGS, sgSETD1A, H3K4me2, ChIP

value: AGS


title: CTRL2_d200_2

description: Library name: 24022a002

value: CTRL


title: CTRL1_d200_3

description: Library name: 24022a007


title: Aged + Control + ICH, replicate 2, scRNA-seq

value: Control + ICH


title: mouse brain, Control, rep1


title: Aged + Control + ICH, replicate 1, scRNA-seq


title: T cells, WT3

status: Public on Jul 24 2025

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each smple

source_name: T cells

extract_protocol:
Total RNA was extracted using TRIzol and the quality and quantity of total RNA were evaluated using an Agilent 2100 Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: T cells

value: PBS


title: T cells, WT1

description: Library name: sample4


title: Low_input_RNAseq_invitro_Tcells

description: Low input RNA-seq (SmartSeq2)

data_processing:
Sequencing reads were demultiplexed (bcl2fastq 2.20), trimmed (trimmomatic 0.36) and aligned (STAR 2.5.2b aligner) to the GRCh37 reference genome. Htseq 0.9.1 was used for gene counting.
Assembly: hg19
Supplementary files format and content: *barcodes.tsv: Raw cell barcodes.
Supplementary files format and content: *RNA_features.tsv.gz: Raw genes.
Supplementary files format and content: *RNA_matrix.mtx.gz: raw gene-barcode matrices.
Supplementary files format and content: *ADT_features.tsv.gz: Raw surface protein antibodies.
Supplementary files format and content: *ADT_matrix.mtx.gz: Raw surface protein antibody-barcode matrices.
Supplementary files format and content: *HTO_features.tsv.gz: Raw hashtag antibodies.
Supplementary files format and content: *HTO_matrix.mtx.gz: Raw hashtag antibody-barcode matrices.
Supplementary files format and content: *TCR_filtered_contig_annotation.tsv.gz: Filtered TCR contig sequences and annotations.
Supplementary files format and content: *BCR_filtered_contig_annotation.tsv.gz: Filtered BCR contig sequences and annotations.
Supplementary files format and content: Low_Input_RNAseq_invitro_Tcells_counts.txt: raw gene counts low-input RNA-seq in-vitro T-cells.
Supplementary files format and content: Low_Input_RNAseq_invitro_Tcells_meta.txt: metadata low-input RNA-seq in-vitro T-cells.

growth_protocol: T-cells were cultured in XVivo 15 (Lonza) supplemented with 5% Human serum (Sigma Aldrich) and 150 U/ml IL2 (Miltenyi Biotec). T-cells were activated by Human T-Activator CD3/CD28 Dynabeads (Life Technologies) for 10 days followed by 4 days of culture without beads. Media and cytokines were refreshed every 2 days.

extract_protocol:
Minipools of 100 viable CD3+ cells (DAPI negative, singlets) were sorted for CD8 high, CD8 mid and CD8 low cells into a 96-well plate containing 10ul lysis buffer (TCL buffer (Qiagen) supplemented with 1% B-mercapthoethanol (Life Technologies)).
Full-length low-input RNA-seq libraries were prepared using the Smart-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

treatment_protocol: CD8+ T-cells were treated with 100ng/ml CXCL16 (R&D)

value: PB

value: CD3+ T-cells


title: T cells, WT2

description: Library name: sample5


title: T cells, CIS3

description: Library name: sample3

value: 40μM cisplatin


title: T cells, CIS2

description: Library name: sample2


title: T cells, CIS1

description: Library name: sample1


title: Day 194 SFTPCC121Y/tdT iAT2s

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: 10X Genomics

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: H5 files

growth_protocol: To generate iAT2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 16, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 17 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI+Y medium, consisting of complete serum-free differentiation medium (cSFDM) base supplemented with 3 µM CHIR99021, 10 ng/ml rhKGF (CK), 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 3’,5’-cyclic monophosphate sodium salt (Sigma), 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI), and 10 μM Y-27632 (Tocris). SFTPCtdTomato+ cells were sorted on days 45, 87, and 182 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 10-14 days through day 194. On day 194, all live cells, irrespective of SFTPCtdTomato expression, were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single-Cell 30 Library Kit (10X Genomics) and loaded on a NextSeq500 (Illumina) with a custom sequencing setting to obtain a sequencing depth of ~40k reads/cell

value: Induced pluripotent stem cell-derived alveolar epithelial type 2 cells (iAT2s)

value: SFTPC C121Y/tdTomato

value: CK+DCI+Y