title: C2(Sup)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
C2.txt

tag: Sex

value: acanthosis nigricans


title: Postmortem, Ventrolateral prefrontal cortex, female, 85 yrs, 4 hr, snRNA-Seq

status: Public on Aug 29 2025

type: SRA

city: Budapest

first: Karolina

last: Pircs

address: Tűzoltó street 37-47

department: Institute of Translational Medicine

country: Hungary

institute: Semmelweis University

description: Library name: AA112_KP_221_VLPFCX_female_ctrl

library_source: transcriptomic single cell

data_processing:
Raw base calls were demultiplexed to obtain sample-specific FastQ files and reads were aligned to the GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics Cell Ranger 7.0.0; RRID:SCR_017344)43 with default parameters and include-introns set to true. The resulting matrix files were used for further analysis. All downstream analysis was done using R (v4.3.1; RRID:SCR_001905) and the standard workflow of Seurat (v4.4.0; RRID:SCR_016341)52. Nuclei with read counts between 1,200 and 100,000, gene counts between 800 and 12,000, and less than 5% mitochondrial transcripts were alone included for the analysis. The data was integrated using Harmony (v1.1.0; RRID:SCR_022206)53, where both sequencing batches and individual samples were regressed out, and the first 39 principal components were chosen. Clusters resolved at a resolution of 0.2 were annotated based on canonical cell type markers of the human prefrontal cortex. Further, any doublets or multiplets detected using scDblFinder (v1.14.0; RRID:SCR_022700)54 were removed.
Assembly: GRCh38
Supplementary files format and content: Compressed .gz files containing tab-separated values and matrix files obtained from Cell Ranger output.

molecule: nuclear RNA

organism: Homo sapiens

source_name: Postmortem Prefrontal Cortex

extract_protocol:
Post mortem tissue collection: Human post mortem brain tissue samples were obtained from the Human Brain Tissue Bank (Semmelweis University, Budapest, Hungary). Tissue samples were collected from 31 individuals who had not been diagnosed with any psychiatric disorder and neurodegenerative disorders. The brains were removed with a PMI of 2 – 12 hours, drop frozen using dry ice, and stored at −80 °C until further dissection. Samples were punched out from the lateral surface of the prefrontal cortices of the diseased subjects using specialized microdissection needles with 8- and 15-mm internal diameters. While most of the samples were dissected from the ventrolateral prefrontal cortex, some originated from the dorsolateral prefrontal cortex and from the middle frontal gyrus (the dorsal part of which belongs to the dorsolateral prefrontal cortex and its ventral part to the ventrolateral prefrontal cortex). The dissected cortical tissue pellets included both gray and white matter portions within the gyrus. Samples were collected in 1.5 mL Eppendorf tubes and stored at −80 °C until further use. Throughout the microdissection procedure, the tissue samples were kept frozen.  Single-nuclei Isolation: The nuclei isolation from the frozen post mortem brain tissue was performed as described previously in Soderstan et. al. 2018 and Jonsson et al 2021. Briefly, the tissue was thawed and dissociated in ice-cold lysis buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, 10 mM tris-HCl (pH 8.0), and 1 mM dithiothreitol] using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion [1.8 M sucrose, 3 mM MgAc, 10 mM tris-HCl (pH 8.0), and 1 mM dithiothreitol] before centrifugation at 30,000 g for 2 hours and 15 minutes. After supernatant removal, the pelleted nuclei were softened for 10 minutes in 50 μl of nuclear storage buffer [15% sucrose, 10 mM tris-HCl (pH 7.2), 70 mM KCl, and 2 mM MgCl2] before being resuspended in 300 μl of dilution buffer [10 mM tris-HCl (pH 7.2), 70 mM KCl, and 2 mM MgCl2] and filtered through a cell strainer (70 μm). Nuclei were stained with Draq7 and run through FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 μm nozzle (reanalysis showed >99% purity). 8,500 nuclei were sorted and used for downstream applications (snRNA Sequencing). Detailed protocol can be found at doi: dx.doi.org/10.17504/protocols.io.5jyl8j678g2w/v1.
Nuclei intended for single-nucleus RNA-sequencing (8,500 nuclei per sample) were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription master mix following the manufacturer’s protocol for the Chromium Next GEM single cell 3′ kit (PN-1000268, 10x Genomics), to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 13 cycles of amplification. Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.

tag: tissue

value: Postmortem Prefrontal Cortex

tag: brain region

value: Ventrolateral prefrontal cortex

value: female

tag: age group

value: Old

tag: age (years)

tag: post mortem_interval_(hours)

tag: cause of_death

tag: pre-manifest alzheimer's_disease

value: Positive

tag: sequencing batch


title: PIP d3 CD45+ rep2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: S58

library_source: transcriptomic

data_processing:
To pre-process FASTQ files, we used the nf-core RNA-seq pipeline version 3.14.0 with default parameters, except for UMI extraction: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*".
In brief, we mapped the paired-end reads to the human genome (Ensembl, release 109) using STAR 2.7.9a and performed downstream quantification with Salmon 1.10.1.
Assembly: mm10
Supplementary files format and content: count tables (.txt) and metadata tables (.txt)

molecule: total RNA

organism: Mus musculus

growth_protocol: After transduction with lentivirus, MEFs were cultured in gelatin-coated plates in DMEM+10%FBS.

extract_protocol:
Total RNA from 5000 cells was extracted using the Qiagen RNeasy Kit following the manufacturer’s protocol. cDNA was transcribed with a RNA, SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio), amplified by 13 to 14 cycles of PCR, and purified with AMPure XP beads (Beckman). cDNA was quantified using a High Sensitivity DNA kit on TapeStation 4200 (Agilent).
Library preparation was performed using a Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were normalized with beads, pooled, and sequenced on an NovaSeq X Series 10B Reagent Kit (300 Cycle) (read length 150-8-8-150).

treatment_protocol: Cells were sorted by FACS.

tag: cell line

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

tag: transduction

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)

tag: time

value: Cells were collected 3 days after viral transduction

tag: sorted cells

value: live(DAPI-) and CD45+


title: C1(Sup)

type: RNA

city: Changsha

first: Jianyun

last: Lu

state: Hunan

address: Tongzipo Road, Yuelu District

country: China

institute: Third Xiangya Hospital, Central South University

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
C1.txt

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  A

source_name: SKIN

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from lesion areas, which were identified by a surgical pathologist using every 10th section stained by May-Giemsa.

value: SKIN

value: Female

tag: disease


title: Postmortem, Ventrolateral prefrontal cortex, male, 80 yrs, 4.5 hr, snRNA-Seq

description: Library name: AA103_KP_222_VLPFCX_male_ctrl

value: male

value: cardiorespiratory insufficiency

value: Negative


title: T3(IP)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
T3.txt

value: normal skin


title: 4-week TH Dagla WT Sample 1

city: Cambridge

first: Morgan

last: Sheng

state: MA

address: 75 Ames St

country: USA

institute: Broad Institute of MIT and Harvard

description: Library name: dagla_4w_TH_WT_1

data_processing:
Reads were aligned to mm10 and gene and isoform level expression leves were estimated using Salmon (version 1.7.0, with arguments -l A --posBias --seqBias --gcBias --validateMapping)
Assembly: mm10
Supplementary files format and content: CSV file contains Salmon's counts estimation for all genes and all samples

molecule: polyA RNA

source_name: Thalamus

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Dagla mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

value: Thalamus

value: WT

tag: age


title: PIB d9 tdT+CD45+ rep5

description: Library name: S56

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)

value: Cells were collected 9 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: PIP d3 CD45+ rep1

description: Library name: S57


title: Postmortem, Ventrolateral prefrontal cortex, male, 76 yrs, 5.5 hr, snRNA-Seq

description: Library name: AA105_KP_290_VLPFCX_male_ctrl

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

tag: Sex

value: Old

value: stroke


title: C3(Sup)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
C3.txt

tag: tissue

value: acanthosis nigricans


title: 4-week TH Dagla -/- Sample 4

description: Library name: dagla_4w_TH_KO_4

value: Dagla -/-


title: T2(IP)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
T2.txt

value: SKIN


title: PIB d9 tdT+CD45+ rep4

description: Library name: S55

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)


title: Postmortem, Ventrolateral prefrontal cortex, female, 80 yrs, 1 hr, snRNA-Seq

description: Library name: AA111_KP_147_VLPFCX_female_ctrl

tag: brain region

value: female

value: acute respiratory insufficiency


title: 4-week TH Dagla -/- Sample 3

description: Library name: dagla_4w_TH_KO_3


title: Postmortem, Ventrolateral prefrontal cortex, male, 75 yrs, 8 hr, snRNA-Seq

description: Library name: AA109_KP_278_VLPFCX_male_ctrl

value: male

tag: age group

value: Negative


title: Postmortem, Ventrolateral prefrontal cortex, male, 74 yrs, 1 hr, snRNA-Seq

description: Library name: AA110_KP_87_VLPFCX_male_ctrl

tag: age (years)

value: acute cardiac insufficiency


title: PIB d9 tdT+CD45+ rep2

description: Library name: S53

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)


title: 4-week TH Dagla -/- Sample 5

description: Library name: dagla_4w_TH_KO_5

value: Thalamus


title: Muscle.60mins.x10Hz-6

first: Ritu

last: Raman

address: 77 Massachusetts Avenue

department: Mechanical Engineering

institute: Massachusetts Institute of Technology

description:
Library name: D24-16139
Singular G4

data_processing:
Fastq files were generated with the Illumina off-line basecaller (olb) v. 1.9.4.
Reads were aligned against mm10 (Feb., 2009) using bwa mem v. 0.7.12-r1039 with flags –t 16 –f, and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5´ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using bedtools v. 2.25.0. In addition, each resulting bam file was randomly down-sampled to a million reads, which were aligned against hg19, and read density across genomic features were estimated for RNA-Seq-specific quality control metrics
Fastq files were processed using the nf-core/rnaseq v 3.11.1 pipeline [https://zenodo.org/records/10171269] in the Nextflow 22.10.4 environment, using the GRCm39 reference genome and ENSEMBL GRCm39.110 murine annotation.
Gene-level expression tables of counts and transcript-per-million (TPM) generated by STAR/Salmon processing were retrieved [Dobin2013, Soneson2015, Patro2017] .
Assembly: GRCm39 / ENSEMBL 110 annotation
Supplementary files format and content: Gene-level raw counts and transcript per million (TPM) data generated by Salmon, tab-separated format

source_name: muscle

growth_protocol: High glucose DMEM w/ l-glutamine, sodium pyruvate and glucose as the base, with 10% fetal bovine serum and 1% pen-strep for growth of these myoblasts. Differentiated using the same DMEM but with 10% inactivated horse serum and 50 ng/ml IGF-1.

extract_protocol:
Followed the Rneasy Mini Kit for RNA extraction
Ten microliters of undiluted total RNA was incubated with 10ul of NEB Dynabeads for polyaA+ RNA selection, eluted, and fragmented in 20ul. Illumina libraries were constructed using NEB Ultra II protocol; 5ul of the fragmented solution using half the amount of reagent and 1,2 PrD instead of enhancer in the ligation step, with 14 PCR cycles of final amplification and TS Singular index barcoding.Library sizes were quantified and verified by QPCR and on a Fragmen t Analyzer before loading for sequencing on a Singular G4 instrument in a 50-base paired-end configuration. Low-input samples were prepared by ribodepletion using the ZapR v2 protocol and mammalian-specific R-probe V2 kit at full volume (7.5 min fragmentation time).

value: muscle

value: myoblast


title: T1(Sup)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
T1.txt

value: Female

value: normal skin


title: 4-week TH Dagla -/- Sample 1

description: Library name: dagla_4w_TH_KO_1


title: Postmortem, Ventrolateral prefrontal cortex, female, 74 yrs, 1.5 hr, snRNA-Seq

description: Library name: AA107_KP_204_VLPFCX_female_ctrl

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

value: Old

tag: post mortem_interval_(hours)


title: PIB d9 tdT+CD45+ rep1

description: Library name: S52

value: Cells were collected 9 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: C3(IP)

value: SKIN

value: acanthosis nigricans


title: T1(IP)


title: Muscle.60mins.x10Hz-5

description:
Library name: D24-16138
Singular G4


title: Postmortem, Ventrolateral prefrontal cortex, male, 73 yrs, 6 hr, snRNA-Seq

description: Library name: AA101_KP_180_VLPFCX_male_ctrl

tag: cause of_death

value: acute cardiac failure;general arteriosclerosis


title: Muscle.60mins.x10Hz-4

description:
Library name: D24-16137
Singular G4


title: 4-week TH Dagla +/- Sample 4

description: Library name: dagla_4w_TH_HT_4

value: Dagla +/-


title: Postmortem, Ventrolateral prefrontal cortex, female, 72 yrs, 1 hr, snRNA-Seq

description: Library name: AA113_KP_260_VLPFCX_female_ctrl

value: female

value: pulmonary embolism

tag: pre-manifest alzheimer's_disease

value: Negative


title: C2(IP)


title: C1(IP)


title: Muscle.60mins.x10Hz-3

description:
Library name: D24-16136
Singular G4


title: PIB d9 tdT+ rep4

description: Library name: S50

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)

value: live(DAPI-) and tdT+


title: 4-week TH Dagla +/- Sample 5

description: Library name: dagla_4w_TH_HT_5

value: Thalamus


title: PIB d9 tdT+CD45+ rep3

description: Library name: S54


title: 4-week TH Dagla -/- Sample 2

description: Library name: dagla_4w_TH_KO_2

value: Dagla -/-


title: Muscle.60mins.x10Hz-2

description:
Library name: D24-16135
Singular G4

value: muscle

value: myoblast


title: Postmortem, Ventrolateral prefrontal cortex, female, 56 yrs, 6 hr, snRNA-Seq

description: Library name: DA823_KP_Sample_211_301

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

value: Middle Age

value: cardiorespiratory insufficiency

tag: sequencing batch


title: Postmortem, Ventrolateral prefrontal cortex, female, 70 yrs, 7 hr, snRNA-Seq

description: Library name: AA108_KP_271_VLPFCX_female_ctrl

value: Old

value: stroke


title: 4-week TH Dagla +/- Sample 3

description: Library name: dagla_4w_TH_HT_3

value: Dagla +/-


title: PIB d9 tdT+ rep3

description: Library name: S49

tag: cell line

value: Cells were collected 9 days after viral transduction


title: Muscle.60mins.x10Hz-1

description:
Library name: D24-16134
Singular G4

tag: cell type


title: 4-week TH Dagla +/- Sample 2

description: Library name: dagla_4w_TH_HT_2

tag: genotype


title: Muscle.60mins.x4Hz-6

description:
Library name: D24-16133
Singular G4


title: PIB d9 tdT+ rep5

description: Library name: S51

tag: transduction


title: PIB d9 tdT+ rep1

description: Library name: S47

tag: time


title: 4-week TH Dagla +/- Sample 1

description: Library name: dagla_4w_TH_HT_1


title: Postmortem, Ventrolateral prefrontal cortex, male, 55 yrs, 1 hr, snRNA-Seq

description: Library name: AA91_KP_69_763

value: male

value: acute myocardial infarction

value: Negative


title: 4-week ST Dagla WT Sample 6

description: Library name: dagla_4w_ST_WT_6

source_name: Striatum

value: Striatum

value: WT


title: Postmortem, Ventrolateral prefrontal cortex, male, 50 yrs, 2 hr, snRNA-Seq

description: Library name: AA93_KP_160_870

value: myocardial infarction


title: PIB d9 CD45+ rep4

description: Library name: S46

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)

tag: sorted cells

value: live(DAPI-) and CD45+


title: Muscle.60mins.x4Hz-4

description:
Library name: D24-16131
Singular G4

value: muscle

value: myoblast


title: 4-week ST Dagla WT Sample 5

description: Library name: dagla_4w_ST_WT_5


title: Muscle.60mins.x4Hz-3

description:
Library name: D24-16130
Singular G4


title: Postmortem, Ventrolateral prefrontal cortex, female, 49 yrs, 6 hr, snRNA-Seq

description: Library name: DA825_KP_Sample_175_720

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

value: female

value: Middle Age

value: suicide drug overdose


title: 4-week ST Dagla WT Sample 4

description: Library name: dagla_4w_ST_WT_4


title: PIB d9 CD45+ rep2

description: Library name: S44

value: Cells were collected 9 days after viral transduction


title: Postmortem, Ventrolateral prefrontal cortex, male, 47 yrs, 1 hr, snRNA-Seq

description: Library name: AA92_KP_156_855

value: male

value: cardiac insufficiency


title: Muscle.60mins.x4Hz-2

description:
Library name: D24-16129
Singular G4


title: PIB d9 CD45+ rep1

description: Library name: S43


title: 4-week ST Dagla WT Sample 3

description: Library name: dagla_4w_ST_WT_3

value: Striatum


title: Muscle.60mins.x4Hz-1

description:
Library name: D24-16128
Singular G4


title: Postmortem, Dorsolateral prefrontal cortex, female, 44 yrs, 5 hr, snRNA-Seq

description: Library name: DA826_KP_Sample_215_A968

value: Dorsolateral prefrontal cortex

value: acute cardiac insufficiency

value: Negative


title: PIB d9 tdT+ rep2

description: Library name: S48

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: live(DAPI-) and tdT+


title: 4-week ST Dagla WT Sample 2

description: Library name: dagla_4w_ST_WT_2

value: WT


title: Postmortem, Ventrolateral prefrontal cortex, male, 42 yrs, 3.5 hr, snRNA-Seq

description: Library name: AA90_KP_65_937


title: PIB d6 tdT+CD45+ rep4

description: Library name: S42

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)

value: Cells were collected 6 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: Muscle.60mins.x1Hz-6

description:
Library name: D24-16127
Singular G4

value: muscle

value: myoblast


title: Postmortem, Ventrolateral prefrontal cortex, male, 53 yrs, 5 hr, snRNA-Seq

description: Library name: AA94_KP_216_A199

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

value: Middle Age

value: pulmonary embolism


title: 4-week ST Dagla WT Sample 1

description: Library name: dagla_4w_ST_WT_1

value: Striatum


title: Muscle.60mins.x4Hz-5

description:
Library name: D24-16132
Singular G4


title: PIB d6 tdT+CD45+ rep3

description: Library name: S41


title: Muscle.60mins.x1Hz-5

description:
Library name: D24-16126
Singular G4


title: PIB d9 CD45+ rep3

description: Library name: S45

value: Cells were collected 9 days after viral transduction

value: live(DAPI-) and CD45+


title: 4-week ST Dagla -/- Sample 5

description: Library name: dagla_4w_ST_KO_5

value: Dagla -/-


title: Postmortem, Middle frontal gyrus, female, 39 yrs, 12 hr, snRNA-Seq

description: Library name: DA818_KP_sample_210_1

value: Middle frontal gyrus

value: female

value: Young

value: suicide hanging

value: Negative


title: PIB d6 tdT+CD45+ rep2

description: Library name: S40

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)

value: Cells were collected 6 days after viral transduction


title: Muscle.60mins.x1Hz-4

description:
Library name: D24-16125
Singular G4

value: muscle

value: myoblast


title: Postmortem, Ventrolateral prefrontal cortex, male, 36 yrs, 6 hr, snRNA-Seq

description: Library name: DA468_KP_sample_136

value: Postmortem Prefrontal Cortex

value: Ventrolateral prefrontal cortex

value: male

value: suicide


title: 4-week ST Dagla -/- Sample 4

description: Library name: dagla_4w_ST_KO_4

value: Striatum


title: PIB d6 tdT+CD45+ rep1

description: Library name: S39

value: live(DAPI-) and tdT+CD45+


title: Muscle.60mins.x1Hz-3

description:
Library name: D24-16124
Singular G4


title: Postmortem, Middle frontal gyrus, female, 36 yrs, 2 hr, snRNA-Seq

description: Library name: DA464_KP_sample_145

value: Middle frontal gyrus


title: PIB d6 tdT+ rep4

description: Library name: S38

value: live(DAPI-) and tdT+


title: Muscle.60mins.x1Hz-2

description:
Library name: D24-16123
Singular G4


title: 4-week ST Dagla -/- Sample 3

description: Library name: dagla_4w_ST_KO_3

value: Dagla -/-


title: Postmortem, Middle frontal gyrus, male, 35 yrs, 6 hr, snRNA-Seq

description: Library name: DA469_KP_sample_243

value: Young


title: 4-week ST Dagla -/- Sample 2

description: Library name: dagla_4w_ST_KO_2


title: 4-week ST Dagla -/- Sample 1

description: Library name: dagla_4w_ST_KO_1


title: Postmortem, Middle frontal gyrus, male, 31 yrs, 7 hr, snRNA-Seq

description: Library name: DA467_KP_sample_234

value: Negative


title: PIB d6 tdT+ rep2

description: Library name: S36

value: mouse embryonic fibroblast


title: Muscle.60mins.Control-6

description:
Library name: D24-16121
Singular G4


title: 4-week ST Dagla +/- Sample 5

description: Library name: dagla_4w_ST_HT_5

value: Dagla +/-


title: Postmortem, Middle frontal gyrus, male, 31 yrs, 8 hr, snRNA-Seq

description: Library name: DA466_KP_sample_171


title: PIB d6 tdT+ rep1

description: Library name: S35

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)


title: Muscle.60mins.Control-5

description:
Library name: D24-16120
Singular G4

value: muscle


title: 4-week ST Dagla +/- Sample 4

description: Library name: dagla_4w_ST_HT_4


title: PIB d6 CD45+ rep3

description: Library name: S34

value: Cells were collected 6 days after viral transduction

value: live(DAPI-) and CD45+


title: Postmortem, Middle frontal gyrus, male, 22 yrs, 8 hr, snRNA-Seq

description: Library name: DA463_KP_sample_249

value: Postmortem Prefrontal Cortex


title: Postmortem, Middle frontal gyrus, male, 25 yrs, 8 hr, snRNA-Seq

description: Library name: DA471_KP_sample_254

value: male


title: PIB d6 CD45+ rep2

description: Library name: S33


title: 4-week ST Dagla +/- Sample 2

description: Library name: dagla_4w_ST_HT_2


title: Muscle.60mins.Control-3

description:
Library name: D24-16118
Singular G4

value: myoblast


title: Muscle.60mins.Control-4

description:
Library name: D24-16119
Singular G4


title: PIB d6 CD45+ rep1

description: Library name: S32


title: Muscle.60mins.Control-2

description:
Library name: D24-16117
Singular G4


title: HARP-01-5062-1

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
Quality control of sequencing reads was assessed using FastQC29 v0.11.7 and MultiQC v1.9
Reads were mapped to the human reference genome (hg38) using STAR27 v2.6.1d
Genomic features were assigned using Subread featureCounts28 v1.6.3
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: Human coronary artery endothelial cells

growth_protocol: Cells were d cultured in EGM-2 MV microvascular endothelial cell growth medium (LONZA, CC-3202) in 5% CO2 incubator at 37 ℃. Cultured cells between passage 5 and passage 8 were used for this study.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep columns (Zymo Research).
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries were sequenced single end (51bp) on an Illumina NovaSeq 6000 at the Genome Technology Center at NYU Langone.

treatment_protocol: Cells were cultured in EGM-2 MV medium containing platelet releasate (v/v, 1:10) from patients with MI or controls for 6 h at 37 ℃. Another group of cells were cultured in EGM-2 MV medium containing CCL3 (100 ng/mL) or PBS for 6 h at 37 ℃.

value: Human coronary artery endothelial cells

tag: batch

value: F

tag: donor

tag: treatment

value: Control platelet releasate


title: HARP-01-5057-1

tag: Sex


title: Muscle.60mins.Control-1

description:
Library name: D24-16116
Singular G4

tag: tissue


title: PIB d3 tdT+CD45+ rep3

description: Library name: S30

value: Cells were collected 3 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: PIB d6 tdT+ rep3

description: Library name: S37

value: live(DAPI-) and tdT+


title: HARP-01-5046-1


title: 4-week ST Dagla +/- Sample 3

description: Library name: dagla_4w_ST_HT_3

value: Striatum

tag: age


title: Muscle.60mins.x1Hz-1

description:
Library name: D24-16122
Singular G4


title: Postmortem, Middle frontal gyrus, male, 18 yrs, 8 hr, snRNA-Seq

description: Library name: DA470_KP_sample_250

tag: brain region

value: Middle frontal gyrus

tag: age group

value: Young

tag: age (years)

value: suicide

value: Negative


title: 4-week SSC Dagla WT Sample 6

description: Library name: dagla_4w_SSC_WT_6

source_name: Somatosensory Cortex

value: Somatosensory Cortex

value: WT


title: PIB d3 tdT+CD45+ rep2

description: Library name: S29

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Pu.1, Irf8, Batf3 (PIB)


title: PIB d3 tdT+CD45+ rep4

description: Library name: S31


title: HARP-01-5033-1


title: 4-week SSC Dagla WT Sample 5

description: Library name: dagla_4w_SSC_WT_5


title: 4-week SSC Dagla WT Sample 4

description: Library name: dagla_4w_SSC_WT_4


title: PIB d3 tdT+CD45+ rep1

description: Library name: S28


title: 4-week SSC Dagla WT Sample 3

description: Library name: dagla_4w_SSC_WT_3


title: PIB d3 tdT+ rep4

description: Library name: S27


title: Muscle.30mins.x10Hz.5

description:
Library name: D24-12398
Singular G4

value: muscle

value: myoblast


title: Muscle.30mins.x10Hz.6

description:
Library name: D24-12399
Singular G4


title: HARP-01-5024-1

value: Human coronary artery endothelial cells

value: F


title: Muscle.30mins.x10Hz.4

description:
Library name: D24-12397
Singular G4


title: 4-week ST Dagla +/- Sample 1

description: Library name: dagla_4w_ST_HT_1

value: Dagla +/-


title: PIB d3 tdT+ rep3

description: Library name: S26

value: Cells were collected 3 days after viral transduction


title: HARP-01-5013-1

value: Control platelet releasate


title: 4-week SSC Dagla WT Sample 1

description: Library name: dagla_4w_SSC_WT_1


title: Muscle.30mins.x10Hz.2

description:
Library name: D24-12395
Singular G4


title: Muscle.30mins.x10Hz.3

description:
Library name: D24-12396
Singular G4


title: PIB d3 tdT+ rep2

description: Library name: S25

value: live(DAPI-) and tdT+


title: PIB d3 tdT+ rep1

description: Library name: S24


title: Muscle.30mins.x10Hz.1

description:
Library name: D24-12394
Singular G4


title: 4-week SSC Dagla -/- Sample 5

description: Library name: dagla_4w_SSC_KO_5

value: Dagla -/-


title: HARP-01-5056-1


title: Muscle.30mins.x4Hz.6

description:
Library name: D24-12393
Singular G4


title: PIB d3 CD45+ rep4

description: Library name: S23

value: live(DAPI-) and CD45+


title: 4-week SSC Dagla -/- Sample 4

description: Library name: dagla_4w_SSC_KO_4


title: HARP-01-5051-1


title: 4-week SSC Dagla -/- Sample 3

description: Library name: dagla_4w_SSC_KO_3


title: Muscle.30mins.x4Hz.5

description:
Library name: D24-12392
Singular G4


title: HARP-01-5027-1


title: Muscle.30mins.x4Hz.4

description:
Library name: D24-12391
Singular G4


title: 4-week SSC Dagla -/- Sample 2

description: Library name: dagla_4w_SSC_KO_2


title: PIB d3 CD45+ rep3

description: Library name: S22


title: HARP-01-5050-1


title: PIB d3 CD45+ rep2

description: Library name: S21


title: 4-week SSC Dagla -/- Sample 1

description: Library name: dagla_4w_SSC_KO_1


title: PIB d3 CD45+ rep1

description: Library name: S20


title: Muscle.30mins.x4Hz.3

description:
Library name: D24-12390
Singular G4


title: HARP-01-5047-1


title: HARP-01-5059-1


title: 4-week SSC Dagla WT Sample 2

description: Library name: dagla_4w_SSC_WT_2


title: 4-week SSC Dagla +/- Sample 5

description: Library name: dagla_4w_SSC_HT_5


title: Muscle.30mins.x4Hz.2

description:
Library name: D24-12389
Singular G4


title: hCD2.MEF rep4

description: Library name: S19

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background

value: live(DAPI-) and YFP-CD45-


title: Muscle.30mins.x4Hz.1

description:
Library name: D24-12388
Singular G4


title: HARP-01-5045-1


title: HARP-01-5044-1


title: 4-week SSC Dagla +/- Sample 4

description: Library name: dagla_4w_SSC_HT_4

value: Somatosensory Cortex


title: 4-week SSC Dagla +/- Sample 3

description: Library name: dagla_4w_SSC_HT_3


title: hCD2.MEF rep2

description: Library name: S17


title: Muscle.30mins.x1Hz.6

description:
Library name: D24-12387
Singular G4


title: HARP-01-5040-1


title: Muscle.30mins.x1Hz.5

description:
Library name: D24-12386
Singular G4


title: 4-week SSC Dagla +/- Sample 2

description: Library name: dagla_4w_SSC_HT_2


title: hCD2.MEF rep1

description: Library name: S16


title: HARP-01-5049-1


title: HARP-01-5035-1


title: Muscle.30mins.x1Hz.4

description:
Library name: D24-12385
Singular G4


title: 4-week SSC Dagla +/- Sample 1

description: Library name: dagla_4w_SSC_HT_1


title: C9a.MEF rep4

description: Library name: S15

value: live(DAPI-) and tdT-CD45-


title: 4-week SN Dagla WT Sample 6

description: Library name: dagla_4w_SN_WT_6

source_name: Substantia Nigra

value: Substantia Nigra

value: WT


title: C9a.MEF rep3

description: Library name: S14

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)


title: HARP-01-5028-1


title: Muscle.30mins.x1Hz.3

description:
Library name: D24-12384
Singular G4

value: muscle

value: myoblast


title: HARP-01-5026-1

value: Human coronary artery endothelial cells

value: F


title: C9a.MEF rep2

description: Library name: S13


title: 4-week SN Dagla WT Sample 5

description: Library name: dagla_4w_SN_WT_5


title: HARP-01-5016-1


title: hCD2.MEF rep3

description: Library name: S18


title: Muscle.30mins.x1Hz.1

description:
Library name: D24-12382
Singular G4


title: Muscle.30mins.Control.6

description:
Library name: D24-12381
Singular G4


title: HARP-01-5015-1


title: C9a.MEF rep1

description: Library name: S12


title: pDC rep5

description: Library name: S11

source_name: pDC

value: pDC

value: splenic plasmacytoid dendritic cells

value: wildtype


title: 4-week SN Dagla WT Sample 3

description: Library name: dagla_4w_SN_WT_3


title: Muscle.30mins.Control.5

description:
Library name: D24-12380
Singular G4


title: HARP-01-5003-1

value: Control platelet releasate


title: pDC rep4

description: Library name: S10


title: Muscle.30mins.Control.4

description:
Library name: D24-12379
Singular G4


title: 4-week SN Dagla WT Sample 1

description: Library name: dagla_4w_SN_WT_1


title: HARP-01-0246-1

value: MI platelet releasate


title: 4-week SN Dagla WT Sample 2

description: Library name: dagla_4w_SN_WT_2


title: HARP-01-0245-1


title: Muscle.30mins.Control.3

description:
Library name: D24-12378
Singular G4


title: pDC rep2

description: Library name: S8


title: 4-week SN Dagla -/- Sample 5

description: Library name: dagla_4w_SN_KO_5

value: Dagla -/-


title: pDC rep3

description: Library name: S9


title: HARP-01-0243-1


title: Muscle.30mins.Control.2

description:
Library name: D24-12377
Singular G4


title: HARP-01-0236-1


title: pDC rep1

description: Library name: S7


title: Muscle.30mins.x1Hz.2

description:
Library name: D24-12383
Singular G4


title: 4-week SN Dagla WT Sample 4

description: Library name: dagla_4w_SN_WT_4


title: 4-week SN Dagla -/- Sample 4

description: Library name: dagla_4w_SN_KO_4


title: 4-week SN Dagla -/- Sample 3

description: Library name: dagla_4w_SN_KO_3


title: MuSC_Taf4a-KO_RNA-seq_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.6.0c (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove multi-mapping reads.
Gene counts were established with featureCounts 1.6.0 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.14.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Muscle stem cells

extract_protocol:
RNA was extracted from 9x10^4 freshly isolated FAC-sorted  MuSCs from control and Taf4asKO mice using  miRNeasy micro Kit (Qiagen).
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer). RNA amounts were normalized and 10ng of total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio).

tag: mouse strain

value: Muscle stem cells

tag: cell state

value: freshly isolated MuSCs


title: 4-week SN Dagla -/- Sample 2

description: Library name: dagla_4w_SN_KO_2


title: HARP-01-0204-1

tag: cell line


title: cDC2 rep3

description: Library name: S6

tag: cell type

value: splenic dendritic cell type 2


title: HARP-01-0177-1


title: MuSC_Taf4a-KO_RNA-seq_2

tag: genotype


title: cDC2 rep1

description: Library name: S4

tag: transduction


title: MuSC_Taf4a-KO_RNA-seq_1


title: 4-week SN Dagla -/- Sample 1

description: Library name: dagla_4w_SN_KO_1

value: Substantia Nigra


title: HARP-01-0174-1


title: 4-week SN Dagla +/- Sample 5

description: Library name: dagla_4w_SN_HT_5

value: Dagla +/-


title: 4-week SN Dagla +/- Sample 4

description: Library name: dagla_4w_SN_HT_4


title: HARP-01-0057-1


title: cDC1 rep3

description: Library name: S3

value: splenic dendritic cell type 1

tag: time


title: MuSC_WT_RNA-seq_3

value: Control


title: HARP-01-0043-1


title: Muscle.30mins.Control.1

description:
Library name: D24-12376
Singular G4

value: muscle


title: MuSC_WT_RNA-seq_2


title: 4-week SN Dagla +/- Sample 3

description: Library name: dagla_4w_SN_HT_3


title: cDC1 rep2

description: Library name: S2

tag: sorted cells


title: HARP-01-0039-1

tag: batch


title: 4-week SN Dagla +/- Sample 2

description: Library name: dagla_4w_SN_HT_2


title: HARP-01-0035-1

tag: donor


title: MuSC_WT_NF-YA_1_igg

library_source: genomic

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.05 and additional parameters "--extsize 100 --nomodel --to-large" (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl data.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.
Library strategy: CUT&Run

molecule: genomic DNA

extract_protocol:
1x106 wild type in vitro cultured muscle stem cells (MuSCs) were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with NF-YA (Sc-17753, Santa Cruz) or mouse IgG ( 12-371B, Millipore) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.
For Cut’n’Run library preparation, precipitated DNA samples was purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). 20ng of DNA was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio).

value: wild type

tag: cut&run antybody

value: Mouse IgG, 12-371B, Millipore

value: activated/proliferating


title: MuSC_WT_RNA-seq_1


title: cDC2 rep2

description: Library name: S5


title: root, PTW, 49 DAS, biol rep 3

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

institute: University Medicine Greifswald

description:
Library name: AM12
gene_RP49vsRC49_results.csv

data_processing:
Mapping using NextGenMap with default parameter and adding --no-unal and --very-sensitive
Counting using featureCounts with Morex V3 GTF
Differential Expression Analysis using DESeq2 independent for organs (leaf and root) and time point (22 days and 49 days) for the treatment Plasma and Control.
Assembly: Hordeum vulgare Morex V3 (Phytozyme)
Supplementary files format and content: The processed data files are in csv format after DESeq2 analysis standard output

organism: Hordeum vulgare

source_name: whole root

growth_protocol: seeds of Hordeum vulgare cv. KWS Kosmos were pre-germinated in Petri dishes on filter paper soaked in 0.5 mM calcium sulphate for 2 days in the dark, then placed in pots with a coarse- and fine-grained quartz sand mixture (ratio 2:1), grown in the greenhouse in a light/dark cycle of 14/10 hours at an air temperature of 22/18 °C, watered daily with defined nutrient solution

extract_protocol:
RNA was extracted using NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel)
mRNA library preparation (poly A enrichment)

treatment_protocol: leaves were sprayed 19, 20 and 21 days after sowing with deionized water or plasma-treated water; plants were harvested on day 22 or 49

value: whole root

value: day 49

tag: treatment

value: sprayed with plasma-treated water


title: 4-week PFC Dagla WT Sample 6

description: Library name: dagla_4w_PFC_WT_6

source_name: Prefrontal Cortex

tag: tissue

value: Prefrontal Cortex

value: WT


title: MuSC_WT_NF-YA_1

value: NF-YA, Sc-17753, Santa Cruz


title: HARP-01-0034-1

value: Human coronary artery endothelial cells

tag: Sex

value: F

value: MI platelet releasate


title: HARP-01-0033-1


title: 4-week SN Dagla +/- Sample 1

description: Library name: dagla_4w_SN_HT_1

value: Substantia Nigra

tag: age


title: root, PTW, 49 DAS, biol rep 1

description:
Library name: AM8
gene_RP49vsRC49_results.csv


title: MuSC_WT_Taf4a_2_igg

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.05 and additional parameters "--extsize 100 --nomodel --to-large" (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
Mapping and counting was repeated similarly versus spike-in organism Escherichia coli str. K-12 substr. MG1655 genome version ASM584v2 (Ensembl release 49).
The raw count matrix was normalized with factors based on E. coli mapped read count.
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl data.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows spike-in normalized counts.
Library strategy: CUT&Run

extract_protocol:
1x10^6 wild type in vitro cultured muscle stem cells (MuSCs) were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with TAF4A (Santa Cruz #sc-136093) or mouse IgG (Santa Cruz, #Sc-136093) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.Ecoli spike-in comes from Mnase enzyme purified from E.coli, it is not added additionally.
For Cut’n’Run library preparation, precipitated DNA samples were purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). For MuSC samples 5ng precipitated DNA was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio).

value: Muscle stem cells


title: MuSC_WT_Taf4a_2

value: Taf4a Sc-136093 Santa Cruz


title: 4-week PFC Dagla WT Sample 5

description: Library name: dagla_4w_PFC_WT_5


title: HARP-01-0242-1


title: root, control, 49 DAS, biol rep 3

description:
Library name: AM6
gene_RP49vsRC49_results.csv

value: sprayed with deionized water


title: HARP-01-0244-1


title: MuSC_WT_Taf4a_1_igg


title: cDC1 rep1

description: Library name: S1

value: splenic dendritic cell type 1

value: wildtype


title: root, control, 49 DAS, biol rep 1

description:
Library name: AM2
gene_RP49vsRC49_results.csv


title: 4-week PFC Dagla WT Sample 3

description: Library name: dagla_4w_PFC_WT_3


title: MuSC_WT_Taf4a_1

value: wild type


title: HARP-01-0231-1


title: HARP-01-0184-1


title: root, PTW, 49 DAS, biol rep 2

description:
Library name: AM10
gene_RP49vsRC49_results.csv


title: 4-week PFC Dagla WT Sample 2

description: Library name: dagla_4w_PFC_WT_2


title: leaf, PTW, 49 DAS, biol rep 3

description:
Library name: AM11
gene_LP49vsLC49_results.csv

source_name: first fully expanded leaf

value: first fully expanded leaf


title: E18.0 Intestine_FACS-sorted blood endothelial cells

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

data_processing:
Raw FASTQ reads were quality and adapter trimmed using TrimGalore! (version 0.6.4 length cutoff 66, quality cutoff 20). The UMI, complex barcode, and sample tags were extracted and demultiplexed using custom scripts (rhapsody-extract-barcode and rhapsody-demultiplex).
Reads were mapped to the GRCm38 reference genome, Esm1-CreERT2 tg/+, and R26-mTmG tg/+ construct sequences with Gencode annotations vM22, using STAR version 2.7.3a (Dobin et al., 2013) (--soloType CB_UMI_Simple –soloCellFilter None –soloFeatures Gene –soloCBstart 1 –soloCBlen 27 –soloUMIstart 28 –soloUMIlen 8 –outFilterMultimapNmax 1 –soloCBwhitelist rhapsody_whitelist.txt).
Assembly: mm10
Supplementary files format and content: Tab-separated values files, MatrixMarket files, and AnnData files

source_name: Intestine

extract_protocol:
For unsorted cells, single cell suspension was obtained by dissociating E18.0 embryo intestines and mesenteries for 30 minutes to 1 hour at 37 °C with Liberase DH (Roche). After multiple washes, the cells were resuspended in red blood cell lysis buffer (Sigma) for 3 min. A total of 40000 cells were loaded onto a microwell cartridge of BD Rhapsody Express system (BD Biosciences). For FACS-sorted blood endothelial cells, single cell suspension was obtained by dissociating E18.0 embryo intestines for 1 hour at 37 °C with Liberase DH (Roche). Cell suspension was stained with conjugated antibodies in FACS buffer for 30 min. GFP+ ECs (around 9000 cells) were complemented with GFP- ECs to reach a total of 40000 cells and loaded onto a microwell cartridge of BD Rhapsody Express system (BD Biosciences)
Single-cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using a BD Rhapsody WTA Reagent kit (BD Biosciences)

value: Intestine

tag: development stage

value: Blood endothelial cells

value: Esm1-CreERT2 tg/+; R26-mTmG tg/+

value: 2 mg  4-hydroxytamoxifen for 24 hours


title: 4-week PFC Dagla WT Sample 1

description: Library name: dagla_4w_PFC_WT_1

value: Prefrontal Cortex

value: WT


title: leaf, PTW, 49 DAS, biol rep 2

description:
Library name: AM9
gene_LP49vsLC49_results.csv

value: day 49

value: sprayed with plasma-treated water


title: 4-week PFC Dagla -/- Sample 5

description: Library name: dagla_4w_PFC_KO_5

value: Dagla -/-


title: E18.0 Mesentery_All unsorted cells

description: BD Rhapsody

source_name: Mesentery

value: Mesentery

value: All cells


title: leaf, PTW, 49 DAS, biol rep 1

description:
Library name: AM7
gene_LP49vsLC49_results.csv


title: HARP-01-0173-1

value: Human coronary artery endothelial cells

value: F

value: MI platelet releasate


title: leaf, control, 49 DAS, biol rep 3

description:
Library name: AM5
gene_LP49vsLC49_results.csv

value: sprayed with deionized water


title: 4-week PFC Dagla WT Sample 4

description: Library name: dagla_4w_PFC_WT_4


title: E18.0 Intestine_All unsorted cells

description: BD Rhapsody


title: 4-week PFC Dagla -/- Sample 4

description: Library name: dagla_4w_PFC_KO_4


title: 4-week PFC Dagla -/- Sample 3

description: Library name: dagla_4w_PFC_KO_3


title: leaf, control, 49 DAS, biol rep 2

description:
Library name: AM3
gene_LP49vsLC49_results.csv


title: HARP-01-0114-1


title: DU102 treated, replicate 1, scRNAseq

city: Shanghai

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver tumor

extract_protocol:
Freshly collected liver tumors from MYC-ON mice were dissected by tissue dissection kit (stemcell). The dissected tissues were filted by 40um filter and fellowed by red cell lysis buffer. Then the cells were centrifuged and washed with PBS buffer. Cells were further stained with PE labelled anti-CD45 antibody (1:500 biolegend) and zombie NIR(biolegend), washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Lived tumor infiltrated CD45+ cells were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of PE signal and APC-cy7 signal.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, sorted CD45+ cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD45+ cells

value: liver tumor

tag: strain

value: 18 weeks old


title: root, control, 49 DAS, biol rep 2

description:
Library name: AM4
gene_RP49vsRC49_results.csv

value: whole root


title: HARP-01-0049-1


title: DU101 treated, replicate 1, scRNAseq

description: 10x Genomics


title: leaf, control, 49 DAS, biol rep 1

description:
Library name: AM1
gene_LP49vsLC49_results.csv

value: first fully expanded leaf


title: HARP-01-0036-1


title: 4-week PFC Dagla -/- Sample 2

description: Library name: dagla_4w_PFC_KO_2


title: CONTROL, replicate 1, scRNAseq

description: 10x Genomics


title: 4-week PFC Dagla -/- Sample 1

description: Library name: dagla_4w_PFC_KO_1


title: HARP-01-0031-1


title: root, PTW, 22 DAS, biol rep 3

description:
Library name: AK12
gene_RP22vsRC22_results.csv

value: day 22


title: NO98_S68

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. Reads Alignment: HISAT2 (default)
2. Expression profiling: Stringtie (default)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: text file containing gene expression profiles

source_name: hepatocellular carcinoma tissue

extract_protocol:
All of specimens were lysed with 1 ml TRIzol. Phenol-chloroform pH 6.7/8.0 was then added for phase separation, and RNA-rich layers were separated by centrifugation. Soluble RNA was precipitated with 2-propanol. The salt was washed away with 75% ethanol and RNA was dissolved in RNase-free water.
TruSeq

value: hepatocellular carcinoma tissue


title: root, PTW, 22 DAS, biol rep 2

description:
Library name: AK10
gene_RP22vsRC22_results.csv


title: 4-week PFC Dagla +/- Sample 5

description: Library name: dagla_4w_PFC_HT_5

value: Prefrontal Cortex

value: Dagla +/-


title: HARP-01-0002-1


title: NO96_S66


title: root, PTW, 22 DAS, biol rep 1

description:
Library name: AK8
gene_RP22vsRC22_results.csv

value: sprayed with plasma-treated water


title: CCL3 100-2

value: CCL3 100 ng/mL


title: HARP-01-0058-1


title: NO94_S64


title: 4-week PFC Dagla +/- Sample 3

description: Library name: dagla_4w_PFC_HT_3


title: 4-week PFC Dagla +/- Sample 4

description: Library name: dagla_4w_PFC_HT_4


title: root, control, 22 DAS, biol rep 3

description:
Library name: AK6
gene_RP22vsRC22_results.csv


title: CCL3 100-1


title: 4-week PFC Dagla +/- Sample 2

description: Library name: dagla_4w_PFC_HT_2


title: NO92_S62


title: 4-week PFC Dagla +/- Sample 1

description: Library name: dagla_4w_PFC_HT_1


title: root, control, 22 DAS, biol rep 2

description:
Library name: AK4
gene_RP22vsRC22_results.csv


title: NO8_S4


title: root, control, 22 DAS, biol rep 1

description:
Library name: AK2
gene_RP22vsRC22_results.csv


title: 4-week HP Dagla WT Sample 6

description: Library name: dagla_4w_HP_WT_6

source_name: Hippocampus

value: Hippocampus

value: WT


title: leaf, PTW, 22 DAS, biol rep 3

description:
Library name: AK11
gene_LP22vsLC22_results.csv


title: PBS-3

value: Human coronary artery endothelial cells

value: PBS


title: NO88_S58


title: leaf, PTW, 22 DAS, biol rep 2

description:
Library name: AK9
gene_LP22vsLC22_results.csv


title: leaf, PTW, 22 DAS, biol rep 1

description:
Library name: AK7
gene_LP22vsLC22_results.csv


title: 4-week HP Dagla WT Sample 4

description: Library name: dagla_4w_HP_WT_4


title: PBS-2

value: F


title: NO84_S56


title: leaf, control, 22 DAS, biol rep 3

description:
Library name: AK5
gene_LP22vsLC22_results.csv

value: sprayed with deionized water


title: NO82_S54


title: 4-week HP Dagla WT Sample 2

description: Library name: dagla_4w_HP_WT_2


title: PBS-1


title: leaf, control, 22 DAS, biol rep 2

description:
Library name: AK3
gene_LP22vsLC22_results.csv


title: T62-P

city: 天津市

first: zhe

last: nian

state: 天津市

address: 天津市和平区气象台路22号

institute: Tianjin Medical University

description: 10x Genomics

data_processing:
The FASTQ files were analyzed with the Cell Ranger Software Suite (version 4.0.0; 10x Genomics) against the GRCh38 human reference genome.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: adrenal gland

extract_protocol:
Resected tumor was transported in MACS Tissue Storage Solution (Miltenyi Biotec) on ice immediately after surgical procurement.
Single cell RNA sequencing libraries were prepared using Chromium Single Cell 3’v3 Reagent Kit (10x Genomics).

value: adrenal gland

value: neuroblastoma

tag: group

value: primary

value: untreated


title: NO80_S52


title: T63-P

address: 天津市和平区气象台路22号

description: 10x Genomics


title: PBS-4


title: NO90_S60


title: 4-week HP Dagla WT Sample 1

description: Library name: dagla_4w_HP_WT_1


title: leaf, control, 22 DAS, biol rep 1

description:
Library name: AK1
gene_LP22vsLC22_results.csv

value: first fully expanded leaf


title: T60-P

address: 天津市和平区气象台路22号

description: 10x Genomics


title: 4-week HP Dagla -/- Sample 5

description: Library name: dagla_4w_HP_KO_5

value: Dagla -/-


title: T59-P

address: 天津市和平区气象台路22号

description: 10x Genomics


title: NO74_S49

value: hepatocellular carcinoma tissue


title: NO72_S47


title: 4-week HP Dagla WT Sample 5

description: Library name: dagla_4w_HP_WT_5


title: 4-week HP Dagla WT Sample 3

description: Library name: dagla_4w_HP_WT_3


title: NO68_S43


title: T57-P

address: 天津市和平区气象台路22号

description: 10x Genomics


title: 4-week HP Dagla -/- Sample 2

description: Library name: dagla_4w_HP_KO_2


title: T62-M

address: 天津市和平区气象台路22号

description: 10x Genomics

value: bone marrow metastases


title: T57-M

address: 天津市和平区气象台路22号

description: 10x Genomics


title: NO64_S41


title: 4-week HP Dagla -/- Sample 1

description: Library name: dagla_4w_HP_KO_1


title: T55-P

address: 天津市和平区气象台路22号

description: 10x Genomics


title: FigS10DE:conserved roles of apoCas9 and crRNA-tracrRNA:dNmeCas9

city: Ann Arbor

first: Zhonggang

last: Hou

state: Michigan

address: 1150 W Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description:
Library name: 202310-106
previous GSM: GSM8209050

library_source: other

data_processing:
Read processing: Sequencing reads were assessed for quality with fastQC (version 0.11.8) and multiQC (version 0.92) to ensure the general quality of the datasets. For the newly acquired spacer sequences, the Read 1 sequences reads were trimmed to extract new spacer instances using Cutadapt (version 2.6) by identifying the flanking Repeat 26 sequences (attgtagcactgcgaaatgagaaagggagctacaac).
Deduplication: For samples with UMIs, the Read 2 sequences of the paired-end reads were processed with Cutadapt to extract the 8-nt UMI sequences by trimming known construct sequences. The newly spacer-UMI sequence combinations were paired with fastq-pair (version 0.4) and processed with UMI-tools (version 1.0.1) for deduplication after alignment. For samples with no UMIs during library construction, no UMI processing was performed (see the next step for an alternative approach to minimize PCR artifacts). For Miseq sample, UMIs are extracted from Read1.
Spacer source identification: The preprocessed spacer sequences were aligned by bowtie2 (version 2.4.1) with the "very-sensitive" preset to the combined alignment reference containing the N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) and the MDA phage genome sequence. For samples with UMIs, aligned spacers were deduplicated using UMI-tools with the directional-adjacency method as noted above. For samples with no UMIs, to handle technical artifacts such as PCR jackpot sites that can over-amplify a subset of spacer sequences, a maximum cap of 5% of the total detected spacer counts on the corresponding Neisseria or phage genome was applied to each unique spacer sequence, i.e., for each unique spacer sequence, if its abundance among total spacers exceeded 5%, its abundance was set to 5% of the total detected spacer count of the given source genome.
Genomic context extraction: Any reads that mapped ambiguously were removed from further analysis using samtools (version 1.9). For each genomic location aligned with the 5' end of any new spacer, the genomic context was extracted as the reference genome sequences flanking the alignment location, including the sequence upstream 10 bp from the alignment sites.
Spacer counting: The numbers of spacers at each unique spacer-aligned location were counted using bedtools2 (version 2.26.0) and custom codes were used to format the genomic context sequences for sequence logo inputs.
Assembly: N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) MDA phage genome: J. Meyer et al., Characterization of MDAPhi, a temperate filamentous bacteriophage of Neisseria meningitidis. Microbiology (Reading) 162, 268-282 (2016).
Supplementary files format and content: For *.MDA.fa files: format: FASTA files, with each header formatted as ">MDA_kan:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on MDA phage genome and counts listed in the headers
Supplementary files format and content: For *.Nme.fa files: format: FASTA files, with each header formatted as ">NC_017501.1:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on Neisseria genome and counts listed in the headers

molecule: other

organism: Neisseria meningitidis 8013

source_name: bacteria

growth_protocol: N. meningitidis (aka meningococcal) strains MC58, 8013, and 8013 mutant derivatives are used in this study. These strains were grown on GC Medium Base (GCB) (BD, 228950) plates with appropriate antibiotics and Kellogg’s supplements I and II (22.2 mM glucose [Fisher Scientific, D16-1], 0.68 mM glutamine [Sigma, G3126], 0.45 mM co-carboxylase [aka thiamine pyrophosphate, Sigma, C8754], 1.23 mM Fe(NO3)3 [Sigma, F8508]). Antibiotic concentrations used were 2.5 μg/mL for erythromycin (Erm), 100 μg/mL for kanamycin (Kan), 100 μg/mL for streptomycin (strp), 2.5 μg/mL for chloramphenicol (cm), and 100 μg/mL for spectinomycin (spc). All solid cultures were incubated at 37 ̊C in a 5% CO2 humidified atmosphere.  JM109 (Promega, L2005) and Mach1 (Invitrogen, C862003) chemically competent E. coli cells were used for plasmid cloning. E. coli BL21 (DE3) (Novagen, 69450-3) cells were used for protein purification. E. coli cells were grown at 37 ̊C in LB broth Lennox or on LB agar plates supplemented, when needed, with 50 μg/mL kanamycin, 50 μg/mL carbenicillin, 20 μg/mL for chloramphenicol or 100 μg/mL spectinomycin.

extract_protocol:
To detect spacer acquisition, 10 ng genomic DNA was used as template to PCR amplify CRISPR’s downstream end using Q5 DNA Polymerase with with primers described in Supplemental Table 1. The following PCR conditions were used: 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 20 s (25 cycles); 72 ̊C for 2 min. PCR products were resolved on 2% agarose gel, stained by SYBR Safe (Invitrogen, S33102), and visualized using a Bio-Rad Chemidoc MP imager (12003154). The adapted “+1” “+2” bands are 66- and 132- nts larger than the un-adapted “0” product derived from parental CRISPR array, due to addition of repeat-spacer units (66-nt each). Adaptation efficiency was measured as the percentage of total CRISPR amplicons with new spacers. Quantification of PCR band intensity was done using Image Lab 6.0 software (Bio-Rad).
UMI library construction: Ligated products from above were used as template for 1st step Q5 PCR to amplify the leader-end of CRISPR array with primers OYZ3624+593 containing partial adaptor. Cycling conditions are 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 25 s (25 cycles); 72 ̊C for 2 min. Following 2% agarose gel electrophoresis, the “+1” adapted band was gel extracted with QIAquick Gel Extraction Kit (Qiagen, 28706). Eluate is used as template for 2nd step Q5 PCR amplification using I5 and I7 index primers to add full Illumina adapter and indexes. 2nd PCR conditions are: 98 ̊C for 30 s; 98 ̊C for 10 s, 65 ̊C for 10 s, 72 ̊C for 25 s (15 cycles); 72 ̊C for 2 min.  Non-UMI library construction: For mutant strains carrying the del_crispr::R26, del_crispr::crispr(sp1), del_crispr::crispr(sp1-2), del_crispr::crispr(sp1-3), del_crispr::crispr(sp1-5), del_crispr::crispr(sp1-7), del_crispr::crispr(sp1-8), del_crispr::crispr(sp1-17), del_crispr::crispr(sp1-25), del_crispr::crispr(sp1-49) alleles, a non-UMI method was used due to the lack of unique restriction site (e.g., FatI) close enough to the newly acquired spacer. 10 ng of total genomic DNA from an adaptation experiment was used as template for 1st step PCR with primers are described in Supplemental Table 1. The following steps for “+1” adapted band gel extraction and 2nd step Q5 PCR were as described in the earlier paragraph.  All final libraries from 2nd step PCR were pooled together, cleaned up using QIAquick PCR Purification Kit, and then purified as one sample by agarose gel electrophoresis and gel extraction. This final pooled library was sequenced on an Illumina sequencing platform, NovaSeq (2x150 bp) at the Univ. of Michigan Advanced Genomics Core.

treatment_protocol: A phage transduction assay was initially performed. Rather than culturing cells on GCB plates with kanamycin, the cells were back-diluted to a concentration of 0.1 OD, and kanamycin was added at a concentration of 40 µg/mL to enrich for transductants. Adaptation assay was performed by incubating diluted culture with or without appropriate inducers, at 37 ̊C in a 5% CO2 humidified atmosphere. Inducer concentrations used were 0.1mM for IPTG (Fisher scientific, BP1755-10). After 24 hrs of induction, genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, 51306) per manufacturer’s instructions with the following minor modification. After cell lysis at 56 ̊C for 40 min, RNase A (1mg/mL, Qiagen 19101) treatment was performed at RT for 2 min.

value: bacteria

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNmeCas9 (D16A+H588A)-FLAG

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: FigS2D:spacer preference analysis:endo dCas9+pLac-Cas1-Cas2 with induction repeat-3

description:
Library name: 202404-25
previous GSM: GSM8209054

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: FigS10DE:conserved roles of apoCas9 and crRNA-tracrRNA:dCjeCas9

description:
Library name: 202310-107
previous GSM: GSM8209051

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dCjeCas9 (D8A+H559A)-FLAG


title: Fig4DE:apoCas9-del_REC with endogenous dual RNA:Cas9+endo dual RNA

description:
Library name: 202402-29
previous GSM: GSM8209053


title: NO60_S37


title: NO62_S39


title: FigS3C:spacer preference analysis:del_tracr with pLac-Cas1-Cas2 induction repeat-3

description:
Library name: 202401-114
previous GSM: GSM8209052


title: FigS7CD:natural short CRISPR isolates:M01 240569 with native cas9-cas1-cas2 repeat-4

description: Library name: 202409-8


title: FigS7CD:natural short CRISPR isolates:M01 240569 with native cas9-cas1-cas2 repeat-3

description: Library name: 202409-7


title: FigS10DE:conserved roles of apoCas9 and crRNA-tracrRNA:No Cas9

description:
Library name: 202310-105
previous GSM: GSM8209049

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty


title: NO58_S35


title: 4-week HP Dagla +/- Sample 4

description: Library name: dagla_4w_HP_HT_4

value: Hippocampus

value: Dagla +/-


title: 4-week HP Dagla +/- Sample 5

description: Library name: dagla_4w_HP_HT_5


title: NO70_S45


title: 4-week HP Dagla -/- Sample 4

description: Library name: dagla_4w_HP_KO_4


title: FigS7CD:natural short CRISPR isolates:M01 240569 with native cas9-cas1-cas2 repeat-2

description: Library name: 202408-8


title: 4-week HP Dagla -/- Sample 3

description: Library name: dagla_4w_HP_KO_3


title: 4-week HP Dagla +/- Sample 2

description: Library name: dagla_4w_HP_HT_2


title: FigS7CD:natural short CRISPR isolates:M01 240569 with native cas9-cas1-cas2 repeat-1

description: Library name: 202408-7


title: NO50_S31


title: 4-week HP Dagla +/- Sample 1

description: Library name: dagla_4w_HP_HT_1


title: NO4_S2


title: FigS8DE:CRISPR homologous recombination :del_CRISPR(R19-S1)

description: Library name: 202304-32


title: FigS8DE:CRISPR homologous recombination :del_CRISPR(R22-S1)

description: Library name: 202304-33


title: FigS8DE:CRISPR homologous recombination :del_CRISPR(R16-S1)

description: Library name: 202304-31


title: LSK – aged + RhoA-inhibitor (Ri) 3

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: Regenerative Medicine

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Library name: scRNA-LSKrhoai3

data_processing:
After performing the quality control of the FASTQ files with FastQC v0.11.5, reads were aligned to the reference genome (GRCm38/mm10, annotation Ensembl 98), filtered, and counted using the «cellranger count» command of Cell Ranger software v7.2.0 (10x Genomics) with default parameters.
Assembly: mm10
Supplementary files format and content: Filtered count matrices in MEX format obtained from CellRanger. The files «*_barcodes.tsv.gz» contain the information of the cell barcodes (columns of the matrix); the files «*_features.tsv.gz» contain the information of the features (rows of the matrix); and the files «*_matrix.mtx.gz» contain the expression counts in sparse matrix format.

source_name: Bone marrow

growth_protocol: Cells were incubated 16h in IMDM 10%FBS 1%P/S.

extract_protocol:
Cells were concentrated to 300-1000 cells/µl. Cell concentration and viability were determined using a TC20™ Automated Cell Counter (Bio-Rad Laboratories, S.A) upon staining the cells with Trypan blue. Cells were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller system (10X Genomics), with a target recovery of 5000 total cells per sample.
cDNA sequencing libraries were prepared using the Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000268), following manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified during 13 cycles and cDNA quality control and quantification were performed on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies). cDNA libraries were indexed by PCR using the PN-1000215 Dual Index Kit TT, Set A plate. Size distribution and concentration of 3' cDNA libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent Technologies).

treatment_protocol: Ri (RhoA inhibitor, Rhosin) was added to one of the aged cell samples to a concentration of 100µM for the 16h incubation commented above.

value: Bone marrow

value: Lin- cKit+ Sca1+ cells (LSK)

value: >80 weeks old

value: RhoA-inhibitor (Ri) treatment


title: FigS7CD:natural short CRISPR isolates:CA40755 with native cas9-cas1-cas2 repeat-2

description: Library name: 202411-21


title: NO42_S27


title: NO44_S28


title: FigS7CD:natural short CRISPR isolates:CA40755 with native cas9-cas1-cas2 repeat-1

description: Library name: 202411-10


title: FigS8DE:CRISPR homologous recombination :del_CRISPR(R13-S1)

description: Library name: 202304-30


title: FigS8DE:CRISPR homologous recombination :del_CRISPR(R25-S1)

description: Library name: 202304-35


title: LSK – young control 3

description: Library name: scRNA-LSKyoung3

value: 10-16 weeks old

value: control


title: FigS7CD:CRISPR evolutionary mimics:sp1-5 with native cas9-cas1-cas2 repeat-4

description: Library name: 202408-10


title: LSK – aged control 3

description: Library name: scRNA-LSKaged3


title: FigS7CD:CRISPR evolutionary mimics:sp1-5 with native cas9-cas1-cas2 repeat-3

description: Library name: 202408-9


title: FigS6J:CRISPR immunity escapers:del_CRISPR(R17-S1)

description: Library name: 202303-81


title: scRNA-Seq - LSK - aged + RhoA-inhibitor (Ri) 1


title: FigS6J:CRISPR immunity escapers:del_CRISPR(R24-S2)

description: Library name: 202303-76


title: scRNA-Seq - LSK - aged + RhoA-inhibitor (Ri) 2


title: NO32_S22

value: hepatocellular carcinoma tissue


title: NO54_S33


title: FigS7CD:CRISPR evolutionary mimics:sp1-5 with native cas9-cas1-cas2 repeat-2

description: Library name: 202409-10


title: NO30_S20


title: FigS6J:CRISPR immunity escapers:del_CRISPR(R8-S3)

description: Library name: 202303-78


title: scRNA-Seq - LSK - aged control 2


title: NO28_S18


title: FigS6J:CRISPR immunity escapers:endo CRISPR WT (25 units of spacer-repeat)

description: Library name: 202303-77


title: scRNA-Seq - LSK - aged control 1


title: FigS7CD:CRISPR evolutionary mimics:sp1 with native cas9-cas1-cas2 repeat-4

description: Library name: 202408-6


title: FigS8DE:CRISPR homologous recombination :endo CRISPR WT (25 units of spacer-repeat)

description: Library name: 202304-29


title: NO26_S16


title: FigS6B:CRISPR genesis evolution:49 units of spacer-repeat

description: Library name: 202303-70


title: NO38_S25


title: FigS7CD:CRISPR evolutionary mimics:sp1 with native cas9-cas1-cas2 repeat-3

description: Library name: 202408-5


title: NO24_S15


title: FigS6B:CRISPR genesis evolution:25 units of spacer-repeat

description: Library name: 202303-69


title: scRNA-Seq - LSK - young control 1


title: FigS7CD:CRISPR evolutionary mimics:sp1 with native cas9-cas1-cas2 repeat-2

description: Library name: 202411-26


title: Mouse 12, scRNAseq, TCR

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE, ROOM 1296

department: Medicine

institute: University of California San Francisco

description: 10x Genomics

data_processing:
Final amplified libraries were purified, quantified and average fragment sizes confirmed by gel electrophoresis using 4200 TapeStation and HS D5000 Screen Tape (Agilent).  Gene expression libraries were sequenced at depth of 20,000 reads per cell. Paired-end, dual indexing sequencing was performed using a NovaSeq 6000 Illumina sequencing system, S4 flow-cell, according to 10x recommended sequencing configuration.
The Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to align the raw sequencing data and to generate count matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colorectal cancer liver metastasis tumor

extract_protocol:
0.5g sections of each tumor were minced into small pieces and digested in 10 mL RPMI containing 2.5% FBS, collagenase IV (1 mg/ml, Sigma), and DNase I (200ug/ml, Sigma) in 37°C water bath for 45 minutes. These were then strained to obtain a single cell suspension, and cell viability >90% was determined by trypan blue exclusion. The single cell suspension was stained with anti-CD45 FITC at 4°C for 30min after the FcR was blocked with anti-mouse CD16/CD32 at 4°C for 10min, and then the cells were washed three times with 3.5 mL of cell staining buffer and centrifuged for 5 minutes at 400g at 4°C. 1.8x10e5 - 6x10e5 sorted CD45+ cells from each sample were diluted as necessary for appropriate input into the 10x Chromium chip after cell concentration was verified by manual counting with a hemocytometer.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: CT26 tumors (control) or CT26/LIGHT-expressing tumors were injected into BALB/c mice via splenic injection. Mice were dosed with intraperitoneal anti-CTLA-4 or isotype control on days 4, 7, 10 and 13 after tumor cell inoculation.

value: Immune cells

value: CT26+isotype control

value: BALB/c

tag: library type

value: VDJ


title: FigS7CD:CRISPR evolutionary mimics:sp1 with native cas9-cas1-cas2 repeat-1

description: Library name: 202411-4

value: bacteria

value: MDAΦ 3+21 hr


title: NO22_S13


title: NO230_S146


title: Mouse 11, scRNAseq, TCR

description: 10x Genomics

value: Colorectal cancer liver metastasis tumor

value: CT26LIGHT+isotype control


title: FigS6B:CRISPR genesis evolution:8 units of spacer-repeat

description: Library name: 202303-66

value: 0.1 mM IPTG


title: FigS7CD:CRISPR evolutionary mimics:single Repeat with native cas9-cas1-cas2 repeat-4

description: Library name: 202408-4


title: NO228_S144


title: Mouse 10, scRNAseq, TCR

description: 10x Genomics


title: FigS6B:CRISPR genesis evolution:17 units of spacer-repeat

description: Library name: 202303-68


title: NO226_S142


title: FigS7CD:CRISPR evolutionary mimics:sp1-5 with native cas9-cas1-cas2 repeat-1

description: Library name: 202409-9


title: FigS7CD:CRISPR evolutionary mimics:single Repeat with native cas9-cas1-cas2 repeat-3

description: Library name: 202408-3


title: FigS6B:CRISPR genesis evolution:7 units of spacer-repeat

description: Library name: 202304-45


title: Mouse 9, scRNAseq, TCR

description: 10x Genomics


title: FigS6B:CRISPR genesis evolution:5 units of spacer-repeat

description: Library name: 202304-44


title: scRNA-Seq - LSK - young control 2


title: FigS7CD:CRISPR evolutionary mimics:single Repeat with native cas9-cas1-cas2 repeat-2

description: Library name: 202409-4


title: Mouse 8, scRNAseq, TCR

description: 10x Genomics


title: FigS7CD:CRISPR evolutionary mimics:single Repeat with native cas9-cas1-cas2 repeat-1

description: Library name: 202409-3


title: FigS6B:CRISPR genesis evolution:3 units of spacer-repeat

description: Library name: 202303-65


title: NO214_S137


title: Mouse 7, scRNAseq, TCR

description: 10x Genomics


title: NO212_S135


title: FigS6B:CRISPR genesis evolution:2 units of spacer-repeat

description: Library name: 202303-64


title: FigS7CD:CRISPR evolutionary mimics, natural short CRISPR isolates:CRISPR WT repeat-4

description: Library name: 202503-10

value: WT


title: FigS6B:CRISPR genesis evolution:1 unit of spacer-repeat

description: Library name: 202303-63


title: Mouse 6, scRNAseq, TCR

description: 10x Genomics


title: FigS7CD:CRISPR evolutionary mimics, natural short CRISPR isolates:CRISPR WT repeat-3

description: Library name: 202411-24


title: NO208_S133


title: NO206_S131


title: FigS7CD:CRISPR evolutionary mimics, natural short CRISPR isolates:CRISPR WT repeat-2

description: Library name: 202411-13


title: Mouse 4, scRNAseq, TCR

description: 10x Genomics


title: FigS6B:CRISPR genesis evolution:single R (No spacer)

description: Library name: 202303-62

value: del_CR::R26, iga-trpB::pLacNmecas1-cas2


title: Mouse 5, scRNAseq, TCR

description: 10x Genomics


title: FigS2D:spacer preference analysis:WT repeat-3

description:
Library name: 202306-14
previous GSM: GSM8209048


title: FigS7CD:CRISPR evolutionary mimics, natural short CRISPR isolates:CRISPR WT repeat-1

description: Library name: 202411-2


title: FigS7CD:natural short CRISPR isolates:CA40755 with native cas9-cas1-cas2 repeat-3

description: Library name: 202411-32


title: FigS3C:spacer preference analysis:del_tracr with pLac-Cas1-Cas2 induction repeat-2

description:
Library name: 202304-57
previous GSM: GSM8209043


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R24-S2) with native cas9-cas1-cas2 repeat-4

description: Library name: 202503-36

value: del_CR(R24-S2), ssiaA-CAT-ctrA::target ps6-N4GATT PAM


title: Mouse 2, scRNAseq, TCR

description: 10x Genomics


title: Mouse 3, scRNAseq, TCR

description: 10x Genomics


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R24-S2) with native cas9-cas1-cas2 repeat-3

description: Library name: 202503-28

value: del_CR(R24-S2), siaA-CAT-ctrA::target ps6-N4GATT PAM


title: NO222_S140


title: NO196_S124


title: Mouse 1, scRNAseq, TCR

description: 10x Genomics


title: Fig2EF:CRISPR role:del_cas9del_CRISPR::R26 with pLac-Cas1-Cas2 induction, FigS4EF:CRISPR role:del_cas9, del_CRISPR::R26

description:
Library name: 202304-49
previous GSM: GSM8209042


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R24-S2) with native cas9-cas1-cas2 repeat-2

description: Library name: 202503-20


title: NO192_S123


title: Mouse 12, scRNAseq, Gene expression

description: 10x Genomics

value: Gene expression


title: NO18_S10


title: FigS2D:spacer preference analysis:WT+pLac-Cas1-Cas2 with induction repeat-3

description:
Library name: 202304-43
previous GSM: GSM8209038


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R24-S2) with native cas9-cas1-cas2 repeat-1

description: Library name: 202503-4


title: NO204_S129


title: Mouse 11, scRNAseq, Gene expression

description: 10x Genomics


title: NO184_S119


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R17-S1) with native cas9-cas1-cas2 repeat-4

description: Library name: 202503-38

value: del_CR(R17-S1), siaA-CAT-ctrA::target ps6-N4GATT PAM


title: Fig4DE:apoCas9-del_REC with endogenous dual RNA:Cas9-del_REC1/2+endo dual RNA

description:
Library name: 202304-24
previous GSM: GSM8209029


title: Mouse 10, scRNAseq, Gene expression

description: 10x Genomics


title: Fig4DE:apoCas9-del_REC with endogenous dual RNA:Cas9-del_BHdel_REC1/2+endo dual RNA

description:
Library name: 202304-25
previous GSM: GSM8209030


title: Mouse 9, scRNAseq, Gene expression

description: 10x Genomics


title: NO202_S127


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R17-S1) with native cas9-cas1-cas2 repeat-3

description: Library name: 202503-30


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dPmuCas9+Pmu sgRNA

description:
Library name: 202304-21
previous GSM: GSM8209028

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dPmuCas9-FLAG+pTR Pmu sgRNA


title: NO190_S121

value: hepatocellular carcinoma tissue


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R17-S1) with native cas9-cas1-cas2 repeat-2

description: Library name: 202503-22


title: NO180_S117


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dPpnCas9+Ppn sgRNA

description:
Library name: 202304-20
previous GSM: GSM8209027

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dPpnCas9-FLAG+pTR Ppn sgRNA


title: Mouse 8, scRNAseq, Gene expression

description: 10x Genomics

value: Immune cells


title: NO174_S115


title: FigS2D:spacer preference analysis:endo dCas9+pLac-Cas1-Cas2 with induction repeat-1

description:
Library name: 202304-46
previous GSM: GSM8209039

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: Mouse 7, scRNAseq, Gene expression

description: 10x Genomics

value: CT26+isotype control

value: BALB/c


title: NO16_S8


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R8-S3) with native cas9-cas1-cas2 repeat-4

description: Library name: 202503-40

value: bacteria

value: del_CR(R8-S3), siaA-CAT-ctrA::target ps6-N4GATT PAM

value: MDAΦ 3+21 hr


title: Mouse 6, scRNAseq, Gene expression

description: 10x Genomics

value: Colorectal cancer liver metastasis tumor


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dAsuCas9+Asu sgRNA

description:
Library name: 202304-19
previous GSM: GSM8209026

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dAsuCas9-FLAG+pTR Asu sgRNA

value: 0.1 mM IPTG


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dHpaCas9+Hpa sgRNA

description:
Library name: 202304-18
previous GSM: GSM8209025

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dHpaCas9-FLAG+pTR Hpa sgRNA


title: NO166_S112


title: NO162_S110


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R8-S3) with native cas9-cas1-cas2 repeat-3

description: Library name: 202503-32


title: Mouse 5, scRNAseq, Gene expression

description: 10x Genomics


title: Mouse 4, scRNAseq, Gene expression

description: 10x Genomics


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNme2Cas9+sgRNA

description:
Library name: 202304-16
previous GSM: GSM8209023

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNme2Cas9-FLAG+pTR sgRNA


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R8-S3) with native cas9-cas1-cas2 repeat-2

description: Library name: 202503-24

value: del_CR(R8-S3), ssiaA-CAT-ctrA::target ps6-N4GATT PAM


title: NO158_S108


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R8-S3) with native cas9-cas1-cas2 repeat-1

description: Library name: 202503-8


title: FigS7AB:CRISPR immunity natural escapers:del_CRISPR(R17-S1) with native cas9-cas1-cas2 repeat-1

description: Library name: 202503-6

value: del_CR(R17-S1), siaA-CAT-ctrA::target ps6-N4GATT PAM


title: Mouse 2, scRNAseq, Gene expression

description: 10x Genomics

value: Gene expression


title: FigS7AB:CRISPR immunity natural escapers:endo CRISPR WT (25 units of spacer-repeat) with native cas9-cas1-cas2 repeat-3

description: Library name: 202503-25

value: WT


title: FigS7AB:CRISPR immunity natural escapers:endo CRISPR WT (25 units of spacer-repeat) with native cas9-cas1-cas2 repeat-4

description: Library name: 202503-33


title: NO156_S106

value: hepatocellular carcinoma tissue


title: NO154_S104


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNmeCas9+sgRNA

description:
Library name: 202304-15
previous GSM: GSM8209022

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNmeCas9-FLAG+pTR sgRNA


title: Mouse 1, scRNAseq, Gene expression

description: 10x Genomics

value: Immune cells


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dPmuCas9

description:
Library name: 202304-14
previous GSM: GSM8209021

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dPmuCas9 (D13A+H580A)-FLAG


title: NO150_S101


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dPpnCas9

description:
Library name: 202304-13
previous GSM: GSM8209020

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dPpnCas9 (D13A+H582A)-FLAG


title: pDC

description: pDC

data_processing:
The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a mm10 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
The resulting expression matrix was used as input to the Seurat library v4.3.0
Assembly: mm10
Supplementary files format and content: 10x Gene Expression matrix

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

tag: cell line

value: pDC

value: splenic plasmacytoid dendritic cells

value: wildtype

tag: sorted cell_type

value: sorted live(DAPI-) and CD11c+SiglecH+B220+BST2+


title: FigS7AB:CRISPR immunity natural escapers:endo CRISPR WT (25 units of spacer-repeat) with native cas9-cas1-cas2 repeat-1

description: Library name: 202503-1

tag: cell type

value: bacteria

tag: genotype

value: MDAΦ 3+21 hr


title: SII CD2 day9

source_name: MEF

value: MEF

value: mouse embryonic fibroblast

value: hCD2Cre/WT Rosa26stopflow-YFP/WT

tag: transduction

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

tag: time

value: Cells were collected 9 days after viral transduction

value: sorted live(DAPI-) and YFP+


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dAsuCas9

description:
Library name: 202304-12
previous GSM: GSM8209019

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dAsuCas9 (D10A+H579A)-FLAG

value: 0.1 mM IPTG


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dHpaCas9

description:
Library name: 202304-11
previous GSM: GSM8209018

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dHpaCas9 (D13A+H581A)-FLAG


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNme3Cas9+sgRNA

description:
Library name: 202304-17
previous GSM: GSM8209024

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNme3Cas9-FLAG+pTR sgRNA


title: NO146_S98

value: hepatocellular carcinoma tissue


title: FigS2F:transcriptome analysis of MDAΦ

description: Library name: 202408-RNASeq-2

value: MDAΦ transducants


title: Mouse 3, scRNAseq, Gene expression

description: 10x Genomics

value: Immune cells

value: Colorectal cancer liver metastasis tumor

value: CT26LIGHT+isotype control

value: BALB/c

value: Gene expression


title: SII Clec9a day9

value: MEF

value: sorted live(DAPI-) and tdTomato+


title: NO144_S96


title: SII CD2 day3

value: mouse embryonic fibroblast

value: hCD2Cre/WT Rosa26stopflow-YFP/WT

value: Cells were collected 3 days after viral transduction


title: NTM2_18_80

city: Tokyo

first: Harutaka

last: Katano

address: 1-23-1 Toyama, Shinjuku

department: Department of Pathology

country: Japan

institute: National Institute of Infectious Diseases

description: Lung FFPE sample from a  patient (NTM2, 18-080)

hyb_protocol: In situ hybridization was performed according to the manufactory manual (User Manual Slide Preparation for RNA Assays, MAN-10184-02, Nanostring). NanoString® ISH probes (1nM 980 plex ISH probe) were used as probes.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed according to the manufacture manual (CosMx SMI Instrument User Manual, MAN-10161-04, Nanostring). After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument. Images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing: Images were segmented to obtain cell boundaries, assign transcripts at the cell-level, and obtain a transcript by cell count matrix. Cells with an average negative control count greater than 0.5 and less than 20 detected features were filtered out.

label: SMI imaging barcodes

source_name: mycobacteria-infected lung tissue

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI, according to the manufactory manual (User Manual Slide Preparation for RNA Assays, MAN-10184-02, Nanostring). Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C.

treatment_protocol: Surgical samples fixed in formalin and paraffin embedded (FFPE) were used for CosMxTM SMI and tissue staining (IHC IF, ISH).

tag: gender

value: F

tag: disease

value: NTM

tag: sample

value: FFPE


title: NO142_S95


title: SII Clec9a day3

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNme3Cas9

description:
Library name: 202304-10
previous GSM: GSM8209017

value: bacteria

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNme3Ccas9 (D16A+H588A)-FLAG

tag: treatment

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: FigS7AB:CRISPR immunity natural escapers:endo CRISPR WT (25 units of spacer-repeat) with native cas9-cas1-cas2 repeat-2

description: Library name: 202503-17

value: WT


title: MTB3_18-79

description: Lung FFPE sample from a  patient (MTB3, 18-079)

label_protocol: In situ hybridization was performed according to the manufactory manual (User Manual Slide Preparation for RNA Assays, MAN-10184-02, Nanostring).

value: M

value: MTB


title: NO140_S93

tag: tissue

value: hepatocellular carcinoma tissue


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNmeCas9

description:
Library name: 202304-08
previous GSM: GSM8209015

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNmeCas9 (D16A+H588A)-FLAG


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:dNme2Cas9

description:
Library name: 202304-09
previous GSM: GSM8209016

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet dNme2Cas9 (D16A+H588A)-FLAG


title: NO14_S6


title: SI8 CD2 day9

value: MEF

value: mouse embryonic fibroblast

value: Cells were transduced with Spib, Irf8 (SI8)

value: Cells were collected 9 days after viral transduction

value: sorted live(DAPI-) and YFP+


title: FigS10FG:conserved roles of apoCas9 and crRNA-tracrRNA:No Cas9

description:
Library name: 202304-07
previous GSM: GSM8209014

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty


title: MTB2_18-78

description: Lung FFPE sample from a  patient (MTB2, 18-078)

value: FFPE


title: NO138_S91


title: SI8 Clec9a day9

value: sorted live(DAPI-) and tdTomato+


title: NTM4_18_77

description: Lung FFPE sample from a  patient (NTM4, 18-077)

value: F

value: NTM


title: NTM1_18_76

description: Lung FFPE sample from a  patient (NTM1, 18-076)


title: FigS2D:spacer preference analysis:WT+pLac-Cas1-Cas2 with induction repeat-2

description:
Library name: 202304-06
previous GSM: GSM8209013

value: bacteria

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: SI8 CD2 day3

value: hCD2Cre/WT Rosa26stopflow-YFP/WT

value: Cells were collected 3 days after viral transduction


title: FigS2D:spacer preference analysis:WT repeat-1

description:
Library name: 202304-03
previous GSM: GSM8209012

value: WT


title: NO136_S89

value: hepatocellular carcinoma tissue


title: NTM3_18-81

description: Lung FFPE sample from a  patient (NTM3, 18-081)


title: NO130_S88


title: SI8 Clec9a day3

value: MEF


title: MTB1_18_72

description: Lung FFPE sample from a  patient (MTB1, 18-072-9)

value: M

value: MTB


title: NO128_S86


title: FigS2D:spacer preference analysis:WT repeat-2

description:
Library name: 202303-84
previous GSM: GSM8209011


title: NO120_S83


title: cDC2

value: splenic dendritic cell type 2

value: wildtype

value: sorted live(DAPI-) and CD11c+MHC-II+CD11b+


title: PIP day9

value: mouse embryonic fibroblast

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)

value: Cells were collected 9 days after viral transduction


title: FigS2D:spacer preference analysis, FigS6B:CRISPR genesis evolution:endo CRISPR WT (25 units of spacer-repeat)

description:
Library name: 202303-51
previous GSM: GSM8209001

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: FigS2CDEFGH:spacer analysis pipeline,FigS6B:CRISPR genesis evolution:endo CRISPR WT (25 units of spacer-repeat)

description:
Library name: 202303-61
previous GSM: GSM8209010

value: bacteria


title: NO118_S81


title: PI4 day9

value: Cells were transduced with Pu.1, Irf4 (PI4)

value: sorted live(DAPI-) and tdTomato+


title: NO112_S77


title: PI4 day3


title: NO110_S75


title: Fig4BC:apoCas9 truncation:apoCas9del_RuvCIII

description:
Library name: 202303-43
previous GSM: GSM8208998

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_RuvCIII-FLAG

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: Fig4BC:apoCas9 truncation:apoCas9del_WED/PI

description:
Library name: 202303-44
previous GSM: GSM8208999

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_PI-FLAG


title: Fig4BC:apoCas9 truncation:apoCas9del_HNH

description:
Library name: 202303-42
previous GSM: GSM8208997

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_HNH-FLAG


title: PIB day9

value: MEF

value: Cells were transduced with Pu.1, Irf8, Baft3 (PIB)


title: NO106_S73

value: hepatocellular carcinoma tissue


title: NO104_S71


title: Fig4BC:apoCas9 truncation:apoCas9del_RuvCII

description:
Library name: 202303-41
previous GSM: GSM8208996

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_RuvCII-FLAG


title: NO102_S70


title: PIB day3

value: Cells were collected 3 days after viral transduction


title: Fig4BC:apoCas9 truncation:apoCas9del_BHdel_REC1/2

description:
Library name: 202303-45
previous GSM: GSM8209000

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_BHdel_REC1/2-FLAG


title: PI8 day9

value: mouse embryonic fibroblast

value: Cells were transduced with Pu.1, Irf8 (PI8)


title: Fig4BC:apoCas9 truncation:apoCas9del_RuvCIdel_BH

description:
Library name: 202303-39
previous GSM: GSM8208994

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_RuvCIdel_BH-FLAG