title: HEK293T,RESTART v3-PRAISE,rep 2

city: Beijing

first: Wenqing

last: Liu

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

institute: Peking University

description: transcriptome-wide quantitative Ψ detection in wildtype HEK293T cells with RESTART v3  treatment

data_processing:
Analysis was performed as previously reported. Briefly, only read 2 was used for subsequent analysis.
Trim_galore first subjected raw to adaptor trimming and filtering of low-quality reads. Duplicated reads were removed by Seqkit (version 0.13.2).The key parameters were: seqkit rmdup -s. umi_tools (version 1.0.0) was used to remove the 8bp UMI in the deduplication read. Six bases after the UMI added during library construction at the 5’ end of inserted sequences and the six bases at the 3’ end of inserted sequences were also removed, using the key parameters: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNNNNNN and umi_tools extract --extract-method=string --3prime --bc-pattern=NNNNNN.
Then the cleaned reads were down-sampled to 40Mb and were mapped to the reference transcriptome(hg38, NCBI Refseq) using PRAISE-tool (https://github.com/Zhe-jiang/PRAISE), and the pseudouridine signals as deletion rate in the transcriptome could be calculated.
We identified putative off-target Ψ sites using the following approach. (1) >15 deletion reads covering each candidate site in restart(+) samples. (2) >100 reads covering each candidate site in restart(-) samples. (3) The deletion rate in restart(-) samples must be less than 1%. (4) The identified off-target Ψ sites must further meet the following criteria: the deletion rate difference in gCtrl, restart v3 and mock groups must be > 20%. (5) For off-target Ψ sites, we applied the statistical test to each of them (contingency table test between restart(+) sample and restart(-) sample), and the P value between the two groups must be <0.000001.
Assembly: GRCh38
Supplementary files format and content: Analysis was performed as previously reported. Briefly, only read 2 was used for subsequent analysis. Trim_galore first subjected raw to adaptor trimming and filtering of low-quality reads. Duplicated reads were removed by Seqkit (version 0.13.2).The key parameters were: seqkit rmdup -s. umi_tools (version 1.0.0) was used to remove the 8bp UMI in the deduplication read. Six bases after the UMI added during library construction at the 5’ end of inserted sequences and the six bases at the 3’ end of inserted sequences were also removed, using the key parameters: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNNNNNN and umi_tools extract --extract-method=string --3prime --bc-pattern=NNNNNN.Then the cleaned reads were down-sampled to 40Mb and were mapped to the reference transcriptome(hg38, NCBI Refseq) using PRAISE-tool (https://github.com/Zhe-jiang/PRAISE), and the pseudouridine signals as deletion rate in the transcriptome could be calculated. We identified putative off-target Ψ sites using the following approach. (1) >15 deletion reads covering each candidate site in restart(+) samples. (2) >100 reads covering each candidate site in restart(-) samples. (3) The deletion rate in restart(-) samples must be less than 1%. (4) The identified off-target Ψ sites must further meet the following criteria: the deletion rate difference in gCtrl, restart v3 and mock groups must be > 20%. (5) For off-target Ψ sites, we applied the statistical test to each of them (contingency table test between restart(+) sample and restart(-) sample), and the P value between the two groups must be <0.000001.

source_name: Epithelial

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was extracted from cells using TRIzol reagent (Life Technologies)
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.

treatment_protocol: For transfection, 2.5 x 105 of HEK293T cells were seeded on 24-well plates (Corning), and all transfections were conducted when cells reached approximately 80% confluency after 20-24h. The plasmids were extracted using EndoFree Mini Plasmid Kit II (TIANGEN BIOTECH, DP118), and were transfected into cells by Lipofectamine LTX reagent (Invitrogen) supplemented with PLUS reagent (Invitrogen) according to the manufacturer’s instructions.

value: Epithelial

value: human embryonic kidney 293 cells


title: Leaves at the tips of the branches (F2 stage) on July 23: Repeat 2

status: Public on Jan 29 2024

type: SRA

city: Changsha

first: Guolong

last: Wu

state: Hunan

address: South of Shaoshan Road No.498

country: China

institute: Central South University Forestry and Technology

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequenceflow-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 sing clc genomic benchwok (parameters- mismath cost: 2 insertion cost: 3 deleton cost-3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NOT PROVIDED
Supplementary files format and content: All_DEG.annot.xlsx

molecule: total RNA

organism: Disanthus cercidifolius subsp. longipes

source_name: Leaves

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) .1.3 ug of total RNA was used for the construction of seguencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER RNA-Seg Library Prep Kit following manufacturer's protocols.

tag: tissue

value: Leaves

tag: developmental stage

value: F2 stage


title: Pt_R_3dpi_rep1

type: RNA

city: Hitachi

first: Tomonori

last: Hirao

state: Ibaraki

address: 3109-1 Ishi, Juo

department: Forest Bio-research Center

country: Japan

institute: Forest Tree Breeding Center, Forestry and Forest Products Research Institute

description: TSK3-1_423736A02_013-03-08_09-13_Area1_532_RMA.calls

hyb_protocol: Hybridized at 42 °C during 17 h with three μg of Cy3 labeled ds-cDNA in the NimbleGen hybridization system.

scan_protocol: Slides were scanned at 2 μm/pixel resolution using an NimbleGen MS 200 scanner (NimbleGen).

data_processing:
Scanned images (TIFF format) were imported into the NimbleScan software version 2.6 (NimbleGen) for grid alignment.
The raw data (.pair file) was background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.). The normalization algorithm is RMA-normalized, averaged gene-level signal intensity.

organism: Pinus thunbergii

label_protocol: Ten micrograms of total RNA were transcribed to double strand (ds) cDNA using a Superscript ds-cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) and  labeled by a NimbleGen One-Color Labeling Kit (NimbleGen, Madison, WI, USA)  in accordance with the NimbleGen gene expression analysis protocol. .

growth_protocol: Resistant and susceptible clones were grafts obtained from the original trees at the FFPRI-FTBC in 2010.

extract_protocol: Total RNA was isolated from 1.5 g of stem that included bark and wood tissue using the RNeasy plant mini kit (QIAGEN) following the protocol supplied by the manufacturer.

treatment_protocol: Inoculation with pine wood nematode was conducted on July 1, 2012. In six susceptible clones and six resistant clones, 2 cm at the tip of the main stem was cut off, the cut edge was quickly crushed with pliers, and 10,000 nematodes that had been suspended in 100 μl sterile water were injected into the cut edge. Stem tissue of inoculated samples was collected 2 cm below the inoculated stem apex at 1, 3, and 7 dpi. A 2 cm segment of stem was cut, frozen immediately in liquid nitrogen, and stored at -80°C. As a control sample, 2 cm at the tip of the main stem was cut off, and 2 cm below the cut stem apex was cut, frozen immediately in liquid nitrogen, and stored at -80°C.

tag: cultivar

value: Tosashimizu 63

tag: phenotype

value: Resistance

tag: inoculated with

value: pine wood nematode

tag: time point

value: 3 day post inoculation (dpi)


title: H1_hESC_teratoma_H3K36me3_ChIP_rep2

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

country: USA

institute: Wayne State University

description: Chromatin IP against H3K36me3

library_source: genomic

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Assembly: hg19
Supplementary files format and content: bedGraph

molecule: genomic DNA

organism: Homo sapiens

source_name: teratoma generated from H1 hESCs

growth_protocol: H1 hESCs were cultured on Matrigel-coated plates in serum-free E8 media at 37oC with 5% CO2 and passaged using EDTA. hESCs were dissociated using EDTA, and 1 million hESCs were injected subcutaneously into SCID-beige mice. Following a period of three to four weeks, mice were euthanized, and teratomas were cleaned and flash frozen.

extract_protocol:
Teratoma tissue was rapidly frozen utilizing liquid nitrogen, and a section was excised using a razor blade. The tissue was then pulverized with liquid nitrogen using a mortar and pestle. The resulting crushed pellet was subsequently crosslinked with formaldehyde sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell line

tag: cell type

value: teratoma

tag: antibody

value: Anti-H3K36me3 antibody (Abcam; ab9050)


title: MNase-seq_231_DOX_0h_control_shRNA-rep2

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

data_processing:
Adapter sequences were removed with cutadapt v1.2.1.
Reads were mapped to the hg19 genome using Bowtie 1.2 with paramters -m 1 -X 2000 --chunkmbs 1024.
Mapped hits were filtered to retain only those with fragment size 120-170bp.
Signal tracks were generated after collapsing mononucleosome-sized fragments to their midpoint coordinate, with conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format

growth_protocol: DMEM High glucose + 10% FBS

extract_protocol:
MNase digested DNAs were purified by Phenol-chloroform extraction with ethanol precipitation
MNase-seq libraries were prepared by NEXTFLEX Rapid DNA-Seq kit (PerkinElmer).

treatment_protocol: For transient GATA3 expression, DOX (1 µg/ml at final) was added to medium. For CHD4 knockdown, MDA-MB-231 cells were infected with lentiviruses encoding CHD4 shRNA. After overnight incubation, the meidum was replaced with fresh medium and the cells were further incubated for 2 days until DOX induction.

tag: genotype

tag: passages


title: Leaves at the tips of the branches (F2 stage) on July 23: Repeat 1


title: Pt_R_7dpi_rep1

description: TSK7-1_423736A03_013-03-08_09-13_Area1_532_RMA.calls

value: 7 day post inoculation (dpi)


title: HEK293T,RESTART v3-PRAISE,rep 1

email: puyulwq@163.com, liuwq21@gamils.com

molecule: polyA RNA

value: WT


title: #3_Resistant

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

country: Germany

institute: DKTK Partner Site Essen/Düsseldorf

description:
MEKi resistant
#3_Resistant

data_processing:
Demultiplexing of the sequencing reads with Illumina CASAVA v. 2.17 or bcl2fastq 2.19
Adapter trimming using Skewer v. 0.1.116 or 0.2.2
Quasi-mapping with salmon v. 0.12
Converting transcript-level counts to gene-level counts and performing of differentially gene expression analysis using DESeq2 v.1.18
Genome_build: mm10
Supplementary_files_format_and_content: csv files of normalized read counts and differential gene expression analysis results

organism: Mus musculus

source_name: Primary cell lines derived from pancreatic cancer of a genetically engineered mouse model

growth_protocol: DMEM high-glucose medium containing 10% fetal bovine serum, 1% penicillin/streptomycin and 1% non-essential amino acids

extract_protocol:
RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega) according to manufacturer’s instruction.
TruSeq Stranded mRNA Kit (Illumina) with 100 ng input RNA

treatment_protocol: To induce resistance, cells were treated with increasing doses of trametinib (LKT) until they grew in 100x of their IC50. One batch was cultivated with 100x IC50 of trametinib in the culture medium (termed resistant ) with medium exchange every 2-3 days on a regular basis. Another batch of each cell line was kept under drug withdrawal and samples were named according their passage number in drug-free medium (P5 and P12)

value: Pancreas

tag: group

value: Resistant


title: H1_hESC_teratoma_H3K36me3_ChIP_rep1

description: Chromatin IP against H3K36me3


title: Young leaves at the tips of the branches (F1 stage) on July 20: Repeat 3

value: F1 stage


title: HEK293T,gctrl-PRAISE,rep 2

description: transcriptome-wide quantitative Ψ detection in wildtype HEK293T cells with gctrl  treatment


title: H1_hESC_teratoma_H3K27ac_ChIP_rep2

description: Chromatin IP against H3K27ac

value: Anti-H3K27ac antibody (Abcam; ab4729)


title: HEK293T,gctrl-PRAISE,rep 1


title: Young leaves at the tips of the branches (F1 stage) on July 20: Repeat 2


title: HEK293T,mock-PRAISE,rep 1

description: transcriptome-wide quantitative Ψ detection in wildtype HEK293T cells without treatment


title: H1_hESC_teratoma_H3K27ac_ChIP_rep1

description: Chromatin IP against H3K27ac


title: Young leaves at the tips of the branches (F1 stage) on July 20: Repeat 1


title: Kat6b WT ALCAR 3331_9 [080923]

status: Public on Jan 28 2024

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
3331_9_ALCAR
080923_3331_9_Kat6b_WT_ALCAR_S27

data_processing:
Thebase calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome by Rsubread version 2.12.3
Fragment (read-pair) counts were summarized by RefSeq Gene ID using the Rsubread featureCounts function
Genes were identified using Rsubreads inbuilt mm39 annotation
Assembly: mm39
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent RefSeq Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: cerebral cortex

growth_protocol: Dissected E16.5 cortices were digested in 200 µl trypsin-EDTA (Sigma, 1006132) for 10 min in a 37oC water bath. Excess trypsin was removed and replaced with 1 ml cortical neuron medium (DMEM/F12 (Gibco, 12500-062), 15.8 mM D-glucose (Sigma, G7021), 5 mM HEPES (Sigma, H-4034), 13.4 mM NaHCO3 (Sigma, G-7021), 100 U/ml penicillin-streptomycin (Gibco, 15140-122), 25 µg/ml Insulin (Sigma, I-6634), 60 M Putrescine dihydrochloride (Sigma, P-5780), 100 µg/ml Apo-transferrin (Sigma, T-2252), 30 nM selenium sodium salt (Sigma S-9133), 20 nM progesterone (Sigma, P-6149), 0.2% BSA (Sigma, A-3311), 1% FCS)(16). Cells were gently triturated, passed through a 100 m cell sieve (Corning, CLS431752) and pelleted (200 g, 5 min). Cells were counted using an automated cell counter (CountessTM, ThermoFisher) and plated onto 12-well plates (Nunc, 150628) or chamber slides (Ibidi, 80826) pre-coated overnight with 0.1% poly-D-lysine (Sigma, P6403). Cells were grown at 37oC in 5% CO2.

extract_protocol:
For RNA isolation, medium was removed and replaced with 200 µl DNA/RNA Shield (Zymo, R1100) followed by an RNA extraction using a kit (RNeasy micro, Qiagen, 74004) according to the manufacturer’s instructions and including the optional DNase I digest.
RNA quantity and quality was assessed using a high sensitivity RNA tape (Agilent, 5067-5579 and 4200 Tapestation, Agilent). 100 ng RNA was used to generate RNA libraries using a sequencing library construction kit (TruSeq RNA Library Prep Kit v2, Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with Vehicle, 1 mM VPA or 1 mM ALCAR for 4 days, with medium changed daily.

tag: litter id

tag: mouse id

tag: kat6b genotype

tag: treatment

value: ALCAR

tag: Sex

value: M

value: cortical neurons

value: cerebral cortex


title: Kat6b WT Vehicle 3332_3 [080923]

description:
3332_3_Vehicle
080923_3332_3_Kat6b_WT_Vehicle_S4

value: Vehicle

tag: tissue


title: Kat6b WT VPA 3331_9 [080923]

description:
3331_9_VPA
080923_3331_9_Kat6b_WT_VPA_S15

value: VPA


title: Kat6b WT ALCAR 3332_3 [080923]

description:
3332_3_ALCAR
080923_3332_3_Kat6b_WT_ALCAR_S28


title: Kat6b WT Vehicle 3331_9 [080923]

description:
3331_9_Vehicle
080923_3331_9_Kat6b_WT_Vehicle_S3


title: Kat6b Dec/+ VPA 3331_7 [080923]

description:
3331_7_VPA
080923_3331_7_Kat6b_dec_pos_VPA_S19

value: Dec/+


title: Pt_S_7dpi_rep1

description: THK7-1_423681A03_2013-03-29_11-31_Area1_532_RMA.calls

value: Takahagi 1

value: Susceptibility

value: pine wood nematode


title: Kat6b WT VPA 3331_6 [080923]

description:
3331_6_VPA
080923_3331_6_Kat6b_WT_VPA_S14

value: F


title: Kat6b Dec/+ Vehicle 3331_7 [080923]

description:
3331_7_Vehicle
080923_3331_7_Kat6b_dec_pos_Vehicle_S7


title: Kat6b Dec/+ ALCAR 3332_5 [080923]

description:
3332_5_ALCAR
080923_3332_5_Kat6b_dec_pos_ALCAR_S32


title: Kat6b Dec/+ Vehicle 3332_5 [080923]

description:
3332_5_Vehicle
080923_3332_5_Kat6b_dec_pos_Vehicle_S8


title: Kat6b WT VPA 3332_3 [080923]

description:
3332_3_VPA
080923_3332_3_Kat6b_WT_VPA_S16


title: Kat6b WT Vehicle 3331_6 [080923]

description:
3331_6_Vehicle
080923_3331_6_Kat6b_WT_Vehicle_S2


title: Kat6b Dec/+ VPA 3332_5 [080923]

description:
3332_5_VPA
080923_3332_5_Kat6b_dec_pos_VPA_S20


title: Kat6b Dec/+ VPA 3331_3 [080923]

description:
3331_3_VPA
080923_3331_3_Kat6b_dec_pos_VPA_S18


title: Kat6b Dec/+ Vehicle 3331_3 [080923]

description:
3331_3_Vehicle
080923_3331_3_Kat6b_dec_pos_Vehicle_S6


title: Pt_R_1dpi_rep2

description: TSK1-2_423736A01_013-03-08_09-13_Area1_532_RMA.calls

value: Tosashimizu 63

value: Resistance

value: 1 day post inoculation (dpi)


title: Pt_S_3dpi_rep2

description: THK3-2_423681A02_2013-03-29_11-31_Area1_532_RMA.calls

value: 3 day post inoculation (dpi)


title: Pt_S_7dpi_rep2

description: THK7-2_423739A03_2013-03-10_07-27_Area1_532_RMA.calls

value: 7 day post inoculation (dpi)


title: Pt_R_7dpi_rep2

description: TSK7-2_423743A03_2013-03-28_16-23_Area1_532_RMA.calls


title: Pt_R_1dpi_rep1

description: TSK1-1_423743A01_2013-03-28_16-23_Area1_532_RMA.calls


title: Kat6b Dec/+ ALCAR 3331_3 [080923]

description:
3331_3_ALCAR
080923_3331_3_Kat6b_dec_pos_ALCAR_S30


title: Kat6b Dec/+ ALCAR 3331_7 [080923]

description:
3331_7_ALCAR
080923_3331_7_Kat6b_dec_pos_ALCAR_S31


title: Kat6b WT VPA 3331_1 [080923]

description:
3331_1_VPA
080923_3331_1_Kat6b_WT_VPA_S13

value: WT


title: Pt_R_3dpi_rep2

description: TSK3-2_423743A02_2013-03-28_16-23_Area1_532_RMA.calls


title: Kat6b WT Vehicle 3331_1 [080923]

description:
3331_1_Vehicle
080923_3331_1_Kat6b_WT_Vehicle_S1


title: Kat6b Dec/+ VPA 3242_1 [080923]

description:
3242_1_VPA
080923_3242_1_Kat6b_dec_pos_VPA_S17


title: Kat6b WT ALCAR 3331_1 [080923]

description:
3331_1_ALCAR
080923_3331_1_Kat6b_WT_ALCAR_S25

value: ALCAR


title: Pt_S_3dpi_rep1

description: THK3-1_423739A02_2013-03-10_07-27_Area1_532_RMA.calls


title: Pt_S_control_rep1

description: TH_0dpi_423671A03_2013-03-03_09-08_Area1_532_RMA.calls

value: none (control)


title: Kat6b Dec/+ Vehicle 3332_5 [300823]

description:
3332_5_Vehicle
300823_3332_5_Kat6b_dec_pos_Vehicle_S8

value: cortical neurons


title: Kat6b Dec/+ ALCAR 3332_5 [300823]

description:
3332_5_ALCAR
300823_3332_5_Kat6b_dec_pos_ALCAR_S32

value: cerebral cortex


title: Kat6b WT ALCAR 3332_3 [300823]

description:
3332_3_ALCAR
300823_3332_3_Kat6b_WT_ALCAR_S28

value: M


title: Kat6b WT VPA 3332_3 [300823]

description:
3332_3_VPA
300823_3332_3_Kat6b_WT_VPA_S16

value: VPA


title: Kat6b WT VPA 3331_9 [300823]

description:
3331_9_VPA
300823_3331_9_Kat6b_WT_VPA_S15


title: Kat6b WT Vehicle 3332_3 [300823]

description:
3332_3_Vehicle
300823_3332_3_Kat6b_WT_Vehicle_S4

value: Vehicle


title: Kat6b Dec/+ ALCAR 3242_1 [080923]

description:
3242_1_ALCAR
080923_3242_1_Kat6b_dec_pos_ALCAR_S29

value: Dec/+


title: Kat6b WT ALCAR 3331_9 [300823]

description:
3331_9_ALCAR
300823_3331_9_Kat6b_WT_ALCAR_S27


title: Pt_S_1dpi_rep2

description: THK1-2_423739A01_2013-03-10_07-27_Area1_532_RMA.calls

value: Takahagi 1

value: Susceptibility


title: Kat6b Dec/+ VPA 3331_7 [300823]

description:
3331_7_VPA
300823_3331_7_Kat6b_dec_pos_VPA_S19


title: Kat6b Dec/+ VPA 3332_5 [300823]

description:
3332_5_VPA
300823_3332_5_Kat6b_dec_pos_VPA_S20

value: F


title: Pt_R_control_rep1

description: TS_0dpi_423671A01_2013-03-03_09-08_Area1_532_RMA.calls

value: Tosashimizu 63


title: Pt_R_control_rep2

description: TS_0dpi_423671A02_2013-03-03_09-08_Area1_532_RMA.calls

value: Resistance


title: Kat6b Dec/+ Vehicle 3331_7 [300823]

description:
3331_7_Vehicle
300823_3331_7_Kat6b_dec_pos_Vehicle_S7


title: Kat6b Dec/+ Vehicle 3242_1 [080923]

description:
3242_1_Vehicle
080923_3242_1_Kat6b_dec_pos_Vehicle_S5


title: Kat6b WT Vehicle 3331_9 [300823]

description:
3331_9_Vehicle
300823_3331_9_Kat6b_WT_Vehicle_S3


title: Kat6b Dec/+ ALCAR 3331_7 [300823]

description:
3331_7_ALCAR
300823_3331_7_Kat6b_dec_pos_ALCAR_S31


title: Kat6b WT VPA 3331_6 [300823]

description:
3331_6_VPA
300823_3331_6_Kat6b_WT_VPA_S14


title: Kat6b Dec/+ VPA 3331_3 [300823]

description:
3331_3_VPA
300823_3331_3_Kat6b_dec_pos_VPA_S18


title: Kat6b WT ALCAR 3331_6 [300823]

description:
3331_6_ALCAR
300823_3331_6_Kat6b_WT_ALCAR_S26


title: Kat6b WT Vehicle 3331_6 [300823]

description:
3331_6_Vehicle
300823_3331_6_Kat6b_WT_Vehicle_S2


title: Kat6b Dec/+ Vehicle 3331_3 [300823]

description:
3331_3_Vehicle
300823_3331_3_Kat6b_dec_pos_Vehicle_S6


title: Kat6b WT VPA 3331_1 [300823]

description:
3331_1_VPA
300823_3331_1_Kat6b_WT_VPA_S13


title: Pt_S_1dpi_rep1

description: THK1-1_423681A01_2013-03-29_11-31_Area1_532_RMA.calls

value: pine wood nematode

value: 1 day post inoculation (dpi)


title: Pt_S_control_rep2

description: TH_0dpi_423671A04_2013-03-03_09-08_Area1_532_RMA.calls


title: WT-IFNy_and_Prmt1_inhibitor-Rep3

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm39/mm39 using the Subread aligner (Rsubread v.2.14.2). Gene-level read counts were obtained by using featureCounts. Rsubread inbuilt gene annotation for mm39 was used for read summarization.
Genes that failed to achieve a CPM (counts per million) expression value of 1 or greater in at least 3 libraries were excluded from analysis. Read counts were converted to log2-CPM, quantile normalized and precision weighted with the voom function of the limma package.
A linear model was fitted to each gene, and the empirical Bayes moderated t-statistic was used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 5% or less.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text files including read counts for each library.

source_name: IFNy and Prmt1-inhibitor treated WT mouse sample, replicate 3

growth_protocol: B16F10 cells were grown in DMEM media supplemented with 5% (v/v) FCS, 1% (v/v) L-glutamine and 1% (v/v) penicillin/streptomycin at 37 degree C in 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from 1x10^6 cells using the RNeasy Mini Kit (Qiagen, Cat#74106) in accordance with the manufacturer's instructions and quality checked using a 4200 TapeStation machine.
One microgram of total RNA per sample was used for NGS library preparation (Illumina TruSeq RNA, Cat#FC-122-2002) as per the manufacturer’s instructions and quality checked using a 4200 TapeStation. NGS libraries were pooled and sequenced using a P2 100-cycle Illumina sequencing kit (Illumina, Cat#20046811) on the NextSeq 2000 sequencing system with paired-end 66bp reads.

treatment_protocol: B16F10 cells were pre-treated with Prmt1-inhibitor GSK3368715 (2.5 µM) for 2 days. Afterwards, untreated wildtype (controls), Prmt1-inhibitor treated or Prmt1-/- B16F10 were cultured for one more day in the presence or absence of mouse IFNγ (1 ng/ml).

tag: strain

value: Adherent, murine melanoma (skin) cell line

value: wildtype

value: IFNy and Prmt1 inhibitor

tag: collection time

value: low passage ~(P5-P10)


title: Prmt1KO-untreated-Rep3

source_name: Untreated Prmt1-KO mouse sample, replicate 3

value: No treatment


title: WT-untreated-Rep3

source_name: Untreated WT mouse sample, replicate 3


title: Prmt1KO-untreated-Rep2

source_name: Untreated Prmt1-KO mouse sample, replicate 2


title: Kat6b Dec/+ ALCAR 3242_1 [300823]

description:
3242_1_ALCAR
300823_3242_1_Kat6b_dec_pos_ALCAR_S29

value: ALCAR

value: cortical neurons

value: cerebral cortex


title: Kat6b WT Vehicle 3331_1 [300823]

description:
3331_1_Vehicle
300823_3331_1_Kat6b_WT_Vehicle_S1

value: WT

value: Vehicle


title: Kat6b WT ALCAR 3331_1 [300823]

description:
3331_1_ALCAR
300823_3331_1_Kat6b_WT_ALCAR_S25


title: Prmt1KO-IFNy-Rep3

source_name: IFNy treated Prmt1-KO mouse sample, replicate 3

value: IFNy


title: WT-IFNy-Rep3

source_name: IFNy treated WT mouse sample, replicate 3


title: WT-Prmt1_inhibitor-Rep2

source_name: Prmt1-inhibitor treated WT mouse sample, replicate 2

value: Prmt1 inhibitor


title: WT-IFNy_and_Prmt1_inhibitor-Rep2

source_name: IFNy and Prmt1-inhibitor treated WT mouse sample, replicate 2


title: Prmt1KO-IFNy-Rep2

source_name: IFNy treated Prmt1-KO mouse sample, replicate 2


title: Prmt1KO-untreated-Rep1

source_name: Untreated Prmt1-KO mouse sample, replicate 1


title: Kat6b Dec/+ ALCAR 3331_3 [300823]

description:
3331_3_ALCAR
300823_3331_3_Kat6b_dec_pos_ALCAR_S30

value: Dec/+

value: F


title: WT-IFNy-Rep1

source_name: IFNy treated WT mouse sample, replicate 1


title: WT-Prmt1_inhibitor-Rep1

source_name: Prmt1-inhibitor treated WT mouse sample, replicate 1


title: Prmt1KO-IFNy-Rep1

source_name: IFNy treated Prmt1-KO mouse sample, replicate 1


title: WT-IFNy_and_Prmt1_inhibitor-Rep1

source_name: IFNy and Prmt1-inhibitor treated WT mouse sample, replicate 1


title: Kat6b Dec/+ Vehicle 3242_1 [300823]

description:
3242_1_Vehicle
300823_3242_1_Kat6b_dec_pos_Vehicle_S5

value: M


title: WT-untreated-Rep1

source_name: Untreated WT mouse sample, replicate 1


title: Kat6b Dec/+ VPA 3242_1 [300823]

description:
3242_1_VPA
300823_3242_1_Kat6b_dec_pos_VPA_S17

value: VPA


title: 5-antATN Spatial Transcriptomics

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
scRNA-seq: Trim input file and remove adapters; spatial: spaceranger mkfastq pipeline demultiplexes base call files and produces fastq files
scRNA-seq: Tag reads with cell barcode and UMI; spatial: spaceranger counts pipeline spatially aligns fastq files based on barcodes
scRNA-seq: Align reads to PhiX, then to mouse; spatial: align reads to mouse genome
scRNA-seq: Aggregate reads and de-duplicate UMIs
scRNA-seq and spatial: Post-processing in R with custom scripts and Seurat
Assembly: scRNA-seq: NCBIM37; spatial transcriptomics: mm10
Supplementary files format and content: Tab delimited file containing count values.
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
scRNA-seq: Microdissect, dissociate, and pool cells across acute brain slices in B6 mice; spatial transcriptomics: flash frozen brains, cryosectioning 10um and place on 10xgenomics visium slides, tissue staining for NeuN and DAPI, permeabilization and library construction following manufacturer's protocol
For scRNA-seq: Cells were placed into 8-well strips containing cell collection buffer, and each strip of cells was flash frozen on dry ice, then stored at -80°C until cDNA synthesis. For cDNA synthesis, cells were lysed by adding 1 µL lysis mix and 1 µL 10 µM barcoded RT primer. The samples were incubated for 5 minutes at 50°C to lyse the cells, followed by 20 minutes at 80°C to inactivate the Proteinase K. Reverse transcription master mix was added to the lysis reaction and incubated at 42°C for 1.5 hour, followed by 10 minutes at 75°C to inactivate reverse transcriptase. PCR was performed, and samples were pooled across the plate to yield approximately 2 mL pooled PCR reaction. From this, 500 µL was purified, washed twice with 75% ethanol, and eluted in 20 µL nuclease-free water. For Visium Spatial transcriptomics: as described by 10x genomics for Visium workflow with 24min permeabilization time

value: Brain


title: 6-postATN Spatial Transcriptomics


title: 2-postATN Spatial Transcriptomics


title: WT-Prmt1_inhibitor-Rep3

source_name: Prmt1-inhibitor treated WT mouse sample, replicate 3

value: Adherent, murine melanoma (skin) cell line


title: WT-untreated-Rep2

source_name: Untreated WT mouse sample, replicate 2

value: wildtype


title: COVID-19_TMA_B_9,Case_12,FOV_23

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

institute: University of Queensland

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were rinsed of excess probes in 2X SSCT for 1 min and were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. 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 for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing: Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. Quality control of the data was conducted based on previously established pipeline for spatial data (standR, Liu et al, Nucleic Acids Research. 2023). Cells with a total transcript count less than 10% of the quantile of the data were filtered out  (16432, or 10.6%), retaining 139127. After removing low quality cells, region of interest (ROI) quality were assessed based on feature sizes and nuclei counts. 3 FOVs with less than 200 cells were removed. The rescaled log2-transformed counts per million (logCPM) of the data is provided as inputs for cell type annotation.    Cell types in the data were determined based on a majority consensus strategy of four widely used annotation methods for scRNAseq data. The 4 methods are reference-based methods Azimuth and CelliD as well as marker-based methods singscore and AUCell. The reference-based methods use the core consensus reference model of the cellular landscape of the lung and nose from Human Lung Cell Atlas (HLCA) as the reference. The filtered logCPM counts data from the quality control step (logCPM) and data from the query dataset (HLCA) were normalized using the SCTransform function in the Seurat R package.The normalized data was passed to each of the 4 methods to generate the respective cell type labels. The final cell type annotation was determined by a majority consensus of at least 2 out of 4 methods. This results in 71.12% assignment of cell types in the dataset.

source_name: lung

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 1:2,000 fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

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

tag: tma

tag: fov

value: rapid autopsy lung

tag: caseid

tag: gender

tag: age

tag: disease


title: COVID-19_TMA_B_9,Case_4,FOV_18


title: COVID-19_TMA_B_9,Case_21,FOV_20


title: COVID-19_TMA_B_9,Case_21,FOV_21


title: COVID-19_TMA_B_9,Case_4,FOV_19


title: COVID-19_TMA_B_9,Case_28,FOV_26


title: COVID-19_TMA_B_9,Case_20,FOV_16


title: COVID-19_TMA_B_9,Case_3,FOV_15


title: COVID-19_TMA_B_9,Case_20,FOV_17


title: COVID-19_TMA_B_9,Case_30,FOV_13


title: COVID-19_TMA_B_9,Case_8,FOV_10


title: COVID-19_TMA_B_9,Case_6,FOV_24


title: COVID-19_TMA_B_9,Case_3,FOV_14


title: WT-IFNy-Rep2

source_name: IFNy treated WT mouse sample, replicate 2

tag: cell line

tag: cell type

tag: genotype

value: low passage ~(P5-P10)


title: COVID-19_TMA_B_9,Case_29,FOV_8


title: COVID-19_TMA_B_9,Case_29,FOV_7


title: COVID-19_TMA_B_9,Case_30,FOV_12


title: COVID-19_TMA_B_9,Case_2,FOV_9


title: COVID-19_TMA_B_9,Case_17,FOV_6


title: COVID-19_TMA_B_9,Case_8,FOV_11


title: COVID-19_TMA_B_9,Case_7,FOV_3


title: COVID-19_TMA_B_9,Case_7,FOV_4


title: COVID-19_TMA_B_9,Case_17,FOV_5


title: COVID-19_TMA_B_9,Case_1,FOV_1


title: COVID-19_TMA_B_10,Case_6,FOV_25


title: COVID-19_TMA_B_10,Case_28,FOV_26


title: COVID-19_TMA_B_9,Case_6,FOV_25


title: COVID-19_TMA_B_9,Case_12,FOV_22


title: COVID-19_TMA_B_10,Case_6,FOV_24


title: COVID-19_TMA_B_10,Case_21,FOV_20


title: COVID-19_TMA_B_10,Case_4,FOV_19


title: COVID-19_TMA_B_10,Case_20,FOV_17


title: COVID-19_TMA_B_9,Case_1,FOV_2


title: COVID-19_TMA_B_10,Case_2,FOV_9


title: COVID-19_TMA_B_10,Case_3,FOV_15


title: COVID-19_TMA_B_10,Case_30,FOV_13


title: COVID-19_TMA_B_10,Case_8,FOV_10


title: COVID-19_TMA_B_10,Case_8,FOV_11


title: COVID-19_TMA_B_10,Case_20,FOV_16


title: COVID-19_TMA_B_10,Case_17,FOV_5


title: COVID-19_TMA_B_10,Case_29,FOV_8


title: COVID-19_TMA_B_10,Case_30,FOV_12


title: COVID-19_TMA_B_10,Case_7,FOV_4


title: PBMC, Treg, EPF/infertile, subject34

city: Adelaide

first: Sarah

last: Robertson

state: South Australia

address: 4 North Terrace

department: Discipline of Obstetrics and Gynaecology

institute: The University of Adelaide

data_processing:
Adapter sequences were trimmed with AdapterRemoval v2.2.1. Read quality was checked with FastQC v0.11.7 (Babraham Bioinformatics, Cambridge, UK) before and after adapter trimming.
Reads were aligned to the GRCh38 genome using STAR v2.5.3 and the resulting BAM files from each sequencing lane were concatenated. Aligned reads were counted with Subread v1.5.2.
R v4.2.1 and R studio v2022.02 were used for differential gene expression (DGE) analyzes. Genes were initially filtered to keep only those with at least 1 CPM in at least 6 libraries.
Using all libraries (Tcon and Treg), DGE between fertile and early pregnancy failure subjects was performed using limma v3.52.2.
Next, the dataset was then divided into Tcon cell samples and Treg cell samples to be further analyzed independently.
For DGE between fertile and early pregnancy failure Tconv cell samples, 3 Tconv samples (I-Tcon-05, I-Tcon-10, I-Tcon-28) lying outside of the 95% CI for the EPF group by principle component analysis were excluded prior to DGE analysis. DGE analysis was performed using limma v3.52.2.
For DGE between fertile and early pregnancy failure Treg cell samples, the data were normalized using RUVSeq v1.30.0 with 6 factors of variation removal (W-6) based on edgeR-ranked P values from a first-pass limma/voom analysis.  1 Treg cell sample (F-Treg-23) lying outside of the 95% CI of the fertile group by principle component analysis after RUVg normalization was excluded and the process was restarted without this sample. After normalization, DE genes were identified using edgeR v3.38.1.
Assembly: GRCh38, AH83216
Supplementary files format and content: tab-delimited text file "All_samples_counts.txt" contains counts per million (cpm) reads for each sample, for the genes that met minimum expression criteria for DGE analysis (at least 1 cpm reads in at least 6 samples)

source_name: PBMC

growth_protocol: T regulatory (Treg) cells (CD4+CD25+CD127low) and T conventional (Tcon) cells (CD4+CD25low/-) were purified from frozen PBMCs by FACS, then rested for 2 hours  at 37⁰C and 5% CO2 in complete X-VIVO culture medium containing 10% fetal bovine serum, 1% Glutamax, 1 mM HEPES and 1% Antibiotic-Antimicotic.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Micro Plus Kit according to the manufacturer's protocols.
46-548ng (mean 200ng) of total RNA was subjected to cDNA library synthesis using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA), NEBNext Ultra II Directional RNA Library Prep Kit from Illumina (San Diego, CA) and NEBNext Multiplex Oligos for Illumina, according to the manufacturer’s protocols. The libraries were quantified with the Universal KAPA Library Quantification Kit (Roche, Basel, Switzerland) and those with sufficient DNA (≥ 2 nM) were pooled to equimolar concentration. Paired-end 150bp sequencing was performed at GENEWIZ (Azenta Life Sciences, Chelmsford, MA) on an Illumina Hi-Seq platform across 5 lanes. Libraries were sequenced to an average read depth of 56.3 million reads per sample.

treatment_protocol: The cells were stimulated in vitrofor 48 hours at a 1:1 ratio with Dynabeads Human T-Expander CD3/CD28 in complete X-VIVO culture medium with 400 U/mL recombinant human IL-2.

value: PBMC

value: CD4+ T regulatory cells

tag: fertility

value: infertile (early pregnancy failure)

value: 48hr CD3/CD28 Dynabeads + rhIL-2


title: COVID-19_TMA_B_10,Case_17,FOV_6


title: COVID-19_TMA_B_10,Case_3,FOV_14


title: COVID-19_TMA_B_10,Case_29,FOV_7


title: COVID-19_TMA_B_10,Case_1,FOV_2


title: COVID-19_TMA_A_9,Case_18,FOV_32


title: PBMC, Treg, EPF/infertile, subject26


title: COVID-19_TMA_B_10,Case_12,FOV_23


title: PBMC, Treg, EPF/infertile, subject27


title: PBMC, Treg, EPF/infertile, subject21


title: COVID-19_TMA_A_9,Case_7,FOV_31


title: COVID-19_TMA_A_9,Case_17,FOV_30


title: COVID-19_TMA_B_10,Case_12,FOV_22


title: COVID-19_TMA_A_9,Case_1,FOV_28


title: COVID-19_TMA_A_9,Case_17,FOV_29


title: COVID-19_TMA_A_9,Case_1,FOV_27


title: PBMC, Treg, EPF/infertile, subject12


title: PBMC, Treg, EPF/infertile, subject2


title: COVID-19_TMA_B_10,Case_1,FOV_1


title: PBMC, Treg, fertile, subject31

value: fertile


title: PBMC, Treg, EPF/infertile, subject14


title: COVID-19_TMA_A_9,Case_8,FOV_23


title: COVID-19_TMA_A_9,Case_30,FOV_26


title: PBMC, Treg, fertile, subject23


title: PBMC, Treg, fertile, subject9


title: COVID-19_TMA_A_9,Case_30,FOV_25


title: COVID-19_TMA_A_9,Case_8,FOV_24


title: COVID-19_TMA_A_9,Case_2,FOV_21


title: COVID-19_TMA_A_9,Case_2,FOV_22


title: PBMC, Treg, fertile, subject30


title: PBMC, Treg, EPF/infertile, subject16


title: PBMC, Treg, fertile, subject3


title: COVID-19_TMA_B_10,Case_7,FOV_3


title: COVID-19_TMA_A_9,Case_31,FOV_20


title: COVID-19_TMA_A_9,Case_31,FOV_19


title: PBMC, Tconv, EPF/infertile, subject34

value: CD4+ T conventional cells


title: PBMC, Tconv, EPF/infertile, subject28


title: PBMC, Treg, fertile, subject1


title: PBMC, Tconv, EPF/infertile, subject27


title: PBMC, Treg, fertile, subject35


title: COVID-19_TMA_A_9,Case_20,FOV_17


title: COVID-19_TMA_A_9,Case_9,FOV_16


title: PBMC, Tconv, EPF/infertile, subject26


title: COVID-19_TMA_A_9,Case_9,FOV_15


title: COVID-19_TMA_A_9,Case_12,FOV_12


title: PBMC, Tconv, EPF/infertile, subject25


title: PBMC, Tconv, EPF/infertile, subject20


title: COVID-19_TMA_A_9,Case_3,FOV_13


title: COVID-19_TMA_A_9,Case_3,FOV_14


title: PBMC, Tconv, EPF/infertile, subject18


title: COVID-19_TMA_B_10,Case_21,FOV_21


title: PBMC, Tconv, EPF/infertile, subject16


title: COVID-19_TMA_A_9,Case_12,FOV_11


title: PBMC, Tconv, EPF/infertile, subject24


title: COVID-19_TMA_A_9,Case_4,FOV_8


title: PBMC, Tconv, EPF/infertile, subject14


title: PBMC, Tconv, EPF/infertile, subject15


title: COVID-19_TMA_A_9,Case_21,FOV_9


title: PBMC, Tconv, EPF/infertile, subject5


title: COVID-19_TMA_A_9,Case_21,FOV_10


title: COVID-19_TMA_A_9,Case_20,FOV_18


title: PBMC, Tconv, EPF/infertile, subject12


title: PBMC, Tconv, EPF/infertile, subject10


title: PBMC, Tconv, EPF/infertile, subject2


title: COVID-19_TMA_A_9,Case_28,FOV_5


title: COVID-19_TMA_A_9,Case_4,FOV_7


title: COVID-19_TMA_A_9,Case_28,FOV_6


title: PBMC, Tconv, fertile, subject35


title: COVID-19_TMA_A_9,Case_16,FOV_4


title: PBMC, Tconv, fertile, subject31


title: COVID-19_TMA_A_9,Case_16,FOV_3


title: PBMC, Tconv, fertile, subject30


title: COVID-19_TMA_A_9,Case_6,FOV_2


title: PBMC, Tconv, fertile, subject23


title: COVID-19_TMA_A_8,Case_18,FOV_32


title: PBMC, Tconv, fertile, subject19


title: PBMC, Tconv, fertile, subject13


title: PBMC, Tconv, fertile, subject11


title: COVID-19_TMA_A_9,Case_6,FOV_1


title: COVID-19_TMA_A_8,Case_17,FOV_29


title: COVID-19_TMA_A_8,Case_17,FOV_30


title: Treg_splenic_bulkRNA_ko3

city: Chicago

first: Deyu

last: Fang

address: 303 E Chicago Avenue

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13 Trimmed reads were aligned using STAR version 020201 Gene counting was performed using htseq-count version 0.6.1p1 Differential expression was performed using DESeq2 version 1.14.1
Assembly: NCBI37/mm10
Supplementary files format and content: bedgraph

source_name: Isolated from spleen of mice in homeostatic conditions

extract_protocol:
nTreg cells were sorted from each of the mice using the Foxp3 YFP reporter.RNA was extracted using the RNeasy Micro Kit (Qiagen, Cat# 74004) from sorted Foxp3+ (YFP+) Treg cells from mouse spleens
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T Regulatory Cells

value: B6 Med1 fl-fl FoxP3 YFP Cre


title: PBMC, Tconv, fertile, subject9


title: PBMC, Tconv, fertile, subject3


title: Treg_splenic_bulkRNA_ko2

value: Isolated from spleen of mice in homeostatic conditions


title: COVID-19_TMA_A_8,Case_1,FOV_27

value: F


title: COVID-19_TMA_A_8,Case_30,FOV_25


title: COVID-19_TMA_A_8,Case_30,FOV_26


title: Treg_splenic_bulkRNA_ko1


title: PBMC, Tconv, fertile, subject1


title: COVID-19_TMA_A_8,Case_2,FOV_22

value: M


title: COVID-19_TMA_A_8,Case_8,FOV_23


title: PBMC, Tconv, fertile, subject32


title: Treg_RM1_ATAC_ko4

data_processing:
Paired end ATACseq reads were aligned to the mouse genome (NCBI37/mm10) using Bowtie2(92) with option ‘‘--very-sensitive-local’’. Mitochondrial reads were excluded from downstream analysis.  Peak calling was performed on each individual sample by MACS2(93) with parameter ‘‘-BAMPE’’. Peaks from different ATACseq replicates and samples were merged using bedtools merge(94). Merged peaks were converted into GTF files and used for HTSeq-count(95). Pairwise comparisons of ATACseq peaks between two conditions were performed using R package DESeq2(96) with reads count of each peak calculated by HTSeq-count.
Assembly: NCBI37/mm10
Supplementary files format and content: tdf

source_name: Isolated from RM1 Tumors

extract_protocol:
50,000 cells were washed in cold phosphate-buffered saline (PBS) to eliminate traces of DNase and buffer. Cell membrane was permeabilized with nuclear lysis buffer (10 mM tris, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL-630).
Then, cells were resuspended in 50uL of transposase reaction mixture (22.5uL nuclease-free water, 25uL of TD buffer and 2.5uL of TDE1 enzyme, Illumina #20034197). Transposition was carried out at 37°C for 22 min, followed by DNA purification with DNA Clean and Concentrator-5 (Zymo Research) according to the manufacturer’s recommendation. Following purification, library fragments were PCR amplified with Nextera XT v2 adapter primers.
Multiplexed and pooled library was sequencing on the NextSeq 500 (Illumina) with 37 nucleotides (nt) paired ends according to the manufacturer’s instructions.

value: Isolated from RM1 Tumors

value: B6 Med1 fl-fl FoxP3 CreERT2

value: Tamoxifen+ RM1 Tumor


title: COVID-19_TMA_A_8,Case_7,FOV_31


title: COVID-19_TMA_A_8,Case_31,FOV_20


title: Treg_splenic_bulkRNA_con2

value: B6 FoxP3 YFP Cre


title: Treg_RM1_ATAC_ko3


title: Treg_splenic_bulkRNA_con1


title: COVID-19_TMA_A_8,Case_31,FOV_19

value: rapid autopsy lung


title: COVID-19_TMA_A_8,Case_20,FOV_18


title: COVID-19_TMA_A_8,Case_20,FOV_17


title: COVID-19_TMA_A_8,Case_1,FOV_28


title: COVID-19_TMA_A_8,Case_9,FOV_16


title: mESC_48h_rep1

city: Lausanne

first: Almut

middle: Sophia

last: Eisele

address: Station 19

country: Switzerland

institute: EPFL

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Lineage barcodes were extracted from the scRNA-seq data using the CellTag pipeline available for download at (https://github.com/morris-lab/BiddyetalWorkflow) after adaptation to the LARRY barcode design. Briefly the CellTag pipeline extracts reads containing a CellTag motif from the processed, filtered, and unmapped reads BAM files produced in intermediate steps of the 10X Genomics Cell Ranger pipeline. To extract LARRY barcodes, the CellTag motif was changed to “([ACTG]{4}TG[ACTG]{4}CA[ACTG]{4}AC[ACTG]{4}GA[ACTG]{4}GT [ACTG]{4} AG[ACTG] {4})” in all scripts. Barcodes with reads from only one UMI, and without perfect match to the reference library were filtered out. A Jaccard score of >0.7 was used to identify cell lineages. No filtering on the number of barcodes expressed per cell was performed. Lineages were called on unfiltered data.
Assembly: mm10
Supplementary files format and content: Cellranger output files and output of lineage assignment pipeline

growth_protocol: CGR8 ES cells  were routinely cultured at 37°C and 5% CO2 on dishes coated with 0.1% gelatin type B in GMEM supplemented with 10% ES cell‐qualified fetal bovine serum, 1% nonessential amino acids, 2 mM l‐glutamine and sodium pyruvate, 100 μM 2‐mercaptoethanol, penicillin and streptomycin (Pen/Strep), homemade leukemia inhibitory factor (LIF), 3 μM CHIR99021 and 0.8 μMPD184352. Cells were passaged by trypsinization every 2-3 days at a ratio of 1:10. For the single cell RNA-seq experiment, cells were switched to N2B27+2i/LIF medium 2 passages beforehand. N2B27+ 2i/LIF medium was composed of a 1:1 mix of DMEM/F12 and Neurobasal medium, supplemented with N2, B27, 1% Pen/Strep, 2 mM L-glutamine, 100 μM 2-mercaptoethanol, LIF, CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were split every 2-3 days at a ratio of 1:10, using accutase and centrifugation.

extract_protocol: Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.1 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: CGR8 cells were transduced with the lentiviral LARRY barcoding library to obtain roughly 1% of GFP+ cells. 72h after infection, live GFP+ cells (live stain 1:500 propidium iodide solution) were sorted on an FACSAria III  into Cellcarrier 96-Ultra 96-well plates. Plates were coated with recombinant human E-cadherin-Fc chimera to reduce colony formation and thereby limit the potential impact of paracrine and direct cell signaling in regulating gene expression of related cells. Coating was performed at 10 μg/ml for 1h at 37°C. After washing the plates with PBS, 1200 cells were sorted into two wells and cells of both wells were collected after 48h for sequencing

value: embryonic stem cells

value: N2B27 medium supplemented with 2i and LIF on E-cadherin coating


title: Treg_RM1_ATAC_ko1


title: COVID-19_TMA_A_8,Case_9,FOV_15


title: Treg_RM1_ATAC_con4

value: B6 FoxP3 CreERT2


title: COVID-19_TMA_A_8,Case_3,FOV_14


title: COVID-19_TMA_A_8,Case_12,FOV_12


title: Treg_splenic_bulkRNA_con3


title: Rec8 in ctf19-9A, rep-3

city: Oklahoma City

first: DEAN

last: DAWSON

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Adapters were trimmed using BBTools/BBDuk and the quality control of reads was done using Fastqc (version 0.11.9). Paired-end sequences were aligned to S.cerevisiae genome (R64-3-1_20210421) with bowtie2 (version 2.5.0) using '-I 10 -X 700  --end-to-end  --very-sensitive --no-mixed --no-discordant  --phred33' arguments.
Bigwig files were generated by deepTools(version 3.4.3) bamcoverage by normalization of each sample for CPM (Counts per Million mapped reads) and the bin size being selected as 10.
BAM files were imported to SeqMonk to quantitate read counts in 20 bp generated probes and to apply DESeq2 analysis to filter by statistical test (p<0.05 after Benjamimi and Hochberg correction with the application of independent intensity filtering) for identification of differences between replicates of WT and ctf19-9A.
Assembly: sacCer3
Supplementary files format and content: bigWig
Library strategy: ChEC-Seq

organism: Saccharomyces cerevisiae

source_name: zygotes

growth_protocol: Three diploid WT or ctf19-9A colonies each obtained from 3 different zygotes (biological replicates) were inoculated separately in YPAD medium for overnight growth at 30 degrees. To induce meiosis, overnight cultures were first shifted to YP acetate media to grow for ~16 hours and then shifted to 1% potassium acetate at 10^8 cells/mL to grow for 4.5 hours.

extract_protocol:
ChEC-seq was performed as described previously (Donczew et al., 2021 [PMID: 34137374]) with an optimized 5min of 2mM CaCl2 incubation in meiotic cells.
Library construction was done using Kapa HyperPrep Kit and TruSeq adapters.

value: zygotes

tag: chec-tag

tag: background

value: X and Y

tag: cell cycle_stage

value: Meiotic prophase I

value: Rec8-3xFLAG-MNase ctf19-9A ndt80-delta


title: Rec8 in ctf19-9A, rep-2


title: COVID-19_TMA_A_8,Case_2,FOV_21


title: COVID-19_TMA_A_8,Case_21,FOV_10


title: Treg_RM1_ATAC_con3

value: T Regulatory Cells

tag: treatment


title: Treg_RM1_ATAC_con2

tag: tissue


title: Rec8 in WT, rep-3

value: Rec8-3xFLAG-MNase ndt80-delta


title: Treg_RM1_ATAC_ko2


title: COVID-19_TMA_A_8,Case_21,FOV_9


title: COVID-19_TMA_A_8,Case_4,FOV_8


title: Rec8 in ctf19-9A, rep-1


title: Treg_RM1_ATAC_con1


title: COVID-19_TMA_A_8,Case_4,FOV_7


title: COVID-19_TMA_A_8,Case_28,FOV_5


title: Rec8 in WT, rep-2


title: COVID-19_TMA_A_8,Case_28,FOV_6


title: Rec8 in WT, rep-1


title: COVID-19_TMA_A_8,Case_3,FOV_13


title: COVID-19_TMA_A_8,Case_16,FOV_4


title: Treg_spleen_ATAC_ko3

source_name: Isolated from Spleens

value: Isolated from Spleens


title: COVID-19_TMA_A_8,Case_16,FOV_3


title: COVID-19_TMA_A_8,Case_6,FOV_2


title: atn_sample14

data_processing:
Trim input file and remove adapters.
Tag reads with cell barcode and UMI
Align reads to PhiX, then to mouse.
Aggregate reads and de-duplicate UMIs.
Post-processing in R with custom scripts and Seurat.
Assembly: NCBIM37
Supplementary files format and content: Tab delimited file containing count values.

source_name: Anterior thalamic nuclei

extract_protocol:
Microdissect, dissociate, and manually harvest cells across acute brain slices in B6 mice.
Cells were placed into 8-well strips containing cell collection buffer, and each strip of cells was flash frozen on dry ice, then stored at -80°C until cDNA synthesis. For cDNA synthesis, cells were lysed by adding 1 µL lysis mix and 1 µL 10 µM barcoded RT primer. The samples were incubated for 5 minutes at 50°C to lyse the cells, followed by 20 minutes at 80°C to inactivate the Proteinase K. Reverse transcription master mix was added to the lysis reaction and incubated at 42°C for 1.5 hour, followed by 10 minutes at 75°C to inactivate reverse transcriptase. PCR was performed, and samples were pooled across the plate to yield approximately 2 mL pooled PCR reaction. From this, 500 µL was purified, washed twice with 75% ethanol, and eluted in 20 µL nuclease-free water.

value: WT

value: Anterior thalamic nuclei


title: Treg_spleen_ATAC_ko2


title: COVID-19_TMA_A_8,Case_12,FOV_11


title: COVID-19_TMA_A_8,Case_6,FOV_1

value: M


title: atn_sample13


title: Treg_spleen_ATAC_ko1

value: B6 Med1 fl-fl FoxP3 CreERT2


title: atn_sample12


title: K562 cells, DualCRISPR at scale screen of putative K562 enhancers, 15 days, replicate 1

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

description: Pooled_and_single_cell_DualCRISPR_screen_results.xlsx

library_source: genomic single cell

data_processing:
For single cell dual-CRISPR screening, Cell Ranger 6.0.1 pipeline was used to process Chromium single-cell data to align reads, generate feature-barcode matrices for the mRNAs, and captured guide RNAs. Seurat 4.0.2 was used to process the single-cell RNA-seq data (Butler et al., 2018). Gene expression matrix was normalized using the “LogNormalize'' method with scale factor of 10,000 and log-transformed. Cell-cycle-related scores were regressed during data scaling. Differential expression tests and p-value calculations were performed by the MAST-fitted model based on whole transcriptome data in all single cells except for genes with mean normalized expression < 0.01 (Finak et al., 2015).
For pooled dual-CRISPR screening, Cutadapt 3.4 was used to extract the unique 20nt protospacer sequences from each pair of guide RNA sequences by locating the U6/H1 promoter sequences from the 5’ end and scaffold sequence from the 3’ end of the 20nt protospacer sequence (U6 promoter, ATATATCTTGTGGAAAGGACGAAA; H1 promoter, ATAAGTTCTGTATGAGACCACTCTT) (Martin, 2011). The read pairs that did not contain the correct promoter and scaffold sequences were not considered. To ensure functional CRISPR guide RNA sequences were counted, the protospacer sequence and the additional 20 bp (for both Lenti-dual-CRISRP-1.0/ Lenti-dual-CRISPR-2.0) into the CRISPR scaffold sequences were kept during the trimming of the sequence reads (tracrRNA sequence, AAGTTAAAAT). Trimmed reads were then mapped to the indexed paired protospacers references generated by Bowtie2 based on our initial library designs, and only aligned reads with mapping quality (MAPQ) score over 23 were used for downstream analyses (Langmead and Salzberg, 2012). MAGeCK RRA was used to identify the significant hits depleted after 15-day culture compared with the day 0 initial cell population, with the cutoff of RRA score < 0.01 (Li et al., 2014). MAGeCK MLE was performed to identify NCREs that confer imatinib resistance, by comparing the 15-day imatinib-treated cell population, 15-day culture cell population and day 0 initial cell population (Li et al., 2015). The NCREs whose loss confers Imatinib resistance were identified as regions that were positively selected (i.e., NCREs with beta scores > mean + 2×s.d.) in the 15-day imatinib-treated populations but are weakly selected in the 15-day culture populations.
Assembly: GRCh37 assembly release 75
Supplementary files format and content: RDS files processed by Seurat containing the polyA-mRNA transcripts and captured CRISPR gRNA molecules count table from single K562 cells transfected with scDual-CRISPR library, pilot screen (~10k cells),  at scale screen (~30k cell) and merged filtered experiment data are included.

growth_protocol: K562 cells were cultured in RPMI 1640 + L-Glutamine (Gibco), 10% fetal bovine serum (Biowest), and 1% Penicillin-Streptomycin (Gibco). 293T cells were cultured in DMEM (Gibco), 10% FBS and 1% Penicillin-Streptomycin. Cell density and culture conditions were maintained according to the ENCODE Cell Culture Guidelines.

extract_protocol:
The single-cell dual-CRISPR library was introduced into K562-Cas9 expressing cells via spin infection at a final MOI of <0.3. After one week, cells that successfully incorporated the single-cell dual-CRISPR system were sorted based on GFP expression using FACS sort. To prepare for single-cell processing, 0.5 × 106 cells at a concentration of 1,500 cells ml-1 in 0.04% BSA-PBS were used for single-cell RNA and guide RNA capture according to the 10x Genomics protocol.
The 10x Genomics Chromium platform was used to generate the single-cell libraries according to the manufacturer’s protocol, which were sequenced on the Illumina NovaSeq 6000 platform.

treatment_protocol: K562/Cas9 cells were infected with the respective virus libraries at a multiplicity of infection = 0.2 by spin-infection. For spin-infection, 3 × 106 cells in each well of a 12-well plate were infected in 1 ml of medium containing 8 μg ml–1 of polybrene. In total, four plates were used for each infection to infect a total of 1.5 × 108 cells, which would result in ~300× to ~500× coverage of the dual-CRISPR libraries. Two days after infection, cells were selected by 2 mg ml–1 of puromycin for a further 6 d. Dead cells were then removed with Histopaque-1077 (Sigma) by centrifuging cells at 400g for 30 minutes at room temperature. For each biological replicate experiment, the lentivirus was produced again and infection was repeated. After puromycin selection, an aliquot of 108 K562/Cas9 cells infected with the respective dual-CRISPR libraries were frozen as the control population (day 0). From the same cell population, 108 K562 cells were further cultured for another 15 days to identify essential NCREs that affect cell growth; and another 108 cells were cultured under 0.1 μM imatinib treatment for 15 days. Dead cells were removed, and drugs were refreshed during the subculture of imatinib-treated cells. On day 15, 108 cells for each culture were collected and frozen for the next step. For 293T cells, procedures were similar, except that the dead cells were removed by refreshing the medium.

value: erythroleukemia

value: Cas9-expressing, DualCRISPR library targeting putative k562 enhancers transfected


title: K562 cells, DualCRISPR at scale screen of putative K562 enhancers, 15 days, replicate 2


title: Treg_spleen_ATAC_con4

value: Tamoxifen+ RM1 Tumor


title: K562 cells, DualCRISPR at scale screen of putative K562 enhancers, 0 day, replicate 1


title: K562 cells, DualCRISPR at scale screen of putative K562 enhancers, 0 day, replicate 2


title: Treg_spleen_ATAC_con3


title: K562 cells, DualCRISPR pilot screen of putative K562 enhancers, 15 days, replicate 1


title: K562 cells, DualCRISPR pilot screen of putative K562 enhancers, 15 days, replicate 2


title: atn_sample11


title: Treg_spleen_ATAC_ko4


title: Treg_spleen_ATAC_con2


title: atn_sample10


title: K562 cells, DualCRISPR pilot screen of putative K562 enhancers, 0 day, replicate 2


title: Treg_spleen_ATAC_con1


title: atn_sample8


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 15 days, replicate 3

value: embryonic kidney cell

value: Cas9-expressing, DualCRISPR library targeting ultraconserved elements transfected


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 15 days, replicate 2


title: KO.d2327 [delta_Bmi1 rep 4]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. Software: Control v2.2.0.4, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation were quantified using Salmon version 1.2.1
Genome_build: mm10 with an ensembl version 101 annotation
Supplementary_files_format_and_content: mmwilson_012522_intCt.txt.gz is a tab separated file of integrer count data
Supplementary_files_format_and_content: mmwilson_012522_l2tpm.txt.gz is a tab separated file of log2 tpm data

source_name: melanocyte stem cells

growth_protocol: Dorsal skin was collected from mice at postnatal day 21 (P21) and placed in a 10 cm dish with cold PBS. Subcutaneous fat was scraped off the dermal side and skin minced into small pieces with razor blades. Tissues were placed in a 15 mL conical tube with 5 mL of 2 mg/mL collagenase I (Worthington) and incubated in a 37°C shaker for 2 hours. Then, warm Trypsin-EDTA (STEMCELL Technologies) supplemented with Deoxyribonuclease I (0.1 mg/mL) was added to each conical tube, and samples were incubated for an additional hour in the 37°C shaker. Tubes were briefly vortexed, and tissue suspension was pipetted up and down with a 10 mL serological pipette for 1 minute each to break up remaining large pieces. Cell suspensions were pelleted at 2000 RPM for 5 minutes at 4°C and then washed in cold PBS prior to filtration through a 70 μm cell strainer. Cell suspension was pelleted, washed in cold PBS, and pelleted again prior to resuspension in cold PBS with DAPI (1:1000, BD Pharmingen). DAPI-stained single cells were sent through a 40 μm cell strainer into a FACS tube. Live cells were selected based on negative DAPI staining. Dct-GFP+, non-autofluorescent cells (based on PerCP-Cy5.5- status) were isolated using a BD FACSAria III.

extract_protocol:
RNA was extracted from  >10,000 Dct-GFP+ sortedf cells with TRIzol using standard phenol chloroform extraction and then purified using the Qiagen RNeasy Micro Kit following the manufacturer’s protocol.
The quality and quantity of RNA samples were determined using an Agilent Femto Pulse. RNA-seq libraries were prepared from 1 ng of total RNA using a TaKaRa SMARTer Stranded Total RNASeq Kit v2 Pico Input Mammalian kit with a 4-min fragmentation and 15 cycles of PCR. After cDNA cleanup, samples were treated with ZapR reagent and library fragments not cleaved by ZapR were further amplified by 15 cycles of PCR. Illumina libraries were validated using the Agilent Fragment Analyzer and quantified by qPCR

tag: strain

value: mixed C57Bl-6;129Sv

value: Bmi1fl/fl, Tyrosinase-Cre, Dct-rtTA, TRE-H2B-GFP

tag: feed

value: doxycycline pellets (Envigo, TD.01306)

value: melanocyte stem cells


title: atn_sample7


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 15 days, replicate 1


title: LS8-Fam83h-mut-RNA-seq-sample2

city: Wuhan

first: Xueqing

last: Zheng

address: Luoyu Road

institute: Wuhan University

data_processing:
Adaptors and low quality bases were trimmed from raw sequencing reads using SOAPnuke (v1.5.2).
The clean reads were mapped to the reference genome GRCm38 using HISAT2 (v2.0.4).
Reads only unambiguously aligned to unique position were preserved to calculate reads number and RPKM (reads per kilobase and per million) value for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all genes in each sample.

source_name: Ameloblast-like cells

growth_protocol: LS8 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from the related cells was extracted using TRIzol Reagent (Ambion) following the manufacturer's instructions.
RNA-seq libraries were prepared with MGIEasy stLFR  Kit following the manufacturer’s instructions and sequenced on the BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: For RNA-seq experiments, LS8 cells were performed lentivirus plasmid package against flag-Fam83h-mut vector (pCMV-Tag2B-FLAG-Fam83h-mut-EGFP) or empty vector (pCMV-Tag2B-EGFP) and were grown in regular medium and collected.

tag: source

value: tooth germ

tag: lentivirus plasmid package


title: WT.d2326 [CTL rep 4]

value: Bmi1fl/fl, Dct-rtTA, TRE-H2B-GFP


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 0 day, replicate 3


title: COVID-19_TMA_B_10,Case_4,FOV_18

tag: tma

tag: fov

value: rapid autopsy lung

tag: caseid


title: atn_sample6


title: atn_sample5


title: LS8-Fam83h-mut-RNA-seq-sample1


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 0 day, replicate 2


title: KO.d2325 [delta_Bmi1 rep 3]


title: K562 cells, DualCRISPR pilot screen of putative K562 enhancers, 0 day, replicate 1


title: LS8-ev-RNA-seq-sample2

value: empty vector


title: WT.d2324 [CTL rep 3]


title: atn_sample4

value: WT


title: atn_sample9

value: Anterior thalamic nuclei


title: K562 cells, DualCRISPR screen of ultraconserved elements, Imatinib 15 day, replicate 2

value: Imatinib


title: KO.d2323 [delta_Bmi1 rep 2]


title: LS8-ev-RNA-seq-sample1


title: KO.d2322 [delta_Bmi1 rep 1]


title: Treg_AOMDSS_scRNA_con3

description: Raw files are unavailable because sequencing core removed them from the university server.

data_processing:
Raw sequencing data, in base call format (.bcl) was demultiplexed using Cell Ranger from 10x Genomics, converting the raw data into FASTQ format.  Cell Ranger was also used for alignment of the FASTQ files to the mouse reference genome (mm10) and to count the number of reads from each cell that align to each gene, generating matrix files for each sample. Matrix files were analyzed using the Seurat R package (Seurat v4.2.1, R version 4.1.0)
Assembly: NCBI37/mm10
Supplementary files format and content: filtered barcodes, features, and matrix gz files

source_name: Isolated from inflamed tumor bearing colon

extract_protocol:
Sixteen thousand cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip K (10X Genomics, PN-1000127), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol.
The cDNA and library were generated using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10X Genomics, PN-1000283) according to the manufacturer’s manual.
The multiplexed libraries were pooled and sequenced on Illumina Novaseq6000 sequencer with paired-end 50 kits using the following read length: 28 bp Read1 for cell barcode and UMI and 90 bp Read2 for transcript. The targeted sequencing depth for gene expression is 25,000 reads per cell.

value: CD45+ Immune Cells

value: B6 FoxP3 YFP Cre

value: DSS+AOM


title: liver,CW1

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

data_processing:
Raw sequencing data format was shown as “.fastq” and the joint sequence (adapter) was removed from the original tags using CUTADAPT 1.9. Low quality and repetitive sequences were filtered to obtain clean data. De novo splicing in TRINITY tool (Version 2.4.0) was selected to assemble the clean reads and then the software was used to perform the transcript clustering based on shared sequences contents. The longest transcript in each cluster was regarded as one Unigene. All obtained Unigenes were annotated based on known databases. Quantitative assessment for transcripts per million (TPM) of each Unigene was executed with the SALMON package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Hipposideros armiger

source_name: liver

extract_protocol:
Commercial RNA simple extraction kit (DP419, TIANGEN, China) was selected to extract the total RNA in liver tissues. 60 mg fresh tissue was ground by high-speed homogenizer (DHFSTPRP-32D, LAWSON, China) with 1 mL lysis buffer RZ to obtain homogenate and then trichloromethane was added. After staying at room temperature for 4 min, the mixture was centrifuged at 12000 rpm to obtain the aqueous phase that was mixed with absolute ethyl alcohol. RD solution was used to remove residual protein impurity in RNA samples and the purified total RNA was stored at RNase-free tubes after repeated centrifugation.
When RNA integrity number > 7.0 and A260/280 > 1.8, messenger RNA (mRNA) with poly A was caught using oligo(dT) dynabeads (25-61005, THERMO FISHER, USA) and then broken into fragmentation with the specific kit (E6150S, NEBNEST, USA). Double-strands complementary DNA was synthesized based on the reverse transcriptase and E. coli DNA polymerase I that were provided by LIANCHUAN BIO TECHNOLOGIES Co., LTD (Hangzhou, China). Paired-ends of the complementary DNA were added with a “A” base, which could combine with the adapter sequence. After the second strand was digested, the sequencing library (300±50 bp) was established by amplifying the target sequences.

value: liver

value: heavy metals exposure


title: K562 cells, DualCRISPR screen of ultraconserved elements, Imatinib 15 day, replicate 1

value: erythroleukemia

value: Cas9-expressing, DualCRISPR library targeting ultraconserved elements transfected


title: K562 cells, DualCRISPR screen of ultraconserved elements, 15 day, replicate 2


title: WT.d2321 [CTL rep 2]

value: mixed C57Bl-6;129Sv


title: Treg_AOMDSS_scRNA_con1

source_name: Isolated from inflamed colon

value: Isolated from inflamed colon

value: T Regulatory Cells


title: Treg_AOMDSS_scRNA_con2

value: Isolated from inflamed tumor bearing colon


title: WT.d2320 [CTL rep 1]

value: Bmi1fl/fl, Dct-rtTA, TRE-H2B-GFP

value: doxycycline pellets (Envigo, TD.01306)

value: melanocyte stem cells


title: atn_sample1

value: WT


title: K562 cells, DualCRISPR screen of ultraconserved elements, 15 day, replicate 1


title: Treg_DSS_scRNA_con2

value: DSS Colitis 6 Days


title: HEK293T cells, DualCRISPR screen of ultraconserved elements, 0 day, replicate 1

value: embryonic kidney cell


title: Itk-/- Th17 rep3

city: Ithaca

first: Avery

last: August

address: 930 Campus Road

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts and cuffnorm v2.2.1 was used to generate FPKM values for annotated genes.
Genes with FPKM and annotation were further analyzed in Genespring for PCA, clustering, and differential gene expression. GSEA was also used to analyze biological pathways and enriched genes based on ratios.
Genome_build: Mouse mm10 (UCSC)

growth_protocol: [mouse husbandry]

extract_protocol:
CD4+ T cells were sorted from lungs, pelleted, frozen at -80C. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from 20ng total RNA per sample using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation, by the RNA Sequencing Core at Cornell University.

treatment_protocol: mice were exposed to 150μg of Saccharopolyspora rectivirgula

tag: itk genotype

value: Itk-/-

value: lungs

value: exposed to 150ug of Saccharopolyspora rectivirgula


title: Treg_DSS_scRNA_con1

value: B6 FoxP3 YFP Cre


title: K562 cells, DualCRISPR screen of ultraconserved elements, 0 day, replicate 2

tag: cell line


title: atn_sample3

value: Anterior thalamic nuclei


title: MLA_4

first: Mengjie

last: Xie

state: Hubei province

address: 99 Ziyang Road, Wuhan City, Hubei Province

institute: Wuhan University Renmin Hospital

data_processing:
Expression values were calculated as FPKM and differential genes were filtered with a 1.5-fold change cutoff and false discovery rate ＜0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: heart

extract_protocol:
Total RNA was extracted using TRIzol reagent and purified with the RNeasy Mini Kit and reversely transcripted into cDNA, according to the manufacturer’s instructions.
The RNA sequencing data were aligned to the reference genomes using the HISAT (Hierarchical Indexing for Sliced Alignment of Transcripts, V2.0.4).

value: heart

value: treat with Dox, tVNS and methyllycaconitine citrate(MLA)


title: Itk-/- Th17 rep1

source_name: Itk-/- CD44+TCRb+CD4+Foxp3-IL17+

tag: cell type


title: MLA_3


title: MLA_5


title: atn_sample2

tag: genotype


title: Itk-/- Th17 rep2


title: K562 cells, scDualCRISPR screen, at scale (~30k cells), scRNAseq

description:
10x Genomics
30k_cell_gRNA_matrix.rds
30k_perturb_cells_gene_exprs.rds
scDualCRISPR_perturb_cell_pGBC_pair_table.rds
scDualCRISPR_perturb_cells_gene_exprs.rds

value: erythroleukemia

value: Cas9-expressing, scDualCRISPR library targeting essential NCREs tranfected


title: K562 cells, DualCRISPR screen of ultraconserved elements, 0 day, replicate 1


title: Treg_RM1_scRNA_ko2

value: Isolated from RM1 Tumors

value: T Regulatory Cells

value: B6 Med1 fl-fl FoxP3 CreERT2

value: Tamoxifen+ RM1 Tumor


title: K562 cells, scDualCRISPR screen, pilot (~10k cells), scRNAseq

description:
10x Genomics
10k_cell_gRNA_matrix.rds
10k_perturb_cells_gene_exprs.rds
scDualCRISPR_perturb_cell_pGBC_pair_table.rds
scDualCRISPR_perturb_cells_gene_exprs.rds


title: MLA_2


title: WT Th17 rep3

source_name: WT CD44+TCRb+CD4+Foxp3-IL17+


title: Treg_RM1_scRNA_con2

value: B6 FoxP3 CreERT2


title: MLA_1


title: WT Th17 rep2

value: WT


title: Treg_RM1_scRNA_ko1


title: Dox+tVNS_5

value: treat with Dox and tragus vagus nerve stimulation (tVNS)


title: HCT116 cells, treatment, replicate 3

city: Shanghai

first: Haojie

last: Chen

state: Shanghai

address: Yueyang Road 320

department: PICB

institute: CAS

data_processing:
Using MAGeCK to process the raw sequencing data
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: sgRNA sequencing

source_name: HCT116 cells

growth_protocol: HCT116 cells were maintained in RPMI 1640  supplemented with 10% fetal bovine serum  and 1% penicillin/streptomycin at 37 °C with 5% CO2.

extract_protocol:
The remaining surviving cells were harvested, and their genomic DNA was isolated and amplified by 2-step PCR using NEBNext Ultra II Q5 Master Mix (M0544L, New England Biolabs, Ipswich, MA, USA) . The PCR products containing the sgRNA sequences were extracted from the gel, quantified, sequenced, and analyzed  by illumina xten platform.
Genomic DNA was isolated and amplified by 2-step PCR using NEBNext Ultra II Q5 Master Mix (M0544L, New England Biolabs, Ipswich, MA, USA)

treatment_protocol: HCT116 cells were plated, transduced with the lentiviral library and selected with puromycin (0.8 µg/mL) as previously reported3. The selected cells were divided into 4 groups and treated with PBS or 10 µM oxaliplatin for 7 days.

value: HCT116 cells

value: oxaliplatin


title: WT Th17 rep1

value: lungs


title: Treg_RM1_scRNA_con1


title: Dox+tVNS_4


title: Dox+tVNS_3


title: HCT116 cells, treatment, replicate 1


title: Betp-Gel@Ran-1

first: huiqin

last: Gao

address: 639 Zhizao’ju Road

institute: Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai,

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform, and 150 bp paired-end reads were generated.
The mapping of 100-bp paired-end reads to genes was undertaken using HTSeq v0.6.0 software,
while fragments per kilobase of transcript per million fragments mapped (FPKM) were also analysed.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample ...

extract_protocol:
Choroidal-retinal flat mounts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Then, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Based on the manufacturer’s instructions, clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: after intravitreal injection of BetP-Gel three months

value: choroidal-retinal flat mounts


title: HCT116 cells, treatment, replicate 2


title: Betp-Gel@Ran-3


title: Dox+tVNS_1


title: wet-AMD-3

source_name: wet-AMD_choroidal-retinal flat mounts

value: CNV mice


title: Dox+tVNS_2

value: heart


title: RNA-seq samples for MDA-MB-468 cells treated with control sgRNA and Cas9, replicate 2

city: Tokyo

first: Takehiro

last: Yamamoto

address: Shinanomachi 35, Shinjuku-ku, tokyo, Japan

department: Biochemistry

institute: Keio University

data_processing:
Base-calling was performed with bcl2fastq program.
Low quality bases, adapters, and other illumina-specific sequences were removed by using Trimmomatic program (v0.38).
The sequence reads were aligned to the human reference genome assembly (GRCh38) using HISAT2 program (v2.1.0).
For estimation of gene expression, StringTie program (v2.1.3b) was employed.
Assembly: GRCh38
Supplementary files format and content: Comma separated values (CSV) file includes fragments per kilobase of exon per million mapped reads (FPKM) counts for each samples.

source_name: breast cancer

growth_protocol: MDA-MB-468 breast cancer cells were maintained in DMEM supplmented with 10% fetal bovine serum (FBS) and antibiotics in 5% CO2 incubator at 37oC.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
The total RNA (1.3 ug) was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit (illumina), according to the manufacturer’s instructions.

value: breast cancer

value: breast mammary gland adenocarcinoma

value: control sgRNA and Cas9


title: HCT116 cells, control

value: PBS


title: RNA-seq samples for MDA-MB-468 cells treated with control sgRNA and Cas9, replicate 3


title: RNA-seq samples for MDA-MB-468 cells treated with control sgRNA and Cas9, replicate 1


title: Mutant PFN1 C71G iMG 1 [A12]

city: Worcester

first: Elaine

last: Lim

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

data_processing:
FastQC
multiqc
STAR aligner (2.7.0a)
HTSeq
Assembly: hg38
Supplementary files format and content: .csv
Supplementary files format and content: expression.csv

source_name: iPSC-derived

extract_protocol:
Total RNA was isolated with Direct-zol RNA Microprep Kit (Zymo Research, R2060) according to the manufacturer’s instructions.
RNA library preparation and sequencing was conducted by Novogene Co., LTD (Beijing, China) with a read length of 150 base pairs.

value: iPSC-derived

value: Induced microglia

value: iMG

value: Mutant


title: WT PFN1 iMG 2 [A13]

value: Control


title: Mutant PFN1 C71G iMG 2 [A14]


title: WT PFN1 iMG 4 [A5]


title: WT PFN1 iMG 1 [A11]


title: Mutant PFN1 C71G iMG 4 [A6]


title: wet-AMD-1


title: Dox_4

value: treated with Dox


title: RNA-seq samples for MDA-MB-468 cells treated with sgRNA for PRMT1 and Cas9, replicate 3

value: sgRNA for PRMT1 and Cas9


title: Dox_5


title: Mutant PFN1 C71G iMG 3 [A4]


title: Dox_3


title: Untreated-3

source_name: Untreated_choroidal-retinal flat mounts

value: Untreated mice


title: Betp-Gel@Ran-2


title: Dox_2


title: Untreated-2


title: RNA-seq samples for MDA-MB-468 cells treated with sgRNA for PRMT1 and Cas9, replicate 1


title: Dox_1


title: Untreated-1


title: RCC4 VHL+  JQ1 R2

status: Public on Jan 27 2024

city: Solna

first: Irene

last: Stevens

address: Tomtebodavägen 23A (Gamma5)

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Reads were mapped to the Ensembl GRCh38 Homo Sapiens reference genome using STAR alignment software version 2.7.8 with Paired End setting
Raw abundance measurements were obtained using Subread package version 2.0.3 featureCounts feature with settings: -t "exon" -g "gene_id".
Differential expression analysis between JQ1 treatment versus DMSO control in both ccRCC4 VHL- and ccRCC4 VHL+ cell lines was done using DESeq2 version 1.30.1. Figures were created in RStudio using ggplot2 version 3.3.6.
The computations and data handling were enabled by resources in project SNIC 2021/22-252 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX, funded by the Swedish Research Council through grant agreement no. 2022-06725.
Supplementary files format and content: tab-delimited text files include Raw Counts Table (pe counts for all 12 samples). And Differential expression Files (ccRCC4 VHL+ treated (JQ1) versus control (DMSO), as well as ccRCC4 VHL-).

source_name: RCC4 VHL +  JQ1

growth_protocol: The clear cell renal cell carcinoma cell line RCC4 with loss of VHL (RCC4 VHL) and the same cell line with VHL reintroduction (RCC4 VHL+) were maintained in high glucose DMEM with 10% FBS (HyClone, EU approved, heat Inactivated, South America) and 1% geneticin (Gibco, Life Technologies, Waltham, MA, USA). All cells were cultured in a humidified environment at +37°C and 5% CO2. RCC4 VHL+ and VHL- cells were transiently transduced with two different lentiviruses carrying one short hairpin RNA against MYC, shMYC1 (TRCN0000039640), shMYC2 (TRCN000003642), or both in combination shMYC1+2 (RCC4 VHL+ shMYC and RCC4 VHL- shMYC). As control, the cells were transduced with a lentivirus with the corresponding scrambled (SCR) control (RCC4 VHL+ shSCR and RCC4 VHL- shSCR). We used 4 μg/ml of polybrene and MOI=5 for both RCC4 VHL+ and RCC4 VHL- cells.

extract_protocol:
RNA from cell lysates will be isolated using Tri-Reagent and RNA will be extracted and purified using DirectZol™ RNA MiniPrep kit (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructons.
DNase treatment was used to reduce the amount of genomic DNA. Ribosomal RNA (rRNA) was depleted from the samples using Ribosomal RNA depletion pools (riboPOOLs) developed by siTOOLs Biotech (Planegg, Germany), to enable sensitive detection of mRNA and non-coding RNA. RNA was reverse transcribed to cDNA fragmentation and size selection was performed to purify sequences that were the appropriate length for the sequencing machine. Once the RNA libraries were prepared, they were sequenced using a NextSeq 2000 instrument obtaining 30-40 million reads per sample.

treatment_protocol: RCC4 cells were treated with MYC inhibitor 5 μM JQ1. As control, DMSO was used. All compounds were from Sigma-Aldrich (St. Louis, MO, USA)

value: VHL reintroduction


title: wet-AMD-2


title: RCC4 VHL+  JQ1 R3

source_name: RCC4 VHL + JQ1


title: RCC4 VHL-  JQ1 R3

source_name: RCC4 VHL -  JQ1

value: loss of VHL


title: RCC4 VHL+ DMSO R3

source_name: RCC4 VHL + DMSO

value: DMSO control


title: RCC4 VHL+ DMSO R2

source_name: RCC4 VHL +  DMSO


title: WT PFN1 iMG 3 [A3]


title: RCC4 VHL-  JQ1 R1


title: RCC4 VHL-  DMSO R3

source_name: RCC4 VHL -  DMSO


title: RCC4 VHL+  JQ1 R1


title: RCC4 VHL+ DMSO R1


title: RCC4 VHL-  JQ1 R2


title: RCC4 VHL-  DMSO R1


title: miR-744-5p

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping  (READemption 0.3.0)
Size filtering: discarding reads shorter than 14 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: Human Genome GRCh37
Supplementary_files_format_and_content: CSV with reads per gene

source_name: HeLa-229 cells

growth_protocol: HeLa cells grown in standard conditions  (DMEM 1 g/L glucose (Life Technologies) supplemented with 10% fetal bovine serum (Biochrom), maintained in a 5% CO2, humidified atmosphere, at 37°C)

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: MicroRNAs were transfected into HeLa-229 cells using a standard reverse transfection protocol (Lipofectamine RNAiMAX, Life Technologies), at a final miRNA concentration of 50 nM. Cells were collected 72h pos-transfection.

tag: transfection


title: RNA-seq samples for MDA-MB-468 cells treated with sgRNA for PRMT1 and Cas9, replicate 2


title: RCC4 VHL-  DMSO R2


title: Muscle_SMAD4_wt_replicate4

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive, Box 3709

department: Cell Biology

institute: Duke University School of Medicine

data_processing:
Read alignment with STAR v2.7.5c
Feature counts and creation of count matrix using Cufflinks v2.2.2, downstream anlysis using DESEQ2
Assembly: mm10
Supplementary files format and content: Tab-separated FPKM-normalized gene counts for each sample

source_name: Mouse Muscle

extract_protocol:
40 h after the CTX injury, MuSCs were isolated from the digested gaskin muscles using FACS and then underwent RNA extraction using the NucleoSpin RNA XS kit from Macherey-Nagel
Smart Seq

treatment_protocol: Treated with cardiotoxin

value: Mouse Muscle

value: Skeletal Muscle Satellite Cells

value: Smad4 f/+:Pax7 CreER/CreER:R26 YFP/YFP

value: Cardiotoxin treatment and Collagenase digestion of tissue


title: Muscle_SMAD4_wt_replicate2


title: Muscle_SMAD4_wt_replicate3


title: Muscle_SMAD4_iKO_replicate1

value: Smad4 f/f:Pax7 CreER/CreER :R26 YFP/YFP


title: Muscle_SMAD4_wt_replicate1


title: Muscle_SMAD4_iKO_replicate2


title: Muscle_NoInjury_replicate3

description: 10X Chromium Next GEM Single Cell 3ʹ v3.1

data_processing:
Filtering of high-quality cells and creation of the Cell-gene matrix was done using CellRanger v6.0.1 (scRNAseq)
Creation of the seurat objects and other down-stream analyses were done using Seurat Version 4.0.0
The raw gene expression counts for all cells were SCT transformed with regression of mitochondrial gene expression, but MuSCs were log-normalized and scaled.
Assembly: mm10
Supplementary files format and content: rds file of seurat object (in R) containingraw gene expression matrix, dimensionality reduction matrices, and other cell-type-related metadata.

source_name: Skeletal Muscle Hindlimb

extract_protocol:
Dissected tissue, snap frozen, homogenized with gentleMACS
Chromium Next GEM Single-Cell 3ʹ Reagent Kits v3.1 (10× Gemomis, CG000204)with size selection using SPRI beads

treatment_protocol: Treated with 1.2% barium chloride (wt/vol in H2O)

value: Skeletal Muscle Hindlimb

value: Tissue disection, Collagenase 2/Dispase digestion. Immune Cell Depleted

value: All Muscle tissue cells

value: C57BL6 mice wt

value: Collagenase digestion of tissue


title: COVID-19_TMA_A_8,Case_8,FOV_24

first: Arutha

last: Kulasinghe

address: 37 kent st

institute: University of Queensland

data_processing: Images were segmented to obtain cell boundaries based on protocol described in He et al, Nature Biotechnology 2022;40(12):1794-806. The transcripts were assigned at the cell-level to obtain a transcript by cell count matrix. Quality control of the data was conducted based on previously established pipeline for spatial data (standR, Liu et al, Nucleic Acids Research. 2023). Cells with a total transcript count less than 10% of the quantile of the data were filtered out  (16432, or 10.6%), retaining 139127. After removing low quality cells, region of interest (ROI) quality were assessed based on feature sizes and nuclei counts. 3 FOVs with less than 200 cells were removed. The rescaled log2-transformed counts per million (logCPM) of the data is provided as inputs for cell type annotation.    Cell types in the data were determined based on a majority consensus strategy of four widely used annotation methods for scRNAseq data. The 4 methods are reference-based methods Azimuth and CelliD as well as marker-based methods singscore and AUCell. The reference-based methods use the core consensus reference model of the cellular landscape of the lung and nose from Human Lung Cell Atlas (HLCA) as the reference. The filtered logCPM counts data from the quality control step (logCPM) and data from the query dataset (HLCA) were normalized using the SCTransform function in the Seurat R package.The normalized data was passed to each of the 4 methods to generate the respective cell type labels. The final cell type annotation was determined by a majority consensus of at least 2 out of 4 methods. This results in 71.12% assignment of cell types in the dataset.

source_name: lung

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

value: rapid autopsy lung

tag: gender

value: F

tag: age

tag: disease


title: Muscle_3DaysPostInjury_replicate1

tag: treatment


title: Muscle_3DaysPostInjury_replicate2

tag: tissue


title: Muscle_NoInjury_replicate1


title: control miR

value: control miR (50nM, 72h)


title: Slide-318-06-07-2022-003-Non-epi

city: Pittsburgh

first: Ayah

middle: N.

last: Al-Bzour

state: Pennsylvania

address: Pittsburgh

department: Department of Medicine, Division of Hematology & Oncology

institute: University of Pittsburgh Medical Center (UPMC)

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 663
DSP-1001660010694-A-F03

data_processing:
*library strategy: GeoMx DSP (RNA-seq)
Illumina FASTQ sequencing files were processed using the GeoMx NGS Pipeline version 2.3.3.10 to generate digital count conversion (DCC) files which were subsequently analyzed using the GeoMx DSP Analysis Suite version 2.4.1 to perform data QC and Q3 normalization using all target groups
Assembly: GeoMx Cancer Transcriptome Atlas
Supplementary files format and content: Processed data files are provided in DCC format

source_name: Stroma

extract_protocol:
Spatial profiling was performed on three regions of interests (ROIs) from formalin fixed paraffin embedded tissue (FFPE) sections for each patient sample. Tumor epithelial compartment (highlighted by pan-cytokeratin, green-fluorescent marker) and the stroma compartment (pan-cytokeratin negative).
This involved library preparation and assessing the quality and quantity of the purified library using Agilent Bioanalyzer and Qubit assays, respectively. NGS libraries were sequenced using the Illumina NextSeq 550 instrument

value: Stroma


title: Muscle_SMAD4_iKO_replicate3


title: Slide2-328-06-23-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 666
DSP-1001660010694-A-G03

source_name: Tumor

value: Tumor


title: Slide2-312-06-23-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 664
DSP-1001660010694-A-F11


title: Slide2-328-06-23-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 667
DSP-1001660010694-A-G04


title: Slide-318-06-07-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 662
DSP-1001660010694-A-F02


title: Slide2-333-06-23-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 668
DSP-1001660010694-A-G07


title: Slide-318-06-07-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 660
DSP-1001660010694-A-E12


title: Slide2-312-06-23-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 665
DSP-1001660010694-A-F12


title: Slide2-333-06-23-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 669
DSP-1001660010694-A-G08


title: Slide-318-06-07-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 661
DSP-1001660010694-A-F01


title: Slide-318-06-07-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 659
DSP-1001660010694-A-E11


title: Slide-343-05-26-22-004-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 656
DSP-1001660010694-A-D12


title: Slide-343-05-26-22-005-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 657
DSP-1001660010694-A-E01


title: Slide-343-05-26-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 655
DSP-1001660010694-A-D11


title: Slide-343-05-26-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 654
DSP-1001660010694-A-D10


title: Slide-318-06-07-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 658
DSP-1001660010694-A-E10


title: Slide-343-05-26-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 652
DSP-1001660010694-A-D08


title: Phgdhfl/fl Cx3cr1-Cre, TEM, rep4

city: Vienna

first: Wolfram

last: Weckwerth

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

data_processing:
The raw reads in fastq format were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated by using HT-seq v0.6
The identified transcripts are further assembled and analyzed for differential analysis with the DESeq2.
Genes with low counts greater than 10
adjusted p-value less than 0.05
Assembly: mm10
Supplementary files format and content: Normalized FPKM values for each sample (tab-delimited text file)

source_name: BMDMS

growth_protocol: Phgdhfl/fl Cx3cr1-Cre and Phgdhfl/fl BMDMs were seeded in a 6-well plate at a density of 1 × 10^6 cells per well and allowed to adhere overnight

extract_protocol:
Total RNA was isolated using the TRl reagent
The NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used for preparing the sequencing libraries

treatment_protocol: Then the media were replaced with AE17-TCM and incubated for 24 hours

value: BMDMS

value: Macrophage

value: macrophage-specific Phgdh KO


title: Phgdhfl/fl Cx3cr1-Cre, TEM, rep3


title: Slide-344-05-26-22-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 651
DSP-1001660010694-A-D07


title: Muscle_NoInjury_replicate2

description: 10X Chromium Next GEM Single Cell 3ʹ v3.1