description:
Library name: D7_Hv1KO_Sham_SC_4
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 4


title: ET1-2_S9_L004

status: Public on Dec 17 2025

type: SRA

city: Houston

first: Weiyi

last: Peng

state: TX

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

country: USA

institute: University of Houston

description:
In vitro screen Sample ET1-2-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET1_Ctrl.gene_summary.txt

library_source: genomic

data_processing:
Genome-wide in vitro immune screen analysis: The MAGeCK (v0.5.9.4) count module was used to calculate the read count of individual gRNAs in different samples with the following parameters: “-l Mouse_v2_CRISPR.library --norm-method total --sample-label Ctrl,ET02,ET1 -n Mouse_v2_CRISPR_191205.count.version2.txt --fastq files.fq”. MAGeCK test module was then applied with parameters “-k Mouse_v2_CRISPR_191205.count.version2.txt -c Ctrl,ET02,ET1 --norm-method total --keep-tmp -n Mouse_v2_CRISPR_191205 _ET_Ctrl --gene-lfc-method secondbest”, to identify the genes whose gRNAs were significant differentially presented between the control and T cell treatment groups at the cutoff using |log2(fold-change)| ≥ 0.25 and p< 0.05.
In vivo screen analysis: For the results from the in vivo immune screen, the sequencing reads were mapped to the ICB sub-library using bowtie (1.2.2) with parameters “--best --strata -a --norc -m 1 -5 6 –S”. Samtools (1.9) was used to calculate the read count of each gRNA. The fold change and statistical significance of genes among the between non-responder and IgG control or responder and IgG control groups were calculated as using a modification of the DrugZ algorithm
Assembly: mm10
Supplementary files format and content: gene_summary.txt, sgrna_summary.txt, count.txt

molecule: genomic DNA

organism: Mus musculus

source_name: Cell line

growth_protocol: ID8 and related derived cell lines were obtained from the American Type Culture Collection (ATCC, Bethesda, MD). All cell lines and their genetically modified cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN), 5 ug/mL of insulin, transferrin and sodium selenite and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA). Cells were grown at 37 °C with 5% CO2. All cell lines were authenticated by short tandem repeat fingerprinting or the expression of tagged markers used for genetic modification. The mycoplasma detection kit (#13100-01, SouthernBiotech, Birmingham, AL) was used to routinely monitor for mycoplasma contamination of cultured cells. The maximum length of time of in vitro cell culture between thawing and use in the described experiments was two weeks.

extract_protocol:
Genomic DNA from all cell samples was extracted by using TRIzol (#15596026; ThermoFisher) according to the manufacturer’s protocol.
DNA fragments containing gRNA sequences were amplified and barcoded with adaptation by nested polymerase chain reaction (PCR) as previously described. The quality and concentration of all PCR products were determined by the Qubit ssDNA high sensitivity assay kit (#Q10212; ThermoFisher) and the bioanalyzer High Sensitivity DNA Kit (#5067-4626 2100; Agilent, Santa Clara, CA) respectively. Samples were then sequenced by Illumina Next-Generation Sequencing (NSG) at the MD Anderson Cancer Center Advanced Technology Genomics Core.
PCR amplicon of gRNA fragments

treatment_protocol: For in vitro CRISPR screen, the mouse improved genome-wide knockout CRISPR Library version 2 consisting of 90,230 gRNAs targeted 18,424 genes was purchased from Addgene and used to generate lentivirus as described above. 1.5× 108 of ID8/GC cells were transduced with pooled library lentivirus at low multiplicity of infection (MOI; ~0.15-0.2) and cultured with growth medium in present of 2ug/ml puromycin to select gRNA-transduced cells. One week after selection, pooled gRNA-transduced tumor cells were washed and seeded incell culture dishes for overnight. For T cell treated groups, cultured Pmel T cells were added at effector: target (ET) ratio of 0.2:1 and 1:1 for 16 hours. For non-T cell treated groups, equal amount of T cell growth medium was added. After treatment, non-adhesive cells including T cells and dead tumor cells were removed by repeated wash using pre-warmed PBS. Adherent cells were harvested by using 0.25% Trypsin-EDTA and washed three times using PBS. Additionally, tumor cells after 48-hour or 7-day puromycin selection were collected to determine the coverage of the genome-wide library in transduced cells before the functional immune screen. Three replicates were performed for all treatment groups, and each sample includes at least 3×107 of transduced cells for genomic DNA isolation using Blood & Cell Culture DNA MAXI Kit as described by the manufacturer’s protocol.  For in vivo CRISPR screen, After construction of the library, ID8/GC cells were transduced to express the pooled in vivo sub-library. Briefly, to generate lentiviral supernatants, HEK293T cells were seeded 16 hours before transfection and transfected with 9μg of lentiviral vectors encoding gRNAs library, along with lentiviral packaging plasmids (3μg of pCMV-VSV-G and 4.5μg of psPAX2) by the jetPRIME transfection reagent according to the manufacturer’s protocol. Viral supernatants were collected 72 hours post-transfection and filtered by 0.45um Syringe Filter Unit to remove cell debris. 1.2x107 ID8/GC cells were transduced with the pooled lentiviral supernatant at a low MOI (~0.15-0.2) and cultured with completed growth media for 48 hours. Then, transduced ID8/GC cells were under the selection pressure with 2μg/mL of puromycin for seven days. Additionally, 3.0x107 sub-library expressing ID8/GC (ID8/GCSL) cells were collected after 7 days of puromycin selection and served as reference samples (Ref). After 7 days of puromycin selection and expansion, ID8/GCSL cells were collected and subcutaneously inoculated into C57BL/6 and NSG mice at 1.0x107 cells per injection into the posterior-lateral flank of the mice. After 3 days post tumor inoculation, tumor-bearing C57BL/6 mice were randomized into two groups to receive anti-PD-1 treatment (N=10) or control (N=5). Intraperitoneal injection of anti-PD-1 at 100μg/per dose, every other day, were used for the mice in anti-PD-1 group. NSG mice bearing pooled tumor cells served as a control to eliminate the genes with essential role in controlling tumor development independent to endogenous immune responses. Additionally, tumor size of all mice was monitored every other day by recording perpendicular diameters taken by calipers. At the end of the treatment cycle of 12 days, tumors were collected to extract genomic DNA as described above.

tag: tissue

value: Cell line

tag: cell line

tag: cell type

value: Murine ovarian cancer cell line

tag: treatment

value: Pmel T cell treated

tag: screen

value: In vitro screen


title: SFI_Pt18

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description:
Library name: Pt18
Pt18

library_source: transcriptomic

data_processing:
Sequenced reads mapped to the GRCh38 reference genome using HISAT2 program
assembly and quantification using the StringTie program
Assembly: GRCh38
Supplementary files format and content: raw read count txt file

molecule: total RNA

organism: Homo sapiens

source_name: kidney

extract_protocol:
FFPE tissues were used.
SureSelectXT RNA Direct Library Preparation Kit

value: kidney

value: Renal cell carcinoma

tag: group

value: SFI


title: ET02-4_S8_L003

description:
In vitro screen Sample ET02-4-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description:
Library name: D7_Hv1KO_Sham_SC_2
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 2

data_processing:
Base calling was performed using CASAVA version 1.8.2 (Illumina, San Diego, CA).
The GENCODE mouse gene annotation (version M33) was used for alignment and quantification.
Gene-level quantification was performed using RSEM version 1.3.3 (PMID: 21816040).
Assembly: Mouse reference genome GRCm39
Supplementary files format and content: Tab-delimited text files containing Ensembl gene identifiers and gene/isoform expression values in TPM (transcripts per million).

molecule: polyA RNA

source_name: Spinal Cord

extract_protocol:
Following euthanasia 7 days and 6 weeks after SCI, mice were perfused with 50 mL of ice-cold normal saline. Total RNA was extracted from the spinal cord, lung, and spleen tissue with the miRNeasy Mini Kit (Qiagen, Cat# 74104).  In brief, approximately 600ul of QIAzol were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to Novogene Bioinformatics Technology Co., Ltd. (Sacramento, CA) for downstream sequencing assays.
Library preparations were carried out by Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp reads). mRNA was enriched through poly-A pulldown.

value: Spinal Cord

tag: strain

tag: Sex

value: male

tag: age

value: 19 to 22 months old

tag: genotype

value: Hv1 knockout

value: Sham

tag: collection time

value: 7 days after SCI

tag: replicate


title: SFI_Pt17

description:
Library name: Pt17
Pt17


title: ET02-4_S8_L002

description:
In vitro screen Sample ET02-4-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


title: SFI_Pt23

description:
Library name: Pt23
Pt23


description:
Library name: D7_Hv1KO_Sham_SC_1
Mouse Spinal Cord, Hv1 knockout, Sham, 7 days after SCI, Replicate 1


title: GTGTAAAC_F7

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description:
Library name: nk_d958_t3_r2
Donor 958, DPI=3, Biological replicate 2

library_source: other

data_processing:
For data pre-processing, sequenced reads were demultiplexed and trimmed using Cutadapt v3.4 to acquire ORF library barcodes (settings: -e 0.1 -m 4 –-discard-untrimmed -g atatcttgtggaaaggacga...tgcatcgatcgagtcagctagctgat), which were subsequently aligned using Bowtie v1.3.0 (settings: -v 0 -m 1 --chunkmbs 2000 --best) 83. Next, the random nucleotide UMIs were extracted from the demultiplexed fastq files, described above, using Cutadapt to identify and trim flanking sequences (settings: -e 0.1 -m 4 --discard-untrimmed -g gatcgagtcagctagctgat...ttaagtcgacaatcaacctc). The ORF barcode reads were matched to the UMIs using the individual read IDs, and the unique barcode-UMI pairs were quantified. Finally, the mini-screen data were analyzed using SAMBA, similar to the CRISPRa screen, but UMIs were used instead of sgRNAs for distinct constructs targeting the same gene.
Assembly: GRCh38.p14
Supplementary files format and content: The processed data file has a tab-delimited format, with the first column as the UMI ID, the second column as the ORF ID, and the following columns with UMI counts for all samples.
Library strategy: CRISPR Screen

molecule: other

source_name: Tumor-infiltrating CAR-PBNK

extract_protocol:
Primary human peripheral blood NK cells from two healthy donors were first transduced with HER2-CAR lentivirus and then with the ORF library lentivirus at an MOI of ~0.2. A total of 20 million library-transduced CAR-NK cells were injected into each HT29 tumor-bearing mouse (n = 5 mice for Donor 0957 and n = 3 for Donor 0958 for each time point). Genomic DNA was extracted from tumors at day 3 and 6 post-treatment, as well as from pre-injection cells, and subjected to NGS to quantify ORF and UMI barcode representations.
To generate the ORF library, the top 35 gene targets (cDNA length ≤ 1 kb) were chosen from the CRISPRa screen, along with five fluorescent reporter genes as null controls. The ORF library was synthesized as individual eBlocks (IDT), pooled at equimolar ratios, and amplified with primers containing four-nucleotide random barcodes (UMIs; NNNN) to introduce molecular redundancy targeting the same gene. The ORF expression vector plasmid was bought from Addgene (#145026). The barcoded ORF library was pool-cloned into the expression vector using Gibson assembly.

value: Tumor-infiltrating CAR-PBNK

value: Primary peripheral blood NK cell

value: Natural Killer cell

value: Donor 958


title: ET02-4_S8_L001

description:
In vitro screen Sample ET02-4-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Cell line


title: GTGTAAAC_F6

description:
Library name: nk_d958_t3_r1
Donor 958, DPI=3, Biological replicate 1


title: SFI_Pt16

description:
Library name: Pt16
Pt16


description:
Library name: D7_Hv1KO_Sham_Lg_5
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 5

source_name: Lung

value: Lung


title: GTGTAAAC_F5

description:
Library name: nk_d957_t3_r5
Donor 957, DPI=3, Biological replicate 5

value: Donor 957


title: ET02-3_S7_L004

description:
In vitro screen Sample ET02-3-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Murine ovarian cancer cell line

value: Pmel T cell treated

value: In vitro screen


title: GTGTAAAC_F4

description:
Library name: nk_d957_t3_r4
Donor 957, DPI=3, Biological replicate 4


title: ET02-3_S7_L003

description:
In vitro screen Sample ET02-3-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


description:
Library name: D7_Hv1KO_Sham_Lg_4
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 4


title: SFI_Pt14

description:
Library name: Pt14
Pt14

value: kidney

value: Renal cell carcinoma

value: SFI


title: SFI_Pt19

description:
Library name: Pt19
Pt19


title: GTGTAAAC_F3

description:
Library name: nk_d957_t3_r3
Donor 957, DPI=3, Biological replicate 3


title: RVI_Pt13

description:
Library name: Pt13
Pt13

value: RVI


description:
Library name: D7_Hv1KO_Sham_Lg_2
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 2

value: male

value: 19 to 22 months old

value: Hv1 knockout


title: ET02-3_S7_L001

description:
In vitro screen Sample ET02-3-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


title: GTGTAAAC_F2

description:
Library name: nk_d957_t3_r2
Donor 957, DPI=3, Biological replicate 2

value: Tumor-infiltrating CAR-PBNK


title: RVI_Pt12

description:
Library name: Pt12
Pt12


description:
Library name: D7_Hv1KO_Sham_Lg_1
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 1

value: Sham

value: 7 days after SCI


title: GTGTAAAC_F1

description:
Library name: nk_d957_t3_r1
Donor 957, DPI=3, Biological replicate 1

value: Primary peripheral blood NK cell

value: Natural Killer cell


title: RVI_Pt11

description:
Library name: Pt11
Pt11


description:
Library name: D7_Hv1KO_SCI_Sp_7
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7

source_name: Spleen

value: Spleen

value: Spinal Cord Injury (SCI)


title: ET02-2_S6_L003

description:
In vitro screen Sample ET02-2-lane3
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Cell line

value: Murine ovarian cancer cell line


description:
Library name: D7_Hv1KO_SCI_Sp_6
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6


title: RVI_Pt10

description:
Library name: Pt10
Pt10


title: ACACTTTG_F9

description:
Library name: nk_d958_t0_r3
Donor 958, DPI=0, Biological replicate 3

value: Donor 958


title: ACACTTTG_F8

description:
Library name: nk_d958_t0_r2
Donor 958, DPI=0, Biological replicate 2


title: ET02-2_S6_L002

description:
In vitro screen Sample ET02-2-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Pmel T cell treated

value: In vitro screen


title: RVI_Pt9

description:
Library name: Pt9
Pt9

value: kidney

value: Renal cell carcinoma


title: SFI_Pt15

description:
Library name: Pt15
Pt15

value: SFI


description:
Library name: D7_Hv1KO_Sham_Lg_3
Mouse Lung, Hv1 knockout, Sham, 7 days after SCI, Replicate 3

value: Lung

value: male

value: 19 to 22 months old


title: ET02-2_S6_L001

description:
In vitro screen Sample ET02-2-lane1
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


title: RVI_Pt8

description:
Library name: Pt8
Pt8

value: RVI


title: ACACTTTG_F7

description:
Library name: nk_d958_t0_r1
Donor 958, DPI=0, Biological replicate 1

value: Tumor-infiltrating CAR-PBNK


title: ACACTTTG_F6

description:
Library name: nk_d957_t0_r3
Donor 957, DPI=0, Biological replicate 3

value: Primary peripheral blood NK cell

value: Donor 957


title: Ctrl2-2_S4_L004

description:
In vitro screen Sample Ctrl2-2-lane4
Mouse_v2_CRISPR_191205.count.version2.txt


title: RVI_Pt7

description:
Library name: Pt7
Pt7


description:
Library name: D7_Hv1KO_SCI_Sp_4
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4

value: Spleen

value: Hv1 knockout

value: 7 days after SCI


title: ACACTTTG_F5

description:
Library name: nk_d957_t0_r2
Donor 957, DPI=0, Biological replicate 2

value: Natural Killer cell


description:
Library name: D7_Hv1KO_SCI_Sp_3
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3

value: Spinal Cord Injury (SCI)


description:
Library name: D7_Hv1KO_SCI_Sp_5
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


title: RVI_Pt6

description:
Library name: Pt6
Pt6


title: ACACTTTG_F4

description:
Library name: nk_d957_t0_r1
Donor 957, DPI=0, Biological replicate 1


title: ET02-2_S6_L004

description:
In vitro screen Sample ET02-2-lane4
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt

value: Cell line

value: Murine ovarian cancer cell line

value: Pmel T cell treated


title: Ctrl2-2_S4_L002

description:
In vitro screen Sample Ctrl2-2-lane2
Mouse_v2_CRISPR_191205.count.version2.txt

value: In vitro screen


description:
Library name: D7_Hv1KO_SCI_Sp_2
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


title: Ctrl2-2_S4_L003

description:
In vitro screen Sample Ctrl2-2-lane3
Mouse_v2_CRISPR_191205.count.version2.txt


title: RVI_Pt5

description:
Library name: Pt5
Pt5

value: kidney

value: Renal cell carcinoma


description:
Library name: D7_Hv1KO_SCI_Sp_1
Mouse Spleen, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1

value: male


title: CACAGGGT_F3

description:
Library name: ctrl_plasmid_t0_r3
Library Plasmid control replicate 3

source_name: Plasmid

value: Plasmid


description:
Library name: D7_Hv1KO_SCI_SC_7
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7

value: Spinal Cord

value: 19 to 22 months old


title: CACAGGGT_F2

description:
Library name: ctrl_plasmid_t0_r2
Library Plasmid control replicate 2


title: ET02-3_S7_L002

description:
In vitro screen Sample ET02-3-lane2
Mouse_v2_CRISPR_191205.count.version2.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.sgrna_summary.txt
Mouse_v2_CRISPR_191205_ET02_Ctrl.gene_summary.txt


title: Ctrl2-1_S3_L004

description:
In vitro screen Sample Ctrl2-1-lane4
Mouse_v2_CRISPR_191205.count.version2.txt


title: RVI_Pt4

description:
Library name: Pt4
Pt4

value: RVI


title: Ctrl2-2_S4_L001

description:
In vitro screen Sample Ctrl2-2-lane1
Mouse_v2_CRISPR_191205.count.version2.txt


title: RVI_Pt3

description:
Library name: Pt3
Pt3


description:
Library name: D7_Hv1KO_SCI_SC_6
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6


title: CACAGGGT_F1

description:
Library name: ctrl_plasmid_t0_r1
Library Plasmid control replicate 1


title: Ctrl2-1_S3_L003

description:
In vitro screen Sample Ctrl2-1-lane3
Mouse_v2_CRISPR_191205.count.version2.txt


title: Ctrl2-1_S3_L002

description:
In vitro screen Sample Ctrl2-1-lane2
Mouse_v2_CRISPR_191205.count.version2.txt


title: RVI_Pt1

description:
Library name: Pt1
Pt1


description:
Library name: D7_Hv1KO_SCI_SC_5
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5


description:
Library name: D7_Hv1KO_SCI_SC_4
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


title: cell_2

description: Library name: cell_2

data_processing:
sgRNA counts were quantified from all samples by trimming, aligning, and quantifying sequencing reads. Briefly, raw fastq files were trimmed down to the sgRNA spacer sequence with Cutadapt v3.4, using a 10% error rate and filtering reads < 15nt long. Spacer sequences were aligned using Bowtie v1.3.0 83, using the following settings: -v0, -m1 --best.
Assembly: Genome-scale SAM CRISPRa single-guide RNA library (Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR- Cas9 complex. Nature 517, 583-588 (2015))
Supplementary files format and content: The processed data file has a tab-delimited format with the first column containing the sgRNA IDs, the second column with gene symbols, and the following columns with sgRNA counts for all samples.
Library strategy: CRISPR Screen

source_name: Tumor-infiltrating CAR-NK92

extract_protocol:
Genomic DNA was extracted from tumors and pre-injected cell pellets using the methods from a previous study. Briefly, each sample was put in a 15 mL Falcon tube and 6 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH adjusted to 8.0) along with 30 μL of 20 mg/mL Proteinase K (Qiagen) were added. These samples were then incubated at 55 °C overnight. After tissue digestion, 30 μL of 10 mg/mL RNase A (Qiagen) was added to the lysed sample, which was then inverted 20 times and incubated at 37 °C for 30 min. Digested tissues were cooled on ice before adding 2 mL cold 7.5 M ammonium acetate (Sigma) to precipitate proteins. Samples were vortexed at high speed for 10 s and then centrifuged at 4,000 g at 4 °C for 15 min. After the spin, the supernatant was transferred to a new 15 mL Falcon tube. 6 mL 100% isopropanol was added to each sample, which were then inverted 50 times and centrifuged at 4,000 g at 4 °C for 10 min. Genomic DNA pellets were visible as a small white pallet in each tube. The supernatant was discarded and 6 mL of 70% ethanol was added to wash the pellet. Each sample was inverted 10 times, and then centrifuged at 4,000 g at 4 °C for 5 min. The supernatant was discarded by pouring, and the remaining ethanol was removed using a pipette to completely remove any liquid. The precipitated genomic DNA was air dried for 30-60 min, and then resuspended in 0.5-1 mL nuclease-free water. Samples were then left overnight at room temperature. The next day, the gDNA solution was vortexed briefly and transferred to Eppendorf tubes. The gDNA concentration was measured using a Nanodrop (Thermo Scientific). For pre-injection cells, gDNA samples were extracted using Blood and Tissue kit (Qiagen) with multiple columns and pooled together for each individual sample.
The sgRNA library readout was performed using a two-step PCR strategy, where the first PCR includes enough genomic DNA to preserve full library complexity (5 μg per reaction * 20 reactions = 100 ug gDNA per sample, 100 ug gDNA / 6.6 pg gDNA/cell / 70,290 sgRNAs > 200-fold coverage), and the second PCR adds appropriate sequencing adapters to the products from the first round PCR (2 μL per reaction, 6 reactions per sample). For PCR#1, a region containing sgRNA cassette was amplified using primers specific to the CRISPR library vector: Forward: 5’-gtgcgccaattctgcagacaaatgg-3’ Reverse: 5’-caggatccaaaaaaagcaccgactc-3’ PCR was performed using Phusion Flash High Fidelity Master Mix (ThermoFisher). For PCR#1, the thermocycling parameters were: 98 oC for 2 min, 25 cycles of (98 oC for 1 s, 62 oC for 5 s, 72 oC for 30 s), and 72 oC for 2 minutes. The final PCR products for each biological sample were pooled and used for amplification with barcoded second PCR primers (Supplementary Tables). Second PCR products were pooled and gel purified from a 2% E-gel EX (Life Technologies) using the QiaQuick Gel Extraction kit (Qiagen). The purified library was then quantified with a gel- based method using the Low-Range Quantitative Ladder (Life Technologies) and dsDNA High Sensitivity Qubit (Life Technologies). Libraries were sequenced with PhiX using an Illumina NovaSeq sequencer at the Yale Center for Genomic Analysis (YCGA).

value: Tumor-infiltrating CAR-NK92

value: Pre-injection control


title: Ctrl2-1_S3_L001

description:
In vitro screen Sample Ctrl2-1-lane1
Mouse_v2_CRISPR_191205.count.version2.txt


title: cell_1

description: Library name: cell_1


title: SK04-RK10331_S23

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include RPM (reads per million) values for each Sample

source_name: Ileum

extract_protocol:
RNA was isolated from FFPE tissue sections using the Qiagen AllPrep RNA/DNA FFPE Kit.
Lexogen QuantSeq 3' mRNA-Seq libraries and single-end 100-bp sequencing was performed

value: Ileum

tag: average ileal_microvillus_length_(µm)

tag: cd microvillus_length_quartile


title: Ctrl1-2_S2_L004

description:
In vitro screen Sample Ctrl1-2-lane4
Mouse_v2_CRISPR_191205.count.version2.txt


description:
Library name: D7_Hv1KO_SCI_SC_3
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3

value: Hv1 knockout

value: 7 days after SCI


description:
Library name: D7_Hv1KO_SCI_SC_2
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2

value: Spinal Cord Injury (SCI)


title: SK13-RK10643_S30


title: tumor_12

description: Library name: tumor_12

value: Natural Killer cell

value: Tumor infiltration


title: Ctrl1-2_S2_L003

description:
In vitro screen Sample Ctrl1-2-lane3
Mouse_v2_CRISPR_191205.count.version2.txt

value: Cell line

value: Murine ovarian cancer cell line


title: SK11-RK10505_S7


title: tumor_11

description: Library name: tumor_11


title: Ctrl1-2_S2_L002

description:
In vitro screen Sample Ctrl1-2-lane2
Mouse_v2_CRISPR_191205.count.version2.txt

value: In vitro screen


description:
Library name: D7_Hv1KO_SCI_SC_1
Mouse Spinal Cord, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1


description:
Library name: D7_Hv1KO_SCI_Lg_7
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 7

value: Lung


description:
Library name: D7_Hv1KO_SCI_Lg_6
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 6

value: male


title: SK06-RK10193_S47


title: Ctrl1-2_S2_L001

description:
In vitro screen Sample Ctrl1-2-lane1
Mouse_v2_CRISPR_191205.count.version2.txt


title: tumor_10

description: Library name: tumor_10


title: Ctrl1-1_S1_L004

description:
In vitro screen Sample Ctrl1-1-lane4
Mouse_v2_CRISPR_191205.count.version2.txt


title: SK10-RK10649_S39


title: SFI_Pt2

description:
Library name: Pt2
Pt2

value: kidney

value: Renal cell carcinoma

value: SFI


title: cell_3

description: Library name: cell_3


description:
Library name: D7_Hv1KO_SCI_Lg_5
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 5

value: 19 to 22 months old


title: Ctrl1-1_S1_L003

description:
In vitro screen Sample Ctrl1-1-lane3
Mouse_v2_CRISPR_191205.count.version2.txt


title: tumor_8

description: Library name: tumor_8

value: Tumor-infiltrating CAR-NK92


title: tumor_7

description: Library name: tumor_7


title: SK11-RK10551_S14


title: SK06-RK10175_S44


description:
Library name: D7_Hv1KO_SCI_Lg_4
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 4


title: Ctrl1-1_S1_L002

description:
In vitro screen Sample Ctrl1-1-lane2
Mouse_v2_CRISPR_191205.count.version2.txt


title: Ctrl1-1_S1_L001

description:
In vitro screen Sample Ctrl1-1-lane1
Mouse_v2_CRISPR_191205.count.version2.txt


title: tumor_6

description: Library name: tumor_6


title: SK07-RK10288_S47


description:
Library name: D7_Hv1KO_SCI_Lg_2
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 2


title: tumor_5

description: Library name: tumor_5


title: SD_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description:
Library name: Sample 6
Gene expression after serum deprivation replicate 3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: AGS

growth_protocol: Human gastric caner cell line AGS was grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO₂.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with complete medium or serum deprivation for 10 days.

value: AGS

value: gastric cancer cells

value: AGS cells treated with serum deprivation replicate 3


title: SK05-RK10282_S21

value: Ileum


description:
Library name: D7_Hv1KO_SCI_Lg_3
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 3

value: Hv1 knockout

value: Spinal Cord Injury (SCI)

value: 7 days after SCI


title: SK08-RK10345_S11


title: tumor_4

description: Library name: tumor_4

value: Natural Killer cell

value: Tumor infiltration


title: tumor_9

description: Library name: tumor_9


title: SD_2

description:
Library name: Sample 5
Gene expression after serum deprivation replicate 2

value: AGS cells treated with serum deprivation replicate 2


description:
Library name: D7_Hv1KO_SCI_Lg_1
Mouse Lung, Hv1 knockout, Spinal Cord Injury (SCI), 7 days after SCI, Replicate 1

value: Lung


title: SK12-RK11006_S12


title: tumor_3

description: Library name: tumor_3


title: tumor_2

description: Library name: tumor_2


title: SK10-RK10652_S42


title: RCaP cells, SBFI-1143 treated, 24 hours, rep3

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

state: New York

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

description: Library name: RCaP_SBFI-1143_24h_3

data_processing:
RNA-seq
Data was analyzed using usegalaxy platform and R
Sample quality was checked using FASTQC and Trimmomatic
The paired-ended sequences were aligned to mm10 using HISAT2
To quantify the number of reads per gene, featureCounts was used
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: prostate cancer cell line

growth_protocol: Mouse RCaP cells were maintained in RPMI640 medium supplemented with 10% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
RNA was isolated using Qiagen Rneasy Mini Kit
RNA library and sequencing was performed by Novogene. mRNA library preparation (poly A enrichment) and sequencing was performed using NovaSeq X Plus (PE150).

treatment_protocol: RCaP  cells were trypsinized, counted, and seeded (6x105 cells/well) in a 100mm plate format in RPMI640 medium supplemented with 2% fetal bovine serum (FBS) and 1% Pencillin/Streptomycin in a humidified atmosphere at 37°C and 5% CO2. After 24 hours of incubation, media was aspirated and replaced with treatment-supplemented media (0.2% DMSO or 15uM SBFI-103). Cells were then treated for 24 hours total, followed by total RNA extraction and quantification

value: prostate cancer cell line

value: RCaP

tag: batch


title: RCaP cells, SBFI-1143 treated, 24 hours, rep4

description: Library name: RCaP_SBFI-1143_24h_4


title: CM_3

description:
Library name: Sample 3
Gene expression after complete medium treatment replicate 3

value: AGS cells treated with complete medium replicate 3


title: RCaP cells, SBFI-1143 treated, 24 hours, rep2

description: Library name: RCaP_SBFI-1143_24h_2


title: SK10-RK10610_S11


title: tumor_1

description: Library name: tumor_1


title: RCC, sample 8

city: New York

first: Fengshen

last: Kuo

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: MSK_8

data_processing:
RNA-seq sequencing reads were aligned against human genome assembly hg19 by STAR 2-pass alignment. Gene level read count values were computed by using the R GenomicAlignments package over aligned reads using UCSC KnownGene in hg19 as the base gene model. The Union Counting mode was used and only mapped paired reads passing alignment quality filtering were considered. Finally, gene (Entrez gene) level FPKM and raw read count values were computed by the R DESeq2 package.
Supplementary files format and content: Comma-separated files including raw count file: MaskID.hg19KnownGene.raw.csv
Supplementary files format and content: Comma-separated files including FPKM count file: MaskID.hg19KnownGene.fpkm.csv

source_name: KRAS mutant URCC

extract_protocol:
20-30mg frozen tissue were homogenized in 1 mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Mini Kit (Qiagen catalog # 217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 25-38 µL RNase-free water
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 8.1-9.2 underwent polyA selection and library preparation using the TruSeq Stranded mRNA LT Kit (Illumina catalog # RS-122-2102) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina).  An average of 72 million paired reads was generated per sample. Ribosomal reads represented 0.04-0.09% of the total reads generated and the percent of mRNA bases averaged 85%

value: Frozen primary tumor tissue

tag: histopathology

value: High grade uRCC

tag: tumor grade


title: RCaP cells, SBFI-1143 treated, 24 hours, rep1

description: Library name: RCaP_SBFI-1143_24h_1

tag: tissue


title: RK10010


title: CM_1

description:
Library name: Sample 1
Gene expression after complete medium treatment replicate 1

tag: cell line

value: AGS cells treated with complete medium replicate 1


title: RCaP cells, SBFI-103 treated, 24 hours, rep4

description: Library name: RCaP_SBFI-103_24h_4

tag: cell type


title: RCC, sample 1

description: Library name: MSK_1

source_name: PRNRP

value: PRNRP


title: RCaP cells, SBFI-103 treated, 24 hours, rep3

description: Library name: RCaP_SBFI-103_24h_3

tag: treatment


title: SK07-RK10208_S9


title: RCaP cells, SBFI-103 treated, 24 hours, rep2

description: Library name: RCaP_SBFI-103_24h_2


title: RK10013


title: SK10-RK10614_S14


title: RCC, sample 4

description: Library name: MSK_4

source_name: KRAS mutant PRCC

value: Papillary RCC


title: Autophagic flux down cells, rep2

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

institute: Seoul National University

description: Library name: CTL_DOWN_2

data_processing:
Paired-end FASTQ files were first merged using NGmerge (v0.2) to remove sequencing adapters and low-quality regions
sgRNA read counts were quantified using MAGeCK count (v0.5.9.5) with the library reference.
Differential sgRNA abundance analysis was performed using MAGeCK test (v0.5.9.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files, read counts from MAGeCK
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted from collected cells
Library was constructed by Cellecta NGS prep kit (#LNGS-120) and following manufacturer’s protocols.

value: epithelial cell


title: SK06-RK10314_S2

value: Ileum


title: Autophagic flux up cells, rep1

description: Library name: CTL_UP_1


title: Cortex, KO, D43, rep1

city: New Haven

first: Michael

last: Scandura

address: 464 Congress Ave

description: Library name: H9_KO

library_source: transcriptomic single cell

data_processing:
To obtain count matrices, scRNA-seq reads were aligned to hg38 human genome and counted with Ensembl genes by count function of CellRanger (v 6.1.2) with default parameters, generating gene-barcode count matrices. Subsequently, the Read10X function of Seurat (v 4.3.0)64 was used to import the count matrices for each group (control and knockout). Quality control was performed to remove low-quality cells. For instance, cells with fewer than 500 or more than 40,000 detected genes were excluded in control sample, while those with fewer than 200 or more than 10,000 genes were excluded in the knockout sample. Additionally, cells with an excessively high percentage of mitochondrial gene expression (above 10%) were excluded.
Following cell filtering, normalization was performed with the NormalizeData function in Seurat, using a scaling factor of 10,000 and log-transformation based on total cell expression. Next, highly variable genes (3,000 in this example) were identified using the FindVariableFeatures function with the VST method. To account for batch effects across samples, Seurat’s anchor-based integration workflow was employed, including SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData. The integrated dataset was then scaled using ScaleData, and principal component analysis (RunPCA) was conducted with 30 principal components. Clustering was performed with FindNeighbors and FindClusters (resolution = 0.7), followed by dimensionality reduction via RunUMAP using the same principal components. As a result of this process, a total of 18 clusters were identified and subsequently annotated according to general organoid markers.
For trajectory analysis, the Monocle3 (v1.3.7) package was used.65 First, the expression matrix was extracted from the Seurat object and converted into a sparseMatrix format. The cell metadata and gene annotation were retrieved from the Seurat object, and a cell_data_set (CDS) was created using the new_cell_data_set function. Cells were then clustered, and a trajectory graph was learned using learn_graph. Pseudotime ordering was performed using order_cells with the UMAP reduction method.
Cell-cell communication analysis was conducted using CellChat (v1.5.0).66 The integrated and annotated Seurat object was imported into CellChat to create a CellChat object. Communication probability was inferred by computing interactions based on curated ligand-receptor databases provided by CellChat. Network aggregation, visualization, and signaling pathway analyses were performed to identify significantly enriched ligand-receptor interactions and pathways across different cell groups, providing insights into intercellular communication within the dataset.
Assembly: hg38
Supplementary files format and content: Processed data files include the filtered gene-barcode expression matrix generated by Cell Ranger (10x Genomics), provided in HDF5 format (filtered_feature_bc_matrix.h5). This file contains gene expression counts for each cell barcode. Quality control metrics and visualization files are available but not included in this submission.

source_name: Cortex

extract_protocol:
Cortical organoids were dissociated using the papain dissociation system per the manufacturer’s instructions. In order to increase cell viability, solutions were oxygenated with 95% O2:5% CO2. In brief, HBSS was used to wash the organoids, then they were dissected into small pieces in the oxygenated papain solution. This solution was then re-equilibrated with 95% O2:5% CO2 and placed in a 37 water bath for an hour. The solution was lightly shaken every 20 minutes during the hour incubation period. After the incubation period was over, light trituration was performed to produce a single cell suspension and albumin-ovomucoid inhibitor solution was used to inactivate the papain. hCOs were then subjected to the 10X Genomics Chromium platform.
To analyze the transcriptomic profile changes induced by KIAA0319 knockout, scRNA-seq was performed using the D43 hCOs samples with or without knockout of KIAA0319 gene (n = 5 WT and n = 5 KIAA0319 -/- hCOs from one batch). Single-cell suspensions were generated and processed using the 10x Genomics Chromium Single Cell 3' Reagent Kit (v3.1) according to the manufacturer's instructions. Libraries were constructed using 10x Genomics Chromium technology targeting the 3′ end of transcripts.

value: Cortex

value: Neural

value: KO


title: Cortex, WT, D43, rep1

description: Library name: H9_WT

value: WT


title: RCC, sample 3

description: Library name: MSK_3


title: SD_1

description:
Library name: Sample 4
Gene expression after serum deprivation replicate 1

value: AGS

value: gastric cancer cells

value: AGS cells treated with serum deprivation replicate 1


title: Autophagic flux up cells, rep2

description: Library name: CTL_UP_2


title: SK06-RK10153_S41


title: CM_2

description:
Library name: Sample 2
Gene expression after complete medium treatment replicate 2

value: AGS cells treated with complete medium replicate 2


title: Basal.5E

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: Basal.5E

data_processing:
Raw sequencing reads were mapped to the GRCh38.p10 genome using STAR v2.7.6a and duplicate reads marked by Picard v2.23.8 and removed from downstream analysis
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: GRCh38.p10
Supplementary files format and content: txt file of RPKM normalized read counts for each detected gene

source_name: Bronchial airways

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: Bronchial airways

value: Basal epithelial cells

tag: sorting markers

value: SiR Tubulin- NGFR+ ITGA6+

value: H1N1 Infection + post IFN-gamma


title: SK06-RK10169_S32


title: RCaP cells, control, 24 hours, rep2

description: Library name: RCaP_DMSO_2

value: prostate cancer cell line

value: RCaP

value: DMSO, 24h


title: TNBC5

first: Minkyu

last: Shim

address: 103, Daehak-ro, Jongno-gu

description: Library name: TNBC5

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: hg38, mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
After surgery, TNBC samples were chopped into submilimeter particles manually and incubated for 30 minutes in a 37℃ 5% CO2 incubator with RPMI-160, supplemented with 1mg/mL hyaluronidase, 1mg/mL collagenase type IV, and 0.5mg/mL DNase I. After tissue digestion, cells were filtered with 70um cell strainers. Erythrocytes were lysed with 3ml ACK lysis buffer on ice for 5 min. The reaction was stopped by adding 10ml 1X PBS. After centrifugation, cells were resuspended with 1ml RPMI-1640 supplemented with 10% FBS. CD11b+ cells were isolated with BD Aria III sorter, and then were immediately sent for scRNA-seq.
Library was performed according to the manufacturer's instructions.

value: tumor

value: TNBC

value: s/p Lt. BCS with SLNB (180 MA), adjuvant chemotherapy and radiation therapy refused s/p neoadjuvant chemotherapy for 6 cycles


title: RCaP cells, control, 24 hours, rep3

description: Library name: RCaP_DMSO_3


title: Secretory.5E

description: Library name: Secretory.5E

value: Secretory epithelial cells

value: SiR Tubulin- NGFR- CD66c+


title: TNBC3

description: Library name: TNBC3

value: s/p Rt. BCS with SLNB (130 MA) s/p adriamycin + cyclophosphamide #4 + cardioxane #6, radiation therapy


title: TNBC4

description: Library name: TNBC4

value: naïve


title: Autophagic flux down cells, rep1

description: Library name: CTL_DOWN_1

value: epithelial cell


title: RCaP cells, control, 24 hours, rep1

description: Library name: RCaP_DMSO_1


title: RCaP cells, SBFI-103 treated, 24 hours, rep1

description: Library name: RCaP_SBFI-103_24h_1


title: TNBC2

description: Library name: TNBC2

value: s/p neoadjuvant chemotherapy for 2 cycles due to progressive disease


title: skeletalmuscle-hiit6

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: UPL25-005097
Column name in miR.Counts1.csv: UPL25-005097_1.trim

data_processing:
FASTQ quality was assessed with FastQC/MultiQC. 3′ adapter trimming (Illumina TGGAATTCTCGGGTGCCAAGG) and length filtering (retain inserts 16–30 nt) were performed within miRge3.0.
Reads were collapsed to unique sequences, then aligned with Bowtie (as implemented in miRge3.0) to mouse miRNA references (miRBase v22.1). Multi-mapping handling followed miRge3.0 defaults.
Assembly: Mus musculus reference: GRCm39 , miRNA annotation: miRBase v22.1 (mouse).
Supplementary files format and content: Matrix of mature miRNA raw counts (CSV): first column = miRNA ID (miRBase v22.1), subsequent columns = sample.

source_name: gastrocnemius muscle

extract_protocol:
~20–30 mg gastrocnemius was homogenized in lysis buffer; total RNA was isolated using Quick-RNA™ Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. RNA quantity and purity were assessed by NanoDrop; integrity was inspected on Agilent TapeStation.
100 ng total RNA per sample was used to prepare small-RNA libraries with NEXTFLEX® Small RNA-Seq Kit v4 (PerkinElmer). 3′/5′ adapters were ligated, cDNA synthesized, bead-cleaned, and PCR-barcoded (17 cycles). Libraries were QC’d on TapeStation, pooled, and sequenced on Illumina NovaSeq X Plus (single-end 75 bp).

treatment_protocol: Mice were randomized into five groups for 6 weeks: Control (PBS i.p.), Lactate (sodium L-lactate 500 mg/kg i.p), HIIT (treadmill intervals with individualized intensity), MCT1/2 inhibitor (AR-C155858 i.p. before sessions), and HIIT + inhibitor. Gastrocnemius muscle was harvested 48 h after the final session.

value: gastrocnemius muscle

value: male

value: BALB/c

value: wild type

value: HIIT


title: SK05-RK10301_S10

value: Ileum


title: RCaP cells, control, 24 hours, rep4

description: Library name: RCaP_DMSO_4

value: prostate cancer cell line

value: RCaP


title: skeletalmuscle-hiit5

description:
Library name: UPL25-005096
Column name in miR.Counts1.csv: UPL25-005096_1.trim


title: Basal.5D

description: Library name: Basal.5D

value: Bronchial airways

value: Basal epithelial cells

value: SiR Tubulin- NGFR+ ITGA6+

value: H1N1 Infection + post IFN-gamma


title: TNBC1

description: Library name: TNBC1

value: tumor

value: TNBC


title: Secretory.5D

description: Library name: Secretory.5D

value: Secretory epithelial cells

value: SiR Tubulin- NGFR- CD66c+


title: SK04-RK10239_S31


title: RK10007


title: RKO cells, OverCX43, rep3

city: Hangzhou

first: Shuo

last: Wang

address: Zijingang Campus

institute: Zhejiang University

data_processing:
Gene differential expression analysis was accomplished by Cuffdiff program in Cufflink’s package.
Benjamini–Hochberg false discovery rate method was applied to correct for multiple hypothesis testing.
The chosen genes were defined as different expression genes as candidates for further analysis, with which P < 0.05, fold change > 1.5 or fold change < 0.67 and any value > 1.
Assembly: hg38
Supplementary files format and content: The files format are tabular. The content are the Expression of gene level and Expression of isoform level.

source_name: RKO

growth_protocol: RKO cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
polyA RNA was isolated by sequencing company.
The cDNA libraries were prepared from high quality RNA using an Illumina TruSeq RNA sample prep kit.

value: RKO

value: colorectal cancer cells

value: Cx43 overexpression


title: skeletalmuscle-hiit4

description:
Library name: UPL25-005095
Column name in miR.Counts1.csv: UPL25-005095_1.trim

value: gastrocnemius muscle

value: male

value: BALB/c


title: Ciliated.5D

description: Library name: Ciliated.5D

value: Ciliated epithelial cells

value: SiR Tubulin+ NGFR-


title: SK08-RK10289_S14

value: Ileum


title: RKO cells, OverCX43, rep2


title: skeletalmuscle-hiit3

description:
Library name: UPL25-005094
Column name in miR.Counts1.csv: UPL25-005094_1.trim

value: wild type

value: HIIT


title: Basal.5C

description: Library name: Basal.5C

value: Bronchial airways

value: Basal epithelial cells

value: SiR Tubulin- NGFR+ ITGA6+


title: SK11-RK10927_S15


title: RKO cells, EV, rep3

value: WT


title: Secretory.5C

description: Library name: Secretory.5C

value: Secretory epithelial cells

value: H1N1 Infection + post IFN-gamma


title: RKO cells, OverCX43, rep1

value: RKO


title: SK10-RK10651_S41


title: skeletalmuscle-hiit1

description:
Library name: UPL25-005092
Column name in miR.Counts1.csv: UPL25-005092_1.trim


title: SK05-RK10343_S7


title: Ciliated.5E

description: Library name: Ciliated.5E


title: RKO cells, EV, rep2

value: colorectal cancer cells


title: SK09-RK10148_S36


title: Basal.5B

description: Library name: Basal.5B


title: RKO cells, EV, rep1


title: skeletalmuscle-lactate6

description:
Library name: UPL25-005091
Column name in miR.Counts1.csv: UPL25-005091_1.trim

value: Lactate administration


title: SK09-RK10590_S56


title: skeletalmuscle-lactate5

description:
Library name: UPL25-005090
Column name in miR.Counts1.csv: UPL25-005090_1.trim

value: gastrocnemius muscle


title: SS3

city: guangzhou

first: haoxian

last: zhou

address: zhongshan 2nd Road

institute: guangdong people hosptial

data_processing:
For Ribo-seq data, cutadapt (v2.0.dev0) was used to trim the relevant adapter sequence and remove the low-quality reads as well as filter reads the outside of 24-35 nt range. Reads aligning to rRNA were removed using bowtie (v1.1.2) with default parameters. The remaining reads were then mapped to the human genome(hg38) using STAR (v2.4.2a) with default options except for the following: --outFilterMismatchNmax 2, --outFilterMultimapNmax 5, --outFilterMatchNmin 16, --alignEndsType EndToEnd. ORFs identification and quantification was performed according to the RiboCode (version 1.2.10) manual with the following parameters: -l no -m 10 -A CTG,GTG,TTG -g -b. The translation efficiency (TE) of ORFs were then calculated by Ribodiff (v0.2.2) analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include expected values for each sample
Library strategy: Ribo-seq

source_name: cell

extract_protocol:
For ribo-seq: The cells were subjected to a treatment with 100 µg/mL cycloheximide for 2 minutes prior to collection. A total of 10 million cells were then washed twice with ice-cold PBS containing 100 µg/ml cycloheximide and promptly frozen in liquid nitrogen. Subsequently, the frozen cells were lysed in 400 µL ice-cold mammalian polysome buffer (composed of 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 0.1% NP-40, 500 U/mL RNase Inhibitor, 1× EDTA-free Complete protease inhibitors, 1 U/µl DNase I, and 100 µg/ml cycloheximide) for 10 minutes on ice. Following lysation, the cell lysate underwent ten passes through a 26-gauge needle and was subsequently clarified by centrifugation at 20,000g for 5 minutes. Approximately 120 µl of the resulting supernatant was treated with 3 µl of RNase I (Life Technologies, AM2294) for 45 minutes at room temperature. The reaction was halted by the addition of SUPERase•In RNase Inhibitor (Life Technologies, AM2694). To purify monosomes, the samples were processed using MicroSpin S-400 HR columns (GE Healthcare, 27-5140-01), and RNA was isolated from the flow-through (approximately 125 µl) using 1 mL RNAzol reagent. To enrich ribosome footprints (RFPs), the RNA samples underwent processing with biotin-labeled probes to eliminate ribosomal RNA fragments. The purified samples were then separated on a 17% 7.5M Urea-PAGE gel. Gel sections ranging in size from 26 nt to 30 nt, as defined by loading with 14-30 ssRNA Ladder Marker (Takara, #3416), were excised for further analysis.
For Ribo-seq, the purified ribosome footprints (RFPs) underwent end-repair and were subsequently processed using an in-house small RNA sequencing protocol, resulting in the conversion of these fragments into libraries. In brief, the RNA fragments were ligated to a pre-adenylated 3' RNA adaptor, followed by ligation to a 5' RNA adaptor. Following reverse transcription, the cDNA was amplified and sequenced using the Illumina Xten platform. For RNA-seq, three micrograms of total RNA were utilized for polyadenylated RNA enrichment with VAHTS mRNA Capture Beads (Vayzme) following the manufacturer’s protocol. The NEBNext Ultra II Directional RNA Library Prep Kit standard protocol (NEB) was employed for library preparation. Subsequently, the libraries were subjected to sequencing on an Illumina HiSeq X Ten platform, generating 150-bp paired-end reads.

value: cell

value: BJ fibroblast

tag: condition

value: senescence


title: skeletalmuscle-lactate4

description:
Library name: UPL25-005089
Column name in miR.Counts1.csv: UPL25-005089_1.trim

value: male

tag: strain

value: BALB/c


title: Secretory.5B

description: Library name: Secretory.5B

value: SiR Tubulin- NGFR- CD66c+


title: Ciliated.5B

description: Library name: Ciliated.5B

value: Ciliated epithelial cells

value: SiR Tubulin+ NGFR-


title: SK04-RK10346_S35

value: Ileum


title: SS2


title: RK10041


title: skeletalmuscle-lactate3

description:
Library name: UPL25-005088
Column name in miR.Counts1.csv: UPL25-005088_1.trim

tag: Sex

value: wild type


title: SS1


title: Ciliated.5C

description: Library name: Ciliated.5C

value: Bronchial airways


title: skeletalmuscle-hiit2

description:
Library name: UPL25-005093
Column name in miR.Counts1.csv: UPL25-005093_1.trim

value: HIIT


title: Secretory.5A

description: Library name: Secretory.5A

value: Secretory epithelial cells

value: H1N1 Infection + post IFN-gamma


title: SK10-RK10653_S43


title: Basal.5A

description: Library name: Basal.5A

value: Basal epithelial cells

value: SiR Tubulin- NGFR+ ITGA6+


title: RK10014


title: SY3

value: young


title: skeletalmuscle-lactate1

description:
Library name: UPL25-005086
Column name in miR.Counts1.csv: UPL25-005086_1.trim

value: gastrocnemius muscle

value: Lactate administration


title: SY2

value: cell

value: BJ fibroblast


title: skeletalmuscle-hiitmct6

description:
Library name: UPL25-005085
Column name in miR.Counts1.csv: UPL25-005085_1.trim

value: male

value: BALB/c

value: HIIT+MCT1/2 inhibitor


title: Ciliated.5A

description: Library name: Ciliated.5A

value: Ciliated epithelial cells

value: SiR Tubulin+ NGFR-


title: Basal.2E.1

description: Library name: Basal.2E.1

value: H1N1 Infection only


title: SK10-RK10625_S24

value: Ileum


title: SK11-RK10545_S11


title: skeletalmuscle-hiitmct5

description:
Library name: UPL25-005084
Column name in miR.Counts1.csv: UPL25-005084_1.trim

value: wild type


title: SY1


title: RNA_CDS+dox_EC_rep2

city: Beijing

first: Yonglin

last: Zhu

state: Beijing

address: D115, School of Medicine

institute: Tsinghua University

data_processing:
Raw reads was first quality controlled (FastQC, version 0.11.7) and trimmed (Trim_Galore, version 0.4.4). The trimmed reads were mapped to the hg38 genome (UCSC) with bowtie2 (version 2.3.5).
For ATAC-seq and ChIP-seq data, Mapped reads were sorted by Samtools, PCR duplicates and reads from mitochondria were removed (Picard tools MarkDuplicates). Then filtered bam files were transferred to bigwig file using the bamCoverage tool from deepTools2. Peaks were called using MACS2 (version 2.2.6).
For RNA-seq data, gene expression (count and FPKM) was calculated using rsem-calculate-expression (RSEM, version 1.2.28)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM  values for all samples (RNA-seq)
Supplementary_files_format_and_content: bigwig files for ATAC-seq and ChIP-seq data

source_name: cultured cells

growth_protocol: Undifferentiated hESCs was cultured in E8 medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase-free DNase.
For RNA-seq, 100ng total RNA was subjected to library preparation following the Smart-seq2 protocol. ATAC-seq libraries were prepared follwing the Omini-ATAC-seq protocol. ChIP-seq libraries were prepared following the Cut&Tag protocol.

treatment_protocol: For EC differentiation, hESCs were first cultured in E8 medium for 1 day, then changed to AATS medium supplemented with 5ng/mL BMP4 and 2μM CHIR99021 for 3 days to induce mesoderm differentiation. After 3 days of induction, cells were replated and cultured in  AATS medium supplemented with 25ng/mL VEGFA165 and 10ng/mL FGF2 for another 5 days.

value: Embryonic stem cells

tag: passage number

value: human embryonic stem cell line H1


title: SK06-RK10196_S50


title: Secretory.2E

description: Library name: Secretory.2E

value: Bronchial airways

value: Secretory epithelial cells

value: SiR Tubulin- NGFR- CD66c+


title: skeletalmuscle-hiitmct4

description:
Library name: UPL25-005083
Column name in miR.Counts1.csv: UPL25-005083_1.trim

value: gastrocnemius muscle

tag: genotype


title: Ciliated.2E

description: Library name: Ciliated.2E


title: skeletalmuscle-lactate2

description:
Library name: UPL25-005087
Column name in miR.Counts1.csv: UPL25-005087_1.trim

value: Lactate administration


title: SK05-RK10347_S22


title: Basal.2E

description: Library name: Basal.2E

value: Basal epithelial cells

value: SiR Tubulin- NGFR+ ITGA6+


title: RNA_CDS+dox_EC_rep1


title: RNA_CDS-dox_EC_rep2


title: skeletalmuscle-hiitmct2

description:
Library name: UPL25-005081
Column name in miR.Counts1.csv: UPL25-005081_1.trim

value: male


title: SK05-RK10296_S43


title: skeletalmuscle-hiitmct3

description:
Library name: UPL25-005082
Column name in miR.Counts1.csv: UPL25-005082_1.trim

value: BALB/c


title: Secretory.2D

description: Library name: Secretory.2D


title: skeletalmuscle-hiitmct1

description:
Library name: UPL25-005080
Column name in miR.Counts1.csv: UPL25-005080_1.trim

value: HIIT+MCT1/2 inhibitor


title: SK05-RK10334_S26


title: Ciliated.2D

description: Library name: Ciliated.2D

value: Ciliated epithelial cells


title: RNA_BCL6B_KO-2_EC_rep2

value: human embryonic stem cell line HUES8


title: skeletalmuscle-control5

description:
Library name: UPL25-005079
Column name in miR.Counts1.csv: UPL25-005079_1.trim

value: PBS injection


title: Basal.2C

description: Library name: Basal.2C

value: H1N1 Infection only


title: skeletalmuscle-control4

description:
Library name: UPL25-005078
Column name in miR.Counts1.csv: UPL25-005078_1.trim

value: wild type


title: SK13-RK10603_S44

value: Ileum


title: Secretory.2C

description: Library name: Secretory.2C


title: SK05-RK10321_S37


title: RNA_CDS-dox_EC_rep1

value: Embryonic stem cells

value: human embryonic stem cell line H1


title: Ciliated.2C

description: Library name: Ciliated.2C

value: Bronchial airways

value: SiR Tubulin+ NGFR-


title: RNA_BCL6B_KO-1_EC_rep1


title: skeletalmuscle-control2

description:
Library name: UPL25-005076
Column name in miR.Counts1.csv: UPL25-005076_1.trim

value: gastrocnemius muscle


title: RNA_BCL6B_KO-1_EC_rep2


title: SK09-RK10583_S52


title: skeletalmuscle-control1

description:
Library name: UPL25-005075
Column name in miR.Counts1.csv: UPL25-005075_1.trim


title: RNA_iCas9_WT_EC_rep1


title: SK05-RK10310_S3


title: SK07-RK10354_S49


title: H3K27ac_EC_rep2


title: RNA_iCas9_WT_EC_rep2


title: SK10-RK10616_S16


title: skeletalmuscle-mct6

description:
Library name: UPL25-005074
Column name in miR.Counts1.csv: UPL25-005074_1.trim

value: MCT1/2 inhibitor


title: Secretory.2B

description: Library name: Secretory.2B

value: Secretory epithelial cells

value: SiR Tubulin- NGFR- CD66c+


title: SK06-RK10174_S43


title: skeletalmuscle-mct4

description:
Library name: UPL25-005072
Column name in miR.Counts1.csv: UPL25-005072_1.trim

value: male


title: Ciliated.2B

description: Library name: Ciliated.2B


title: skeletalmuscle-mct5

description:
Library name: UPL25-005073
Column name in miR.Counts1.csv: UPL25-005073_1.trim

value: BALB/c


title: RNA_BCL6B_KO-2_EC_rep1


title: SK08-RK10238_S16


title: H3K27ac_EC_rep1


title: skeletalmuscle-control3

description:
Library name: UPL25-005077
Column name in miR.Counts1.csv: UPL25-005077_1.trim


title: Secretory.2A

description: Library name: Secretory.2A


title: Ciliated.2A

description: Library name: Ciliated.2A


title: H3K27me3_EC_rep2


title: SK06-RK10225_S10


title: RK10021


title: skeletalmuscle-mct3

description:
Library name: UPL25-005071
Column name in miR.Counts1.csv: UPL25-005071_1.trim


title: Basal.2B

description: Library name: Basal.2B

value: Basal epithelial cells

value: SiR Tubulin- NGFR+ ITGA6+


title: skeletalmuscle-mct2

description:
Library name: UPL25-005070
Column name in miR.Counts1.csv: UPL25-005070_1.trim


title: Basal.1E

description: Library name: Basal.1E

value: Uninfected


title: H3K4me3_EC_rep2


title: skeletalmuscle-mct1

description:
Library name: UPL25-005069
Column name in miR.Counts1.csv: UPL25-005069_1.trim


title: SK05-RK10283_S13


title: H3K27me3_EC_rep1


title: H3K4me3_EC_rep1


title: Secretory.1E

description: Library name: Secretory.1E


title: Ciliated.1E

description: Library name: Ciliated.1E

value: Ciliated epithelial cells


title: SK12-RK11017_S22


title: Basal.2A

description: Library name: Basal.2A

value: H1N1 Infection only


title: SK07-RK10207_S8


title: H3K27ac_EPC_rep2


title: the quadriceps of D-gal+MSCs mice 4

city: Jinan

first: Jia

last: Song

state: Select...

address: No.107 Wenhua Xi Road, Jinan,Shandong Province

institute: Qilu Hospital of Shandong University

description: Library name: MSC4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time,Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence.Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: xlsx. file including raw counts for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated  using TRIzol reagent (Invitrogen). 2ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following manufacturer's protocols.

value: skeletal muscle


title: Basal.1D

description: Library name: Basal.1D


title: H3K27ac_EPC_rep1


title: the quadriceps of D-gal+MSCs mice 2

description: Library name: MSC2


title: Secretory.1D

description: Library name: Secretory.1D


title: SK04-RK10304_S38

value: Ileum


title: the quadriceps of D-gal+MSCs mice 1

description: Library name: MSC1


title: H3K27me3_EPC_rep1

value: Embryonic stem cells


title: Ciliated.1D

description: Library name: Ciliated.1D


title: SK05-RK10307_S2


title: SK05-RK10332_S27


title: Basal.1C

description: Library name: Basal.1C


title: H3K4me3_EPC_rep2

value: human embryonic stem cell line H1


title: SK09-RK10145_S35


title: Secretory.1C

description: Library name: Secretory.1C

value: Bronchial airways


title: the quadriceps of D-gal+PBS mice 2

description: Library name: PBS2


title: the quadriceps of D-gal+MSCs mice 3

description: Library name: MSC3


title: SK06-RK10285_S3


title: the quadriceps of D-gal+PBS mice 1

description: Library name: PBS1


title: H3K27ac_VMC_rep2


title: SK10-RK10626_S25


title: Basal.1B

description: Library name: Basal.1B


title: Pf strain NF54 infected PHH, 5C treated, sequencing replicate 1

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

data_processing:
The sequencing endline fastq files were quality checked using FASTQC (ver. 0.11.9). The reads were subsequently trimmed for quality (-q 30) and adapter removal using the Trim_Galore software (ver. 0.6.7). The trimmed reads were aligned onto the Homo sapiens ver. 38 genome using STAR aligner (ver. 2.7.10a). The reads mapped onto the respective genomes were counted using the –quantMode GeneCounts option in STAR.
Reads mapping only to sense strand were corrected for batch effects stemming from different hepatocyte donors using the Combat-seq tool (sva package ver. 3.44.0). The batch corrected counts were used for subsequent differential expression analysis (for conditions/treatments) in DESEq2 package (ver. 1.36.0) in RStudio (ver. 4.2.2 “Innocent and Trusting”).
PCA plot for the various sequenced libraries/samples was generated using plotPCA command. Volcano plots for differentially expressed genes and genes of interest were generated using custom scripts and ggplot2 (ver. 3.4.2) in R.
Gene Ontology enrichment analysis was performed in using the clusterProfiler tool (ver. 4.4.4) with subsequent dot-plots generated using inbuilt functions in ggplot2. Heatmaps for differentially expressed genes were generated using the Morpheus online tool by Broad Institute.
Assembly: Plasmodium falciparum 3D7 genome version 59; Homo sapiens genome version GRCh38
Supplementary files format and content: tab-delimited txt files containing batch corrected Combat-seq counts for genes
Supplementary files format and content: tab-delimited txt files containing normalized counts for genes from DESeq2

organism:
Plasmodium falciparum
Homo sapiens

source_name: Plasmodium falciparum NF54 infected primary human hepatocytes

extract_protocol:
Freshly isolated or in vitro cultured hepatocytes (mock or treatment) were homogenized in TRIzol solution and cryopreserved at -80°C. RNA was subsequently isolated using the Zymo research Direct zol RNA purification kit (Cat. No. #R2053)
RNA sequencing libraries from isolated/purified RNA were prepared using the Kapa mRNA Hyperprep Kit (Cat. No. #KK8581) using slight modifications of the manufacturer’s instructions for mRNA enrichment method. The input total RNA for the various libraries was selected between 150ng, 250ng or 500ng. The enriched mRNA was fragmented at 94°C  for 6min and dA tailing performed at 55°C for 15min. In order to better capture the AT rich Pf transcriptome we modified the PCR protocol as follows: Initial denaturation at 98°C for 2min; Cycling denaturation at 98°C for 20sec, annealing + extension at 62°C for 2min; final extension at 62°C for 3min. We selected PCR cycles for library amplification (12, 11 and 10 respectively) based on starting input total RNA amount.


title: Secretory.1B

description: Library name: Secretory.1B


title: the quadriceps of D-gal+PBS mice 4

description: Library name: PBS4


title: Pf strain NF54 infected PHH, iwp2 treated, sequencing replicate 1

value: Plasmodium falciparum NF54 infected primary human hepatocytes


title: H3K27me3_VMC_rep2


title: H3K27ac_VMC_rep1


title: Ciliated.1B

description: Library name: Ciliated.1B

value: SiR Tubulin+ NGFR-


title: RK10011


title: H3K27me3_VMC_rep1


title: SK07-RK10201_S5


title: Basal.1A

description: Library name: Basal.1A


title: SK05-RK10299_S14


title: Pf strain NF135 infected PHH, 5C treated, sequencing replicate 2

source_name: Plasmodium falciparum NF135 infected primary human hepatocytes


title: the quadriceps of D-gal+PBS mice 3

description: Library name: PBS3


title: H3K4me3_VMC_rep2


title: Pf strain NF54 infected PHH, mock treated, sequencing replicate 1

value: Mock


title: SK06-RK10241_S6


title: H3K4me3_EPC_rep1


title: Secretory.1A

description: Library name: Secretory.1A

value: Secretory epithelial cells


title: H3K4me3_VMC_rep1


title: H3K27me3_EPC_rep2


title: Ciliated.1C

description: Library name: Ciliated.1C


title: Pf strain NF135 infected PHH, iwp2 treated, sequencing replicate 2

value: Plasmodium falciparum NF135 infected primary human hepatocytes


title: SK09-RK10230_S34


title: Ciliated.1A

description: Library name: Ciliated.1A


title: H3K27ac_hESC_rep2


title: Pf strain NF135 infected PHH, mock treated, sequencing replicate 2


title: SK11-RK10953_S36


title: LL045.Flu.Flu.AIM

description: Library name: LL045.Flu.Flu.AIM

data_processing:
Raw sequencing reads were mapped to the GRCh38.p10 genome using STAR v2.7.6a and duplicate reads marked by Picard v2.23.8 and removed from downstream analysis
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: GRCh38.p10
Supplementary files format and content: txt file of RPKM normalized read counts for each detected gene
Supplementary files format and content: CM_FluCMV2023.geneRpkm.detected.RPM.3.exon.txt

source_name: Lung

value: Lung

value: CD25+ CD137+ CD8+ T cell

value: Influenza peptide stimulated


title: H3K27ac_hESC_rep1


title: LL045.Flu.Negative.AIM

description: Library name: LL045.Flu.Negative.AIM

value: CD69+ CD8+ T cell

value: Unstimulated


title: Pf strain NF135 infected PHH, iwp2 treated, sequencing replicate 1


title: SK06-RK10339_S53

source_name: Ileum


title: SK05-RK10349_S33


title: LL037.CMV.CMV.AIM

description: Library name: LL037.CMV.CMV.AIM

value: CMV peptide stimulated


title: H3K27me3_hESC_rep1


title: SK10-RK10611_S12


title: LL037.Flu.Flu.AIM

description: Library name: LL037.Flu.Flu.AIM


title: H3K4me3_hESC_rep2


title: Non-allergic control 4

type: other

city: Madrid

first: Jose Antonio

last: Cañas

state: Madrid

address: Av. Reyes Catolicos 2

department: Inmunology

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

hyb_protocol: EPIC Illumina

scan_protocol: Methylation EPIC-8 v2.0 Array

data_processing:
DMRCate
Average beta

label: Cy3 and Cy36

source_name: Peripheral whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Total blood DNA was extracted using the DNA Blood Kit (Qiagen, Hilden, Germany), according to standard instructions

value: Peripheral whole blood


title: LL037.Negative.AIM

description: Library name: LL037.Negative.AIM


title: SK05-RK10319_S25


title: H3K4me3_hESC_rep1


title: CMANIE Patient 2 (Post-treatment)

label: Cy3 and Cy35


title: LL035.Flu.Flu.AIM

description: Library name: LL035.Flu.Flu.AIM


title: SK10-RK10662_S54


title: CMANIE Patient 6 (Pre-treatment)

label: Cy3 and Cy34


title: ATAC_EC_rep2


title: SK04-RK10348_S33


title: LL035.Flu.Negative.AIM

description: Library name: LL035.Flu.Negative.AIM


title: CMANIE Patient 2 (Pre-treatment)

label: Cy3 and Cy33


title: LL033.CMV.CMV.AIM

description: Library name: LL033.CMV.CMV.AIM


title: ATAC_EPC-2_rep2


title: SK05-RK10308_S17


title: Pf strain NF135 infected PHH, 5C treated, sequencing replicate 1


title: H3K27me3_hESC_rep2


title: Pf strain NF135 infected PHH, mock treated, sequencing replicate 1


title: ATAC_EPC-2_rep1


title: CMAIE Patient 12 (Post-treatment)

label: Cy3 and Cy31


title: LL033.CMV.Negative.AIM

description: Library name: LL033.CMV.Negative.AIM


title: SK05-RK10336_S29


title: SK08-RK10292_S8


title: LL031.CMV.CMV.AIM

description: Library name: LL031.CMV.CMV.AIM


title: LL031.Flu.Flu.AIM

description: Library name: LL031.Flu.Flu.AIM


title: SK05-RK10329_S36


title: CMAIE Patient 13 (Pre-treatment)

label: Cy3 and Cy30


title: CMAIE Patient 12 (Pre-treatment)

label: Cy3 and Cy29


title: ATAC_EPC-1_rep1


title: ATAC_EPC-1_rep2


title: LL031.Negative.AIM

description: Library name: LL031.Negative.AIM


title: SK06-RK10149_S39


title: Non-allergic control 3

label: Cy3 and Cy28


title: ATAC_VMC_rep2


title: LL029.CMV.CMV.AIM

description: Library name: LL029.CMV.CMV.AIM


title: ATAC_EC_rep1


title: SK05-RK10322_S40


title: CMANIE Patient 1 (Post-treatment)

label: Cy3 and Cy27


title: ATAC_VMC_rep1


title: SK11-RK10678_S2


title: CMAIE Patient 13 (Post-treatment)

label: Cy3 and Cy32


title: LL029.Flu.Flu.AIM

description: Library name: LL029.Flu.Flu.AIM


title: CMANIE Patient 5 (Pre-treatment)

label: Cy3 and Cy26


title: RK10002


title: ATAC_hESC_rep2


title: LL029.Negative.AIM

description: Library name: LL029.Negative.AIM


title: CMANIE Patient 1 (Pre-treatment)

label: Cy3 and Cy25


title: ATAC_hESC_rep1


title: SK05-RK10337_S28


title: LL028.Flu.Flu.AIM

description: Library name: LL028.Flu.Flu.AIM


title: CMAIE Patient 11 (Post-treatment)

label: Cy3 and Cy24


title: RNA_EC_rep2


title: SK12-RK11016_S21


title: CMAIE Patient 10 (Post-treatment)

label: Cy3 and Cy23


title: LL028.Flu.Negative.AIM

description: Library name: LL028.Flu.Negative.AIM


title: RK10075


title: SK05-RK10350_S32


title: RNA_EPC-2_rep2


title: CMAIE Patient 11 (Pre-treatment)

label: Cy3 and Cy22


title: SK06-RK10226_S4


title: LL026.CMV.Negative.AIM

description: Library name: LL026.CMV.Negative.AIM


title: RNA_EPC-2_rep1


title: CMAIE Patient 10 (Pre-treatment)

label: Cy3 and Cy21


title: LL025.CMV.CMV.AIM

description: Library name: LL025.CMV.CMV.AIM


title: SK05-RK10330_S24


title: RNA_EPC-1_rep2


title: Non-allergic control 2

label: Cy3 and Cy20


title: LL025.CMV.Negative.AIM

description: Library name: LL025.CMV.Negative.AIM


title: CMANIE Patient 3 (Pre-treatment)

label: Cy3 and Cy19


title: RNA_EPC-1_rep1


title: RNA_VMC_rep2


title: LL025.Flu.Flu.AIM

description: Library name: LL025.Flu.Flu.AIM


title: SK06-RK10168_S31


title: CMAIE Patient 9 (Post-treatment)

label: Cy3 and Cy18


title: SK10-RK10619_S18


title: CMAIE Patient 8 (Post-treatment)

label: Cy3 and Cy17


title: RNA_EC_rep1


title: RNA_VMC_rep1


title: LL026.CMV.CMV.AIM

description: Library name: LL026.CMV.CMV.AIM


title: LL010.CMV.CMV.AIM

description: Library name: LL010.CMV.CMV.AIM


title: LL025.Flu.Negative.AIM

description: Library name: LL025.Flu.Negative.AIM


title: CMAIE Patient 7 (Post-treatment)

label: Cy3 and Cy16


title: RNA_hESC_rep2


title: LL010.CMV.Negative.AIM

description: Library name: LL010.CMV.Negative.AIM


title: SK06-RK10171_S34


title: SK10-RK10612_S13


title: CMAIE Patient 9 (Pre-treatment)

label: Cy3 and Cy15


title: RNA_hESC_rep1


title: SK10-RK10646_S38


title: CMAIE Patient 8 (Pre-treatment)

label: Cy3 and Cy14


title: 9149

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Library name: Sample 36

data_processing:
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline, which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file contains information about positions correlated with age in the control group (48 samples) along with their annotations; the corresponding positions in diseased cows (48 samples) are also available.
Library strategy: EM-seq

organism: Bos taurus

source_name: Blood

growth_protocol: The cows were raised in the same conditions on the farm

extract_protocol:
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction, enzymatic methyl-seq (EM-seq) library preparation and whole-genome sequencing
Libraries were pooled at equimolar concentrations and sequenced using Illumina NovaSeq technology, generating approximately 450 million 150-bp paired-end reads per library.During library preparation, there is a DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines

value: Blood

value: Low Production


title: SK04-RK10240_S2

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include RPM (reads per million) values for each Sample

value: Ileum


title: shCLGN3

city: hefei

first: yan

last: sitong

address: 安徽医科大学第一附属医院研工部

institute: 安徽医科大学

description:
Library name: sample6
sh-CLGN

data_processing:
Raw sequencing data underwent rigorous quality filtering, including the removal of adapter-containing reads, reads with ambiguous bases, and reads where over 50% of bases exhibited Qphred scores ≤20. Cleaned reads were subsequently assessed for Q20, Q30, and GC content.The reference genome index was constructed using HISAT2 v2.0.5, and the paired-end cleaned reads were aligned to the reference genome. Quantification was performed using featureCounts. The gene expression levels were standardized based on factors such as gene length to obtain FPKM values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: HCC

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) . ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: HCC

value: hepatocytes

value: CLGN knock down

value: shCLGN


title: shCLGN2

address: 安徽医科大学第一附属医院研工部

description:
Library name: sample5
sh-CLGN


title: SK10-RK10624_S23

first: Tzipi

last: Braun

extract_protocol:
RNA was isolated from FFPE tissue sections using the Qiagen AllPrep RNA/DNA FFPE Kit.
Lexogen QuantSeq 3' mRNA-Seq libraries and single-end 100-bp sequencing was performed


title: 9148

description: Library name: Sample 35


title: CMAIE Patient 7 (Pre-treatment)

label: Cy3 and Cy13


title: SK10-RK10641_S37


title: 9119

description: Library name: Sample 34


title: shCLGN1

address: 安徽医科大学第一附属医院研工部

description:
Library name: sample4
sh-CLGN


title: CMANIE Patient 4 (Post-treatment)

label: Cy3 and Cy12


title: 9065

description: Library name: Sample 33


title: NC3

address: 安徽医科大学第一附属医院研工部

description:
Library name: sample3
sh-NC

value: WT

value: shcontrol


title: CMANIE Patient 4 (Pre-treatment)

label: Cy3 and Cy11


title: SK05-RK10327_S38


title: 8164

description: Library name: Sample 32


title: CMAIE Patient 5 (Post-treatment)

label: Cy3 and Cy10


title: 8155

description: Library name: Sample 31


title: CMAIE Patient 3 (Post-treatment)

label: Cy3 and Cy9


title: SK04-RK10248_S3


title: SK07-RK10130_S21


title: 8137

description: Library name: Sample 30


title: NC1

address: 安徽医科大学第一附属医院研工部

description:
Library name: sample1
sh-NC


title: CMAIE Patient 1 (Post-treatment)

label: Cy3 and Cy8


title: POU4F3nT+ in d140 cochlear organoids with T4

city: Indianapolis

first: Tsubasa

last: Saeki

state: IN

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

description: Library name: T4_d140_POU4F3+

data_processing:
Illumina’s CellRanger v4.0.0 program generated BCL files, which were demultiplexed and converted to FASTQ files via bcl2fastq Conversion Software (Illumina). The FASTQ files were then aligned to the GRCh38-3.0.0 human reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner. Mapped reads were grouped by cell barcode, and single-cell gene expression was quantified using unique molecular identifiers (UMIs). The resulting filtered gene-barcode (count) matrices were used as input for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: Gene expression matrix

source_name: cochlear organoids

growth_protocol: PAX2-2A-nGFP/POU4F3-2A-ntdTomato hESCs were dissociated with Accutase and distributed at 2500-3500 cells per well onto low-adhesion 96-well U-bottom plates in E8fn containing Y-27632. 100μL of E8fn was added to each well after >4 h of incubation. After 48 h of incubation (day 0; d0), aggregates were washed in Essential 6 medium and transferred to new 96-well U-bottom plates with 100 μL of E6 medium with Normocin (E6n) containing FGF-2, SB-431542, and 2% Martigel. On d3, FGF-2 and LDN-193189 were added. Culture media was changed on d7 and d8 with E6n containing CHIR99021, LDN, and FGF-2. On d11, aggregates were washed and transferred to 6-well culture dishes in Organoid Maturation Medium (OMM) containing 1% Matrigel and CHIR99021. OMM consists of a 50:50 mixture of advanced DMEM:F12 and Neurobasal Medium with N2 Supplement, B27 minus Vitamin A, GlutaMAX, β-Mercaptoethanol, and Normocin. Cultures were maintained in OMM containing CHIR99021 and Purmorphamine from d13-18, and maintained in OMM containing Purmorphamine and IWP2 from d18-22, with media changes on d15, 18, and 20, then maintained in OMM for the remainder of the culture.

extract_protocol:
Aggregates were dissected to enrich POU4F3nT+ cells 2-3 days prior to single-cell dissociation. On the day of cell sorting, aggregates were incubated with Accumax at 37°C for 120 min. During incubation, the samples were mechanically dissociated by gentle pipetting with wide-orifice P1000 tips. After confirming that most cells, especially those with reporter expression, were completely dissociated, they were filtered through a 40-μm cell strainer and then transferred into 2-ml tubes. After spinning down at 200 ×g for 5 min, dissociated cells were resuspended in FACS buffer consisting of 2% fetal bovine serum in 1× DPBS. Then, cells were collected into a 5-ml round-bottom polypropylene tube. Simultaneously, the above protocol prepared size control cells from wild-type WA25 hESCs. Cells were stored on ice in the dark prior to sorting. tdTomato-positive populations were collected and cleaned using a SORP Aria or SORP Fusion (BD Bioscience).
scRNA-seq for all samples was performed using the 10x Genomics Chromium 3’ v3 platform for cDNA library construction and the NovaSeq 6000 system (Illumina) for sequencing.

value: cochlear organoids


title: NC2

address: 安徽医科大学第一附属医院研工部

description:
Library name: sample2
sh-NC


title: CMAIE Patient 5 (Pre-treatment)

label: Cy3 and Cy7


title: POU4F3nT+ in d109 cochlear organoids with T4

description: Library name: T4_d109_POU4F3+


title: 8056

description: Library name: Sample 29


title: SK08-RK10342_S53

address: Derech Sheba 2


title: POU4F3nT+ in d109 cochlear organoids without T4

description: Library name: CTR_d109_POU4F3+


title: CMAIE Patient 3 (Pre-treatment)

label: Cy3 and Cy6


title: SK05-RK10328_S31


title: SK07-RK10200_S4


title: 7135

description: Library name: Sample 26


title: 8049

description: Library name: Sample 28


title: CMAIE Patient 1 (Pre-treatment)

label: Cy3 and Cy5


title: SK06-RK10194_S48


title: G121,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,8092

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

institute: University of Minnesota

description: Library name: G121

data_processing:
Read quality for each sample was first assessed with FASTQC
Trimming and additional QC for each sample with Trim Galorev0.6.4
Globin and rRNA reads were filtered out using bowtie2v2.4.2
Remaining reads were alligned to the GRCh38 genome using STARv2.7.10b
Assembly: GRCh38 (Ensemble v 112)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: PBMC

extract_protocol:
Qiagen RNeasy Micro Kit
KAPA mRNA HyperPrep kit

treatment_protocol: The study interventions are shown in Fig. 1. At baseline and approximately 4 weeks later, participants received a DNA vaccine, which included a p24 conserved element (CE) 1/2 plasmid (4 mg) with an IL-12 DNA plasmid (2 mg) split into two separate injections administered via electroporation using the TriGrid Delivery System (TDS-IM v1.0; Ichor Medical Systems). At 12 weeks, they received the p24CE 1/2 plasmid (4 mg) with a p55gag plasmid (2 mg) and IL-12 plasmid (2 mg) split into two separate injections administered via electroporation. At approximately week 20, participants received an MVA62B boost via intramuscular injection. At week 24, participants received intravenous infusions of 10-1074 (30 mg/kg) and VRC07-523LS (20mg/kg). From weeks 25-33, participants received weekly subcutaneous injections of 60 mg of lefitolimod (2 injections per dose, 1-9 doses, see “Safety”). At approximately week 34, they received a second infusion of each of the two bNAbs and 48 hours later interrupted ART. Clinical laboratory values, including plasma HIV RNA levels, were checked weekly from week 34-58 and then at least every other week for the remainder of the ATI. ART was reinitiated for any one of the following outcomes: (1) plasma HIV RNA > 50,000 copies RNA/mL for four weeks, (2) plasma HIV RNA > 10,000 copies RNA/mL for 6 weeks, (3) plasma HIV RNA > 2000 copies RNA/ml for 12 weeks, or (4) plasma HIV RNA > 400 copies/RNA for 24 weeks. ART could also be reinitiated for confirmed CD4+ T cell decline below 350 cells/uL, the presence of severe acute retroviral syndrome, concerns about HIV transmission due to high-risk sexual behavior, acute SARS-CoV-2 infection or need for COVID-19 or Mpox vaccination, or at the request of the participant or their primary care clinician. Following reinitiation of ART, participants were seen at 1, 2, and 6 months to confirm virologic suppression.

tag: disease state

value: HIV

value: PBMC

tag: time

value: Baseline

tag: patient id

tag: patient status

value: Controller

tag: hiv viral_load


title: 7089

description: Library name: Sample 24


title: G119,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,1292

description: Library name: G119

value: Noncontroller


title: Blood, ALFQA, Week 24 Day 2, 15U034

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

description:
Library name: 15U034_ALFQA_W24D2
Column name in TMM_counts.txt:15U034_ALFQA_W24D2

data_processing:
Raw sequencing data were converted to FASTQ using bcl2fastq2 v.2.20.0 (Illumina)
Low quality bases were removed using Trimmomatic v0.39 and FastQC v0.11.860.
Reads were mapped to the Rhesus Macaque genome (Mmul_10) using HISAT2 v2.1.061.
Subread featureCounts v1.6.4 was used for gene expression quantification of protein-coding genes, and trimmed mean of M values (TMM)-based normalization was implemented within edgeR v3.36.062.
Genes aligning to highly divergent regions of the genome, deriving from mitochondria, coding for ribosomal proteins and hemoglobin-related genes were excluded from the count matrix. Only genes with counts above 10 in a minimum of 15 samples were retained.
Assembly: Mmul_10
Supplementary files format and content: tab-delimitted text file contains TMM-normalized counts for all samples.

organism: Macaca mulatta

extract_protocol:
Total RNA was extracted from 10,000-100,000 or 30,000-6.5 million cryopreserved PBMC using the Single Cell RNA Purification Kit (Norgen Biotek Corp) or the PureLink RNA Mini Kit (ThermoFisher Scientific)
Amplified cDNA was made from 6.66-10ng of RNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio Inc.), spiked with 5μL of 1:20,000 diluted ERCC Mix 1 or 2 (ThermoFisher Scientific). Sequence-ready libraries were generated using the Illumina DNA Library Prep Kit, quantified on a MiSeq.

value: peripheral blood cells

value: ALFQA


title: Blood, ALFQA, Week 24 Day 2, 14U045

description:
Library name: 14U045_ALFQA_W24D2
Column name in TMM_counts.txt:14U045_ALFQA_W24D2

value: Blood


title: SK07-RK10313_S48

city: Ramat Gan

institute: Sheba Medical Center at Tel Hashomer

tag: average ileal_microvillus_length_(µm)

tag: cd microvillus_length_quartile


title: SK12-RK11008_S13

tag: tissue


title: 7030

description: Library name: Sample 21

value: Low Production


title: 7080

description: Library name: Sample 23


title: G117,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,2251

description: Library name: G117


title: G115,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,2908

description: Library name: G115


title: Blood, ALFQA, Week 24 Day 2, 13U013

description:
Library name: 13U013_ALFQA_W24D2
Column name in TMM_counts.txt:13U013_ALFQA_W24D2


title: SK10-RK10622_S21

value: Ileum


title: Blood, ALFQ, Week 24 Day 2, 17U011

description:
Library name: 17U011_ALFQ_W24D2
Column name in TMM_counts.txt:17U011_ALFQ_W24D2

value: ALFQ


title: 7024

description: Library name: Sample 19

value: Control


title: 7028

description: Library name: Sample 20


title: RK10024


title: G113,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,1408

description: Library name: G113


title: G123,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,8106

description: Library name: G123


title: Blood, ALFQ, Week 24 Day 2, 16U010

description:
Library name: 16U010_ALFQ_W24D2
Column name in TMM_counts.txt:16U010_ALFQ_W24D2


title: G109,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,8012

description: Library name: G109


title: SK04-RK10323_S37


title: 6133

description: Library name: Sample 18


title: 6126

description: Library name: Sample 17


title: Blood, ALFQ, Week 24 Day 2, 15U033

description:
Library name: 15U033_ALFQ_W24D2
Column name in TMM_counts.txt:15U033_ALFQ_W24D2


title: SK06-RK10143_S37


title: SK06-RK10231_S12


title: Blood, ALFQA, Week 24 Day 2, 14U044

description:
Library name: 14U044_ALFQA_W24D2
Column name in TMM_counts.txt:14U044_ALFQA_W24D2


title: Blood, ALFQ, Week 24 Day 2, 14U026

description:
Library name: 14U026_ALFQ_W24D2
Column name in TMM_counts.txt:14U026_ALFQ_W24D2


title: Blood, ALFQ, Week 24 Day 2, 14U012

description:
Library name: 14U012_ALFQ_W24D2
Column name in TMM_counts.txt:14U012_ALFQ_W24D2


title: 6096

description: Library name: Sample 16


title: SK07-RK10139_S29


title: G107,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,2594

description: Library name: G107


title: Blood, ALFQ, Week 24 Day 2, 13U037

description:
Library name: 13U037_ALFQ_W24D2
Column name in TMM_counts.txt:13U037_ALFQ_W24D2


title: SK11-RK10542_S8


title: G105,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,2523

description: Library name: G105


title: 6046

description: Library name: Sample 13


title: 6085

description: Library name: Sample 15


title: Intermediate mesoderm (IM) cells with RA signaling- IM with RA signaling

city: Daejeon

first: In Hwan

last: Tae

address: 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Library name: IM2

data_processing:
Sequencing reads were processed with the Cell Ranger version 7.0.1 (10X Genomics, CA, USA) using the Human reference transcriptome GRch38 from ensembl. From the gene expression matrix, downstream analysis was carried out with R version 4.0.2. Quality control, filtering, data clustering and visualization, and differential expression analysis was carried out using WinSeurat program (Ebiogen Inc, Korea) based on Seurat version 4.2.0. For each individual dataset, genes expressed in cells < 500 UMIs and < 300 genes were removed from the gene expression matrix.
Assembly: GRch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human intermediate mesoderm cells

extract_protocol:
Single-cell suspensions were made from human kidney organoid using TrypLE (Thermo Fisher, 12604013), and then filtered through a 40 uM mesh strainer (Corning, CLS431750) to isolate single cells.
Single-cell RNA-sequencing libraries were then prepared using the Chromium Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. libraries were sequenced in multiplex on the Novaseq 6000 sequencer (Illumina, San Diego, CA) to produce on average a minimum of 60,000 reads per single cell

value: human intermediate mesoderm cells


title: Blood, ALFA, Week 24 Day 2, 15U036

description:
Library name: 15U036_ALFA_W24D2
Column name in TMM_counts.txt:15U036_ALFA_W24D2

value: ALFA


title: 6042

description: Library name: Sample 12


title: Blood, ALFA, Week 24 Day 2, 17U041

description:
Library name: 17U041_ALFA_W24D2
Column name in TMM_counts.txt:17U041_ALFA_W24D2


title: Intermediate mesoderm (IM) cells - IM CTL

description: Library name: IM1


title: SK07-RK10133_S23


title: SK07-RK10214_S13


title: UOK120 cells, shNR1D1 biol rep 3

city: Nanjing

first: Yanwen

last: Lu

state: jiangsu

address: No. 22 Hankou Rd., Gulou District, Nanjing, Jiangsu 210093, P.R.China

institute: Nanjing University

data_processing:
reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the follwing assembly analysis. Thus, to get high quality clean reads.
We aligned reads of all samples to the research species referencegenome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie with default parameters.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes counts values for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values counts for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using RNA easy mini plus kit (Qiagen). 1.3 ug RNA was used for the construction of the squencing libraries.
RNA libraries for RNA-seq  were prepared using SMARTER mrna-seq library Prep kit following manufacturer's protocols

value: Kidney

tag: cell line

value: Xp11.2 translocation renal carcinoma cell lines


title: SK12-RK11015_S20


title: G111,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,2887

first: Michael

description: Library name: G111


title: SK09-RK10589_S55


title: SK06-RK10170_S33


title: Blood, ALFA, Week 24 Day 2, 14U043

description:
Library name: 14U043_ALFA_W24D2
Column name in TMM_counts.txt:14U043_ALFA_W24D2

tag: cell type


title: 5133

description: Library name: Sample 10


title: Blood, ALFA, Week 24 Day 2, 14U018

description:
Library name: 14U018_ALFA_W24D2
Column name in TMM_counts.txt:14U018_ALFA_W24D2

tag: treatment


title: 6004

description: Library name: Sample 11


title: G003,Baseline,HIV/Gag vaccine/bNAbs-TLR9 agonist/bNAbs,1408

description: Library name: G003


title: 6060

description: Library name: Sample 14


title: SK12-RK11010_S15


title: UOK120 cells, shNR1D1 biol rep 2


title: UOK120cells, shControl biol rep 2

value: shRNA(nc)


title: 5124

description: Library name: Sample 8


title: 5132

description: Library name: Sample 9


title: UOK120 cells, shNR1D1 biol rep 1


title: Blood, AH, Week 24 Day 2, 17U033

description:
Library name: 17U033_AH_W24D2
Column name in TMM_counts.txt:17U033_AH_W24D2

value: AH


title: SK05-RK10333_S23


title: SK12-RK11013_S18


title: 5104

description: Library name: Sample 7