title: Patient61_Sample11

description: COUNTS_TABLE_RAW4: P61_S11


title: Patient71_Sample18

status: Public on Jan 30 2023

type: SRA

city: New York

first: Angelica

last: Galianese

state: New York

address: 615 W 164th Street, Apt 21C

country: USA

institute: Columbia University

description: COUNTS_TABLE_RAW10: P71_S18

library_source: transcriptomic

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples

molecule: total RNA

organism: Homo sapiens

source_name: nasopharyngeal samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.

tag: tissue

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: Patient61_Sample6

description: COUNTS_TABLE_RAW4: P61_S6


title: Patient71Sample_17

description: COUNTS_TABLE_RAW10: P71S_17


title: mnp-20-0716

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: CNS tumor tissue

label_protocol: Illumina

extract_protocol: DNA from FFPE tissue was extracted using a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: "material"

value: FFPE tissue

tag: "tumor type"

value: Medulloblastoma, non-WNT/SHH

tag: "patient age (years)"

tag: "patient gender"

value: female

tag: "tumor location"

value: cerebellum


title: Patient61_Sample8

description: COUNTS_TABLE_RAW4: P61_S8


title: Patient61_Sample7

description: COUNTS_TABLE_RAW4: P61_S7


title: Patient72_Sample4

description: COUNTS_TABLE_RAW9: P72_S4


title: Patient71_Sample15

description: COUNTS_TABLE_RAW10: P71_S15


title: Patient71_Sample14

description: COUNTS_TABLE_RAW10: P71_S14


title: Patient71_Sample16

description: COUNTS_TABLE_RAW10: P71_S16


title: mnp-20-0019

value: Primitive neuroectodermal tumor

value: male

value: temporal lobe


title: Patient61_Sample4

description: COUNTS_TABLE_RAW4: P61_S4


title: 71B4, Whole muscle lysate, WTlFlox

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description:
Muscle_lysate_counts.txt
Muscle_lysate_metadata.txt

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

organism: Mus musculus

source_name: Hindlimb (skeletal muscle)

extract_protocol:
Muscle were digested by using RNeasy Micro Kit (Qiagen, # 74004) and RNeasy Fibrous Tissue Mini Kit (Qiagen #  74704) to isolate RNA from sorted cells and the TA muscle, respectively, single cell suspension stained and MPs were sorted as follow: CD45- CD31- Sca1+ Tdtomato+Alpha7-
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 using the High Output 75 cycle kit (Illumina) to generate paired-end 43bp × 43bp reads.

value: Hindlimb (skeletal muscle)

tag: time

value: Muscle resting state, 56 days post tamoxifen

tag: cell type

value: Whole muscle lysate

tag: sorted cell type

value: Total tissue lysate

tag: genotype

value: WTlFlox


title: 71B3, Whole muscle lysate, WTlFlox


title: mnp-20-0857

value: Anaplastic astrocytoma

value: third ventricle, parietal lobe


title: Patient61_Sample3

description: COUNTS_TABLE_RAW4: P61_S3


title: B16F10 tumor, PBS treated, D6, bio rep 1 [T6PBS1]

city: Cambridge

first: Joseph

middle: R

last: Palmeri

state: MA

address: 500 Main St., Attn: 76-291: Joseph Palmeri

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description: 75-nt kit

data_processing:
Data preprocessing and count matrix construction were performed using the Smart-seq2 Multi-Sample v2.2.0 Pipeline (RRID:SCR_018920) on Terra
.
Assembly: GENCODE mouse (M21) reference genome
Supplementary files format and content: Seurat object containing count matrices and sample metadata
Supplementary files format and content: Metadata spreadsheet containing sample information
Supplementary files format and content: Count matrix containing counts each sample
Supplementary files format and content: Gene metadata spreadsheet

molecule: polyA RNA

source_name: B16F10 tumor

extract_protocol:
Total RNA was extracted using RNAeasy plus mini kit
RNA-sequencing was performed by the BioMicro Center at MIT using a modified version of the SCRB-seq protocol (https://www.biorxiv.org/content/10.1101/003236v1)

treatment_protocol: C57Bl/6 mice were inoculated with 1e6 B16F10 cells subcutaneously on their flank. Mice were then subseqently treated with either PBS, Tx, Tx + anti-CD4, or anti-CD4. Tx is defined as 200µg or TA99 given intraperitoneally on day 7 post tumor inoculation and 36.1 µg of anti-4-1BB-LAIR given intratumorally on day 8 post tumor inoculation. Anti-CD4 treatment (clone GK1.5) was given at a dose of 400 µg intraperitoneally on days 6, 9, and 12. Tumors and tumor draining lymph nodes were harvested on days 11 or day 14 (denoted as D3 and D6, defined relative to anti-4-1BB-LAIR treatment day). Samples were enriched for CD45+ cells using a magnetic bead postiive isolation step prior to RNA extratction.

tag: strain

value: B16F10 tumor

tag: cell line

value: Primary CD45+ cells

value: CD45+ Immune cells

tag: treatment

value: PBS

tag: timepoint


title: 73A7, Whole muscle lysate, WT

tag: tissue

value: WT


title: 73A5, Whole muscle lysate, WT


title: Patient61_Sample2

description: COUNTS_TABLE_RAW4: P61_S2

value: nasopharyngeal samples

tag: subject


title: mnp-20-0903

value: FFPE tissue

value: Medulloblastoma, non-WNT/SHH

value: female

value: fourth ventricle


title: Patient71_Sample12

description: COUNTS_TABLE_RAW10: P71_S12

tag: geographic location


title: Patient61_Sample5

description: COUNTS_TABLE_RAW4: P61_S5

tag: collection date


title: Patient70_Sample10

description: COUNTS_TABLE_RAW9: P70_S10


title: 74A3, Mesenchymal progenitors, WTlFlox

description:
MP_counts.txt
MP_metadata.txt

value: Hindlimb (skeletal muscle)

value: Mesenchymal progenitors

value: Sorted on CD45- CD31- Sca1+ tdtomato+ alpha7-


title: Patient70_Sample8

description: COUNTS_TABLE_RAW9: P70_S8


title: mnp-20-1114

tag: "material"

value: Odontogenic tumor

value: male


title: 71B5, Whole muscle lysate, WTlFlox

value: Muscle resting state, 56 days post tamoxifen

value: Whole muscle lysate

value: Total tissue lysate

value: WTlFlox


title: mnp-20-0509

tag: "tumor type"

value: Pilocytic Astrocytoma

value: medulla oblongata


title: Patient61_Sample1

description: COUNTS_TABLE_RAW4: P61_S1


title: Patient71_Sample13

description: COUNTS_TABLE_RAW10: P71_S13


title: 72B7, Mesenchymal progenitors, WTlFlox

description:
MP_counts.txt
MP_metadata.txt

value: Muscle resting state, 14 days post tamoxifen


title: Patient60_Sample15

description: COUNTS_TABLE_RAW4: P60_S15

value: nasopharyngeal samples


title: Patient60_Sample14

description: COUNTS_TABLE_RAW4: P60_S14


title: Patient69_Sample12

description: COUNTS_TABLE_RAW10: P69_S12


title: 74A1, Mesenchymal progenitors, WTlFlox

description:
MP_counts.txt
MP_metadata.txt


title: Patient69_Sample11

description: COUNTS_TABLE_RAW7: P69_S11


title: mnp-20-0177

value: FFPE tissue

value: Pineoblastoma

tag: "patient age (years)"

value: pineal region


title: Patient69_Sample10

description: COUNTS_TABLE_RAW7: P69_S10


title: Patient60_Sample13

description: COUNTS_TABLE_RAW4: P60_S13


title: Patient60_Sample12

description: COUNTS_TABLE_RAW4: P60_S12


title: mnp-20-1109

tag: "patient gender"

value: cerebellum


title: Patient69_Sample8

description: COUNTS_TABLE_RAW10: P69_S8


title: 72B8, Mesenchymal progenitors, WT

description:
MP_counts.txt
MP_metadata.txt

value: Hindlimb (skeletal muscle)

value: WT


title: Patient60_Sample11

description: COUNTS_TABLE_RAW4: P60_S11


title: Patient69_Sample9

description: COUNTS_TABLE_RAW7: P69_S9


title: mnp-20-1201

value: female

tag: "tumor location"

value: orbital frontal cortex


title: 74A2, Mesenchymal progenitors, WT

description:
MP_counts.txt
MP_metadata.txt

tag: time

value: Mesenchymal progenitors

value: Sorted on CD45- CD31- Sca1+ tdtomato+ alpha7-


title: Patient69_Sample7

description: COUNTS_TABLE_RAW7: P69_S7


title: Patient60_Sample10

description: COUNTS_TABLE_RAW4: P60_S10


title: DKO+GCS-100 osteoclast biol rep 3

city: Wuhan

first: Lingxin

last: Zhu

state: Hubei

address: 237 Luoyu Road, Hongshan District, School and Hospital of Stomatology, Wuhan University

country: China

institute: Wuhan University

description:
Gene expression data
1900-LZ-9

data_processing:
Data were aligned using the STAR aligner and featureCounts v1.6.4 software, and reads per kilobase of transcript per million mapped read values on gene level were estimated for ensemble transcriptome.
DESeq2 was used to estimate significance between any two experimental groups.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow-derived

growth_protocol: Bone marrow cells were isolated from wild-type mice and myeloid specific Mmp9/Mmp14-deleted mice cultured on plastic substrata for differentiation into osteoclasts with M-CSF and RANKL.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The construction of libraries was generated using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.
QuantSeq 3’ mRNA-Seq Library

treatment_protocol: Bone marrow-derived macrophages were cultured with 20 ng/ml M-CSF and 30 ng/ml RANKL for 4 days in the presence or absence of GCS-100.

value: Bone marrow-derived

tag: cell type

value: Primary osteoclast

value: M-CSF/RANKL plus GCS-100


title: mnp-20-0893

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: male

value: cerebellum, fourth ventricle


title: Patient60_Sample9

description: COUNTS_TABLE_RAW4: P60_S9

value: nasopharyngeal samples


title: mnp-20-0051

value: FFPE tissue

value: Medulloblastoma, non-WNT/SHH

value: fourth ventricle


title: Patient60_Sample8

description: COUNTS_TABLE_RAW4: P60_S8


title: mnp-20-0617

value: Intraocular medulloepithelioma


title: 73C3, Mesenchymal progenitors, WT

description:
MP_counts.txt
MP_metadata.txt

value: Hindlimb (skeletal muscle)

value: Muscle resting state, 14 days post tamoxifen

tag: sorted cell type


title: DKO+GCS-100 osteoclast biol rep 2

description:
Gene expression data
1900-LZ-8

tag: genotype


title: DKO+GCS-100 osteoclast biol rep 1

description:
Gene expression data
1900-LZ-7


title: Patient60_Sample6

description: COUNTS_TABLE_RAW4: P60_S6


title: Patient69_Sample5

description: COUNTS_TABLE_RAW7: P69_S5


title: Patient69_Sample4

description: COUNTS_TABLE_RAW7: P69_S4


title: mnp-20-0905

value: Pilocytic Astrocytoma

value: female

value: cerebellum


title: DKO osteoclast biol rep 2

description:
Gene expression data
1900-LZ-5

value: M-CSF/RANKL


title: Patient69_Sample3

description: COUNTS_TABLE_RAW7: P69_S3


title: Patient69_Sample2

description: COUNTS_TABLE_RAW7: P69_S2


title: DKO osteoclast biol rep 1

description:
Gene expression data
1900-LZ-4

value: Bone marrow-derived


title: Patient60_Sample4

description: COUNTS_TABLE_RAW4: P60_S4


title: Patient60_Sample3

description: COUNTS_TABLE_RAW4: P60_S3


title: Patient69_Sample1

description: COUNTS_TABLE_RAW9: P69_S1


title: wild-type osteoclast biol rep 3

description:
Gene expression data
1900-LZ-3

value: Primary osteoclast

value: wild-type


title: Patient69_Sample6

description: COUNTS_TABLE_RAW7: P69_S6


title: mnp-20-1053


title: Patient60_Sample2

description: COUNTS_TABLE_RAW4: P60_S2


title: DKO osteoclast biol rep 3

description:
Gene expression data
1900-LZ-6


title: Patient68_Sample20

description: COUNTS_TABLE_RAW10: P68_S20


title: wild-type osteoclast biol rep 1

description:
Gene expression data
1900-LZ-1


title: Patient60_Sample1

description: COUNTS_TABLE_RAW4: P60_S1


title: mnp-20-0953


title: mnp-20-0219

value: Ganglioglioma

value: frontal lobe


title: Patient68_Sample21

description: COUNTS_TABLE_RAW10: P68_S21


title: wild-type osteoclast biol rep 2

description:
Gene expression data
1900-LZ-2


title: Patient68_Sample19

description: COUNTS_TABLE_RAW10: P68_S19


title: Patient60_Sample7

description: COUNTS_TABLE_RAW4: P60_S7


title: Patient59_Sample3

description: COUNTS_TABLE_RAW4: P59_S3


title: Patient59_Sample4

description: COUNTS_TABLE_RAW4: P59_S4


title: Patient60_Sample5

description: COUNTS_TABLE_RAW4: P60_S5


title: Patient59_Sample5

description: COUNTS_TABLE_RAW4: P59_S5


title: mnp-20-1468

value: male

value: temporal lobe


title: Patient68_Sample18

description: COUNTS_TABLE_RAW10: P68_S18

value: nasopharyngeal samples


title: Patient68_Sample17

description: COUNTS_TABLE_RAW10: P68_S17


title: mnp-20-1255

value: FFPE tissue

value: Diffuse midline glioma, H3 K27-mutated

value: pons


title: Patient68_Sample22

description: COUNTS_TABLE_RAW10: P68_S22


title: Patient59_Sample1

description: COUNTS_TABLE_RAW4: P59_S1


title: mnp-20-1467

value: Embryonal tumor with multilayered rosettes (ETMR)


title: mnp-20-0336

value: Medulloblastoma, non-WNT/SHH

value: cerebellum, fourth ventricle, pons


title: mnp-20-1004

value: CNS sarcoma

value: primary somatosensory cortex, primary motor cortex


title: Patient68_Sample15

description: COUNTS_TABLE_RAW7: P68_S15


title: Patient57_Sample6

description: COUNTS_TABLE_RAW4: P57_S6


title: Patient57_Sample7

description: COUNTS_TABLE_RAW4: P57_S7


title: Patient68_Sample13

description: COUNTS_TABLE_RAW7: P68_S13


title: mnp-20-1102

value: Pilocytic Astrocytoma

value: female

value: cerebellum


title: mnp-20-0787

value: cerebellum, fourth ventricle


title: Patient68_Sample12

description: COUNTS_TABLE_RAW10: P68_S12


title: Patient57_Sample5

description: COUNTS_TABLE_RAW4: P57_S5


title: mnp-20-0800

value: brain stem, cerebellum


title: mnp-20-0239

value: Low-grade astrocytoma, NOS

value: pons, cerebellum


title: Patient57_Sample3

description: COUNTS_TABLE_RAW4: P57_S3


title: Patient64_Sample5

description: COUNTS_TABLE_RAW7: P64_S5


title: mnp-20-1223

value: male

value: frontal lobe


title: Patient64_Sample6

description: COUNTS_TABLE_RAW9: P64_S6

value: nasopharyngeal samples


title: Patient68_Sample16

description: COUNTS_TABLE_RAW10: P68_S16


title: Patient59_Sample2

description: COUNTS_TABLE_RAW4: P59_S2


title: Patient64_Sample4

description: COUNTS_TABLE_RAW7: P64_S4


title: mnp-20-0677

value: FFPE tissue

value: spinal cord


title: Patient57_Sample2

description: COUNTS_TABLE_RAW4: P57_S2


title: Patient64_Sample3

description: COUNTS_TABLE_RAW7: P64_S3


title: Patient57_Sample1

description: COUNTS_TABLE_RAW4: P57_S1


title: Patient68_Sample14

description: COUNTS_TABLE_RAW7: P68_S14


title: Patient64_Sample2

description: COUNTS_TABLE_RAW7: P64_S2


title: Patient55_Sample3

description: COUNTS_TABLE_RAW4: P55_S3


title: mnp-20-1216

value: Medulloblastoma, SHH


title: Patient63_Sample3

description: COUNTS_TABLE_RAW7: P63_S3


title: Patient55_Sample4

description: COUNTS_TABLE_RAW4: P55_S4


title: mnp-20-1253

value: Retinoblastoma

value: hypothalamus


title: Patient54_Sample6

description: COUNTS_TABLE_RAW4: P54_S6


title: mnp-20-0690

value: Anaplastic astrocytoma

value: temporal lobe


title: Patient55_Sample2

description: COUNTS_TABLE_RAW4: P55_S2


title: Patient63_Sample2

description: COUNTS_TABLE_RAW7: P63_S2


title: Patient57_Sample4

description: COUNTS_TABLE_RAW4: P57_S4


title: Patient64_Sample1

description: COUNTS_TABLE_RAW9: P64_S1


title: mnp-20-0873

value: Pilocytic Astrocytoma

value: parietal lobe


title: Patient55_Sample5

description: COUNTS_TABLE_RAW4: P55_S5


title: mnp-20-1397

value: Glioblastoma (GBM)

value: female

value: parietal lobe, occipital lobe


title: Patient60_Sample26

description: COUNTS_TABLE_RAW7: P60_S26


title: Patient54_Sample5

description: COUNTS_TABLE_RAW4: P54_S5


title: Patient63_Sample1

description: COUNTS_TABLE_RAW7: P63_S1


title: Patient55_Sample1

description: COUNTS_TABLE_RAW4: P55_S1


title: mnp-20-0545

value: frontal lobe, temporal lobe


title: mnp-20-0078

value: Atypical teratoid/rhabdoid tumor (AT/RT)

value: cerebellum


title: mnp-20-1090

value: Medulloblastoma, non-WNT/SHH


title: Patient60_Sample25

description: COUNTS_TABLE_RAW7: P60_S25

value: nasopharyngeal samples


title: Patient54_Sample3

description: COUNTS_TABLE_RAW4: P54_S3


title: mnp-20-0137

value: FFPE tissue

value: male

value: orbital frontal cortex


title: Patient53_Sample4

description: COUNTS_TABLE_RAW1: P53_S4


title: Patient60_Sample22

description: COUNTS_TABLE_RAW7: P60_S22


title: Patient54_Sample2

description: COUNTS_TABLE_RAW4: P54_S2


title: Patient60_Sample23

description: COUNTS_TABLE_RAW7: P60_S23


title: Patient60_Sample24

description: COUNTS_TABLE_RAW7: P60_S24


title: Patient60_Sample19

description: COUNTS_TABLE_RAW7: P60_S19


title: mnp-20-0291


title: Patient51_Sample7

description: COUNTS_TABLE_RAW3: P51_S7


title: Patient53_Sample1

description: COUNTS_TABLE_RAW1: P53_S1


title: Patient53_Sample3

description: COUNTS_TABLE_RAW1: P53_S3


title: Patient60_Sample17

description: COUNTS_TABLE_RAW13: P60_S17


title: Patient60_Sample18

description: COUNTS_TABLE_RAW13: P60_S18


title: Patient54_Sample4

description: COUNTS_TABLE_RAW4: P54_S4


title: Patient51_Sample5

description: COUNTS_TABLE_RAW3: P51_S5


title: mnp-20-0461

value: fourth ventricle


title: mnp-20-0185

value: Anaplastic pilocytic astrocytoma


title: Patient51_Sample4

description: COUNTS_TABLE_RAW3: P51_S4


title: Patient59_Sample19

description: COUNTS_TABLE_RAW7: P59_S19


title: Patient51_Sample3

description: COUNTS_TABLE_RAW3: P51_S3


title: mnp-20-1031

value: Ganglioneuroblastoma

value: primary somatosensory cortex, primary motor cortex


title: Patient59_Sample21

description: COUNTS_TABLE_RAW7: P59_S21


title: mnp-20-1416

value: Pilocytic Astrocytoma

value: cerebellum, fourth ventricle


title: Patient60_Sample21

description: COUNTS_TABLE_RAW7: P60_S21


title: Patient60_Sample16

description: COUNTS_TABLE_RAW13: P60_S16


title: mnp-20-1059

value: medulla oblongata


title: mnp-20-1429

value: cerebellum, fourth ventricle, pons


title: Patient51_Sample8

description: COUNTS_TABLE_RAW3: P51_S8


title: Patient51_Sample6

description: COUNTS_TABLE_RAW3: P51_S6


title: Patient60_Sample20

description: COUNTS_TABLE_RAW13: P60_S20


title: Patient59_Sample20

description: COUNTS_TABLE_RAW7: P59_S20


title: mnp-20-1583


title: Patient59_Sample18

description: COUNTS_TABLE_RAW7: P59_S18


title: mnp-20-0744

value: Low-grade astrocytoma, NOS


title: Patient51_Sample2

description: COUNTS_TABLE_RAW3: P51_S2


title: mnp-20-1267

value: Oligoastrocytoma

value: female


title: Patient59_Sample17

description: COUNTS_TABLE_RAW7: P59_S17


title: Patient50_Sample7

description: COUNTS_TABLE_RAW6: P50_S7


title: Patient51_Sample1

description: COUNTS_TABLE_RAW3: P51_S1


title: Patient50_Sample5

description: COUNTS_TABLE_RAW6: P50_S5


title: Patient59_Sample16

description: COUNTS_TABLE_RAW7: P59_S16


title: mnp-20-0470

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: temporal lobe, occipital lobe


title: Patient50_Sample4

description: COUNTS_TABLE_RAW6: P50_S4

value: nasopharyngeal samples


title: Patient59_Sample15

description: COUNTS_TABLE_RAW7: P59_S15


title: mnp-20-0803

value: FFPE tissue

value: Anaplastic astrocytoma


title: mnp-20-1561

value: Glioblastoma (GBM)

value: frontal lobe


title: Patient59_Sample12

description: COUNTS_TABLE_RAW13: P59_S12


title: mnp-20-0796

value: spinal cord


title: Patient49_Sample4

description: COUNTS_TABLE_RAW3: P49_S4


title: Patient59_Sample11

description: COUNTS_TABLE_RAW7: P59_S11


title: Patient50_Sample6

description: COUNTS_TABLE_RAW6: P50_S6


title: Patient50_Sample3

description: COUNTS_TABLE_RAW6: P50_S3


title: mnp-20-0132

value: Medulloblastoma, non-WNT/SHH

value: male


title: Patient59_Sample14

description: COUNTS_TABLE_RAW13: P59_S14


title: Patient59_Sample9

description: COUNTS_TABLE_RAW7: P59_S9


title: Patient50_Sample1

description: COUNTS_TABLE_RAW6: P50_S1


title: mnp-20-0426

value: Choroid plexus papilloma

value: parietal lobe


title: Patient49_Sample2

description: COUNTS_TABLE_RAW3: P49_S2


title: Patient59_Sample10

description: COUNTS_TABLE_RAW7: P59_S10


title: Patient59_Sample7

description: COUNTS_TABLE_RAW7: P59_S7


title: Patient49_Sample1

description: COUNTS_TABLE_RAW3: P49_S1


title: Patient49_Sample3

description: COUNTS_TABLE_RAW3: P49_S3


title: mnp-20-1440

value: Germinoma

value: hypothalamus


title: mnp-20-0753

value: Pilocytic Astrocytoma

value: temporal lobe


title: mnp-20-1354

value: female

value: cerebellum


title: Patient49_Sample5

description: COUNTS_TABLE_RAW3: P49_S5


title: Patient59_Sample6

description: COUNTS_TABLE_RAW7: P59_S6


title: Patient58_Sample2

description: COUNTS_TABLE_RAW7: P58_S2


title: Patient59_Sample13

description: COUNTS_TABLE_RAW13: P59_S13


title: mnp-20-1251

value: Dysembryoplastic neuroepithelial tumor (DNET)

value: parietal lobe, occipital lobe


title: mnp-20-1122

value: FFPE tissue

value: Atypical teratoid/rhabdoid tumor (AT/RT)


title: Patient50_Sample2

description: COUNTS_TABLE_RAW6: P50_S2

value: nasopharyngeal samples


title: Patient48_Sample9

description: COUNTS_TABLE_RAW2: P48_S9


title: Patient57_Sample8

description: COUNTS_TABLE_RAW7: P57_S8


title: Patient57_Sample9

description: COUNTS_TABLE_RAW7: P57_S9


title: Patient58_Sample1

description: COUNTS_TABLE_RAW7: P58_S1


title: mnp-20-1250

value: Anaplastic ganglioglioma


title: mnp-20-1370


title: Patient48_Sample7

description: COUNTS_TABLE_RAW2: P48_S7


title: Patient48_Sample11

description: COUNTS_TABLE_RAW2: P48_S11


title: Patient48_Sample8

description: COUNTS_TABLE_RAW2: P48_S8


title: Patient59_Sample8

description: COUNTS_TABLE_RAW7: P59_S8


title: Patient48_Sample10

description: COUNTS_TABLE_RAW2: P48_S10


title: mnp-20-0990


title: mnp-20-1210


title: Patient48_Sample6

description: COUNTS_TABLE_RAW2: P48_S6


title: Patient55_Sample12

description: COUNTS_TABLE_RAW11: P55_S12


title: Patient56_Sample2

description: COUNTS_TABLE_RAW9: P56_S2


title: Patient56_Sample1

description: COUNTS_TABLE_RAW9: P56_S1


title: mnp-20-0318

value: Descriptive diagnosis


title: Patient48_Sample5

description: COUNTS_TABLE_RAW2: P48_S5


title: Patient48_Sample3

description: COUNTS_TABLE_RAW2: P48_S3


title: Patient48_Sample2

description: COUNTS_TABLE_RAW2: P48_S2


title: Patient55_Sample11

description: COUNTS_TABLE_RAW11: P55_S11


title: Patient48_Sample4

description: COUNTS_TABLE_RAW2: P48_S4


title: mnp-20-1508

value: Embryonal tumor with multilayered rosettes (ETMR)

value: occipital lobe


title: Patient56_Sample3

description: COUNTS_TABLE_RAW9: P56_S3


title: Venus negative, scRNA-seq

city: Milwaukee

first: Yi-Guang

last: Chen

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreatic islets

extract_protocol:
Pancreata from 9-12-week-old NOD.Il2V/+ female mice were inflated using a 30-gauge needle by injecting 3-5 mL of HBSS containing 0.5 U/mL collagenase P solution and 10 μg/mL DNase into the bile duct. The inflated pancreas was digested at 37°C for 15 min. Digested pancreata were washed three times with 10 mL of HBSS containing 2% FBS. Each individual pancreas was then suspended in 5 mL complete RPMI 1640.  Islets were visualized under a dissecting microscope and hand-picked.  Pelleted islets were suspended in 200 μL of enzyme free cell dissociation buffer.  Cells were then washed with 500 μL of HBSS, resuspended in RPMI 1640. Islet cells were stained with antibodies for CD45.1, CD4, CD8, CD11c, and CD19, and sorted into Venus+ and Venus- CD4 T cells on a FACSAria III (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: pancreatic islets

value: CD4 T cells

tag: age

value: 9-12 weeks

tag: strain

tag: group

value: Venus negative

tag: Sex


title: Patient48_Sample1

description: COUNTS_TABLE_RAW2: P48_S1

tag: tissue


title: Patient55_Sample10

description: COUNTS_TABLE_RAW11: P55_S10

tag: subject


title: Patient46_Sample10

description: COUNTS_TABLE_RAW2: P46_S10

tag: geographic location


title: Venus positive, scRNA-seq

description: 10x Genomics

value: Venus positive


title: Patient55_Sample13

description: COUNTS_TABLE_RAW12: P55_S13

tag: collection date


title: IMPA5

city: Chengdu

first: changsheng

last: he

address: No. 16, South Section, 1st Ring Roa

institute: southwest minzu university

data_processing:
Find_circ and CIRI2 software
The raw reads obtained by sequencing were filtered with removed the low-quality reads to obtain clean reads
The expression statistics of known and novel circRNAs in each sample was performed, and the raw counts were normalized using TPM
Normalized expression level = (readCount*1,000,000) / libsize (libsize is the sum of the circRNA read count).
For small RNA libraries, we used novoaligen software to align clean reads with the miRBase database to identify known miRNAs, and used mirDeep software to predict Novel miRNAs
Supplementary files format and content: Novoaligen and samtools software for quantitative analysis, using RPM (reads per million) for standardization

organism: Capra hircus

source_name: intramuscular fat

extract_protocol:
Total RNA of IMPA and IMA was isolated using TRIzol reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA concentrations were quantified using NanoDrop spectrophotometer and Agilent 2100 Bioanalyzer.

value: intramuscular fat

value: intramuscular preadipocytes

value: WT

tag: treatment

value: adipogenic differentiation

value: Day 0


title: Patient55_Sample9

description: COUNTS_TABLE_RAW11: P55_S9


title: T2DM_Mac_D7_rHDL_rep3_S50

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
RNA-Seq reads were first trimmed to remove low-quality bases, poly(A) and Illumina adapter using cutadapt (version 2.8).
Subsequently, the reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with the mm10 mouse genome and the STAR aligner for read mapping and the Ensembl GRCm38 release 93 gene annotations for counting reads in transcripts. The following gene biotypes were retained in the gene expression matrix: protein coding, lincRNA and antisense.
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA was isolated from FACS sorted ECs and Macrophagess from ischemic muscles using Arcturus PicoPure RNA isolation Kit (Applied Biosystems)
Lexogen QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) was used to prepare 3′ RNA-Seq libraries. The double stranded DNA concentrations were quantified using a 5200 Fragment Analyzer (Part # M5310AA, Agilent Technologies), which gave similar concentrations for each sample that ranged from 1.7 to 4.3 ng/ μL. The molar concentration of cDNA molecules in the individual libraries was calculated from the DNA concentration and the region average size. Aliquots containing an equal number of nmoles of molecules from each library were pooled to give a pooled library with a concentration of 10 nM molecules. After library preparation, libraries were pooled and sequenced using single-end sequencing with 75 bp reads on an Illumina NextSeq500 instrument (Illumina, San Diego, CA).

treatment_protocol: Unilateral hindlimb ischemia was induced by ligating femoral artery proximal to the bifurcation of superficial and deep femoral artery in control and type 2 diabetic mice. Mice were  were administered with reconstituted ApoA-I nanoparticles with phosphatidyl serine core (rHDL) intravenously starting 2 days post-HLI with doses every 2 days until scarification with Saline injections serving as controls. Ishcemic muscle macrophages and endothelial cells were FACS sorted at 3 and 7 days after  ischemia induction.

value: IGF-II/LDLR-/-ApoB100/100 , with C57BL/6J background

value: reconstituted HDL (rHDL)-ApoA-I

value: Ischemic Macrophages

tag: time point

value: 7 days post femoral artery ligation

tag: replicate

tag: disease state

value: Diabetic


title: T2DM_Mac_D7_rHDL_rep2_S49


title: IMPA4


title: Patient46_Sample8

description: COUNTS_TABLE_RAW2: P46_S8

value: nasopharyngeal samples


title: Patient55_Sample7

description: COUNTS_TABLE_RAW11: P55_S7


title: Patient55_Sample8

description: COUNTS_TABLE_RAW12: P55_S8


title: IMPA3


title: Patient55_Sample6

description: COUNTS_TABLE_RAW12: P55_S6


title: T2DM_Mac_D7_rHDL_rep1_S48


title: IMPA2


title: Patient46_Sample9

description: COUNTS_TABLE_RAW2: P46_S9


title: T2DM_Mac_D3_rHDL_rep3_S44

value: 3 days post femoral artery ligation


title: Patient54_Sample7

description: COUNTS_TABLE_RAW9: P54_S7


title: Patient46_Sample7

description: COUNTS_TABLE_RAW2: P46_S7


title: Patient54_Sample1

description: COUNTS_TABLE_RAW9: P54_S1


title: Patient46_Sample6

description: COUNTS_TABLE_RAW2: P46_S6


title: T2DM_Mac_D3_rHDL_rep2_S43


title: Patient46_Sample5

description: COUNTS_TABLE_RAW2: P46_S5


title: IMA5

value: intramuscular adipocytes

value: Day 3


title: Hdac1 vs WT replicate 4

type: RNA

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Biological replicate 4 of 4. WT or Hdac1 mutant were harvest at 3rd instar stage

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Hi-RPM Gene Expression Hybridization Kit,) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Gene Expression Wash Buffer Kit and dry.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Drosophila melanogaster

source_name: Oregon-R Wild type

label_protocol: 15 µg of total RNA were primed with 2 µl of 2.5 µg/µl anchored Oligo-(dT)20 primer at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen).  After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min. to degrade RNA. Neutralize the hydrolysis reaction by adding 25μL 1M HEPES pH 7.4. After clean by QIAquick(Qaigen), cDNA were elute from column by 60 μl 0.1M NaHCO3 pH 9.0.  Add elute into a tube contain Alexa 555 or 647 NHS ester. Couple the dye at room temperature in the dark for 60-90 min. Stop the reaction by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Immediately purify the labeled cDNA through QIAquick column.

growth_protocol: Fly grew at 25 degree C, harvest at 3rd instar stage

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
After DNaseI treatment, RNA were purified by RNeasy kit (Qiagene)

tag: background strain

value: Oregon-R

tag: genotype/variation

value: Wild type

tag: Stage

value: 3rd instar larvae

label: Alexa Fluor 647

source_name: Oregon-R Hdac1 mutant


title: T2DM_Mac_D3_rHDL_rep1_S42

tag: cell type


title: Patient53_Sample5

description: COUNTS_TABLE_RAW7: P53_S5


title: Patient46_Sample4

description: COUNTS_TABLE_RAW2: P46_S4


title: Hdac1 vs WT replicate 3

description: Biological replicate 3 of 4. WT or Hdac1 mutant were harvest at 3rd instar stage


title: Hdac1 vs WT replicate 2

description: Biological replicate 2 of 4. WT or Hdac1 mutant were harvest at 3rd instar stage


title: T2DM_EC_D7_rHDL_rep3_S38

value: Ischemic Endothelial cells


title: IMA4

value: intramuscular fat

tag: genotype

tag: time


title: Hdac1 vs WT replicate 1

description: Biological replicate 1 of 4. WT or Hdac1 mutant were harvest at 3rd instar stage


title: Patient46_Sample3

description: COUNTS_TABLE_RAW2: P46_S3


title: Patient52_Sample6

description: COUNTS_TABLE_RAW7: P52_S6


title: Patient46_Sample1

description: COUNTS_TABLE_RAW2: P46_S1


title: IMPA1

value: intramuscular preadipocytes

value: WT


title: T2DM_EC_D7_rHDL_rep1_S36

tag: strain


title: IMA1

value: adipogenic differentiation


title: T2DM_EC_D3_rHDL_rep3_S31

value: IGF-II/LDLR-/-ApoB100/100 , with C57BL/6J background


title: Patient52_Sample4

description: COUNTS_TABLE_RAW7: P52_S4


title: Patient52_Sample5

description: COUNTS_TABLE_RAW7: P52_S5


title: IMA3


title: Patient45_Sample3

description: COUNTS_TABLE_RAW3: P45_S3


title: T2DM_EC_D3_rHDL_rep4_S32

value: reconstituted HDL (rHDL)-ApoA-I


title: Patient46_Sample2

description: COUNTS_TABLE_RAW2: P46_S2


title: IMA2


title: Patient45_Sample2

description: COUNTS_TABLE_RAW3: P45_S2


title: T2DM_EC_D7_rHDL_rep2_S37


title: Patient53_Sample2

description: COUNTS_TABLE_RAW7: P53_S2


title: Patient52_Sample2

description: COUNTS_TABLE_RAW7: P52_S2


title: T2DM_EC_D3_rHDL_rep2_S30


title: Patient52_Sample3

description: COUNTS_TABLE_RAW7: P52_S3


title: T2DM_AEC_D7_rHDL_rep4_S25

source_name: Adductor Muscle

value: Arterial Endothelial cells


title: Patient48_Sample21

description: COUNTS_TABLE_RAW10: P48_S21


title: RNA-trNK-unstim-2

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

data_processing:
For RNA-Seq, sequence reads were mapped to the mouse (mm10) genome with hisat2 (2.1.0) with default settings and we kept one hit if multiple reads were mapped to the same position for each RNA-Seq library.For each RNA-Seq sample, gene expression was quantified using featureCounts function in Subread package.
For ATAC-Seq, quality trimming and primer removal of ATAC-Seq reads were performed with Trimmomatic, using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned against mm10 using Bowtie2. The aligned reads were sorted using samtools, and duplicates were marked and removed using PICARD. ATAC-seq coverage tracks were obtained using bamCoverage from Deeptools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for RNA-Seq samples
Supplementary files format and content: bigWig file for each ATAC-Seq sample

source_name: RNA,Liver trNK,unstim

extract_protocol:
RNA was harvested using Single Cell Full Length mRNA-Amplification Kit (Vazyme). 5ng total RNA was used for the construction of sequencing libraries. DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)
RNA libraries for RNA-seq or DNA libraries for ATAC-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)

treatment_protocol: Single-cell suspension of liver was centrifuged and resuspended in RPMI 1640 containing 10% FBS. Then, the cells were kept unstimulated or stimulated by phorbol 12-myristate 13-acetate (PMA, 50 ng/mL) and ionomycin (1 μg/mL), in presence or absence of IL-21 (20 ng/mL) or IL-18 (10 ng/mL), for 5 hours at 37 °C in 5% CO2 atmosphere. A protein transport inhibitor Brefeldin A (Invitrogen) was added after the first hour.

value: liver

value: trNK

value: No treatment


title: Patient52_Sample1

description: COUNTS_TABLE_RAW7: P52_S1

value: nasopharyngeal samples


title: ATAC-trNK-PI-ATAC

library_source: genomic

source_name: ATAC,Liver trNK,PI21

value: 50 ng/mL PMA, 1 ug/mL ionomycin, 20 ng/mL IL-21


title: Patient45_Sample1

description: COUNTS_TABLE_RAW3: P45_S1


title: Patient45_Sample4

description: COUNTS_TABLE_RAW3: P45_S4


title: ATAC-trNK-unstim-ATAC

source_name: ATAC,Liver trNK,unstim


title: RNA-trNK-unstim-1


title: T2DM_AEC_D7_rHDL_rep3_S24

value: 7 days post femoral artery ligation

value: Diabetic


title: Patient48_Sample20

description: COUNTS_TABLE_RAW10: P48_S20


title: ATAC-trNK-PI21-ATAC

source_name: ATAC,Liver trNK,PI

value: 50 ng/mL PMA, 1 ug/mL ionomycin


title: Patient44_Sample6

description: COUNTS_TABLE_RAW1: P44_S6


title: Patient44_Sample5

description: COUNTS_TABLE_RAW1: P44_S5


title: RNA-trNK-PI21-2

source_name: RNA,Liver trNK,PI21


title: T2DM_AEC_D7_rHDL_rep2_S23


title: Patient48_Sample18

description: COUNTS_TABLE_RAW10: P48_S18


title: T2DM_AEC_D7_rHDL_rep1_S22


title: T2DM_EC_D3_rHDL_rep1_S29

value: 3 days post femoral artery ligation


title: Patient44_Sample3

description: COUNTS_TABLE_RAW1: P44_S3


title: Patient48_Sample19

description: COUNTS_TABLE_RAW10: P48_S19


title: Patient48_Sample17

description: COUNTS_TABLE_RAW7: P48_S17


title: Patient44_Sample2

description: COUNTS_TABLE_RAW1: P44_S2


title: Patient48_Sample16

description: COUNTS_TABLE_RAW7: P48_S16


title: T2DM_AEC_D7_PBS_rep2_S17

value: PBS


title: RNA-trNK-PI18-2

source_name: RNA,Liver trNK,PI18

value: 50 ng/mL PMA, 1 ug/mL ionomycin, 10 ng/mL IL-18


title: Patient44_Sample1

description: COUNTS_TABLE_RAW1: P44_S1

source_name: nasopharyngeal samples


title: RNA-trNK-PI-2

source_name: RNA,Liver trNK,PI


title: T2DM_AEC_D7_PBS_rep3_S18


title: RNA-trNK-PI-1


title: RNA-trNK-PI21-1


title: T2DM_AEC_D7_PBS_rep1_S16


title: Patient44_Sample4

description: COUNTS_TABLE_RAW1: P44_S4


title: Patient43_Sample3

description: COUNTS_TABLE_RAW5: P43_S3


title: RNA-trNK-PI18-1


title: Patient48_Sample14

description: COUNTS_TABLE_RAW7: P48_S14


title: Patient43_Sample2

description: COUNTS_TABLE_RAW5: P43_S2


title: Patient43_Sample1

description: COUNTS_TABLE_RAW5: P43_S1


title: RNA-cNK-unstim-1

source_name: RNA,Liver cNK,unstim

value: cNK


title: Patient48_Sample13

description: COUNTS_TABLE_RAW7: P48_S13


title: RNA-cNK-unstim-2

value: WT


title: Patient42_Sample7

description: COUNTS_TABLE_RAW1: P42_S7


title: Patient48_Sample12

description: COUNTS_TABLE_RAW10: P48_S12


title: Patient34_Sample13

description: COUNTS_TABLE_RAW13: P34_S13


title: Patient42_Sample5

description: COUNTS_TABLE_RAW1: P42_S5


title: Patient42_Sample8

description: COUNTS_TABLE_RAW1: P42_S8


title: T2DM_AEC_D3_PBS_rep3_S6


title: Patient47_Sample2

description: COUNTS_TABLE_RAW9: P47_S2


title: Patient48_Sample15

description: COUNTS_TABLE_RAW7: P48_S15


title: RNA-cNK-PI21-2

source_name: RNA,Liver cNK,PI21


title: T2DM_AEC_D3_rHDL_rep3_S12


title: T2DM_AEC_D3_rHDL_rep1_S10


title: Patient42_Sample4

description: COUNTS_TABLE_RAW1: P42_S4


title: T2DM_AEC_D3_PBS_rep1_S4


title: T2DM_AEC_D3_rHDL_rep2_S11


title: Control_Mac_D7_rHDL_rep1_S45

value: Ischemic Macrophages

value: Normal


title: RNA-cNK-PI21-1


title: RNA-cNK-PI18-2

source_name: RNA,Liver cNK,PI18


title: RNA-cNK-PI18-1


title: Patient47_Sample1

description: COUNTS_TABLE_RAW9: P47_S1


title: T2DM_AEC_D3_PBS_rep2_S5

value: IGF-II/LDLR-/-ApoB100/100 , with C57BL/6J background


title: Patient42_Sample6

description: COUNTS_TABLE_RAW1: P42_S6


title: Control_Mac_D7_rHDL_rep2_S46

value: reconstituted HDL (rHDL)-ApoA-I


title: RNA-cNK-PI-2

source_name: RNA,Liver cNK,PI

value: liver


title: RNA-Uterus-trNK-2

source_name: RNA,Uterus,trNK

value: uterus

value: trNK


title: Patient34_Sample12

description: COUNTS_TABLE_RAW13: P34_S12

value: nasopharyngeal samples


title: Control_Mac_D7_rHDL_rep3_S47

source_name: Gastrocnemius muscle


title: Patient42_Sample3

description: COUNTS_TABLE_RAW1: P42_S3


title: Patient34_Sample11

description: COUNTS_TABLE_RAW13: P34_S11


title: Control_Mac_D3_rHDL_rep2_S40


title: RNA-cNK-PI-1


title: Patient42_Sample2

description: COUNTS_TABLE_RAW1: P42_S2


title: Control_Mac_D3_rHDL_rep3_S41


title: Patient28_Sample9

description: COUNTS_TABLE_RAW11: P28_S9


title: Patient28_Sample8

description: COUNTS_TABLE_RAW12: P28_S8


title: Patient28_Sample7

description: COUNTS_TABLE_RAW12: P28_S7


title: Patient16_Sample8

description: COUNTS_TABLE_RAW13: P16_S8


title: RNA-Uterus-cNK-1

source_name: RNA,Uterus,cNK

value: No treatment


title: Patient41_Sample1

description: COUNTS_TABLE_RAW5: P41_S1


title: RNA-Uterus-trNK-1


title: Control_EC_D7_rHDL_rep3_S35

value: Ischemic Endothelial cells

value: 7 days post femoral artery ligation


title: Control_Mac_D3_rHDL_rep1_S39


title: Control_EC_D7_rHDL_rep2_S34


title: Patient41_Sample2

description: COUNTS_TABLE_RAW5: P41_S2


title: Patient42_Sample1

description: COUNTS_TABLE_RAW1: P42_S1


title: Patient40_Sample4

description: COUNTS_TABLE_RAW1: P40_S4


title: RNA-Spleen-cNK-2

source_name: RNA,Spleen,cNK

value: spleen


title: Control_EC_D7_rHDL_rep1_S33


title: Patient40_Sample3

description: COUNTS_TABLE_RAW1: P40_S3


title: Patient40_Sample2

description: COUNTS_TABLE_RAW1: P40_S2


title: RNA-SGs-trNK-2

source_name: RNA,SGs,trNK

value: salivary glands


title: RNA-Uterus-cNK-2


title: Control_EC_D3_rHDL_rep3_S28

value: 3 days post femoral artery ligation


title: Patient40_Sample1

description: COUNTS_TABLE_RAW1: P40_S1


title: Patient16_Sample3

description: COUNTS_TABLE_RAW13: P16_S3


title: Patient16_Sample4

description: COUNTS_TABLE_RAW13: P16_S4


title: RNA-SGs-trNK-1


title: Patient16_Sample5

description: COUNTS_TABLE_RAW13: P16_S5


title: Control_EC_D3_rHDL_rep2_S27


title: RNA-SGs-cNK-2

source_name: RNA,SGs,cNK


title: Patient39_Sample5

description: COUNTS_TABLE_RAW3: P39_S5


title: Control_EC_D3_rHDL_rep1_S26


title: Patient16_Sample7

description: COUNTS_TABLE_RAW13: P16_S7


title: Patient16_Sample6

description: COUNTS_TABLE_RAW13: P16_S6


title: Patient16_Sample2

description: COUNTS_TABLE_RAW13: P16_S2


title: Patient39_Sample3

description: COUNTS_TABLE_RAW3: P39_S3


title: RNA-SGs-cNK-1


title: RNA-Spleen-cNK-1


title: Control_AEC_D7_rHDL_rep3_S21

source_name: Adductor Muscle

value: Arterial Endothelial cells


title: Patient16_Sample1

description: COUNTS_TABLE_RAW13: P16_S1


title: Patient39_Sample2

description: COUNTS_TABLE_RAW3: P39_S2


title: Control_AEC_D7_rHDL_rep2_S20


title: RNA-Liver-trNK-2

source_name: RNA,Liver,trNK


title: Control_AEC_D7_rHDL_rep1_S19


title: Patient39_Sample1

description: COUNTS_TABLE_RAW3: P39_S1


title: RNA-Liver-trNK-1


title: Patient11_Sample9

description: COUNTS_TABLE_RAW10: P11_S9


title: Patient11_Sample8

description: COUNTS_TABLE_RAW10: P11_S8


title: Control_AEC_D7_PBS_rep3_S15

value: PBS


title: Patient11_Sample7

description: COUNTS_TABLE_RAW10: P11_S7


title: Patient38_Sample9

description: COUNTS_TABLE_RAW1: P38_S9


title: Patient38_Sample7

description: COUNTS_TABLE_RAW1: P38_S7


title: Patient39_Sample4

description: COUNTS_TABLE_RAW3: P39_S4


title: RNA-Liver-cNK-1

source_name: RNA,Liver,cNK

value: cNK

value: WT


title: Patient38_Sample8

description: COUNTS_TABLE_RAW1: P38_S8


title: TABLE-seq_RNA30ng_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Bowtie2 (version 2.3.5.1) was used to map trimmed reads to the mouse reference genome mm9 and Tsin-H3.1-flag plasmid construct reference. PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES = true’ in cDNA data.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
BEDtools (version 2.92.2) and bedGraphToBigWig (version 4) (https://www.encodeproject.org/software/bedgraphtobigwig/) were used with the following parameters ‘genomecov --scaleFactor 10,000,00/(the number of reads mapped to mm9 or Tsin-H3.1-flag plasmid construct reference)’. Normalized signals were visualized in Integrative Genomics Viewer (IGV)  (version 2.6.3).
Assembly: mm9
Assembly: Tsin-H3.1-flag plasmid construct reference
Supplementary files format and content: BigWig files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample of TABLE-seq

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM beta-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). HEK293T cells were cultured in DMEM supplemented with 10% FBS and 1% antibiotic solution (penicillin/streptomycin). All cells were grown at 37 C and 5% CO2.

extract_protocol:
RNA extraction was performed by RNeasy Plus Mini Kit (Qiagen, Cat. #74134).
2 μl 100 μM 5ph_Tn5a and 2 μl 100 μM Tn5a_N6_invert_dT were added to 16 μl H2O. Samples were annealed by 95 C for 5 min and ramped to 25 C at 5 C/min. 1 μl Exo I, 3 μl 10X Exo I reaction buffer, and 6 μl H2O were added and incubated at 37 C for 30 min, followed by 80 C for 15 min. The annealed adaptors were purified by 2X of VAHTS DNA clean beads, eluted into 20 μl H2O, and stored at -20 C until usage.    10 μl tagmented ssDNA or cDNA was mixed with 2 μl annealed adaptors, 0.5 μl T4 DNA ligase (Takara, Cat. #2011A), 2 μl 10X ligation buffer, 2.5 μl 40% PEG6000, 3 μl H2O, and incubated at 20 C for 1 hour. The ligated DNA was purified by 0.8X VAHTS DNA clean beads and eluted into 10 μl H2O. The purified DNA was amplified by primers with sequencing indexes. 1 μl 10 μM forward primer, 1 μl 10 μM reverse primer, 8 μl DNA, and 10 μl 2X HIFI PCR Master Mix (NEB, Cat. #M0541L) were mixed and amplified at 72 C for 5 min, 98 C for 30 sec, 20 cycles of 98 C for 10 sec and 63 C for 10 sec, then 72 C for 1 min, 16 C to hold. PCR products were purified by 0.9X VAHTS DNA clean beads and eluted into 20 μl H2O. The concentrations of DNA were detected by Equalbit 1X dsDNA HS Working Solution (Vazyme, Cat. #121-01-AA). The libraries were sequenced on an Illumina NovaSeq platform with pair-end reads of 150 bp.
TABLE-seq

tag: genet type


title: Patient38_Sample6

description: COUNTS_TABLE_RAW1: P38_S6


title: Patient11_Sample6

description: COUNTS_TABLE_RAW10: P11_S6


title: Control_AEC_D3_rHDL_rep2_S8

value: Normal


title: TABLE-seq_RNA30ng_rep2


title: Control_AEC_D3_rHDL_rep1_S7


title: Control_AEC_D7_PBS_rep2_S14


title: Control_AEC_D3_rHDL_rep3_S9


title: Patient5_Sample20

description: COUNTS_TABLE_RAW10: P5_S20


title: Patient5_Sample16

description: COUNTS_TABLE_RAW10: P5_S16


title: Patient5_Sample17

description: COUNTS_TABLE_RAW10: P5_S17


title: Control_AEC_D7_PBS_rep1_S13


title: RNA-Liver-cNK-2


title: Patient38_Sample5

description: COUNTS_TABLE_RAW1: P38_S5


title: Patient38_Sample1

description: COUNTS_TABLE_RAW1: P38_S1


title: Control_AEC_D3_PBS_rep3_S3


title: Patient5_Sample18

description: COUNTS_TABLE_RAW10: P5_S18


title: Patient38_Sample3

description: COUNTS_TABLE_RAW1: P38_S3


title: Patient5_Sample19

description: COUNTS_TABLE_RAW10: P5_S19


title: Control_AEC_D3_PBS_rep2_S2


title: Patient38_Sample4

description: COUNTS_TABLE_RAW1: P38_S4


title: Patient4_Sample16

description: COUNTS_TABLE_RAW7: P4_S16


title: Patient4_Sample17

description: COUNTS_TABLE_RAW7: P4_S17


title: Control_AEC_D3_PBS_rep1_S1


title: Patient37_Sample3

description: COUNTS_TABLE_RAW1: P37_S3


title: Patient4_Sample15

description: COUNTS_TABLE_RAW7: P4_S15


title: Patient37_Sample2

description: COUNTS_TABLE_RAW1: P37_S2


title: Patient5_Sample15

description: COUNTS_TABLE_RAW10: P5_S15


title: AloPmouse.RepF.AA.Cmpd4w12wTerm.KT.30_S30

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

description:
S30
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

data_processing:
Base calling was done by bcl2fastq from Illumina.
Reads were mapped with Hisat2 (version 2.0.1-beta).
Counts were generated with featurecounts (1.4.4).
TPMs were generated using Sailfish (version 0.7.6).
All processing was wrapped together with bcbio 0.9.5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: combined.counts.txt: Tab-delimited text file includes counts.
Supplementary_files_format_and_content: combined.gene.sf.tpm.txt: Tab-delimited text file includes TPMs.

source_name: Dorsal skin (approx 50 mg), 8w Off Tx, Cmpd4w12wTerm

extract_protocol:
RNA was prepared according to a standard phenol-chloroform total RNA extraction method where skin samples were homogenized in Qiazol®, added chloroform, vortexed and centrifuged for phase separation. The RNA containing phase was ethanol precipitated and purified on an Applied Biosystems 6100 Nucleic Acid Prep Station.
RNA was diluted to 50ng/ul and used as input to create RNA libraries using TruSeq Stranded Total RNA with RiboGold depletion (Illumina, CA, USA) following standard instructions with the exception that no fragmentation of samples were made due to low RIN-values. Libraries were validated on the Fragment Analyzer platform (AATI, IA, USA) using standard sensitivity NGS analysis kit. Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. The pool was then sequenced using a High Output 2 x 76 bp kit on an Illumina NextSeq500.

treatment_protocol: 4 week daily oral servings for free eating.

tag: strain/background

tag: gender

value: Female

tag: age

value: approx 30w at termination

value: AA

tag: group

value: 8w Off Tx

value: Dorsal skin

tag: dose

value: 100 mg/kg po od

value: RepF


title: AloPmouse.RepE.AA.Cmpd4w12wTerm.KT.29_S29

description:
S29
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

tag: tissue

tag: treatment

value: RepE


title: Patient38_Sample2

description: COUNTS_TABLE_RAW1: P38_S2

source_name: nasopharyngeal samples

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: AloPmouse.RepA.AA.Cmpd4w12wTerm.KT.25_S25

description:
S25
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

tag: genotype/variation

tag: replicate

value: RepA


title: Patient4_Sample9

description: COUNTS_TABLE_RAW7: P4_S9


title: Patient4_Sample13

description: COUNTS_TABLE_RAW7: P4_S13


title: Patient37_Sample1

description: COUNTS_TABLE_RAW1: P37_S1


title: Patient36_Sample7

description: COUNTS_TABLE_RAW1: P36_S7


title: Patient36_Sample10

description: COUNTS_TABLE_RAW1: P36_S10


title: Patient4_Sample8

description: COUNTS_TABLE_RAW7: P4_S8


title: Patient36_Sample4

description: COUNTS_TABLE_RAW1: P36_S4


title: AloPmouse.RepB.AA.Cmpd4w12wTerm.KT.26_S26

description:
S26
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: RepB


title: Patient36_Sample8

description: COUNTS_TABLE_RAW1: P36_S8


title: Patient36_Sample3

description: COUNTS_TABLE_RAW1: P36_S3


title: Patient4_Sample14

description: COUNTS_TABLE_RAW7: P4_S14


title: AloPmouse.RepC.AA.Cmpd4w12wTerm.KT.27_S27

description:
S27
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: RepC


title: Patient36_Sample6

description: COUNTS_TABLE_RAW1: P36_S6


title: AloPmouse.RepF.AA.Cmpd4wNoTerm.KT.24_S24

description:
S24
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: Dorsal skin (approx 50 mg), Systemic JAKi, Cmpd4wNoTerm

value: Systemic JAKi


title: AloPmouse.RepC.AA.Cmpd4wNoTerm.KT.21_S21

description:
S21
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient36_Sample9

description: COUNTS_TABLE_RAW1: P36_S9


title: AloPmouse.RepD.AA.Cmpd4w12wTerm.KT.28_S28

description:
S28
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: RepD


title: Patient4_Sample12

description: COUNTS_TABLE_RAW7: P4_S12


title: AloPmouse.RepE.AA.Cmpd4wNoTerm.KT.23_S23

description:
S23
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AloPmouse.RepD.AA.Cmpd4wNoTerm.KT.22_S22

description:
S22
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient4_Sample6

description: COUNTS_TABLE_RAW7: P4_S6


title: Patient36_Sample2

description: COUNTS_TABLE_RAW1: P36_S2


title: Patient4_Sample10

description: COUNTS_TABLE_RAW7: P4_S10


title: AloPmouse.RepA.AA.Cmpd4wNoTerm.KT.19_S19

description:
S19
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient36_Sample5

description: COUNTS_TABLE_RAW1: P36_S5


title: Patient4_Sample11

description: COUNTS_TABLE_RAW7: P4_S11


title: AloPmouse.RepB.AA.Cmpd4wNoTerm.KT.20_S20

description:
S20
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AloPmouse.RepF.Ctrl.12w.KT.18_S18

description:
S18
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: Dorsal skin (approx 50 mg), Healthy, untreated

value: Ctrl

value: Healthy


title: Patient36_Sample1

description: COUNTS_TABLE_RAW1: P36_S1


title: Patient4_Sample7

description: COUNTS_TABLE_RAW7: P4_S7


title: Patient3_Sample9

description: COUNTS_TABLE_RAW7: P3_S9


title: AloPmouse.RepC.Ctrl.12w.KT.15_S15

description:
S15
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient35_Sample5

description: COUNTS_TABLE_RAW1: P35_S5


title: AloPmouse.RepD.Ctrl.12w.KT.16_S16

description:
S16
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient35_Sample6

description: COUNTS_TABLE_RAW1: P35_S6


title: AloPmouse.RepB.Ctrl.12w.KT.14_S14

description:
S14
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient2_Sample1

description: COUNTS_TABLE_RAW7: P2_S1


title: AloPmouse.RepA.Ctrl.12w.KT.13_S13

description:
S13
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Patient4_Sample4

description: COUNTS_TABLE_RAW7: P4_S4


title: Patient4_Sample5

description: COUNTS_TABLE_RAW7: P4_S5


title: AloPmouse.RepF.AA.Vec12w.KT.06_S6

description:
S6
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

source_name: Dorsal skin (approx 50 mg), Alopecia, untreated

value: Alopecia


title: Patient3_Sample7

description: COUNTS_TABLE_RAW7: P3_S7


title: AloPmouse.RepE.Ctrl.12w.KT.17_S17

description:
S17
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: Female


title: Patient3_Sample8

description: COUNTS_TABLE_RAW7: P3_S8


title: Patient35_Sample4

description: COUNTS_TABLE_RAW1: P35_S4


title: Patient34_Sample10

description: COUNTS_TABLE_RAW3: P34_S10


title: Patient3_Sample10

description: COUNTS_TABLE_RAW7: P3_S10


title: Patient35_Sample2

description: COUNTS_TABLE_RAW1: P35_S2


title: Patient35_Sample3

description: COUNTS_TABLE_RAW1: P35_S3


title: Patient34_Sample9

description: COUNTS_TABLE_RAW3: P34_S9


title: Patient1_Sample13

description: COUNTS_TABLE_RAW12: P1_S13


title: Epithelium organoid, Smad2/3-LTF, A83-01, Rep 4

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads alignment and quantification of gene expression was performed using Salmon 1.4.0.
Read count extraction and normalization were performed using DEseq2 1.32.0.
Assembly: GRCm39
Supplementary files format and content: Comma-separated text file containing normalized counts values for each sample.

source_name: Endometrium

extract_protocol:
Total mRNA was extracted from the endometrial organoids of 4 different mice per genotype using the DirectZol kit from Zymo.
RNA was ensured to have a high quality RIN score and subjected to library preparation and sequencing using the Ultra Low Input Library Preparation Kit (SMART Seq v4, Takara, Inc)

value: Endometrium

tag: cell type

value: Epithelium

value: Smad2flox/flox; Smad3flox/flox-Ltfcre/+


title: Patient35_Sample1

description: COUNTS_TABLE_RAW1: P35_S1


title: Epithelium organoid, Smad2/3-LTF, A83-01, Rep 3

tag: genotype


title: Patient1_Sample14

description: COUNTS_TABLE_RAW12: P1_S14


title: Patient1_Sample11

description: COUNTS_TABLE_RAW12: P1_S11


title: Patient34_Sample8

description: COUNTS_TABLE_RAW3: P34_S8


title: Patient1_Sample12

description: COUNTS_TABLE_RAW11: P1_S12


title: AloPmouse.RepC.AA.Vec12w.KT.03_S3

description:
S3
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: approx 30w at termination

value: AA

value: Dorsal skin


title: AloPmouse.RepE.AA.Vec12w.KT.05_S5

description:
S5
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: RepE


title: Patient1_Sample10

description: COUNTS_TABLE_RAW11: P1_S10

value: nasopharyngeal samples


title: AloPmouse.RepD.AA.Vec12w.KT.04_S4

description:
S4
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: Epithelium organoid, Smad2/3-LTF, A83-01, Rep 1


title: Patient34_Sample7

description: COUNTS_TABLE_RAW3: P34_S7


title: Patient1_Sample9

description: COUNTS_TABLE_RAW12: P1_S9


title: Epithelium organoid, Smad2/3-LTF, A83-01, Rep 2


title: AloPmouse.RepB.AA.Vec12w.KT.02_S2

description:
S2
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt


title: AloPmouse.RepA.AA.Vec12w.KT.01_S1

description:
S1
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt

value: RepA


title: Patient34_Sample6

description: COUNTS_TABLE_RAW3: P34_S6


title: Patient34_Sample5

description: COUNTS_TABLE_RAW3: P34_S5


title: Patient1_Sample8

description: COUNTS_TABLE_RAW10: P1_S8


title: Epithelium organoid, Smad2/3-LTF, Control, Rep 4

value: DMSO


title: F4/80lowTAMs_melanoma-day21_rep2

city: New Haven

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

data_processing:
TruSeq technology supports massively parallel sequencing using a proprietary reversible terminator-based method that enables detection of single bases as they are incorporated into growing DNA strands. A fluorescently-labeled terminator is imaged as each dNTP is added and then cleaved to allow incorporation of the next base. Since all four reversible terminator-bound dNTPs are present during each sequencing cycle, natural competition minimizes incorporation bias.
After image acquisition, raw data is transferred from its local site to a High Performance Computing (HPC) cluster through an infrastructure developed by Yale’s HPC Resource Center. There, the data is transformed into sequence by means of Illumina’s Pipeline software package, which consists of three executables: Firecrest, Bustard, and Gerald.
Firecrest performs image analysis. For each raw TIF file, clusters are identified; intensities are extracted; X,Y positions are determined; and noise levels are calculated. Thereafter, images are filtered, and, in this way, clusters are sharpened, background noise is mitigated, and scale is adjusted.
Bustard performs base calling. Using the output from Firecrest, Bustard produces sequences of bases from each cluster and assigns each base a confidence level. It does so by deconvolving signal from each cluster and applying correction for cross-talk (the overlap between the frequency emissions of the fluorophores); and phasing and pre-phasing (the phenomenon whereby a molecule in a given cluster is ahead or behind its current incorporation cycle, respectively).
Gerald performs sequence analysis. Gerald filters low quality base calls based on user-defined criteria; aligns sequences to an elected reference genome; visualizes the results; and generates statistics, diagnostic quality control plots, and summary tables. ELAND (Efficient Large-Scale Alignment of Nucleotide Databases), a Gerald alignment program, can efficiently align for up to two errors up to 32mers from a reference genome; PhageAlign, another Gerald alignment program, can exhaustively align all possible alignments up to an arbitrary edit distance (PhageAlign is accordingly slow, and therefore only recommended for reference genomes less than, or equal to, 2-megabases).

growth_protocol: 0.5x106 YUMM1.7 melanoma cells were injected intradermally in C57Bl/6J female mice, and mice were not treated following tumor initiation. Tumors were harvested at day 21 and processed into single-cell suspension through enzymatic digestion, according to standard protocols.

extract_protocol:
Sorted cells were spinned down and lysed by resuspending in 1mL RLT buffer and RNA was extracted using RNeasy mini plus kit (Qiagen). 200ng-1ug of Purified total RNA suspended in nuclease-free H2O (15-25ul) was submitted per sample.
RNA quality control protocol: RNA had an OD260/280 ratio of 1.8-2 and an OD260/230 ratio of 1.8-2. RNA integrity was verified in an Agilent Technologies 2100 Bioanalyzer through an Eukaryote Total RNA Pico Series II assay. For this poly_A-based library preps, high-quality RNA had a bioanalyzer RIN score of 7 or higher.
https://www.illumina.com/systems/sequencing-platforms/miseq.html
https://medicine.yale.edu/keck/ycga/sequencing/illumina/9_21599_284_12501_v1.pdf

treatment_protocol: Tumor single-cell suspensions were stained for FACS sorting in a FACSAria instrument, and Live+CD45+CD11b+F480+ (F4/80high or F4/80low) cells were collected for RNA extraction.

tag: tissue of origin

value: intradermal YUMM1.7 murine melanoma

value: WT

tag: age at time of tumor induction

value: 8 w/o

tag: days post-tumor inoculation


title: Patient1_Sample7

description: COUNTS_TABLE_RAW10: P1_S7


title: Epithelium organoid, Smad2/3-LTF, Control, Rep 3


title: F4/80lowTAMs_melanoma-day21_rep3

tag: strain


title: Patient34_Sample4

description: COUNTS_TABLE_RAW3: P34_S4


title: Epithelium organoid, Smad2/3-LTF, Control, Rep 2


title: Patient34_Sample3

description: COUNTS_TABLE_RAW3: P34_S3


title: Epithelium organoid, Smad2/3-LTF, Control, Rep 1


title: Patient1_Sample6

description: COUNTS_TABLE_RAW10: P1_S6


title: F4/80lowTAMs_melanoma-day21_rep1

tag: gender


title: Epithelium organoid, Smad2/3-FF, A83-01, Rep 4

value: Smad2flox/flox; Smad3flox/flox


title: Patient34_Sample2

description: COUNTS_TABLE_RAW3: P34_S2


title: F4/80highTAMs_melanoma-day21_rep2


title: Patient34_Sample1

description: COUNTS_TABLE_RAW3: P34_S1


title: Patient1_Sample4

description: COUNTS_TABLE_RAW10: P1_S4


title: F4/80highTAMs_melanoma-day21_rep3


title: Epithelium organoid, Smad2/3-FF, A83-01, Rep 3


title: F4/80highTAMs_melanoma-day21_rep1


title: Patient33_Sample4

description: COUNTS_TABLE_RAW2: P33_S4


title: Epithelium organoid, Smad2/3-FF, A83-01, Rep 1


title: Patient Sample PS10 [Microbial reads]

city: ropar

first: srivatsava

last: naidu

state: punjab

address: bhara phool

department: biomedical engineering

country: India

institute: indian institute of technology ropar

description: processed data file: One_Codex_PS_Results.xlsx

data_processing:
Adapter removal pre-processing using Cutadapt
Human genome alignment using Bowtie2
miRBase (v. 22) for miRNAs alignments, and gencode (v. 19) annotation file for other RNA species alignments.
WG Rescue alignment using Bowtie2 and read counting using FeatureCount, differential expression analysis using RUVseq and DESeq2
Microbial species alignment using ONE CODEX platform
Genome_build: hg19
Supplementary_files_format_and_content: Text files-read counts, Excel sheet -microbial reads

extract_protocol:
Total RNA was isolated from cell-free saliva of healthy donors and OSCC patients using TRIzol method
Small RNA library was prepared using Ion Total RNA-Seq Kit v2.0 as per manufacturer's instructions

tag: subject status

value: oral squamous cell carcinoma patient

tag: organ

value: Oral cavity

tag: type of saliva

value: Unstimulated

tag: tissue/sample type

value: Saliva


title: Epithelium organoid, Smad2/3-FF, A83-01, Rep 2

tag: tissue

value: Endometrium

value: Epithelium

tag: treatment


title: Patient Sample PS8 [Microbial reads]


title: Epithelium organoid, Smad2/3-FF, Control, Rep 3


title: Patient33_Sample3

description: COUNTS_TABLE_RAW2: P33_S3

tag: subject

tag: geographic location


title: Patient33_Sample5

description: COUNTS_TABLE_RAW2: P33_S5

tag: collection date


title: Patient33_Sample1

description: COUNTS_TABLE_RAW2: P33_S1


title: Patient Sample PS9 [Microbial reads]


title: TABLE-seq_TN5_100ng_rep2


title: Patient32_Sample6

description: COUNTS_TABLE_RAW3: P32_S6


title: Patient Sample PS4 [Microbial reads]


title: Patient Sample PS5 [Microbial reads]


title: Patient33_Sample2

description: COUNTS_TABLE_RAW2: P33_S2


title: Patient1_Sample5

description: COUNTS_TABLE_RAW10: P1_S5


title: Patient32_Sample5

description: COUNTS_TABLE_RAW3: P32_S5


title: Patient32_Sample7

description: COUNTS_TABLE_RAW3: P32_S7


title: Patient 3, scRNAseq

city: Chongqing

first: Shen

last: Zhang

address: No. 288 Tianwen avenue, Nanan district

department: Obstetrics and Gynecology Department

institute: The Second Affiliated Hospital of Chongqing Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
After the biopsy, the endometrial tissues were processed immediately. The two-stage dissociation protocol was performed. Briefly, the tissues were washed with DMEM/F12 medium (Gibco) and subsequently minced into small pieces. Then, the minced tissues were dissociated in DMEM/F12 supplemented with 1% Penicillin-Streptomycin (Gibco, 15140122), 0.4 mg/mL Collagenase V (Sigma, C9263), 1.25 U/mL Dispase II (Sigma, D4693) at 37 °C for 1 h with agitation. The supernatant was collected as the stromal fibroblast-enriched suspension. The pellet was the glandular and luminal fragments, which was further dissociated in TrypLE Select (Gibco, 12563-011) at 37 °C for 20 min. The cells were collected as the epithelium-enriched portion.
Cell counting and quality control were performed following the manufacturer’s instructions. Then, the two portions were mixed and loaded into Chromium microfluidic chips (Chromium Next GEM Chip G Single Cell Kit, 10X Genomics) with 3’ chemistry and barcoded with a 10×Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed to generate barcoded cDNA. Next, sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) and Dynabeads™ MyOne™ SILANE (Life, 37005D) according to the manufacturer’s instructions. The single-cell libraries were sequenced in paired-end reads on a NovaSeq 6000 platform (Illumina).

tag: Sex

value: female

tag: fecundity

value: infertile

tag: disease state

value: recurrent implantation failure

tag: endometrial preparation

value: hormonal replacement therapy

tag: phase

value: mid-secretory


title: Patient 2, scRNAseq

description: 10x Genomics


title: Epithelium organoid, Smad2/3-FF, Control, Rep 1

tag: cell type

tag: genotype


title: Epithelium organoid, Smad2/3-FF, Control, Rep 2


title: Patient 1, scRNAseq

description: 10x Genomics


title: Patient Sample PS3 [Microbial reads]


title: Patient Sample PS2 [Microbial reads]


title: TABLE-seq_TN5_50ng_rep2


title: Patient Sample PS1 [Microbial reads]


title: TABLE-seq_TN5_25ng_rep2


title: Patient Sample PS7 [Microbial reads]


title: Healthy cohort HC22 [Microbial reads]

description: processed data file: One_Codex_Results_HC.xlsx

source_name: Saliva_Healthy control

value: Healthy control


title: TABLE-seq_TN5_50ng_rep1


title: TABLE-seq_TN5_25ng_rep1


title: Patient32_Sample2

description: COUNTS_TABLE_RAW3: P32_S2

value: nasopharyngeal samples


title: TABLE-seq_TN5_100ng_rep1


title: Healthy cohort HC15 [Microbial reads]


title: Patient31_Sample5

description: COUNTS_TABLE_RAW3: P31_S5


title: Patient32_Sample3

description: COUNTS_TABLE_RAW3: P32_S3


title: Healthy cohort HC21 [Microbial reads]


title: Patient31_Sample4

description: COUNTS_TABLE_RAW3: P31_S4


title: Healthy cohort HC12  [Microbial reads]


title: Patient31_Sample6

description: COUNTS_TABLE_RAW3: P31_S6


title: Patient Sample PS9

description: processed data file: LincRNA_matrix_file.txt, miRNA_matrix_file.txt, Protein_coding_matrix_file.txt, Total_transcripts_matrix_file.txt


title: TABLE-seq_37C15min_rep2


title: TABLE-seq_37C30min_rep1


title: TABLE-seq_37C5min_rep2


title: Patient32_Sample1

description: COUNTS_TABLE_RAW3: P32_S1


title: TABLE-seq_37C30min_rep2


title: Healthy cohort HC18 [Microbial reads]


title: Patient31_Sample3

description: COUNTS_TABLE_RAW3: P31_S3


title: Patient31_Sample2

description: COUNTS_TABLE_RAW3: P31_S2


title: Patient32_Sample4

description: COUNTS_TABLE_RAW3: P32_S4


title: Patient31_Sample1

description: COUNTS_TABLE_RAW3: P31_S1


title: Patient Sample PS10


title: TABLE-seq_37C15min_rep1


title: Patient Sample PS8


title: TABLE-seq_37C5min_rep1


title: TABLE-seq_16C30min_rep2


title: Patient Sample PS7


title: Patient30_Sample2

description: COUNTS_TABLE_RAW5: P30_S2


title: TABLE-seq_16C30min_rep1


title: Patient Sample PS4


title: Patient Sample PS5


title: Patient30_Sample1

description: COUNTS_TABLE_RAW5: P30_S1


title: Patient29_Sample2

description: COUNTS_TABLE_RAW5: P29_S2


title: Patient Sample PS2


title: Patient Sample PS3


title: TABLE-seq_16C15min_rep2


title: TABLE-seq_16C15min_rep1


title: Patient Sample PS1


title: Healthy cohort HC22


title: Patient28_Sample4

description: COUNTS_TABLE_RAW5: P28_S4


title: Patient28_Sample5

description: COUNTS_TABLE_RAW5: P28_S5


title: TABLE-seq_RNA300pg_rep1


title: TABLE-seq_RNA300pg_rep2


title: Healthy cohort HC18


title: Patient28_Sample2

description: COUNTS_TABLE_RAW5: P28_S2


title: Healthy cohort HC12


title: Patient28_Sample1

description: COUNTS_TABLE_RAW5: P28_S1


title: TABLE-seq_RNA3ng_rep2


title: Patient27_Sample6

description: COUNTS_TABLE_RAW2: P27_S6


title: TABLE-seq_RNA30pg_rep2


title: TABLE-seq_16C5min_rep2


title: Patient28_Sample6

description: COUNTS_TABLE_RAW5: P28_S6


title: Healthy cohort HC21


title: TABLE-seq_RNA30pg_rep1


title: Patient27_Sample5

description: COUNTS_TABLE_RAW2: P27_S5


title: TABLE-seq_16C5min_rep1


title: TABLE-seq_RNA3ng_rep1


title: Patient27_Sample4

description: COUNTS_TABLE_RAW2: P27_S4


title: TABLE-seq_RNA300ng_rep2


title: Patient28_Sample3

description: COUNTS_TABLE_RAW5: P28_S3


title: LC873

city: Stanford

first: Gabor

last: Boross

state: CA

address: 450 Serra Mall

institute: Stanford University

description: barcode region of lentiviral backbones from genomic DNA from bulk tumor-bearing lungs were PCR-amplified and high-throughput DNA sequenced

library_source: other

data_processing:
For genomic barcoded DNA, the sgIDs (specific for given guideRNA and so genotype of the tumor) and barcodes (specific to tumor) were identified from fastq files and tumor size (cell number) was calculated by normalizing the number of reads to  three benchmarks “spike-in” cell lines with custom R and python scripts.
Assembly: mm10
Supplementary files format and content: The oncogene_negative_fitness_landscape_LUAD_tumor_sizes.csv file contains all tumor sizes (number of cells) for all tumors/expansions. The mouse genotype, sample title, guideRNA are shown in comma separated text table.
Library strategy: Ultra-deep sequencing of DNA barcode amplicon

molecule: other

source_name: Autochthonous lung tumor

growth_protocol: Autochthonous lung tumors were initiated in mice below with Lenti-sgTSTriple-pool/Cre lentiviral pool  and harvested after 3 months.  KrasLSL-G12D;T (KT)  R26LSL-Tomato;H11LSL-Cas9 (TC)  Lkb1f/f;TC  (Lkb1;TC)  Keap1f/f;TC (Keap1;TC)

extract_protocol:
Following homogenization and overnight protease K digestion, genomicDNA was extracted from the lung lysates using standard phenol-chloroform and ethanolprecipitation methods.
Q5 High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amplify the sgID-BC region from 50 ng of DNA from dissected tumors or 32 μg of bulk lung genomic DNA. The unique dual-indexed primers used were Forward: AATGATACGGCGACCACCGAGATCTACAC- 8 nucleotides for i5 index-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-6 to 9 random nucleotides for increasing the diversity-GCGCACGTCTGCCGCGCTG and Reverse: CAAGCAGAAGACGGCATACGAGAT-6 nucleotides for i7 index-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-9 to 6 random nucleotides for increasing the diversity-CAGGTTCTTGCGAACCTCAT. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter, A63881) using a double size selection protocol. The concentration and quality of the purified libraries were determined using the Agilent High Sensitivity DNA kit (Agilent Technologies, 5067-121791801811821831841851861871881891901911921931941951961974626) on the Agilent 2100 Bioanalyzer (Agilent Technologies, G2939BA). The libraries were pooled based on lung weights to ensure even reading depth, cleaned up again using AMPure XP beads, and sequenced (read length 2x150bp) on the Illumina HiSeq 2500 platform (Admera Health Biopharma Services).

value: Autochthonous lung tumor


title: LC854


title: LC860


title: Patient27_Sample2

city: New York

first: Angelica

last: Galianese

address: 615 W 164th Street, Apt 21C

institute: Columbia University

description: COUNTS_TABLE_RAW2: P27_S2

data_processing:
single end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
paired end: For producing count tables: We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0).
For producing unmapped reads: Produced with Pandora (Abate et al., 2015; Wang et al). The Pandora workflow takes RNA-seq data as input and produces the annotated microbial reads present in the sample as outputs. The pipeline runs through five main modules: 1) mapping to the human host genome using STAR (Dobin et al., 2013) and bowtie2 (Langmead & Salzberg, 2012); 2) processing of the host-mapped reads with featureCounts (Liao et al., 2014)  to obtain the host gene expression profile; 3) de-novo assembly of host-subtracted short (2x100bp) reads using Trinity (Grabherr et al., 2011) to create long contiguous full-length transcripts (contigs); 4) contigs alignment to curated sets of NCBI sequences from viruses, bacteria, fungi and other eukaryotic parasites with BLAST (Altschul et al., 1990); and 5) filtering and parsing the BLAST results into a report specifying the detected microbial abundances in the sample.
Assembly: single end: NCBI/build37.2
Assembly: paired end: GRCh38
Raw counts provided for all samples

extract_protocol:
Nasopharyngeal swabs were collected from each participant using a minitip flock swab (VWR catalog no. 10755-196; Copan Diagnostics) and immediately placed in a 15 mL tube containing 2 mL of DNA/RNA Shield (Product no. R1100-250; Zymo). Samples were separated into two 1 mL aliquots, and stored at −80°C. After thawing, RNA extraction was done using Zymo Quick-RNA™ Microprep Kit RNA extraction kit (ZYMO, R1050) including the recommended on column DNase I treatment step for 15 min. An Agilent Bioanalyzer was used for quality control prior to library creation
For single end samples: RNA RIBOZERO 30M SE100. For paired end samples: RNA RIBOZERO 20M PE100. Then proceed with library construction using Illumina TruSeq  chemistry.


title: Healthy cohort HC15


title: LC845


title: Patient27_Sample3

description: COUNTS_TABLE_RAW2: P27_S3


title: Patient29_Sample1

description: COUNTS_TABLE_RAW5: P29_S1


title: TABLE-seq_unfrag_rep2

value: WT


title: TABLE-seq_unfrag_rep1


title: Patient27_Sample1

description: COUNTS_TABLE_RAW2: P27_S1


title: TABLE-seq_frag_rep2


title: LC863


title: TABLE-seq_frag_rep1


title: CM3119

value: KT


title: TABLE-seq_RNA300ng_rep1


title: Patient26_Sample3

description: COUNTS_TABLE_RAW5: P26_S3


title: Patient26_Sample4

description: COUNTS_TABLE_RAW5: P26_S4


title: CM3123


title: dUTP_based_rep2


title: dUTP_based_rep1


title: Mouse

city: xian

first: Cangang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
The 10x Genomics Cell Ranger (3.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Genome_build: Fish:GRCz11, Frog:Xenopus_laevis_v2, Mouse:GRCm38, Rat:Rnor_6.0, Pig:Sscrofa11, Monkey:Mmul_8, Human:GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices).

extract_protocol:
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted 7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Splenocytes were sorted from the spleens of  seven vertebrate species

value: Splenocytes

tag: strain


title: CM3042


title: Patient26_Sample2

description: COUNTS_TABLE_RAW5: P26_S2


title: prenatal valproic acid treatment rep4

city: Kaifeng

first: Yijie

address: Jinming Avenue

institute: Henan University

description: single cell

data_processing:
bcl2fastq Conversion Software version 2.19 was used to convert bcl files to fastq files
The fastq files of each sample were aligned to the mm10 genome assembly using the 10X genomics  software cellranger(version 3.1.0) with default parameters. The matrix of all samples were aggregated using 'cellranger aggr' command
The Seurat (version 3.2.2) was used to perform data normalization, batch effect removing, cell clustering and dimension reduction. Specifically, cells that contained fewer than 100 genes  or more than 10% mitochondrial transcripts were removed. The count of each gene was normalized to the sequencing depth of the cell, multiplied by a scale factor 10000 and log-transformed. The top 2000 variable genes were selected and PCA was performed on these variable genes. The first 30 PCA components were used for the UMAP dimension reduction to obtain a two-dimensional representation of the cell state. For clustering, we used FindClusters function with resolution 0.9.
Genome_build: mm10
Supplementary_files_format_and_content: each sample contain three files which generated by 'cellranger count' command, it's a sparse matrix that contain the gene UMI count of each cell
Supplementary_files_format_and_content: Autism_gene_count_matrix.tsv.gz  is a gzipped matrix table with filtered gene UMI counts for every gene and every cell

source_name: female hippocampus

extract_protocol:
the hippocampus were cut into pieces and transferred it to a 1.5 mL microcentrifuge tube with 2 mg/mL isolation solution, containing pronase (Sigma, Cat# P6911-1G) and 50 μg/mL DNaseІ (Sigma, cat. no. D5025) in 1 mL Hibernate A (Invitrogen, cat. no. A1247501)/B27 (Invitrogen, cat. no. 17504) medium (HABG). The tissue and solution were mixed for 30 min at 37℃ in a horizontal shaker at 200 rpm. After incubation, the tissue was gently triturated by polished tips, and the single cells were released. The purified cells were obtained by density gradient centrifugation at 800 g for 15 min, resuspended in 1x PBS (calcium and magnesium-free) containing 1% BSA, and then centrifuged at 200 g for 2 min. Single cells were concentrated and resuspended in the desired medium.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prenatal valproic acid treatment

value: hippocampus


title: CM3046


title: Patient25_Sample3

description: COUNTS_TABLE_RAW1: P25_S3


title: prenatal valproic acid treatment rep3

description: single cell


title: prenatal valproic acid treatment rep1

description: single cell

source_name: male hippocampus

value: male


title: CM3121


title: Patient25_Sample2

description: COUNTS_TABLE_RAW1: P25_S2


title: CM3117


title: Patient25_Sample4

description: COUNTS_TABLE_RAW1: P25_S4


title: prenatal valproic acid treatment rep2

description: single cell


title: LC866


title: Patient26_Sample5

description: COUNTS_TABLE_RAW5: P26_S5


title: CM3122


title: CM3063


title: Patient26_Sample1

description: COUNTS_TABLE_RAW5: P26_S1


title: CM3062


title: Patient24_Sample6

description: COUNTS_TABLE_RAW1: P24_S6


title: Patient25_Sample1

description: COUNTS_TABLE_RAW1: P25_S1


title: prenatal saline treatment rep4

description: single cell

value: prenatal saline treatment


title: prenatal saline treatment rep3

description: single cell


title: Patient24_Sample4

description: COUNTS_TABLE_RAW1: P24_S4


title: LC902

value: TC


title: prenatal saline treatment rep2

description: single cell


title: LC904


title: LC910


title: Patient24_Sample3

description: COUNTS_TABLE_RAW1: P24_S3


title: prenatal saline treatment rep1

description: single cell


title: Patient24_Sample1

description: COUNTS_TABLE_RAW1: P24_S1


title: Patient24_Sample5

description: COUNTS_TABLE_RAW1: P24_S5


title: LC846


title: Patient24_Sample2

description: COUNTS_TABLE_RAW1: P24_S2


title: RT2119


title: LC903


title: Patient23_Sample4

description: COUNTS_TABLE_RAW4: P23_S4


title: RT2106


title: RT2115


title: Patient23_Sample1

description: COUNTS_TABLE_RAW4: P23_S1


title: L_C3

first: Li

last: Shen

state: Zhejiang Province

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) with TopHat v2.0.14 coupled with Bowtie v2.1.0. The mapped reads were subjected to Cufflinks v2.2.1 with the reference annotation (UCSC gene models) to calculate the FPKM values of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: the processed data files contain the FPKM values of each gene (gene id, FPKM value)

source_name: mouse liver

growth_protocol: old mice with a standard diet after MDL-800 supplementation or a standard diet.

extract_protocol:
Mouse livers were directly lysed and used for cDNA synthesis using the SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 634936).
After amplification, the cDNA samples were fragmented using a Covaris M220 sonicator (Covaris). Sequencing libraries were made with the fragmented cDNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instructions (New England Biolabs, E7370).

value: liver

tag: diet

value: standard diet


title: Patient22_Sample5

description: COUNTS_TABLE_RAW3: P22_S5


title: L_C2


title: L_C1


title: RT2104


title: Patient23_Sample3

description: COUNTS_TABLE_RAW4: P23_S3


title: L_M1

value: standard diet after MDL-800 supplementation


title: L_M2


title: L_C4


title: LC907


title: L_M3


title: RT2117


title: Patient22_Sample4

description: COUNTS_TABLE_RAW3: P22_S4


title: Patient23_Sample2

description: COUNTS_TABLE_RAW4: P23_S2


title: Patient22_Sample3

description: COUNTS_TABLE_RAW3: P22_S3


title: S_hira_2

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to TAIR10 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: The expression levels (FPKM) of differentially expressed genes after shade treatment.

organism: Arabidopsis thaliana

source_name: 6-day-old white light-grown treated with 1 hr shade seedlings

growth_protocol: 6-day-old white light-grown Col-0 (WT), pif7, asf1ab, and hira seedlings treated with 1 hr shade.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: With 1 hr shade (R/FR=0.4) treatment

value: whole seedlings

tag: age

value: hira

value: shade


title: Patient22_Sample1

description: COUNTS_TABLE_RAW3: P22_S1


title: 10X_Bone_Marrow_Mouse_AML_T2_2

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
T2_N_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

data_processing:
ScRNA-seq alignment process was completed by cellranger(version 2.1.0)
Seurat V3 workflow
Genome_build: mm10 mouse genome references for mouse and hg19 human genome references
Supplementary_files_format_and_content: txt files with gene counts, rds files with annotation and umap information

source_name: AML_BM_T2_10X genomics

extract_protocol:
Preparation: Whole Bone Marrow (WBM) are isolated from mouse tibiae, femora and ilia leg bones by crushing in 2%FBS(PBS) buffer, add 1:1000 DNase1 and then translate into 15mL BD tube, centrifuge at 1200rpm, RT for 3min. Then discard the supernatant and add 3mL 1XACK lysis buffer to resuspend bone marrow pellet on ice for 3~5 min, and then add PBS (more than lysis buffer) to terminate lysis reaction, centrifuge at 1200rpm, RT for 3min. Discard the supernatant and then add 0.04% PBS-BSA buffer to resuspend cell pellet and then filtered through a 40μm cell strainer. More than 80% of the living cells in the sample and the density of living cells ranged from 600 to 1200 cells/μl was preferable. Sample quality is measured using Bio-rad TC20 automated cell counter.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform and modified SMART-seq2 protocol based on published previously (Fuchou Tang, 2010).

tag: strain background

tag: tissue type

value: AML

tag: time point

value: BM

tag: strategy

value: 10X genomics


title: S_hira_3

tag: tissue

tag: treatment


title: 10X_Bone_Marrow_Mouse_AML_T3_1

description:
T3-1L_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

source_name: AML_BM_T3_10X genomics


title: S_hira_1


title: Patient21_Sample5

description: COUNTS_TABLE_RAW5: P21_S5

value: nasopharyngeal samples

tag: subject

tag: geographic location

tag: collection date


title: 10X_Bone_Marrow_Mouse_AML_T1_1

description:
T1_L_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

source_name: AML_BM_T1_10X genomics


title: Patient21_Sample4

description: COUNTS_TABLE_RAW5: P21_S4


title: Patient22_Sample2

description: COUNTS_TABLE_RAW3: P22_S2


title: 10X_Bone_Marrow_Mouse_AML_T2_1

description:
T2_2R_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds


title: 10X_Bone_Marrow_Mouse_AML_T0

description:
T0_all_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

source_name: AML_BM_T0_10X genomics


title: Patient21_Sample2

description: COUNTS_TABLE_RAW5: P21_S2


title: 10X_Bone_Marrow_Mouse_AML_T3_2

description:
T3-2L_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds


title: Patient21_Sample3

description: COUNTS_TABLE_RAW5: P21_S3


title: 10X_Bone_Marrow_Mouse_Normal_1

description:
Normal_HSC_S1_L001_R1_001.fastq.gz
processed data file:
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_all.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_all_unspliced.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_Malignant_at_T3.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_PLC.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis.rds
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point_counts.csv
mmu_10X_scRNA_Landscape_of_leukemogenesis_tipping_point.rds
mmu_10X_scRNA_Landscape_of_Malignant_all_counts.csv
mmu_10X_scRNA_Landscape_of_Malignant_all.rds

source_name: Normal_BM__10X genomics

value: Normal


title: S_asf1ab_3


title: Patient21_Sample1

description: COUNTS_TABLE_RAW5: P21_S1


title: S_pif7_3