title: PHH, Control, Day2, B

city: Miami

first: Emmanuel

last: Thomas

state: Florida

address: 1550 NW 10th Ave Rm 119, Papanicalaou Bldg

department: Department of Pathology

institute: University of Miami Miller School of Medicine

data_processing:
Alignment, splice junction, and novel transcript identifications were performed using STAR aligner, with UCSC human  genome ver. hg38 and GENCODE gene annotation ver. GRCh38.p7 (GRCm38.p5) as references.
Feature Counts was used for counting number of reads per transcript. Post-alignment quality assessment was performed using Picard tools.
RStudio (v2021.09.1 build 372) software utilizing R environment v4.1.2 is used for post-DESeq2 analysis in plotting DEGs.
Assembly: hg38, GRCh38.p7
Supplementary files format and content: Gene count files include RPKM values for each sample with corresponding p-values and comparative fold-change between conditions. DESeq2 output gene count file in .xlsx spreadsheet format

source_name: Primary

growth_protocol: PHH cells derived from human patient liver resections were maintained in Power Media (Takara) supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA from cells were isolated using the RNeasy Mini Kit with DNase treatment (Qiagen, 74106). RNA was quantified using Qubit (Thermo Fischer Scientific) and RNA integrity (RIN) was analyzed using BioAnalyzer 2100 lab-on-chip (Agilent) for a RIN score >7.0. 1.3 ug of total RNA was used for the construction of sequencing libraries.
Stranded total-RNA RNA-Seq libraries were synthesized using Illumina TruSeq Total Stranded with RiboZero Gold ribosomal RNA depletion, following manufacturer's protocols. Resulting libraries were quantified and balanced using Qubit (Thermo Fischer Scientific), BioAnalyzer HS lab-on-chip (Agilent), and qPCR (Roche/Kapa).

treatment_protocol: Plated Primary Hepatocytes infected for 48 hours with HCV JFH-1 MOI = 1, or uninfected (Control)

value: Primary

value: Patient-Derived Primary Human Hepatocytes

value: WT

tag: treatment

value: Control; No Treatment

value: Day 2


title: PHH, Control, Day2, A

status: Public on Aug 19 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: time


title: Non-small cell lung cancer, 0.24 MG/KG, Collected -2 days relative to first dose (RNA_80859833_EQ9101590)

city: Houston

first: David

middle: S

last: Hong

state: TX

address: 1515 Holcombe Boulevard Unit 455

institute: University of Texas M.D. Anderson Cancer Center

description:
SUBJID: 80859833
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

data_processing:
Transcript levels were quantified by the Personalis ACE Cancer Transcriptome Analysis pipeline (Menlo Park, CA)
STAR version 2.4.2a-p1 was used to align reads to the US National Center for Biotechnology Information hs37d5 annotation 105 reference genome
Assembly: hs37d5 annotation 105 reference genome
Supplementary files format and content: comma-separated value files include TPM values for genes expressed in >5% of samples and had standard deviation >1 for expression in log2 TPM

source_name: tumor biopsy

extract_protocol:
AllPrep DNA/RNA FFPE Tissue Kit (QIAGEN)
SureSelect Target Enrichment Kit (Agilent) and TruSeq Rapid SBS (Illumina)

tag: disease state

value: Non-small cell lung cancer

value: utomilumab

tag: dose

tag: Stage

value: UNKNOWN

tag: response to_prior_therapy

value: REFRACTORY

tag: best objective_response

value: Stable disease

tag: tissue

value: tumor biopsy

tag: subjid


title: PHH, +HCV JFH-1, Day2, A

value: 48 hour HCV JFH-1; MOI = 1


title: DSGC, P12, HB9-GFP, down, rep6

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_5

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 v2.1.0. SAM files were converted to BAM files using SAMtools v1.3.1. Transcript abundance estimation and normalization were performed using the Cuffquant and Cuffnorm tools, respectively, in Cufflinks v2.2.1. Downstream analyses were performed using Monocle2 in R v3.5.1.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas were dissected in cold Hibernate A medium (BrainBits) lacking Ca2+, Mg2+, and phenol red. Retinas were dissociated in papain (Worthington, LS003126), 1.1 mM EDTA, and 5.5 mM Cysteine-HCl dissolved in Hibernate A (no Ca2+, Mg2+, or phenol red) for 30 min at 37°C. Cells were then incubated with Brilliant Violet 421-conjugated Anti-CD11b antibody (1:300; BioLegend, Catalog No. 101251) for 30 min at 4 C to label CD11b+ microglia, which can be CTB-Alexa 647+. Cells were incubated with propidium iodide to label dead cells. Single GFP+ CTB-Alexa 647+ CD11b– and GFP– CTB-Alexa 647+ CD11b– cells were sorted into individual tubes containing 3500 U/ml RNase inhibitor (New England Biolabs), 140 U/ml DNase (New England Biolabs), and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter, Miami, FL).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

value: Retina

value: ON-OFF DSGC

tag: age

tag: preferred direction

value: down


title: PHH, +HCV JFH-1, Day2, B


title: SKM-28z CAR-T cells, Day9 [sample1]

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke v1.5.2 (parameter- -l 15 -q 0.2 -n 0.05)
Trimmed sequence reads were mapped to hg19 using HISAT2 v2.0.4 (Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8)
Sequence reads were mapped to genes using Bowtie2
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited text files include TPM values as matrix file

source_name: PBMC

growth_protocol: PBMC was prepared using lymphoprep and stimulated with plate-coated anti-CD3 mAb and 100U/ml IL-2 in AIM-V medium supplemented with 10% AB serum.

extract_protocol:
On day 9 and 13, CAR positive cells were labelled with biotin-anti-mouse IgG (Jackson Laboratory) and streptavidin-PE and sorted on FACSAriaII cell sorter.
RNA was harvested using Rneasy mini kit (Qiagen). 0.4 ~ 2.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer's protocols.

treatment_protocol: Retrovirus supernatants for each CAR was obtained using Phoenix-Ampho packaging cell line and infected to activated PBMC using retronectin (Takara) following manufacturer's instruction.

value: PBMC

value: SKM-28z CAR-T cells

tag: Sex

value: male

value: Retrovirus-mediated CAR induction

value: Day 9


title: Non-small cell lung cancer, 0.24 MG/KG, Collected 0 days relative to first dose (RNA_80852642_EQ9197552)

description:
SUBJID: 80852642
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: STAGE IV

value: Objective progression


title: DSGC, P10, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_11


title: DSGC, P10, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_8


title: Non-small cell lung cancer, 1.2 MG/KG, Collected 5 days relative to first dose (RNA_80853139_EQ9100835)

description:
SUBJID: 80853139
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Non-small cell lung cancer

value: 1.2 MG/KG


title: Melanoma, 1.2 MG/KG, Collected 36 days relative to first dose (RNA_80839833_EQ9192353)

description:
SUBJID: 80839833
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Melanoma

value: utomilumab

value: UNKNOWN


title: DSGC, P10, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_9


title: DSGC, P10, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_7


title: Melanoma, 1.2 MG/KG, Collected 8 days relative to first dose (RNA_80839833_EQ9405660)

value: REFRACTORY

value: tumor biopsy


title: DSGC, P10, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_6

value: Retina


title: DSGC, P8, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_2

value: ON DSGC

value: up


title: DSGC, P14, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_9

value: ON-OFF DSGC

value: down


title: Non-small cell lung cancer, 1.2 MG/KG, Collected  days relative to first dose (RNA_80849833_EQ9109368)

description:
SUBJID: 80849833
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Annotation is not available.

value: RELAPSED

value: Not Evaluable


title: Melanoma, 1.2 MG/KG, Collected 42 days relative to first dose (RNA_80839633_EQ9409814)

description:
SUBJID: 80839633
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: STAGE IV


title: DSGC, P8, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_1


title: DSGC, P8, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_0


title: Melanoma, 1.2 MG/KG, Collected 13 days relative to first dose (RNA_80835739_EQ9409536)

description:
SUBJID: 80835739
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Objective progression


title: Melanoma, 1.2 MG/KG, Collected 0 days relative to first dose (RNA_80024179_EQ9109063)

description:
SUBJID: 80024179
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Non-small cell lung cancer, 0.24 MG/KG, Collected 15 days relative to first dose (RNA_80835298_EQ9404950)

description:
SUBJID: 80835298
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Non-small cell lung cancer


title: DSGC, P8, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_2


title: Melanoma, 1.2 MG/KG, Collected 41 days relative to first dose (RNA_80832642_EQ9195919)

description:
SUBJID: 80832642
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: 1.2 MG/KG


title: DSGC, P8, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_0


title: Non-small cell lung cancer, 1.2 MG/KG, Collected 13 days relative to first dose (RNA_80831225_EQ9196696)

description:
SUBJID: 80831225
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Stable disease


title: Melanoma, 1.2 MG/KG, Collected 10 days relative to first dose (RNA_80832642_EQ9190255)

value: Melanoma

value: utomilumab


title: DSGC, P8, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_1


title: DSGC, P7, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_1


title: Non-small cell lung cancer, 1.2 MG/KG, Collected 26 days relative to first dose (RNA_80831097_EQ9402646)

description:
SUBJID: 80831097
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P7, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_2


title: Melanoma, 0.24 MG/KG, Collected 50 days relative to first dose (RNA_80830063_EQ9407657)

description:
SUBJID: 80830063
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: UNKNOWN

value: REFRACTORY


title: Melanoma, 0.24 MG/KG, Collected 50 days relative to first dose (RNA_80889833_EQ9105729)

description:
SUBJID: 80889833
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: STAGE IIIB

value: tumor biopsy


title: Melanoma, 0.24 MG/KG, Collected -5 days relative to first dose (RNA_80889833_EQ9104162)


title: DSGC, P7, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_1

value: Retina

value: ON DSGC


title: Non-small cell lung cancer, 0.24 MG/KG, Collected 2 days relative to first dose (RNA_80888993_EQ9108035)

description:
SUBJID: 80888993
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P7, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_0

value: down


title: Melanoma, 0.24 MG/KG, Collected 21 days relative to first dose (RNA_80830063_EQ9402545)


title: DSGC, P5, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_5

value: up


title: Melanoma, 1.2 MG/KG, Collected -168 days relative to first dose (RNA_80839633_EQ9407918)

description:
SUBJID: 80839633
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: RELAPSED


title: Non-small cell lung cancer, 1.2 MG/KG, Collected 1 days relative to first dose (RNA_80881225_EQ9108700)

description:
SUBJID: 80881225
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P7, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_0


title: Melanoma, 1.2 MG/KG, Collected -1 days relative to first dose (RNA_80800063_EQ9109819)

description:
SUBJID: 80800063
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P5, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_6


title: DSGC, P5, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_4


title: DSGC, P5, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_3


title: Melanoma, 1.2 MG/KG, Collected 21 days relative to first dose (RNA_80069965_EQ9105076)

description:
SUBJID: 80069965
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P5, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_1


title: Melanoma, 1.2 MG/KG, Collected -16 days relative to first dose (RNA_80069313_EQ9200553)

description:
SUBJID: 80069313
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P5, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_2


title: Melanoma, 1.2 MG/KG, Collected 0 days relative to first dose (RNA_80068993_EQ9109913)

description:
SUBJID: 80068993
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Melanoma, 1.2 MG/KG, Collected -4 days relative to first dose (RNA_80065739_EQ9406089)

description:
SUBJID: 80065739
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Melanoma, 0.24 MG/KG, Collected 1 days relative to first dose (RNA_80088197_EQ9191944)

description:
SUBJID: 80088197
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P5, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_0


title: DSGC, P5, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_5


title: Melanoma, 0.24 MG/KG, Collected 21 days relative to first dose (RNA_80061212_EQ9102038)

description:
SUBJID: 80061212
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Melanoma, 1.2 MG/KG, Collected 0 days relative to first dose (RNA_80088077_EQ9298784)

description:
SUBJID: 80088077
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Melanoma, 0.24 MG/KG, Collected 0 days relative to first dose (RNA_80087554_EQ9107277)

description:
SUBJID: 80087554
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: Melanoma, 0.24 MG/KG, Collected 56 days relative to first dose (RNA_80085298_EQ9292432)

description:
SUBJID: 80085298
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P4, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_2


title: Melanoma, 0.24 MG/KG, Collected 0 days relative to first dose (RNA_80086103_EQ9107268)

description:
SUBJID: 80086103
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Partial response


title: DSGC, P5, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_1


title: DSGC, P5, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_0


title: Melanoma, 0.24 MG/KG, Collected -7 days relative to first dose (RNA_80085298_EQ9203967)

value: STAGE IV


title: Melanoma, 0.24 MG/KG, Collected 104 days relative to first dose (RNA_80084533_EQ9208669)

description:
SUBJID: 80084533
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P4, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_2


title: Melanoma, 0.24 MG/KG, Collected 43 days relative to first dose (RNA_80081318_EQ9191377)

description:
SUBJID: 80081318
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Objective progression


title: DSGC, P4, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_3


title: Melanoma, 0.24 MG/KG, Collected 0 days relative to first dose (RNA_80084179_EQ9101098)

description:
SUBJID: 80084179
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression


title: DSGC, P4, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_0


title: DSGC, P4, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_1


title: Melanoma, 0.24 MG/KG, Collected 0 days relative to first dose (RNA_80081318_EQ9197586)


title: WholeIleum2-4

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
R2 Illumina reads were corrected using R-corrector
3’ polyA tails longer than 10 bases were trimmed using custom Perl scripts
R2 longer than 25 bases were re-paired using BBMap
Read were aligned using CellRanger v4.0.6
Genome_build: Sus Scrofa 11.1
Genome_build: Annotation build: Sus Scrofa 11.1.97
Supplementary_files_format_and_content: Raw count matrix (matrix.mtx), cell barcodes (barcode.tsv) & gene feature table (feature.tsv) files in gun zipped format

organism: Sus scrofa

source_name: Ileum

extract_protocol:
10X Chromium Single Cell Gene Expression assay with v2 chemistry was used to constuct single-cell cDNA libraries
Libraries were prepared for 2x100 paired end sequencing using standard Illumina protocols

value: Ileum

tag: tissue dissection

value: Whole cross section of ileum

tag: breed

value: Mixed-breed

value: Seven weeks

tag: gender

value: Male


title: DSGC, P4, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_0


title: DSGC, P5, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_4


title: DSGC, P5, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_2


title: DSGC, P5, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_3


title: Melanoma, 1.2 MG/KG, Collected 0 days relative to first dose (RNA_80086842_EQ9100890)

description:
SUBJID: 80086842
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

value: Melanoma

tag: treatment

value: utomilumab

value: 1.2 MG/KG

value: Not Evaluable


title: DSGC, P12, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_3

value: Retina

tag: cell type


title: DSGC, P12, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_4

value: ON DSGC

tag: genotype


title: WholeIleum2-2


title: WholeIleum2-1


title: DSGC, P12, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_2


title: WholeIleum2-3


title: DSGC, P4, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_1


title: DSGC, P12, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_0


title: DSGC, P12, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_5

value: down


title: WholeIleum1-1

value: Female


title: PP2-3

value: Ileum with Peyer's patches


title: DSGC, P12, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_4


title: WholeIleum1-3


title: PP2-4


title: DSGC, P12, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_1


title: WholeIleum1-2


title: DSGC, P12, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_2


title: DSGC, P12, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_5

value: up


title: DSGC, P12, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_0


title: PP2-1


title: PP1-4


title: PP2-2


title: DSGC, P10, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_5


title: DSGC, P10, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_6


title: PP1-3


title: PP1-2


title: DSGC, P10, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_3


title: PP1-1


title: DSGC, P10, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_4


title: DSGC, P12, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_3


title: PBMC2-4

source_name: Blood

value: Blood

value: PBMC


title: DSGC, P12, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_1


title: DSGC, P10, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_2


title: PBMC2-3


title: DSGC, P10, Spig1-GFP, up, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_1


title: PBMC2-2


title: DSGC, P10, Spig1-GFP, up, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_0


title: PBMC2-1


title: PBMC1-4


title: DSGC, P10, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_4


title: PBMC1-3


title: DSGC, P10, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_3


title: PBMC1-2


title: PBMC1-1


title: DSGC, P10, Spig1-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_0


title: DSGC, P8, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_4

value: ON-OFF DSGC


title: DSGC, P8, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_2


title: NoPP2-1

value: Ileum

value: Ileum without Peyer's patches


title: NoPP2-4

value: Mixed-breed

value: Seven weeks


title: DSGC, P8, HB9-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_5


title: DSGC, P8, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_3


title: NoPP2-2

value: Male


title: NoPP2-3


title: DSGC, P8, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_1


title: Nopp1-2


title: Nopp1-3


title: DSGC, P8, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_0


title: DSGC, P5, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_4


title: Nopp1-1


title: DSGC, P5, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_1


title: DSGC, P10, Spig1-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_2


title: DSGC, P10, Spig1-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_1


title: DSGC, P5, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_0


title: mature_leaves_Col-0_DNAmeth

city: Wuhan

first: Qiangwei

last: Zhou

state: Hubei

address: Hongshan district, shizishan #1

country: China

institute: Huazhong Agricultural university

library_source: genomic

data_processing:
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using Fastp
The cleaned reads were then mapped to the TAIR10 reference genome using BatMeth2
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: mature leaves Col-0

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photo-period, and two- and five-week-old plants were used for all experiments.

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturer's instructions.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

value: mature leaves

value: mature leaves from five-week

value: wild type


title: mature_leaves_ddcc_DNAmeth

source_name: mature leaves ddcc

value: ddcc


title: mature_leaves_met1-3_DNAmeth

source_name: mature leaves met1-3


title: young_shoots_met1-3_DNAmeth

source_name: young shoots met1-3

value: young shoots

value: young shoots from two-week old seedlings


title: DSGC, P5, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_2

value: Retina

value: down


title: DSGC, P4, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_6


title: young_shoots_ddcc_DNAmeth

source_name: young shoots ddcc


title: Nopp1-4

value: Female


title: young_shoots_Col-0_DNAmeth

source_name: young shoots Col-0


title: DSGC, P4, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_4


title: DSGC, P4, HB9-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_5


title: mature_leaves_met1-3_RNA_rep2

data_processing:
Trimmomatic fitered the raw reads
The cleaned reads were mapped to the TAIR10 reference genome using Hisat2.
gene expression was quantified using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...

extract_protocol:
Total RNA was isolated from the indicated tissues using a RNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 74904).
The RNA was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations.

value: mature leaves from five-week old


title: DSGC, P5, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_3


title: DSGC, P4, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_3


title: mature_leaves_met1-3_RNA_rep1


title: DSGC, P4, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_2


title: mature_leaves_ddcc_RNA_rep3


title: DSGC, P5, HB9-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_5


title: DSGC, P4, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_1


title: DSGC, P4, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_0


title: DSGC, P14, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_6


title: mature_leaves_met1-3_RNA_rep3


title: mature_leaves_ddcc_RNA_rep1


title: mature_leaves_ddcc_RNA_rep2


title: mature_leaves_Col-0_RNA_rep3


title: DSGC, P14, HB9-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_5


title: WholeIleum1-4

value: Whole cross section of ileum


title: young_shoots_met1-3_RNA_rep2


title: DSGC, P14, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_3

value: ON-OFF DSGC


title: DSGC, P14, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_4


title: DSGC, P14, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_2


title: DSGC, P14, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_1


title: mature_leaves_Col-0_RNA_rep2


title: young_shoots_met1-3_RNA_rep1


title: young_shoots_met1-3_RNA_rep3


title: DSGC, P10, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_10


title: DSGC, P14, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_0


title: mature_leaves_mddcc_INPUT_rep2

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the TAIR10 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

source_name: mature leaves mddcc

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.

tag: development stage

value: mddcc

tag: chip antibody


title: mature_leaves_mddcc_INPUT_rep1


title: DSGC, P12, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_4


title: mature_leaves_mddcc_RNAPII_rep2

value: RNAPII


title: DSGC, P12, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_3


title: mature_leaves_mddcc_RNAPII_rep1


title: DSGC, P12, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_2


title: DSGC, P12, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_1


title: mature_leaves_mddcc_H3K9me2_rep1


title: mature_leaves_mddcc_H3K27ac_rep2


title: DSGC, P12, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_0


title: mature_leaves_mddcc_H3K9me2_rep2


title: DSGC, P10, HB9-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_4


title: mature_leaves_Col-0_RNA_rep1


title: mature_leaves_mddcc_H3K4me1_rep2


title: mature_leaves_mddcc_H3K27me3_rep2


title: 1772-158-161-Tomato-minus_1710-763

city: Uppsala

first: Longlong

last: Luo

address: Husargatan 3

department: Dermatology and Venereology, Department of Medical Sciences

country: Sweden

institute: Uppsala University

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: *_expression_for_R.tab: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell.

source_name: Dorsal skin

growth_protocol: Ivl-CreERT2/R26-tdTomato mice were housed together with sex-matched littermates and fed ad libitum. All animal experiments were performed in accordance with the Swedish legislation.

extract_protocol:
Female mice were sacrificed at p57, hair cycle stages were determined by H&E staining of adjacent dorsal skin. Clipped and disinfected dorsal skin was isolated, dermal and adipose tissue was removed and strips of skin were floated on trypsin (Sigma) for 2h at 32°C. Epidermal tissue was subsequently scraped into S-MEM / 1% BSA and single cells were isolated by pipetting multiple times with an automatic pipette. The resulting cell suspension was filtered through 70 µm and 40 µm cell strainers, resuspended in Defined Keratinocyte Serum-free Medium (DK-SFM) without supplement (Life Technologies) and stained with α-CD49f-A647, α-LY6A-PE-Cy7 and α-CD34-FITC (all 1:50, BD Biosciences) for 1h. After incubation, cells were washed and Sytox Blue (1:1000, Life Technologies) was added 2min prior to FACS. From the suspension, Tomato-traced and non-traced live basal interfollicular epidermis cells (Sytox blue-neg/CD49f+/LY6A+/CD34-neg) were sorted into 400μl of DK-SFM with 0.1 mg/ml DNase I (Stem Cell Technologies) and stored on ice until capturing on the Fluidigm C1 chip.
Before capturing, the cell suspension was carefully resuspended and two times passed through a 20 µm cell strainer. Epidermal cells were captured on a medium microfluidic chip (designed for cells from 10 µm – 17 µm) using the Fluidigm C1 Autoprep System. 14 µl filtered cell suspension (about 750 cells / µl in DK-SFM with DNase I) was mixed with 6 µl C1 Suspension Reagent and 14 µl were loaded onto the chip. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments, Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: Mice were treated 2 days prior to sacrifice i.p. with 10 μg/g(mouse) of Tamoxifen dissolved in corn oil.

tag: strain

value: Dorsal interfollicular epidermis

value: Post natal day 57

value: Tamoxifen ip (10ug/g) 2 days before

tag: sorted population

value: Non-traced cells (Tomato-minus)


title: mature_leaves_mddcc_H3K27ac_rep1

value: mature leaves


title: 1772-146-140-Tomato-plus_2209-761

value: Traced cells (Tomato-plus)


title: mature_leaves_mddcc_H3K27me3_rep1


title: 1772-146-139-Tomato-minus_2209-760


title: DSGC, P10, HB9-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_3


title: DSGC, P10, HB9-GFP, down, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_2


title: mature_leaves_mddcc_H3K4me1_rep1


title: DSGC, P10, HB9-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_5


title: mature_leaves_mddcc_H3K9ac_rep1


title: DSGC, P10, HB9-GFP, down, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_1


title: Lrig1-low cells from colonic tumors_S15

city: Copenhagen

first: Malte

last: Thodberg

address: Blegdamsvej 3B, Building 7 (Maersk Tower)

department: CBMR

country: Denmark

institute: University of Copenhagen

data_processing:
Read QC with TRIMMOMATIC with "HEADCROP:6", "CROP:68", "SLIDINGWINDOW:5:20", "MINLEN:30", "2>"
Mapping with HISAT2 default parameters
Quantification with featureCounts from SUBREAD on mm10 RefSeq genes
Genome_build: mm10
Supplementary_files_format_and_content: TXT file holding expression matrix (counts)

source_name: Lrig1-low cells from colonic tumors

growth_protocol: Colonic epithelium from Lrig1-eGFP-IRES-CreERT2 x APCmin mice. Colonic tumors were dissected from the neighboring tissue and manually minced

extract_protocol:
RNA was extracted using the PicoPure RNA isolation kit (ThermoFisher)
Libraries were prepared using SMARTer Stranded Total RNA-Seq Pico Input Mammalian v2 Kit (Takara) for a maximum of 8 cycles according to the manufacturers recommendations. Non-coding RNA species (rRNA and tRNA) were excluded using specific probes during the integral library preparation step.
Paired-end RNA sequencing was performed with NextSeq sequencer using NextSeq 500 High Output v2 Kit (75 cycles) (Illumina).

treatment_protocol: Cells were harvested using EDTA chelation method (10mM for 30 min.), dissociated with TryplE and dispase and sorted for Lrig1 expression using the eGFP reporter. Lineage-positive cells (CD45+ and CD31+) were excluded and only EpCam+ were sorted

tag: disease state

value: Tumor

value: low

value: colon


title: Cochlea, postnatal 28, replicate 1

city: Omaha

first: Jian

last: Zuo

state: Nebraska

address: 1006 N 20th St, Criss II, 313

department: Biomedical Sciences

institute: Creighton University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlear

extract_protocol:
Dissection of 14 cochlear tissues from 7 mice was completed in less than 15 minutes from the time point of euthanizing the mice. The tissues were then incubated with 1 mg/ml Collagenase IV for 10 minutes at room temperature (RT). At the end of incubation, collagenase was inactivated by adding an equal volume of DMEM/F-12 media with 10% fetal bovine serum (FBS). Tissues were then gently triturated with a trimmed 200ul pipette to dissociate cells; after transferring half of the media to a new tube, tissues were then triturated with a new 200ul pipette for further dissociating the tightly connected cells. All dissociated cells were passed through multiple 40 µm strainers. Cells were lysed within GEMs generated by the 10x Genomics Chromium System.
Libraries were constructed in accordance with the protocol of Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1.

value: Inner Ear

value: Cochlear


title: Cochlea, postnatal 14, replicate 1

description: 10x Genomics


title: NS.1454.002.NEBNext_dual_i7_E10---NEBNext_dual_i5_E10.35C [Control]

city: Windsor

first: Javad

last: Sadeghi

state: Ontario

address: 2990 Riverside Dr W

department: GLIER

country: Canada

institute: University of Windsor

data_processing:
To remove potentially contaminating rRNA sequences, raw sequences were filtered against eight default rRNA databases using SortMeRNA v2.1
The non-rRNA sequences were then quality-filtered using the default parameters with Trimmomatic v0.38
This filtering step removed poor-quality sequences as well as adapter sequence that was required for RNA sequencing
The non-rRNA sequences were aligned to the Chinook salmon (GCF_002872995.1_Otsh_v1.0; https://www.ncbi.nlm.nih.gov/assembly/GCF_002872995.1/) reference genome using the splicing aligner HISAT2
Assembly: GCF_002872995.1
Supplementary files format and content: FeatureCounts, was used to calculate the number of transcript sequence fragments assigned to each gene

organism: Oncorhynchus tshawytscha

source_name: Hindgut

extract_protocol:
TRIzol® reagent (Life Technologies, Mississauga, ON, CAT=15596018)
RNA sequencing libraries were prepared and sequenced at the McGill University and Genome Quebec Innovation Centre (McGill University, Montreal, QC) using the Illumina NovaSeq 6000 S4 PE100 protocol and 100-bp paired-end sequencing

treatment_protocol: Control

value: Hindgut

value: Epithelia

value: Diploid

value: Control


title: mature_leaves_mddcc_H3K4me3_rep1

value: mature leaves from five-week old

value: mddcc


title: DSGC, P10, HB9-GFP, down, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_0

value: Retina

value: ON-OFF DSGC

value: down


title: Lrig1-high cells from normal colonic epithelium_S14

value: Normal

value: high


title: mature_leaves_mddcc_H3K9ac_rep2

value: mature leaves


title: H524-Input

city: Daegu

first: Hyo-Gyoung

last: Kang

address: Hoguk-ro, Buk-gu

department: Cell and Matrix Research Institute, School of Medicine

country: South Korea

institute: Kyungpook National University

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic 0.38.
The cleaned reads were aligned to the human genome (hg19) using Bowtie (version 1.1.2 parameter set -n 2 -m 1 -X 500) (Langmead et al., 2009), allowing up to two nucleotide mismatches to the reference genome per seed and returning only uniquely mapped reads. Mapped data (SAM file format) were sorted and indexed using SAMtools (version 1.9) (Li et al., 2009). Then, duplicate reads were excluded using a MarkDuplicates module in Picard (version 1.118).
Peaks were called in the aligned sequence data using a model-based analysis of ChIP-seq (MACS2 version 2.1.1) (Zhang et al., 2008). The following parameters were used: macs2 callpeak -t ChIP.bam -c Input.bam -g hs -q 0.05 --call-summits --keep-dup 1.
ChIPseeker (version 1.18.0) (Yu et al., 2015), a bioconductor package within R (version 3.5.1) to facilitate batch annotation of enriched peaks, was used to identify nearby genes and transcripts from the peaks obtained from MACS2.
Assembly: UCSC hg19
Supplementary files format and content: bed, bigwig

growth_protocol: Small cell lung cancer cells were cultured at 37˚C in a humidified atmosphere with 5% CO2 in Corning® RPMI medium (Corning Inc., Corning, NY, USA) supplemented with 10% Corning® Fetal Bovine Serum (Corning Inc., Corning, NY, USA), and 100 U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIPSeq library preparation was performed with TruSeq® ChIP Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed on an Illumina NovaSeq 6000.

treatment_protocol: Untreated

tag: cell line

value: Small cell lung cancer

value: Untreated


title: 1772-158-158-Tomato-plus_1710-762

value: Female

tag: tissue

value: Dorsal interfollicular epidermis

value: Post natal day 57

value: Tamoxifen ip (10ug/g) 2 days before

value: Traced cells (Tomato-plus)


title: Lrig1-low cells from normal colonic epithelium_S13

value: low

value: colon


title: mature_leaves_met1-3_INPUT_rep2

value: mature leaves from five-week old


title: H524-Promoter

value: H3K4me3 (Abcam, #ab8580)


title: NS.1454.002.NEBNext_dual_i7_F12---NEBNext_dual_i5_F12.35A [Control]

value: Hindgut

value: Epithelia

value: Diploid

value: Control


title: Cochlea, postnatal 28, replicate 2

description: 10x Genomics

value: Inner Ear

value: Cochlear


title: H524-NeuroD1

value: Small cell lung cancer

value: NeuroD1(Cell signaling #4373)


title: mature_leaves_met1-3_INPUT_rep1

value: mature leaves


title: H82-Promoter

value: Untreated


title: NS.1454.002.NEBNext_dual_i7_H11---NEBNext_dual_i5_H11.35B [Control]


title: mature_leaves_mddcc_H3K4me3_rep2

value: mddcc


title: H82-Input


title: mature_leaves_met1-3_RNAPII_rep2

value: RNAPII


title: NS.1454.002.NEBNext_dual_i7_C12---NEBNext_dual_i5_C12.12C [Control]


title: Lrig1-high cells from colonic tumors_S12

source_name: Lrig1-high cells from colonic tumors

value: Tumor

value: high


title: Lrig1-low cells from colonic tumors_S11

value: low

value: colon


title: mature_leaves_met1-3_H3K9me2_rep1

value: mature leaves from five-week old


title: NS.1454.002.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.139A [Probiotic treatment]

treatment_protocol: These samples received Probiotics for 10 days and after 10 days humanely euthanized immediately in an overdose solution of clove oil

value: Hindgut

value: Probiotics


title: NS.1454.002.NEBNext_dual_i7_A11---NEBNext_dual_i5_A11.12B [Control]

value: Epithelia

value: Diploid


title: H82-NeuroD1


title: mature_leaves_met1-3_RNAPII_rep1


title: Lrig1-high cells from colonic tumors_S08


title: Lrig1-low cells from colonic tumors_S07


title: mature_leaves_met1-3_H3K27ac_rep2


title: Lrig1-high cells from normal colonic epithelium_S06

value: Normal


title: NS.1454.002.NEBNext_dual_i7_D12---NEBNext_dual_i5_D12.139C [Probiotic treatment]


title: NS.1454.002.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.12A [Control]

value: Control


title: mature_leaves_met1-3_H3K9me2_rep2


title: Lrig1-high cells from normal colonic epithelium_S10


title: NS.1454.002.NEBNext_dual_i7_D10---NEBNext_dual_i5_D10.115B [Probiotic treatment]


title: Lrig1-high cells from colonic tumors_S04


title: NS.1454.002.NEBNext_dual_i7_G11---NEBNext_dual_i5_G11.139B [Probiotic treatment]


title: Lrig1-low cells from colonic tumors_S03


title: mature_leaves_met1-3_H3K4me1_rep2


title: NS.1454.002.NEBNext_dual_i7_A10---NEBNext_dual_i5_A10.115C [Probiotic treatment]


title: mature_leaves_met1-3_H3K27ac_rep1


title: mature_leaves_met1-3_H3K9ac_rep1


title: mature_leaves_met1-3_H3K9ac_rep2


title: Lrig1-high cells from normal colonic epithelium_S02


title: mature_leaves_met1-3_H3K27me3_rep1


title: Lrig1-low cells from normal colonic epithelium_S05


title: NS.1454.002.NEBNext_dual_i7_B11---NEBNext_dual_i5_B11.115A [Probiotic treatment]


title: NS.1454.002.NEBNext_dual_i7_B12---NEBNext_dual_i5_B12.91B [Antibiotic treatment]

treatment_protocol: These samples received antibiotics for 10 days and after 10 days humanely euthanized immediately in an overdose solution of clove oil

value: Antibiotics


title: mature_leaves_met1-3_H3K27me3_rep2


title: NS.1454.002.NEBNext_dual_i7_G9E12---NEBNext_dual_i5_G9.67C [Antibiotic treatment]


title: Lrig1-low cells from normal colonic epithelium_S09


title: mature_leaves_met1-3_H3K4me3_rep1


title: NS.1454.002.NEBNext_dual_i7_E12---NEBNext_dual_i5_E12.67B [Antibiotic treatment]


title: mature_leaves_met1-3_H3K4me3_rep2


title: OWT_3DPI_3

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

description: YoungOld.GRCm38_99.rsem.genes.resultsTPM

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Reads were trimmed with cutadapt version 1.7.1
Reads were mapped against reference transcriptome GRCm38_99 and gene expression levels were calculated with RSEM version 1.3.1
Genome_build: GRCm38, Ensembl genebuild 99
Supplementary_files_format_and_content: Tab-delimited text file name with normalized TPM values for each gene and sample.

source_name: Satellite cells

extract_protocol:
Cells were isolated from skeletal muscle
Total RNA was isolated from freshly-sorted satellite cells with the PicoPure RNA Isolation Kit (KIT0204), NEBNext Single Cell/Low Input RNA Library Prep Kit was used for library preparation.
Cells were processed for RNA extraction right after sorting. Total RNA was extracted with the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher) together with on-column DNA digestion. Both RNA isolation kits were used according to the manufacturer's instructions. RNA concentration was measured with NanoDrop 2000/2000c (Thermo Fisher).
RNA integrity and library preparation were checked with a BioAnalyzer (RNA Pico Chip, Agilent). For the in vitro-based RNA-Seq, low input library preparation and single-end sequencing was performed in the Centre de Regulació Genomica (CRG) genomics unit using the HiSeqTM Sequencing Kit and the TruSeq v3 Cluster (Illumina). For the RNA-seq experiment in freshly isolated cells standard Directional RNA-seq library preparation and single-end sequencing (Illumina HiSeq 2500) was performed in the Genomic Unit of Centro Nacional de Investigaciones Cardiovasculares (CNIC).

value: Freshly sorted satellite cells

value: WT

value: old (24 months old)

tag: muscle state

value: 3 days after injury (Cardiotoxin)


title: OWT_3DPI_1

treatment_protocol: Cells were isolated from skeletal muscle

tag: age


title: OWT_1DPI_3

value: 1 day after injury (Cardiotoxin)


title: OWT_3DPI_2


title: NS.1454.002.NEBNext_dual_i7_G12---NEBNext_dual_i5_G12.91A [Antibiotic treatment]


title: mature_leaves_ddcc_INPUT_rep2

value: mature leaves

value: ddcc


title: mature_leaves_ddcc_INPUT_rep1


title: Lrig1-low cells from normal colonic epithelium_S01

value: low


title: mature_leaves_met1-3_H3K4me1_rep1


title: YWT_1DPI_7

value: young (3 months old)


title: OWT_1DPI_1


title: mature_leaves_ddcc_H3K9me2_rep1

value: mature leaves from five-week old


title: YWT_1DPI_6


title: EPCs, oscillating shear stress, 12h [Sample_OS1]

city: Weifang

first: lan

middle: lan

last: li

state: shandong

address: Weifang Medical University, Weifang, Shandong, 261053, China

institute: weifang medical university

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N or low quality reads from raw data.
Sequencing reads were mapped to the human genome (GRCh38) using HISAT2.
Read counts of each gene were obtained by HTSeq-count.
FPKM of each gene was calculated using Cufflinks.
Assembly: GRCh38.p12
Supplementary files format and content: FPKM_allsamples.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: umbilical cord blood

growth_protocol: EPCs were cultured in complete endothelial growth medium-2 (EGM-2, supplemented with an EGM-2 Bullet kit, including 10% fetal calf serum).

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (NovaSeq 6000) and 150 bp paired-end reads were generated.

treatment_protocol: OSS (±3.5 dynes/cm2, 1 Hz frequency) was applied to EPCs using a Flexcell flow STR-4000 parallel plate flow chamber system (Flexcell STR-4000, USA).

value: umbilical cord blood

value: endothelial progenitor cells

value: oscillating shear stress


title: mature_leaves_ddcc_H3K9me2_rep2


title: EPCs, oscillating shear stress, 12h [Sample_OS3]


title: EPCs, oscillating shear stress, 12h [Sample_OS2]


title: W1286-2

type: RNA

city: Shanghai

first: Jiahui

last: Yu

address: No.800, Xiangyin Road, Yangpu District, Shanghai

institute: Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, China

hyb_protocol: RNA was fragmented and hybridized into array probes with GeneChip hybridization oven 645, and GeneChip fluidics station 450 with Affymetrix GeneChip Hybridization Wash and Stain Kit.

scan_protocol: GeneChip Scanner 3000 was used to scan the images. And get the raw intensities of each sample.

data_processing: Then RMA algorithm was used to normalize the raw data and get the normalized data.

label_protocol: not provided

extract_protocol: Total RNA was analyzed by Agilent 2100. Amplified RNA was prepared using GeneChip 3' IVT Express Kit, then purified.

treatment_protocol: Total RNA was extracted from HGC27 human cells.

value: normal


title: W1286-3


title: mature_leaves_ddcc_H3K27ac_rep2


title: YWT_1DPI_5


title: W1286-1


title: W1290-3

value: ncRuPAR over expression


title: OWT_1DPI_2


title: C57 Injury biol rep 4 [C57Bl-6N_8_MI_remote_S46]

city: INDIANAPOLIS

first: Loren

middle: J.

last: Field

state: Indiana

address: 1044 West Walnut, R4-376

department: Medicine

institute: Indiana University

data_processing:
The sequence data were mapped to the mouse reference genome mm10 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: mouse reference genome mm10
Supplementary files format and content: excel table including raw counts, log2 fold change, p-values and FDR

source_name: Heart (septum and left ventricle)

extract_protocol:
Rneasy Plus Mini Kit
KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

value: Heart (septum and left ventricle)

value: female

value: permanent coronary artery ligation


title: mature_leaves_ddcc_RNAPII_rep2

value: RNAPII


title: W1290-1


title: EPCs, static condition, 12h [Sample_J2]

value: WT

value: static condition


title: C57 Injury biol rep 3 [C57Bl-6N_7_MI_remote_S45]


title: mature_leaves_ddcc_RNAPII_rep1


title: OWT_QSC_2

value: Freshly sorted satellite cells

value: old (24 months old)

value: resting non-injured muscle


title: mature_leaves_ddcc_H3K27ac_rep1

value: mature leaves

value: ddcc


title: EPCs, static condition, 12h [Sample_J1]


title: C57 Injury biol rep 2 [C57Bl-6N_6_MI_remote_S44]


title: C57 Injury biol rep 1 [C57Bl-6N_5_MI_remote_S43]


title: EPCs, static condition, 12h [Sample_J3]


title: C57 Normal biol rep 4 [C57Bl-6NCR_4_no_injury_S38]

value: None; control


title: mature_leaves_ddcc_H3K9ac_rep2

value: mature leaves from five-week old


title: OWT_QSC_1


title: mature_leaves_ddcc_H3K4me1_rep2


title: mature_leaves_ddcc_H3K9ac_rep1


title: OWT_QSC_3


title: Raji_Bryo_Rep3

city: Seattle

first: Rimas

last: Orentas

state: Washington

address: 1100 Olive Way NE

department: BTCCCR

institute: Seattle Children's Research Institute

data_processing:
Base calling by CASAVA base recognition
Data filtration: remove reads with adapter contamination, when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Alignment: HISAT2,2.0.5, parameter default.
Quantification: featureCounts, 1.5.0-p3
Diffrential gene expression analysis: DESeq2, 1.20.0, |log2(FoldChange)| >= 1 & padj <= 0.05
Assembly: hg38
Supplementary files format and content: Count matrixs includes FPKM value for each sample
Supplementary files format and content: Diffrential gene expression matrix includes fold change and p value for each sample

source_name: Raji

growth_protocol: Raji cells were cultured in RPMI media supplemented with L-glutamine and 10% FBS

extract_protocol:
Qiagen RNeasy kit
polyA enrichment mRNA library preparation

treatment_protocol: Raji cells were treated with 1nM Bryostatin-1 or DMSO overnight at 37C.

value: Raji

value: Burkitt's lymphoma cell

value: GFP-ffluc

value: 1nM Bryostatin-1


title: Raji_Bryo_Rep2


title: mature_leaves_ddcc_H3K4me1_rep1


title: YWT_QSC_5

value: young (3 months old)


title: C57 Normal biol rep 3 [C57Bl-6NCR_3_no_injury_S37]

value: Heart (septum and left ventricle)

value: female


title: YWT_QSC_6


title: mature_leaves_ddcc_H3K27me3_rep2


title: YWT_QSC_4


title: W1290-2

value: ncRuPAR over expression


title: Raji_DMSO_Rep3

value: DMSO


title: C57 Normal biol rep 1 [C57Bl-6NCR_1_no_injury_S35]


title: YDrp1KO_3DPI_4

value: 3 days after injury (Cardiotoxin)


title: YDrp1KO_3DPI_3

value: Freshly sorted satellite cells


title: Raji_DMSO_Rep2


title: DBA Injury biol rep 4 [DBA-2J_8_MI_remote_S42]

value: permanent coronary artery ligation


title: mature_leaves_ddcc_H3K27me3_rep1


title: mature_leaves_ddcc_H3K4me3_rep2


title: Raji_Bryo_Rep1


title: Raji_DMSO_Rep1


title: DBA Injury biol rep 3 [DBA-2J_7_MI_remote_S41]


title: YDrp1KO_3DPI_1


title: RPE1-TP53KO cells 2

city: Amsterdam

first: Job

last: de Lange

address: Boelelaan 1117

department: Human Genetics

country: Netherlands

institute: Amsterdam UMC location Vrije Universiteit

data_processing:
FASTQ files were clipped and cleaned with fastp
The trimmed FASTQs were mapped to human reference genome (hg19), using HISAT2
sam to  bam convesion , sorting and indexing performed using SAMTOOLS
The gene-level reads were counted  by featurecount . Multi-mapping reads were also counted by assigning fractional counting
Raw counts were normalized by the  trimmed mean of m-values using R/EdgeR package
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include raw read counts per sample
Supplementary files format and content: tab-delimited text files include TMM normalized log2-transformed count per million per sample

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen)
Samples were enriched for mRNA using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2

value: Retinal pigment epithelium

value: untreated


title: mature_leaves_ddcc_H3K4me3_rep1

value: mature leaves

value: ddcc


title: YDrp1KO_3DPI_2


title: mature_leaves_Col-0_INPUT_rep2

value: mature leaves from five-week old

value: wild type


title: C57 Normal biol rep 2 [C57Bl-6NCR_2_no_injury_S36]

value: None; control


title: DBA Injury biol rep 2 [DBA-2J_6_MI_remote_S40]


title: PAXIP1 knockout, RPE1-TP53KO cells 3

description: RPE1-hTert-iCas9-TP53/puroKO-PAXIP1KO.r3


title: mature_leaves_Col-0_INPUT_rep1


title: YWT_3DPI_3


title: DBA Injury biol rep 1 [DBA-2J_5_MI_remote_S39]


title: PAXIP1 knockout, RPE1-TP53KO cells 2

description: RPE1-hTert-iCas9-TP53/puroKO-PAXIP1KO.r2


title: RPE1-TP53KO cells 1


title: mature_leaves_Col-0_RNAPII_rep2

value: RNAPII


title: YWT_3DPI_1


title: PAXIP1 knockout, RPE1-TP53KO cells 1

description: RPE1-hTert-iCas9-TP53/puroKO-PAXIP1KO.r1


title: mature_leaves_Col-0_H3K9me2_rep2


title: YDrp1KO_1DPI_3

value: 1 day after injury (Cardiotoxin)


title: DBA Normal biol rep 3 [DBA-2J_3_no_injury_S33]


title: DBA Normal biol rep 2 [DBA-2J_2_no_injury_S32]


title: DBA Normal biol rep 1 [DBA-2J_1_no_inury_S31]


title: YWT_3DPI_2

value: young (3 months old)


title: mature_leaves_Col-0_H3K9me2_rep1


title: YDrp1KO_1DPI_4


title: mature_leaves_Col-0_RNAPII_rep1


title: DBA Normal biol rep 4 [DBA-2J_4_no_injury_S34]

value: Heart (septum and left ventricle)


title: ESCO2 mutant, RPE1-TP53KO cells 3

description: RPE1-hTert-iCas9-TP53/puroKO-ESCO2mut.r3


title: DDX11 knockout, RPE1-TP53KO cells 3


title: mature_leaves_Col-0_H3K27ac_rep1


title: ESCO2 mutant, RPE1-TP53KO cells 2

description: RPE1-hTert-iCas9-TP53/puroKO-ESCO2mut.r2


title: YWT_1DPI_3


title: YWT_1DPI_4


title: DDX11 knockout, RPE1-TP53KO cells 1


title: YWT_1DPI_2


title: ESCO2 mutant, RPE1-TP53KO cells 1

description: RPE1-hTert-iCas9-TP53/puroKO-ESCO2mut.r1


title: YDrp1KO_1DPI_2


title: YDrp1KO_1DPI_1


title: mature_leaves_Col-0_H3K27ac_rep2


title: YWT_1DPI_1


title: Naive P14 cells 3

city: Munich

first: Lorenz

last: Kretschmer

state: Bavaria

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

country: Germany

institute: TU Munich

description: bulkRNA-Seq of 10000 cells

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (Version 2.5.4). Read counts per gene locus were obtained using htseq-count (Version 0.11.4).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization and differential expression analysis. Batch effects were identified using sva (Version 3.34.0) and subsequently modelled in the design formula of DESeq2.
Assembly: mm10
Supplementary files format and content: Matrix table, in txt format, with raw read counts per gene locus from htseq-count.

source_name: splenic CD8+ T cells

extract_protocol:
10000 cells were sorted of each population. Rneasy Plus Mini Kit (Quiagen) was used for RNA isolation according to the manufacturer's protocol.
SMART-Seq V4 Ultra Low Input RNA Kit (Takara) was used according to the manufacturer's protocol for library contruction.

value: CD8+ T cells

value: spleen


title: mature_leaves_Col-0_H3K9ac_rep1

source_name: mature leaves Col-0


title: DDX11 knockout, RPE1-TP53KO cells 2


title: mature_leaves_Col-0_H3K4me1_rep2


title: mature_leaves_Col-0_H3K4me1_rep1


title: 1-9 P2 (P16); US

city: San Diego

first: Jaimie

last: Mayner

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

data_processing:
Data was processed through STAR, with gene alignement trough samTools and featureCounts
Count matrix was analyzed using R software 4.0.3
DeSeq2 was used for normalization, Relative Log Expression, and adjusted p-values
Assembly: hg38
Supplementary files format and content: Excel Workbook with normalized counts using DESeq2's median of ratios values for Unsorted Samples with column delinated sample IDs
Supplementary files format and content: Excel workbook with normalized counts using DESeq2's median of ratios values for WA and SA Samples with column delinated sample IDs

growth_protocol: VSMCs were differentiated from iSPCs through lateral plate mesoderm as described in:  Cheung, C., Bernardo, A., Pedersen, R. et al. Directed differentiation of embryonic origin–specific vascular smooth muscle subtypes from human pluripotent stem cells. Nat Protoc 9, 929–938 (2014).

extract_protocol:
RNA was extracted using the miRNeasy Kit from Qiagen and manufacturers instructions
Library was built using the Illumina TruSeq Stranded RNA and High Throughput Library Prep Kit.

treatment_protocol: VSMCs were sampled from multiple differentiation batches (as indicated by passage number of iPSCs at time of differentiation) and from different time points post differentiation (as indicated by passage number of VSMCs at time of sample extraction). RR WT VSMCs were seeded into a collagen coated microfluidic device, allowed to attach overnight, and then exposed to fluidic shear stress, resulting  in a population that detached (weakly adherent, WA) and a population that remained adherent in the channel (strongly adherent, SA). Unsorted (US) control included cells not seeded into the device, and those cultured overnight in the device but not exposed to fluidic shear stress (USID).

value: iPSC derived VSMC

value: RR KO

value: Unsorted

tag: iPSc passage_number

tag: vsmc passage_number


title: Naive P14 cells 2

description: bulkRNA-Seq of 10000 cells


title: mature_leaves_Col-0_H3K27me3_rep2


title: 1-9 P1 (P19); US


title: mature_leaves_Col-0_H3K4me3_rep2


title: mature_leaves_Col-0_H3K27me3_rep1


title: YDrp1KO_QSC_3

value: Freshly sorted satellite cells

value: resting non-injured muscle


title: YWT_QSC_3


title: 1-9 P0 (P21); US


title: CD62L-_Ly108-_P14_spleen_LCMV_Clone_13_d28pi_2

description: bulkRNA-Seq of 10000 cells


title: CD62L-_Ly108+_P14_spleen_LCMV_Clone_13_d28pi_1

description: bulkRNA-Seq of 10000 cells


title: Naive P14 cells 1

description: bulkRNA-Seq of 10000 cells


title: YDrp1KO_QSC_2


title: CD62L-_Ly108-_P14_spleen_LCMV_Clone_13_d28pi_3

description: bulkRNA-Seq of 10000 cells


title: mature_leaves_Col-0_H3K9ac_rep2


title: mature_leaves_Col-0_H3K4me3_rep1


title: CD62L+_Ly108+_P14_spleen_LCMV_Clone_13_d28pi_2

description: bulkRNA-Seq of 10000 cells


title: CD62L+_Ly108+_P14_spleen_LCMV_Clone_13_d28pi_1

description: bulkRNA-Seq of 10000 cells


title: CD62L-_Ly108+_P14_spleen_LCMV_Clone_13_d28pi_3

description: bulkRNA-Seq of 10000 cells


title: young_shoots_met1-3_INPUT_rep2

value: young shoots

value: young shoots from two-week old seedlings


title: 1-5 P2 (P46); USID

value: RR WT

value: Unsorted Cultured in Device


title: YWT_QSC_1


title: 1-5 P2 (P46); SA

value: Strongly Adherent


title: 1-5 P9 (P46); SA


title: 1-5 P9 (P46); WA

value: Weakly Adherent


title: Lung2 d10 NB (sample 217395 VDJ)

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

institute: University Clinic Erlangen

description:
217395_Lung_2_filtered_contig_annotations.csv
Sample 3 VDJ

data_processing:
Demultiplexing, FASTQ generation with cellranger v2.1.1
Alignment to mm10 and clonotyping with cellranger v3.0.1
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Output Cellranger 5' Gene Expression: tsv, mtx. Contains only detected cellular barcodes. For Targeted Gene Expression samples, non-targeted genes are removed from the filtered matrix.
Supplementary_files_format_and_content: Output Cellranger 5' TCR: csv. High-level annotations of each high-confidence, cellular contig.

source_name: CD4+4get+ primary lung cells

extract_protocol:
Single cell suspension to be prepared with10x Chromium Single Cell 5′ Solution (Gene Expression Ananlysis and TCR-specific VDJ library)
Cells were subjected to 10x Chromium Single Cell 5′ Solution v2 library prep kit for gene expression analysis and TCR-specific VDJ analysis according to the manufacturer’s instructions
Single Cell RNAseq

treatment_protocol: At day 10 after Nb infection lungs and MLNs of IL-4eGFP reporter (4get) mice were harvested. Lungs were perfused with PBS, cut into small pieces and digested with the commercial “Lung Dissociation kit” (Miltenyi) according to manufacturer’s instructions. Digested lungs and complete MLNs were gently mashed through a 100 μm cell strainer. For lung cells a 40% percoll purification was applied and erythrocytes were lysed with ACK-buffer (0.15 M NH4Cl, 1 mM KHO3, 0.1 mM Na2EDTA). Then samples of both organs were treated with Fc-receptor blocking antibody (anti-CD16/32, clone 2.4G2, BioXCell, West Lebanon, NH) and stained with anti-CD4-Percp-Cy5.5 antibody (clone: RM4-5). IL-4eGFP+CD4+ cells were sorted.

value: Lung

value: d10 post Nippostrongylus brasiliensis infection


title: 1-5 P9 (P46); USID


title: MLN2 d10 NB  (sample 217396 VDJ)

description:
217396_MLN_2_filtered_contig_annotations.csv
Sample 4 VDJ

source_name: CD4+4get+ primary mesenteric lymph node cells

value: Mesenteric Lymph Node


title: NS.1454.002.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.67A [Antibiotic treatment]

value: Hindgut

value: Epithelia

value: Diploid

value: Antibiotics


title: young_shoots_met1-3_RNAPII_rep1

source_name: young shoots met1-3

value: RNAPII


title: YWT_QSC_2

value: young (3 months old)


title: 1-5 P8 (P46); SA

value: iPSC derived VSMC


title: MLN1 d10 NB (sample 217394 VDJ)

description:
217394_MLN_1_filtered_contig_annotations.csv
Sample 2 VDJ


title: YDrp1KO_QSC_1

value: Freshly sorted satellite cells

value: resting non-injured muscle


title: Lung1 d10 NB (sample 217393 VDJ)

description:
217393_Lung_1_filtered_contig_annotations.csv
Sample 1 VDJ


title: young_shoots_met1-3_H3K9me2_rep1

value: young shoots

value: young shoots from two-week old seedlings


title: MLN2 d10 NB  (sample 217396 GEX Rapid Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217396_MLN_2_barcodes.tsv.gz
217396_MLN_2_features.tsv.gz
217396_MLN_2_matrix.mtx.gz
Sample 4 GEX Rapid Run


title: young_shoots_met1-3_RNAPII_rep2


title: CD62L-_Ly108-_P14_spleen_LCMV_Armstrong_d28pi_3

description: bulkRNA-Seq of 10000 cells

value: CD8+ T cells

value: spleen


title: CD62L-_Ly108-_P14_spleen_LCMV_Armstrong_d28pi_2

description: bulkRNA-Seq of 10000 cells


title: 1-5 P8 (P46); WA

value: RR WT

value: Weakly Adherent


title: 1-5 P2 (P46); WA


title: young_shoots_met1-3_H3K9me2_rep2


title: CD62L-_Ly108-_P14_spleen_LCMV_Armstrong_d28pi_1

description: bulkRNA-Seq of 10000 cells


title: CD62L-_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_2

description: bulkRNA-Seq of 10000 cells


title: 1-5 P8 (P46); US

value: Unsorted


title: SKBR3, siAKTIP 1

city: Pokfulam

first: Lydia

last: Cheung

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: University of Hong Kong

data_processing:
Sequencing reads were first filtered for adapter sequence, low quality sequence and rRNA sequence. Reads with read length ≥40 bp retained were aligned to the human genome GRCh38 using STAR version 2.5.2. Differentially expressed genes were identified using DESeq2 version 1.26.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files which include FPKM, TPM, count values and gene ID

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen).
2ug RNA was used for library preparation using KAPA Stranded mRNA-Seq Kit (Roche).
RNA sequencing was performed on the Illumina NovaSeq 6000 system.

value: Breast cancer

value: Breast cancer cells

value: AKTIP knockdown


title: young_shoots_met1-3_H3K27ac_rep2


title: young_shoots_met1-3_H3K9ac_rep1


title: SKBR3, siAKTIP 2


title: young_shoots_met1-3_INPUT_rep1


title: CD62L-_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_1

description: bulkRNA-Seq of 10000 cells


title: young_shoots_met1-3_H3K4me1_rep2


title: CD62L+_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_1

description: bulkRNA-Seq of 10000 cells


title: Lung2 d10 NB (sample 217395 GEX Rapid Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217395_Lung_2_barcodes.tsv.gz
217395_Lung_2_features.tsv.gz
217395_Lung_2_matrix.mtx.gz
Sample 3 GEX Rapid Run

value: Lung

value: d10 post Nippostrongylus brasiliensis infection


title: CD62L+_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_2

description: bulkRNA-Seq of 10000 cells


title: MCF7, siAKTIP 2


title: young_shoots_met1-3_H3K27ac_rep1


title: CD62L+_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_3

description: bulkRNA-Seq of 10000 cells


title: MLN1 d10 NB (sample 217394 GEX Rapid Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217394_MLN_1_barcodes.tsv.gz
217394_MLN_1_features.tsv.gz
217394_MLN_1_matrix.mtx.gz
Sample 2 GEX Rapid Run

value: Mesenteric Lymph Node


title: young_shoots_met1-3_H3K9ac_rep2


title: Lung1 d10 NB (sample 217393 GEX Rapid Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217393_Lung_1_barcodes.tsv.gz
217393_Lung_1_features.tsv.gz
217393_Lung_1_matrix.mtx.gz
Sample 1 GEX Rapid Run


title: SKBR3, mock 2

value: WT


title: young_shoots_met1-3_H3K4me1_rep1


title: MLN2 d10 NB  (sample 217396 GEX HighOutput Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217396_MLN_2_barcodes.tsv.gz
217396_MLN_2_features.tsv.gz
217396_MLN_2_matrix.mtx.gz
Sample 4 GEX HighOutput Run


title: Lung2 d10 NB (sample 217395 GEX HighOutput Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217395_Lung_2_barcodes.tsv.gz
217395_Lung_2_features.tsv.gz
217395_Lung_2_matrix.mtx.gz
Sample 3 GEX HighOutput Run


title: Lung1 d10 NB (sample 217393 GEX HighOutput Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217393_Lung_1_barcodes.tsv.gz
217393_Lung_1_features.tsv.gz
217393_Lung_1_matrix.mtx.gz
Sample 1 GEX HighOutput Run


title: MCF7, siAKTIP 1


title: BM Adult

city: Zollikerberg

first: Sonia

last: Tugues

address: 104 Forchstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: 10X Genomics

data_processing:
Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v4 workflow.
Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 4.0).
Assembly: GRCm38.p6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Group 1 innate lymphoid cells

extract_protocol:
1) Livers were cut immediately after dissection and kept in ice-cold digestion buffer (1.0 mg/ml Collagenase IV, 2 mg/ml DNase, 5% FBS in HBSS with Ca2++/Mg2++) to prevent loss of hepatic ILCs due to prolonged exposure to accumulating lactate. Embryos were removed from the uterus of pregnant mice and dissected under a microscope. All organs were digested with gentle rocking at 37°C for 20-30 min. After digestion, cells were passed through a 100 μm filter and washed, followed by 3 min incubation in ACK (Ammonium-Chloride-Potassium, Sigma Aldrich) buffer to lyse erythrocytes 2) For harvesting of bone marrow cells, tibiae and femora were carefully separated from surrounding muscle and connective tissue, crushed in a mortar, and passed through a 100 μm filter, followed by lysis of erythrocytes.
Sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared following manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.

value: Group 1 innate lymphoid cells

value: 6-8 weeks old


title: MLN1 d10 NB (sample 217394 GEX HighOutput Run)

description:
Sample was sequenced in two runs (Rapid Rund and HighOutput Run). Combined data was used to generate processed data files.
217394_MLN_1_barcodes.tsv.gz
217394_MLN_1_features.tsv.gz
217394_MLN_1_matrix.mtx.gz
Sample 2 GEX HighOutput Run


title: BM P10

description: 10X Genomics

source_name: Bone marrow

value: Bone marrow

value: P(ostnatal day) 10


title: Hobit KO P10

description: 10X Genomics

source_name: Liver

value: Liver


title: young_shoots_met1-3_H3K27me3_rep2

city: Wuhan

first: Qiangwei

last: Zhou

address: Hongshan district, shizishan #1

institute: Huazhong Agricultural university

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the TAIR10 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow(H3K4me3,H3K27ac,PII)/broad(H3K27me3,H3K4me1,H3K9me2) parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

value: young shoots

value: young shoots from two-week old seedlings


title: shPNISR 3

city: Guangzhou

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: All of the cells were cultured at 37°C in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HC8 cells transfected with  shNC plasmid or shPNISR plasmid

value: colorectal cancer cell

value: HCT8 cells transfected with shPNISR plasmid


title: young_shoots_met1-3_H3K27me3_rep1


title: MCF7, mock 1


title: Hobit KO Adult

description: 10X Genomics


title: Vehicle Nap EtOH bio rep3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

data_processing:
Reads were trimmed by Cutadapt and filtered using fastq_quality_filter as part of FASTX-toolkit with parameters including “-q 20” and “-p 90”. The reference genome and gene annotation files of Homo sapiens were retrieved from GENCODE (release 31) (https://www.gencodegenes.org/). Read mapping was performed by means of Subread aligners in Rsubread package with only uniquely mapped reads reported in the final alignment and read summarisation. Principal Component Analysis (PCA) plot was carried out using all protein-coding genes and long noncoding RNAs with RPKM value ≥ 1 in at least one sample. Subsequently, log2(RPKM+1) transformation and quantile normalization were applied.
Quantification was carried out by featureCounts function in R. Significant differences in gene expression were identified using DESeq2 with the following cut-offs: log2FoldChange > 1 (or < -1) and an FDR-adjusted P value of < 0.05. After this analysis, only protein-coding genes were retained based on the gene biotype labels. Overrepresentation enrichment analysis of DEGs were identified using WebGestalt for gene ontology (GO) terms and pathways, with a significance enrichment level set at an FDR < 0.05.
Supplementary files format and content: gene read counts plain text table

source_name: Ishikawa celss

growth_protocol: were cultured (50:50 DMEM/F12, 0.5 % GSP, 10 % charcoal-stripped FBS) at 37 °C and in 5 % CO2. Cells were cultured to 70 % confluence and seeded into 6-well plates.

extract_protocol:
Following treatment, cells were harvested by trypsinization and lysed in QIAzol Lysis Reagent. RNA was extracted using the miRNeasy Mini RNA Extraction kit (Qiagen, UK) as per manufacturer’s instructions.
Total RNA (100 ng) was used for library preparation using the Illumina TruSeq® Stranded Total kit, according to the manufacturer’s guidelines.
The libraries were sequenced by the Next Generation Sequencing Facility at the University of Leeds, using the NextSeq 500 (Illumina, California, USA) to generate single end 75 bp reads.

treatment_protocol: The cultures were treated with either 1) basal media (as above), 2) vehicle control (70 % ethanol, EtOH) or 3), 0.1 mg/ml P4, 4) 1.0 mg/ml P4, or 5) 1.0 mg/ml P4, for 24 hrs.

value: Ishikawa celss

value: Endomerial epithelial adenocarcinoma

value: Treatment of cells with vehicle control (70% EtOH)  for 24 hrs


title: Vehicle Nap P4 bio rep3

value: Treatment of cells with vehicle control (Nap) and Progesterone for 24 hrs


title: young_shoots_met1-3_H3K4me3_rep2


title: Hobit KO E18

description: 10X Genomics

value: E(mbryonic day) 18.5


title: shPNISR 2


title: shPNISR 1


title: young_shoots_met1-3_H3K4me3_rep1


title: PSAT1_P4 bio rep3

value: Treatment of cells with recombinant human PSAT1 and Progesterone for 24 hrs


title: WT P10

description: 10X Genomics


title: young_shoots_ddcc_RNAPII_rep2

source_name: young shoots ddcc

value: ddcc

value: RNAPII


title: MCF7, mock 2

value: Breast cancer

value: Breast cancer cells

value: WT


title: WT E18

description: 10X Genomics

value: Group 1 innate lymphoid cells


title: Control bio rep3

value: No treatment of cells control medium


title: shNC 3

value: HCT8 cells transfected with shNC plasmid


title: shNC 2


title: Vehicle Nap P4 bio rep2


title: young_shoots_ddcc_RNAPII_rep1

value: young shoots

value: young shoots from two-week old seedlings


title: shNC 1

value: colorectal cancer cell


title: TCF7-GFP+_P14_T_cells

description: scRNAseq

data_processing:
Cell Ranger (version 5.0.0; 10x Genomics) was used for demultiplexing and alignment (resulting in the bam file) as well as counting (resulting in the mtx and tsv files) using default parameters
velocyto (version 0.17.17) performed counting of spliced and unspliced RNA molecules (based on bam file) to create loom file
Python software package SCANPY (version 1.6) was used for downstream analysis
Cells were filtered out that express < 200 genes and >4500 genes, >20000 counts,  > 15% mitochondrial genes. Genes were filtered out that were present in < 3 cells.
Cell cycle, percent mito and n_counts were regressed out
Assembly: mouse reference genome GRCm38
Supplementary files format and content: Output of the Cell Ranger Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized)
Supplementary files format and content: unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10x genomics)
Chromium Single Cell 3′ Library Construction Kit (10x genomics)

value: spleen


title: young_shoots_ddcc_INPUT_rep2


title: Vehicle Nap bio rep2

value: Ishikawa celss

value: Endomerial epithelial adenocarcinoma

value: Treatment of cells with vehicle control (Nap)  for 24 hrs


title: young_shoots_ddcc_H3K9me2_rep2


title: Vehicle Nap EtOH bio rep2

value: Treatment of cells with vehicle control (70% EtOH)  for 24 hrs


title: DLD1 shNAT10_rep3 IP for acRIP-seq

description: DLD1 shNAT10-3-IP-ac4C

data_processing:
library strategy: acRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
ac4C peaks were identified using exomePeak R package (v2.13.2) under parameters:  “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Differential ac4C peak were identified using exomePeak R package under parameters:“PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200” .
GO and KEGG analysis were performed using clusterprofile R package (v3.6.0).
ac4C-RNA-related genomic features were visualized using Guitar R package (v1.16.0).Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 12 -rna”.
Assembly: GRCh38
Supplementary files format and content: fpkm; peaks

source_name: DLD1 cell

growth_protocol: Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).

extract_protocol:
the fragmented RNA was incubated with Anti-N4-acetylcytidine (ac4C) antibody (abcam, ab252215) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The ac4C-enriched RNA was purified by Zymo RNA clean and concentrator-25 kit (Zymo Research, R1017)
The library was prepared by EpiTM mini longRNA-seq kit (Epibiotek, E1802). Both the input samples without IP and the ac4C IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: 100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Acetylated RNA immunoprecipitation was performed using EpiTM ac4C immunoprecipitation kit (Epibiotek, R1815).

value: CRC cell line

tag: passage

tag: molecule type

value: ac4C RNA


title: young_shoots_ddcc_INPUT_rep1

value: ddcc


title: young_shoots_ddcc_H3K9me2_rep1


title: T3

first: hua

middle: rong

last: Liu

state: Shanghai

address: 130 Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

description: colon tissues from AOM plus DSS induced mouse CRC models

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: CD45+cells in  colon tissues with high-grade intraepithelial neoplasia

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Male C57BL/6 mice were injected (day 0) intraperitoneally with 12 mg/kg body weight of azoxymethane (AOM), followed by ad libitum access to three dextran sodium sulfate (DSS) (at a final concentration of 2.5%)/water cycles (7 days of DSS and 14 days of water).  CD45+cells in  colon tissues with low/high-grade (T1/T3) intraepithelial neoplasia and the healthy control tissues were purified by FACS for single cell sequencing.

value: model building at 6-8 weeks of age


title: PSAT1 bio rep3

value: Treatment of cells with recombinant human PSAT1 for 24 hrs


title: DLD1 shNAT10_rep3 input for acRIP-seq

description: DLD1 shNAT10-3-input-ac4C

value: totalRNA


title: C

description: colon tissues from Healthy mice

source_name: CD45+cells in normal colon tissues from healthy mouse


title: PSAT1_P4 bio rep2

value: Treatment of cells with recombinant human PSAT1 and Progesterone for 24 hrs


title: DLD1 shNAT10_rep2 IP for acRIP-seq

description: DLD1 shNAT10-2-IP-ac4C


title: PSAT1 bio rep2


title: young_shoots_ddcc_H3K27ac_rep2

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 10 min and quenched with 0.2 M glycine at room temperature.


title: young_shoots_ddcc_H3K27ac_rep1


title: Control bio rep2

value: No treatment of cells control medium


title: DLD1 shNAT10_rep1 IP for acRIP-seq

description: DLD1 shNAT10-1-IP-ac4C


title: Vehicle Nap P4 bio rep1

value: Treatment of cells with vehicle control (Nap) and Progesterone for 24 hrs


title: T1

source_name: CD45+cells in  colon tissues with low-grade intraepithelial neoplasia


title: DLD1 shNAT10_rep2 input for acRIP-seq

description: DLD1 shNAT10-2-input-ac4C


title: young_shoots_ddcc_H3K9ac_rep2

value: young shoots


title: Vehicle Nap bio rep1


title: young_shoots_ddcc_H3K9ac_rep1

value: young shoots from two-week old seedlings