title: KYSE410 Hypoxia rep1

description:
K410expression_matrix.txt
K410H1_S56

value: esophageal cancer cell line

value: ambient o2 concentration:0.50percent duration of hypoxia

tag: time point

value: 48 hours


title: KYSE410 Normoxia rep2

status: Public on Dec 01 2024

type: SRA

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

description:
K410expression_matrix.txt
K410N2_S39

library_source: transcriptomic

data_processing:
bcl2fastq,v2.20
fastp,0.22.0
HISAT2,2.2.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was harvested using TRIzol™ Reagent (ThermoFisher). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS VAHTS mRNA Capture Beads and VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina  following manufacturer's protocols.

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: ambient o2 concentration:21percent duration of hypoxia


title: KYSE410 Normoxia rep3

description:
K410expression_matrix.txt
K410N3_S40


title: Con2

city: Guangzhou

first: Xiaofei

last: Zhang

address: 1838 North Guangzhou Avenue

department: Department of Gynecology and Obstetrics

institute: Nanfang Hospital, Southern Medical University

data_processing:
Raw reads obtained by Illumina HiSeq2500 sequencing are filtered first: remove the adapters at both ends of reads, remove reads with fragment length <17nt and low-quality reads, etc. complete the preliminary filtering of data and obtain high-quality data (clean reads).  Genome-wide reads distribution map was obtained by aligning clean reads with reference genome, and ncRNA classification annotation was performed on clean reads.  The miRNA expression was calculated, miRNA expression clustering and miRNA differential expression analysis among samples.
Assembly: hg38
Supplementary files format and content: Microsoft Excel  Worksheet (.xls) file includes counts for each sample

source_name: Follicular fluid exosomes

extract_protocol:
Follicular fluid from POI patients and control group patients were collected. Exosomes from follicular fluid were extracted by ultracentfugation method, total RNA from exosomes was extracted by trizol method, and sRNA of 18-30nt was screened for high throughput sequencing
The library construction process mainly includes the following steps: extraction of total RNA or purified sRNA fragments of the sample, connection of connector successively, reverse transcription into cDNA, and then PCR amplification. Then the target fragment library was recovered by cutting glue, and the qualified library was sequenced.

tag: tissue

value: Follicular fluid exosomes

value: Normal ovarian reserve


title: Con1


title: HC618110941

type: RNA

city: Beijing

first: Yin

last: Wu

state: -- select

address: No. 8 Gongti south street road, Chaoyang district

department: Heamotologic department

institute: Capital Medical University Beijing Chaoyang Hospital

description: see next sheet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Primeview Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: NDMM bone marrow plasmacells, CD138 magnetic beads sorted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: primary plasmacells were sortted from bone marrow of newly diagnosed multiple myeloma patients using CD138 magnetic beads according to the manufacturer's instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: no

tag: batch

value: Batch 4

tag: gender

value: M

tag: age

tag: time at diagnosis

tag: type

value: IgG-Lambda

tag: riss

value: I

tag: treatment strategy

value: NO

tag: best respose

value: SD

tag: chromosome

tag: FISH

value: negtive

tag: os(months)


title: KYSE150 Hypoxia rep3

description:
K150expression_matrix.txt
K150H3_S55

tag: time point


title: KYSE410 Hypoxia rep2

description:
K410expression_matrix.txt
K410H2_S57

tag: cell line


title: KYSE150 Hypoxia rep2

description:
K150expression_matrix.txt
K150H2_S54

tag: cell type


title: KYSE410 Normoxia rep1

description:
K410expression_matrix.txt
K410N1_S38

tag: genotype


title: G2529SGLB

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description: PGAL1-FLO11, SG liquid B

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

organism: Saccharomyces cerevisiae

source_name: yeast cell culture

label_protocol: Affymetrix IVT labeling

growth_protocol: 6 hour growth

extract_protocol: Qiagen RNeasy mini-kit

treatment_protocol: quick-frozen in acid phenol

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SG

tag: growth medium

value: liquid


title: G2529SGLC

description: PGAL1-FLO11, SG liquid C


title: HC618110928

description: see next sheet

tag: batch

tag: gender

tag: age

value: II

value: CTD*6, ASCT ，T maintenance

value: VGPR


title: AGS-NC_2

city: Changsha

first: wenjie

last: Feng

state: hunan

address: Xiangya Street

department: burn and reconstruction department

institute: central south university

description: AGS_NC_3 FPKM

data_processing:
SOAPnuke software developed by BGI
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke software benchwork (parameter- Quality limit: -n 0.01 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --polyX 50 --minReadLen 150 )
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text files include RPKM for each sample

source_name: stomach

extract_protocol:
RNA was harvested using total RNA extract kit (Solarbio ,China).1.5ug total RNA was used for constructIon sequencing libraries
RNA libraries for RNA-seg were prepared using  DNBSEQ Eukaryotic mRNA library Prep Kit following manufacturer's protocols

tag: tissue

value: stomach

value: AGS

value: gastric cancer cell

tag: treatment

value: ANGPTL4 victor 2


title: HC618110927

description: see next sheet

value: Batch 4

value: F

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

tag: treatment strategy

value: CTD*2 MP*2

tag: best respose

value: PD


title: AGS-OE_2

description: AGS_OE_3 FPKM

tag: cell line

value: ANGPTL4 oe 2


title: G2529SGLA

description: PGAL1-FLO11, SG liquid A


title: AGS-NC_1

description: AGS_NC_2 FPKM

tag: cell type

value: ANGPTL4 victor 1


title: KYSE150 Normoxia rep2

description:
K150expression_matrix.txt
K150N2_S51

value: esophageal cancer cell line

tag: genotype

value: WT

value: ambient o2 concentration:21percent duration of hypoxia

tag: time point


title: HC618110930

description: see next sheet

value: M

value: IgG-Lambda

value: III

value: PDD*4 ,ASCT, PDD*1 PTD*3, PT maintenance

tag: chromosome

value: ND

tag: FISH


title: AGS-OE_1

description: AGS_OE_2 FPKM

value: stomach

value: AGS

value: gastric cancer cell

value: ANGPTL4 oe 1


title: HC618110923

description: see next sheet

value: Batch 4

value: kappa

value: II

value: PDD*4 ,ASCT,BD maintenance

value: CR

value: negtive


title: G2529LB

description: PGAL1-FLO11, SD liquid B

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

tag: growth medium

value: liquid


title: AGS-OE

description: AGS_OE_1 FPKM

tag: tissue

value: ANGPTL4 oe


title: G2529LC

description: PGAL1-FLO11, SD liquid C


title: KYSE150 Hypoxia rep1

description:
K150expression_matrix.txt
K150H1_S53

value: esophageal cancer cell line

value: WT

tag: treatment

value: ambient o2 concentration:0.50percent duration of hypoxia

value: 48 hours


title: HC618110919

description: see next sheet

tag: batch

tag: gender

value: M

tag: age

tag: time at diagnosis

value: IgA-Lambda

value: BD*2 VRD*6,ID maintenance

value: PR

value: hypodiploids


title: HC618110925

description: see next sheet

value: Batch 4

value: F

tag: type

tag: riss

value: II

tag: treatment strategy

value: PAD*4,ASCT,BTD maintenance

tag: best respose

value: CR MRD-

value: ND


title: G2529SGSC

description: PGAL1-FLO11, SG agar C

value: 6 hrs

value: SG

value: agar


title: KYSE150 Normoxia rep3

description:
K150expression_matrix.txt
K150N3_S52

tag: cell line

tag: cell type

value: esophageal cancer cell line

tag: genotype

value: WT

value: ambient o2 concentration:21percent duration of hypoxia

tag: time point


title: AGS-NC

description: AGS_NC_1 FPKM

value: stomach

value: AGS

value: gastric cancer cell

value: ANGPTL4 control cell


title: HC618110916

description: see next sheet

value: IgA-Lambda

value: MR

tag: chromosome

tag: FISH

tag: os(months)


title: G2529SGSA

description: PGAL1-FLO11, SG agar A

tag: genotype/variation

tag: growth time

tag: nutrient composition

tag: growth medium


title: G2529LA

description: PGAL1-FLO11, SD liquid A

value: SD

value: liquid


title: KYSE150 Normoxia rep1

description:
K150expression_matrix.txt
K150N1_S50

tag: treatment


title: G2529SGSB

description: PGAL1-FLO11, SG agar B


title: D456, NT, 3

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
We processed the raw files using aRNA-pipe which implements STAR for alignment and HTSeq for the generation of count tables
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2,5,2b for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Assembly: hg37
Supplementary files format and content: tab delimited text file for raw counts of all samples

source_name: GBM 456

growth_protocol: DMEM/F12 basal media (Invitrogen) supplemented with epidermal growth factor (EGF), fibroblast growth factor, sodium pyruvate, penicillin/streptomycin, and the B27 equivalent GEM21 (Gemini Bio Products)

extract_protocol:
Norgen Total RNA kit plus DNase treatment according to the manufacturer's protocol
We used 800 ng of total RNA as input to the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB cat# E7490S). PolyA depleted RNA was used as input to the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB cat# E7530S). Libraries were barcoded using the NEBNext Multiplex Oligos for Illumina (NEB cat# E7335S).

treatment_protocol: GBM 456 cells were transiently co-transfected with psPAX2, pCMV-VSVG and shRNA constructs using FuGENE® HD Transfection Reagent (Promega) as previously reported(67). Virus titer was determined using Lenti-X qRT-PCR Titration Kit (Takara). Lentivirus pLenti6.3/V5 GCH1 (HsCD00941202) was purchased from DNASU while pLenti6.3 EV was purchased from Addgene. For lentivirus expressing GCH1 shRNAs (TRCN0000050744 and TRCN0000050745) and non-targeting control shRNA were purchased from Sigma. Both shRNA constructs were designed against the GCH1 coding sequence. The shRNA sequences were as follows: GCH1 Sh4:5’CCATATTGGTTATCTTCCT’3’ and GCH1 Sh5: 5’GATGTCCTAAACGATGCTA3’

value: GBM 456

value: glioblastoma

value: Control

value: shRNA


title: D456, GCH1, sh5, 3

value: GCH1 KD


title: D456, GCH1, sh4, 3


title: D456, GCH1, oe, 3

value: GCH1 OE

value: genetic modification


title: Donor #4 Fibrosa

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive NE

department: Biomedical Engineering

institute: Georgia Tech & Emory University

description:
all_donors_gene_counts.csv
all_donors_metadata.csv
all_donors.rds

library_source: transcriptomic single cell

data_processing:
scRNAseq data files were processed and aligned to the human reference genome (GRCh38) using CellRanger from 10X Genomics
The generated h5 files for each sample were processed with Seurat R package (v3) for further analysis
Quality checks to retain cells with 200-8,000 unique feature counts and less than 20% of mitochondrial counts were performed. All datasets were then merged, normalized, scaled, clustered, and visualized by UMAP. Cell types were annotated using known markers for VEC, VIC, MΦ, and T-cells. Clusters with low expression of all annotation markers were designated as Stromal cells. Clusters with expression of more than 1 annotation marker subset were labeled as Transitional (Trans) cells. Multiple clusters of the same cell type were designated numbers (e.g., VEC1, VEC2).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aortic valve

extract_protocol:
Briefly, 500 units/mL of collagenase type I (MP Biomedical), 500 units/mL of collagenase type II (MP Biomedical), 150 units/mL collagenase Type XI (Sigma-Aldrich), 60 units/mL hyaluronase type Is (Sigma-Aldrich), and 60 units/mL DNASE I (Zymo) were dissolved in HBSS without calcium and magnesium and filtered through a 0.45 um syringe filter. One and a half AV leaflets were placed in a 35 mm dish with the desired layer for isolation face-up, then 2 mL of dissociation buffer was placed on the upwards facing layer and incubated for 45 min at 37 ºC. After incubation, cells from the layer in contact with the dissociation buffer were gently scraped off using a sterile cotton swab, blocked with 1 mL of fetal bovine serum (FBS) and passed through a 70 μm cell strainer. The suspension was centrifuged for 5 min at 500 x g and resuspended in > 50 μL of 2% BSA in PBS at a concentration of 1000 cells/μL.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

tag: tissue

value: Aortic valve

tag: layer

value: Fibrosa

tag: disease stage

value: Moderate Fibrosis

tag: sex-age

tag: race

value: Hispanic


title: Donor #5 Ventricularis

value: Ventricularis

value: Fibrocalcification

value: White


title: G2529SC

description: PGAL1-FLO11, SD agar C

value: 6 hrs

value: agar


title: D456, GCH1, sh5, 2

tag: cell line


title: HC618110910

description: see next sheet

tag: batch

value: Batch 4

tag: gender

value: F

tag: age

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

value: II

tag: treatment strategy

value: BD*7 ,Rd maintenance

tag: best respose

value: PR

value: complicated


title: G2529SA

description: PGAL1-FLO11, SD agar A

tag: genotype/variation

tag: growth time

tag: nutrient composition

value: SD


title: Donor #4 Leftover 2

tag: tissue

value: Aortic valve

value: Mixed


title: D456, NT, 2

value: GBM 456

tag: cell type

value: glioblastoma

tag: genotype

value: Control

tag: treatment

value: shRNA


title: Donor #5 Fibrosa

tag: layer

value: Fibrosa

tag: disease stage

value: Fibrocalcification

tag: sex-age

tag: race

value: White


title: G2529SB

description: PGAL1-FLO11, SD agar B

value: 6 hrs

tag: growth medium

value: agar


title: G85SGLB

description: wild-type, SG liquid B

value: wild-type

value: SG

value: liquid


title: HC618110911

description: see next sheet

tag: batch

value: Batch 4

tag: gender

value: M

tag: age

tag: time at diagnosis

value: IgG-K

value: II

value: CR,MRD+

tag: chromosome

tag: FISH

value: negtive


title: Donor #4 Leftover 1

value: Aortic valve

value: Mixed

value: Moderate Fibrosis

value: Hispanic


title: HC618110908

description: see next sheet

value: F

tag: type

value: IgA-Lambda

tag: riss

value: III

tag: treatment strategy

value: BCD*9, RD-R maintenance

tag: best respose

value: CR

value: hypodiploids


title: Donor #4 Leftover 3

tag: tissue


title: G85SGLC

description: wild-type, SG liquid C

tag: genotype/variation

value: wild-type

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SG

value: liquid


title: HC618110905

description: see next sheet

value: Batch 4

value: IgG-Lambda

value: II

value: BCD*9, Thal maintenance

tag: os(months)


title: HC618110906

description: see next sheet

value: M

value: IgG-K

value: PR


title: NUP98/NSD1+ RUNX1/ZNF423+ AML blasts from NSG mice, RNA-seq

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: spleen

extract_protocol:
Mononuclear cells derived from the patient were isolated from bone marrow using lymphocyte monocyte separation medium (GE Healthcare); Mononuclear cells were isolated from spleen of PDX mice using mouse mononuclear cell isolate kit (Solarbio)
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

tag: disease state

value: Acute myeloid leukemia (AML)

value: spleen

tag: cell line

value: primary cell

tag: cell type

value: mononuclear cells

tag: cell source

value: PDX mice


title: Donor #4 Ventricularis

value: Aortic valve

tag: layer

value: Ventricularis

tag: disease stage

value: Moderate Fibrosis

tag: sex-age

tag: race

value: Hispanic


title: D456, GCH1, sh4, 2

value: GBM 456

value: glioblastoma

tag: genotype

value: GCH1 KD

tag: treatment

value: shRNA


title: D456, GCH1, oe, 2

value: GCH1 OE

value: genetic modification


title: HC618110901

description: see next sheet

tag: batch

value: Batch 4

tag: gender

value: M

tag: age

tag: time at diagnosis

tag: type

value: IgG-Lambda；Lambda

tag: riss

value: I

tag: treatment strategy

value: BCD*2、Rd maintenance

tag: chromosome

value: complicated

tag: FISH


title: D456, NT, 1

tag: cell line

tag: cell type

value: Control


title: HC618110909

description: see next sheet

value: IgA-Lambda

value: II

value: PDDT*4 ，ASCT， BD， T maintenance

tag: best respose

value: CR MRD+


title: G2300LB

description: flo11 knockout, SD liquid B

tag: genotype/variation

value: flo11 knockout

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

tag: growth medium

value: liquid


title: G85SGLA

description: wild-type, SG liquid A

value: wild-type

value: SG


title: HC618110903

description: see next sheet

value: Batch 4

value: IgD-Lambda

value: PAD*5 ,BD*1

value: CR

tag: os(months)


title: HC618110904

description: see next sheet

tag: batch

value: M

value: IgG-Lambda

value: III

value: PAD*5,PCTD*3, PCETD*1 ,VT-DECP

value: PR


title: G2300LC

description: flo11 knockout, SD liquid C


title: Donor #3 Fibrosa

tag: tissue

value: Aortic valve

tag: layer

value: Fibrosa

tag: disease stage

value: Mild Fibrosis

tag: sex-age

tag: race

value: White


title: Donor #3 Leftover

value: Mixed


title: G85SGSC

description: wild-type, SG agar C

value: 6 hrs

value: agar


title: Donor #3 Ventricularis

value: Ventricularis


title: Donor #2 Fibrosa

value: Black


title: HC618091410

description: see next sheet

value: Batch 2

tag: gender

tag: age

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

value: II

tag: treatment strategy

value: VGPR


title: D456, GCH1, sh5, 1

tag: cell line

value: GBM 456

tag: cell type

value: glioblastoma

tag: genotype

value: GCH1 KD

tag: treatment

value: shRNA


title: D456, GCH1, oe, 1

value: GCH1 OE

value: genetic modification


title: D456, GCH1, sh4, 1


title: QR27, case

city: New York

first: Bin

last: Xu

state: NY

address: 1051 Riverside Dr

department: Psychiatry

institute: Columbia University

description: total RNA size fractionated prior to library preparation

data_processing:
Raw reads were subjected to ACGT101-miR (LC Sciences, Houston, TX, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18∼26 nucleotide were mapped to specific species precursors in miRBase (v22.0) by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
The unique sequences mapping to human mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known human  precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two mentioned mapped   5p and 3p sequences were defined as known miRNAs.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
Assembly: Hg38, Ensembl version 98
Supplementary files format and content: Differentially expressed miRNA between case and control
Supplementary files format and content: raw counts

source_name: iPSC-derived cerebral organoid

growth_protocol: Cerebral Organoids were generated as described in Rao et. al

extract_protocol:
Total RNA extraction with miRNA enrichment was performed using the Vana™ miRNA Isolation Kit (Thermo Fisher Scientific, AM1561).
Approximately 1 ug of total RNA was used to prepare small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA) and single-end sequencing 50bp on an Illumina Hiseq 2500 (following the vendor’s recommended protocol) was conducted

value: iPSC-derived cerebral organoid

value: mixed, iPSC-derived cerebral organoid

value: 70DIV IPSC derived cerebral organoid


title: Donor #1 Fibrosa

value: Aortic valve

value: Fibrosa

value: Non-Diseased


title: QR20, control

value: Wild type


title: HC618091407

description: see next sheet

value: Batch 2

value: M

value: IgA-Lambda,IgG-Lambda

value: III

value: VAD*1, PDD*6, ASCT

tag: best respose

value: sCR

tag: chromosome

value: complicated

tag: FISH

value: ND

tag: os(months)


title: Q6, case

tag: tissue


title: Donor #1 Leftover

tag: layer

value: Mixed

tag: disease stage

tag: sex-age

value: Black


title: Q5, control

value: iPSC-derived cerebral organoid


title: G85SGSB

description: wild-type, SG agar B

tag: genotype/variation

value: wild-type

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SG

tag: growth medium

value: agar


title: G85SGSA

description: wild-type, SG agar A


title: G2300SA

description: flo11 knockout, SD agar A

value: flo11 knockout

value: SD


title: G2300SC

description: flo11 knockout, SD agar C


title: G2300LA

description: flo11 knockout, SD liquid A

value: liquid


title: Donor #1 Ventricularis

value: Aortic valve

value: Ventricularis

value: Non-Diseased

tag: race


title: HC618091405

description: see next sheet

tag: batch

value: Batch 2

tag: gender

value: M

tag: age

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

value: II

tag: treatment strategy

value: BCD*2 BTD*3, RCD maintenance

value: PR


title: Q2, control

value: iPSC-derived cerebral organoid

tag: cell line

tag: cell type

value: mixed, iPSC-derived cerebral organoid

tag: genotype

value: Wild type

tag: treatment

value: 70DIV IPSC derived cerebral organoid


title: G2300SB

description: flo11 knockout, SD agar B

value: 6 hrs

value: agar


title: HC618091403

description: see next sheet

value: IgG-Lambda

value: III

tag: best respose

tag: chromosome

value: ND

tag: FISH

tag: os(months)


title: G2468LC

description: msb2 knockout, SD liquid C

tag: genotype/variation

value: msb2 knockout

tag: growth time

tag: nutrient composition

value: SD

tag: growth medium

value: liquid


title: HC618091406

description: see next sheet

tag: batch

value: Batch 2

tag: gender

value: F

tag: age

value: Lambda

value: I

value: CR MRD-

value: complicated


title: HC618091404

description: see next sheet

value: M

tag: time at diagnosis

tag: type

tag: riss

value: PDD*4, ASCT, PDD*1 PTD*3

value: VGPR


title: Q1, case

tag: tissue

value: iPSC-derived cerebral organoid

tag: cell line

tag: cell type

value: mixed, iPSC-derived cerebral organoid

value: 70DIV IPSC derived cerebral organoid


title: HCT116 p53-/--KD-2

first: Lixiao

last: Zhou

address: Yuhangtang road

institute: Zhejiang University

data_processing:
Agilent 2100 Bioanalyzer to determine the quality of RNA
 Illumina HiSeq sequence database
Next-Generation Sequencing
Assembly: hg19
Supplementary files format and content: FPKM values

source_name: colon cancer cell line

extract_protocol:
Cells are collected and then treated with  Trizol reagent, and the RNA were extracted using precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: colorectal cancer

value: HCT116 cell line

tag: genotype

value: p53 null


title: G2468LB

description: msb2 knockout, SD liquid B

value: msb2 knockout

value: 6 hrs

value: SD


title: G2468LA

description: msb2 knockout, SD liquid A

value: liquid


title: G4_3

city: shanghai

first: Jiam

last: Gao

address: 197 Rui Jin 2nd Road

institute: Shanghai Institute of Hematology,Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: adipogenic differentiation

data_processing:
Raw sequencing reads were parsed (includes demultiplexing, barcode trimming, and adaptor removal)  and quality control using software of trimmomatic and FASTQC.
The clean reads were mapped to the human genome assembly hg38/GRCh38 using HISAT2.
Uniquely mapped reads were extracted for gene expression quantifiing by using the FeatureCounts software.
Differential expression analysis of RNA-Seq data in two groups was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: NUGC-4 cells, IN10018+Criozotinib, 24h

growth_protocol: NUGC-4 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Scientific). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared from samples by using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: NUGC-4 cells was treatment of 24h with 1uM IN10018 or  1uM Crizotinib, combination IN10018( 1uM) and Crizotinib (1uM ).

value: Diffuse gastric cancer cell line

value: WT

tag: treatment

value: IN10018+Criozotinib, 24h


title: Donor #2 Leftover

value: Aortic valve

tag: layer

value: Mixed

tag: disease stage

value: Mild Fibrosis

tag: sex-age

tag: race

value: Black


title: HCT116 p53-/--KD-1


title: HC219103019

description: see next sheet

value: Batch 3

value: M

value: IgG-K

value: II

tag: treatment strategy

tag: best respose

value: VGPR

tag: chromosome

value: ND

tag: FISH


title: G4_2

description: adipogenic differentiation


title: HC618110956

description: see next sheet

tag: batch

value: Batch 4

tag: gender

tag: age

tag: time at diagnosis

value: IgD-Lambda

value: MR

tag: os(months)


title: G4_1

description: adipogenic differentiation

tag: cell line

tag: cell type


title: HC219103025

description: see next sheet

tag: type

value: IgG-k

tag: riss

value: VRD*7, RD-R maintenance

value: VGPR MRD+


title: HC219103020

description: see next sheet

value: kappa

value: III

value: PR


title: HC219103018

description: see next sheet

value: F

value: IgG-Lambda

value: VRD*5,RD*2,R maintenance

value: CR


title: HCT116 p53-/--scr-2

tag: disease

value: colorectal cancer

value: HCT116 cell line

tag: genotype

value: p53 null


title: HCT116 p53-/--scr-3


title: HC219103017

description: see next sheet

value: Batch 3

value: M

value: Lambda

value: II

value: ND


title: HCT116 p53-/--KD-3


title: G3_3

description: adipogenic differentiation

source_name: NUGC-4 cells, Criozotinib, 24h

value: Diffuse gastric cancer cell line

value: WT

tag: treatment

value: Criozotinib, 24h


title: G3_2

description: adipogenic differentiation


title: G3_1

description: adipogenic differentiation


title: G2434LC

description: [pRS316], SD liquid C

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

tag: growth medium

value: liquid


title: G2434LB

description: [pRS316], SD liquid B


title: G2434LA

description: [pRS316], SD liquid A


title: G2432LC

description: [pRS316-MSB2*], SD liquid C


title: HC219103014

description: see next sheet

value: IgA-k

tag: treatment strategy

value: VRD*2, RCD*1,ICD*1,VRD*2/IRD*7

tag: best respose

value: Scr

tag: chromosome

tag: FISH


title: HCT116 p53-/--scr-1

value: colorectal cancer


title: HC219103015

description: see next sheet

tag: batch

tag: gender

tag: age

tag: time at diagnosis

value: VRD*4 ,IRD*1 RD*1,TD-T maintenance

value: CR


title: G2_3

description: adipogenic differentiation

source_name: NUGC-4 cells, IN10018, 24h

tag: cell line

tag: cell type


title: HCT116 p53+/+-KD-1

tag: disease

value: HCT116 cell line

value: p53 WT


title: G2432LB

description: [pRS316-MSB2*], SD liquid B


title: HCT116 p53+/+-KD-3

tag: genotype


title: HC219103016

description: see next sheet

value: Batch 3

value: F

tag: type

value: IgG-K

tag: riss

value: I

value: VRD*5，IRd*5，R maintenance

value: CR MRD+


title: HCT116 p53+/+-KD-2


title: G2_2

description: adipogenic differentiation

value: Diffuse gastric cancer cell line

value: WT

tag: treatment


title: HCT116 p53+/+-scr-2


title: HCT116 p53+/+-scr-3


title: G2432LA

description: [pRS316-MSB2*], SD liquid A

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

value: liquid


title: G2468SB

description: msb2 knockout, SD agar B

value: msb2 knockout

tag: growth medium

value: agar


title: HC219103013

description: see next sheet

value: M

value: IgD-Lambda

value: II

tag: treatment strategy

value: VRD*6 ASCT,R maintenance

tag: best respose

value: sCR，MRD-


title: G2_1

description: adipogenic differentiation


title: HC219103012

description: see next sheet

tag: batch

value: Batch 3

value: kappa

value: III

tag: chromosome

tag: FISH

value: 1q21（+3),CCND1+，MAF -,FGFR3 -

tag: os(months)


title: G2468SC

description: msb2 knockout, SD agar C


title: HC219103011

description: see next sheet

tag: gender

tag: age

tag: time at diagnosis

value: VRD*1,RCD*3 ICD*8，IR maintenance

value: CR

value: 1q21（+3） ，TP53 -，IGH/FGFR3


title: HC219103009

description: see next sheet

value: F

value: IgG-L

value: VRD*8,R maintenance

value: FGFR3 +


title: HC219103010

description: see next sheet

value: IgA-k

value: BD*1 BCD*5 TD*2, Rd*2-R maintenance

value: VGPR

value: 1q21+,FGFR3+，IGH-,MAF -


title: G2468SA

description: msb2 knockout, SD agar A

value: msb2 knockout

value: 6 hrs

value: SD

value: agar


title: PAH_Lung_15

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

data_processing:
Basecalls was performed using bcl2fastq v1.3.0
Sequenced reads were mapped to the human genome assembly (GRCh38) with STAR v2.6.1a with the following options: STAR --readFilesCommand zcat --quantMode TranscriptomeSAM --outFilterMismatchNmax 999 --sjdbGTFfile /home/dnanexus/Homo_sapiens.GRCh38.98.gtf --genomeDir ./home/dnanexus/genome --outSAMstrandField intronMotif --sjdbScore 1 --alignIntronMin 20 --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --alignSJoverhangMin 8 --alignMatesGapMax 1000000 --outFileNamePrefix /home/dnanexus/outputs/ --outFilterMismatchNoverReadLmax 0.04 --outWigStrand Unstranded --runThreadN 16
The quantification of the transcriptome-mapped reads was perfomred using RSEM v1.3.1 with the following command: rsem-calculate-expression --no-bam-output --bam --paired-end --num-threads 8
The raw counts generated from rsem were normalized using the cpm function from edgeR v3.14.0
Assembly: hg38
Supplementary files format and content: csv file for genes counts for Lung samples

source_name: Human Lung

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer’s instructions. RNA quality was checked, and RNA was quantified using a NanoDrop spectrophotometer.
RNA libraries were prepared using the TruSeq® Stranded mRNA Library

tag: tissue

value: Lung

tag: condition

value: PAH


title: G1_3

description: adipogenic differentiation

source_name: NUGC-4 cells, Control, 24h

tag: cell line

tag: cell type

value: Diffuse gastric cancer cell line

tag: genotype

value: WT

value: Control, 24h


title: G1_2

description: adipogenic differentiation

tag: treatment


title: G1_1

description: adipogenic differentiation


title: G2434SB

description: [pRS316], SD agar B

tag: genotype/variation

tag: growth time

tag: nutrient composition


title: PAH_Lung_14


title: NUP98/NSD1+ RUNX1/ZNF423+ AML blasts from patient, RNA-seq

source_name: bone marrow

tag: disease state

value: Acute myeloid leukemia (AML)

value: bone marrow

value: primary cell

value: mononuclear cells

tag: cell source

value: patient


title: G2434SA

description: [pRS316], SD agar A

tag: growth medium


title: G2434SC

description: [pRS316], SD agar C


title: PAH_Lung_13


title: HCT116 p53+/+-scr-1

tag: disease

value: colorectal cancer

value: HCT116 cell line

value: p53 WT


title: shUSP27X_3

city: Weifang

first: Zhenhai

last: Yu

address: No.288 Shengli East Street

institute: Weifang Medical University

data_processing:
After the library was constructed, the library was first diluted to 1.5ng/ul using a Qubit 2.0 Fluorometer for initial quantification.
The insert size of the library was detected using Agilent 2100 bioanalyzer, and the effective library concentration was accurately quantified by qRT-PCR after the insert size was as expected (effective library concentration above 2nM)
After passing the library inspection, the different libraries are pooled according to the effective concentration and the target downstream data volume required for Illumina sequencing.
Sequenced fragments are converted into sequence data (reads) by CASAVA base identification of image data measured by high-throughput sequencers

source_name: MCF7 cells

extract_protocol:
RNA was extracted from tissues or cells using standard extraction methods, and then the RNA samples were strictly controlled. The quality control method was mainly through Agilent 2100 bioanalyzer: accurate detection of RNA integrity.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: MCF7 cells

value: breast cancer cells

value: USP27X knockdown


title: G2432SC

description: [pRS316-MSB2*], SD agar C

value: 6 hrs

value: SD

value: agar


title: HC219103007

description: see next sheet

tag: batch

value: Batch 3

value: F

tag: type

value: Lambda

tag: riss

value: II

tag: treatment strategy

tag: chromosome

tag: FISH

tag: os(months)


title: PAH_Lung_12

tag: tissue

value: Lung

tag: condition

value: PAH


title: shUSP27X_2

tag: cell line

tag: cell type

tag: genotype


title: HC219103008

description: see next sheet

tag: gender

value: M

tag: age

tag: time at diagnosis

value: IgA-k

tag: best respose


title: G2432SB

description: [pRS316-MSB2*], SD agar B

tag: genotype/variation

tag: growth time

tag: nutrient composition

tag: growth medium


title: HC219103006

description: see next sheet

tag: batch

tag: type

value: IgA-L

tag: riss

tag: treatment strategy

value: VRD*4 VRCD*1 BiVRCD*1 ,VRCD*1

value: PD

value: 1q21（+3）、TP53 mutation


title: shUSP27X_1

value: MCF7 cells

value: breast cancer cells


title: HC219103004

description: see next sheet

value: kappa

value: BCD*8 ICD*3

value: CR MRD+

tag: chromosome

value: ND

tag: FISH


title: HC219103005

description: see next sheet

value: Batch 3

value: F

value: III

value: BD*1 BDT*1

value: 1q21（+4），TP53 - ，IGH/FGFR3

tag: os(months)


title: G2432SA

description: [pRS316-MSB2*], SD agar A

value: 6 hrs

value: SD

value: agar


title: HC219103003

description: see next sheet

value: M

value: IgG-K

value: II

value: BCD*2, PACD*2，ICED,ICETD

value: MR


title: PAH_Lung_10

tag: tissue

value: Lung

tag: condition

value: PAH


title: PAH_Lung_11


title: 1128LCb

description: [pRS313-STE11-4], SD liquid C

value: liquid


title: HC219103002

description: see next sheet

tag: gender

value: Lambda

value: 髓内达sCR，MRD-

value: ND

value: IGH-


title: shNC_3

tag: cell line

value: MCF7 cells

tag: cell type

value: breast cancer cells

tag: genotype

value: WT


title: PAH_Lung_9


title: 1128LBb

description: [pRS313-STE11-4], SD liquid B

tag: genotype/variation

value: 6 hrs

value: SD


title: shNC_2


title: shNC_1


title: shNC-ATAC

city: Wuhan

first: Hanyang

last: Hu

state: Please Select

address: School of Basic Medical Sciences, Wuhan University

institute: Wuhan University

library_source: genomic

data_processing:
Raw reads of ChIP-seq and ATAC-seq were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned to the hg19 build of the human genome using Subread aligner v2.0.0.
MACS2 and Homer were used to find peaks
Assembly: hg19
Supplementary files format and content: BED format for peaks

molecule: genomic DNA

source_name: shNC-ATAC

growth_protocol: HTR8/SVneo cells were grown in RPMI-1640 media supplemented with 10% fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin

extract_protocol:
For ATAC-seq, nuclei were isolated in cold lysis buffer (10mM Tris-HCL [pH 7.4], 10 mM NaCl, 3mM MgCl2, 0.1% NP-40) by centrifugation at 500Xg for 10 min.
ATAC-seq libraries were prepared using the Nextera DNA Library Prep Kit, puified using the Qiagen MinElute Reaction Cleanup Kit, amplified by PCR and purified using Kapa Pure Beads.

treatment_protocol: Cells were treated with 30 mM glucose for 24 hour

value: HTR8/SVneo cells

value: immortalized first-trimester invasive trophoblast cell line

value: control


title: PAH_Lung_8


title: HC219103001

description: see next sheet

value: Batch 3

value: M

tag: age

tag: time at diagnosis

value: IgA-Lambda

value: II

value: VRD*4 ,PTD ,VRCD,ASCT, R maintenance

tag: best respose

value: PR


title: shM3-ATAC

value: METTL3 knockdown


title: PAH_Lung_5

value: Lung

value: PAH


title: shNC_H3K27ac_IP

extract_protocol:
For ChIP-seq, chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
DNAs purified from input and IP samples were subjected to library generation using HyperPlus Library Preparation Kit

tag: antibody


title: PAH_Lung_7


title: PAH_Lung_6


title: 1128LAb

description: [pRS313-STE11-4], SD liquid A

tag: growth time

tag: nutrient composition

tag: growth medium

value: liquid


title: HC219050849

description: see next sheet

tag: batch

value: Batch 1

tag: type

value: kappa

tag: treatment strategy

tag: chromosome


title: PAH_Lung_3

tag: tissue

tag: condition


title: PAH_Lung_4


title: shNC_H3K27ac_Input

tag: cell line


title: HC219050850

description: see next sheet

tag: gender

value: F

value: PCL

tag: riss

value: III

tag: FISH

tag: os(months)


title: shNC_ARID1A_IP

value: HTR8/SVneo cells

tag: cell type

value: immortalized first-trimester invasive trophoblast cell line

tag: genotype


title: 85C0b

description: wild-type, t=0, SD liquid C

growth_protocol: 0 hours growth

tag: genotype/variation

value: wild-type

value: 0 hrs

value: SD


title: 1066LBb

description: [pRS313], SD liquid B

tag: growth time

value: 6 hrs


title: 1066LCb

description: [pRS313], SD liquid C

tag: nutrient composition


title: HC219050847

description: see next sheet

tag: age

tag: time at diagnosis

value: IgA-L

value: II

tag: best respose

value: CR

value: 1q21 +、IGH +


title: 85A0b_2

description: wild-type, t=0, SD liquid A

tag: growth medium


title: 85B0b

description: wild-type, t=0, SD liquid B


title: HC219050848

description: see next sheet

tag: batch

value: M

tag: type

value: NS

tag: treatment strategy

value: PTD*4 ,PDDT*1 PVDD*1 PCAD ,R maintenance

value: MR

tag: chromosome


title: HC219050845

description: see next sheet

value: Batch 1

tag: gender

value: kappa

value: BCD*6 ICD*5


title: HC219050846

description: see next sheet

tag: riss

value: PDD*5 ,VRD*1

value: CR MRD+


title: PAH_Lung_1

tag: tissue

value: Lung

tag: condition

value: PAH


title: shNC_ARID1A_Input

tag: cell line

value: HTR8/SVneo cells

tag: cell type

value: immortalized first-trimester invasive trophoblast cell line

value: control


title: shM3_H3K27ac_IP

tag: genotype

value: METTL3 knockdown

tag: antibody


title: Control_Lung_18

value: Control


title: 1066LAb

description: [pRS313], SD liquid A

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

value: liquid


title: 1128SC

description: [pRS313-STE11-4], SD agar C

value: agar


title: shM3_H3K27ac_Input


title: Control_Lung_17


title: 1128SB

description: [pRS313-STE11-4], SD agar B


title: HC219050843

description: see next sheet

value: F

tag: age

tag: time at diagnosis

value: Lambda

value: II

value: PDD*4，ASCT，R maintenance

tag: best respose

tag: FISH

value: MAF-


title: HC219050842

description: see next sheet

tag: batch

value: Batch 1

tag: type

value: IgG-K

value: III

tag: treatment strategy

value: PDD*5,  ASCT, VRD*4, R maintenance

value: CR MRD+


title: Control_Lung_16

value: Lung


title: shM3_ARID1A_IP

value: HTR8/SVneo cells

value: immortalized first-trimester invasive trophoblast cell line

value: METTL3 knockdown


title: PAH_Lung_2

value: PAH


title: shM3_ARID1A_Input


title: Control_Lung_15

value: Control


title: 1128SA

description: [pRS313-STE11-4], SD agar A

value: 6 hrs

value: SD

tag: growth medium

value: agar


title: HC219050844

description: see next sheet

tag: gender

value: M

value: IgA-k

tag: riss

value: VRD*3 ,RD*1

value: VGPR

tag: chromosome

value: ND


title: Control_Lung_14

tag: tissue

tag: condition


title: shNC_METTL3_IP

tag: cell line

tag: cell type

tag: genotype

value: control

tag: antibody


title: 1066SB

description: [pRS313], SD agar B

tag: genotype/variation

tag: growth time

tag: nutrient composition


title: 1066SC

description: [pRS313], SD agar C


title: HC219050841

description: see next sheet

value: Batch 1

tag: age

tag: time at diagnosis

value: IgG-L

value: III

value: BTD*2, BD*2, ID*2, RD maintenance

tag: best respose

tag: FISH

tag: os(months)


title: shNC_METTL3_Input

value: HTR8/SVneo cells

value: immortalized first-trimester invasive trophoblast cell line


title: HC219050836

description: see next sheet

tag: batch

tag: gender

tag: type

value: IgG-K

value: II

tag: treatment strategy

value: VRD*5，RCD*7,R maintenance


title: Control_Lung_13

tag: tissue

value: Lung

tag: condition

value: Control


title: HC219050838

description: see next sheet

value: F

value: Lambda

tag: riss

value: BCD*2 VRCD*2

value: MR

tag: chromosome


title: shM3_METTL3_IP

tag: cell line

tag: cell type

tag: genotype

value: METTL3 knockdown

tag: antibody


title: Control_Lung_12


title: Control_Lung_11


title: G85_F0

description: wild-type, t=0, SD agar F

tag: genotype/variation

value: wild-type

tag: growth time

value: 0 hrs

tag: nutrient composition

value: SD

tag: growth medium

value: agar


title: shM3_METTL3_Input


title: G85_E0

description: wild-type, t=0, SD agar E


title: 1066SA

description: [pRS313], SD agar A

value: 6 hrs


title: KG1a-ATRA+VbP

first: xibao

last: yu

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Hematology

institute: Jinan University

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Then Tophat v2.0.9 was used to map the cleaned reads to the GRCh38 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: AML cell lines HEL and KG1a cells were cultured in RPMI 1640 containing 10% fetal bovine serum.

extract_protocol:
After treating with ATRA, VbP, combination of ATRA and VbP for 72 h, the HEL and KG1a cells were harvested and RNA was extracted with TRIzol reagent. Amplified cDNA was successively converted into short read sequencing libraries using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®. Hisat2 (version:2.0.4).
Libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: The cells were treated with ATRA, VbP, combination of ATRA and VbP.

value: Blood

tag: age

value: 59 years

value: wild type

tag: treatment

value: ATRA+VbP


title: Control_Lung_10


title: KG1a-VbP

value: VbP


title: HC219050833

description: see next sheet

tag: batch

value: Batch 1

tag: gender

tag: time at diagnosis

value: kappa

value: II

value: Dara-VMP

tag: best respose

value: VGPR

tag: FISH


title: HC219050834

description: see next sheet

value: M

tag: type

value: IgD-L

tag: riss

tag: treatment strategy

value: PCD*1,PCDT*2,PCDT*2 ASCT, R maintenance

value: CR MRD-

value: ND


title: Control_Lung_9

tag: tissue

value: Lung

tag: condition

value: Control


title: HC219050832

description: see next sheet

value: IgG-K

value: PDD*6 ,ID-I maintenance

tag: chromosome

value: negtive


title: 847SB

description: tec1 knockout, SD agar B

tag: genotype/variation

value: tec1 knockout

value: 6 hrs

value: SD

value: agar


title: 847SC

description: tec1 knockout, SD agar C

tag: growth time


title: KG1a-ATRA

value: Blood

value: 59 years

tag: genotype

value: wild type

tag: cell line

value: ATRA


title: Control_Lung_8


title: Control_Lung_7


title: KG1a-Ctrl

tag: age

value: DMSO


title: 847LC

description: tec1 knockout, SD liquid C

tag: nutrient composition

tag: growth medium

value: liquid


title: 847SA

description: tec1 knockout, SD agar A


title: Control_Lung_5


title: HEL-VbP

description: HEL-VbP

source_name: HEL

value: 30 years

value: HEL

tag: treatment

value: VbP


title: HC219050839

description: see next sheet

source_name: NDMM bone marrow plasmacells, CD138 magnetic beads sorted

tag: batch

value: Batch 1

tag: gender

value: M

tag: time at diagnosis

value: IgA-k

value: III

value: VGPR

tag: os(months)


title: Control_Lung_6

value: Lung

value: Control


title: HEL-ATRA

description: HEL-ATRA


title: G85_D0

description: wild-type, t=0, SD agar D

source_name: yeast cell culture

value: wild-type

value: 0 hrs

value: SD

value: agar


title: 847LB

description: tec1 knockout, SD liquid B

value: tec1 knockout

value: 6 hrs


title: HC219050829

description: see next sheet

tag: type

tag: riss

value: II

value: VRD*4 ,IRD*,4 RD maintenance

tag: best respose

value: CR ,MRD+

tag: FISH

value: IGH+


title: HC219050830

description: see next sheet

value: Batch 1

value: Lambda

tag: treatment strategy

value: VRD*6, ASCT，VRD*2，VR maintenance

value: CR

tag: chromosome


title: HEL-Ctrl

description: HEL-Ctrl

tag: tissue

value: Blood

value: 30 years

value: wild type

value: HEL

value: DMSO


title: HC219050831

description: see next sheet

value: F

value: kappa

value: III

value: PDD*1, R maintenance

value: PR

value: ND


title: Control_Lung_4

value: Lung

tag: condition

value: Control


title: Control_Lung_3


title: 527SC

description: Kss1K42R, SD agar C

tag: genotype/variation

tag: growth time

value: 6 hrs

value: SD

value: agar


title: 847LA

description: tec1 knockout, SD liquid A

value: tec1 knockout

tag: nutrient composition

value: liquid


title: Control_Lung_2


title: HC219050827

description: see next sheet

value: Batch 1

value: M

tag: age

value: IgG-K

value: II

value: BTD*8，T maintenance

value: sCR MRD+


title: HEL-ATRA+VbP

description: HEL-ATRA+VbP

value: Blood

value: 30 years

tag: genotype

value: wild type

tag: cell line

value: HEL

tag: treatment

value: ATRA+VbP


title: 527SB

description: Kss1K42R, SD agar B

tag: growth medium


title: 527SA

description: Kss1K42R, SD agar A


title: HC219050825

description: see next sheet

tag: batch

tag: gender

value: F

tag: time at diagnosis

value: PCL

value: III

value: VRDD*3 NR,V-DECP

value: NR

value: TP53 -,MAF-,IGH/CCND1

tag: os(months)


title: HC219050835

description: see next sheet

value: Batch 1

tag: type

tag: riss

value: I

value: VRD*8,VBiRD*4, Rd-R maintenance

tag: best respose

value: PR

tag: FISH


title: Control_Lung_1

tag: tissue

value: Lung

tag: condition

value: Control


title: HC219050828

description: see next sheet

tag: treatment strategy

value: VRDD*2 ,VRD*2, RD maintenance

value: CR MRD-

tag: chromosome


title: D15

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

data_processing:
Transcript Quantification: FASTA (fasta.gz) files were quantified using CellRanger. The specific command was 'cellranger count' with  all  paramters set as default.
Preprocessing: filtered count matrices from CellRanger were read into R and processed using Seurat (v4.0.4). The reminaing cells were filtered for total genes, total umis and mitochondrial percentage.
Analysis: Sample replicates were merged  and analysed using Seurat's standard workflow.
Genome_build: GRCh38, https://uswest.ensembl.org/info/data/ftp/index.html
Supplementary_files_format_and_content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post CellRanger filtering pre Seurat filtration.

source_name: D15 Enteric Neural Crest Crestosphere

growth_protocol: A previously established 12-day protocol was used to induce enteric neural crest (ENC) (Barber et al., 2019; Fattahi et al., 2016). ENC crestospheres were formed during D12–D15 by removing ENC induction crest medium C on D12 and detaching the ENC monolayers using accutase (30 min, 37 C, 5% CO2), and re-suspended the ENC cells in NC-C medium [FGF2 (10 ng ml-1), CHIR 99021 (3 μM), N2 supplement (10 μl ml-1), B27 supplement (20 μl ml-1), glutagro (10 μl ml-1), and MEM NEAAs (10 μl ml-1) in neurobasal medium] and transferred them to ultra-low-attachment plates to form free-floating 3D enteric crestospheres. On D14, cells were fed with fresh medium. On D15, enteric crestospheres medium was switched to ENC medium [GDNF (10 ng ml-1), ascorbic acid (100 μM), N2 supplement (10 μl ml-1), B27 supplement (20 μl ml-1), glutagro (10 μl ml-1), and MEM NEAAs (10 μl ml-1) in neurobasal medium]. Feeding continued every other day with ENC medium until D30-D40, after which, feeding frequency could be reduced to once or twice per week but at a higher volume.

extract_protocol:
Cells were washed twice in PBS and dissociated with accutase (Stemcell Tech) at 37 C. After 1 h (30 min for D10 and D15 samples) cells were triturated with a wide bore pipet tip and passed through a 37μm reversible cell strainer. The single cell containing filtrate was collected in 4mL cold complete media. After washing cells were washed with PBS, counted and proceeded to library preparation
snRNA-seq libraries were prepared with Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics). The libraries were sequenced at UCSF Center for Advanced Technology.

treatment_protocol: No special treatment was performed.

value: hPSC-derived Enteric Neural Crest Crestosphere

tag: plating

value: Suspension

tag: differentiation replicate


title: D10

source_name: D10 Enteric Neural Crest Induction

tag: cell line

value: Adherent (Geltrex)


title: HC219050826

description: see next sheet

value: M

tag: age

value: Lambda

value: II

value: PCDD*1, PCDT*1

value: MR


title: RNA-seq_RNAi-ABCA1-seRNA-3

city: WuHan

first: shuai

last: mei

address: 1095# Jiefang Ave

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

extract_protocol:
RNAi-Ctrl or RNAi-ABCA-seRNATHP1 cells were collected and the RNA was extracted using Trizol (Thermo Fisher Scientific，15596018).
The sequencing library was conducted by NEBNext UltraTM RNA Library Prep Kit (NEB #E749), and purified by AMPure XP system, according to the standard Illumina protocols.

tag: genotype


title: HC219050824

description: see next sheet

tag: batch

value: F

value: IgA-Lambda

value: negtive


title: HC219050823

description: see next sheet

value: Batch 1

tag: gender

value: IgG-Lambda

value: III

value: BD


title: 527LB

description: Kss1K42R, SD liquid B

tag: genotype/variation

tag: growth time

value: 6 hrs

tag: nutrient composition

value: SD

tag: growth medium

value: liquid


title: SD-GC

description: wild-type, SD gelatin C

value: wild-type

value: gelatin


title: RNA-seq_RNAi-ABCA1-seRNA-2


title: 527LA

description: Kss1K42R, SD liquid A


title: HC219050821

description: see next sheet

value: M

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

value: VRD*1, VTD*2

tag: best respose

value: PR


title: SD-GB

description: wild-type, SD gelatin B


title: HC219050819

description: see next sheet

value: I

tag: treatment strategy

value: NO

tag: FISH


title: HC219050818

description: see next sheet

value: F

value: IgD-Lambda

value: VAD&IE*12, EPA&EP*4，Radiation

value: VGPR MRD+

tag: chromosome


title: HC219050822

description: see next sheet

value: Batch 1

value: Lambda

value: II

value: VRD*5, ASCT，R maintenance


title: 527LC

description: Kss1K42R, SD liquid C

value: 6 hrs

value: SD

value: liquid


title: HT1080, 24h, PI, coll, r1

city: London

first: Oscar

last: Maiques

address: Charterhouse Square

department: Tumour Microenvironment

country: United Kingdom

institute: Queen Mary's University of London- Cancer Research UK Barts Centre

description: 24h treatment with PI

hyb_protocol: cRNA were hybridized to Affymetrix GeneChip HGU133plus2 arrays using the standard Affymetrix protocol

scan_protocol: scanned by a GeneArray@ 2500 Scanner (Affymetrix).

data_processing:
Microarray data analysis was performed using R (version 2.9.2) (http://www.R-project.org) and Bioconductor version (2.4)48.
Signal data were normalized using the robust multichip average (RMA) algorithm from the Affy49 package with default parameters

source_name: 24h_Protease_inhibitors_in thick collagen matrix

label_protocol: iotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HT1080 cells were maintained in DMEM containing 10% fetal calf serum (FCS). Fibrillar bovine dermal collagen (no. 5005-B; PureCol, Advanced BioMatrix) was prepared at 1.7 mg ml−1 in DMEM: 100 μl per well in 96-well plates; 300 μl per well in 24-well plates, 700 μl per well in 12-well plates. After collagen gel polymerization for 4 h, cells were seeded on top of collagen in medium containing 10% FCS, allowed to adhere for 24 h and treatments added. For collagen concentration of collagen Collagen I matrices were prepared using FibriCol (CellSystems) prepared at 10 mg ml−1.

extract_protocol: RNA was extracted from HT1080 cells treated with protease inhibitors for 4 and 24 hours seeded on top of collagen I using Trizol (Invitrogen, Carlsbad, CA) followed by Quiagen RNeasy Midi Kit.

treatment_protocol: Protease inhibitor mix: 100 µM GM6001, 50 µM Pepstatin A, 250 µM E64, 2 µM Aprotinin, 2 µM Leupeptin. GM6001 and H1152 was from Merck Millipore (Hertfordshire, UK); Pepstatin, E-64, Aprotinin and Leupeptin were from Sigma-Aldrich (Dorset, UK)

tag: cell type

value: Fibrosarcoma cell

tag: treatment

value: 24h treatment with proteinase kinase inhibitor cocktail


title: RNA-seq_RNAi-ABCA1-seRNA-1

tag: cell line


title: HT1080, 24h, PI, coll, r2

description: 24h treatment with PI


title: HT1080, 24h, PI, coll, r3

description: 24h treatment with PI


title: SD-GA

description: wild-type, SD gelatin A

value: wild-type

value: gelatin


title: SLAD-LC

description: wild-type, SLAD liquid C

value: SLAD


title: HT1080, 4h, PI, coll, r2

description: 4h treatment with PI

source_name: 4h_Protease_inhibitors_in thick collagen matrix

value: 4h treatment with proteinase kinase inhibitor cocktail


title: HC219050817

description: see next sheet

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: F

tag: age

value: kappa

value: VRD*2 ，PDD*2，TD maintenance

value: CR


title: HT1080, 4h, PI, coll, r3

description: 4h treatment with PI


title: HT1080, 4h, PI, coll, r1

description: 4h treatment with PI


title: RNA-seq_RNAi-Ctrl-3

tag: genotype


title: RNA-seq_RNAi-Ctrl-1


title: RNA-seq_THP1si-MED23-3

extract_protocol:
THP1 cells were seeded into 6 well and induced to be attacted. then, the cells were transfected with si-negetive control (si-NC) or si-MED23 siRNA. After 48 hours, the cells were washed by cold 1X PBS buffer. the RNA was extracted using Trizol (Thermo Fisher Scientific，15596018).
The sequencing library was conducted by NEBNext UltraTM RNA Library Prep Kit (NEB #E749), and purified by AMPure XP system, according to the standard Illumina protocols.


title: RNA-seq_THP1si-MED23-1


title: SLAD-LB

description: wild-type, SLAD liquid B

extract_protocol: Qiagen RNeasy mini-kit


title: SLAD-LA

description: wild-type, SLAD liquid A


title: HC219050814

description: see next sheet

tag: batch

value: Batch 1

tag: gender

value: PDD*6 ,RCD*6 RD maintenance

value: CR MRD-


title: RNA-seq_RNAi-Ctrl-2


title: SD-LB

description: wild-type, SD liquid B

tag: genotype/variation

tag: growth time


title: RNA-seq_THP1_si-NC1


title: SD-LA

description: wild-type, SD liquid A

tag: nutrient composition

tag: growth medium


title: HC219050813

description: see next sheet

tag: time at diagnosis

tag: type

value: IgA-L

value: II

value: VGPR

value: 1q21+，FGFR3 -

tag: os(months)


title: HC219050815

description: see next sheet

value: M

value: IgG-L

tag: riss

tag: treatment strategy

value: NO


title: HT1080, vehicle, coll, r2

description: Untreated

source_name: untreated_in thick collagen matrix

value: Fibrosarcoma cell

value: Untreated


title: SLAD-SB

description: wild-type, SLAD agar B

value: wild-type

value: 6 hrs

value: SLAD

value: agar


title: HC219050810

description: see next sheet

value: F

value: kappa

value: I

value: BCDT*2, PCD*1,RCD*2, ASCT，R maintenance

tag: best respose

value: CR MRD+

tag: chromosome

tag: FISH


title: HC219050811

description: see next sheet

value: Batch 1

value: Lambda

value: III

value: BCD*2, VRD*4, VRCD*2, VBiRD，IRCD,TMD,CETD*4,CAR-T

value: MR


title: RNA-seq_THP1si-MED23-2

tag: cell line


title: HT1080, vehicle, coll, r3

description: Untreated

tag: cell type

tag: treatment


title: HC219050812

description: see next sheet

tag: batch

value: M

tag: age

value: IgG-K

value: II

value: PDD*9, VRD*1, R maintenance

value: VGPR MRD+


title: HT1080, vehicle, coll, r1

description: Untreated

value: Fibrosarcoma cell

value: Untreated


title: SLAD-SC

description: wild-type, SLAD agar C

tag: genotype/variation

value: wild-type

value: 6 hrs

value: SLAD

value: agar


title: SD-LC

description: wild-type, SD liquid C

tag: growth time

value: SD

value: liquid


title: RNA-seq_THP1si-NC3

tag: genotype


title: RNA-seq_THP1si-NC2


title: si-ABCA1-seRNA-LXRβ

data_processing:
Library strategy: CUT&TAG
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bowtie2.
The bam file generated by the unique mapped reads as an input file, transformed to bigwig flies using deeptools software .
The deeptools computeMatrix and plotHeatmap tools were used for chromatin characteristics analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools

extract_protocol:
Libraries for high-throughput sequence were amplified with HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, TD903) according to the protocol. A universal adapter i5 and a uniquely adapter i7 primer gets from TruePrep Index Kit V4 for Illumina (Vazyme Biotech, TD501) with different barcoded for each sample. Using thermocycler with a heated-lid to amplify libraries under suitable conditions. PCR production purify was performed with 1.2X volume of VAHTS DNA Clean Beads (vazyme, N411-01) relative to PCR products according to the manufacture’s. Finally, libraries were eluted with 22ul sterilized ultrapure water and separated by magnetic stand
THP-1 macrophages were counted and harvested at room temperate. And then, cells were re-suspended with 500ul wash buffer and centrifuged for 3min at 600×g. Subsequently, cells were aliquoted 100ul in prepared ConA beads and incubated on a rotating platform for 10min at room temperate. Then, indicated primary antibodies and second antibodied were combined with cells. Hyperactive Tn5 transposon was applied to accurately cleavage DNA sequences near the target proteins. 300ul tagmentation buffer was added into product and incubated in 37°C for 1h to fragment the DNA sequences. At last, DNA was extracted for follow-up experiments


title: HC219050809

description: see next sheet

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

value: Batch 1

tag: gender

value: F

value: BCD*7, RCD*5, RD-R maintenance

value: CR MRD+


title: si-ABCA1-seRNA-LXRα


title: HC219050804

description: see next sheet

value: M

tag: time at diagnosis

value: IgA-L

value: TD*1,PTD*2 VRD*2 ASCT，VR maintenance


title: HC219050805

description: see next sheet

tag: type

value: IgA-k

value: I

value: MR


title: si-ABCA1-seRNA-RXRα


title: SLAD-SA

description: wild-type, SLAD agar A

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

tag: nutrient composition

tag: growth medium


title: SD-SC

description: wild-type, SD agar C


title: SD-SB

description: wild-type, SD agar B


title: HC219050806

description: see next sheet

tag: riss

value: II

tag: treatment strategy

value: BCD*2 BTD*2 RD*4，R maintenance


title: 230119-79_S15 [Day 10, replicate 6]

city: Uppsala

first: Alma

last: Hansen

address: Ulls väg 2B

country: Sweden

institute: Statens veterinärmedicinska anstalt

description:
230119-79_S15
Sample79

data_processing:
trimmed with Trimmomatic v0.39 using the standard Illumina adapter library, SLIDINGWINDOW:4:20 and MINLEN:50
Reads were mapped to a merged version of the reference genomes with STAR v. 2.7.2b, using default settings
Reads mapping to features were counted using HTSeq v. 0.9.1, with strandedness set on reverse, i.e. -s reverse, and otherwise default settings
Read counts loaded into R and, using edgeR, each sample was CPM normalized with regards to library size and genes filtered out that had few/no reads mapping to them across samples
Assembly: GRCg6a/pEimTen1.1
Supplementary files format and content: comma separated text files containing raw gene counts for each gene and sample, one for the chicken data and one for E. tenella

organism: Gallus gallus

source_name: Chicken caecum

extract_protocol:
TRIzol (ThermoFischer Scientific) / choloroform extraction
TruSeq stranded mRNA library preparation kit with polyA selection (Illumina) according to manufacturer’s protocol

tag: tissue

value: Chicken caecum

value: Eimeria tenella

tag: timepoint

value: Day 10


title: si-NC-LXRβ

description: si-NC-LXRBeta

tag: cell line

value: si-NC-LXRBeta


title: 221228-80_S5 [Day 3, replicate 6]

description:
221228-80_S5
Sample80

value: Day 3


title: SD-SA

description: wild-type, SD agar A

value: wild-type

value: 6 hrs

value: SD

value: agar


title: HC219050803

first: Yin

last: Wu

description: see next sheet

value: Batch 1

value: M

value: Lambda

value: BCDT*4 ,BCD*7，RCD*8，R maintenance

tag: best respose

value: CR MRD+

tag: chromosome

tag: FISH


title: IgG-HepG2


title: HC219050802

description: see next sheet

tag: batch

tag: age

value: IgG-K

value: VTD*5, ITD*2, VRD*1

value: PR

value: ND


title: 221228-79_S15 [Day 10, replicate 6]

description:
221228-79_S15
Sample79

value: Chicken caecum

tag: treatment

value: Eimeria tenella


title: si-NC-RXRα

description: si-NC-RXRalpha

tag: genotype

value: si-NC-RXRalpha


title: 230119-78_S10 [Day 1, replicate 6]

description:
230119-78_S10
Sample78

value: Day 1


title: si-NC-LXRα

description: si-NC-LXRalpha

value: si-NC-LXRalpha


title: HC219050801

description: see next sheet

tag: gender

value: F

value: IgA-k

value: I

value: RD*4 RCD*10,Rd-R maintenance

value: CR

value: negtive


title: G85_C0

first: Gregory

last: Carter

description: wild-type, t=0, SD agar C

tag: genotype/variation

value: wild-type

tag: growth time

value: 0 hrs

value: SD

value: agar


title: 230119-80_S5 [Day 3, replicate 6]

description:
230119-80_S5
Sample80

value: Day 3


title: RNAi-ABCA1-seRNA-LXRβ


title: 221228-78_S10 [Day 1, replicate 6]

description:
221228-78_S10
Sample78


title: 230119-67_S14 [Day 10, replicate 5]

description:
230119-67_S14
Sample67

value: Day 10


title: RNAi-Ctrl-LXRβ

description: RNAi-Ctrl-LXRBeta

value: RNAi-Ctrl-LXRBeta


title: P2631_Sample-TA-762 [CTLX183]

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

country: France

institute: INRAE

data_processing:
Reads were trimming of adaptor sequences and removal of reads containing ambiguous base calls (FASTX-Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html),
Reads were filtered according to their size (15–40 nt).
Reads quantification and annotation were performed using then cPRO-seq pipeline (Chen et al., 2012).
The sequence reads were aligned against the Bos taurus btau5.0.1 genome as miRBase_v22.1 using the miRDeep2 package (Friedlander et al., 2012)
A miRDeep2.0.1.2 score ≥ 0 as a cut-off threshold was used.
Assembly: Bos taurus btau5.0.1 genome as miRBase_v22.1
Supplementary files format and content: Tab-delimited text file for each sample

organism: Capra hircus

source_name: Omental adipose tissue

extract_protocol:
Total RNAs were extracted from on average of 1 g of powdered of AT and 750 µl of Trizol LS, using a miRVana kit (Thermo Fisher Sciences, USA) following the manufacturer’s instruction. The concentration and quality of the RNAs were estimated by spectrophotometry NanodropTH (ND-1000, NanoDrop Technologies LLC, Wilmington, DE, USA) and using the Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA), respectively.
Small RNA-Seq librairies were generated from 2 mg of total RNA using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer’s instructions. Briefly, during the first step, RNA adapters were sequentially ligated to each end of the RNA; firstly the 3′ RNA adapter (5′ TGGAATTCTCGGGTGCCAAGG 3′) which is specifically designed to target miRNAs and other small RNAs, then the 5′ RNA adapter (5′ GTTCAGAGTTCTACAGTCCGACGATC 3′). Small RNA ligated with 3′ and 5′ RNA adapters were reverse transcribed, and PCR amplified (30 s at 98 °C; [10 s at 98 °C, 30 s at 60 °C, 15 s at 72 °C] × 13 cycles; 10 min at 72 °C) to obtain cDNA. Acrylamide gel purifications of 140–160 nt amplified cDNA (corresponding to cDNA obtained from small RNA + 120 nt from the adapters) were performed. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Libraries were loaded in the flow cell at 2.8 nM and clusters were generated using Cbot and sequenced on HiSeq 4000 (Illumina) as single end 50 base reads, according to the manufacturer’s instructions.

treatment_protocol: Eleven lactating Alpine goats were at peak of lactation (48 ± 2 days postpartum, at the beginning of the experiment). For a 2-wk pre-experimental period, the goats were fed a standard diet of orchardgrass hay with a 35:65 forage-to-concentrate ratio. During the 48 h before slaughter, five goats received the standard diet ad libitum (control) while the others six were food deprived.

value: Omental adipose tissue

value: Control


title: RNAi-Ctrl-LXRα

description: RNAi-Ctrl-LXRalpha

value: RNAi-Ctrl-LXRalpha


title: RNAi-ABCA1-seRNA-LXRα


title: MZ B cells from Akt mice - replicate 3

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

description: Gene expession data of marginal B cells from the spleen of AKTboe mice

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.

data_processing: In DRFZ with GeneChip Operating System (GCOS, Affymetrix) generated CHP and CEL files were analyzed at INRAE, France (Luc Jouneau). Only chips, which fulfilled all chip and hybridization quality criteria, were selected for analysis. Normalization has been performed using R package GCRMA. To detect which probe sets were expressed in a given sample and to get Present/Marginal/Absent calls mas5calls function of affy R package was used. Differential expression was detected using limma R package.

organism: Mus musculus

source_name: CD19(+)CD21(hi)CD23(lo)CD1d(hi) B cells from the spleen of AKTboe mice

growth_protocol: Cell suspensions were prepared from spleens of CD19Cre (Rickert et al. 1997) and AktBOE (B cells overexpressing a constitutively active variant of Akt (CD19crex ROSA-LoxP-STOP-LoxP- Akt) female mice (7-8 weeks old; 4 mice/group). Red blood cell lysis was performed using self-made RBC lysis buffer. Cells were incubated with anti-CD43 beads (Miltenyi #130-049-801) and CD43 negative cells were collected from AutoMacs. After FcγR block, cell suspensions were stained with CD19 APC-Cy7 (Biolegend #115529 at 1/200), CD21 A647 (DRFZ clone 7G6 at 1/200), CD23-bio (BD # 553137 at 1/200)/SA-PeCy7 (BD #557598 at 1/400), CD1d PE(Biolegend #123510 at 1/400). No bin channel was used. Cells were sorted as Dapi-negative, CD19+ and CD1dlowCD23+CD21+ for FOB cells and CD1dhighCD23-CD21high for MZ B cells.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: strain

value: female

value: spleen


title: RNAi-Ctrl-RXRα

description: RNAi-Ctrl-RXRalpha

value: RNAi-Ctrl-RXRalpha


title: IgG-THP-1


title: MZ B cells from CD19Cre mice - replicate 3

description: Gene expession data of marginal B cells from the spleen of Cd19-cre mice

source_name: CD19(+)CD21(hi)CD23(lo)CD1d(hi) B cells from the spleen of Cd19-cre mice

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: P2631_Sample-TA-67 [CTLX186]

value: 48h Feed Deprivation


title: 230119-68_S9 [Day 1, replicate 5]

description:
230119-68_S9
Sample68

value: Chicken caecum

value: Eimeria tenella

value: Day 1


title: MZ B cells from Akt mice - replicate 1


title: 221228-68_S9 [Day 1, replicate 5]

description:
221228-68_S9
Sample68


title: P2631_Sample-TA-81 [CTLX184]


title: MZ B cells from CD19Cre mice - replicate 2


title: FO B cells from CD19Cre mice - replicate 3

description: Gene expession data of follicular B cells from the spleen of Cd19-cre mice

source_name: CD19(+)CD21(lo)CD23(+)CD1d(lo) B cells from the spleen of Cd19-cre mice


title: FO B cells from CD19Cre mice - replicate 1


title: FO B cells from CD19Cre mice - replicate 2


title: ATAC-seq_RNAi-ABCA1-seRNA-3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis.
Peaks were annotated by using homer's annotatePeaks.pl.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using MACS

extract_protocol:
4x10^5 THP-1 cells were collected, washed by cold 1X PBS. And then, the cell pellets were re-suspended in 50ul cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) to generate the nuclei pellets. Next, the nuclei pellets were resuspended in the transposition reaction mix (25 μl TD, 2.5 μl TDE1, 22.5 μl Nuclease Free H2O), incubated at 37°C for 30minutes. the DNA was purified by Qiagen MinElute PCR Purification Kit
The assays for transposase-accessible chromatin with high throughput sequencing (ATAC) assays were performed in Jiayin Biotechnology Ltd


title: 221228-67_S14 [Day 10, replicate 5]

description:
221228-67_S14
Sample67


title: G85_B0

address: 600 Main Street

institute: The Jackson Laboratory

description: wild-type, t=0, SD agar B

value: wild-type

tag: nutrient composition

tag: growth medium


title: 66_S67 [Day 2, replicate 6]

description:
66_S67
Sample66

value: Day 2


title: P2631_Sample-TA-747 [CTLX179]


title: P2631_Sample-TA-62 [CTLX182]


title: ATAC-seq_RNAi-ABCA1-seRNA-2


title: MZ B cells from Akt mice - replicate 2


title: P2631_Sample-TA-23 [CTLX181]


title: MZ B cells from CD19Cre mice - replicate 1


title: ATAC-seq_RNAi-ABCA1-seRNA-1


title: 230119-57_S7 [Day 1, replicate 3]

description:
230119-57_S7
Sample57


title: RNAi-ABCA1-seRNA-RXRα


title: 66_S54 [Day 2, replicate 6]

description:
66_S54
Sample66


title: P2631_Sample--TA-802 [CTLX180]


title: ATAC-seq_RNAi-Ctrl-3

value: RNAi-Ctrl


title: G85_A0

description: wild-type, t=0, SD agar A

value: 0 hrs

value: SD

value: agar


title: Gene expression profiles of intestine in response to GDE5 deficiency exp1

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: gut-specific GDE5 (Gpcpd1) deficient

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of intestine were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Male wild-type and gut-specific GDE5 (Gpcpd1) deficient mice (20 weeks) were fed normal diet.

value: GDE5 KO

source_name: wild-type


title: P2631_Sample-TA-808 [CTLX177]

value: Omental adipose tissue


title: 230119-59_S8 [Day 1, replicate 4]

description:
230119-59_S8
Sample59


title: Gene expression profiles of intestine in response to GDE5 deficiency exp2


title: P2631_Sample-TA-61 [CTLX176]


title: 221228-59_S8 [Day 1, replicate 4]

description:
221228-59_S8
Sample59


title: P2631_Sample-TA-724 [CTLX178]


title: P2631_Sample-TA-827 [CTLX175]


title: 230119-53_S4 [Day 3, replicate 5]

description:
230119-53_S4
Sample53

value: Day 3


title: 54_S64 [Day 4, replicate 6]

description:
54_S64
Sample54

value: Day 4


title: ATAC-seq_RNAi-Ctrl-2


title: stage1_pp121_replicate2

data_processing:
Transcript Quantification: FASTA (fasta.gz) files were quantified using CellRanger. The specific command was 'cellranger count' with  parameters '--include-introns --nosecondary' all other paramters were default.
Preprocessing: filtered count matrices fromCellRanger were read into R and processed using Seurat (v4.0.4). The reminaing cells were filtered for total genes, total umis and mitochondrial percentage.
Analysis: Sample replicates were merged and analysed using Seurat's standard workflow.
Genome_build: GRCh38; https://uswest.ensembl.org/info/data/ftp/index.html
Supplementary_files_format_and_content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post CellRanger filtering pre Seurat filtration.

source_name: Stage 1 Enteric Ganglioid

extract_protocol:
Ganglioids were washed twice in PBS and dissociated with accutase (Stemcell Tech) at 37 C. After 20 minutes incubation, the ganglioids were triturated with a wide bore pipet tip and passed through a 37μm reversible cell strainer. The single cell containing filtrate was collected in 4mL cold complete media and put on ice. The remaining undissociated cells were incubated for an additional 20 minutes at 37 C with fresh accutase, followed by trituration and filtering. The cell suspension was centrifuged 5 minutes at 500 rcf at 4 C to remove media. The cells were resuspended in cold lysis buffer (10mM Tris-HCl, 10mM Nal, 3mM MgCl2, 0.1% Nonidet™ P40 substitute and incubated on ice for 3 minutes. The cells were then centrifuged and washed twice in wash buffer (1X PBS, 1.0% BSA, 0.2U/μL Protector RNase inhibitor (Sigma-Aldrich)). Finally, the cells were filtered twice in MACS smart strainer (Miltenyi Biotec) and nuclear viability and count were measured using acridine orange and propidium iodide on the CellDrop™ cell counter (DeNovix).
snRNA-seq libraries were prepared with Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics). The libraries were sequenced at UCSF GenomicsCoLab.
single nuclei RNA-seq

treatment_protocol: For PP121 samples we added 2 uM PP121 to media D15-D20.

value: hPSC-derived Stage 1 Enteric Ganglioid

tag: plating

value: Suspension

tag: differentiation replicate


title: 54_S77 [Day 4, replicate 6]

description:
54_S77
Sample54

tag: tissue

tag: timepoint


title: ATAC-seq_RNAi-Ctrl-1

tag: cell line


title: SG3, scRNAseq

city: Zhoushan

first: Jiwei

last: Chen

state: Zhejiang

address: Ocean College Zhejiang University

institute: Ocean College Zhejiang University

description: 10X Genomics

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

organism: Phaeodactylum tricornutum

source_name: silicified cells

extract_protocol:
The prepared nuclear suspensions of the diatom cells (SG-Pt and WT-Pt) were mixed with cDNA reverse transcription reagents, 10x barcode gel beads, and sequencing oil for Chromium Chip B in the small chamber of the microfluidic device. The "double cross" system of the microfluidic device was used to form gel beads-in-emulsion. The formed GEMs (gel beads in emulsion) were transferred to PCR tubes and placed in a PCR machine for reverse transcription. Then, the reverse transcription primers containing 30 nt oligo-dT on the gel beads were used to reverse transcribe the poly-A RNA in the collected nuclei into cDNA with Barcode and UMI information. The reverse transcribed cDNA was purified using the SPRIselect magnetic bead system and amplified using PCR.
The prepared cDNA was fragmented using a fragment enzyme, and suitable fragments of 350-500 bp were selected using magnetic beads. The fragments were then subjected to end repair to add PolyA and adapter-linked Read2 sequencing primers. The cDNA library containing P5 and P7 adapters was constructed by PCR amplification. The library was purified using the SPRIselect magnetic bead system, and the concentration of cDNA was measured using Qubit. The size of the prepared cDNA fragments was checked using Agilent 2100. Cluster generation and the first round of sequencing primer hybridization were performed according to the Illumina User Guide. The Flow cell with clusters was loaded onto the sequencer, and paired-end sequencing was performed using the Paired-end program. The entire sequencing process was controlled by Illumina's Data collection software, and real-time data analysis was performed to obtain raw sequencing data.

value: silicified cells

tag: cell type

value: oval shaped


title: WT1, scRNAseq

description: 10X Genomics

source_name: non-silicified cells

value: non-silicified cells

value: fusiform shaped


title: stage1_pp121_replicate1


title: 221228-53_S4 [Day 3, replicate 5]

description:
221228-53_S4
Sample53

value: Chicken caecum

value: Eimeria tenella


title: WT_Female_rep4

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Raw reads were demultiplexed and quality of pre-aligned data was computed by FastQC
Reads were aligned to the GRCm39 mouse reference genome with STAR 2.7.10b
Data was then further processed by featureCounts v2.0.6 to obtain read counts at the gene level
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files with raw counts for each Sample.

source_name: nucleus ambiguus

growth_protocol: This study was conducted using from male and female WT and Ren-aChAT-KO mice. All mice were housed in a temperature and humidity-controlled facility with ad libitum access to Teklad diet and chlorinated water.

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific).
RNA libraries were prepared using Takara low-input, SMART-seq stranded preparation kit according to manufacturer protocol

treatment_protocol: There were 4 untreated groups:WT male=6, Ren-aChAT-KO male=6, WT female=4, Ren-aChAT-KO female=6.

value: nucleus ambiguus

value: Wild Type

value: Female


title: WT_Female_rep3


title: 221228-57_S7 [Day 1, replicate 3]

description:
221228-57_S7
Sample57

value: Day 1


title: 221228-50_S3 [Day 3, replicate 4]

description:
221228-50_S3
Sample50


title: Brain_PBS_24h_sample_3

city: Solna

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

institute: Karolinska Institute

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: Scanning was done using the GeneChip® Scanner 3000 7G

data_processing: The raw data was normalized in Expression Console, provided by Affymetrix (http://www.affymetrix.com), using the robust multi-array average (RMA) method. Subsequent analysis of the gene expression data was carried out in the statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). In order to search for the differentially expressed genes between the X and Y groups, an empirical Bayes moderated t-test was applied using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg.

label: Biotin

source_name: vascular fragments of ipsilateral brain hemisphere, 24h post MCAO, PBS treated

label_protocol: 10 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA from the entire expressed genome according to the Nugen Technologies, Inc. protocols Ovation® Pico WTA System V2 (M01224v2) and Encore Biotine Module (M01111v5).

growth_protocol: Mice were supplied with a standard mouse diet and were housed in 12h light/dark cycle with free access tow ater and food.

extract_protocol: Total RNA extracted using Qiagen kit following manufacturer's instructions. RNA concentration was measured with ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA).

treatment_protocol: Mice were either treated with imatinib or PBS 3 times before MCAO for the 3h post MCAO mice and an additional 4th time for the 24h post MCAO mice.

tag: Sex

value: male

value: brain vascular fragments

tag: developmental stage

value: adult


title: Brain_imatinib_24h_sample_2

source_name: vascular fragments of ipsilateral brain hemisphere, 24h post MCAO, Imatinib treated


title: Brain_imatinib_24h_sample_1


title: 468CS-3

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.87 whole genome
Fragments per kilobase per million mapped fragments (FPKM) were calculated using a protocol from Trapnell, C. et al, Nature  biotechnology, 2010.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: FPKM values
Supplementary_files_format_and_content: raw gene counts
Supplementary_files_format_and_content: DESeq2.normailized counts

source_name: MDA-MB-468 cells treated with CS-6

growth_protocol: MDA-MB-468 cells were cultured on 10 cm plates according to the ATCC protocol.

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-468 cells were treated with CS-6 (18 nmol/L) or DMSO for 24 h

value: breast cancer cell line


title: stage1_control_replicate2

value: control


title: Brain_PBS_24h_sample_1


title: Brain_PBS_24h_sample_2


title: 468CS-2


title: stage1_control_replicate1

value: hPSC-derived Stage 1 Enteric Ganglioid


title: 230119-50_S3 [Day 3, replicate 4]

description:
230119-50_S3
Sample50

value: Day 3


title: Brain_imatinib_24h_sample_3


title: 49_S59 [Day 3, replicate 6]

description:
49_S59
Sample49


title: 49_S72 [Day 3, replicate 6]

description:
49_S72
Sample49


title: Brain_imatinib_3h_sample_1

source_name: vascular fragments of ipsilateral brain hemisphere, 3h post MCAO, Imatinib treated


title: 468NC-3

source_name: MDA-MB-468 cells treated with DMSO

value: DMSO


title: Brain_PBS_3h_sample_3

source_name: vascular fragments of ipsilateral brain hemisphere, 3h post MCAO, PBS treated


title: Brain_imatinib_3h_sample_2


title: Brain_PBS_3h_sample_2


title: WT_Female_rep1


title: 47_S58 [Day 3, replicate 5]

description:
47_S58
Sample47

source_name: Chicken caecum


title: 468NC-1


title: WT_Male_rep2

value: Male


title: WT_Male_rep5


title: 468CS-1


title: sh1

city: Zhenjiang

first: Yong

last: Peng

state: 未选择

address: No. 8, Power Road

institute: Zhenjiang First People's Hospital

description:
Library name: sample-5
sh1-FPKM

data_processing:
The total RNA was extracted by Trizol, and the concentration and purity of the extracted RNA were further examined by UV spectrophotometer; the total RNA of the three groups of cells was analyzed by Fragment Analyzer for quality identification. The total RNA obtained from the three groups of cells was analyzed by Fragment Analyzer to identify the quality of the extracted RNA, and the unqualified samples were filtered. The total RNA of the three groups of cells was identified by Fragment Analyzer, and the unqualified samples were filtered out and library construction was performed. The quality of the sequencing data was evaluated by FastQC software; the sequencing data were compared with hg38, and the genome annotation file Homo_sapiens and Bowtie2 analysis software were used to analyze the sequences obtained. The sequences were genetically annotated using the genome annotation file Homo_sapiens and Bowtie2 analysis software.
Assembly: HG38
Supplementary files format and content: gz./XLS

source_name: AGS

extract_protocol:
Total RNA from AGS gastric cancer cell line was extracted by Trizol. The total RNA of the three groups of cells was identified by Fragment Analyzer, and the unqualified samples were filtered out and library construction was performed. The sequencing data were evaluated by FastQC software to remove low-quality reads, splice reads, and unknown bases with N>5% in the sequencing data. The sequencing data were evaluated by FastQC software to remove low-quality reads, reads with junctions, and reads with unknown base N>5% to obtain high-quality sequencing data.
1. Isolation of target DNA/RNA. 2. Enzymatically or mechanically section the fragment. 3. Ligate segments into prepared vector. 4. Transform into host cells. 5. Screen and identify positive clones. 6. Verify the size and sequence of the insert.

value: AGS

value: human gastric cancer cell line

value: cancer gene


title: WT_Male_rep1


title: 47_S71 [Day 3, replicate 5]

description:
47_S71
Sample47

value: Chicken caecum

value: Eimeria tenella


title: P1

description:
Library name: sample-2
P1-FPKM

value: shControl


title: 45_S66 [Day 2, replicate 5]

description:
45_S66
Sample45

value: Day 2


title: WT_Male_rep4

value: nucleus ambiguus

value: Wild Type


title: sh2

description:
Library name: sample-6
sh2FPKM


title: Brain_PBS_3h_sample_1

value: male

value: brain vascular fragments


title: WT_Female_rep2

value: Female


title: WT_Male_rep3


title: P2

description:
Library name: sample-3
P2-FPKM


title: 468NC-2

value: breast cancer cell line


title: 230119-46_S2 [Day 3, replicate 3]

description:
230119-46_S2
Sample46


title: 38_S76 [Day 4, replicate 5]

description:
38_S76
Sample38

value: Day 4


title: sh

description:
Library name: sample-4
sh-FPKM


title: 221228-46_S2 [Day 3, replicate 3]

description:
221228-46_S2
Sample46

value: Day 3


title: AP2_M1_KO_RNASEQ_3

city: Nanning

first: Dandan

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

data_processing:
For CUT&Tag analysis, the paired-end reads were filtered and then aligned to the Eimeria tenella reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify CUT&Tag peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
RNA-seq analysis was performed based on the reference genome of Eimeria tenella  (ToxoDB-69). Briefly, Paired-end clean reads were aligned to the reference genome using Hisat2. Read counts were calculated for each gene using the sorted bam files from htseq-count. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR. Gene expression with a fold change >4 or < -4 and p adjust < 0.01 was considered as significantly differentially expressed.
Assembly: ToxoDB-69_Eimeria tenella 2021
Supplementary files format and content: bigwig, narrowPeak

organism: Eimeria tenella

source_name: sporozoites

growth_protocol: The E. tenella Houghton strain stably expressing Cas9 (EtHCYA) was used for the construction of knockout strain, and wild type E. tenella Houghton (EtH) strain was used for gene overexpression strain construction. These strains were maintained and propagated through one- to four-weeks-old sanhuang chickens. Chickens were reared in a coccidia-free environment and provided with water and feed free of coccidiostat and antibiotics.

extract_protocol:
For RNA-SEQ analysis, total RNAs from the sporozoites of EtHCYA and AP2-M1-KO strains were isolated using Trizol regent, and the genomic DNA was removed by DNase Ⅰ (Tiangen Biotech Co., Ltd, Beijing, China). The purity, concentration and integrity of RNAs were tested using NanoPhotometer® (IMPLEN, CA, USA), Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.  For CUT&Tag analysis, the fresh sporozoites of EtH and AP2-M1-OE strains (1×107 for each experiment) were prepared as described above. Library construction was performed by formaldehyde crosslinked CUT&Tag using the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (Novoprotein, Nanjing, China) according to the manufacturer's instructions. Briefly, fresh sporozoites were treated with 1% formaldehyde for 10 min at room temperature, and the cross-link was terminated by 1×Glycine solution. Then, the sporozoites were washed and bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-Flag mAb, Abmart, Shanghai, China) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG, Proteintech, USA) for 1 h at room temperature. The parasites were then resuspended with 65 μL of tagmentation Buffer (ChiTag pAG-Tn5 buffer + 1 μL of 0.7 M MgCl2) and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by 5 μL stop buffer and 1 μL proteinase K at 55°C for 2 h. DNA extraction was performed using Tagment DNA Extract Beads.
For CUT&Tag Library construction, Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations (NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina B box, Novoprotein, Suzhou, China).  For RNA-seq library construction, Illumina sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Sequencing was performed using the Illumina Novaseq 6000 platform (Beijing Novogene Technology Co., Ltd) to generate 150 bp paired-end reads.

value: sporozoites

value: Houghton

value: AP2_M1 knockout strain


title: EtHCYA_RNASEQ_3

value: Cas9-expressing Eimeria tenella strain


title: KO_Female_rep1

value: KO of Chat


title: 45_S53 [Day 2, replicate 5]

description:
45_S53
Sample45

value: Chicken caecum


title: P

description:
Library name: sample-1
p-FPKM

value: AGS

value: human gastric cancer cell line

value: cancer gene