title: cDC1_FF_rep3

description: cDC1 feeder free

value: feeder free


title: 231-H3B-2

status: Public on Jun 17 2025

type: SRA

city: Wuhan

first: Chen

last: Zeyu

state: Huibei

address: No. 1095, Jiefang Avenue

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: Sample 11
Column name in gene_count.csv:231-H3B-2

library_source: transcriptomic

data_processing:
Initial quantification was performed using Qubit 2.0, diluting the library to 1.5 ng/ul, followed by detection of the insert size of the library using Agilent 2100, and after the insert size met expectations, qRT-PCR was performed to accurately quantify the effective concentration of the library (effective library concentration above 2 nM) to ensure library quality.
After passing the library inspection, the different libraries were pooled according to the effective concentration and the target amount of data to be sequenced by Illumina
The raw sequencing reads (raw reads) contain low-quality, spliced reads, so we use the default parameters of fastp for quality control to filter the unqualified reads, and the resulting clean reads are used for subsequent analysis.
Clean Reads were quickly and accurately compared with the reference genome using HISAT2 software to obtain information on the positioning of Reads on the reference genome
Assembly: GRCh38
Supplementary files format and content: csv file includes gene counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

growth_protocol: MHCC-97H, MDA-MB-231 and HCT-116 cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
RNA is extracted from cells using Trizol
RNA is extracted from cells using standard extraction methods, followed by rigorous quality control of the RNA samples, primarily by means of an Agilent 2100 bioanalyzer: precise detection of RNA integrity

treatment_protocol: DMSO or 20 nM H3B-8800 in the presence of 10% FBS until 24hrs.

tag: tissue

value: breast cancer

tag: cell line

tag: cell type

value: breast cancer cell lines

tag: genotype

value: WT

tag: treatment

tag: time

value: day 1


title: cDC1_FF_rep2

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: cDC1 feeder free

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) was used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts were obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: hg38
Supplementary files format and content: comma-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes normalized counts for each sample

molecule: polyA RNA

source_name: in vitro classical type 1 DCs (cDC1)

growth_protocol: CD34+ cells are differentiated with recombinant human cytokines as described in the associated manuscript.

extract_protocol:
RNA isolation was performed using Qiagen micro RLT kits and RNA quality was analyzed using Agilent RNA 6000 Nano kit and samples had a RIN value above 9.5.
Illumina Stranded mRNA library was prepared using 100 ng of RNA sequencing procedures are carried out using NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) and performed a 50 bp paired end sequencing with a total of 60 million read coverage using NovaSqq 6000

treatment_protocol: conventional type I (CD141+Clec9A+) and type 2 (CD1c+FCERA+) dendritic cells from the in vitro cultures were enriched by flow cytometry

value: in vitro classical type 1 DCs (cDC1)


title: BY4741_EtOH_4hr_bio_rep2

city: Kunigami-gun

first: Yuta

last: Yamazaki

address: Tancha 1919-1

country: Japan

institute: Okinawa Institute of Science and Technology

description:
Library name: Sample32
colomn name in all_counts_BY4741.csv EtOH-4hr_rep2

data_processing:
Raw sequence data in FASTQ format generated by NovaSeq 6000 were used for further analysis. The quality of the reads was analyzed by FastQC software (v0.11.9). We removed the low-quality reads and adaptors using trimmomatic software (v0.39). The quality of the raw reads and cleaned reads were compared using FastQC software. The reads from S. cerevisiae were mapped to the reference genome (R64-1-1) using STAR software (v2.7.8). To map the reads from S. pastorianus, we generated a reference genome from previously published S. pastorianus genome information using Yeast Annotation Pipeline. Then, the reads from S. pastorianus were mapped to the annotated genome information using STAR software. Quantification of reads was performed by featureCounts software (v2.0.1).
Assembly: R64-1-1 for S. cerevisiae. BBYY00000000.1 (GeneBank) for S. pastorianus
Supplementary files format and content: Comma separated values files includes raw counts for each sample

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741

growth_protocol: We cultured yeasts in YPD media (1% yeast extract, 2% bacto peptone, and 2% glucose) at 25℃.

extract_protocol:
We extracted total RNA using an RNeasy mini kit (QIAGEN, Germany). We added 600 µl of RTL buffer and glass beads to the cell pellets. The cells were disrupted by shaking at 3000 rpm for 2 min with cooling using TOMMY Micro Smash MS-100R. The cell debris was removed by centrifuging at 12,000 rpm for 2 min at 4℃. 350 µl of the supernatant was mixed with an equal volume of 70 % EtOH. We transferred the mixture to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We added 350 µl of RW1 buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. To remove residual DNA, we added an RNase-Free DNase Set (QIAGEN, Germany) to the column. After 15 min digestion at room temperature, we added RW1 buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We added 500 µl of RPE buffer to the column and centrifuged it at 10,000xg for 20 seconds at 4℃. We repeated this process twice. We collected RNA by adding 50 µl of RNase-free water to the column and centrifuging it at 10,000xg for 30 seconds at 4℃. We measured the RNA concentration by nanodrop. The quality and integrity of the RNA samples were assessed using an Agilent 2200 TapeStation (Agilent Technologies)
We prepared the library using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). For indexing, we used NEBNext Multiplex Oligos for Illumina (NEB #E6440). We followed the manufacturer's protocol to prepare the libraries.

treatment_protocol: S. cerevisiae and S. pastorianus were cultured in 100 ml YPD media overnight until OD595 reached 0.1–0.2. The cultures were separated into two aliquots and transferred to 150 ml YPD (total 200 ml x2). We incubated them until OD595 reached around 0.1. From one of the aliquots, we took 20 ml of the culture (control). We then added 6 ml of YPD and 14 ml of 99.5 % EtOH (7% EtOH). In another aliquot, we added 200 µl of 10% SDS (0.01% SDS). We collected the culture 0.5, 1, 2, 4, 8, and 20 hr after the addition of SDS or EtOH (Fig. 1B). The cells were washed twice with PBS, flash-frozen by liquid nitrogen, and stored in -80℃ until lysis. Three biological replicates were collected in all conditions.

value: Saccharomyces cerevisiae BY4741

value: Yeast cells

value: 7% EtOH


title: CJ B6 6M AL-50W F4

city: Houston

first: EMRE

last: AKSAN

state: TX

address: 6501 Fannin St NB302

department: Ophthalmology

institute: Baylor College of Medicine

description: Library name: DP_74361

data_processing:
Quality control was performed using Rosalind platform with default trimming settings.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files with normalized gene expression counts (e.g., TPM or DESeq2-normalized counts) for all samples.

organism: Mus musculus

source_name: conjunctiva

extract_protocol:
Total RNA was extracted from cornea and conjunctiva tissues using RNeasy Mini Kit (Qiagen).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer’s instructions.

value: conjunctiva

tag: strain

value: ad libitum feeding


title: 231-H3B-1

description:
Library name: Sample 10
Column name in gene_count.csv:231-H3B-1


title: 231-DMSO-3

description:
Library name: Sample 9
Column name in gene_count.csv:231-DMSO-3

value: DMSO


title: cDC1_FF_rep1

description: cDC1 feeder free


title: BY4741_EtOH_8hr_bio_rep2

description:
Library name: Sample35
colomn name in all_counts_BY4741.csv EtOH-8hr_rep2


title: BY4741_EtOH_4hr_bio_rep1

description:
Library name: Sample31
colomn name in all_counts_BY4741.csv EtOH-4hr_rep1


title: CJ B6 6M AL-50W F1

description: Library name: DP_74358


title: BY4741_EtOH_2hr_bio_rep3

description:
Library name: Sample30
colomn name in all_counts_BY4741.csv EtOH-2hr_rep3


title: cDC1_OP9_rep2

description: cDC1 cultured in OP9

value: OP9 feeder


title: K B6 6M CR 50W F7

description: Library name: DP_74357

source_name: cornea

value: cornea

value: calorie-restricted feeding


title: 231-DMSO-1

description:
Library name: Sample 7
Column name in gene_count.csv:231-DMSO-1


title: cDC1_DLL1_rep3

description: cDC1 cultured in DLL1

value: DLL1 feeder


title: BY4741_EtOH_2hr_bio_rep2

description:
Library name: Sample29
colomn name in all_counts_BY4741.csv EtOH-2hr_rep2


title: cDC1_DLL1_rep2

description: cDC1 cultured in DLL1


title: 231-DMSO-2

description:
Library name: Sample 8
Column name in gene_count.csv:231-DMSO-2


title: BY4741_EtOH_1hr_bio_rep3

description:
Library name: Sample27
colomn name in all_counts_BY4741.csv EtOH-1hr_rep3


title: K B6 6M CR 50W F2

description: Library name: DP_74354


title: 97H-H3B-3

description:
Library name: Sample 6
Column name in gene_count.csv:97H-H3B-3

source_name: liver cancer

value: liver cancer

value: liver cancer cell lines


title: K B6 6M CR 50W F3

description: Library name: DP_74355


title: 97H-H3B-2

description:
Library name: Sample 5
Column name in gene_count.csv:97H-H3B-2


title: ms_mo_7

city: Cambridge

first: Fatima

last: Gunter-Rahman

state: MA

address: 77 Massachusetts Ave

institute: MIT

library_source: transcriptomic single cell

data_processing:
CellRanger was used to align sequencing reads to hg38 (CellRanger  6.0.1 for the four pilot samples in batch 1, and 6.1.2 for the rest of the samples. All batches had representation from both MO and control groups). CellBender 0.3.0 was used to remove ambient noise from droplets with nuclei, and to identify empty droplets.
Assembly: hg38
Supplementary files format and content: counts matrix for each nuclei and gene

molecule: nuclear RNA

source_name: placenta

extract_protocol:
Nuclei were isolated from placental samples following a modified version of the Allen Brain institute protocol for nuclei extraction. Briefly, tissue was homogenized using an electric pulsator and via dounces in a glass tissue homogenizer. A series of two washes was used to remove debris, and then nuclei were stained with DAPI. Flow cytometry was used to count 10,000 nuclei per sample, with gating based on DAPI-positive cells.
The standard Chromium 10X v3.1 kit instructions were followed to generate the single-nucleus RNA-seq data.

value: placenta

tag: facing side

value: ms

tag: condition

value: MO

tag: batch


title: BY4741_EtOH_1hr_bio_rep2

description:
Library name: Sample26
colomn name in all_counts_BY4741.csv EtOH-1hr_rep2

value: WT


title: ms_mo_6


title: CJ B6 6M AL-50W F3

description: Library name: DP_74360


title: 97H-H3B-1

description:
Library name: Sample 4
Column name in gene_count.csv:97H-H3B-1

value: day 1


title: K B6 6M CR 50W F1

description: Library name: DP_74353


title: BY4741_EtOH_1hr_bio_rep1

description:
Library name: Sample25
colomn name in all_counts_BY4741.csv EtOH-1hr_rep1

value: Saccharomyces cerevisiae BY4741


title: K B6 6M AL-50W F5

description: Library name: DP_74352


title: ms_lean_3

value: Lean


title: ms_mo_5


title: 97H-DMSO-3

description:
Library name: Sample 3
Column name in gene_count.csv: 97H-DMSO-3


title: K B6 6M CR 50W F4

description: Library name: DP_74356


title: cDC1_DLL1_rep1

description: cDC1 cultured in DLL1

value: in vitro classical type 1 DCs (cDC1)


title: K B6 6M AL-50W F4

description: Library name: DP_74351


title: BY4741_EtOH_0.5hr_bio_rep3

description:
Library name: Sample24
colomn name in all_counts_BY4741.csv EtOH-0.5hr_rep3

value: Yeast cells

value: 7% EtOH


title: BY4741_EtOH_0.5hr_bio_rep2

description:
Library name: Sample23
colomn name in all_counts_BY4741.csv EtOH-0.5hr_rep2


title: 97H-DMSO-1

description:
Library name: Sample 1
Column name in gene_count.csv: 97H-DMSO-1

value: DMSO


title: BY4741_EtOH_2hr_bio_rep1

description:
Library name: Sample28
colomn name in all_counts_BY4741.csv EtOH-2hr_rep1


title: fs_mo_6

value: fs


title: fs_lean_4


title: K B6 6M AL-50W F3

description: Library name: DP_74350

value: cornea

value: ad libitum feeding


title: BY4741_EtOH_0.5hr_bio_rep1

description:
Library name: Sample22
colomn name in all_counts_BY4741.csv EtOH-0.5hr_rep1


title: K B6 6M AL-50W F2

description: Library name: DP_74349


title: BY4741_SDS_20hr_bio_rep3

description:
Library name: Sample21
colomn name in all_counts_BY4741.csv SDS_001-20hr_rep3


title: K B6 6M AL-50W F1

description: Library name: DP_74348


title: BY4741_SDS_20hr_bio_rep2

description:
Library name: Sample20
colomn name in all_counts_BY4741.csv SDS_001-20hr_rep2


title: fs_mo_5


title: fs_mo_4


title: 09H054 simvastatin 24 hr

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8
Sequenced reads were mapped to the reference genome using CASAVA 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: primary human AML cells

growth_protocol: Primary human AML cells were not grown in culture.

extract_protocol:
RNA was extracted using TRIzol reagent as recommended by manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Frozen aliquots of primary human AML cell were thawed, and exposed for 24 hours to 330 nmol/L simvastatin, or 1100 nmol/L atorvastatin, or 0.1% DMSO in serum-free cytokine-supplemented media containing 500 nmol/L stemregenin and 500 nmol/L UM729.

value: bone marrow

tag: phenotype

value: statin resistant

value: primary human AML cells

tag: compound

value: simvastatin


title: 09H054 atorvastatin 24 hr

value: atorvastatin


title: 09H054 control 24 hr

value: control


title: m_KO_Th9_3

city: Los Angeles

first: Sai

last: Xiao

state: California

address: 1500 E. Duarte Road

institute: City of Hope

data_processing:
The raw reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to the reference genome with orientation mode using STAR (version 2.7.4).
Peak calling results with IP and input libraries were generated by exomePeak2.
The m6A binding motif was analyzed by HOMER (version 4.11).
Called peaks were annotated by intersection with gene and transcript architecture using bedtools (version 2.30.0) . The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files. The DEGs were detected with R package edgeR (version v. 3.28.1)
Assembly: mm10
Supplementary files format and content: comma-delimited text files contain raw counts values
Supplementary files format and content: comma-delimited text files contain includes callpeak sites

source_name: Th9 cells

growth_protocol: WT and Ythdf2-KO Th9 cells were grown in RPMI1640 (Gibco) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Gibco).

extract_protocol:
For m6A-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen). Fragmented mRNA (5 μg mRNA) was used for m6A immunoprecipitation (m6A-IP) using an m6A antibody (Synaptic, 202003) following the standard protocol of the Magna MeRIP m6A Kit (Merck Millipore). For Ythdf2 RIP-seq, fifty million Th9 cells were harvested and washed twice with cold PBS, and the cell pellet was lysed with two volumes of lysis buffer [10 mM HEPES pH 7.6, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 Protease Inhibitor cocktail (Thermo Fisher Scientific), and 400 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)]. The lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. One-tenth volume of cell lysate was saved as input. The rest of the cell lysate was incubated with 5 μg anti-YTHDF2 (MBL, Cat No. RN123PW) that was pre-coupled with Protein A magnetic beads (Invitrogen, Cat: 10001D) at 4℃ for 2h with gentle rotation. Afterward, the beads were washed five times with 1 ml ice-cold washing buffer (50 mM HEPES pH 7.6, 200 mM NaCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, and 200 U/mL RNase inhibitor). Immunoprecipitated samples were subjected to Proteinase K digestion in wash buffer supplemented with 1% SDS and 2 mg/mL Proteinase K (Thermo Fisher Scientific) incubated with shaking at 1200 rpm at 55℃ for 1 h. Total RNA was extracted from both input and immunoprecipitated RNA by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo Research).  For bulk RNA-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen).
RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina NovaSeq 6000  machine with 100-bp paired-end reads (PE100).
m6a-seq, RIP-seq, poly-RNA-seq

value: Th9 cells


title: 97H-DMSO-2

description:
Library name: Sample 2
Column name in gene_count.csv: 97H-DMSO-2

value: liver cancer

value: liver cancer cell lines

value: WT

value: day 1


title: BY4741_SDS_20hr_bio_rep1

description:
Library name: Sample19
colomn name in all_counts_BY4741.csv SDS_001-20hr_rep1

value: Saccharomyces cerevisiae BY4741

value: Yeast cells


title: ms_mo_4

value: placenta

value: ms

value: MO


title: m_KO_Th9_2


title: 09H042 simvastatin 24 hr


title: ms_lean_2

value: Lean


title: BY4741_SDS_8hr_bio_rep3

description:
Library name: Sample18
colomn name in all_counts_BY4741.csv SDS_001-8hr_rep3


title: m_WT_Th9_3


title: 09H042 control 24 hr

value: bone marrow


title: m_KO_Th9_1


title: 09H042 atorvastatin 24 hr

value: statin resistant


title: ms_mo_2


title: BY4741_SDS_8hr_bio_rep2

description:
Library name: Sample17
colomn name in all_counts_BY4741.csv SDS_001-8hr_rep2


title: BY4741_SDS_4hr_bio_rep3

description:
Library name: Sample15
colomn name in all_counts_BY4741.csv SDS_001-4hr_rep3


title: m_WT_Th9_2


title: ms_mo_3


title: BY4741_SDS_8hr_bio_rep1

description:
Library name: Sample16
colomn name in all_counts_BY4741.csv SDS_001-8hr_rep1


title: 09H010 simvastatin 24 hr

value: statin sensitive

value: primary human AML cells


title: 09H010 control 24 hr


title: fs_lean_3

value: fs


title: m_WT_Th9_1


title: BY4741_SDS_4hr_bio_rep2

description:
Library name: Sample14
colomn name in all_counts_BY4741.csv SDS_001-4hr_rep2


title: fs_mo_3


title: Th9_RIP2


title: Th9_RIP1


title: fs_lean_2


title: 08H112 simvastatin 24 hr

value: simvastatin


title: 09H010 atorvastatin 24 hr

value: atorvastatin


title: BY4741_SDS_2hr_bio_rep3

description:
Library name: Sample12
colomn name in all_counts_BY4741.csv SDS_001-2hr_rep3


title: fs_mo_2


title: 08H112 control 24 hr

value: control


title: ms_lean_1


title: BY4741_SDS_2hr_bio_rep2

description:
Library name: Sample11
colomn name in all_counts_BY4741.csv SDS_001-2hr_rep2


title: KO_Th9_MeRIP3

data_processing:
The raw reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to the reference genome with orientation mode using STAR (version 2.7.4).
Peak calling results with IP and input libraries were generated by exomePeak2.
The m6A binding motif was analyzed by HOMER (version 4.11).
Called peaks were annotated by intersection with gene and transcript architecture using bedtools (version 2.30.0) . The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files. The DEGs were detected with R package edgeR (version v. 3.28.1)
Assembly: mm10
Supplementary files format and content: comma-delimited text files contain raw counts values
Supplementary files format and content: comma-delimited text files contain includes callpeak sites
Library strategy: m6a-seq

value: Th9 cells


title: 08H112 atorvastatin 24 hr


title: ms_mo_1


title: BY4741_SDS_2hr_bio_rep1

description:
Library name: Sample10
colomn name in all_counts_BY4741.csv SDS_001-2hr_rep1

value: WT


title: BY4741_SDS_1hr_bio_rep3

description:
Library name: Sample9
colomn name in all_counts_BY4741.csv SDS_001-1hr_rep3


title: fs_mo_1


title: WT_Th9_MeRIP3


title: 08H050 control 24 hr


title: KO_Th9_MeRIP1


title: 08H050 simvastatin 24 hr


title: 08H050 atorvastatin 24 hr


title: KO_Th9_MeRIP2


title: BY4741_SDS_1hr_bio_rep2

description:
Library name: Sample8
colomn name in all_counts_BY4741.csv SDS_001-1hr_rep2


title: fs_lean_1


title: BY4741_SDS_4hr_bio_rep1

description:
Library name: Sample13
colomn name in all_counts_BY4741.csv SDS_001-4hr_rep1


title: WT_Th9_MeRIP2


title: 05_BE_RNA

city: Heidelberg

first: Dominik

last: Lindenhofer

address: Meyerhofstraße 1

country: Germany

institute: EMBL Heidelberg

description: SDR-seq

data_processing:
Barcode identification, count matrices consisting of either cell-reads (gDNA and RNA) or cell-UMIs (RNA) were generated using SDRranger (https://github.com/hawkjo/SDRranger).
Assembly: Targeted references were constructed for the PCR amplicons for gDNA and RNA libraries. Sequences for this study were extracted from the human GRCh38 assembly
Supplementary files format and content: Tab-separated values and matrix files.  The gDNA processed files contain read matrices for cell vs gDNA site with reads.
Library strategy: scDNA-scRNA-seq (SDR-seq)

extract_protocol:
Human iPSCs were fixed in either PFA or glyoxal, in-situ reverse transcription was performed and cells were subjected to the Tapestri machine from MissionBio (v2). Multiplexed PCR amplified both gDNA and RNA simultenously in the same cell together with cell barcoding.
For POP a common library for both gDNA and RNA was prepared. For all other runs separate sequencing libraries were performed for both gDNA and RNA.

value: human iPSCs


title: WT_Th9_MeRIP1


title: BY4741_SDS_0.5hr_bio_rep3

description:
Library name: Sample6
colomn name in all_counts_BY4741.csv SDS_001-0.5hr_rep3

value: Saccharomyces cerevisiae BY4741


title: 07H160 simvastatin 24 hr


title: 07H160 control 24 hr


title: 05_BE_gDNA

description: SDR-seq

library_source: genomic

molecule: genomic DNA


title: BY4741_SDS_0.5hr_bio_rep2

description:
Library name: Sample5
colomn name in all_counts_BY4741.csv SDS_001-0.5hr_rep2

value: Yeast cells


title: 07H160 atorvastatin 24 hr


title: SKOV3ip1 cells, BARD1 siRNA_3, biol rep 3, 48h

first: Emine

last: Bayraktar

address: 1881 East Road

institute: MD Anderson Cancer Center

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data orRaw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files which contain sequences of readsand corresponding base quality.
The sequencing reads/raw reads often contain low-quality reads or reads with adapters, which will affect the quality of downstreamanalysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads.
Raw reads filtering is as follows: Removing reads with adapter contamination. Removing reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). Removing reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Performed alignments with HISAT2 (http://ccb.jhu.edu/software/hisat2/faq.shtml) to the reference.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium

source_name: SKOV3ip1 tumors

growth_protocol: SKOV3ip1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 0.1% gentamicin sulfate.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s instructions.
Library was prepared using Poly(A) capture for mrAN enrichment. RNA fragmentation and cDNA reverse transcription per Novogene protocol.

treatment_protocol: SKOV3ip1 cells were transfected with either BARD1 or control siRNA. Briefly, siRNA (2 μg) was incubated with 6 µL of Lipofectamine 2000 transfection reagent (Invitrogen, Carlsbad, CA) for 20 minutes at room temperature and then added to cells cultured in 6-well plate at 60% confluence and incubated for 48 hours.

value: SKOV3ip1 tumors

value: ovarian adenocarcinoma

value: BARD1 siRNA


title: scRNA-seq, WT mouse olfactory epithelium, UNO - open (R)

city: Aurora

first: Stephen

middle: William

last: Santoro

state: Colorado

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

description: 10X Genomics

data_processing:
Gene count matrix generated with Cellranger count (v6.0.1)
SeuratObject created from cellranger output using standard Seurat pipeline
SeuratObject filtered to remove cells with percent mitochrondrial content > 12% or nFeatures_RNA < 750
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: gzipped matrix file, gene raw count matrix output from cellranger count
Supplementary files format and content: barcodes.tsv.gz: gzipped text file of cell barcodes corresponding to matrix.mtx.gz
Supplementary files format and content: features.tsv.gz: gzipped text file of genes corresponding to matrix.mtx.gz
Supplementary files format and content: RDS: R data file containg SeuratObject

source_name: Olfactory epithelium

extract_protocol:
Immediately following dissection at PD 28, olfactory epithelia halves were dissociated into single cells, fluorescently stained for cell viability, subjected to fluorescence-activated cell sorting to remove dead cells, quantified, and captured using a Chromium instrument (10X Genomics).
Single cell RNA libraries were generated using a Single Cell 3’ HT Kit (10X Genomics).

treatment_protocol: Samples are from the open and closed sides of the olfactory epithelium of a PD 28 mouse that was UNO-treated at PD14.

value: Olfactory epithelium

tag: age

value: PD 28

tag: Sex

value: male

value: unilateral naris occlusion (PD14)

tag: side

value: open (right)

value: all olfactory epithelial cells


title: BY4741_SDS_0.5hr_bio_rep1

description:
Library name: Sample4
colomn name in all_counts_BY4741.csv SDS_001-0.5hr_rep1


title: scRNA-seq, WT mouse olfactory epithelium, UNO - closed (L)

description: 10X Genomics

value: closed (left)


title: SKOV3ip1 cells, BARD1 siRNA_2, biol rep 2, 48h


title: 07H099 simvastatin 24 hr

value: bone marrow

value: statin sensitive

value: primary human AML cells

value: simvastatin


title: SKOV3ip1 cells, BARD1 siRNA_1, biol rep 1, 48h

value: WT


title: BY4741_control_bio_rep3

description:
Library name: Sample3
colomn name in all_counts_BY4741.csv control-1-rep3

value: Saccharomyces cerevisiae BY4741


title: SKOV3ip1 cells, Control siRNA_3, biol rep 3, 48h

value: Control siRNA


title: BY4741_SDS_1hr_bio_rep1

description:
Library name: Sample7
colomn name in all_counts_BY4741.csv SDS_001-1hr_rep1

value: Yeast cells


title: 07H099 atorvastatin 24 hr

value: atorvastatin


title: Gene Expression scRNAseq

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: 10X Genomics

data_processing:
The gene expression data were mapped and gene level quantification was performed using the cellranger (ver. 6.1.2) count function, with the expect-cells parameter set to 50,000 and the transcriptome parameter set to the 10x Genomics mouse reference genome (refdata-gex-mm10-2020-A). Feature barcode fastqs were processed using kallisto (ver. 0.48.0), bustools (0.39.3), and kite (https://github.com/pachterlab/kite; git commit aafc8c8) software to generate GEM (gel bead in emulsion)-specific barcode count tables. GEM barcodes were corrected and filtered using the bustools correct function with the 10x Genomics known barcodes allow list: 737K-august-2016.txt. All raw count tables were imported into R (ver. 4.2.0) and processed with functions from the tidyverse package (ver. 1.3.1). The cellranger classified cell-containing GEM barcodes (e.g., filtered_feature_bc_matrix) were used to limit the GEMs found in the feature barcode tables. Raw gene expression and normalized tetramer count tables were imported into R and processed with the Seurat R package (ver. 4.1.1). Gene expression data was normalized using the SCTransform method.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
Single cell suspensions were individually prepared from the pancreas of 13 non-diabetic (10-13 weeks) NOD mice by injection of collagenase (Cizyme, VitaCyte) into the common bile duct followed by mechanical disruption and Lympholyte1.1 (Cedarlane Labs) density centrifugation. InsC-ChgA:I-Ag7, InsC-ChgA:I-Ag7, InsBP8G:I-Ag7 and InsBP8E:I-Ag7 tetramers were generated by adding TotalSeq reagents containing streptavidin conjugated with PE and unique oligonucleotide barcodes (C0966, C0968, C0969, and C0954; BioLegend), respectively. Cells were stained with TotalSeq PE tetramers paired with traditional APC tetramers, with dual PE+ and APC+ cells being identified as tetramer+. The pancreas cells from each mouse were stained with different CD45 TotalSeq hashtag antibodies conjugated with unique oligonucleotide barcodes (C0301-C0313; BioLegend). The samples were then pooled and 55,000 live, lineage-, CD90.2+, CD4+ tetramer+ cells were single cell sorted using a FACS Aria II (BD Biosciences). Cells were processed for sequencing using the Chromium Single Cell Mouse TCR Amplification Kit (PN-1000254; 10x Genomics). Two libraries, gene expression and feature barcode (tetramer and hashtag oligos), were pooled and sequenced in one lane of a NovaSeq 6000 using 2x151 bp paired-end read chemistry.
10x Genomics Chromium Next GEM Single Cell 5' Kit v2 (PN-1000263)

value: pancreas

value: Non-obese diabetic (NOD)

value: 10 weeks


title: ALT treated adult-3

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned to the mouse genome (mm10/GRCm38) using STAR.
The featureCounts program was used to generate raw counts for each gene.
Assembly: (mm10/GRCm38)
Supplementary files format and content: The raw counts are stored in .csv format.
Supplementary files format and content: DESEQ2 median of ratios normalized counts are also stored in .csv format

source_name: dorsal skin

extract_protocol:
Skin tissue total RNA were extracted with RNeasy Mini Kit and Dendritic cell RNA were extracted with Rneasy micro plus kit (Qiagen) as per manufacturer’s instructions
Whole skin tissue derived libraries were generated with NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 and Dendritic cell derived libraries were generated with Revelo™ RNA-Seq High Sensitivity library preparation kit per manufacturer’s instructions.

treatment_protocol: Neonate an adult mice were intradermally injected with house dust mite extract (HDM), Alternaria alternata Extract (ALT)and PBS controls. Full thickness skin biopsy were isolated 6 days after allergens inoculation. For Dendritic cell sorting, neoante mice were intraperitonealy injected with Corticosterone or DMSO for 30 minutes, and then were intradermally injected with HDM or PBS for 9 hours.

value: dorsal skin

value: wild type

value: one ALT injection wait for 6days


title: BY4741_control_bio_rep1

description:
Library name: Sample1
colomn name in all_counts_BY4741.csv control-1-rep1


title: YKK2941_EtOH_20hr_bio_rep3

description:
Library name: Sample78
colomn name in all_counts_YKK2941 EtOH-20hr_rep3

organism: Saccharomyces pastorianus

source_name: S. pastorianus Weihenstephan 34/70

value: S. pastorianus Weihenstephan 34/70

value: 7% EtOH


title: 06H088 simvastatin 24 hr

value: bone marrow

value: statin resistant


title: BY4741_control_bio_rep2

description:
Library name: Sample2
colomn name in all_counts_BY4741.csv control-1-rep2


title: SKOV3ip1 cells, Control siRNA_1, biol rep 1, 48h

value: SKOV3ip1 tumors

value: ovarian adenocarcinoma


title: T47D cells, normoxia, total RNA, biol rep 4

city: Solna

first: Kathleen

middle: Diane

last: Watt

address: Tomtebodevägen 23

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
RNA sequencing read quality was assessed using FastQC v.0.11.8 and MultiQC.
Sequencing adapters and reads mapping to ribosomal RNA were removed using BBDuk from the BBTools suite (http://jgi.doe.gov/data-and-tools/bb-tools/) prior to alignment to hg38 using HISAT2 with default settings.
Reads were summarized using the featureCounts function of the Rsubread R package with default settings and RefSeq gene definitions.
Assembly: GRCh38
Supplementary files format and content: Matrix of raw gene expression counts based on RefSeq gene definitions.

growth_protocol: T47D cells (ATCC, Manassas, Virginia, USA) were grown in RPMI-1640 Medium (Gibco, Cat#11875093) with 10% fetal bovine serum (FBS) (Corning).  Cells were maintained at 37 °C with 5% CO2. H9 hESCs were obtained from WiCell and the use of hESCs was approved by the Stem Cell Oversight Committee of Canada. hESCs were cultured on plates prepared with Corning® Matrigel® hESC-Qualified Matrix (#07181, Stemcell Technologies) and fed daily using pre-warmed mTeSR™1 feeder-free medium supplemented with mTeSR™1 5X Supplement (#85850, Stemcell Technologies). Colony quality, confluence, and spontaneous differentiation was visually monitored daily and differentiated colonies were manually scraped off the plate. hESCs were passaged using StemPro™ EZPassage™ Disposable Stem Cell Passaging Tool (23181010, Thermo Fisher). All cells were maintained at 37°C and 5% CO2 in a humidified environment.

extract_protocol:
Cells (8 x 106 cells per condition) were seeded in 15cm plates 24h prior to the experiment. Media was changed before cells were exposed to normoxia or hypoxia (0.5% O2) for 24h or 48h. Cells were pre-treated with 100 μg/ml cycloheximide for 5 min and scraped in ice-cold, cycloheximide supplemented (100 μg/ml) PBS, using rubber scrapers. Cells were then pelleted in 15 ml conical tubes at 240 ×g for 5 min at 4°C, and lysed on ice in 500 μl of hypotonic lysis buffer (5 mM Tris–HCl, pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg/ml cycloheximide, 1 mM DTT, 0.5% Triton, 0.5% sodium deoxycholate) for 15 min. Subsequently, lysates were cleared through a 15 min, 20 817 ×g centrifugation at 4°C. Cleared lysates were diluted with hypotonic lysis buffer to set their optical density (OD) at 260 nm to 10–20. Sucrose gradients (5–50%) were generated in polypropylene tubes (Beckman Coulter, 331372, 14×89 mm) using a gradient maker (Biocomp Gradient Master 108), according to the manufacturer's instructions. A volume of 500μl was removed from the top of the sucrose gradient to allow for sample loading. Lysates were then layered over the top of linear sucrose gradients and centrifuged at 4°C for 2 hat 222 228× g (36 000 rpm) using an ultracentrifuge (Beckman Coulter, Optima XPN-80, rotor SW41Ti), while 10% of the sample was kept for total cytosolic mRNA extraction. Ultracentrifuged samples were fractionated into 2 ml tubes using a density gradient fractionation system (Brandel, BR-188-177), resulting in 12 fractions of 800 μl each. Input samples, as well as sucrose gradient fractions, were mixed with 1000 μl of TRIzol LS reagent (Invitrogen) and kept at −80°C for subsequent RNA isolation.
RNAseq libraries for total and polysome-associated mRNA fractions from T47D, H9, cells cultured under hypoxia (1% O2) and normoxia  (20% O2) were prepared using the Smart-seq2 protocol as previously described83. RNA quantity and quality was assessed by Qubit (Life Technologies) and Bioanalyzer (Agilent Technologies), and 10 ng of RNA was used as input material. After pre-amplification PCR 70 pg of cDNA underwent tagmentation in a total volume of 20 uL using the Nextera XT Kit (Illumina). Sequencing was then performed at the SciLifeLab National Genomics Infrastructure (NGI, Sweden) facility using the NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 50-base paired-end setup using the ‘NovaSeqStandard’ workflow and S1 flow cell.

treatment_protocol: For hypoxia experiments media was changed to fresh full-serum media and cells were incubated in normoxia (regular incubator) or hypoxia (Biospherix OxyCycler model C42 or ProOx model C21 chambers housed in a regular incubator) at 1% O2 for either 24 (H9 cells) or 48 hrs (T47D).

value: Human breast cancer

value: normoxia (20% oxygen, 24 hrs)

tag: rna type

value: total cytosolic mRNA


title: YKK2941_EtOH_20hr_bio_rep2

description:
Library name: Sample77
colomn name in all_counts_YKK2941 EtOH-20hr_rep2

value: Yeast cells

value: WT


title: Feature Barcodes scRNAseq

description: 10X Genomics

value: pancreas


title: HDM treated adult-3

value: one HDM injection wait for 6days


title: 06H088 atorvastatin 24 hr

value: primary human AML cells

value: atorvastatin


title: YKK2941_EtOH_20hr_bio_rep1

description:
Library name: Sample76
colomn name in all_counts_YKK2941 EtOH-20hr_rep1


title: T47D cells, normoxia, total RNA, biol rep 3


title: 06H045 simvastatin 24 hr

value: statin sensitive

value: simvastatin


title: HDM treated adult-2

value: dorsal skin

value: wild type


title: YKK2941_EtOH_8hr_bio_rep3

description:
Library name: Sample75
colomn name in all_counts_YKK2941 EtOH-8hr_rep3

value: S. pastorianus Weihenstephan 34/70

value: 7% EtOH


title: T47D cells, normoxia, total RNA, biol rep 2


title: 06H045 control 24 hr

value: bone marrow

value: control


title: HDM treated adult-1


title: SKOV3ip1 cells, Control siRNA_2, biol rep 2, 48h

value: SKOV3ip1 tumors

value: ovarian adenocarcinoma

value: Control siRNA


title: YKK2941_EtOH_8hr_bio_rep2

description:
Library name: Sample74
colomn name in all_counts_YKK2941 EtOH-8hr_rep2

value: Yeast cells


title: 07H099 control 24 hr


title: ALT treated adult-2

value: one ALT injection wait for 6days


title: T47D cells, normoxia, total RNA, biol rep 1

value: Human breast cancer

value: normoxia (20% oxygen, 24 hrs)

value: total cytosolic mRNA


title: PBS treated adult-3

value: one PBS injection wait for 6days


title: PBS treated adult-2


title: T47D cells, normoxia, polysomal RNA, biol rep 4

value: polysome-associated mRNA


title: YKK2941_EtOH_8hr_bio_rep1

description:
Library name: Sample73
colomn name in all_counts_YKK2941 EtOH-8hr_rep1

value: WT


title: ALT treated adult-1

value: dorsal skin


title: 04H030 simvastatin 24 hr

value: statin sensitive

value: primary human AML cells

value: simvastatin


title: YKK2941_EtOH_4hr_bio_rep3

description:
Library name: Sample72
colomn name in all_counts_YKK2941 EtOH-4hr_rep3

value: S. pastorianus Weihenstephan 34/70

value: 7% EtOH


title: 06H088 control 24 hr

value: bone marrow

value: statin resistant

value: control


title: 04H030 control 24 hr


title: T47D cells, normoxia, polysomal RNA, biol rep 3


title: PBS treated adult-1

value: wild type


title: 04H030 atorvastatin 24 hr

value: atorvastatin


title: HDM treated neonate-6

value: one HDM injection wait for 6days


title: T47D cells, normoxia, polysomal RNA, biol rep 2

value: Human breast cancer

value: normoxia (20% oxygen, 24 hrs)


title: YKK2941_EtOH_4hr_bio_rep1

description:
Library name: Sample70
colomn name in all_counts_YKK2941 EtOH-4hr_rep1

value: Yeast cells


title: T47D cells, DMSO, total RNA, biol rep 4

description: Library name: T47D_DMSO_rep4

growth_protocol: T47D cells (ATCC, Manassas, Virginia, USA) were grown in RPMI-1640 Medium (Gibco, Cat#11875093) with 10% fetal bovine serum (FBS) (Corning).  Cells were maintained at 37 °C with 5% CO2 in a humidified environment.

extract_protocol:
RNA isolation was performed using TRIZOL.
RNAseq libraries for total RNA fractions from C48 and DMSO-treated T47D cells were prepared at the Institute for Research in Immunology and Cancer (IRIC) Genomics Platform at the University of Montreal (Canada).  RNA quantity and quality was assessed by Qubit (Life Technologies) and Bioanalyzer (Agilent Technologies). Samples were sequenced on the NextSeq500 platform with a 75-base single-end setup.

treatment_protocol: For compound 48 (C48) (Axon Medchem, #2809/batch1) treatments, media was replaced with fresh RPMI 10% FBS containing 10 µM C48 or the equivalent volume of DMSO as vehicle control. Cells were treated with DMSO for 48h, or 24h DMSO followed by 24h 10µM C48 additional 24h.

value: DMSO (24 hrs)


title: T47D cells, normoxia, polysomal RNA, biol rep 1

value: polysome-associated mRNA


title: HDM treated neonate-5

value: dorsal skin


title: T47D cells, hypoxia, total RNA, biol rep 4

value: hypoxia (1% oxygen, 24 hrs)

value: total cytosolic mRNA


title: T47D cells, DMSO, total RNA, biol rep 3

description: Library name: T47D_DMSO_rep3


title: YKK2941_EtOH_2hr_bio_rep3

description:
Library name: Sample69
colomn name in all_counts_YKK2941 EtOH-2hr_rep3

value: WT


title: 06H045 atorvastatin 24 hr

value: statin sensitive

value: primary human AML cells


title: T47D cells, hypoxia, total RNA, biol rep 3


title: HDM treated neonate-4


title: T47D cells, DMSO, total RNA, biol rep 1

description: Library name: T47D_DMSO_rep1


title: T47D cells, DMSO, total RNA, biol rep 2

description: Library name: T47D_DMSO_rep2


title: HDM treated neonate-3


title: YKK2941_EtOH_2hr_bio_rep1

description:
Library name: Sample67
colomn name in all_counts_YKK2941 EtOH-2hr_rep1

value: S. pastorianus Weihenstephan 34/70

value: 7% EtOH


title: T47D cells, hypoxia, total RNA, biol rep 2


title: T47D cells, hypoxia, total RNA, biol rep 1


title: YKK2941_EtOH_4hr_bio_rep2

description:
Library name: Sample71
colomn name in all_counts_YKK2941 EtOH-4hr_rep2


title: HDM treated neonate-2


title: HDM treated neonate-1


title: YKK2941_EtOH_1hr_bio_rep2

description:
Library name: Sample65
colomn name in all_counts_YKK2941 EtOH-1hr_rep2


title: T47D cells, hypoxia, polysomal RNA, biol rep 4


title: YKK2941_EtOH_1hr_bio_rep3

description:
Library name: Sample66
colomn name in all_counts_YKK2941 EtOH-1hr_rep3


title: T47D cells, C48, total RNA, biol rep 4

description: Library name: T47D_C48_rep4


title: YKK2941_EtOH_1hr_bio_rep1

description:
Library name: Sample64
colomn name in all_counts_YKK2941 EtOH-1hr_rep1


title: T47D cells, C48, total RNA, biol rep 3

description: Library name: T47D_C48_rep3


title: T47D cells, hypoxia, polysomal RNA, biol rep 3


title: ALT treated neonate-3

value: one ALT injection wait for 6days


title: ALT treated neonate-2

value: wild type


title: T47D cells, C48, total RNA, biol rep 1

description: Library name: T47D_C48_rep1


title: T47D cells, hypoxia, polysomal RNA, biol rep 2


title: YKK2941_EtOH_0.5hr_bio_rep3

description:
Library name: Sample63
colomn name in all_counts_YKK2941 EtOH-0.5hr_rep3


title: YKK2941_EtOH_2hr_bio_rep2

description:
Library name: Sample68
colomn name in all_counts_YKK2941 EtOH-2hr_rep2


title: T47D cells, hypoxia, polysomal RNA, biol rep 1


title: YKK2941_EtOH_0.5hr_bio_rep2

description:
Library name: Sample62
colomn name in all_counts_YKK2941 EtOH-0.5hr_rep2


title: PBS treated neonate-4

value: one PBS injection wait for 6days


title: 01_POP

description: SDR-seq

library_source: other

molecule: other

value: human iPSCs


title: YKK2941_EtOH_0.5hr_bio_rep1

description:
Library name: Sample61
colomn name in all_counts_YKK2941 EtOH-0.5hr_rep1


title: H9 cells, normoxia, total RNA, biol rep 4

value: Human embryonic stem cell


title: OG21

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing:
Lexogen Platform
Assembly: HG19
Supplementary files format and content: read count

growth_protocol: Patient-derived CRC-SCs were maintained in DMEM/F12 advanced supplemented with 1% L-glutamine, 1% penicillin-streptomycin, 0.6% glucose solution, 2% B27,1% N2, 10ng/ml hbFGF, 20 ng/ml EGF in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Qiagen miRNeasy micro kit
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)

treatment_protocol: Patient-derived CRC-SCs were treated with 10μM of EM127 for 24 hours.

value: colon

tag: patient

value: N

value: treated


title: H9 cells, normoxia, total RNA, biol rep 3

value: normoxia (20% oxygen, 24 hrs)


title: YKK2941_SDS_20hr_bio_rep3

description:
Library name: Sample60
colomn name in all_counts_YKK2941 SDS_001-20hr_rep3

value: Yeast cells


title: OG20

source_name: tumor tissue

tag: tissue

value: tumor tissue

value: untreated


title: PBS treated neonate-2

value: dorsal skin


title: H9 cells, normoxia, total RNA, biol rep 1

tag: cell line

value: total cytosolic mRNA


title: PBS treated neonate-1


title: YKK2941_SDS_20hr_bio_rep2

description:
Library name: Sample59
colomn name in all_counts_YKK2941 SDS_001-20hr_rep2

tag: cell type

value: WT


title: YKK2941_SDS_20hr_bio_rep1

description:
Library name: Sample58
colomn name in all_counts_YKK2941 SDS_001-20hr_rep1

value: S. pastorianus Weihenstephan 34/70

tag: genotype


title: OG19

source_name: normal tissue

value: normal tissue

tag: treatment


title: T47D cells, C48, total RNA, biol rep 2

description: Library name: T47D_C48_rep2

value: Human breast cancer


title: OG18

value: M


title: H9 cells, normoxia, polysomal RNA, biol rep 4

value: polysome-associated mRNA


title: YKK2941_SDS_8hr_bio_rep3

description:
Library name: Sample57
colomn name in all_counts_YKK2941 SDS_001-8hr_rep3


title: H9 cells, normoxia, polysomal RNA, biol rep 3


title: ALT treated neonate-1

value: wild type

value: one ALT injection wait for 6days


title: KO 2

city: nanjing

first: Qi

last: Wang

state: Jiangsu

address: The First Affiliated Hospital of Nanjing Medical University, 300 Guang Zhou Road

institute: The first affliated hospital of nanjing medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow-derived macrophages

extract_protocol:
BMDMs were isolated from Xbp1FL/FL and Xbp1M-KO mice and lysed in TRIzol reagent (Invitrogen, Carlsbad, CA) after LPS stimulation for 6 h, and then Xbp1FL/FL or Xbp1M-KO BMDMs RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strian

value: 6-8 weeks


title: KO 3


title: OG16

value: colon


title: KO 1


title: OG17


title: H9 cells, normoxia, polysomal RNA, biol rep 1

value: Human embryonic stem cell


title: OG15

value: L

value: treated


title: WT 3


title: YKK2941_SDS_8hr_bio_rep1

description:
Library name: Sample55
colomn name in all_counts_YKK2941 SDS_001-8hr_rep1

value: Yeast cells


title: PBS treated neonate-3

value: one PBS injection wait for 6days


title: YKK2941_SDS_4hr_bio_rep3

description:
Library name: Sample54
colomn name in all_counts_YKK2941 SDS_001-4hr_rep3


title: H9 cells, hypoxia, total RNA, biol rep 3

value: hypoxia (1% oxygen, 24 hrs)


title: YKK2941_SDS_4hr_bio_rep2

description:
Library name: Sample53
colomn name in all_counts_YKK2941 SDS_001-4hr_rep2


title: OG14

value: tumor tissue

value: untreated


title: WT 2


title: H9 cells, hypoxia, total RNA, biol rep 1

value: total cytosolic mRNA


title: OG13

value: normal tissue


title: YKK2941_SDS_2hr_bio_rep3

description:
Library name: Sample51
colomn name in all_counts_YKK2941 SDS_001-2hr_rep3

value: S. pastorianus Weihenstephan 34/70

value: WT


title: YKK2941_SDS_4hr_bio_rep1

description:
Library name: Sample52
colomn name in all_counts_YKK2941 SDS_001-4hr_rep1


title: WT 1


title: H9 cells, hypoxia, polysomal RNA, biol rep 4

value: polysome-associated mRNA


title: H9 cells, hypoxia, polysomal RNA, biol rep 3


title: OG12

value: K


title: YKK2941_SDS_8hr_bio_rep2

description:
Library name: Sample56
colomn name in all_counts_YKK2941 SDS_001-8hr_rep2


title: OG11


title: H9 cells, hypoxia, polysomal RNA, biol rep 1


title: YKK2941_SDS_2hr_bio_rep2

description:
Library name: Sample50
colomn name in all_counts_YKK2941 SDS_001-2hr_rep2


title: OG10


title: HSC_CCl4_Tom-2

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v. 0.23.2) (parameters - Quality >= Q15, N base limit = 10)
Trimmed sequence reads were mapped to GRCm39 using STAR aligner (v. 2.7.11a) with default parameters
Read count exxtraction were performed using featureCounts (v. 2.0.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes tpm for each Sample

source_name: liver

extract_protocol:
Cells were lysed using lysis buffer from SMART-Seq® Stranded Kit (Takara)
Libraries were generated using SMART-Seq® Stranded Kit according to manufacturer's instruction

treatment_protocol: Mice were injected intraperitoneally with carbon tetrachloride (1 ml/kg of body weight), diluted in corn oil at a ratio of 1:5, twice a week for 8 weeks

value: liver

value: Hepatic stellate cell


title: H9 cells, hypoxia, total RNA, biol rep 4


title: OG09

value: colon

value: J


title: T47D Input, normoxia, biol rep3

data_processing:
Raw H3K4me3 fastq files were processed using the nf-core/chipseq pipeline v.1.2.0 (available at https://github.com/nf-core/chipseq). Reads were aligned to GRCh38/hg38 in paired-end mode and all other parameters were kept as default.
The filtered aligned reads were extracted from the BAM files and re-aligned to a custom index of 5’UTR sequences using Bowtie (version 1.2.2) (settings: -v 2 -X 1000 -a). This custom index was created from genomic sequence regions corresponding to RefSeq transcripts with 2,000 bp of genomic sequence added upstream of the annotated TSS, and 10,000 bp added downstream of the TSS.
Bedtools genomeCoverageBed (v2.29.1) was then used to compute the genome coverage of H3K4me3 with -dz and -pc options, and -scale to normalize for library size. The cumulative sum of H3K4me3 coverage was calculated for each genomic region corresponding to RefSeq transcripts, and genomic regions were trimmed at the position where 95% of cumulative H3K4me3 signal had already occurred.
In order to reduce file sizes and computation time, the position (relative to the transcription start site), and the H3K4me3 coverage were collected for every 0.1% increase in the cumulative sum of H3K4me3 signal, such that each genomic region corresponding to RefSeq transcripts would have 1,000 data points summarizing the distribution of the histone mark.
Assembly: GRCh38/hg38 for genomic alignment, and RefSeq rel_109.20201120 for transcript annotations.
Supplementary files format and content: BAM files aligned to modified RefSeq reference described above.
Supplementary files format and content: CDF files (ZZZ tab separated) in the format: RefSeq ID, cumulative sum of H3K4me3 read coverage, positions relative to the transcription start site where the cumulative sum of read coverage increases by 0.1%, and read coverage at these positions, scaled to total library size. This file format was created§ to easily summarize and load large bam files into R, and reduce computation times.

extract_protocol:
Post hypoxia treatment, control and treated cells were washed 2x in PBS and collected (500 rcf for 5 minutes at 4°C) and flash frozen. Prior to each ChIP, antibodies were conjugated overnight at 4°C in ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF, 50 ug/mL BSA) with 50/50 mix of Dynabeads™ Protein A (Thermo Fisher, 10001D) and Dynabeads™ Protein G (Thermo Fisher, 10003D) at a ratio of 6 ug of antibody to 25 uL of beads per sample. Prior to IP, beads were washed 2x with ChIP Buffer 1 and resuspended in 25 uL of ChIP Buffer 1. Frozen cells were washed twice in Buffer N (15 mM Tris Base, 15 mM NaCl, 60 mM KCl, 8.5% sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 1x protease inhibitor, 50 ug/mL BSA), then resuspended in 2x cell pellet volume of Buffer N and lysed for 10 minutes on ice in equivalent volume of 2x Lysis Buffer (1x Buffer N, 0.6% NP-40). Nuclei was pelleted (500 rcf for 5 minutes at 4°C) and resuspended in 6x cell pellet volume of Buffer N, then spun through Sucrose Cushion (15 mM Tris Base, 15 mM NaCl, 60mM KCl, 30% sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 1x protease inhibitor, 50 ug/mL BSA) at 500 rcf for 12 minutes at 4°C. Nuclei pellet was resuspended in 2x cell pellet volume of Buffer N. 2 uL of nuclei suspension was diluted with 18 uL of 2 M NaCl in triplicate, vortexed, and sonicated with a water bath sonicator (30x cycle of 30 seconds on, 30 seconds off) prior to measuring the chromatin concentration with NanoDrop Spectrophotometer (Thermo Fisher). Concentration of nuclei suspension was then adjusted to 1 ug/uL and separated into 100ug chromatin aliquots. Nuclei suspensions were prewarmed for 2 minutes at 37°C, then 1.52 uL of MNase (Worthington Biochemical Corporation, LS004797) was added for 12 minutes at 37 °C on a ThermoMixer (Eppendorf) set to 900 rpm. Digestion was stopped by adding 1/10 volume of MNase Stop Buffer (100 mM EDTA and 10 mM EGTA) and placing nuclei on ice. 5M NaCl was slowly added to the suspension to a concentration of 0.6 M on the slowest vortex setting to release the chromatin, insoluble nuclei was then pelleted (18,000 rcf, 1 minute, 4 °C), and supernatant was run through hydroxyapatite (HAP) chromatography. 15 uL of soluble chromatin was saved for visualization and the rest of the soluble chromatin was added to 0.07 g of HAP resin (Bio-Rad, #157-0021) rehydrated in HAP Buffer 1 (5 mM NaPO4 pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF) and rotated for 10 minutes at 4 °C. HAP mixture was run through Ultrafree-MC Centrifugal Filter (Millipore, UFC30HV25) at 600 rcf for 30 seconds at 4 °C and 15 uL of flow-through was saved for visualization. Then the column was washed 4x with 200uL HAP Buffer 1, 4x with 200 uL HAP Buffer 2 (5 mM NaPO4 pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF), and eluted 3x with 100 uL of HAP Elution Buffer (500 mM NaPO4 pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF). Flowthrough after each step was saved for visualization. Chromatin concentration was measured again in triplicate with the combined HAP elutions using NanoDrop. Final chromatin concentration was adjusted to 20 ng/uL using ChIP Buffer 1 prior to IP. 15 uL of chromatin was set aside for input control and chromatin was added to beads conjugated with H3K4me3 antibody (Epigentek, A4033). Chromatin and bead mixture was rotated for 10 minutes at 4 °C, washed 2x with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% glycerol, 0.1% NP-40, 200 uM PMSF, 50 ug/mL BSA), washed 1x ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% NP-40, 200 uM PMSF, 50 ug/mL BSA), and washed 1x with TE buffer, transferring beads to a new tube after each wash step. DNA was finally eluted in 50 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% SDS) at 600 rpm for 10 minutes at 55 °C on a ThermoMixer. 35 uL of ChIP Elution Buffer was also added to the input control to bring the final volume to 50 uL. To both input and eluted ChIP DNA, 2 uL of 5 M NaCl, 1uL of 500 mM EDTA, and 1 uL of 20 mg/mL Proteinase K was added and incubated for 2 hours at 55 °C and DNA was purified using MinElute PCR Purification Kit (Qiagen, 28004). DNA as eluted in ultrapure H2O and concentration was measured before and after purification using Qubit dsDNA Quantitation, High Sensitivity (Thermo Fisher, Q32851). Finally, HAP input and elutions were visualized using 2% agarose gel in 1x TBE ran at 140 V for 40 minutes to confirm fragment sizes.
ChIP DNA was sent to the McGill University and Genome Quebec Innovation Center, where it was further validated via Bioanalyzer, followed by shotgun library preparation, and library sequencing via Illumina NovaSeq6000. H3K4me3 ChIP DNA was sequenced to a depth of about 50 million reads and input samples were sequence to a depth of about 150 million reads.

value: Human breast cancer

tag: chip antibody

value: normoxia (20% oxygen, 48 hrs)


title: YKK2941_SDS_1hr_bio_rep3

description:
Library name: Sample48
colomn name in all_counts_YKK2941 SDS_001-1hr_rep3

value: Yeast cells


title: T47D Input, normoxia, biol rep2


title: OG08


title: HSC_CCl4-2


title: YKK2941_SDS_1hr_bio_rep2

description:
Library name: Sample47
colomn name in all_counts_YKK2941 SDS_001-1hr_rep2


title: YKK2941_SDS_2hr_bio_rep1

description:
Library name: Sample49
colomn name in all_counts_YKK2941 SDS_001-2hr_rep1


title: HSC_CCl4-1


title: YKK2941_SDS_1hr_bio_rep1

description:
Library name: Sample46
colomn name in all_counts_YKK2941 SDS_001-1hr_rep1


title: HSC_CCl4_Tom-3


title: HSC_CCl4-3


title: OG06

value: I


title: T47D H3K4me3, ChIP, normoxia, biol rep3

value: H3K4me3 (Epigentek, A4033)


title: HSC_Tom-3


title: OG05


title: T47D H3K4me3, ChIP, normoxia, biol rep2


title: OG07


title: YKK2941_SDS_0.5hr_bio_rep2

description:
Library name: Sample44
colomn name in all_counts_YKK2941 SDS_001-0.5hr_rep2


title: YKK2941_SDS_0.5hr_bio_rep3

description:
Library name: Sample45
colomn name in all_counts_YKK2941 SDS_001-0.5hr_rep3


title: HSC_CCl4_Tom-1


title: T47D H3K4me3, ChIP, normoxia, biol rep1


title: OG04

value: treated


title: HSC_Tom-2

value: untreated


title: YKK2941_SDS_0.5hr_bio_rep1

description:
Library name: Sample43
colomn name in all_counts_YKK2941 SDS_001-0.5hr_rep1


title: HSC_Tom-1


title: OG03

value: H


title: HSC-3


title: YKK2941_control_bio_rep3

description:
Library name: Sample42
colomn name in all_counts_YKK2941 control-1-rep3


title: T47D Input, hypoxia, biol rep2

value: hypoxia (1% oxygen, 48 hrs)


title: OG02

value: tumor tissue


title: T47D Input, normoxia, biol rep1


title: YKK2941_control_bio_rep2

description:
Library name: Sample41
colomn name in all_counts_YKK2941 control-1-rep2

value: S. pastorianus Weihenstephan 34/70

value: WT


title: T47D Input, hypoxia, biol rep1


title: YKK2941_control_bio_rep1

description:
Library name: Sample40
colomn name in all_counts_YKK2941 control-1-rep1


title: HSC-1


title: OG01

value: normal tissue


title: OG00

value: G


title: T47D H3K4me3, ChIP, hypoxia, biol rep3


title: OF99


title: T47D H3K4me3, ChIP, hypoxia, biol rep2


title: GFP+ cells, SF3B1 gRNA2

city: Hong Kong

first: Jingkai

address: The University of Hong Kong, Pokfulam

institute: University of Hong Kong

description:
Library name: Sample 8
Column name in count.txt: SF3B1_gRNA2

data_processing:
Raw sequencing data (in .fastq format) were subjected to quality assessment using FastQC v0.12.1. The terminal 12-base pairs of all reads were trimmed using Trimmomatic v0.39 to remove low-quality bases with abnormal nucleotide frequency distributions (threshold: Phred score < 20). Processed reads were aligned to the Gallus gallus GRCg6a reference genome (Ensembl release 112) using STAR v2.7.11b. A raw count matrix was generated from the aligned .bam files using featureCounts v1.5.3 (from Subread package) counting at gene level.
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Gallus gallus

source_name: Trunk neural crest

extract_protocol:
Approximately 50,000 GFP+ cells per treatment were collected for RNA extraction using RNAqueous-Micro Kit (Ambion) and genomic DNA was removed by TURBO DNase treatment for 30 min. RNA quality was assayed using an Agilent 2100 Bioanalyzer. Only samples with an RNA integrity number (RIN) ≥8.0 and a 28S/18S ribosomal ratio ≥ 1.0 were selected for further processing.
cDNA libraries were constructed using the Illumina Stranded mRNA Prep kit

value: Trunk neural crest

value: Primary cells

value: Neural crest cells

value: SF3B1 knockout


title: OF98

value: colon


title: T47D Input, hypoxia, biol rep3

value: Human breast cancer


title: GFP+ cells, PHF5A gRNA2

description:
Library name: Sample 6
Column name in count.txt: PHF5A _gRNA2

value: PHF5A knockout


title: GFP+ cells, SF3B1 gRNA1

description:
Library name: Sample 7
Column name in count.txt: SF3B1_gRNA1


title: Conglobate Gland, dsMock, rep3

city: Barcelona

first: Jose Luis

last: Maestro

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37-49

department: Complexity of Life

country: Spain

institute: Institute of Evolutionary Biology

description:
Library name: Sample 7
GC_dspolyh_6

data_processing:
Quality control of libraries with FastQC
Read filtering and trimming with Trimmomatic
Read alignment with HISAT2
Read count summary with Feature Counts
Assembly: GenBank genome assembly: GCA_003018175.1
Supplementary files format and content: Excel spreadsheet containing raw gene counts for each sample

organism: Blattella germanica

source_name: Conglobate Gland

growth_protocol: Blattella germanica specimens used for RNA-seq analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
RNA was isolated using the HigherPurity Tissue Total RNA Purification kit (Canvax).
mRNA libraries from conglobate gland were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: We sequenced four replicates for each of the mRNA-seq libraries. Specimens were injected two micrograms of dsRNA according to their treatment (dsILP8 or dsMock).

value: Conglobate Gland


title: T47D H3K4me3, ChIP, hypoxia, biol rep1

value: H3K4me3 (Epigentek, A4033)


title: H9 Input, normoxia, biol rep3

value: Human embryonic stem cell

value: normoxia (20% oxygen, 24 hrs)


title: Conglobate Gland, dsMock, rep2

description:
Library name: Sample 6
GC_dspolyh_5


title: OF97

value: F

value: treated


title: H9 Input, normoxia, biol rep2


title: GFP+ cells, PHF5A gRNA1

description:
Library name: Sample 5
Column name in count.txt: PHF5A_gRNA1


title: GFP+ cells, DLC1 gRNA2

description:
Library name: Sample 4
Column name in count.txt: DLC1_gRNA2

value: DLC1 knockout


title: Conglobate Gland, dsILP8, rep4

description:
Library name: Sample 4
GC_dsILP8_8


title: OF96

value: tumor tissue

value: untreated


title: H9 Input, normoxia, biol rep1


title: OF95

value: normal tissue


title: HSC-2

value: liver

value: Hepatic stellate cell


title: GFP+ cells, DLC1 gRNA1

description:
Library name: Sample 3
Column name in count.txt: DLC1_gRNA1

value: Trunk neural crest

value: Primary cells

value: Neural crest cells


title: H9 H3K4me3, ChIP, normoxia, biol rep3


title: Conglobate Gland, dsILP8, rep3

description:
Library name: Sample 3
GC_dsILP8_5


title: OF94

value: colon

value: E


title: Conglobate Gland, dsILP8, rep2

description:
Library name: Sample 2
GC_dsILP8_4

value: Conglobate Gland


title: Conglobate Gland, dsMock, rep4

description:
Library name: Sample 8
GC_dspolyh_8


title: OF93


title: H9 H3K4me3, ChIP, normoxia, biol rep2

value: H3K4me3 (Epigentek, A4033)


title: GFP+ cells, scrambled gRNA, replicate 1

description:
Library name: Sample 1
Column names in count.txt: ctrl_gRNA_rep1

value: Scrambled


title: H9 H3K4me3, ChIP, normoxia, biol rep1

value: Human embryonic stem cell

value: normoxia (20% oxygen, 24 hrs)


title: OF92


title: Conglobate Gland, dsMock, rep1

description:
Library name: Sample 5
GC_dspolyh_1


title: H9 Input, hypoxia, biol rep3

value: hypoxia (1% oxygen, 24 hrs)


title: 07_Species_Mix_RNA

description:
Library name: 07_Species_Mix_RNA
SDR-seq

data_processing:
Barcode identification, count matrices consisting of either cell-reads (gDNA and RNA) or cell-UMIs (RNA) were generated using SDRranger (https://github.com/hawkjo/SDRranger).
Assembly: Targeted references were constructed for the PCR amplicons for gDNA and RNA libraries. Sequences for this study were extracted from the human GRCh38 assembly
Supplementary files format and content: Tab-seperated values and matrix files
Library strategy: scDNA-scRNA-seq (SDR-seq)

organism:
Homo sapiens
Mus musculus

extract_protocol:
Human iPSCs were fixed in either PFA or glyoxal, in-situ reverse transcription was performed and cells were subjected to the Tapestri machine from MissionBio (v3). Multiplexed PCR amplified both gDNA and RNA simultenously in the same cell together with cell barcoding.
For POP a common library for both gDNA and RNA was prepared. For all other runs separate sequencing libraries were performed for both gDNA and RNA.

value: human iPSCs

tag: cell line_2

tag: cell type_2

value: mouse fibroblasts


title: 07_Species_Mix_gDNA

description:
Library name: 07_Species_Mix_gDNA
SDR-seq


title: OF90

value: D

value: tumor tissue

value: untreated


title: OF91

value: treated


title: WT, no memory, time 20, rep 3

city: València

first: Joan

last: Serrano Quílez

state: València

address: Jaume Roig, 11

institute: CSIC

data_processing:
RNAseq data were obtained after Illumina sequencing and fastq files were obtained from Macrogen server
The quality of the raw sequencing data was checked by fastQC and trimmomatic program was used to withdraw the adapter sequences and the bases with a low base quality from the ends.
bases of reads which had a window size lower than 4 and a mean quality lower than 15 and the reads shorter than 36 bp were also trimmed.
Trimmed reads were mapped using sacCer3 as a reference genome with HISAT2, splice-aware aligner, and StringTie
Assembly: sacCer3
Supplementary files format and content: tab-delimited text containing raw reads for each sample
Supplementary files format and content: tab-delimited text containing TMM-normalised reads for each sample

growth_protocol: For all samples, yeast cells were growth until exponential phase (O.D.600 = 0.7) in rich medium (YPD).

extract_protocol:
A 10 mL aliquote is collected from each culture, washed twice with pure water and celular pellet was then frozen in liquid nitrogen. Total RNA was extracted with hot acid phenol protocol.
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: A cell culture was split into two flasks. One of them (memory) was exposed to a first 20 min heat shock and, after a 60 min recovery phase at optimal conditions, to a second 20 min heat shock. In the meantime, the other flask (no memory) was only exposed to a single 20 min heat shock. The heat shocks were performed by adding media at 51 ºC.

value: wt

tag: memory

value: No

tag: time


title: WT, no memory, time 0, rep 3


title: H9 Input, hypoxia, biol rep2


title: WT, no memory, time 15, rep 3


title: HS_4day_rep3

city: Madrid

first: Pilar

last: Sánchez Testillano

state: Madrid

address: C/ Ramiro de Maeztu, 9

department: Biotechnology

institute: Margarita Salas Center of Biological Research (CIB)

description: count matrix column name: ERRA220002009-1a

data_processing:
High clean quality reads were selected among the resulting raw read data for all replicates of both experiments. This filtering process was done with through fastp (v0.22.0) (Trimming adapters, filtering reads with >10% uncertain nucleotides and quality score < 5 for more than 50 % of the read sequence)
Clean reads were mapped to a B. napus reference genome assembly (NCBI GenBank accession no. GCA_000751015.1), using HiSAT2 splice sensitive alignment software (Chalhoub et al., 2014; Handa, 2003). Parameters chosen for HiSAT2 alignment were default: Unstranded RNA-seq library specification, maximum mismatch penalty : 6, minimum mismatch penalty : 2, read gap penalty : 5, read extend penalty : 3, 5 hits to report per read, a minimum and maximum intron length of 20bp and 500,000 bp respectively, allowing soft clipping and no requirement of long anchors. (read documentation for more details)
Expression quantification representing counts of clean reads mapped completely or incompletely to each gene model was obtained through HTSeqCount software (v0.11.1) (Anders et al., 2015; Putri et al., 2022), and normalized values were obtained through DESeq2 Variance Stabilized Transformation (Love et al., 2014)
NOTE: The 'ERRA220002009-1a' sample was identified as an outlier and was therefore excluded prior to obtaining the normalized dataset.
Assembly: AST_PRJEB5043_v1 (Darmor-bzh)
Supplementary files format and content: CSV-delimited text file includes raw counts for each sample, VST normalized counts

organism: Brassica napus

growth_protocol: Plants of Brassica napus L. were germinated and grown in growth chambers under controlled conditions, as previously described (Berenguer et  al., 2020). Vacuolated Microspores (VM) or late unicellular microspores at the most responsive stage of embryogenesis were isolated from flower buds with as described in Berenguer et  al., 2020. Microspore cultures were obtained after the buds were sterilized for 20 min in a 5% commercial bleach, rinsed 6 times in distilled water, crushed in a cold mortar with NLN-13 medium, filtered through a  48 μm nylon mesh, suspended in NLN-13 medium, and put into 4 consecutive cycles of centrifugation with NLN-13 medium resuspension at 185 x g for 5 min at 4º C. Final culture cell density was then adjusted to 10,000 cells/mL before culture heat shock treatment.

extract_protocol:
Each culture sample (10,000 cells/mL) was centrifuged, the medium removed and the pellet frozen in liquid nitrogen, ground to fine powder and stored at -80°C until RNA extraction was performed. Total RNA from culture samples in both experiments was extracted using RNeasy Plant Microkit (Quiagen) following the manufacturer’s instructions. To ensure that the RNA was completely free of DNA contamination, samples were treated with Turbo DNase (ThermoFisher, Waltham, MA, USA), and the quality and concentration of RNA was analyzed using NanoDrop ND-1000 (ThermoFisher, Waltham, MA, USA).
Non-directional cDNA libraries for each RNA sample were synthesized, assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and sequenced on an Illumina Novaseq platform and 150bp paired-end reads were generated by Novogene Co., Ltd (Cambridge, Europe)

treatment_protocol: Final microspore cultures were subjected to heat stress at 32ºC and were maintained at this temperature from initiation until the embryos reached proembryo structures at 4d. Microspore cultures at the vacuolated microspore stage lacking embryogenic cells (VM) and microspore cultures having a significant amount of embryogenic cells after heat shock treatment (PE) were sampled at timepoints 0d and 4d of the treated cultures.

tag: developmental stage_pollen_used

value: stress-treated microspores (proembryo stage)

value: microspores and proembryos

value: cultivar Topas, line DH-4079

value: heat shock


title: HS_4day_rep2

description: count matrix column name: ERRA220002008-1a


title: OF89

value: colon

value: normal tissue


title: OF88

value: C


title: H9 H3K4me3, ChIP, hypoxia, biol rep3

value: Human embryonic stem cell

value: H3K4me3 (Epigentek, A4033)


title: H9 Input, hypoxia, biol rep1

value: hypoxia (1% oxygen, 24 hrs)


title: WT memory, time 15, rep 3

value: Yes


title: GFP+ cells, scrambled gRNA, replicate 2

description:
Library name: Sample 2
Column names in count.txt: ctrl_gRNA_rep2

value: Trunk neural crest

value: Primary cells

value: Neural crest cells

value: Scrambled


title: HS_4day_rep1

description: count matrix column name: ERRA220002007-1a


title: VacuolatedMicrospore_rep3

description: count matrix column name: ERRA220002006-1a

value: microspores before stress

value: vacuolated microspores

value: untreated


title: WT, memory, time 0, rep 3

value: wt


title: OF87

value: tumor tissue


title: OF86


title: H9 H3K4me3, ChIP, hypoxia, biol rep1


title: Conglobate Gland, dsILP8, rep1

description:
Library name: Sample 1
GC_dsILP8_2

value: Conglobate Gland


title: mip6d, no memory, time 20, rep 3

value: No


title: VacuolatedMicrospore_rep2

description: count matrix column name: ERRA220002005-1a

value: cultivar Topas, line DH-4079


title: OF85

value: colon

value: B

value: treated


title: DMSO_3

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v2.0.0) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.38.1).
Assembly: hg38
Supplementary files format and content: raw counts

source_name: LNCaP Cell treated with DMSO

growth_protocol: Culture LNCaP cells in RPMI 1640 with 10% FBS in 10cm cell culture dishes

extract_protocol:
Trizol reagent RNA isolation followed by isopropanol precipitation and 75% ethanol wash.
cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were then denatured, and neutralized, before loading to NovaSeq 6000 sequencer

treatment_protocol: Seed cells into 10 cm cell culture dishes and allow to attach to plate 24 hours. Treat cells with DMSO control or MP18/Cpd17 @ 500 nM for 72 hours. Harvest cells and isolate RNA with Trizol reagent.

value: LNCaP Cell Line

tag: replicate

value: Biological Replicate 3

tag: agent

value: DMSO


title: mip6d, no memory, time 15, rep 3


title: VacuolatedMicrospore_rep1

description: count matrix column name: ERRA220002004-1a


title: DMSO_2

value: Biological Replicate 2


title: WT, memory, time 20, rep 3

value: Yes


title: OF83

value: normal tissue


title: Tension SDX cells bio4

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

data_processing:
The data was processed using Cell Ranger v7.1.0 pipeline from 10x Genomics with the commands "cellranger mkref" and "cellranger count" to generate single-cell transcript abundance matrices named filtered_feature_bc_matrix.h5.
Assembly: Populus trichocarpa (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002775.5/)
Supplementary files format and content: hd5

organism: Populus trichocarpa

source_name: Tension SDX

growth_protocol: Five to twelve-month-old trees of P. trichocarpa used for bending treatment were propagated from branch cutting and grown in the glasshouse or walk-in growth chamber (16/8 h light/dark cycle, 24-26℃) at National Taiwan University (Taipei, Taiwan). For all experiments, stems were collected from below the 8th internodes.

extract_protocol:
The protoplast isolation of SDX mainly followed our previously established protocol (Lin et al., 2014). The stems of normal or tension/opposite woods were cut into 8-cm segments and then debarked. The cell wall of the debarked stems were digested with cellulose-macerozyme solution (0.25 M mannitol, 20mM MES, pH 5.7, 20 mM KCl, 10 mM CaCl2．2H2O, 0.1% BSA, 1.5% cellulase R10, 0.4% macerozyme R10) for 3 hours at room temperature. After cell wall digestion, the stems were transferred into the modified MMG solution (4 mM MES, 0.25 M mannitol, 20 mM KCl) with shaking for 1 min to release SDX protoplasts. The SDX protoplasts were filtered through a 70-μm cell strainer and then centrifuged at 900g for 3 min at room temperature, and the filtered protoplasts were resuspended with the modified MMG solution. These protoplasts were further sorted. For cell sorting, a solution of FDA (fluorescein diacetate) at a final concentration of 0.008 mg/ml was used to stain live protoplasts. The staining process involved incubation for 5 minutes at room temperature in the dark. Subsequently, the stained protoplasts were centrifuged at 900g for 3 minutes at room temperature and then resuspended in the modified MMG solution. The FDA-stained SDX protoplasts were filtered through a 40-μm cell strainer and sorted using the BD FACSAria™ III cell sorter. A 488 nm laser was employed to select the FDA-stained SDX protoplasts. The sorting process involved narrowing down the selection based on forward-scattered light-height (FSC-H) and side-scattered light-height (SSC-H), followed by selection based on fluorescein isothiocyanate-area (FITC-A) and side-scattered light-area (SSC-A).
Single-cell sequencing libraries of four biological replicates for vertical, tension, and opposite stem differentiating xylem (SDX) in P. trichocarpa were generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics). The number of cells loaded following to the instructions in the 10x Genomics manual aimed at minimizing the formation of doublets or multiplets.

treatment_protocol: The stems of P. trichocarpa trees were bent from vertical to an angle of 90° to a horizontal line and maintained for 18 or 21 days. The bending point of the stem was fixed at a height of 115 cm (Fig. S2). The stem segments were collected from the bending point for 16 cm above and 16 cm below both. Trees treated with 18-day bending were used for protoplast isolation and scRNA-seq. Trees treated with 18- or 21-day bending were used for the anatomical dissection of stems.

value: Tension SDX

value: wild type


title: Tension SDX cells bio3


title: DMSO_1

value: Biological Replicate 1


title: MP18_3

source_name: LNCaP Cell treated with Cpd17/MP18


title: mip6d, memory, time 15, rep 3


title: Tension SDX cells bio2


title: mip6d, memory, time 20, rep 3


title: MP18_2


title: OF81

value: A

value: untreated


title: H9 H3K4me3, ChIP, hypoxia, biol rep2

value: Human embryonic stem cell

value: H3K4me3 (Epigentek, A4033)

value: hypoxia (1% oxygen, 24 hrs)


title: mip6d, memory, time 0, rep 3


title: OF80

value: colon


title: MP18_1


title: Tension SDX cells bio1


title: WT, no memory, time 20, rep 2

value: wt

value: No


title: OR14

growth_protocol: HCT-116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

treatment_protocol: HCT-116 cells were treated with 5μM of EM127 for 24 hours.

tag: type

value: treated

tag: treatment time


title: Opposite SDX cells bio4

source_name: Opposite SDX

value: Opposite SDX


title: WT, no memory, time 15, rep 2


title: WT, no memory, time 0, rep 2


title: mip6d, no memory, time 0, rep 3


title: OF84

tag: patient

value: B

value: tumor tissue


title: Opposite SDX cells bio2


title: OF82

tag: tissue


title: OR13

tag: cell line


title: WT, memory, time 20, rep 2

value: Yes


title: OR11


title: Opposite SDX cells bio1

tag: cell type


title: OR12


title: WT memory, time 15, rep 2

tag: genotype


title: Vertical SDX cells bio5

source_name: Vertical SDX

value: Vertical SDX


title: OR09

tag: treatment


title: Vertical SDX cells bio4


title: OR10


title: WT, memory, time 0, rep 2


title: Vertical SDX cells bio3


title: OR08

value: KO


title: mip6d, no memory, time 20, rep 2


title: mip6d, no memory, time 15, rep 2


title: Opposite SDX cells bio3

value: wild type


title: B. subtilis RNC-6 Treatment 2 (pH 5.0)-2

city: Noida

first: Rajnish

middle: Prakash

last: Singh

address: A 10, A Block, Block A, Industrial Area, Sector 62, Noida

country: India

institute: Jaypee Institute of Information Technology

description: Library name: Sample 6

data_processing:
data preprocessing: fastqc, Trim_galore, bbnorm
Assembly: Trinity
Quantification: Kallisto
Assembly: denovo
Supplementary files format and content: transcripts.counts.matrix.tsv, tsv format, contains transcript expression and annotation for all samples
Supplementary files format and content: transcripts.fasta.gz, gzipped fasta format, contains assembled transcript sequences

organism: Bacillus subtilis

source_name: bacterial

extract_protocol:
Xploregen Kit Based Method
Qiagen mrna library kit is used for the preparation of libraries according to the manufacturer's protocols

value: bacterial


title: NR2F2-deleted_in vitro_Adipocytes_10-days_rep3

type: RNA

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

description: In vitro differentiation

hyb_protocol: GeneChip HT WT PLUS Reagent Kit

scan_protocol: Affymetrix standard 24-peg microarray protocol

data_processing: Transcriptome Analysis Console (TAC) ver 4.0

label: biotin

source_name: Subcutaneous adipose stem-like cells

label_protocol: GeneChip HT WT PLUS Reagent Kit

growth_protocol: Homozygous NR2F2 floxed dams were provided either control (Soybean oil) or omega-6 rich (safflower oil) diets at the time of mating and underwent normal gestation/lactation, when pups were sacrificed for subcutaneous adipocyte stem-like cell isolation by FACS.

extract_protocol: Trizol followed by Qiagen Clean-up

treatment_protocol: Isolated ASCs were plated for 24-hours, NR2F2 was deleted using Adenovirus-Cre-GFP relative to Adenovirus-GFP controls. Cells recovered for 2-days and were differentiated into adipocytes for 10-days

tag: age

value: Postnatal day-12 pups

value: primary adipocyte stem-like cells were differentiated


title: NR2F2-deleted_in vitro_Adipocytes_10-days_rep2

description: In vitro differentiation


title: Vertical SDX cells bio2


title: B. subtilis RNC-6 Treatment 1 (pH 5.0)-1

description: Library name: Sample 5


title: Control_in vitro_Adipocytes_10-days_rep2

description: In vitro differentiation


title: Control_in vitro_Adipocytes_10-days_rep3

description: In vitro differentiation


title: OR07

value: untreated


title: mip6d, no memory, time 0, rep 2


title: SKN-1t[NDNN] transgenic rep4

city: Seattle

first: Nicolas

last: Lehrbach

state: WA

address: 1100 Fairview Ave. N, Seattle, WA 98109-102.

institute: Fred Hutchinson Cancer Center

data_processing:
STAR v2.7.7a(https://pubmed.ncbi.nlm.nih.gov/23104886/) with 2-pass mapping was used to align paired-end reads to WBcel235 genome assembly and quantify gene-level counts based on ENSEMBL gene annotation v52. FastQC 0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RNA-SeQC 2.3.4 (https://pubmed.ncbi.nlm.nih.gov/22539670/) were used to check read QC metrics.
Assembly: WBcel235
Supplementary files format and content: plain text containing gene-by-sample count matrix

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: For each sample/genotype, animals were bleach synchronized and hatched overnight rotating in M9 at 20°C. ~2000 synchronized L1 larvae were plated onto 9cm NGM plates. The animals were then allowed to grow to L4 stage before collection. Animals were washed 3x with M9 before resuspending the worm pellet in 1mL of TRIzol reagent (product #) and then stored at -80°C.

extract_protocol:
TriZol
TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA)

value: whole animal

value: unc-119(ed3) III; mgTi42(SKN-1t[NDNN])

value: synchronized L4 stage animals

tag: strain


title: Control_in vitro_Adipocytes_10-days_rep1

description: In vitro differentiation


title: OR06


title: mip6d, memory, time 20, rep 2


title: NR2F2-deleted_in vitro_Adipocytes_10-days_rep1

description: In vitro differentiation


title: OR05

value: control


title: SKN-1t[DNDD] transgenic rep4

value: unc-119(ed3) III; mgTi41(SKN-1t[DNDD])


title: mip6d, memory, time 15, rep 2


title: SKN-1t[NNNN] transgenic rep4

value: unc-119(ed3) III; mgTi21(SKN-1t[NNNN])


title: B. subtilis RNC-6 Treatment 1 (pH 4.0)-1

description: Library name: Sample 3


title: B. subtilis RNC-6 Control-2

description: Library name: Sample 2


title: OR04


title: B. subtilis RNC-6 Control-1

description: Library name: Sample 1


title: mip6d, memory, time 0, rep 2


title: SKN-1t[NDNN] transgenic rep3


title: OR03


title: control (non-transgenic) rep4


title: Tumor, NFAT.mteth.IL15.IL21_good response, #93

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

description: 10X Genomics

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.0.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.0.1 (STAR 2.7.2a). Sequenced reads were aligned to a custom human and mouse reference sequence containing CAR T. Sequenced reads were also aligned to the Total Seq C antibody Streptavidin and cell hashes HTO1, HTO2, and HTO3.
Assembly: GRCh38_mm10
Supplementary files format and content: feature_bc_matrix.h5

source_name: Tumor

extract_protocol: Freshly collected spleens or tumors were processed using Papain Dissociation System (Worthington Biochemical Corporation) according to manufacturer's protocol. In brief, each specimen were minced in the papain solution containing DNase and incubated in 37 degrees in a CO2 incubator for 30 minutes. The cloudy supernatant was collected, and was layered on top of Earle's Balanced Salt Solution containing 10% of albumin-ovomucoid inhibitor. The samples were centrifuged, and the pelleted cells were resuspended in PBS. Tumor #83 and #93 were submitted for scRNA-seq as is. All the other samples were incubated with the hIL-15 PE-conjugated antibody, and given TotalSeq™-C0951 PE Streptavidin. Spleen samples were also hashtagged as follows. Splenocyte #12: TotalSeq-C0251, barcode seq. GTCAACTCTTTAGCG; #17: TotalSeq-C0252, barcode seq. TGATGGCCTATTGGG; #18: TotalSeq-C0253, barcode seq. TTCCGCCTCTCTTTG; Splenocyte #83: TotalSeq-C0251, barcode seq. GTCAACTCTTTAGCG; #93; TotalSeq-C0252, barcode seq. TGATGGCCTATTGGG; #87; TotalSeq-C0253, barcode seq. TTCCGCCTCTCTTTG. #12, #17, and #18 were combined into one sample, and #83, #93, and #87 were combined into one sample.

value: Tumor

value: Neuroblastoma

value: ffLuc +, GFP +

value: GPC2-CAR T w/ NFAT.mteth.IL15.IL21


title: mig,replicate2,scRNAseq

city: Wuhan

first: Zhou

last: Haoyu

address: LuoYu road

institute: Wuhan University

description: 13X Genomics

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger(v5.0.1)
Assembly: ensembl_102
Supplementary files format and content: tab_seperated values files and matrix files

organism: Rattus norvegicus

source_name: skin

extract_protocol:
Tissue samples are collected at day 4 and immediately cut into 2-3 mm tissue block using a scalpel in tissue preservation solution. After centrifuging, tissue preservation solution is removed. The tissue block is transferred into a centrifuge tube and enzymed under 37 ℃ for digestion. Repetitive pipetting is done every 15-20 mins. After 30 mins, tissue digestion is examined via trypan blue staining until no obvious tissue block exists and the digestion stops. 40 µm cell strainer is used to filter the cell suspension. The residual cells are cleaned using the 2-3mL precooled complete DMEM medium in which the cleaning solution is filtered and collected into a centrifuge tube. Centrifuge at 300g and 4 ℃ for 5 mins and discard the supernatant. Then, red blood cell lysis buffer at room temperature is added to resuspend cells and lyse the red blood cells for 5 mins. Equal amounts of PBS-BSA (0.04 %) solution are added to stop the lysis of the red blood cells. Solutions are centrifuged at 300 g and 4 ℃ for 5 mins and discard the supernatant. Cell status is observed via trypan blue staining in which then the Dead Cell Removal Kit can be used to remove dead cells and debris. PBS-BSA (0.04%) is used to wash cells. A right amount of PBS-BSA (0.04%) is used to resuspend the precipitation followed by counting the cells using a hemacytometer.
The cellular suspension is stained with 0.4% trypan blue to assess cell viability under microscopic observation. Prepared single-cell suspension is then partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs are reverse transcribed into cDNAs. The reaction system is configured for breaking GEMs. After reacting at the suitable temperature for a fixed period, the products are purified. The reaction system is configured for PCR. After reacting at the suitable temperature for a fixed period, the products are purified. The reaction system is configured. A certain amount of cDNA amplified products is taken. The cDNAs are subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand. Finally, the products are purified. The reaction system is configured. Then, the cDNAs are subjected to adaptor ligation. Finally, the products are purified. The PCR reaction system is configured. Amplification is processed via PCR. The products are then purified. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: skin

value: migrasomes injected


title: WT, no memory, time 15, rep 1

value: wt

value: No


title: SKN-1t[DNDD] transgenic rep3


title: B. subtilis RNC-6 Treatment 2 (pH 4.0)-2

description: Library name: Sample 4

value: bacterial


title: mig,replicate1,scRNAseq

description: 12X Genomics


title: Tumor, teth.mIL15.IL21_good response, #83

description: 10X Genomics

value: GPC2-CAR T w/ mteth.IL15.IL21


title: WT, no memory, time 0, rep 1


title: SKN-1t[NNNN] transgenic rep3


title: ctrl,replicate2,scRNAseq

description: 11X Genomics

value: migrasomes uninjected


title: Spleen, combined and hashtagged, #83, #87, #93 FBC

description: 10X Genomics

source_name: Splenocytes

value: Splenocytes

value: GPC2-CAR T w/ mteth.IL15.IL21 or NFAT.mteth.IL15.IL21


title: control (non-transgenic) rep3

value: whole animal

value: synchronized L4 stage animals


title: WT, memory, time 20, rep 1

value: Yes


title: Spleen, combined and hashtagged, #83, #87, #93

description: 10X Genomics


title: ctrl,replicate1,scRNAseq

description: 10X Genomics


title: WT memory, time 15, rep 1


title: SKN-1t[NDNN] transgenic rep2

value: unc-119(ed3) III; mgTi42(SKN-1t[NDNN])


title: WT, memory, time 0, rep 1


title: SKN-1t[DNDD] transgenic rep2

value: unc-119(ed3) III; mgTi41(SKN-1t[DNDD])


title: Tumor, NFAT.mteth.IL15.IL21_poor response, #18 FBC

description: 10X Genomics

value: Tumor

value: Neuroblastoma


title: 473A ATAC ad 2.6

city: lexington

first: ka wing

last: Fong

state: KY

address: 760 press ave

institute: University of Kentucky

description: Library name: 473A ATAC ad 2.6

data_processing:
Paired-end sequencing reads were trimmed using Trimmomatic(v0.39) to remove adapters and low quality bases. Trimmed reads were mapped to the human reference genome assembly GRCh37 (hg19) using Bowtie2 (v2.3.5.1), allowing fragments up to 2kb to be aligned.
The alignment result was further filtered by SAMtools to remove reads unmapped, not primary alignment, reads failing platform, reads mapped to mitochondria, reads mapped to ENCODE blacklisted genomic regions and multi-mapped reads.
PCR duplicates were removed using Picard(v2.26.8). Peaks were called by MACS2(v2.2.7.1). The coverage track bigwig files were generated with bin size 10 and were normalized by reads per genome coverage using deeptools (v3.5.1).
Assembly: GRCH37
Supplementary files format and content: bigwig
Supplementary files format and content: narrowpeak file

growth_protocol: LNCaP and C4-2B cells were grown in RPMI + 10% FBS and 1% PS.

extract_protocol:
For CUT&RUN assay, 0.5x10^6  cells bound to Concanavalin A-coated beads were incubated with indicated primary antibodies and secondary antibody.  pA-MNase was used to digest chromatin/DNA bound by the antibodies-protein complex in CUT&RUN, followed by Proteinase K digestion and PCI extraction. For ATAC-seq, 50,000 cells were collected, then washed once by 1×PBS and tagmented in 1×TD buffer with 2.5 μl Tn5, 0.01% digitonin, and 0.3×PBS. The reactions were incubated at 37 °C for 30 min in a thermomixer with 300 rpm mixing. The tagmented DNA was purified using the DNA Clean & Concentrator-5 kit.
CUT&RUN libraries were prepared from 15-20ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 160-320bp (CUT&RUN) in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). All CUT&RUN Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000. ATAC-seq Libraries were amplified and adapter dimers and primer dimers were cleaned up.

treatment_protocol: LNCaP and C4-2B cells were infected by lentivirial supernatent containing shTRIM28, shRb, lenti-HAF TRIM28-WT and S473A for 4 days before being harvested for CUT&RUN assay.

value: Human prostate cancer cells

tag: chip antibody


title: 473A ATAC ad 2.5

description: Library name: 473A ATAC ad 2.5


title: Tumor, NFAT.mteth.IL15.IL21_poor response, #18

description: 10X Genomics

value: ffLuc +, GFP +

value: GPC2-CAR T w/ NFAT.mteth.IL15.IL21


title: WT, no memory, time 20, rep 1

value: wt


title: WT ATAC ad 2.2

description: Library name: WT ATAC ad 2.2


title: mip6d, no memory, time 20, rep 1

value: No


title: SKN-1t[NNNN] transgenic rep2

value: unc-119(ed3) III; mgTi21(SKN-1t[NNNN])


title: control (non-transgenic) rep2


title: mip6d, no memory, time 15, rep 1


title: Tumor, NFAT.mteth.IL15.IL21_good response, #17

description: 10X Genomics


title: WT ATAC ad 2.1

description: Library name: WT ATAC ad 2.1


title: mip6d, no memory, time 0, rep 1


title: TRIM28 473A rep2

description: Library name: TRIM28 473A rep2

data_processing:
Paired-end sequencing reads were trimmed using Trimmomatic(v0.39) to remove adapters and low quality bases. Trimmed reads were mapped to the human reference genome assembly GRCh37 (hg19) using Bowtie2 (v2.3.5.1), allowing fragments up to 2kb to be aligned.
The alignment result was further filtered by SAMtools to remove reads unmapped, not primary alignment, reads failing platform, reads mapped to mitochondria, reads mapped to ENCODE blacklisted genomic regions and multi-mapped reads.
PCR duplicates were removed using Picard(v2.26.8). Peaks were called by MACS2(v2.2.7.1). The coverage track bigwig files were generated with bin size 10 and were normalized by reads per genome coverage using deeptools (v3.5.1).
Assembly: GRCH37
Supplementary files format and content: bigwig
Supplementary files format and content: narrowpeak file
Library strategy: CUT&Run