title: LC06_PRE_CD45_021

city: Seoul

first: Soomin

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Cancer Research Institute

description: Library name: TA3761 | 021 | CD45+

data_processing:
Several QC steps were performed in accordance with the manufacturer’s guidelines. To ensure high-quality data, technical QC was performed using the following settings: flag segments with less than 1,000 raw reads, flag segments when less than 80% of raw reads were aligned, flag segments when sequencing saturation was less than 50%, negative probe count geomean was less than 10, no template control count was greater than 1,000, minimum nuclei count was less than 200, and minimum surface area was less than 16,000 µm2. Biological probe QC was performed excluding probes from the target count calculation in all segments if (geomean probe in all segments)/(geomean probes within target) ≤ 0.1, and if the failed grubs outlier test in ≥ 20% of the segments. A marginal threshold of the target frequency above 1% was set, and only 14,214 biological probes remained after this process.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: EGFR-mutant NSCLC_tumor, immune.xlsx
Supplementary files format and content: Q3 normalization
Library strategy: Spatial Transcriptomics

source_name: tissue

growth_protocol: We obtained formalin-fixed, paraffin-embedded (FFPE) tissue sections from 25 patients.

extract_protocol:
For spatial transcriptomic profiling, tissue sections from multiple patients were placed on the same slide (three slides in total), and 4 μm sections of the tissue microarray (TMA) were used for histological analysis following hematoxylin and eosin staining. Serial sections were stained simultaneously with fluorescently labeled antibodies to detect pan-cytokeratin (NanoString, AE1/AE3, cat. #121301310), and DNA-binding dye (ThermoFisher, Syto13, cat. #S7575) was then applied to the slides. Using the instrument’s web interface, ROIs up to 660 × 785 μm were selected and outlined by two experienced pathologists (JK and YKJ).
Library preparation was performed according to manufacturer instruction (Nanostring DSP-Genomics Library Preparation Protocol, Nanostring Technologies, Seatle, WA) (Merritt et al., 2020). Photocleaved oligonucleotides from each ROI were PCR amplified using Illumina’s i5/i7 dual-indexing system to preserve ROI identity. PCR products were pooled and purified with two rounds of AMPure XP beads (Beckman Coulter, Brea, CA). Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA) was used to measure library concentration and purity. Paired-end (275 bp reads) sequencing was performed on an Illumina NextSeq instrument. Reads were then aligned to analyte barcodes with Bowtie

treatment_protocol: As shown in the table, our dataset includes lung adenocarcinoma (LADC) and non-small cell lung cancer (NSCLC) before and after EGFR-TKI treatment.

value: tissue

tag: egfr-tki state

value: PRE

tag: region type

value: immune


title: Tumour, Menuetto, Mouse1130

status: Public on Jan 03 2025

type: SRA

city: Parkville

first: John

middle: E

last: La Marca

state: VIC

address: 1G Royal Parade

department: Blood Cells and Blood Cancer

country: Australia

institute: Walter and Eliza Hall Institute

description:
Library name: InVivo Menuetto Sample 6
mouse1130_tumour

library_source: other

data_processing:
Reads were mapped to sgRNA library files using MAGeCK v0.5.9
Supplementary files format and content: Processed data files for each screen contain raw sgRNA counts for each sample
Library strategy: CRISPR Screen

molecule: other

organism: Mus musculus

source_name: spleen

extract_protocol:
DNA was extracted using the DNeasy cell and tissue kit (QIAGEN) or Puregene kit (QIAGEN) according to the manufacturer's instructions.
Libraries were prepared and sequenced on the Illumina NextSeq 2000 using NextSeq 2000 P4 XLEAP-SBS Reagents, or on the Illumina MiSeq using a MiSeq Reagent Kit according to the manufacturer's instructions.

tag: tissue

value: spleen

tag: cell type

value: Lymphoma

tag: genotype

tag: treatment

value: In vivo

tag: crisprlibrary

value: Menuetto


title: HeLa_P65_10min_Rep2_pDBF

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
OINC-seq (Oxidation-Induced Nucleotide Conversion sequencing)
Adapters were trimmed from reads using Cutadapt.
RNA oxidation events (as seen as mutations) were quantified using PIGPEN (https://github.com/TaliaferroLab/OINC-seq)
Assembly: hg38 and GRCz11
Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.

extract_protocol:
RNA was extracted using Trizol and DNase treated for 30 min at 37C.
Single amplicon libraries were constructed using gene-specific RT-PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.

tag: cell line

value: HeLa

value: plus DBF


title: HA-EZH1 ChIP-seq at 16h, biological replicate 3

city: Thuwal

first: Valerio

last: Orlando

country: Saudi Arabia

institute: KAUST

library_source: genomic

data_processing:
Raw data was quality-checked and trimmed with BBDuk (version December 10, 2015) (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/). Since the datasets contained a spike-in from Drosophila melanogaster, the high-quality reads were mapped against the mouse genome (version mm10) and against the D. melanogaster genome (version BDGP6) with the software BWA (version 0.7.17). Afterwards, from the mouse-derived mapping reads, PCR duplicates were removed with Picard MarkDuplicates (version 2.8.1) (http://broadinstitute.github.io/picard/) and only reads being properly paired with a mapping quality equal or higher than 30 were kept with SAMtools (version 1.7). Peak calling was performed using MACS2 (version 2.2.4) using a q-value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: ChIP-seq peaks (depending on the mark, narrowPeak or broadPeak format). BigWig files.

molecule: genomic DNA

source_name: skeletal muscle

extract_protocol: TruSeq ChIP Library Preparation Kit followed by sequencing with NovaSeq6000

value: skeletal muscle


title: LC05_POST_CD45_019

description: Library name: TA3761 | 019 | CD45+

value: POST


title: HeLa_P65_10min_Rep2_mDBF

value: minus DBF


title: HA-EZH1 ChIP-seq at 16h, biological replicate 2


title: HeLa_P65_10min_Rep1_pDBF


title: LC06_PRE_PanCK_020

description: Library name: TA3761 | 020 | PanCK+

value: tumor


title: LC05_POST_PanCK_019

description: Library name: TA3761 | 019 | PanCK+


title: LC06_PRE_CD45_020

description: Library name: TA3761 | 020 | CD45+


title: HA-EZH1 ChIP-seq at 16h, biological replicate 1


title: LC05_POST_PanCK_018

description: Library name: TA3761 | 018 | PanCK+


title: HeLa_P65_10min_Rep1_mDBF


title: LC04_PRE_PanCK_017

description: Library name: TA3761 | 017 | PanCK+


title: LC05_POST_CD45_018

description: Library name: TA3761 | 018 | CD45+


title: HA-EZH1 ChIP-seq at 12h, biological replicate 3


title: HeLa_P65_10min_Rep3_pDBF


title: LC04_PRE_CD45_017

description: Library name: TA3761 | 017 | CD45+


title: LC04_PRE_CD45_016

description: Library name: TA3761 | 016 | CD45+


title: LC04_PRE_PanCK_016

description: Library name: TA3761 | 016 | PanCK+


title: A549,sgControl,WGBS

city: Beijing

first: Zhou

last: Xindi

state: Beijing

address: 30 Shuangqing Road

department: School of Medicine

country: China

institute: Tsinghua University

description: Control

data_processing:
Illumina HiSeq 2000 reads were trimmed and clipped for quality control.
Reads were mapped with Homo_sapiens.GRCh38 to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads.
Identical reads (potential PCR or optical duplicates) were flattened to 1 read.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: bedGraph

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
genomic DNA isolated  and bisulfite treated
The genomic DNAs of A549 control and UHRF1 KO tumor cells were isolated using the NucleoSpin Blood Mini kit for DNA from cells and tissue. The EZ DNA Methylation-GoldTM Kit  were used for DNA bisulfite conversion of genomic DNA (400ng) according to the manufacturers’ instructions. The DNA bisulfite converted DNA were then used for WGBS and focused bisulfite sequencing.

treatment_protocol: UHRF1 sgRNA was cloned in to lentiCRISPRv2-hygro and transfection with lentivirus then selected with hygromycin.

value: tumor cell

value: Contro


title: LC06_PRE_PanCK_021

description: Library name: TA3761 | 021 | PanCK+


title: HeLa_P65_05uM_Rep2

value: 5uM DBF


title: HeLa_P65_10min_Rep3_mDBF


title: LC04_PRE_PanCK_015

description: Library name: TA3761 | 015 | PanCK+


title: HA-EZH1 ChIP-seq at 20h, biological replicate 1


title: LC04_PRE_CD45_015

description: Library name: TA3761 | 015 | CD45+


title: HA-EZH1 ChIP-seq at 12h, biological replicate 1


title: LC04_PRE_PanCK_014

description: Library name: TA3761 | 014 | PanCK+


title: HeLa_P65_05uM_Rep1


title: PVA_HSC_rTSP1 Plus aCD36_3

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Reads were checked for quality (FastQC v0.11.5) and processed using the Digital Expression Explorer 2 (DEE2) workflow
Adapter trimming was performed with Skewer (v0.2.2)
Further quality control was performed with Minion, part of the Kraken package
Filtered reads were mapped to the mouse reference genome GRCm38 using STAR aligner and gene-wise expression counts were generated using the “-quantMode GeneCounts” parameter.
The R package edgeR was used to calculate FPKM
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for all samples in this subseries

source_name: Bone Marrow

growth_protocol: FACS purified HSCs were cultured ex vivo for 11 days in a polyvinyl alcohol based expansion medium containing 10 ng/mL murine SCF and 100 ng/mL murine TPO.

extract_protocol:
Cells were FACS sorted into TRIzol-LS and total RNA was purified as per manufacturer’s protocol. 2 ng total RNA was utilized as input for library preparation.
Libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit following manufacturer's protocols.

treatment_protocol: To analyze transcriptional alterations within HSCs cultured in the presence of recombinant Thbs1 and a neutralizing antibody targeting CD36, RNA Seq analysis was performed on FACS purified HSPCs.

value: Bone Marrow

value: Primary cells

value: Hematopoietic stem cell

value: Control

tag: age

value: 4 month old

value: rThbs1 Plus anti-CD36 antibody


title: HeLa_P65_05min_Rep3_mDBF


title: PVA_HSC_rTSP1 Plus aCD36_1


title: PVA_HSC_rTSP1 Plus aCD36_2


title: HeLa_P65_05min_Rep3_pDBF


title: LC03_POST_PanCK_013

description: Library name: TA3761 | 013 | PanCK+

value: tissue


title: LC03_PRE_PanCK_010

description: Library name: TA3761 | 010 | PanCK+

value: PRE


title: HeLa_P65_05min_Rep2_pDBF

value: HeLa


title: LC02_POST_PanCK_009

description: Library name: TA3761 | 009 | PanCK+


title: PVA_HSC_rTSP1_3


title: HeLa_P65_05uM_Rep3


title: LC02_POST_CD45_009

description: Library name: TA3761 | 009 | CD45+

value: immune


title: HA-EZH1 ChIP-seq at 12h, biological replicate 2

value: skeletal muscle


title: HeLa_P65_05min_Rep2_mDBF


title: PVA_HSC_rTSP1_2


title: LC02_POST_CD45_008

description: Library name: TA3761 | 008 | CD45+

value: POST


title: LC02_POST_PanCK_008

description: Library name: TA3761 | 008 | PanCK+


title: HeLa_P65_05min_Rep1_pDBF

value: plus DBF


title: LC02_POST_PanCK_007

description: Library name: TA3761 | 007 | PanCK+

value: tumor


title: LC02_POST_CD45_007

description: Library name: TA3761 | 007 | CD45+


title: PVA_HSC_rTSP1_1


title: HeLa_P65_05min_Rep1_mDBF

value: minus DBF


title: LC04_PRE_CD45_014

description: Library name: TA3761 | 014 | CD45+


title: LC02_PRE_PanCK_006

description: Library name: TA3761 | 006 | PanCK+


title: LC03_PRE_PanCK_011

description: Library name: TA3761 | 011 | PanCK+


title: Aged_TSPKO_BMEC_3

description: RS.03684462_Aged.TSPKO.BMEC.3_RS.03677334

treatment_protocol: To perform RNA Seq analysis of BMECs derived from aged Thbs1 knockout mice, 18 month-old knockout mice were utilized, along with young (3 month-old) and aged (18 month-old) control mice. Mice were intravitally labeled with an antibody targeting VEcadherin via retro-orbital sinus injections 10 minutes prior to sacrifice. Mice were euthanized and their long bones harvested to isolate BMECs by FACS for performing RNA Seq analyses.

value: Endothelial cell

value: Aged Thbs1 knockout

value: 18 month


title: HeLa_P65_03uM_Rep3

value: 3uM DBF


title: LC01_POST_PanCK_004

description: Library name: TA3761 | 004 | PanCK+


title: LC02_PRE_PanCK_005

description: Library name: TA3761 | 005 | PanCK+


title: HeLa_P65_03uM_Rep1


title: LC01_POST_CD45_004

description: Library name: TA3761 | 004 | CD45+


title: Aged_TSPKO_BMEC_2

description: RS.03684461_Aged.TSPKO.BMEC.2_RS.03677333

value: Bone Marrow

value: Primary cells


title: LC01_POST_PanCK_003

description: Library name: TA3761 | 003 | PanCK+


title: Aged_Control_BMEC_3

description: RS.03684459_Aged.Cntl.BMEC.3_RS.03677331

value: Aged Control


title: Aged_TSPKO_BMEC_1

description: RS.03684460_Aged.TSPKO.BMEC.1_RS.03677332


title: LC03_POST_PanCK_012

description: Library name: TA3761 | 012 | PanCK+


title: HeLa_P65_02min_Rep3_pDBF


title: Aged_Control_BMEC_2

description: RS.03684458_Aged.Cntl.BMEC.2_RS.03677330


title: LC02_PRE_CD45_005

description: Library name: TA3761 | 005 | CD45+


title: LC02_PRE_CD45_006

description: Library name: TA3761 | 006 | CD45+


title: LC01_POST_CD45_003

description: Library name: TA3761 | 003 | CD45+


title: LC01_PRE_CD45_002

description: Library name: TA3761 | 002 | CD45+


title: LC01_PRE_PanCK_001

description: Library name: TA3761 | 001 | PanCK+


title: HeLa_P65_02min_Rep3_mDBF


title: LC01_PRE_CD45_001

description: Library name: TA3761 | 001 | CD45+


title: Aged_Control_BMEC_1

description: RS.03684457_Aged.Cntl.BMEC.1_RS.03677329


title: LC25_PRE_PanCK_023

description: Library name: TA3765_TA3766 | 023 | PanCK+


title: Young_Control_BMEC_3

value: Young Control

value: 3 month


title: LC25_PRE_CD45_023

description: Library name: TA3765_TA3766 | 023 | CD45+

value: tissue

value: PRE


title: HeLa_P65_02min_Rep2_mDBF

value: HeLa


title: HeLa_P65_02min_Rep2_pDBF


title: HeLa_P65_03uM_Rep2


title: LC25_PRE_PanCK_022

description: Library name: TA3765_TA3766 | 022 | PanCK+


title: LC25_PRE_CD45_022

description: Library name: TA3765_TA3766 | 022 | CD45+

value: immune


title: Young_Control_BMEC_2


title: HeLa_P65_02min_Rep1_pDBF


title: Young_Control_BMEC_1


title: LC24_PRE_CD45_021

description: Library name: TA3765_TA3766 | 021 | CD45+


title: LC01_PRE_PanCK_002

description: Library name: TA3761 | 002 | PanCK+


title: LC24_PRE_PanCK_021

description: Library name: TA3765_TA3766 | 021 | PanCK+


title: Aged_TSPKO_MSC_3

treatment_protocol: To perform RNA Seq analysis of BM MSCs derived from aged Thbs1 knockout mice, 18 month-old knockout mice were utilized, along with young (3 month-old) and aged (18 month-old) control mice. Mice were intravitally labeled with an antibody targeting VEcadherin via retro-orbital sinus injections 10 minutes prior to sacrifice. Mice were euthanized and their long bones harvested to isolate BM MSCs by FACS for performing RNA Seq analyses.

value: Mesenchymal stromal cell


title: LC24_PRE_PanCK_020

description: Library name: TA3765_TA3766 | 020 | PanCK+


title: HeLa_P65_02min_Rep1_mDBF


title: HeLa_P65_01uM_Rep3

value: 1uM DBF


title: LC24_PRE_CD45_020

description: Library name: TA3765_TA3766 | 020 | CD45+


title: LC24_PRE_PanCK_019

description: Library name: TA3765_TA3766 | 019 | PanCK+

value: tumor


title: Aged_TSPKO_MSC_2


title: LC24_PRE_CD45_019

description: Library name: TA3765_TA3766 | 019 | CD45+


title: LC24_PRE_PanCK_018

description: Library name: TA3765_TA3766 | 018 | PanCK+


title: HeLa_P65_01uM_Rep1


title: LC24_PRE_CD45_018

description: Library name: TA3765_TA3766 | 018 | CD45+


title: LC23_PRE_PanCK_017

description: Library name: TA3765_TA3766 | 017 | PanCK+


title: Aged_Control_MSC_3


title: LC23_PRE_CD45_017

description: Library name: TA3765_TA3766 | 017 | CD45+


title: HeLa_P65_01min_Rep3_pDBF

value: plus DBF


title: LC23_PRE_PanCK_016

description: Library name: TA3765_TA3766 | 016 | PanCK+


title: Aged_Control_MSC_2


title: HeLa_P65_01min_Rep3_mDBF

value: minus DBF


title: LC23_PRE_CD45_016

description: Library name: TA3765_TA3766 | 016 | CD45+


title: LC22_POST_PanCK_015

description: Library name: TA3765_TA3766 | 015 | PanCK+

value: POST


title: LC22_POST_CD45_015

description: Library name: TA3765_TA3766 | 015 | CD45+


title: HeLa_P65_01min_Rep2_pDBF


title: Aged_Control_MSC_1

value: 18 month


title: LC22_POST_PanCK_014

description: Library name: TA3765_TA3766 | 014 | PanCK+


title: LC22_POST_CD45_014

description: Library name: TA3765_TA3766 | 014 | CD45+


title: HeLa_P65_01min_Rep2_mDBF


title: Young_Control_MSC_2


title: Young_Control_MSC_3


title: LC21_PRE_PanCK_012

description: Library name: TA3765_TA3766 | 012 | PanCK+


title: HeLa_P65_01uM_Rep2


title: HeLa_P65_01min_Rep1_pDBF


title: LC21_PRE_CD45_012

description: Library name: TA3765_TA3766 | 012 | CD45+


title: Young_Control_MSC_1


title: LC21_PRE_CD45_013

description: Library name: TA3765_TA3766 | 013 | CD45+


title: HeLa_P65_01min_Rep1_mDBF


title: Aged_TSPKO_MSC_1

value: Aged Thbs1 knockout


title: Aged_TSPKO_HSC_5

treatment_protocol: To analyze aging associated transcriptional alterations within HSCs, RNA Seq analysis was performed on FACS purified HSCs isolated from young (3 month-old), aged (18 month-old) mice and aged (18 month-old) Thbs1 knockout mice.

value: Bone Marrow

value: Hematopoietic stem cell


title: LC20_POST_ABCP_PanCK_010

description: Library name: TA3765_TA3766 | 010 | PanCK+


title: Aged_TSPKO_HSC_4

value: Primary cells


title: HeLa_P65_00uM_Rep3


title: LC20_POST_ABCP_CD45_010

description: Library name: TA3765_TA3766 | 010 | CD45+


title: HeLa_P65_00uM_Rep2


title: LC20_POST_ABCP_PanCK_011

description: Library name: TA3765_TA3766 | 011 | PanCK+


title: LC15_PRE_PanCK_009

description: Library name: TA3765_TA3766 | 009 | PanCK+


title: HeLa_P65_00uM_Rep1


title: LC15_PRE_CD45_009

description: Library name: TA3765_TA3766 | 009 | CD45+


title: LC15_PRE_PanCK_008

description: Library name: TA3765_TA3766 | 008 | PanCK+


title: HeLa_P65_00min_Rep3_pDBF


title: LC21_PRE_PanCK_013

description: Library name: TA3765_TA3766 | 013 | PanCK+


title: LC15_PRE_CD45_008

description: Library name: TA3765_TA3766 | 008 | CD45+


title: LC08_POST_PanCK_007

description: Library name: TA3765_TA3766 | 007 | PanCK+


title: LC08_POST_CD45_007

description: Library name: TA3765_TA3766 | 007 | CD45+


title: HeLa_P65_00min_Rep3_mDBF


title: LC08_POST_CD45_006

description: Library name: TA3765_TA3766 | 006 | CD45+


title: Aged_Control_HSC_5

value: Aged Control


title: Aged_Control_HSC_4


title: LC08_POST_PanCK_006

description: Library name: TA3765_TA3766 | 006 | PanCK+


title: HeLa_P65_00min_Rep2_pDBF


title: LC05_PRE_CD45_005

description: Library name: TA3765_TA3766 | 005 | CD45+


title: HeLa_P65_00min_Rep2_mDBF


title: LC05_PRE_PanCK_005

description: Library name: TA3765_TA3766 | 005 | PanCK+


title: LC04_POST_PanCK_004

description: Library name: TA3765_TA3766 | 004 | PanCK+


title: LC20_POST_ABCP_CD45_011

description: Library name: TA3765_TA3766 | 011 | CD45+


title: Aged_Control_HSC_2


title: LC04_POST_CD45_004

description: Library name: TA3765_TA3766 | 004 | CD45+


title: Aged_Control_HSC_3


title: HeLa_P65_00min_Rep1_pDBF


title: HeLa_P65_00min_Rep1_mDBF


title: Aged_TSPKO_HSC_3


title: LC05_PRE_PanCK_003

description: Library name: TA3765_TA3766 | 003 | PanCK+


title: LC05_PRE_CD45_003

description: Library name: TA3765_TA3766 | 003 | CD45+


title: LC24_POST_ABCP_PanCK_002

description: Library name: TA3765_TA3766 | 002 | PanCK+


title: LC23_POST_PanCK_001

description: Library name: TA3765_TA3766 | 001 | PanCK+


title: Aged_Control_HSC_1


title: Aged_TSPKO_HSC_2


title: Aged_TSPKO_HSC_1


title: LC23_POST_CD45_001

description: Library name: TA3765_TA3766 | 001 | CD45+


title: LC19_PRE_CD45_026

description: Library name: TA3763_repeat | 026 | CD45+


title: LC19_PRE_PanCK_026

description: Library name: TA3763_repeat | 026 | PanCK+


title: Young_Control_HSC_5

value: Young Control

value: 3 month


title: HeLa_H2B_MALAT1_Rep4_pDBF


title: LC19_PRE_CD45_025

description: Library name: TA3763_repeat | 025 | CD45+

value: tissue

value: PRE


title: HeLa_H2B_MALAT1_Rep3_mDBF

value: HeLa


title: LC19_POST_CD45_024

description: Library name: TA3763_repeat | 024 | CD45+

value: immune


title: LC19_POST_PanCK_023

description: Library name: TA3763_repeat | 023 | PanCK+


title: Young_Control_HSC_2


title: HeLa_H2B_MALAT1_Rep2_pDBF


title: Young_Control_HSC_3


title: LC19_PRE_PanCK_024

description: Library name: TA3763_repeat | 024 | PanCK+


title: Young_Control_HSC_1


title: HeLa_H2B_MALAT1_Rep4_mDBF


title: HeLa_H2B_MALAT1_Rep2_mDBF


title: LC18_POST_CD45_022

description: Library name: TA3763_repeat | 022 | CD45+


title: HeLa_H2B_MALAT1_Rep1_pDBF


title: PVA_HSC_rThbs1 Plus IgM_3

treatment_protocol: To analyze transcriptional alterations within HSCs cultured in the presence of recombinant Thbs1 and its neutralizing antibody, RNA Seq analysis was performed on FACS purified HSPCs.

value: Control

value: 4 month old

value: rThbs1 Plus IgM antibody


title: LC18_POST_CD45_020

description: Library name: TA3763_repeat | 020 | CD45+


title: LC18_POST_PanCK_021

description: Library name: TA3763_repeat | 021 | PanCK+

value: tumor


title: LC18_POST_CD45_021

description: Library name: TA3763_repeat | 021 | CD45+

value: POST


title: HeLa_H2B_MALAT1_Rep1_mDBF

value: minus DBF


title: LC18_PRE_PanCK_019

description: Library name: TA3763_repeat | 019 | PanCK+


title: PVA_HSC_rThbs1 Plus IgM_2


title: LC18_POST_PanCK_020

description: Library name: TA3763_repeat | 020 | PanCK+


title: LC18_PRE_CD45_019

description: Library name: TA3763_repeat | 019 | CD45+


title: PVA_HSC_rThbs1 Plus IgM_1


title: HeLa_H2B_MALAT1_Rep3_pDBF

value: plus DBF


title: LC19_PRE_PanCK_025

description: Library name: TA3763_repeat | 025 | PanCK+


title: Young_Control_HSC_4

value: Bone Marrow


title: HeLa_H2B_GAPDH_Rep4_pDBF


title: LC18_PRE_CD45_017

description: Library name: TA3763_repeat | 017 | CD45+


title: LC18_PRE_PanCK_018

description: Library name: TA3763_repeat | 018 | PanCK+


title: PVA_HSC_rThbs1 Plus A4.1_3

value: Hematopoietic stem cell

value: rThbs1 Plus A4.1 antibody


title: HeLa_H2B_GAPDH_Rep4_mDBF


title: LC18_POST_PanCK_022

description: Library name: TA3763_repeat | 022 | PanCK+


title: PVA_HSC_rThbs1 Plus A4.1_2

value: Primary cells


title: LC18_POST_CD45_016

description: Library name: TA3763_repeat | 016 | CD45+


title: LC18_POST_PanCK_016

description: Library name: TA3763_repeat | 016 | PanCK+


title: HeLa_H2B_GAPDH_Rep3_pDBF


title: PVA_HSC_rThbs1 Plus A4.1_1


title: HeLa_H2B_GAPDH_Rep3_mDBF


title: LC17_POST_PanCK_015

description: Library name: TA3763_repeat | 015 | PanCK+


title: LC17_POST_CD45_014

description: Library name: TA3763_repeat | 014 | CD45+


title: LC16_POST_CD45_013

description: Library name: TA3763_repeat | 013 | CD45+


title: HeLa_H2B_GAPDH_Rep2_pDBF


title: PVA_HSC_rThbs1_2


title: LC16_POST_PanCK_013

description: Library name: TA3763_repeat | 013 | PanCK+


title: LC15_POST_PanCK_011

description: Library name: TA3763_repeat | 011 | PanCK+


title: PVA_HSC_rThbs1_3


title: HeLa_H2B_GAPDH_Rep1_pDBF


title: PVA_HSC_Control_3

value: Vehicle (PBS)


title: LC15_POST_PanCK_009

description: Library name: TA3763_repeat | 009 | PanCK+


title: LC15_POST_PanCK_010

description: Library name: TA3763_repeat | 010 | PanCK+


title: LC17_POST_PanCK_014

description: Library name: TA3763_repeat | 014 | PanCK+


title: PVA_HSC_Control_2


title: HeLa_H2B_GAPDH_Rep1_mDBF


title: LC15_POST_CD45_007

description: Library name: TA3763_repeat | 007 | CD45+


title: LC18_PRE_PanCK_017

description: Library name: TA3763_repeat | 017 | PanCK+


title: HeLa_H2B_GAPDH_Rep2_mDBF


title: LC15_POST_PanCK_008

description: Library name: TA3763_repeat | 008 | PanCK+


title: LC15_POST_CD45_006

description: Library name: TA3763_repeat | 006 | CD45+


title: H2B_pDBF_rep4

molecule: polyA RNA


title: LC17_POST_CD45_015

description: Library name: TA3763_repeat | 015 | CD45+


title: LC14_POST_CD45_004

description: Library name: TA3763_repeat | 004 | CD45+


title: PVA_HSC_rThbs1_1


title: H2B_pDBF_rep3


title: LC15_POST_PanCK_007

description: Library name: TA3763_repeat | 007 | PanCK+


title: Young_TSPKO_Female_HSC_2

description: RS.03684449_Yng.TSPKO.Female.HSC.2_RS.03677321

treatment_protocol: To analyze transcriptional alterations within HSCs due to deletion of Thbs1, RNA Seq analysis was performed on FACS purified HSCs isolated from young (4 month-old) control and Thbs1 knockout mice.

value: Thbs1 knockout


title: PVA_HSC_Control_1


title: Young_TSPKO_Female_HSC_3

description: RS.03684450_Yng.TSPKO.Female.HSC.3_RS.03677322


title: LC14_POST_PanCK_004

description: Library name: TA3763_repeat | 004 | PanCK+

value: tissue


title: H2B_pDBF_rep1


title: H2B_pDBF_rep2


title: LC15_POST_PanCK_006

description: Library name: TA3763_repeat | 006 | PanCK+


title: LC14_POST_CD45_003

description: Library name: TA3763_repeat | 003 | CD45+


title: LC15_PRE_PanCK_005

description: Library name: TA3763_repeat | 005 | PanCK+

value: PRE


title: Young_TSPKO_Female_HSC_1

description: RS.03684448_Yng.TSPKO.Female.HSC.1_RS.03677320


title: LC14_PRE_CD45_002

description: Library name: TA3763_repeat | 002 | CD45+


title: LC14_POST_PanCK_003

description: Library name: TA3763_repeat | 003 | PanCK+


title: LC14_PRE_PanCK_002

description: Library name: TA3763_repeat | 002 | PanCK+


title: LC13_POST_PanCK_025

description: Library name: TA3762 | 025 | PanCK+


title: Young_Control_Female_HSC_3

description: RS.03684447_Yng.Cntl.Female.HSC.3_RS.03677319


title: LC14_PRE_PanCK_001

description: Library name: TA3763_repeat | 001 | PanCK+


title: H2B_mDBF_rep4

value: HeLa


title: H2B_mDBF_rep3


title: H2B_mDBF_rep2


title: LC13_PRE_CD45_024

description: Library name: TA3762 | 024 | CD45+

value: immune


title: LC13_POST_CD45_025

description: Library name: TA3762 | 025 | CD45+


title: Young_Control_Female_HSC_2

description: RS.03684446_Yng.Cntl.Female.HSC.2_RS.03677318

value: Control


title: LC13_PRE_CD45_023

description: Library name: TA3762 | 023 | CD45+


title: LC13_PRE_PanCK_024

description: Library name: TA3762 | 024 | PanCK+


title: H2B_mDBF_rep1


title: LC13_PRE_PanCK_023

description: Library name: TA3762 | 023 | PanCK+


title: LC12_POST_ABCP_CD45_022

description: Library name: TA3762 | 022 | CD45+


title: sham_if3_s3

city: Dresden

first: Björn

middle: H

last: Falkenburger

address: Fetscherstrasse 74

department: Neurology

country: Germany

institute: TU Dresden

data_processing:
Reads were mapped to the mouse genome GRCm39 UCSC M29 using Salmon pseudoaligner
Differential gene expression analysis was performed using DESeq2 version 1.40.2 following the standard workflow and using default parameters.
Assembly: mm39
Supplementary files format and content: comma-seperated value file contains raw counts

source_name: Brain

growth_protocol: Twelve week old mice were randomly allocated into ad libitum (AL) or intermittent fasting (IF).  IF was initiated at CET 15:00 (2 hours prior to lights off) for 24 hours on Mondays, Wednesdays and Fridays (alternate day fasting for 3/7 days per week). Food access was controlled by transferring mice daily between fresh cages with or without food. Mice in the AL groups were also transferred between cages at the same time to standardize handling.  All mice had free access to water throughout the study.

extract_protocol:
Total RNA from substantia nigra lysate was extracted using the RNeasy Lipid Tissue Mini Kit
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Mice were either fasted for one day, or subjected to the IF paradigm for 1 week (i.e., 3 days of fasting), or maintained on AL diet for 1 week.

value: Brain

value: Substantia nigra

value: Sham

value: Intermitted fasting one week


title: H2B_GAPDH_intspan_Rep3_pDBF


title: Young_Control_Female_HSC_1

description: RS.03684445_Yng.Cntl.Female.HSC.1_RS.03677317

value: 4 month old


title: H2B_GAPDH_intspan_Rep2_mDBF

value: minus DBF


title: LC12_PRE_CD45_020

description: Library name: TA3762 | 020 | CD45+


title: sham_if1_s2

value: Intermitted fasting one day


title: H2B_GAPDH_intspan_Rep3_mDBF


title: LC12_PRE_PanCK_021

description: Library name: TA3762 | 021 | PanCK+

value: tumor


title: LC12_PRE_CD45_021

description: Library name: TA3762 | 021 | CD45+


title: LC11_PRE_PanCK_019

description: Library name: TA3762 | 019 | PanCK+


title: sham_if3_s1


title: LC12_POST_ABCP_PanCK_022

description: Library name: TA3762 | 022 | PanCK+


title: LC12_PRE_PanCK_020

description: Library name: TA3762 | 020 | PanCK+


title: sham_if3_s2


title: sham_if1_s3


title: H2B_GAPDH_intspan_Rep1_mDBF


title: LC11_PRE_CD45_018

description: Library name: TA3762 | 018 | CD45+


title: H2B_GAPDH_intspan_Rep1_pDBF

value: plus DBF


title: LC11_PRE_CD45_019

description: Library name: TA3762 | 019 | CD45+


title: H2B_GAPDH_intspan_Rep2_pDBF


title: LC11_POST_PanCK_017

description: Library name: TA3762 | 017 | PanCK+

value: POST


title: LC11_POST_PanCK_016

description: Library name: TA3762 | 016 | PanCK+


title: sham_al_s3

value: Ad libitum diet


title: LC11_POST_CD45_017

description: Library name: TA3762 | 017 | CD45+


title: LC11_POST_CD45_016

description: Library name: TA3762 | 016 | CD45+


title: sham_al_s2


title: LC10_POST_PanCK_015

description: Library name: TA3762 | 015 | PanCK+


title: LC10_POST_CD45_015

description: Library name: TA3762 | 015 | CD45+


title: sham_al_s1


title: H2B_GAPDH_exon_Rep3_pDBF


title: asyn_if_s3

growth_protocol: Mice were randomly allocated into ad libitum (AL) or intermittent fasting (IF) groups two weeks after surgery (rAAV aSyn – AL, rAAV aSyn – IF).  IF was initiated at CET 15:00 (2 hours prior to lights off) for 24 hours on Mondays, Wednesdays and Fridays (alternate day fasting for 3/7 days per week).  Food access was controlled by transferring mice daily between fresh cages with or without food.  Mice in the AL groups were also transferred between cages at the same time to standardize handling.  All mice had free access to water throughout the study.

treatment_protocol: IF was started two weeks after surgery and carried out for 10 weeks.

value: Intermitted fasting 10 weeks


title: H2B_GAPDH_exon_Rep2_pDBF


title: H2B_GAPDH_exon_Rep2_mDBF


title: asyn_if_s2


title: sham_if1_s1


title: LC10_POST_PanCK_014

description: Library name: TA3762 | 014 | PanCK+

value: tissue


title: LC09_POST_PanCK_013

description: Library name: TA3762 | 013 | PanCK+


title: LC10_POST_CD45_014

description: Library name: TA3762 | 014 | CD45+


title: LC09_POST_CD45_012

description: Library name: TA3762 | 012 | CD45+


title: H2B_GAPDH_exon_Rep1_mDBF


title: H2B_GAPDH_exon_Rep3_mDBF


title: asyn_al_s3

value: Ad libitum diet 10 weeks


title: H2B_GAPDH_exon_Rep1_pDBF

value: HeLa


title: LC11_PRE_PanCK_018

description: Library name: TA3762 | 018 | PanCK+

value: PRE


title: LC08_POST_PanCK_010

description: Library name: TA3762 | 010 | PanCK+


title: LC09_POST_CD45_013

description: Library name: TA3762 | 013 | CD45+

value: immune


title: asyn_if_s1

value: Brain


title: LC08_POST_CD45_010

description: Library name: TA3762 | 010 | CD45+


title: LC09_POST_PanCK_012

description: Library name: TA3762 | 012 | PanCK+


title: ATP5MC1_pDBF_rep3


title: LC09_PRE_PanCK_011

description: Library name: TA3762 | 011 | PanCK+


title: LC09_PRE_CD45_011

description: Library name: TA3762 | 011 | CD45+


title: asyn_al_s2

value: Substantia nigra


title: LC08_POST_CD45_009

description: Library name: TA3762 | 009 | CD45+


title: H3K27me3 ChIP-seq at 32h, biological replicate 3

data_processing:
Raw data was quality-checked and trimmed with BBDuk (version December 10, 2015) (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/). Since the datasets contained a spike-in from Drosophila melanogaster, the high-quality reads were mapped against the mouse genome (version mm10) and against the D. melanogaster genome (version BDGP6) with the software BWA (version 0.7.17). Afterwards, from the mouse-derived mapping reads, PCR duplicates were removed with Picard MarkDuplicates (version 2.8.1) (http://broadinstitute.github.io/picard/) and only reads being properly paired with a mapping quality equal or higher than 30 were kept with SAMtools (version 1.7). Peak calling was performed using MACS2 (version 2.2.4) using a q-value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: ChIP-seq peaks (depending on the mark, narrowPeak or broadPeak format)

extract_protocol: TruSeq ChIP Library Preparation Kit followed by sequencing with NextSeq500

value: skeletal muscle

value: C3H/C2C12 cell line (ATCC_CRL-1772)

tag: antibody


title: asyn_al_s1


title: ATP5MC1_pDBF_rep2


title: H3K27me3 ChIP-seq at 32h, biological replicate 2


title: LC08_PRE_PanCK_008

description: Library name: TA3762 | 008 | PanCK+


title: ATP5MC1_mDBF_rep2


title: LC08_PRE_CD45_008

description: Library name: TA3762 | 008 | CD45+


title: LC08_PRE_CD45_007

description: Library name: TA3762 | 007 | CD45+


title: ATP5MC1_ND3_Rep3_pDBF


title: ATP5MC1_mDBF_rep3


title: CD8pos_TmuColonized

city: Stanford

first: Colin

middle: J

last: Raposo

state: CA

address: 240 Pasteur Drive, BMI 4600

department: Pathology

institute: Stanford University

description: Library name: Tmu

library_source: transcriptomic single cell

data_processing:
scRNA-seq data was processed using CellRanger Count (v6.0.0; 10X genomics) aligned to the mm10 genome.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: Ileum

growth_protocol: WT SPF mice were colonized via oral feeding with 1e6 protist Tritrichomonas musculus for 21 days prior to sacrifice.

extract_protocol:
At 21 days post-colonization, the distal 10cm of the small intestine (ileum) was excised and the intraepithelial lymphocytes were isolated. Cells were stained with viability dye and surface antibodies. Live CD8a+ T cells were FACS sorted into RPMI supplemented with 10% FBS. After sorting, samples were pooled and loaded into the Chromium Controller (10x Genomics).
scRNA and TCR libraries were prepared according to manufacturer's instructions (10X Genomics 5’ v2).

value: Ileum

value: 1e6 Tmu


title: CD8pos_SPF

description: Library name: SPF


title: H3K27me3 ChIP-seq at 28h, biological replicate 2


title: ATP5MC1_ND3_Rep3_mDBF

value: minus DBF


title: LC08_POST_PanCK_009

description: Library name: TA3762 | 009 | PanCK+

value: tumor


title: ATP5MC1_pDBF_rep1

value: plus DBF


title: LC08_PRE_PanCK_007

description: Library name: TA3762 | 007 | PanCK+


title: H3K27me3 ChIP-seq at 28h, biological replicate 3


title: ATP5MC1_mDBF_rep1


title: ATP5MC1_ND3_Rep1_pDBF


title: ATP5MC1_ND3_Rep2_pDBF


title: H3K27me3 ChIP-seq at 24h, biological replicate 2


title: LC08_PRE_CD45_005

description: Library name: TA3762 | 005 | CD45+


title: H3K27me3ChIP-seq at 28h, biological replicate 1


title: ATP5MC1_ND3_Rep2_mDBF


title: LC08_PRE_PanCK_005

description: Library name: TA3762 | 005 | PanCK+


title: LC08_PRE_CD45_006

description: Library name: TA3762 | 006 | CD45+


title: H3K27me3 ChIP-seq at 24h, biological replicate 1


title: H3K27me3 ChIP-seq at 24h, biological replicate 3


title: RAkt5974

city: Miaoli County

first: Li-Rung

last: Huang

address: No.35, Keyan rd. Zhunan town

country: Taiwan

institute: National Health Research Institutes

description: The total RNA was isolated from FACSorted CD90.1+ CD8+ T cells

data_processing:
The original raw data from Illumina are transformed to Sequenced Reads by base calling using CASAVA v1.8 software. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.
The TopHat2 algorithm (v2.0.12) is chosen for mapping sequences to a reference Genome and can be divided into three parts:(1) Align reads to a reference transcriptome (optional). (2) Map reads to the exons. (3) Reads are segmented and then mapped to the adjacent exons.
Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is the most commonest method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010). HTSeq software (v0.6.1) was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Genome_build: mm10
Supplementary_files_format_and_content: Excel, abundance measurements (FPKM) for each gene (n=52592) in each sample (n=18)

source_name: activated CD8+ T cells overexpressing Akt1 intracellularly and CD90.1 on the surface under anti-CD3/anti-CD28 restimulation for 24 hours

growth_protocol: CD8+ T cells isolated from the spleens of Cor93 TCR transgenic mice were subjected to anti-CD3/anti-CD28 bead activation in T-cell medium for 3 days.

extract_protocol:
TRIZOL
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: The activated Cor93-specific CD8+ T cells were transduced with retroviruses carrying the control CD90.1 plasmid, Akt1-CD90.1 plasmid or Akt2-CD90.1 plasmid at day 1 post activation. The activated CD8+ T cells were harvested at day 3 post activation and were re-stimulated with anti-CD3/anti-CD28 beads for 24 hours. The transduced CD8+ T cells at day 3 post activation or under restimulation for 24 hours were FACSorted based on CD90.1 expression and were subjected to RNA extraction.

tag: strain

value: spleen

value: HBV Cor93 specific CD8+ T cells

value: retrovirus transduction to induce reporter protein, CD90.1, and Akt1 expression followed by anti-CD3/anti-CD28 restimulation for 24 hours


title: LC08_PRE_PanCK_006

description: Library name: TA3762 | 006 | PanCK+

value: tissue


title: H3K27me3 ChIP-seq at 32h, biological replicate 1


title: RAkt5975

source_name: activated CD8+ T cells overexpressing Akt2 intracellularly and CD90.1 on the surface under anti-CD3/anti-CD28 restimulation for 24 hours

value: retrovirus transduction to induce reporter protein, CD90.1, and Akt2 expression followed by anti-CD3/anti-CD28 restimulation for 24 hours


title: RAkt5977


title: RAkt5976


title: LC07_POST_PanCK_003

description: Library name: TA3762 | 003 | PanCK+

value: POST


title: H3K27me3 ChIP-seq at 20h, biological replicate 3


title: LC07_POST_CD45_004

description: Library name: TA3762 | 004 | CD45+


title: RAkt5973


title: ATP5MC1_ND3_Rep1_mDBF

value: HeLa


title: LC07_POST_PanCK_004

description: Library name: TA3762 | 004 | PanCK+


title: RAkt5972


title: H3K27me3 ChIP-seq at 20h, biological replicate 2


title: ATP5MC1_CO1_Rep3_pDBF


title: ATP5MC1_CO1_Rep2_pDBF


title: LC06_POST_PanCK_001

description: Library name: TA3762 | 001 | PanCK+


title: R2A5970

source_name: activated CD8+ T cells overexpressing CD90.1 on the surface under anti-CD3/anti-CD28 restimulation for 24 hours

value: retrovirus transduction to induce reporter protein, CD90.1, expression followed by anti-CD3/anti-CD28 restimulation for 24 hours


title: ATP5MC1_CO1_Rep3_mDBF


title: H3K27me3 ChIP-seq at 16h, biological replicate 3


title: H3K27me3 ChIP-seq at 20h, biological replicate 1


title: R2A5969


title: Akt5968

source_name: activated CD8+ T cells overexpressing Akt2 intracellularly and CD90.1 on the surface

value: retrovirus transduction to induce reporter protein, CD90.1, and Akt2 expression


title: H3K27me3 ChIP-seq at 16h, biological replicate 2


title: ATP5MC1_CO1_Rep1_pDBF


title: Akt5967


title: H3K27me3 ChIP-seq at 16h, biological replicate 1


title: ATP5MC1_CO1_Rep1_mDBF


title: Akt5965


title: PARP7KO HA Rep2

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

description: Library name: Sample 7

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novogene output.
The raw RNA seq paired end fastq files were quantified using the Salmon tool with “libtype” flag as automatic and mm10 version of the Salmon index file.
The index was generated using the salmon “index” flag with the mm10 transcripts fasta file supplied.
he “tximport” import function from the tximport package) was used to import the Salmon quantification data for further processing using DESeq2
Differential expression analysis was done with DESeq2
Assembly: mm10
Supplementary files format and content: Salmon counts and abundance matrix

source_name: Pancreatic tumor

growth_protocol: CR705 cells were maintained in RPMI (1.0 g/L glucose; Sigma-Aldrich), supplemented with 10% v/v heatinactivated fetal bovine serum (FBS; Sigma-Aldrich), 1% v/v L-glutamine (Sigma-Aldrich), and 1% v/v penicillin-streptomycin, (P/S; Sigma-Aldrich). Cells were cultured at 37°C, with 100% humidity and 5% CO2. Cells were subcultured when the cells reached 80% confluency.

extract_protocol:
Total RNA isolation kit (BioRad, Hercules, CA, USA) according to manufacturer’s instructions. Subsequently, High-Capacity cDNA Reverse Transcription kit (Applied Biosystems, Waltham, MA, USA) was used to generate cDNA.
RNA Seq libraries were prepared using Novogene RNA seq library Kit

treatment_protocol: CR705AhrKO cells were generated using CRISPR/Cas9 using pSpCas9(BB)-2APuro (PX459) (plasmid #62988) from Addgene (Watertown, MA, USA). The guide oligos were 5´-AAACTCTAAGCGACACAGAGACCGC-3´ and 5´-CACCGCGGTCTCTGTGTCGCTTAGA-3´. The resulting gRNA oligos were annealed and cloned into the PX459 plasmid. The plasmid was transfected, puromycin selected, and T7 assays were done to determine the presence insertions or deletions (indels) as previously described. Genomic DNA from multiple clones was harvested, and the region surrounding the target site of the Ahr gene was amplified and sequenced to confirm knockout. The primers used to amplify the gRNA target sequence were: Forward 5´- TGTTTCGTCGGTAGAGCAGT-3´ and reverse 5´-AGTCCTAGCCCCAATCAGTCT-3´. After screening, multiple clones were chosen and subsequently expanded and further analyzed. CR705 cells were also transfected with empty PX459 plasmid and treated with puromycin before being expanded. CR705 PX459 cells are referred to as Cas9 control cells in this study.

value: Pancreatic tumor

value: pancreatic cancer

value: HA


title: PARP7KO HA Rep3

description: Library name: Sample 8


title: LC07_POST_CD45_003

description: Library name: TA3762 | 003 | CD45+

value: immune


title: H3K27me3 ChIP-seq at 12h, biological replicate 2

value: skeletal muscle

value: C3H/C2C12 cell line (ATCC_CRL-1772)


title: PARP7KO HA Rep1

description: Library name: Sample 6


title: PARP7KO HA Rep4

description: Library name: Sample 9


title: Akt5964

source_name: activated CD8+ T cells overexpressing Akt1 intracellularly and CD90.1 on the surface

value: retrovirus transduction to induce reporter protein, CD90.1, and Akt1 expression


title: Akt5963


title: H3K27me3 ChIP-seq at 12h, biological replicate 1


title: WTC11 ADNP Het

last: Yan

email: linda.lee2@mssm.edu, nan.yang1@mssm.edu

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Mount Sinai

description: 10x Genomics

data_processing:
Cellranger (v7.0) was used to align reads to the GRCh38 human and mm10 mouse reference transcriptomes (GRCh38_and_mm10-2020-A) with default alignment parameters to generate count matrices.
Data was filtered to retain only genes annotated to the human genome, and features were filtered for detection in a minimum of 3 cells and 200 features per cell. Samples further filtered for genes between 500-6000 and maximum of 20% reads mapping mitochondria
Samples were merged, normalized (natural-log transformed) and counts scale by factor of 10,000.
Assembly: GRCh38/hg38
Supplementary files format and content: barcodes.tsv file from cellranger output
Supplementary files format and content: features.tsv file from cellranger output
Supplementary files format and content: matrix.mtx file from cellranger output

source_name: WTC11 (iPSC)

growth_protocol: For PSC-iGABAs, cells were transduced with FUW-TetO-Ascl1-T2A-puromycin, FUW-TetO-Dlx2-IRES-hygromycin, and FUW-rtTA lentiviruses. Twenty-four hours later, the medium was replaced by N2 media (1xN2 supplement, 1xNEAA in DMEM-F12 media) containing Doxycycline (2 µg/mL) to induce transgene expression. Selection of transduced cells was achieved with N2 media containing antibiotics for 3 days. Selection media was replaced with N2 media containing 4 µM AraC for an additional three days. On day 8, GABAergic neurons were dissociated using Accutase and replated with mouse glial cells at a density of 104,000 cells/cm2 on Geltrex-coated plates. Two weeks post-transgene induction, doxycycline was withdrawn, and the culture was maintained in Neurobasal A media supplemented with 1xB27, 1xGlutamax, and 1% fetal bovine serum. Mature neurons were used for various assays on day 35 after co-culture. For NPC-iGABAs, PSC lines with stable inducible ASCL1-DLX2 integration were dissociated into single cells using Accutase and plated at 43300,000 cells/ cm2 onto GelTrex-coated wells in KSR media supplemented with 2 μM Chroman1. From days 1-10, the cells underwent daily full medium changes with LDN193189 (100 nM), SB431542 (10 μM) and XAV939 (2 μM). Starting on day 11, N2 media supplemented with Doxycycline (2 µg/mL) and DAPTwas used to induce ASCL1 and DLX2 expression and promote synchronized neural differentiation. Doxycycline was discontinued either 3 or 7 days later, and DAPT was removed after 7 days. Neurons were then dissociated and re-plated with mouse glial cells Subsequent steps were consistent with those used in other GABAergic neuron differentiation method.

extract_protocol:
DIV35 neurons were washed once with D-PBS, lifted using Accutase and RNA was extracted with TRIzol following the provider’s instructions. Following isolation, the RNA was treated with TURBO DNA-free kit. Total RNA (1μg) was used per sample for library preparation and sequencing.
Chromium Single Cell 3’ Reagent V3 kit was used for library preparation according to the manufacturer’s specifications. Barcoded libraries were sequenced using the Illumina NovaSeq with 150 bp paired-end reads to an average depth of approximately 3x104 reads per cell.

treatment_protocol: To generate genetically modified PGP1 and WTC11 iPSCs with the ADNP p.Tyr719* variant, we altered the nucleotide sequence NM_015339.4.2157C to G. Additionally, we inserted hemagglutinin (HA) tags immediately after Tyr719 to detect the resulting truncated proteins. In parallel, as a control, we inserted HA tags at the 3’ end of the endogenous ADNP gene in the PGP1 line. sgRNAs targeting proximal regions were designed using the CHOPCHOP online tool (https://chopchop.cbu.uib.no/) and cloned into the lentiCRISPRv1 plasmid (Addgene Plasmid #49535) using the Golden Gate Assembly protocol. The gene-targeting template plasmid used to generate the HA-tagged ADNP p.Tyr719* allele includes a puromycin-resistance cassette flanked by LoxP sites for Cre-recombinase mediated deletion, positioned after the HA tag sequence, and the 5′ and 3′ DNA homology arms. A similar gene-targeting template was used to generate the HA-tagged ADNP allele. The day before transfection, human iPSCs were dissociated into single cells with Accutase and plated at 250,000 cells per well in six-well plates containing StemFlex medium with Chroman1. For transfection, the template vector (1 μg) and the CRISPRv1-gRNA (0.5 μg) were incubated with Lipofectamine Stem Transfection Reagent (10 μl) and OptiMEM (250 μl, Invitrogen) for 10 minutes, then added dropwise to the iPSCs. Selection with puromycin (1μg/ml) in StemFlex medium started 24-48 hours after transfection and continued for approximately 10 days until stable colonies formed. Individual colonies were picked with a P200 pipette tip under a microscope. Heterozygous and homozygous ADNP p.Tyr719-HA* iPSC clones, as well as heterozygous ADNP-HA iPSC clones, were confirmed by PCR. The puromycin-resistance cassette was removed using Cre-recombinase.

value: WTC11 (iPSC)

value: induced GABAergic neurons

value: Heterozygous

value: small molecules and Ascl1 + Dlx2


title: WTC11 WT

description: 10x Genomics

value: Wildtype


title: R2A5971

value: spleen

value: HBV Cor93 specific CD8+ T cells


title: PARP7KO HA Rep5

description: Library name: Sample 10


title: Akt5961


title: SUZ12 ChIP-seq at 32h, biological replicate 2


title: LC06_POST_PanCK_002

description: Library name: TA3762 | 002 | PanCK+

value: tissue

value: POST

value: tumor


title: PGP1 ADNP Het

description: 10x Genomics

source_name: PGP1 (iPSC)

value: PGP1 (iPSC)


title: PGP1 ADNP Homo

description: 10x Genomics

value: Homozygous


title: WT HA Rep4

description: Library name: Sample 4

value: Pancreatic tumor

value: pancreatic cancer

value: WT

value: HA


title: H3K27me3ChIP-seq at 12h, biological replicate 3

value: skeletal muscle

value: C3H/C2C12 cell line (ATCC_CRL-1772)


title: SUZ12 ChIP-seq at 32h, biological replicate 3


title: ATP5MC1_CO1_Rep2_mDBF

value: HeLa

value: minus DBF


title: S2A5960

source_name: activated CD8+ T cells overexpressing CD90.1 on the surface

value: retrovirus transduction to induce reporter protein, CD90.1, expression


title: PGP1 WT

description: 10x Genomics

value: induced GABAergic neurons

value: Wildtype

value: small molecules and Ascl1 + Dlx2


title: SUZ12 ChIP-seq at 32h, biological replicate 1


title: WT HA Rep3

description: Library name: Sample 3


title: S2A5959

value: spleen

value: HBV Cor93 specific CD8+ T cells


title: WT HA Rep2

description: Library name: Sample 2


title: S2A5957


title: SUZ12 ChIP-seq at 28h, biological replicate 2


title: Dual-Smadi

description: 10x Genomics

data_processing:
Cellranger (v7.0) was used to align reads to the GRCh38 human and mm10 mouse reference transcriptomes (GRCh38_and_mm10-2020-A) with default alignment parameters to generate count matrices.
Data was filtered to retain only genes annotated to the human genome, and features were filtered for detection in a minimum of 3 cells and 200 features per cell. Samples further filtered for genes between 500-6000 and maximum of 20% reads mapping mitochondria
Samples were merged, normalized (natural-log transformed) and counts scale by factor of 10,000.
Assembly: GRCh38/hg38
Supplementary files format and content: barcodes.tsv file from cellranger output
Supplementary files format and content: fetures.tsv file from cellranger output
Supplementary files format and content: matrix.mtx file from cellranger output
Supplementary files format and content: AD_methods_counts_matrix.txt contains counts from seurat object
Supplementary files format and content: AD_methods_metadata.csv contains metadata from seurat object
Supplementary files format and content: dual_smad_counts_matrix.txt contains counts from seurat object
Supplementary files format and content: dual_smad_emtadata.csv contains metadata from seurat object

value: small molecules


title: WT HA Rep1

description: Library name: Sample 1


title: WT HA Rep5

description: Library name: Sample 5


title: 7DNPC-iNs

description: 10x Genomics

value: PGP1 (iPSC)


title: Zeb_WT_pDBF_Rep2

organism: Danio rerio

source_name: 2 dpf embryos

value: 2 dpf embryos

value: wildtype

value: plus DBF


title: 3DNPC-iNs

description: 10x Genomics


title: SUZ12 ChIP-seq at 28h, biological replicate 3


title: PSC-iNs

description: 10x Genomics

value: Ascl1 + Dlx2


title: Zeb_WT_pDBF_Rep3


title: CR705, PARP7KO, Rep8

data_processing:
The raw RNA sequence paired-end fastq files were quantified using the Salmon tool with “libtype” flag as automatic and mm10 version of the Salmon index file. The index was generated using the salmon “index” flag with the mm10 transcripts fasta file supplied. The “tximport” import function from the tximport package (v1.26.1) was used to import the Salmon quantification data for further processing including differential expression analysis by DESeq2. For all comparisons, WT tumour samples were considered as the control. Significant genes were considered as those with absolute log fold change greater than 1 and Benjamin Hochberg false discovery rate value of differential expression less than 0.01 and tested using the Wald Test implemented in DESeq2.
Assembly: mm10
Supplementary files format and content: counts and abundance generated by tximport

source_name: Pancreas

growth_protocol: CR705 cells derived from a spontaneous pancreatic tumour in a LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx1-Cre (KPC) mouse were used in this study [29]. Cells were maintained in RPMI culture medium (1.0 g/L glucose), supplemented with 10% v/v heat-inactivated fetal bovine serum (FBS), 1% v/v L-glutamine and 1% v/v penicillin-streptomycin. Cells were cultured at 37°C with 100% humidity and 5% CO2, and subcultured when confluency reached 80%.

extract_protocol:
Total RNA was isolated from approximately 100 mg of tumours from CR705 WT or PARP7KO cells using the Aurum™ Total RNA isolation kit (BioRad) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using Strand-specific TruSeq RNA-seq library Prep Kit following manufacturer's protocols.

value: Pancreas

value: Pancreatic Cancer


title: SUZ12 ChIP-seq at 24h, biological replicate 3

value: skeletal muscle

value: C3H/C2C12 cell line (ATCC_CRL-1772)


title: Zeb_WT_pDBF_Rep1


title: Hela_Paired_Damage_RNA

first: Dongsheng

last: Bai

address: 101 Avenue of the Americas

institute: New York Genome Center

description: Paired-Damage

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Assembly: hg38,mm10
Supplementary files format and content: bigwig file
Library strategy: paired-damage

molecule: nuclear RNA

source_name: Hela cell

extract_protocol:
Sub-libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome depletion; the DNA oxidative damage sites were treated with enzymatic labeling with biotin and tagmentated with identical barcoded assembled pA-Tn5, followed by reverse transcription with paired barcoded RT primers. After 2 rounds of Ligation-based combinatorial barcoding, nuclei were lysed and gDNA and RNA were purified with 1X SPRI beads; next, DNA and RNA libraries were amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).

treatment_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in DMEM (Gibco, 10569010) supplemented with 10% fetal bovine serum (Gibco, 16000044) and 1% penicillin-streptomycin (Gibco, 10378016) at 37 °C with 5% CO2. Cells were not authenticated or tested for mycoplasma. Cells were sown on plates 48 hours before treatment with H2O2 at the density of 3×105 cells per culture dish. Subconfluent cells were treated with H2O2, in a complete medium, at the final concentration of 200 µM (Thermo Scientific Chemicals, 202465000) for 2 hours at 37°C 5% CO2. After treatment, the medium was replaced with complete medium without H2O2 for additional incubation. The frontal cortex of male C57BL/6J mice at 8 weeks and 11 months was purchased from Jackson Laboratories and maintained in dry ice. Single-cell suspensions were prepared from douncing of the frozen tissues, in Douncing Buffer with protease/RNase inhibitor cocktail (DBI: 0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.5 (Invitrogen, 15567027), 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U μL−1 RNase OUT and 0.5 U μL−1 SUPERase Inhibitor) supplemented with 0.1% Triton-X100 (Sigma T9284). The cell suspension was then filtered by 30-μm Cell-Tric (Sysmex) and spun down for 10 min, at 1,000 g and 4 °C. After the cell pellets were washed with DBI and spun down again, cold NIB-HEPES buffer was added to resuspend the nuclei pellets, incubated on ice for 10 min and centrifuged for 10 min at 600 g, 4 °C. Cells were washed with 1 mL cold NIB-HEPES buffer and centrifuged for 10 min at 600 g, 4 °C before proceeding to Paired-Damage experiments. The nuclei were counted by a cell counter before proceeding to Paired-Damage experiments immediately.

value: Hela cell

value: Cancer cell

value: WT

value: hydrogen peroxide treatment


title: CR705, PARP7KO, Rep7


title: Hela_Paired_Damage_DNA

description: Paired-Damage


title: CR705, PARP7KO, Rep5


title: Hela_48hr_bulk_RNA

description: RNA-seq

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Assembly: hg38
Supplementary files format and content: bigwig file

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in DMEM (Gibco, 10569010) supplemented with 10% fetal bovine serum (Gibco, 16000044) and 1% penicillin-streptomycin (Gibco, 10378016) at 37 °C with 5% CO2. Cells were not authenticated or tested for mycoplasma. Cells were sown on plates 48 hours before treatment with H2O2 at the density of 3×105 cells per culture dish.

extract_protocol:
RNA-seq libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
Nuclear RNA was reverse transcribed, nuclei were lysed and cDNA were purified with 1X SPRI beads; next, cDNA library was amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. Amplied cDNA was tagmentated by Tn5. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).

treatment_protocol: Subconfluent cells were treated with H2O2, in a complete medium, at the final concentration of 200 µM (Thermo Scientific Chemicals, 202465000) for 2 hours at 37°C 5% CO2. After treatment, the medium was replaced with complete medium without H2O2 for additional incubation from 0 hour to 48 hours.


title: SUZ12 ChIP-seq at 24h, biological replicate 2


title: Zeb_WT_mDBF_Rep3

value: minus DBF


title: Hela_24hr_bulk_RNA

description: RNA-seq


title: CR705, PARP7KO, Rep9


title: SUZ12 ChIP-seq at 20h, biological replicate 2


title: SUZ12 ChIP-seq at 20h, biological replicate 1


title: CR705, PARP7KO, Rep4


title: Zeb_WT_mDBF_Rep2


title: CR705, PARP7KO, Rep2


title: Hela_0hr_bulk_RNA

description: RNA-seq


title: SUZ12 ChIP-seq at 24h, biological replicate 1


title: SUZ12 ChIP-seq at 28h, biological replicate 1


title: SUZ12 ChIP-seq at 16h, biological replicate 2


title: Zeb_WT_mDBF_Rep1


title: SUZ12 ChIP-seq at 16h, biological replicate 3


title: Zeb_NES_pDBF_Rep1

value: Halo-NES


title: Hela_6hr_bulk_RNA

description: RNA-seq


title: CR705, PARP7KO, Rep1


title: Zeb_NES_mDBF_Rep2


title: SUZ12 ChIP-seq at 20h, biological replicate 3


title: CR705, PARP7KO, Rep6


title: Zeb_NES_mDBF_Rep1


title: CR705, PARP7KO, Rep3


title: Zeb_NES_pDBF_Rep2


title: Hela_control_bulk_RNA

description: RNA-seq

value: Control


title: CR705, WT, Rep7


title: Hela_2hr_bulk_RNA

description: RNA-seq


title: Hela_48hr_bulk_damage

description: bulk damagenome

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Assembly: hg38
Supplementary files format and content: bigwig file
Library strategy: paired-damage-seq

extract_protocol:
Damagenome libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome depletion; the DNA oxidative damage sites were treated with enzymatic labeling with biotin and tagmentated with identical barcoded assembled pA-Tn5, nuclei were lysed and gDNA and RNA were purified with 1X SPRI beads; next, DNA libraries were amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).


title: ZF_NES_MALAT1_Rep4_plus


title: SUZ12 ChIP-seq at 16h, biological replicate 1


title: CR705, WT, Rep6


title: SUZ12 ChIP-seq at 12h, biological replicate 3


title: CR705, WT, Rep5


title: ZF_NES_MALAT1_Rep4_minus


title: Hela_24hr_bulk_damage

description: bulk damagenome


title: SUZ12 ChIP-seq at 12h, biological replicate 2


title: CR705, WT, Rep4


title: ZF_NES_MALAT1_Rep3_minus


title: SUZ12 ChIP-seq at 12h, biological replicate 1


title: Hela_2hr_bulk_damage

description: bulk damagenome


title: CR705, WT, Rep3


title: Hela_6hr_bulk_damage

description: bulk damagenome


title: ZF_NES_MALAT1_Rep2_plus


title: Hela_0hr_bulk_damage

description: bulk damagenome


title: CR705, WT, Rep2


title: Bio-EZH1 ChIP-seq at 32h, biological replicate 3


title: Bio-EZH1 ChIP-seq at 32h, biological replicate 2


title: Hela_control_bulk_damage

description: bulk damagenome


title: CR705, WT, Rep1


title: ZF_NES_MALAT1_Rep1_plus


title: Hela_48hr_bulk_ATAC

description: ATAC-seq

extract_protocol:
ATAC-seq libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
DNA open chromatin regios were tagmentated with Tn5, nuclei were lysed and gDNA were purified with 1X SPRI beads; next, DNA library was amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).


title: Bio-EZH1 ChIP-seq at 32h, biological replicate 1


title: KO6_S22

city: New York City

first: Coen

last: van Solingen

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

data_processing:
Quality control of sequencing reads was assessed using FastQC (v.0.11.7)
Reads were mapped to mouse reference genome mm39 using STAR (v2.6.1d).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: mm39
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: lung

growth_protocol: Mice were inoculated with influenza strain PR8 and were euthanized 4 days later. Lungs were harvested and snapfrozen. Four mice of each groups were used.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x150bp configuration, single index, per lane

treatment_protocol: Lungs were isolated at Day=4 after inoculation with influenza.Lungs were homogenized and RNA was isolated using trizol.

value: lung

value: bone marrow derived macrophages

value: KO

value: flu


title: KO4_S20


title: Bio-EZH1 ChIP-seq at 28h, biological replicate 3

source_name: skeletal muscle


title: ZF_NES_MALAT1_Rep3_plus

value: 2 dpf embryos

value: plus DBF


title: ZF_NES_GAPDH_Rep4_plus


title: Bio-EZH1 ChIP-seq at 28h, biological replicate 2


title: ZF_NES_MALAT1_Rep2_minus


title: KO3_S19


title: Hela_6hr_bulk_ATAC

description: ATAC-seq


title: ZF_NES_GAPDH_Rep4_minus


title: KO1_S18


title: Hela_2hr_bulk_ATAC

description: ATAC-seq


title: Bio-EZH1 ChIP-seq at 28h, biological replicate 1


title: ZF_NES_GAPDH_Rep3_plus


title: Bio-EZH1 ChIP-seq at 24h, biological replicate 3


title: Bio-EZH1 ChIP-seq at 24h, biological replicate 2


title: ZF_NES_GAPDH_Rep3_minus


title: Hela_0hr_bulk_ATAC

description: ATAC-seq


title: WT5_S17


title: Hela_control_bulk_ATAC

description: ATAC-seq


title: Bio-EZH1 ChIP-seq at 24h, biological replicate 1


title: ZF_NES_MALAT1_Rep1_minus


title: WT3_S15


title: ZF_NES_GAPDH_Rep2_plus


title: Hela_24hr_bulk_ATAC

description: ATAC-seq


title: WT2_S14


title: Bio-EZH1 ChIP-seq at 20h, biological replicate 3


title: FB23-2_3_MeRIP

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
For data analysis, the data analysis employed the following pipeline to identify m6A peaks. We used HISAT2 to map reads to the reference genome Homo sapiens (GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software.
Cuffdiff was used to calculate differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: peak

source_name: Cell line

extract_protocol:
Total RNA was isolated and purified with TRIzol reagent (Invitrogen, USA) following the manufacturer's procedure. Poly (A) RNA was extracted using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, USA).
Then Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA) was used to randomly fragment RNA and m6A-specific antibody (Synaptic Systems, cat.202003, Germany) was applied for immunoprecipitation (IP). Then input and IP RNA samples were subjected into next-generation sequencing on an illumina Novaseq™ 6000.

treatment_protocol: MHCC97H cells were treated with or without FB23-2 (2 μM) for 48 hours, then cells were harvested for the next MeRIP-seq

value: Cell line

tag: cut&tag antibody

value: m6A-specific antibody (Synaptic Systems, cat.202003)


title: FB23-2_2_MeRIP


title: ZF_NES_GAPDH_Rep2_minus

data_processing:
OINC-seq (Oxidation-Induced Nucleotide Conversion sequencing)
Adapters were trimmed from reads using Cutadapt.
RNA oxidation events (as seen as mutations) were quantified using PIGPEN (https://github.com/TaliaferroLab/OINC-seq)
Assembly: hg38 and GRCz11
Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.

extract_protocol:
RNA was extracted using Trizol and DNase treated for 30 min at 37C.
Single amplicon libraries were constructed using gene-specific RT-PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.


title: WT1_S13


title: Bio-EZH1 ChIP-seq at 20h, biological replicate 2

value: skeletal muscle


title: ZF_NES_GAPDH_Rep1_plus


title: DMSO_3_MeRIP

value: DMSO


title: FB23-2_1_MeRIP


title: WT-veh sample 3

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs) were prepared by flushing the marrow from the tibiae and femorae of 6- to 8-week-old mice. Cells were differentiated into macrophages in DMEM supplemented with 10% FBS, 1% P/, and 15% L929-conditioned media for 7 days.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x50bp configuration, single index, per lane

treatment_protocol: BMDM were treated with IFNBeta (1000 U/mL) or vehicle control for 8 hours

value: Vehicle


title: ZF_NES_GAPDH_Rep1_minus


title: Bio-EZH1 ChIP-seq at 20h, biological replicate 1

value: C3H/C2C12 cell line (ATCC_CRL-1772)


title: DMSO_2_MeRIP


title: WT-veh sample 1

value: WT


title: Bio-EZH1 ChIP-seq at 16h, biological replicate 3


title: ZF_H2B_MALAT1_Rep4_plus


title: DMSO_1_MeRIP


title: ZF_H2B_MALAT1_Rep3_plus


title: ZF_H2B_MALAT1_Rep4_minus


title: WT-IFN sample 3

value: IFN


title: Bio-EZH1 ChIP-seq at 16h, biological replicate 1


title: FB23-2_3

data_processing:
For RNA-seq data, we used HISAT2 to map reads to the reference genome of Homo sapiens GRCh38.
The mapped reads of each sample were assembled using StringTie with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare. After the final transcriptome was generated, stringTie was used to perform expression levels for mRNAs by calculating FPKM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA samples from FB23-2 treatment and DMSO groups were isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. Poly (A) RNA is purified using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using a magnesium RNA Fragmentation Module (NEB, cat. e6150, USA). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next to synthesize the cDNA library. At last, we performed the paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol. The differential gene expression was examined using a standard Illumina sequence analysis pipeline.

treatment_protocol: MHCC97H cells were treated with or without FB23-2 (2 μM) for 48 hours, then cells were harvested for the next RNA-seq


title: WT-IFN sample 2


title: Bio-EZH1 ChIP-seq at 12h, biological replicate 3


title: ZF_H2B_MALAT1_Rep3_minus

value: minus DBF


title: FB23-2_2


title: WT-IFN sample 1


title: KO-veh sample 3


title: Bio-EZH1 ChIP-seq at 12h, biological replicate 2


title: Bio-EZH1 ChIP-seq at 12h, biological replicate 1


title: ZF_H2B_MALAT1_Rep2_plus


title: WT-veh sample 2


title: ZF_H2B_MALAT1_Rep2_minus


title: KO-veh sample 2


title: DMSO_3


title: ZF_H2B_MALAT1_Rep1_plus


title: KO-veh sample 1


title: AGS cell lines, control，24h, rep3

city: Hohhot

first: Liu

last: Fangyuan

state: Inner Mongolia

address: No. 1 Tongdao North Street

institute: Affiliated Hospital of Inner Mongolia Medical University

description: Library name: sample12

data_processing:
Illumina Novaseq platform for basecalling
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality.
RSEM was used to count the reads numbers mapped to each gene. Andthen FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depthandgene length for the reads count at the same time, and is currently the most commonlyusedmethod for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: AGS

growth_protocol: AGS and MKN74 celllines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
The treatment group treated cells with AKG for 24 hours, while the control group was treated with PBS.  Trizol reagent for RNA collecting and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using standard llumina protocols

treatment_protocol: Collecting cells after treatment of 24h post AGS and MKN74 cellines with a-KG

value: AGS

value: PBS


title: DMSO_2


title: ZF_H2B_MALAT1_Rep1_minus


title: DMSO_1


title: KO-IFN sample 3


title: ZF_H2B_GAPDH_Rep4_plus


title: Bio-EZH1 ChIP-seq at 16h, biological replicate 2


title: AGS cell lines, control，24h, rep1

description: Library name: sample10


title: KO-IFN sample 2


title: AGS cell lines, control，24h, rep2

description: Library name: sample11


title: AGS cell lines, α-KG treated，24h, rep3

description: Library name: sample9

value: α-KG


title: ZF_H2B_GAPDH_Rep4_minus


title: A549,sgUHRF1,rep1

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline and RPKM counts were calculated
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Tab-delimited text file includes RPKMs for each sample.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Candidate gene sgRNA was cloned in to lentiCRISPRv2-hygro and transfection with lentivirus then selected with hygromycin.

value: tumor cell

value: UHRF1 KO


title: A549,sgUHRF1,rep2


title: FB23-2_1


title: ZF_H2B_GAPDH_Rep3_plus


title: A549,sgNTC,rep2

value: non-targeting control


title: AGS cell lines, α-KG treated，24h, rep2

description: Library name: sample8


title: AGS cell lines, α-KG treated，24h, rep1

description: Library name: sample7


title: Molino-3

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 (v2.20).
The ‘TGGAATTCTCGGGTGCCAAGG’ adapter was removed for all samples of small RNA-seq using the Cutadapt (v2.5). Reads without an adapter and shorter than 18bp were discarded. We excluded reads aligning to rRNAs, scaRNAs, snoRNAs, and snRNAs.  Additionally reads aligning to tRNAs were removed. As annotated tRNAs for Astyanax mexicanus 2.0 are unavailable, we used tRNAscan-SE (v2.0.6) to search for Astyanax mexicanus 2.0 tRNAs using Danio rerio (GRCz11) tRNAs from GtRNAdb
The reads remaining after filtering (rRNAs, scaRNAs, snoRNAs, snRNAs and tRNAs) from all samples were concatenated and the miRDeep2 (v3) tool was used to identify novel miRNAs. First, the mapper.pl module was used to align the reads to Astyanax mexicanus 2.0 genome from NCBI (Assembly GCF_000372685.2). Next miRDeep2.pl module was run on the mapped arf file using the reference genome and know mature Danio rerio miRNAs from miRbase (v22) as supporting miRNAs from related species.
To quantify the expression of each novel miRNA in all the samples we used quantifier.pl module in mirdeep2 and aligned the sequenced reads to the novel precursor miRNAs using the default parameters.
Assembly: Astyanax mexicanus 2.0
Supplementary files format and content: miRNA_counts.txt

organism: Astyanax mexicanus

source_name: embryos

extract_protocol:
Small RNA (<200nt) was extracted using the mirVana RNA isolation kit (Catalog number: AM1560) according to the manufacturer's instructions
Libraries were made according to the manufacturer’s directions for the TruSeq Small RNA Library Prep Kit (Illumina, Cat. No. RS-200-0012)
RNA-Resulting libraries were size selected for 145-160bp fragments using Novex 6% TBE gels (Invitrogen, Cat. No. EC6265BOX) to retain only the small RNA inserts
Libraries were pooled, requantified, and sequenced as 75bp single reads on an Illumina NextSeq 500 instrument high-output flow cell

treatment_protocol: WT embryos collected at 24hpf

tag: time

value: 24 hours post fertilization

value: embryos

tag: morph

value: Molino


title: A549,sgNTC,rep1


title: Molino-2


title: MKN74 cell lines, control，24h, rep3

description: Library name: sample6


title: ZF_H2B_GAPDH_Rep2_plus

value: 2 dpf embryos

value: plus DBF


title: A549,ICAM-1 low,rep2

source_name: cell line

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: A549 cells were stained with anti-ICAM1 antibody and sorted  by FACS

value: cell line

value: wild-type

value: FACS sort ICAM1-low subset


title: Molino-1

value: WT


title: MKN74 cell lines, control，24h, rep2

description: Library name: sample5


title: A549,ICAM-1 low,rep1


title: ZF_H2B_GAPDH_Rep2_minus


title: Tinaja-3

value: Tinaja


title: MKN74 cell lines, control，24h, rep1

description: Library name: sample4


title: ZF_H2B_GAPDH_Rep1_plus


title: A549,ICAM-1 high,rep2

value: FACS sort ICAM1-high subset


title: KO-IFN sample 1

value: bone marrow derived macrophages

value: KO

value: IFN


title: ZF_H2B_GAPDH_Rep1_minus

value: minus DBF


title: MKN74 cell lines, α-KG treated，24h, rep3

description: Library name: sample3

value: α-KG


title: MKN74 cell lines, α-KG treated，24h, rep2

description: Library name: sample2


title: A549,ICAM-1 high,rep1

value: tumor cell


title: Human Stellate Cells treated (R3)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
Library name: D12_R3
Human Stellate Cells treated (R3)

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE V26
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: Homo Sapiens genome hg38
Supplementary files format and content: RSEM output

source_name: Liver

extract_protocol:
RNA from cells was obtained using the Quick RNA-Microprep Kit (Zymo, Cat#R1050), following the manufacturer’s instructions. For 3D cultures, total RNA from 6 pooled spheroids were extracted using the same kit.
Sequencing libraries were prepared following the protocol included with the kit TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E)

value: Liver

value: Human Stellate Cells

value: treated with RORA


title: CD138+cells from multiple myeloma_Replicate 10

city: Wuhan

first: Chunyan

last: Sun

state: HUBEI

address: 1277 Jiefang Dadao, Wuhan 430022, China

department: Hematology

institute: Wuhan Union Hospital

data_processing:
FastQC 0.11.5 software was used for basecalling.
Raw sequencing data was first filtered by Trimmomatic (version 0.39), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Sequenced reads were mapped to GRCh38 whole genome using STRA software (version 2.7.5c) with default parameters.
The expression of novel lncRNA and genome annotated known lncRNA were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
LncRNA differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow CD138+ cells

extract_protocol:
Bone marrow CD138+ cells were obtained from multiple myeloma patients and normal individuals by magnetic bead separation. The cells were treated with TRIzol to extract total RNA according to manufactures' instrctions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Multiple Myeloma

value: CD138+ cells

tag: gender

value: female


title: Human Stellate Cells treated (R2)

description:
Library name: D12_R2
Human Stellate Cells treated (R2)


title: Pachon-3

value: 24 hours post fertilization

value: embryos

value: Pachon


title: ZF_H2B_GAPDH_Rep3_minus

value: 2 dpf embryos


title: MG1655, CNMA, 60min, rep3

city: Gdansk

first: Dariusz

last: Nowicki

state: pomorskie

address: Wita Stwosza 59

department: Bacterial Molecular Genetics

country: Poland

institute: University of Gdansk

data_processing:
Galaxy platform v 23.0
Sequence trimming after FastQC v0.11.9 was performed using Trimmomatic v0.38.1 (adapter sequence: TruSeq2, paired-ended, for Illumina GAII). Reads were mapped to eschColi_K12 reference genome using HISAT2 (Forward (FR); Spliced alignment options:Penalty for canonical/non-canonical - 0/3, Penaulty function - Constant [f(x) = B] where constant term B=0
Rstudio R-4.3.1 environment was employed to DEGs (DESEq 1.40.2) analysis using BAM files from HISAT2
Assembly: GCA_000005845, Ensembl July 2023
Supplementary files format and content: .xlsx file includes raw count data and DEGs analysis (p ≤ 0.001 and log2FC ≥ 1.5) for each sample

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Escherichia coli MG1655 cultured in fresh LB, aerobically with shaking at 37°C

extract_protocol:
RNA was harvested using RNase Mini Kit  (Qiagen) followed by additional pufification step with DNAse I (Qiagen). Samples where then validated using Bioanalyzer 2100
TruSeq total RNA stranded with NebNext Ribodepletion kit (bacteria)

treatment_protocol: CNMA (Sigma) was added to treated samples (OD=0.1) from 1M stock solution in DMSO to final concantration 0.94mM. Then, cultures were incubated in aerobic contitions by 30 and 60 min. Untreated bacteria were used as a control.

value: bacterial cell

value: WT

value: CNMA


title: Human Stellate Cells treated (R1)

description:
Library name: D12_R1
Human Stellate Cells treated (R1)


title: MKN74 cell lines, α-KG treated，24h, rep1

description: Library name: sample1


title: CD138+cells from multiple myeloma_Replicate 9


title: CD138+cells from multiple myeloma_Replicate 8


title: Pachon-2


title: Pachon-1


title: MG1655, CNMA, 60min, rep2


title: CD138+cells from multiple myeloma_Replicate 7


title: Human Stellate Cells untreated (V2)

description:
Library name: D12_V2
Human Stellate Cells untreated (V2)

value: untreated


title: Surface-3

value: Surface


title: MG1655, CNMA, 60min, rep1


title: MG1655, CNMA, 30min, rep3


title: CD138+cells from multiple myeloma_Replicate 6

value: male


title: Tinaja-2

value: Tinaja


title: Tinaja-1


title: Human Stellate Cells untreated (V1)

description:
Library name: D12_V1
Human Stellate Cells untreated (V1)

value: Liver


title: Surface-1


title: CD138+cells from multiple myeloma_Replicate 5


title: MG1655, CNMA, 30min, rep2


title: MG1655, CNMA, 30min, rep1


title: The S1Tr brain region in acute stress

city: qingdao

first: xufeng

last: xu

address: No. 16 Jiangsu Road

institute: qingdao university

description: Library name: S1Tr-sample 1

data_processing:
The 10x visium spatial transcriptome library was sequenced using the Illumina NovaSeq PE150 strategy
Assembly: mus musculus
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene lDs;matrix.mtx: gene expresion count data in Matrix Market Exchange Format
Library strategy: spatial transcriptomics

source_name: brain S1TR region

extract_protocol:
The parts containing the target brain regions in the control group and the experimental group were removed and placed together, embedded by optimal cutting temperature compound (OCT), and cut into the virus expression area by frozen section. The brain slices with a thickness of 10 μm were sectioned for spatial transcriptome sequencing
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium SpatialGene Expression Slides 8 Reagent kit according to manufacturer's construction

treatment_protocol: Mice received FST stress (non-stress mice as control), followed 2 hours later by rapidly extracting the whole brains and placed on a precooled metal plate.

value: brain S1TR region

value: neurons


title: CD138+cells from multiple myeloma_Replicate 3

value: Multiple Myeloma


title: CD138+cells from multiple myeloma_Replicate 2

value: CD138+ cells


title: NOD.Tnfrsf9-/-.Foxp3-EGFP knockout (CD137 knockout)

city: Milwaukee

first: Yi-Guang

state: WI

address: 8701 Watertown Plank Rd.

department: Pediatrics (Endocrinology) and Microbiology & Immunology

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger v7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix file

source_name: pancreatic islets

extract_protocol:
10X Genomics Single Cell 3' v2
Single Cell 3' v2

value: pancreatic islets

value: Foxp3+ CD4 T cells (Tregs) and CD8 T cells


title: KYSE70 xenograft, VVD-065 treated rep4

city: San Diego

first: Brent

last: Kuenzi

address: 5820 Nancy Ridge Dr

department: Biology

institute: Vividion Therapeutics

data_processing:
Fastq files were initially analyzed by fastqc. Reads were aligned with STAR to GENCODE v24 (hg38).  Aligned reads were quantified by salmon. Counts were summarized to gene level using tximport. Differentially expressed genes were determined using DESeq2
Assembly: hg38
Supplementary files format and content: counts = raw unnormalized counts summarized to gene level

growth_protocol: Following the acclimation period (3-7 days), immunodeficient mice, NSG (Jackson Laboratory) were inoculated subcutaneously into the dorsal flank with a cell suspension of 90% viable tumor cells in 0.2 ml of serum-free RPMI-1640: HC Matrigel (Corning, catalogue no. # 354262) (1:1 v/v) delivering tumor cells (5 x 10^6 cells/ mouse)

extract_protocol:
RNA from frozen cell pellets was extracted using standard protocols by Novogene (Novogene Corporation Inc, Sacramento, CA)
Standard library preparation and sequencng was performed by Novogene (Novogene Corporation Inc, Sacramento, CA)

treatment_protocol: VVD-065 was administered at the indicated dose level by oral gavage


title: KYSE70 xenograft, VVD-065 treated rep3


title: NOD.Foxp3-EGFP (wildtype)

description: 10x Genomics


title: KYSE70 xenograft, VVD-065 treated rep2


title: KYSE70 xenograft, VVD-065 treated rep1


title: Human Stellate Cells untreated (V3)

description:
Library name: D12_V3
Human Stellate Cells untreated (V3)

value: Human Stellate Cells


title: Cet_ICAM1_D1_2

first: Zhou

last: Xindi

address: 30 Shuangqing Road

institute: Tsinghua University

description: 10x Genomics

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

source_name: Tumor

extract_protocol:
Single-cell suspensions were obtained from mice bearing MC38-EGFR treated with Cetuximab and Cet×ICAM1-D1 on day 14. Cells were stained with Live & DEAD Zombie NIR Fixable Viability Kit and anti-mouse-CD45 . Equally numbers of alive CD45+ cells were sorted by FACS AriaIII (BD) from each sample of Cetuximab and Cet×ICAM1-D1 treated tumors then pooled together, respectively. The cells were washed with PBS for library construction of scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor


title: KYSE70 xenograft, vehicle treated rep4

value: vehicle


title: CD138+cells from multiple myeloma_Replicate 1

value: female


title: CD138+cells from normal_Replicate 3

value: Normal


title: Cet_ICAM1_D1_1

description: 10x Genomics

value: WT


title: Surface-2

value: 24 hours post fertilization

value: embryos


title: CD138+cells from normal_Replicate 2


title: KYSE70 xenograft, vehicle treated rep2


title: KYSE70 xenograft, vehicle treated rep3


title: Cetxuiamb_1

description: 10x Genomics

value: Cetuximab


title: KYSE70 xenograft, vehicle treated rep1


title: C_9

status: Public on Jan 02 2025

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base calling and making fastq files were performed using software provided with the 10X Genomics Cell Ranger (cellranger mkfastq v3.0).
Count data were calculated from fastq files using software provided with the 10X Genomics Cell Ranger (cellranger count v3.0).
Count data were normalized to compare across samples using software provided with the 10X Genomics Cell Ranger (cellranger aggr v3.0).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (read count) for each cell.

source_name: PBMC

extract_protocol: A single-cell RNA-seq library was prepared from PBMC using Chromium Single Cell 3' Library Kit v2 (10x Genomics) following the manufacturer’s instructions.

value: PBMC

value: Control


title: C_10


title: CD138+cells from normal_Replicate 1

value: male


title: C_7


title: CD138+cells from multiple myeloma_Replicate 4


title: C_6


title: C_8


title: C_4


title: C_5


title: C_3


title: C_1


title: ALS_31

value: Rapid ALS


title: ALS_32

value: Non-rapid ALS


title: ALS_30


title: ALS_36


title: ALS_33


title: ALS_34


title: Cetxuiamb_2

city: Beijing

description: 10x Genomics


title: ALS_23


title: ALS_21


title: ALS_18


title: ALS_29


title: ALS_22


title: ALS_16


title: ALS_14


title: ALS_26


title: ALS_25


title: ALS_13


title: ALS_28


title: ALS_27


title: ALS_10


title: C_2


title: ALS_11


title: ALS_35


title: ALS_17


title: ALS_9


title: ALS_20


title: ALS_7


title: ALS_3


title: ALS_6


title: Oln93 del Sox10, transduced with lentivirus containing Sox9,  biological replicate 1

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

data_processing:
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina
Sequencing libraries were validated using the NGS Kit on an Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified using the Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina HiSeq2500 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x100 bp single-end configuration.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using cutadapt v1.9.1. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL (Rnor5) using the STAR aligner v.2.52.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 v.1.16.1 was used for differential gene expression analysis and normalization
Assembly: Rn5
Supplementary files format and content: tab-delimited text files containing counts and DESeq results

organism: Rattus norvegicus

source_name: Oln93 cell line

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Genome-edited Oln93 cells that lack Sox10 were transduced with lentiviruses containing mouse coding sequences  of Sox8, Sox9 and Sox10

value: Oln93 cell line

value: Sox10 Deletion

value: transduced with Sox9 containing lentivirus


title: Oln93 del Sox10, transduced with lentivirus containing Sox9,  biological replicate 2


title: Oln93 del Sox10, transduced with lentivirus containing Sox8,  biological replicate 1

value: transduced with Sox8 containing lentivirus


title: Oln93 del Sox10, transduced with lentivirus containing Sox8,  biological replicate 2


title: ALS_24


title: ALS_19


title: Oln93 del Sox10, transduced with lentivirus containing Sox10,  biological replicate 2

value: transduced with Sox10 containing lentivirus


title: Oln93 del Sox10, transduced with lentivirus containing Sox10,  biological replicate 1