title: human OFC, OF9, CONTROL

city: New York

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
human: TopHat 2.0.8b and Cufflinks 2.1.1; rat: STAR
Assembly: human: GRCh37; rat: mRatBN7.2
Supplementary files format and content: human FPKM (csv); rat raw counts (CSV)

source_name: orbitofrontal cortex

extract_protocol:
human: Total RNA was extracted using Invitrogen ToTally RNA Kit (Life Technologies); rat: RNA extraction from the isolated tissue was conducted by TRIzol and isopropanol precipitation
human: RNA-seq libraries were prepared from 1 ug of total RNA using Illumina’s TruSeq RNA library preparation kit V2; rat: Using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), reverse transcription was performed on polyadenylated transcripts, along with second-strand synthesis of full-length cDNA and amplification of the product (Azenta Life Sciences, Chelmsford, MA).

value: orbitofrontal cortex

value: CONTROL


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_3_doublings

status: Public on Oct 20 2025

type: SRA

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
3 doublings after release from starvation

library_source: genomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
time points  were separated by barcode and the 5bp barcode was removed from the read sequence
reads were mapped to the yeast S288C genome using BLAT
Paired end read count distribution in 10bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands
the genome average read count value was calculated and the data were normalized to one and the F and R counts were averaged for each bp. ChIP reads were then normalized to their corresponding input.
Assembly: Saccer1
Supplementary files format and content: tab-delimited text files of input normalized read density in 10bp windows for indicated time points. R indicated repetitive regions.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast derived from S288C with the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus. The strain has the gene for CreEBD78 recombinase integrated into the HIS3 locus.

growth_protocol: Cells were grown in YPD or YPGal (for over expression Sir3 (oeSir3) cells) for 48hrs at 30°C till saturation and growth arrest. In the tag switch experiment, estradiol was added for 16hrs to induce the HA to T7 tag switch. Cells were then released into fresh media (for oeSir3 cells the estradiol step was skipped and cells were kept in starvation for 72hrs) and aliquots were fixed with formaldehyde at indicated times for several cell generations.

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were sonicated. Anti-HA, anti-T7 or anti-TAP ChIPs were performed as indicated.
ChIP and input DNA samples, were treated with RNAse A, blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read), and PCR amplified and size selected by gel purification.
Illumina multiplex ChIP-seq with custom in line 5bp barcodes

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: cell cycle

value: exit from starvation after nutrient depletion

tag: cell type

value: yeast


title: H1_B_S1D3_1

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx

library_source: transcriptomic single cell

data_processing:
We processed Smart-seq3 scRNA-seq data beginning with the removal of index, primer, and adaptor sequences from the paired-end reads, utilizing Trimmomatic software (version 0.39). Post-trimming, the forward reads (Read 1) were aligned to the Homo sapiens reference genome (hg38) employing HISAT2 (version 2.1.0). The aligned reads were then annotated to gene features using the featureCounts tool (version 2.0.0), taking into account both 5' and internal fragments.  For 10x Genomics scRNA-seq data, initial processing was performed with the Cell Ranger software (version 3.0.1) using default parameters and the GRCh38 reference genome (version 3.0.0).The initial processing of raw snATAC-seq data was conducted using the cellranger-atac software, version 1.2.0, employing the standard parameters and referencing the refdata-cellranger-atac-GRCh38-1.2.0 genome assembly.
Assembly: hg38
Supplementary files format and content: sparse matrix: read count
Supplementary files format and content: fragments.tsv

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: hESC and hiPSC lines were maintained cultured on surfaces coated with Matrigel (Corning, Cat#354230) and cultured in mTeSR1 media (Stem Cell Technologies, Cat#85850) at 37°C. The cells were passaged using Versene solution (ThermoFisher Scientific, Cat#15040066), and routine screenings for Mycoplasma contamination were performed employing the MycoBlue Mycoplasma Detector Kit (Vazyme, Cat#D101).     For differentiation experiments, hESCs and hiPSCs were dissociated to single-cell suspensions using TrypLE™ Express Enzyme (ThermoFisher Scientific, Cat#12605) and plated at a density of 0.53 x 106 cells/cm2 on surface coated with Matrigel diluted 1:30 (Corning, Cat#356231) in mTeSR1 media. This medium was supplemented with 10 μM Y-27632 (Selleckchem, Cat#S1049) to enhance cell survival. Differentiation was initiated within 24 hours post-seeding. Prior to introducing differentiation media, cells were washed with 1× DPBS without Mg2+ and Ca2+ (Meilunbio, Cat#MA0015). The cells were cultured at 37 °C with 5% (vol/vol) CO2.     The differentiation of stem cells into pancreatic lineages was conducted following modified versions of the protocols established by Rezania et al. and Hogrebe et al., herein referred to as protocols A and B, respectively. Additionally, a novel differentiation protocol developed within this study is referred to as protocol C.

extract_protocol:
SC-derived cells or islets were dissociated into single cells with 0.25% trypsin at 37 °C for 3-5 min, and the digestion was halted by adding 0.4 volumes of FBS. Partially dissociated SC-islets underwent a secondary trypsinization at 37°C for 3 minutes to ensure complete dissociation. Cells from both dissociation steps were pooled for further analysis. Retrieved grafts from the renal capsule were finely minced and enzymatically dissociated using 0.25% trypsin at 37°C for 5 minutes. The enzymatic reaction was halted by adding 0.4 volumes of FBS.
ScRNA-seq via the Smart-seq3 method was carried out in accordance with established procedures. Briefly, individual cells were sorted into 384-well plates containing lysis buffer (0.3 μL per well). The reverse transcription of mRNA was facilitated using a 0.1 μL aliquot of reverse transcription mix, followed by pre-amplification employing a 0.6 μL aliquot of PCR mix. A diluted sample of the resulting cDNA from each cell was analyzed using quantitative PCR (qPCR) employing ChamQ™ SYBR® qPCR Master Mix (Vazyme, Q321-02) and primers targeting ACTB: forward 5’-ACAGAGCCTCGCCTTTGCC-3’ and reverse 5’-GATATCATCATCCATGGTGAGCTGG-3’. Cells exhibiting cycle threshold (Ct) values under 21 for ACTB were selected for library preparation. To differentiate human cells within grafts, GAPDH expression was quantified using specific primers: forward 5’-CTCTGCTCCTCCTGTTCGAC-3’ and reverse 5’-GCGCCCAATACGACCAAATC-3’, considering cells as human if Ct values were below 25 and melting temperatures surpassed 85°C. Library construction was performed utilizing the TruePrep DNA Library Prep Kit (Vazyme, Cat#TD501), and sequencing was conducted on the MGIseq-2000 platform, generating 100 bp paired-end reads.     For 10x Genomics scRNA-seq, cells purified through FACS were processed on a Chromium controller. This step was followed by cDNA synthesis and library preparation in line with the protocols provided with the Single Cell 3′ Reagent Kit v3.1. The prepared libraries were then sequenced using the Illumina HiSeq 4000 system, yielding 150 bp paired-end reads.Cell suspensions were initially stained with DAPI to facilitate the sorting of live single cells utilizing the FACSAria™ Fusion flow cytometer. Subsequent to sorting, nuclei were isolated in accordance with the protocols detailed in the Chromium NEXT GEM Single Cell ATAC Reagent Kits v2 (10x Genomics). The prepared libraries were then subjected to sequencing on the NovaSeq 6000 platform, achieving 50 bp paired-end reads.     In the context of protocol A, one set of samples consisted of a composite of cells from stages S2D2, S4D3, S5D3, and S6D3, combined in a ratio of 1:2:2:3. An alternative set comprised cells from stages S3D2, S4D3, and S5D3, merged in a ratio of 1:2:3. Within the framework of protocol C, one sample amalgamated cells from stages S2D2, S3D3, S4D3, and S5D3, in a ratio of 1:2:2:3, whereas another ensemble included cells from stages S2D4, S3D3, and S4D3, in a ratio of 1:2:3.

tag: cell line

tag: Stage

tag: batch

tag: treatment

value: B


title: HeLa, SETDB1KO, rep3

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Reads that aligned to the hg19 rDNA genomic sequences were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the hg19 genome using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
Read counts from biological triplicates were determined and samples were downsampled to the same read depth using custom scripts utilising SAMTools.
Differential analysis was performed using a custom R script adapting DESeq2 (Love et al., 2014). For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: hg19
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing read-count normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for hg19 refGene genes.

molecule: total RNA

source_name: HeLa

growth_protocol: HeLa cells were grown in DMEM + 10% (v/v) FBS, and hTERT-RPE-1 cells were grown in DMEM/F12 HAM + 10% (v/v) FBS. Cells cultured at 37 degrees, 5% CO2 in a humidifed cell culture incubator.

extract_protocol:
Cells were washed in PBS, and RNA extracted using the Qiagen Rneasy minikit, following the manufacturer's instructions.
RNA was depleted for ribosomal RNA by the Oxford genomics centre, and library preparation performed using their standard protocols (https://www.well.ox.ac.uk/ogc/guides/)

treatment_protocol: Where siRNA treatment was required, cells were transfected with 4 siRNAs per gene (SMARTPool, Dharmacon). Briefly, 3 µl tranfection reagent (Oligofectamine (HeLa), or Mirus-TX2 (hTERT-RPE-1)) was added to 100 µl OptiMem medium. Following 5 min incubation at room temperature, 60 pM siRNA SMARTPool was added, the tube gently inverted, and incubated at room temperature for 30 mins. Following incubation, siRNA mixes were added drop-wise to cells in a 6-well plate, and incubated for 96 h at 37 degrees, 5% CO2.

value: HeLa

tag: genotype

value: SETDB1 KO


title: H1_B_S1D3_2


title: human OFC, OF84, CONTROL

country: USA

tag: tissue


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_2_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
second doubling after release from starvation


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_1_doubling

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
first doubling after release from starvation


title: H1_B_S1D2_2


title: H1_B_S1D2_1


title: HeLa, SETDB1KO, siPPP6C, rep3

description: SETDB1KO_siPPP6C.vs.WT.TotalRNAseq_DESeq2.csv

value: SETDB1 KO; PPP6C siRNA


title: human OFC, OF83, CONTROL


title: HeLa, SETDB1KO, rep1


title: H1_B_S1D1_2


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_30min_after_release

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
30min after release from starvation


title: human OFC, OF81, CONTROL


title: HeLa, WT, rep3

value: WT


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_0min_after_release

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
0min after release from starvation


title: H1_B_S1D1_1


title: H1_AA3_S2D4_2


title: HeLa, WT, rep2


title: HeLa, SETDB1KO, siPPP6C, rep1


title: human OFC, OF75, CONTROL


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_midlog

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
cells in log phase before starvation


title: HeLa, WT, rep1


title: ABE_PCSK9_Edit_3

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description:
Library name: VK2494
Hybrid Capture Sequencing
ABE_PCSK9.hybrid_capture.PCSK9.pivot_tabe.add_chi_square_stats.csv

data_processing:
1. adapter trimming -a AGATCGGAAGAGC -A AGATCGGAAGAGC. 2. FLASH merge R1 and R2. Unmerged reads are treated as individual molecule. 3. UMI-deduplication for merged and unmerged reads using https://github.com/aryeelab/umi 4. bwa mapping to hg38
5. CRISPRessoWGS is used to quantify indel frequency and base editing frequency.
Assembly: hg38
Supplementary files format and content: tsv format

source_name: Primary Human Hepatocytes

extract_protocol:
Genomic DNA extracted from edited primary T - cells or unedited control cells using Agencourt DNAdvance according to manufacturer’s protocol.
Genomic DNA from edited primary T - cells or unedited control cells used to perform hybrid capture sequencing according to manfacturer's instructions. CBE and ABE libraries were pooled and loaded separately on NextSeq 2000 and NovaSeq X with paired-end sequencing 146 15 15 146 cycles according to the manufacturer’s instructions

treatment_protocol: Primary Human T-cells were nucleofected with respective editors like ABE8e, eA3A-BE3, and Cas9-3xNLS mRNA, cultured in X-VIVO media with cytokines, and harvested cells at day 5 after electroporation.

value: Primary Human Hepatocytes

tag: sample group


title: human OFC, OF72, CONTROL


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_12_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
12 doublings after release from starvation


title: H1_AA2_S2D4_2


title: human OFC, OF71, HEROIN

value: HEROIN


title: H1_AA3_S2D4_1


title: HeLa, SETDB1KO, rep2


title: ABE_PCSK9_Edit_2

description:
Library name: VK2502
Hybrid Capture Sequencing
ABE_PCSK9.hybrid_capture.PCSK9.pivot_tabe.add_chi_square_stats.csv


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_4_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
4 doublings after release from starvation


title: H1_AA2_S2D4_1


title: ABE_PCSK9_Edit_1

description:
Library name: VK2501
Hybrid Capture Sequencing
ABE_PCSK9.hybrid_capture.PCSK9.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF82, CONTROL


title: human OFC, OF70, CONTROL


title: H1_AA1+CH1_S2D4_2


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_3_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
3 doublings after release from starvation


title: human OFC, OF7, CONTROL


title: Sir3_HAtoT7_switch_figS6_T7-ChIP_before_switch

description:
Sir3-T7 ChIP timecourse of exit from starvation replicate
sonication followed by anti-T7 ChIP
48h incubation starvation cells


title: H1_AA1+CH1_S2D4_1


title: human OFC, OF8, CONTROL


title: ABE_PCSK9_Control_3

description:
Library name: VK2500
Hybrid Capture Sequencing
ABE_PCSK9.hybrid_capture.PCSK9.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF69, CONTROL


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_1_doubling

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
first doubling after release from starvation


title: ABE_PCSK9_Control_2

description:
Library name: VK2499
Hybrid Capture Sequencing
ABE_PCSK9.hybrid_capture.PCSK9.pivot_tabe.add_chi_square_stats.csv


title: ABE_PCSK9_Control_1

description:
Library name: VK2498
Hybrid Capture Sequencing


title: human OFC, OF68, CONTROL


title: H1_AA1_S2D4_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: ABE_Control_3

description:
Library name: VK2468
Hybrid Capture Sequencing

source_name: Human peripheral blood

value: Human peripheral blood

value: Primary Human T-cells

value: CD4+ CD8+


title: H1_AA1_S2D4_1


title: human OFC, OF66, CONTROL


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_0min_after_release

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
0min after release from starvation


title: human OFC, OF67, HEROIN


title: H1_A_S7D7_4

value: A


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_before_switch

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
48h incubation starvation cells


title: human OFC, OF65, HEROIN


title: ABE_mRNA_CIITA_Edit_3

description:
Library name: VK2466
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S7D7_2


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_30min_after_release

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
30min after release from starvation


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_midlog

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
cells in log phase before starvation


title: Sir3_HAtoT7_switch_fig4_Input_5_doublings

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
5 doublings after release from starvation


title: H1_A_S7D7_3


title: ABE_mRNA_CD7_Edit_3

description:
Library name: VK2465
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: ABE_mRNA_CBLB_Edit_3

description:
Library name: VK2464
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF64, CONTROL


title: human OFC, OF60, HEROIN


title: H1_A_S7D7_1


title: Sir3_HAtoT7_switch_fig4_Input_4_doublings

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
4 doublings after release from starvation


title: H1_A_S7D3_4


title: human OFC, OF59, HEROIN


title: Sir3_HAtoT7_switch_figS6_HA-ChIP_2_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation replicate
sonication followed by anti-HA ChIP
second doubling after release from starvation


title: ABE_mRNA_PDCD1_Edit_3

description:
Library name: VK2467
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF58, CONTROL


title: H1_A_S7D3_2


title: ABE_Control_2

description:
Library name: VK2460
Hybrid Capture Sequencing


title: Sir3_HAtoT7_switch_fig4_Input_2_doublings_replicate

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
second doubling after release from starvation


title: H1_A_S7D3_3


title: human OFC, OF54, HEROIN


title: H1_A_S7D3_1


title: Sir3_HAtoT7_switch_fig4_Input_90min_after_release

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
1h30min after release from starvation


title: ABE_mRNA_CD7_Edit_2

description:
Library name: VK2457
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF55, HEROIN


title: ABE_mRNA_PDCD_Edit_2

description:
Library name: VK2459
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: Sir3_HAtoT7_switch_fig4_Input_2_doublings


title: ABE_mRNA_CBLB_Edit_2

description:
Library name: VK2456
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S7D2_2

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: Sir3_HAtoT7_switch_fig4_Input_30min_after_release

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
30min after release from starvation


title: H1_A_S7D2_3


title: human OFC, OF51, CONTROL


title: human OFC, OF52, HEROIN


title: Sir3_HAtoT7_switch_fig4_Input_1_doubling

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
first doubling after release from starvation


title: ABE_mRNA_B2M_Edit_3

description:
Library name: VK2463
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: ABE_mRNA_B2M_Edit_2

description:
Library name: VK2455
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF50, HEROIN


title: Sir3_HAtoT7_switch_fig4_Input_3_doublings

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
3 doublings after release from starvation


title: Sir3_HAtoT7_switch_fig4_Input_2h_after_switch

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
starvation cells 18 hrs after estradiol addition


title: H1_A_S7D2_1


title: ABE_Control_1

description:
Library name: VK2452
Hybrid Capture Sequencing


title: human OFC, OF5, CONTROL


title: H1_A_S7D14_3


title: Sir3_HAtoT7_switch_fig4_Input_after_switch

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
starvation cells 16 hrs after estradiol addition


title: ABE_mRNA_PDCD_Edit_1

description:
Library name: VK2451
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S7D14_2


title: Sir3_HAtoT7_switch_fig4_Input_before_switch

description:
Input from Sir3 tag switch timecourse
sonication followed by DNA extraction before ChIP
48h incubation starvation cells


title: ABE_mRNA_CIITA_Edit_1

description:
Library name: VK2450
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF48, HEROIN


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_5_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
5 doublings after release from starvation


title: ABE_mRNA_CD7_Edit_1

description:
Library name: VK2449
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF47, HEROIN


title: ABE_mRNA_CBLB_Edit_1

description:
Library name: VK2448
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: ABE_mRNA_B2M_Edit_1

description:
Library name: VK2447
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_3_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
3 doublings after release from starvation


title: H1_A_S7D1_3

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: human OFC, OF45, CONTROL


title: human OFC, OF46, HEROIN


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_4_doublings

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
4 doublings after release from starvation


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_2_doublings_replicate

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
second doubling after release from starvation


title: human OFC, OF44, HEROIN


title: H1_A_S7D1_2


title: Cas9_Control_3

description:
Library name: VK2526
Hybrid Capture Sequencing


title: ABE_mRNA_CIITA_Edit_2

description:
Library name: VK2458
Hybrid Capture Sequencing
ABE_CRL.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S7D14_4


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_90min_after_release

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
1h30min after release from starvation


title: H1_A_S7D1_1


title: Cas9_mRNA_PDCD1_Edit_3

description:
Library name: VK2525
Hybrid Capture Sequencing
Cas9.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF42, HEROIN


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_30min_after_release

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
30min after release from starvation


title: human OFC, OF49, CONTROL


title: H1_A_S6D7_3


title: H1_A_S7D14_1


title: H1_A_S7D1_4


title: Cas9_mRNA_CIITA_Edit_3

description:
Library name: VK2524
Hybrid Capture Sequencing
Cas9.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF41, HEROIN


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_2_doublings


title: H1_A_S6D7_2


title: Cas9_mRNA_CD7_Edit_3

description:
Library name: VK2523
Hybrid Capture Sequencing
Cas9.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF4, CONTROL


title: H1_A_S6D7_1


title: human OFC, OF39, CONTROL


title: H1_A_S6D6_3


title: Cas9_mRNA_CBLB_Edit_3

description:
Library name: VK2522
Hybrid Capture Sequencing
Cas9.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF38, HEROIN


title: Cas9_mRNA_B2M_Edit_3

description:
Library name: VK2521
Hybrid Capture Sequencing
Cas9.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_2h_after_switch

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
starvation cells 18 hrs after estradiol addition


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_after_switch

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
starvation cells 16 hrs after estradiol addition


title: Cas9_Control_2

description:
Library name: VK2520
Hybrid Capture Sequencing


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_before_switch

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
48h incubation starvation cells


title: H1_A_S6D6_1


title: H1_A_S6D6_2


title: Cas9_mRNA_PDCD_Edit_2

description:
Library name: VK2519
Hybrid Capture Sequencing
Cas9.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF36, CONTROL


title: human OFC, OF37, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_5_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
5 doublings after release from starvation


title: Cas9_mRNA_CIITA_Edit_2

description:
Library name: VK2518
Hybrid Capture Sequencing
Cas9.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S6D5_1

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: human OFC, OF35, HEROIN


title: human OFC, OF34, CONTROL


title: Cas9_mRNA_CD7_Edit_2

description:
Library name: VK2517
Hybrid Capture Sequencing
Cas9.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF33, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_4_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
4 doublings after release from starvation


title: Sir3_HAtoT7_switch_fig4_T7-ChIP_1_doubling

description:
Sir3-T7 ChIP timecourse of exit from starvation
sonication followed by anti-T7 ChIP
first doubling after release from starvation


title: H1_A_S6D4_2


title: H1_A_S6D4_3


title: Cas9_mRNA_B2M_Edit_2

description:
Library name: VK2515
Hybrid Capture Sequencing
Cas9.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF32, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_3_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
3 doublings after release from starvation


title: human OFC, OF31, HEROIN


title: H1_A_S6D4_1


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_30min_after_release

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
30min after release from starvation


title: Cas9_Control_1

description:
Library name: VK2514
Hybrid Capture Sequencing


title: H1_A_S6D3_3


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_90min_after_release

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
1h30min after release from starvation


title: H1_A_S6D5_2


title: Cas9_mRNA_PDCD_Edit_1

description:
Library name: VK2513
Hybrid Capture Sequencing
Cas9.hybrid_capture.PDCD1.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S6D3_2


title: human OFC, OF30, CONTROL


title: human OFC, OF3, CONTROL


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_2_doublings

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
second doubling after release from starvation


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_1_doubling

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
first doubling after release from starvation


title: H1_A_S6D3_1


title: Cas9_mRNA_CIITA_Edit_1

description:
Library name: VK2512
Hybrid Capture Sequencing
Cas9.hybrid_capture.CIITA.pivot_tabe.add_chi_square_stats.csv


title: Cas9_mRNA_CD7_Edit_1

description:
Library name: VK2511
Hybrid Capture Sequencing
Cas9.hybrid_capture.CD7.pivot_tabe.add_chi_square_stats.csv


title: Cas9_mRNA_CBLB_Edit_2

description:
Library name: VK2516
Hybrid Capture Sequencing
Cas9.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_2_doublings_replicate

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
second doubling after release from starvation, replicate


title: human OFC, OF29, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_2h_after_switch

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
starvation cells 18 hrs after estradiol addition


title: H1_A_S6D2_3

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: Cas9_mRNA_CBLB_Edit_1

description:
Library name: VK2510
Hybrid Capture Sequencing
Cas9.hybrid_capture.CBLB.pivot_tabe.add_chi_square_stats.csv


title: human OFC, OF28, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_after_switch

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
starvation cells 16 hrs after estradiol addition


title: H1_A_S6D2_2


title: Cas9_mRNA_B2M_Edit_1

description:
Library name: VK2509
Hybrid Capture Sequencing
Cas9.hybrid_capture.B2M.pivot_tabe.add_chi_square_stats.csv


title: H1_A_S6D2_1


title: human OFC, OF27, HEROIN


title: Sir3_HAtoT7_switch_fig4_HA-ChIP_before_switch

description:
Sir3-HA ChIP timecourse of exit from starvation
sonication followed by anti-HA ChIP
48h incubation starvation cells


title: H1_A_S6D1_3


title: human OFC, OF26, CONTROL


title: SEN

city: Mountain View

first: Gabriel

last: Meca-Laguna

state: CA

address: 110 Pioneer Way, Suite J

institute: Lifespan Research Institute

description: Library name: SEN

data_processing:
The snRNA-Seq. was processed, explored, and visualized using Trailmaker/Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/). For ambient RNA discrimination, a False Discovery Rate (FDR) was calculated for each cell barcode using the emptyDrops function. Barcodes with an FDR value < 0.1 were used. Additionally, a hard Unique Molecular Identifier (UMI) threshold of > 500 UMIs allowed further distinction between real cells and empty droplets. Barcodes with over 10% mitochondrial gene content were filtered out. Outliers in the relationship between the number of expressed genes and the number of UMIs were identified and excluded by fitting a linear regression model and using a stringent 0.001 p-value criteria. Barcodes with a high probability of being a doublet were excluded using scDblFinder. After quality control, 668 non-senescent cells and 626 SEN were analyzed. To correct for batch effects, the Harmony integration method was selected. Data was LogNormalized, and the 2000 top highly variable genes (HVGs) were selected. For two-dimensional data visualization, the top 20 principal components were used and data was embedded using Uniform Manifold Approximation and Projection (UMAP). Cell clusters were identified using the Louvain algorithm with a resolution of 0.3. Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Lung fibroblasts

extract_protocol:
For nuclei isolation, fibroblasts were transferred into pre-chilled 1.5 mL Eppendorf tubes and dissociated using the 10x Genomics Nuclei Isolation Kit (10X Genomics; Cat# PN: 1000494).
Single-cell libraries were prepared using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics; Cat# PN: 1000323) on the Chromium X instrument, following the manufacturer’s protocol.

value: Lung fibroblasts

value: Fibroblast

value: Senescent (SEN, 24 hours of doxorubicin 300 nM and cultured for 9 more days)


title: human OFC, OF25, HEROIN

value: orbitofrontal cortex


title: H1_A_S6D1_2


title: W303, cisplatin 1h, replicate 1

city: Tokyo

first: Sihan

last: Li

address: Shirokanedai 4-6-1, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Library name: W303cis_1_1h

library_source: other

data_processing:
Sequencing data were trimmed with Cutadapt v2.6 and demultiplexed using FASTX-toolkit v0.0.14.
Reads were initially filtered by mapping to noncoding RNA genes using Bowtie2 v2.3.5.
Unaligned reads were then mapped to the SacCer3 genome sequence with STAR v2.7.1a. Alignments to the transcriptome were generated and the number of reads mapped to each gene was counted using the "--quantMode TranscriptomeSAM GeneCounts" parameters.
The distance from the 5’ ends of reads to the A-sites was estimated for each read length using riboWaltz.
The positions and counts of A-sites on each transcript were analyzed using RiboPlot. Reads of 29-36 nt were used for the MS2-tagged dataset, while reads of 21-22 nt and 27-29 nt were used for the cisplatin treatment dataset.
Assembly: sacCer3
Supplementary files format and content: Files ending with "ReadsPerGene.txt" are tab-delimited text files including raw read counts for each gene.
Supplementary files format and content: Files ending with "position_RPM.txt" are tab-delimited text files providing nucleotide positions relative to the start and stop codons, along with reads per million (RPM) of A-site occurrences for each transcript.
Library strategy: Ribo-Seq

molecule: other

source_name: Saccharomyces cerevisiae

growth_protocol: For the MS2-tagged dataset, cells carrying pGAL7p-rDNA plasmids were grown in synthetic complete (SC) medium containing 2% galactose to induce transcription from the GAL7 promoter. Cells were incubated at 30°C with shaking to an optical density at 600 nm (OD600) of 0.6-0.8. For the cisplatin treatment dataset, cells were grown in SC medium containing 2% glucoase at 30°C with shaking to an OD600 of 0.5.

extract_protocol:
For the MS2-tagged dataset, cells were harvested by centrifugation and lysed in IXA-100 buffer (50 mM Tris-HCl pH 7.5, 100 mM KCl, 12 mM Mg(OAc)₂, 0.01% NP-40, 1 mM DTT, 100 μg/mL CHX, 1 mM PMSF, and cOmplete Mini EDTA-free Protease Inhibitor Cocktail (Roche), 1 tablet/10 mL). Ribosomes carrying plasmid-derived 18S rRNA with an MS2 binding sequence were isolated by incubation with MS2 coat protein bound to anti-FLAG beads and eluted with IXA buffer containing FLAG peptide. For the cisplatin treatment dataset, cells were collected by rapid filtration through 0.45 μm membrane filters and lysed in ribo-seq lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X, 1 mM DTT, 100 µg/mL CHX, 25 U/mL TURBO™ DNase (Invitrogen)). Purified ribosomes or cell lysates (containing 10 μg of RNA) were treated with RNase I (Epicentre) at 10 U/µL at 23°C for 45 min. The reaction was quenched by placing the samples on ice and adding 10 µL of SUPERase·In™ RNase Inhibitor (Ambion). Ribosomes were sedimented through a sucrose cushion (1 M sucrose, 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL CHX, 20 U/mL SUPERase·In™ RNase Inhibitor) and resuspended in 120 µL of splitting buffer (20 mM Tris-HCl pH 7.5, 300 mM NaCl, 1% Triton-X, 5 mM EDTA, 1 mM DTT, 100 µg/mL CHX, 20 U/mL SUPERase·In™ RNase Inhibitor). After passing through a 100K MWCO centrifugal filter unit, the flow-through fraction was collected and mixed with 300 µL of TRIzol reagent (Thermo Fisher Scientific). RNA was then purified using the Direct-zol Microprep Kit (ZYMO RESEARCH) following the manufacturer's instructions.
RNA fragments of 19-34 nt were extracted from 15% TBE-Urea gels (Invitrogen) and dephosphorylated with T4 Polynucleotide Kinase (NEB). Linker oligonucleotides were pre-adenylated using the 5′ DNA Adenylation Kit (NEB) and ligated to the dephosphorylated RNA fragments using T4 RNA Ligase 2, Truncated (NEB). RNA fragments were recovered from gels and mixed with customized biotinylated oligos against specific rRNA regions. Fragments from noncoding RNA were captured with Hydrophilic Streptavidin Magnetic Beads (NEB) and discarded. The noncoding RNA-depleted RNA fragments were then subjected to reverse transcription using ProtoScript II Reverse Transcriptase (NEB), circularization with CircLigase™ II ssDNA Ligase (Epicentre), and subsequent PCR amplification using Phusion High-Fidelity DNA Polymerase (NEB) to generate libraries. Oligo Clean & Concentrator (ZYMO RESEARCH) was used throughout the library preparation to purify RNA/DNA fragments from each reaction.

treatment_protocol: For the cisplatin treatment dataset, cells were treated with either 600 µM cisplatin or 1% DMSO (vehicle control) for 1 hour once OD600 reached 0.5.

tag: strain

value: Saccharomyces cerevisiae

value: 600 µM cisplatin, 1 hr


title: W303, DMSO 1h, replicate 2

description: Library name: W303dmso_2_1h

value: 1% DMSO, 1 hr


title: human OFC, OF23, HEROIN


title: scRNAseq HTO human microglia 7

city: Antwrepen

first: Renzo

last: Mancuso

address: Universiteitsplein 1

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: Library name: MIND_LIB60_HTO

data_processing:
The FASTQ files were aligned by Cellranger (v.7.1.0) against the human genome database (GRCh38, Ensembl 98, refdata-gex-GRCh38-2020-A).
Assembly: GRCh38, Ensembl 98, refdata-gex-GRCh38-2020-A
Supplementary files format and content: cellranger output

molecule: protein

source_name: Brain

growth_protocol: Microglia progenitors were generated following the MIGRATE protocol.

extract_protocol:
Single cell: At 3 (C9-HRE, C9-ISO) or 6 months (CTRL and C9KO) of age, xenotransplanted mice were euthanized with an overdose of sodium pentobarbital and immediately perfused with ice-cold 1x DPBS (Gibco, Cat. no. 14190-144) supplemented with 5 U of heparin (LEO). After perfusion, one brain hemisphere per mouse was placed in FACS buffer (1X DPBS, 2% FCS and 2 mM EDTA) + 5 µM actinomycin D (ActD; Sigma, Cat. no. A1410-5MG) for transcriptomics. Brains were dissociated using Miltenyi Neural Tissue Dissociation Kit P (Miltenyi, Cat. no. 130-092-628) supplemented with 5 µM ActD. Samples were then passed through a 70-µm strainer (BD2 Falcon), washed in 10 ml of ice-cold FACS buffer with 5 µM ActD and spun at 300g for 15 min at 4 °C. ActD was included during tissue collection and enzymatic dissociation to stop transcriptional activity, and it was stopped following the myelin removal step to minimize toxicity from prolonged exposure. After dissociation, myelin was removed using 30% isotonic Percoll (GE Healthcare, Cat. no. 17-5445-02) solution. Cells resuspended in Percoll were centrifuged at 300g for 15 min at 4 °C. After centrifugation, layers of myelin and cellular debris were discarded and FC receptors were blocked in FcR blocking solution (1:10, Miltenyi, Cat. no. 130-092-575) in cold FACS buffer for 10 min at 4 °C. Cells were then washed in 5 ml of FACS buffer, pelleted and incubated with the following antibodies: PE-Pan-CD11b (1:100, Miltenyi, Cat. no. 130-113-806), BV421-mCD45 (1:100, BD Biosciences, Cat. no. 563890), APC-hCD45 (1:50, BD Biosciences, Cat. no. 555485), Total-Seq A cell hashing antibodies (1:500, BioLegend) and viability dye (1:2.000, eFluor 780, Thermo Fisher Scientific, Cat. no. 65-0865-14), in cold FACS buffer for 30 min at 4 °C. Cells were then washed, pelleted down, resuspended in 500 µl of FACS buffer. Cells were passed through a 35-µm strainer before sorting and loaded into the input chamber of a MACSQuant Tyto Cartridge. Human cells were sorted based on CD11b and hCD45 expression at 4 °C (Fig. S5a).
Single cell: The DNA libraries were generated following the manufacturer’s instructions (CG000315 Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 Dual Index). Hashtag oligo libraries were prepared according to the manufacturer’s instructions (BioLegend, Total-Seq A Antibodies and Cell Hashing with 10x Single Cell 3′ Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR.

value: Brain

value: Microglia

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0251-APP KI hCSF1 KI-C-LINE TotalSeq-A0252-APP KI hCSF1 KI-C-LINE TotalSeq-A0255-APP KI hCSF1 KI-C-LINE TotalSeq-A0257-APP KI hCSF1 KI-C-LINE TotalSeq-A0258-APP KI hCSF1 KI-C9KO TotalSeq-A0259-APP KI hCSF1 KI-C9KO TotalSeq-A0260-APP KI hCSF1 KI-C9KO


title: scRNAseq GEX human microglia 7

description: Library name: MIND_LIB60_GEX

value: GEX


title: NS

description: Library name: NS

value: Non-senescent (NS) control


title: human OFC, OF20, CONTROL

value: CONTROL


title: W303, DMSO 1h, replicate 1

description: Library name: W303dmso_1_1h


title: H1_A_S5D3_3


title: Sir3D_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the yeast S288C and the S.pombe genomes using BLAT
The read density distribution was determined for each species in each dataset separately. The average S.pombe genomic read density per bp (F and R reads were processed together) was determined for each dataset. For spike-in normalization, S.cerevisiae read densities per bp were then divided with the corresponding S.pombe average genomic read density.
Normalized read densities for each gene were aligned by the transcription start site and divided into sense and antisense transcripts. The median read density for each gene (from the tss to the end of the coding sequence) was then determined for each transcript. Intron regions were excluded from the calculation. Median read densities for each gene in each replicate of each time point were finally divided by the genome average mRNA S.cerevisiae/S.pombe count ratio for the whole time course of the corresponding replicate, to allow for direct comparisons between replicates and strains.
Assembly: Saccer1 and Schizosaccharomyces pombe (assembly ASM294v2)
Supplementary files format and content: tab-delimited text files of  normalized median read densities for each gene in indicated strains and time points.

growth_protocol: Cells were grown in YPD or YPGal (for Sir3 over expression  (oeSir3) cells) for 72hrs at 30°C till saturation and growth arrest.  Cells were then released into fresh media and aliquots were flash frozen in liquid N2 in a timecourse for several cell generations. S.pombe  cells  (strain FY2319, courtesy of S. Forsburg) were grown in YES.

extract_protocol:
Cells were resuspended in Trizol, cell walls were broken with bead beating and total RNA was extracted and DNAseI treated. Extracted total RNA amounts were measured with  the Qubit fluorimeter and the Nanodrop spectrophotometer and the quality was checked by a Bioanalyzer scan (Agilent). Each S.cerevisiae total RNA extract was mixed with the S.pombe total RNA extract at a mass ratio of 10:1.
total RNA was used to make stranded Illumina RNA_seq libraries with the Illumina  TruSeq Stranded mRNA kit or the Illumina Stranded mRNA Prep Ligation kit .

treatment_protocol: Cells were flash frozen in liquid N2

value: exit from growth arrest after nutrient depletion

value: yeast


title: scRNAseq HTO human microglia 6

description: Library name: MIND_LIB59_HTO

value: TotalSeq-A0259-APP KI hCSF1 KI-C-LINE TotalSeq-A0258-APP KI hCSF1 KI-C-LINE TotalSeq-A0257-APP KI hCSF1 KI-C-LINE TotalSeq-A0256-APP KI hCSF1 KI-C-LINE TotalSeq-A0254-APP KI hCSF1 KI-C9KO TotalSeq-A0255-APP KI hCSF1 KI-C9KO TotalSeq-A0251-APP KI hCSF1 KI-C9KO


title: human OFC, OF2, HEROIN

value: HEROIN


title: H1_A_S5D3_2

value: A


title: scRNAseq GEX human microglia 6

description: Library name: MIND_LIB59_GEX


title: Sir3D_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: H1_A_S5D3_1


title: human OFC, OF19, HEROIN


title: human OFC, OF18, HEROIN


title: Sir3D_mRNA_Fig6_90min_after_release

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: scRNAseq HTO human microglia 5

description: Library name: MIND_LIB28_HTO

value: TotalSeq-A0251-APP NLGF hCSF1 KI-C9KO TotalSeq-A0260-APP KI hCSF1 KI-C9KO


title: H1_A_S5D2_3


title: W303, cisplatin 1h, replicate 2

description: Library name: W303cis_2_1h


title: human OFC, OF16, HEROIN

value: orbitofrontal cortex


title: Sir3D_mRNA_Fig6_30min_after_release

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: H1_A_S5D2_2


title: scRNAseq HTO human microglia 4

description: Library name: MIND_LIB27_HTO

value: TotalSeq-A0252-APP NLGF hCSF1 KI-C9KO TotalSeq-A0253-APP NLGF hCSF1 KI-C9KO TotalSeq-A0254-APP NLGF hCSF1 KI-C9KO


title: scRNAseq GEX human microglia 5

description: Library name: MIND_LIB28_GEX


title: human OFC, OF15, HEROIN


title: H1_A_S6D1_1


title: H1_A_S5D2_1


title: Sir3D_mRNA_Fig6_5min_after_release

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,


title: Sir3D_mRNA_Fig6_starvation

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,


title: human OFC, OF14, HEROIN


title: scRNAseq GEX human microglia 4

description: Library name: MIND_LIB27_GEX


title: H1_A_S5D1_3


title: scRNAseq HTO human microglia 3

description: Library name: MIND_LIB19_HTO

value: TotalSeq-A0251-APP NLGF hCSF1 KI-C9-1 ISO TotalSeq-A0253-APP NLGF hCSF1 KI-C9-1 TotalSeq-A0255-APP NLGF hCSF1 KI-C9-1 TotalSeq-A0257-APP NLGF hCSF1 KI-C9-2 ISO TotalSeq-A0259-APP NLGF hCSF1 KI-C9-2 ISO TotalSeq-A0260-APP NLGF hCSF1 KI-C9-2 ISO TotalSeq-A0252-APP NLGF hCSF1 KI-C9-2 ISO


title: scRNAseq GEX human microglia 3

description: Library name: MIND_LIB19_GEX


title: H1_A_S5D1_2


title: human OFC, OF13, CONTROL


title: human OFC, OF11, HEROIN


title: Sir3D_mRNA_Fig6_midlog

description:
mRNA from a Sir3 deletion mutant in a  timecourse after exit from starvation
yeast derived from S288C (MRL5.1 ( MATa  ura3-delta  leu2-delta  his3-delta  met15-delta sir3-delta:KANR))
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: Sir2D_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
second doubling after release from starvation,


title: scRNAseq HTO human microglia 2

description: Library name: MIND_LIB17_HTO

value: TotalSeq-A0251-APP KI hCSF1 KI-C9-1 ISO TotalSeq-A0252-APP KI hCSF1 KI-C9-1 ISO TotalSeq-A0253-APP KI hCSF1 KI-C9-1 ISO TotalSeq-A0254-APP KI hCSF1 KI-C9-1 ISO TotalSeq-A0255-APP KI hCSF1 KI-C9-1 TotalSeq-A0256-APP KI hCSF1 KI-C9-1


title: H1_A_S5D1_1


title: human OFC, OF10, HEROIN


title: scRNAseq GEX human microglia 2

description: Library name: MIND_LIB17_GEX

value: Brain


title: Sir2D_mRNA_Fig6_90min_after_release

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
1h30min after release from starvation,


title: H1_A_S4D3_2


title: scRNAseq HTO human microglia 1

description: Library name: MIND_LIB14_HTO

value: Microglia

value: TotalSeq-A0253-APP KI hCSF1 KI-C9KO A1#I TotalSeq-A0254-APP KI hCSF1 KI-C9KO A1#I TotalSeq-A0255-APP KI hCSF1 KI-C9KO A1#I TotalSeq-A0256-APP KI hCSF1 KI-C9KO A1#I


title: NC-RKO.

city: Nanjing

first: Weizhen

last: Liu

state: Jiangsu

address: No.138,Xianlin Avenue,Qixia District

institute: Nanjing University Of Chinese Medicine

description: Library name: sample1

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

source_name: RKO

growth_protocol: The human CRC cell line RKO were purchased from the National Collection of Authenticated Cell Cultures and cultured in DMEM supplemented with 10% fetal bovine serum (Gibco, USA).

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

treatment_protocol: Two groups of RKO cells  were transfected with siNC and siHNRNPM separately.

value: RKO

value: Human Colorectal Adenocarcinoma Cells

value: WT

value: control RKO cells


title: scRNAseq GEX human microglia 1

description: Library name: MIND_LIB14_GEX

value: GEX


title: Sir2D_mRNA_Fig6_5min_after_release

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
5min after release from starvation,

value: exit from growth arrest after nutrient depletion

value: yeast


title: Carcinoma, scRNAseq

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

description: 10x Genomics

data_processing:
Illumina bcl files were basecalled, demultiplexed and aligned to the mouse mm10 genome using CellRanger software v7.2.0 (10x Genomics). The output of CellRanger was used to run the Python package ‘velocyto’ v0.17 and produce loom files for each sample with RNA velocity estimations [https://www.nature.com/articles/s41586-018-0414-6 ].
Assembly: mm10
Supplementary files format and content: loom (HDF5) files

organism: Mus musculus

source_name: anorectal transition zone

extract_protocol:
Freshly collected cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions with the Chromium Single Cell Controller (10x Genomics). .
Preparation for RNA sequencing followed the standard Drop-seq library (10X Genomics Chromium system), including cell identification, counting, and viability assessment, cell encapsulation, single cell 3’ reagent preparation, and massive parallel sequencing (Illumina HiSeq).

value: Transition Zone

value: anorectal transition zone

tag: age

value: 4-8 weeks old

tag: condition

value: Carcinoma


title: H1_A_S4D2_2

value: A


title: C9orf72 patient line-isogenic_diff10_d32

description: Library name: Sample_30

data_processing:
The analysis was performed in-house with a standardized pipeline integrated in GenomeComb (115). The pipeline used fastq-mcf for adapter clipping. Reads were aligned to the hg38 genome reference (116) using STAR (117) in 2-pass mode and the resulting sam file converted to cram using samtools (118). Bam files were sorted.
Assembly: GRCh38
Supplementary files format and content: normalized_counts.txt (normalized using size factors estimated via the median ratio method as implemented in DESeq2)

source_name: iPSC

extract_protocol:
Cells were harvested and RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004)
Strand-specific RNA-seq libraries were prepared using the internal standard operating procedure (SOP) of BGI, based on the DNBSEQ platform.

treatment_protocol: Cells were harvested and RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004). and sequencing.  Genes that were not expressed in any sample were removed. Raw gene counts were normalized using size factors estimated via the median ratio method described by Anders and Huber (122), and subsequently transformed using the variance stabilizing transformation (VST) from the DESeq2 package (v1.44.0)

value: iPSC

value: Microglia progenitor

value: C9orf72 patient line - isogenic control


title: Dysplasia, scRNAseq

description: 10x Genomics

value: Dysplasia


title: H1_A_S4D2_1


title: C9orf72 patient line_diff10_d32

description: Library name: Sample_29

value: C9orf72 HRE patient line


title: Hyperplasia, replicate 2, scRNAseq

description: 10x Genomics

value: Hyperplasia


title: Sir2D_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
first doubling after release from starvation,


title: Sir2D_mRNA_Fig6_midlog

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
log phase before arrest in starvation,


title: H1_A_S4D3_3

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: Hyperplasia, replicate 1, scRNAseq

description: 10x Genomics


title: Sir3_3xHA_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: Sir3_3xHA_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: H1_A_S4D1_2


title: C9orf72 patient line-isogenic_diff9_d25

description: Library name: Sample_26


title: Normal, scRNAseq

description: 10x Genomics

value: Normal


title: Sir2D_mRNA_Fig6_30min_after_release

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
30min after release from starvation,


title: E14_Bahd1_YA5_res_rep2

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed. Raw read counts were used for differential gene expression analysis by DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

growth_protocol: E14 cells were grown in DMEM plus 15% of FBS and 1% of antibiotics, 0.1mM of β-Mercaptoethanol, 0.1mM of Nonessential amino acids and 1000units/ml of leukemia inhibitory factor (LIF).

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit.
RNA libraries were made with standard Illumina protocols and sequenced by Nextseq SE75 kit.

treatment_protocol: For BAHD1 knockout (KO) assay,  gRNA-Cas9 complex was introduced into cell via electroporation. Plasmidis coding wild type (WT) or mutant BAHD1 with BAH domain mutation Y637A were introduced into Bahd1 KO E14 cells. For RNA-seq experiments, cells were grown in regular medium and collected.

value: Bahd1 YA5 res


title: H1_A_S4D3_1


title: H1_A_S3D2_2


title: C9orf72 patient line-isogenic_diff8_d25

description: Library name: Sample_24


title: KDM-RKO

description: Library name: sample2

value: RKO

value: Human Colorectal Adenocarcinoma Cells

value: HNRNPM knockdown

value: siHNRNPM treated RKO cells


title: E14_Bahd1_YA1_res_rep2

value: Bahd1 YA1 res


title: Sir2D_mRNA_Fig6_starvation

description:
mRNA from a Sir2 deletion mutant in a  timecourse after exit from starvation
yeast from the YSC1053_KO deletion library (GE Healthcare/Dharmacon) (MATa ura3-delta leu2-delta his3-delta 1 met15-delta Sir2-delta::KanR)
trizol extraction, DNAse I treatment, oligodT magnetice bead purification
72h incubation, starvation after growth in glucose,

value: exit from growth arrest after nutrient depletion

value: yeast


title: H1_A_S4D1_1


title: H1_A_S3D2_1


title: H1_A_S3D2_3


title: E14_Bahd1_YA5_res_rep1


title: Sir3_3xHA_mRNA_Fig6_90min_after_release

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: C9orf72 patient line_diff9_d25

description: Library name: Sample_25


title: Sir3_3xHA_mRNA_Fig6_30min_after_release

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: C9orf72 patient line-isogenic_diff10_d25

description: Library name: Sample_28


title: C9orf72 patient line_diff10_d25

description: Library name: Sample_27


title: Sir3_3xHA_mRNA_Fig6_5min_after_release

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: H1_A_S3D1_2


title: E14_Bahd1_YA1_res_rep1


title: Sir3_3xHA_mRNA_Fig6_starvation

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: H1_A_S3D1_1


title: E14_Bahd1_WT16_res_rep2

value: Bahd1 WT16 res


title: C9orf72 patient line-isogenic_diff7_d32

description: Library name: Sample_22


title: Sir3_3xHA_mRNA_Fig6_midlog

description:
mRNA from a  Sir3_3xHA hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated before the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: H1_A_S2D2_2

value: A


title: C9orf72 patient line_diff7_d32

description: Library name: Sample_21

value: iPSC


title: E14_Bahd1_WT16_res_rep1


title: Sir3_3xT7_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: C9orf72 patient line-isogenic_diff7_d25

description: Library name: Sample_20

value: Microglia progenitor


title: H1_A_S2D1_1


title: H1_A_S2D1_2


title: C9orf72 patient line_diff7_d25

description: Library name: Sample_19


title: Sir3_3xT7_mRNA_Fig6_90min_after_release

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: Sir3_3xT7_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: H1_A_S1D2_2


title: H1_A_S2D2_1


title: Sir3_3xT7_mRNA_Fig6_30min_after_release

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: C9orf72 patient line_diff4_d32

description: Library name: Sample_17


title: E14_Bahd1_KO_rep2

value: Bahd1 KO


title: Sir3_3xT7_mRNA_Fig6_5min_after_release

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: C9orf72 patient line-isogenic_diff4_d32

description: Library name: Sample_18

value: C9orf72 patient line - isogenic control


title: E14_Bahd1_WT2_res_rep1

value: Bahd1 WT2 res


title: E14_Bahd1_KO_rep1


title: C9orf72 patient line_diff8_d25

description: Library name: Sample_23

value: C9orf72 HRE patient line


title: H1_A_S1D2_1


title: C9orf72 patient line-isogenic_diff4_d25

description: Library name: Sample_16


title: E14_parent_rep2

value: parent


title: Sir3_3xT7_mRNA_Fig6_starvation

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: H1_A_S1D1_2


title: C9orf72 patient line_diff4_d25

description: Library name: Sample_15


title: E14_Bahd1_WT2_res_rep2


title: E14_parent_rep1


title: Sir3_3xT7_mRNA_Fig6_midlog

description:
mRNA from a  Sir3_3xT7 hypomorph strain in a  timecourse after exit from starvation phase
yeast derived from the wt1 strain with  the loxP-3xHA-loxpP-3xT7 tags switch cassette fused to the Sir3 C-terminus, isolated after the estradiol induced tag-switch.
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: H1_A_S1D1_1

description:
cellname.smartseq3.tsv
genename.smartseq3.tsv
readcount.smartseq3.mtx


title: R8d 2

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
The read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.1) with read count
Assembly: CaprahircusARS1

organism: Capra hircus

source_name: CiMEC cells

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

extract_protocol:
Extract total RNA from each sample,then use Ribo-Zero™ Gold Kits（Human/Mouse/Rat） to delete Rrna
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina using 1μg of total RNA.

treatment_protocol: GEFs were seeded at a density of 5×104 cells per well of a 4-well plate or 5×105 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium. The next day, the fibroblast medium was replaced by R induction medium. The culture was continued for 8 days, and the induction medium was refreshed every 2 days. On day 8, those induced cells with primary colonies were named R-8d cells/CiMECs-P0 and were further passaged at a ratio of 1:3 every 3-4 days; the cells were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with goat MEC culture medium changed every 2 days. The culture plates or dishes were precoated with Matrigel® Matrix (Corning, 356230).

value: CiMEC cells

value: induced mammary epithelial cells

value: WT

value: reprogramming


title: Sir3_wt2_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: C9KO_diff6_d32

description: Library name: Sample_13

value: BIONi010-C C9orf72KO


title: Sir3_wt2_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: R8d 1


title: Sir3_wt2_mRNA_Fig6_90min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: C9KO_diff5_d25

description: Library name: Sample_11


title: C_line_diff5_d25

description: Library name: Sample_12


title: Sir3_wt2_mRNA_Fig6_30min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: R6d 1


title: C_line_diff4_d25

description: Library name: Sample_10


title: R4d 2


title: R6d 2


title: Postn-KO, rep 3

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description:
Library name: shPostn_C
shPostn.rep3

data_processing:
Transcripts were quantified with salmon and summarized to gene-level counts using tximport.
Assembly: mm10
Supplementary files format and content: comma-separated values containing gene read counts

source_name: sarcoma cells sorted ex vivo from mouse tumors

growth_protocol: Syngeneic tumor cell line p53KO Ccne1 OE was generated in-house. First, mesenchymal stem cells were harvested from female C57/Bl6 p53KO mice, transduced using a retroviral vector for the overexpression of Ccne1 and RFP fluorescent tracer, and expanded in vitro. To generate immortalized tumor cell line, cells were passaged twice through female wild-type (C57/Bl6) recipient mice via subcutaneous transplantation, and re-harvested. Resulting tumor cell lines were briefly expanded in vitro in DMEM+FBS.  To generate Postn-WT and Postn-KO genotypes, the p53KO Ccne1 OE cell line was further transduced with viral vectors encoding either a hairpin against Postn, or a scrambled (control) sequence.  Cell lines were transplanted into experimental mice to generate sarcoma tumors. Tumors were harvested and RFP+ tumor cells were sorted for RNA-seq.

extract_protocol:
Total RNA was extracted using TRIzol.
DNBSEQ eukaryotic strand-specific mRNA libraries were prepared by BGI.

value: p53 KO Ccne1 OE

value: undifferentiated pleimorphic sarcoma cells

value: shPostn


title: Sir3_wt2_mRNA_Fig6_5min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,

value: exit from growth arrest after nutrient depletion

value: yeast


title: R4d 1


title: Sir3_wt2_mRNA_Fig6_starvation

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: Postn-KO, rep 2

description:
Library name: shPostn_B
shPostn.rep2

value: sarcoma cells sorted ex vivo from mouse tumors


title: R3d 2


title: C_line_diff6_d32

description: Library name: Sample_14

value: iPSC

value: Microglia progenitor


title: R2F+ISG15

type: RNA

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description:
Gene expression data from total RNA of mouse cell lines
R2F_rISG15.sst-rma-gene-full.chp

hyb_protocol: Microarray analysis were conducted as followed the standard Affymetrix procedures.

scan_protocol: Hybridized slides were scanned by Affymetrix Gene Chip scanner 3000 7G system.

data_processing: Raw data were generated using Partek Genomics Suite version 7 software.

label: biotin

source_name: R2F cells treated with recombinant ISG15

label_protocol: Genome-wide gene expression analysis was performed using the Affymetrix Human Clariom S Assay.

growth_protocol: Immortalized fibroblasts (S1F and R2F) were stably cultured in dishes with DMEM with 10% fetal bovine serum at 37°C in an incubator supplied with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent and purified using RNeasy mini kit.

treatment_protocol: treated with 300 ng/ml ISG15 recombinant protein

value: SV-40 transformed human fibroblast cell line

value: recombinant ISG15


title: C_line_diff4_d32

description: Library name: Sample_8


title: Sir3_wt2_mRNA_Fig6_midlog

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (JOY1 (S288C(BY4741 parent): MATa  ura3D  leu2D  his3D  met15D  bar1D:HIS5)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,


title: R2F+PBS

description:
Gene expression data from total RNA of mouse cell lines
R2F_CTL.sst-rma-gene-full.chp

source_name: R2F cells treated with vehicle control

value: vehicle control, PBS


title: Postn-KO, rep 1

description:
Library name: shPostn_A
shPostn.rep1


title: C9KO_diff4_d32

description: Library name: Sample_7


title: R3d 1


title: Sir3_wt1_mRNA_Fig6_2_doublings_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
second doubling after release from starvation,


title: Sir3_wt1_mRNA_Fig6_1_doubling_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
first doubling after release from starvation,


title: C9KO_diff3_d32

description: Library name: Sample_5


title: Postn-WT, rep 3

description:
Library name: shSCR_C
shSCR.rep3

value: shSCR


title: R2d 2

value: CiMEC cells


title: Sir3_wt1_mRNA_Fig6_90min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
1h30min after release from starvation,


title: R2d 1

value: induced mammary epithelial cells


title: C9KO_diff4_d25

description: Library name: Sample_9


title: R1d 2

value: WT


title: Postn-WT, rep 1

description:
Library name: shSCR_A
shSCR.rep1


title: Sir3_wt1_mRNA_Fig6_30min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
30min after release from starvation,


title: W303, MS2-purified 18S: G1645A/A1754G, replicate 2

description: Library name: purified_b2

value: Saccharomyces cerevisiae

value: Expressing pGAL7p-rDNA (18S:GA/AG-MS2 binding site)


title: C_line_diff2_d25

description: Library name: Sample_4


title: R1d 1

value: reprogramming


title: Sir3_wt1_mRNA_Fig6_5min_after_release

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
5min after release from starvation,


title: C9KO_diff2_d25

description: Library name: Sample_3

value: BIONi010-C C9orf72KO


title: S1F+ISG15

description:
Gene expression data from total RNA of mouse cell lines
S1F_rISG15.sst-rma-gene-full.chp

source_name: S1F cells treated with recombinant ISG15


title: W303, MS2-purified 18S: G1645A/A1754G, replicate 1

description: Library name: purified_b1


title: C_line_diff1_d32

description: Library name: Sample_2


title: Sir3_wt1_mRNA_Fig6_starvation

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
72h incubation, starvation after growth in glucose,


title: C9KO_diff1_d32

description: Library name: Sample_1


title: R0d 2

source_name: GEF cells

value: GEF cells

value: Fibroblast cells


title: S1F+PBS

description:
Gene expression data from total RNA of mouse cell lines
S1F_CTL.sst-rma-gene-full.chp

source_name: S1F cells treated with vehicle control


title: W303, MS2-purified 18S: WT, replicate 2

description: Library name: purified_w2

value: Expressing pGAL7p-rDNA (18S:WT-MS2 binding site)


title: R0d 1


title: Sir3_wt1_mRNA_Fig6_midlog

description:
mRNA from a wt Sir3 strain in a  timecourse after exit from starvation phase
yeast derived from S288C (NKI12318 (MATa his3d200 leu2d0 lys2d0 met15d0 trp1d63 ura3d0 bar1::HisG HIS3  Pgpd_CRE_EBD78)) .
trizol extraction, DNAse I treatment, oligodT magnetic bead purification
log phase before arrest in starvation,

value: exit from growth arrest after nutrient depletion

value: yeast


title: W303, MS2-purified 18S: WT, replicate 1

description: Library name: purified_w1


title: C_line_diff3_d32

description: Library name: Sample_6

value: iPSC

value: Microglia progenitor


title: Postn-WT, rep 2

description:
Library name: shSCR_B
shSCR.rep2

value: sarcoma cells sorted ex vivo from mouse tumors

value: p53 KO Ccne1 OE

value: undifferentiated pleimorphic sarcoma cells


title: MacacaPFCsnRNA_Y4_2_1

status: Public on Oct 19 2025

first: Suijuan

last: Zhong

state: Haidian

address: No.19 Xinjiekouwai Street

institute: Beijing Normal University

description:
Library name: MacacaPFCsnRNA_Y4_2_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz

data_processing:
Barcode filtering and sequence alignment were performed with software Cell Ranger (http://10xgenomics.com). Reads were aligned to the human and macaque reference genome (Macaca_fascicularis 5.0.98)
raw counts extraction, normalization, dimensional reduction analysis and further downstream analysis were mainly performed with the R package Seurat
Assembly: Macaca_fascicularis_5.0.98
Supplementary files format and content: .tar.gz files include filtered_feature_bc_matrix for macaque samples

molecule: nuclear RNA

organism: Macaca fascicularis

source_name: prefrontal cortex

extract_protocol:
Macaque prefrontal cortex samples across developmental stages were collected in ice-cold oxygenated artificial cerebrospinal fluid at PH 7.4.  Samples were transferred into 2 ml ice-cold EZ PREP and were homogenized by grinding with a glass Dounce tissue grinder . Transfer the tissue homogenate into a 15 ml tube, add 2 ml of EZ PREP, incubate on ice for 5 minutes and centrifuge at 500 g at 4℃ for 5 minutes. The supernatant was removed and the nuclei were resuspended in 4 ml ice-cold EZ PREP, and the incubation and centrifugation were repeated once.
The libraries were generated by using the Chromium Next GEM Single Cell 3' Kit v3 according to the 10x GENOMICS official instructions, and processed on the Illumina platform for sequencing with 150 bp paired-end reads

value: prefrontal cortex


title: MacacaPFCsnRNA_Y4_1_2

description:
Library name: MacacaPFCsnRNA_Y4_1_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz

growth_protocol: Macaque prefrontal cortex samples across developmental stages were collected in ice-cold oxygenated artificial cerebrospinal fluid at PH 7.4.  Samples were transferred into 2 ml ice-cold EZ PREP and were homogenized by grinding with a glass Dounce tissue grinder . Transfer the tissue homogenate into a 15 ml tube, add 2 ml of EZ PREP, incubate on ice for 5 minutes and centrifuge at 500 g at 4℃ for 5 minutes. The supernatant was removed and the nuclei were resuspended in 4 ml ice-cold EZ PREP, and the incubation and centrifugation were repeated once.


title: MacacaPFCsnRNA_Y2_2_2

description:
Library name: MacacaPFCsnRNA_Y2_2_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_Y4_1_3

description:
Library name: MacacaPFCsnRNA_Y4_1_3
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_Y2_2_1

description:
Library name: MacacaPFCsnRNA_Y2_2_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_Y2_1_1

description:
Library name: MacacaPFCsnRNA_Y2_1_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_Y1_1_2

description:
Library name: MacacaPFCsnRNA_Y1_1_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_Y1_1_1

description:
Library name: MacacaPFCsnRNA_Y1_1_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_M6_1_2

description:
Library name: MacacaPFCsnRNA_M6_1_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_P0_3_1

description:
Library name: MacacaPFCsnRNA_P0_3_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: set2-set16-me3-2, ChIP

first: Hua

address: 38 Xueyuan Rd

description: Library name: set2-set16-me3-2

data_processing:
ChIP-seq data was processed as in Ho et al. (61). Fastq files were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using trim_galore (version 0.6.4), then ChIP-seq trimmed fastq reads were aligned to C. elegans genome version WBcel235 using bowtie2 (version 2.3.5.1) with default parameters. Bam files were then sorted and indexed using samtools (version 1.10). ChIP enrichment was normalized by dividing to input using DeepTools bamCompare (v3.3.0) with the following parameters: RPKM, bin-size of 10bp, ignore duplicates, extend reads to 200bp and remove ENCODE blacklisted regions (https://github.com/Boyle-Lab/Blacklist/). C. elegans enhancers were obtained from Jänes et al. (62). Genome-wide data was visualized using the Integrative Genomics Viewer (v2.6.1, Robinson et al., 2011(63).
For RNA-seq, the raw fastq files (stranded SE75) were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using trim_galore (version 0.6.4), then mapped to WBcel235 whole genome using HISAT 2.2.1 with default parameters. The number of reads mapped to genes was determined with featureCounts (Version 1.6.4). FPKM stands for Fragments Per Kilobase of transcript per Million mapped reads at gene level. The resulting read count data were processed by DESeq2 (v1.35.0) to identify differentially expressed transcripts among experimental groups. Genes with log2 fold change > ± 1 and Padj <0,01 were considered to have significant expression change.
Assembly: WBcel235
Supplementary files format and content: bigWig

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C.elegans strains were grown at 20°C on NGM (Nematode Growth Medium) plates seeded with E.Coli OP50 bacteria, following standard procedures (Brenner, 1974), unless otherwise stated. Double mutants were generated by standard genetic crosses.

extract_protocol: Young adult animals were selected for these analyses as they can be highly synchronised. Chromatin extraction from large animal’s population was performed as described in Zaghet et al. 2021. Briefly, animals (at young adult stage) were collected and fixed for 10 minutes with a solution of 1% formaldehyde.

value: whole organism

tag: chip antibody


title: MacacaPFCsnRNA_Y2_1_2

description:
Library name: MacacaPFCsnRNA_Y2_1_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_M6_2_1

description:
Library name: MacacaPFCsnRNA_M6_2_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_P0_1_2

description:
Library name: MacacaPFCsnRNA_P0_1_2
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_P0_1_1

description:
Library name: MacacaPFCsnRNA_P0_1_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: set2-set16-input-me3, ChIP

description: Library name: set2-set16-input-me3


title: set2-set16-me3-1, ChIP

description: Library name: set2-set16-me3-1


title: set16-me1-2, ChIP

description: Library name: set16-me1-2


title: MacacaPFCsnRNA_E110_1_1

description:
Library name: MacacaPFCsnRNA_E110_1_1
filtered_feature_bc_matrix_prenatalmacaque.tar.gz


title: MacacaPFCsnRNA_E110_1_2

description:
Library name: MacacaPFCsnRNA_E110_1_2
filtered_feature_bc_matrix_prenatalmacaque.tar.gz


title: set16-me1-1, ChIP

description: Library name: set16-me1-1


title: MacacaPFCsnRNA_M6_1_1

description:
Library name: MacacaPFCsnRNA_M6_1_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_P0_2_1

description:
Library name: MacacaPFCsnRNA_P0_2_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_E90_1_2

description:
Library name: MacacaPFCsnRNA_E90_1_2
filtered_feature_bc_matrix_prenatalmacaque.tar.gz


title: set-2input-me3, ChIP

description: Library name: set-2input-me3


title: MacacaPFCsnRNA_Y4_1_1

description:
Library name: MacacaPFCsnRNA_Y4_1_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: MacacaPFCsnRNA_E90_1_1

description:
Library name: MacacaPFCsnRNA_E90_1_1
filtered_feature_bc_matrix_prenatalmacaque.tar.gz


title: set16-input-me1, ChIP

description: Library name: set16-input-me1


title: Con_16

city: Fushan

first: Jianhua

state: Guangdong

address: No. 12, Jinsha Avenue, Shunde District, Foshan, Guangdong, P.R. China

institute: Department of Laboratory Medicine Shunde Hospital of Guangzhou University of Chinese Medicine

data_processing:
The original data obtained from high-throughput sequencing were converted to raw sequence reads by base calling, and the results were stored in FASTQ format.
Low-quality reads and reads without primers were discarded. PCR and sequencing errors were corrected by unique molecular identifiers (UMIs).
The reads with same UMI were one clone. Only duplicate reads with different UMIs will be kept in downstream processing. A clonotype was defined by the CDR3 amino acid sequence for further analysis.
TCRβ V, D, J gene and clonotype defined according to IMGT59 and Igblast; TCRβ VDJ combination defined by MIXCR. We performed mRNA-Seq profiling on 70 samples.Reads mapped to the IPD-IMGT/HLA database and HLA -HD determining HLA alleles using mRNA-seq results
Categorical variables were described as count (%), and two group comparison was performed using Fisher’s exact test. Continuous variables were expressed as median and interquartile range (IQR) values and compared by Mann–Whitney U test between groups. Spearman correlation coefficient was calculated to assess the association between two vectors of quantitative variables. The significance of monotonic trend across multiple groups was assessed by Cuzick's test . The significance of overlap between tow gene sets was assessed by hypergeometric test (the “dhyper” function of R software). All statistical analyses were performed using R software (version 4.0.2). A two-sided P-value lower than 0.05 was considered as statistically significant. Given the exploratory nature of the present study, unadjusted p-values not accounting for multiple testing were used to screen COVID-19 associated TCR variables.

source_name: Peripheral Blood

extract_protocol:
PBMC, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy


title: Con_15


title: set-2-2-me3, ChIP

description: Library name: set-2-2-me3


title: MacacaPFCsnRNA_Y1_2_1

description:
Library name: MacacaPFCsnRNA_Y1_2_1
filtered_feature_bc_matrix_postnatalmacaque.tar.gz


title: set-16input-me3, ChIP

description: Library name: set-16input-me3


title: Con_13


title: Con_14


title: Con_12


title: set-2-1-me3, ChIP

description: Library name: set-2-1-me3


title: Con_11


title: n2-me3-2, ChIP

description: Library name: n2-me3-2


title: set-16-1-me3, ChIP

description: Library name: set-16-1-me3


title: Con_8


title: n2-me3-1, ChIP

description: Library name: n2-me3-1


title: Con_10


title: n2-me1-2, ChIP

description: Library name: n2-me1-2


title: Con_5


title: n2-input-me3, ChIP

description: Library name: n2-input-me3


title: n2-me1-1, ChIP

description: Library name: n2-me1-1


title: Con_7


title: Con_6


title: n2-2-me3, ChIP

description: Library name: n2-2-me3


title: Con_4


title: set-16-2-me3, ChIP

description: Library name: set-16-2-me3


title: Con_2


title: Con_3


title: Con_1


title: RP_10

value: Re-detectable positive


title: input-etoh-2, ChIP

description: Library name: input-etoh-2

value: ethanol


title: n2input-me3, ChIP

description: Library name: n2input-me3


title: input-auxin-2, ChIP

description: Library name: input-auxin-2

value: Auxin


title: input-etoh-1, ChIP

description: Library name: input-etoh-1


title: RP_9


title: input-auxin-1, ChIP

description: Library name: input-auxin-1


title: Con_9


title: IP-etoh-2, ChIP

description: Library name: IP-etoh-2


title: RP_8


title: RP_7


title: IP-auxin-2, ChIP

description: Library name: IP-auxin-2


title: IP-etoh-1, ChIP

description: Library name: IP-etoh-1


title: RP_5


title: n2-input-me1, ChIP

description: Library name: n2-input-me1


title: IP-auxin-1, ChIP

description: Library name: IP-auxin-1


title: RP_6


title: RP_4


title: n2-1-me3, ChIP

description: Library name: n2-1-me3


title: RP_3


title: N2-1-4, RNA

description: Library name: N2-1-4


title: N2-1-3, RNA

description: Library name: N2-1-3


title: N2-1-2, RNA

description: Library name: N2-1-2


title: RP_1


title: Re_14

value: Convalescent


title: N2-1-1, RNA

description: Library name: N2-1-1


title: tm1630-1-4, RNA

description: Library name: tm1630-1-4


title: tm1630-1-2, RNA

description: Library name: tm1630-1-2


title: tm1630-1-1, RNA

description: Library name: tm1630-1-1


title: Re_10


title: Re_12


title: 1804-2-4, RNA

description: Library name: 1804-2-4


title: Re_11


title: tm1630-1-3, RNA

description: Library name: tm1630-1-3


title: Re_8


title: Re_9


title: 1804-1-2, RNA

description: Library name: 1804-1-2


title: Re_7


title: Re_6


title: 1804-1-3, RNA

description: Library name: 1804-1-3


title: Re_5


title: 1504-1804-1-4, RNA

description: Library name: 1504-1804-1-4


title: 1804-1-1, RNA

description: Library name: 1804-1-1


title: 1504-1804-1-3, RNA

description: Library name: 1504-1804-1-3


title: Re_4


title: 1504-1804-1-2, RNA

description: Library name: 1504-1804-1-2


title: RP_2


title: Re_3


title: 1504-1-4, RNA

description: Library name: 1504-1-4


title: Re_1


title: Se-1

value: Symptomatic


title: Re_13


title: 1504-1-3, RNA

description: Library name: 1504-1-3


title: Mo_16


title: 1504-1-1, RNA

description: Library name: 1504-1-1


title: Mo_15


title: ethanol4, RNA

description: Library name: ethanol4


title: 1504-1-2, RNA

description: Library name: 1504-1-2


title: Mo_14


title: ethanol3, RNA

description: Library name: ethanol3


title: Mo_13


title: ethanol2, RNA

description: Library name: ethanol2


title: Mo_11


title: Mo_12


title: Auxin3, RNA

description: Library name: Auxin3


title: 1504-1804-1-1, RNA

description: Library name: 1504-1804-1-1


title: Auxin4, RNA

description: Library name: Auxin4


title: Mo_10


title: Mo_8


title: Re_2


title: Auxin2, RNA

description: Library name: Auxin2


title: Mo_9


title: Mo_7


title: Mo_6


title: 100 μg BKC treated pancreas control group 2

city: Busan

first: Tae Hwan

last: Shin

address: Nakdong-daero 550 beon-gil

department: Health Sciences

country: South Korea

institute: Dong-A University

description: Library name: B100-4_P

data_processing:
Trimmomatics (ver. 0.38) was used for a program that performs trimming depending on various parameters on illumina paired-end or single-end.
HISAT2 (ver. 2.1.0) was used for a fast and sensitive alignment program for mapping next-generation sequencing reads to genomes. Its first implementation based on an extension of BWT for graphs, designed a graph FM index (GFM). In addition to using one global GFM index, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
StringTie (ver. 2.1.3b) was used for a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
edgeR (ver. 3.40.2) is used for differential expression analysis of RNA-seq expression profiles with biological replication.
Assembly: The Rattus norvegicus reference genome (GRCr8) and its corresponding annotation files were obtained from NCBI.
Supplementary files format and content: FPKM

organism: Rattus norvegicus

source_name: pancreas

growth_protocol: Six-week-old male Sprague-Dawley (SD) rats (Doo Yeol Biotech, Seoul, Korea) were acclimatized for 1 week before the experiment. Rats were housed in an individually ventilated cage system with controlled temperature and humidity (i.e., 20–25°C, 50 ± 10% humidity, and a 12-h light/dark cycle). The water and feed were supplied ad libitum. All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of the Korea Institute of Radiology and Medical Science (approval number: KIRAMS 2024-0014).

extract_protocol:
Quantitative RNA sequencing was performed with adrenal glands, heart, and pancreas at 24 h after the 10th intratracheal instillation. Collected organs were added 1 mL of TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) per 50 mg of organ tissues. The paired adrenal glands per animal were pooled, and the heart was dissected in the left ventricular area. Samples weighed approximately 50 mg and were stored in TRIzol at -80℃ in a deep freezer until RNA purification.
Total RNA was isolated using a RNeasy Mini kit (Qiagen, Valencia, CA, USA), and the RNA integrity was analyzed using a Bioanalyzer (Agilent, Santa Clara, CA, USA). RNA samples with RNA integrity values greater than 9 were selected to prepare the mRNA sequencing library. The library was prepared using a TruSeq Stranded mRNA library kit (Illumina, San Diego, CA, USA).

treatment_protocol: Single-dose instillation of benzalkonium Chloride (BKC) induced approximately 40% polymorphonuclear leukocytes (PMNs) at a dose of 200 μg/rat, whereas less than 10% PMNs were observed at 100 μg/rat. Therefore, the doses for repeated exposure were selected as 50 and 100 μg/rat. Repeated instillations (total 10 times) were conducted every 3 days, starting from 7 weeks of age. Rats were euthanized on day 31 (24 h after the final administration).

value: pancreas

value: wildtype

value: 100 μg BKC


title: 100 μg BKC treated pancreas control group 1

description: Library name: B100-1_P


title: Auxin1, RNA

description: Library name: Auxin1


title: Mo_5


title: Mo_4


title: Vehicle treated pancreas control group 2

description: Library name: VEH-3_P

value: Vehicle


title: Mo_3


title: Vehicle treated pancreas control group 1

description: Library name: VEH-2_P