title: H3K27ac-CUTandTag_CD8_24h_WT_rep2

description:
Library name: H3K27ac-CUTandTag_CD8_24h_WT2
H3K27ac-CUTandTag_CD8_24h_WT.bw

value: WT


title: Col-0 whole seedling, 4h ethylene treated, rep4

status: Public on Aug 10 2026

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description:
Library name: 211004_Ath_SC_Ath_3do_col_4ET_4_1_10xRNA
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell by gene matrices were generated with Cellranger v3.1.0
Assembly: TAIR10 genome; Araport 11 transcriptome
Supplementary files format and content: harmony.rds, Seurat object that contains the snRNA-seq dataset of whole seedlings
Supplementary files format and content: apical_clusters.rds, Seurat object that contains cells that compose the apical seedling
Supplementary files format and content: spatial_multiome_imputed_250825.rds, Seurat object that contains cells related to the spatial multi-modal integration
Supplementary files format and content: GA_subclust26_multiome_imputed_250825.rds, Seurat object that contains the AHR (cluster 26) cells

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Arabidopsis seedlings were grown at 23C in complete darkness for 72h prior to harvest

extract_protocol:
1.5g pulverized frozen tissue was extracted in 10 mL nuclei purification buffer (NPB; 20 mM MOPS pH 7, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, 1X protease inhibitors (Sigma), 1:1000 SUPERase (Thermo), at 4 oC for 10 min with gentle agitation. The nuclei-containing extract was sequentially filtered through 70 µm (Fisher) and 30 µm (Miltenyi) filters at 4 oC. The filtered extract was then homogenized using a pre-chilled Dounce homogenizer with 10 loose pestle strokes followed by 10 tight pestle strokes. Nuclei were pelleted by centrifugation at 700 x g for 5 min at 4 °C and resuspended in 3 mL NPB. A discontinuous gradient of 15% / 45% optiprep was prepared by diluting 60% Optiprep (Sigma) to 50% with 120 mM Tris-Cl, pH 8.0, 150 mM KCl, 30 mM MgCl2, and further diluted to 15% or 45% with NPB containing 1:1000 SUPERase. The nuclear pellet was resuspended in 3 mL NPB, gently layered onto the 15%/45% OptiPrep gradient, and centrifuged at 1500 × g for 15 min at 4 oC. Following centrifugation, the nuclei were collected from the 15%/45% OptiPrep interface, washed with 10 mL of 1X PBS (Corning), and pelleted by centrifugation at 500 × g for 5 min at 4 oC. The nuclei were resuspended in 1 mL of PBS, stained with 3 µg of Hoechst 33342, placed on ice, and taken to the Flow Cytometry Core for Fluorescence-Activated Nuclei Sorting (FANS). A BD Influx sorter with a 100-μm nozzle was used to sort nuclei in 1x PBS with sheath fluid at 20 PSI; nuclei were kept at 4 °C during the purification process. Debris was excluded first by gating using forward and side scatter pulse area parameters (FSC-A and SSC-A in log scale), then exclusion of aggregates using pulse width parameters (FSC-W and SSC-W), and finally gating on Hoechst-positive nuclei. Hoechst was excited with a 405nm laser at 100mW and detected using the 460/50BP filter. The Hoechst-positive nuclei were sorted using the '1-drop pure' mode directly into 1.5mL Eppendorf tubes containing 1x PBS, 0.5% BSA, and 1:1,000 SUPERase.
Following FANS, nuclei were centrifuged at 500 × g for 5 min; the supernatant was aspirated, and the nuclei were resuspended in 50 µl of PBS, BSA, and RNase inhibitors and quantified using a hemocytometer (Incyto). 10,000 nuclei, or the total nucleus suspension if fewer than 10,000 nuclei were collected, were used as input for the 10x Genomics Single Cell 3’ Gene Expression v3 reagents. Sequencing libraries were constructed following the manufacturer’s instructions and were sequenced with the Illumina NovaSeq 6000.

treatment_protocol: Control plants were treated with Zero grade air in sealed chambers at a rate of 30mL / min. Treated plants were exposed to 10 ppm ethylene gas at a flow rate of 30mL / min for the indicated treatment lengths.

tag: tissue

value: Whole seedling

tag: genotype

tag: treatment

value: 4h ethylene


title: RNF213-knockout HeLa cells treated with palmitate for 1 h

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

description: Library name: B2

library_source: transcriptomic

data_processing:
Basecalling was performed with RTAVersion ver. 3.4.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a.
Assembly: GRCh38
Supplementary files format and content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0

molecule: polyA RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: Parental and RNF213-knockout HeLa cells, derived from cervical cancer, were obtained from American Type Culture Collection (ATCC, VA, USA), and cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10 % fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin (Nacalai Tesque). All cells were maintained in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from HeLa cells using Sepasol®-RNA I Super G (Nacalai Tesque). PolyA(+) RNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA, USA).
RNA libraries were constructed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

treatment_protocol: HeLa cells are treated with 0.5 mM sodium palmitate (Nacalai Tesque) for 0, 1, 3, 6, 12, or 18 h.

tag: cell line

value: HeLa

tag: cell type

value: cervical cancer cell line

value: RNF213 knockout

value: treated with palmitate for 1 h


title: SJWLM071786_X2_DYE1777_T0

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
Library name: SJWLM071786_X2
2671584

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

molecule: total RNA

source_name: Tumor

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

value: Tumor

tag: batch


title: H3K27ac-CUTandTag_CD8_24h_WT_rep1

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: H3K27ac-CUTandTag_CD8_24h_WT1
H3K27ac-CUTandTag_CD8_24h_WT.bw

library_source: genomic

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of  WT and H2AZ-cKO. The sorted naïve T cells were stimulated with anti-CD3 and anti-CD28 antibodies (Abs) for 6 or 24 h.  Then the naive CD8 T or activated CD8 T cells were collected for ATAC-seq and CUT&Tag assay. ATAC-seq library was constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD501-01),  following the manufacturer’s instructions. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z, H3K4me3, H3K27me3, H3K27ac and PolII S5P antibody in T cells. Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904).
CUT&Tag libraries was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904), following the manufacturer’s instructions.

value: spleen

value: naive CD8+ T cell

tag: cell subset


title: Col-0 whole seedling, 2h ethylene treated, rep4

description:
Library name: 211004_Ath_SC_Ath_3do_col_2ET_4_1_10xRNA
10x Genomics

value: 2h ethylene


title: SJWLM071784_X1_DYE1776_2D

description:
Library name: SJWLM071784_C2
2671583

source_name: Cells

value: Cells


title: RNF213-knockout HeLa cells treated with palmitate for 0 h

description: Library name: B1

value: treated with palmitate for 0 h


title: H3K27ac-CUTandTag_CD8_24h_IgG-Ctr

description:
Library name: H3K27ac-CUTandTag_CD8_24h_IgG
H3K27ac-CUTandTag_CD8_24h_IgG.bw


title: K-562–Cas9, sgPTBP1+sgPTBP2, rep3

city: Philadelphia

first: Junwei

last: Shi

state: PA

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

description:
Library name: K562_PTBP1_PTBP2_DKO_rep3
countsMOLM13.csv

data_processing:
Sequencing reads were aligned to human genome GRCh38.p13 using STAR 2.7.10a. Raw read counts were generated using STAR's --quantMode GeneCounts option.
Assembly: GRCh38.p13
Supplementary files format and content: countsMOLM13.csv contains raw counts for all MOLM-13 and K-562 samples aligned to the human genome, while countsMV411.csv contains the raw counts for the MV4-11 samples. Columns are samples and rows are genes labeled by Ensembl gene ID.

source_name: blood

growth_protocol: MOLM-13–Cas9 and K-562–Cas9 were grown in RPMI-1640 medium with 10% bovine calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2. MV4-11–Cas9 cells were grown similarly, but without the pen/strep.

extract_protocol:
RNA was extracted from cells with TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit with in-column treatment of DNase I for 15 min. at room temperature. RNA quality was evaluated with RNA 6000 Nano Bioanalyzer kit (Agilent), and RNA with RIN ≥ 9 was used for further library construction.
MOLM-13 and K-562 RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Briefly, 1 μg of total RNA was poly-A selected and fragmented with NEBNext Poly (A) mRNA Magnetic Isolation Module, followed by first and second strand cDNA synthesis. The libraries were end-repaired, linked with the Illumina adaptors, and PCR amplified with 9 cycles. The libraries were sequenced on the Illumina NovaSeq 6000 platform with 2×100-base paired-end reads. MV4-11 RNA-seq libraries were constructed similarly by Novagene, and those libraries were sequenced on a NovaSeq X Plus with 2×150-base paired-end reads.

treatment_protocol: MOLM-13 and K-562 cells were lentivirally transduced with CRISPR single guide RNAs against PTBP1 (sgPTBP1_3), PTBP2 (sgPTBP2_2), both, or the non-targeting control Rosa26 (Mus musculus locus). MV4-11 cells were transduced with either of two PTBP1 sgRNAs (sgPTBP1_1 or sgPTBP1_3) or the two controls Rosa26 or EMX1. For the infection, cells and lentivirus were centrifuged at 650×g for 25 minutes at room temperature with 8 µg/mL Polybrene. Cells were harvested 5 days post-infection.

value: blood

value: chronic myeloid leukemia

tag: genetic modification


title: SJWLM071784_X1_DYE1775_3D

description:
Library name: SJWLM071784_C1
2671582


title: H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO_rep2

description:
Library name: H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO2
H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO.bw


title: Col-0 whole seedling, 8h ethylene treated, rep3

description:
Library name: 210816_Ath_SC_Ath_3do_col_8ethylene_3_1_10xRNA
10x Genomics

value: 8h ethylene


title: SJWLM071784_X1_DYE1774_T0

description:
Library name: SJWLM071784_X1
2671581


title: K-562–Cas9, sgPTBP1+sgPTBP2, rep2

description:
Library name: K562_PTBP1_PTBP2_DKO_rep2
countsMOLM13.csv


title: Col-0 whole seedling, 72h ethylene treated, rep5

description:
Library name: 210816_Ath_SC_Ath_3do_col_72ethylene_5_1_10xRNA
10x Genomics

value: 72h ethylene


title: SJEWS049193_X2_DYE1773_VT

description:
Library name: SJEWS049193_C6
2671580

value: VT

value: EWS


title: H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO_rep1

description:
Library name: H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO1
H3K27ac-CUTandTag_CD8_24h_H2AZ-cKO.bw


title: Col-0 whole seedling, 72h ethylene treated, rep4

description:
Library name: 210816_Ath_SC_Ath_3do_col_72ethylene_4_1_10xRNA
10x Genomics

value: Whole seedling


title: SJEWS049193_X2_DYE1772_2D

description:
Library name: SJEWS049193_C4
2671579


title: K-562–Cas9, sgPTBP2, rep3

description:
Library name: K562_PTBP2_KO_rep3
countsMOLM13.csv


title: K-562–Cas9, sgPTBP1+sgPTBP2, rep1

description:
Library name: K562_PTBP1_PTBP2_DKO_rep1
countsMOLM13.csv


title: H3K27ac-CUTandTag_CD8_0h_WT_rep2

description:
Library name: H3K27ac-CUTandTag_CD8_0h_WT2
H3K27ac-CUTandTag_CD8_0h_WT.bw

value: WT

value: unstimulated


title: Col-0 whole seedling, 8h ethylene treated, rep1

description:
Library name: 210702_Ath_SC_Ath_3do_col_8ethylene_1_1_10xRNA
10x Genomics


title: SJEWS049193_X2_DYE1771_3D

description:
Library name: SJEWS049193_C2
2671578


title: K-562–Cas9, sgPTBP2, rep2

description:
Library name: K562_PTBP2_KO_rep2
countsMOLM13.csv


title: Col-0 whole seedling, 4h ethylene treated, rep1

description:
Library name: 210702_Ath_SC_Ath_3do_col_4ethylene_1_1_10xRNA
10x Genomics

value: 4h ethylene


title: H3K27ac-CUTandTag_CD8_0h_WT_rep1

description:
Library name: H3K27ac-CUTandTag_CD8_0h_WT1
H3K27ac-CUTandTag_CD8_0h_WT.bw


title: H3K27ac-CUTandTag_CD8_0h_N-IgG-Ctr

description:
Library name: H3K27ac-CUTandTag_CD8_0h_N-IgG
H3K27ac-CUTandTag_CD8_0h_N-IgG-Ctr.bw


title: SJEWS049193_X2_DYE1770_T0

description:
Library name: SJEWS049193_X2
2671577


title: K-562–Cas9, sgPTBP2, rep1

description:
Library name: K562_PTBP2_KO_rep1
countsMOLM13.csv


title: Col-0 whole seedling, 2h ethylene treated, rep1

description:
Library name: 210702_Ath_SC_Ath_3do_col_2ethylene_1_1_10xRNA
10x Genomics


title: H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO_rep2

description:
Library name: H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO2
H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO.bw


title: SJEWS071785_X2_DYE1769_VT

description:
Library name: SJEWS071785_C5
2671576


title: H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO_rep1

description:
Library name: H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO1
H3K27ac-CUTandTag_CD8_0h_H2AZ-cKO.bw


title: SJEWS030393_X1_DYE1768_VT

description:
Library name: SJEWS030393_C5
2671575


title: Col-0 whole seedling, 72h ethylene treated, rep3

description:
Library name: 210520_Ath_SC_Ath_3do_col_72ethylene_3_1_10xRNA
10x Genomics


title: K-562–Cas9, sgPTBP1, rep2

description:
Library name: K562_PTBP1_KO_rep2
countsMOLM13.csv


title: K-562–Cas9, sgPTBP1, rep3

description:
Library name: K562_PTBP1_KO_rep3
countsMOLM13.csv


title: ATAC_CD8T_6h_WT_rep3

description:
Library name: ATAC_CD8T_6h_WT3
ATAC_CD8T_6h_WT.bw


title: Col-0 whole seedling, 72h ethylene treated, rep2

description:
Library name: 210520_Ath_SC_Ath_3do_col_72ethylene_2_1_10xRNA
10x Genomics


title: SJEWS063834_X1_DYE1767_VT

description:
Library name: SJEWS063834_C4
2671574


title: K-562–Cas9, sgPTBP1, rep1

description:
Library name: K562_PTBP1_KO_rep1
countsMOLM13.csv


title: Col-0 whole seedling, 72h ethylene treated, rep1

description:
Library name: 210520_Ath_SC_Ath_3do_col_72ethylene_1_1_10xRNA
10x Genomics


title: ATAC_CD8T_6h_WT_rep2

description:
Library name: ATAC_CD8T_6h_WT2
ATAC_CD8T_6h_WT.bw


title: ATAC_A2780 TxCpR Rep2

first: Wonyoung

last: Choi

address: 3 N Dunlap St

department: Pathology

institute: UTHSC

description:
Library name: A2780 TxCpR Rep2
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_TxCpR_2

data_processing:
The paired-end reads were aligned to the reference genome with Bowtie2 under the --very-sensitive setting (bowtie2 --very-sensitive -x hg38_genome_index -X 2000 -1 sample_1.fastq -2 sample_2.fastq). Duplicate reads were subsequently removed using Picard MarkDuplicates (v1.141) to minimize technical artifacts. Chromatin accessibility peaks for all samples were identified with MACS2 peak calling (macs2 callpeak --verbose 3 --treatment sample.bam -g hs -B -q 0.05 --extsize 200 --nomodel --shift -100 --nolambda --keep-dup all -f BAMPE --outdir dir --call-summits). To make the universal peakset for all samples, we followed the method from previous TCGA ATAC-seq paper17. An iterative removal strategy was applied first within each sample, retaining the most significant peak and discarding directly overlapping peaks until a fixed-width, non-redundant set was obtained. The same procedure was then applied across samples to remove redundancies and generate a unified peak set. To correct for differences in sequencing depth and quality, MACS2 peak scores (-log10 p-value) were normalized to “score per million,” calculated as the peak score divided by the total score sum for the sample and scaled to one million. This normalization enabled direct comparison across samples and facilitated construction of a final merged peak set.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts of ATAC-seq peaks for each sample

extract_protocol:
ATAC-seq library preparation and sequencing reactions were conducted at Azenta Life Sciences (South Plainfield, NJ, USA).
Cells were quantified and assessed for viability using a Countess Automated Cell Counter (ThermoFisher Scientific, Waltham, MA, USA). Cells were aliquoted for continued ATAC-Seq. After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 minutes at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples. Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to a SPRI Bead cleanup to yield purified DNA libraries.

value: Ovarian cancer cells

value: Cisplatin/Paclitaxel


title: K-562–Cas9, sgRosa26, rep3

description:
Library name: K562_control_rep3
countsMOLM13.csv


title: Col-0 whole seedling, 24h control, rep4, lane4

description:
Library name: 210421_Ath_SC_Ath_3do_Col_24control_4_4_10xRNA
10x Genomics

value: 24h control


title: ATAC_CD8T_6h_WT_rep1

description:
Library name: ATAC_CD8T_6h_WT1
ATAC_CD8T_6h_WT.bw

value: spleen

value: naive CD8+ T cell


title: ATAC_A2780 TxCpR Rep1

description:
Library name: A2780 TxCpR Rep1
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_TxCpR_1


title: K-562–Cas9, sgRosa26, rep2

description:
Library name: K562_control_rep2
countsMOLM13.csv


title: ATAC_A2780 TxR Rep2

description:
Library name: A2780 TxR Rep2
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_TxR_2

value: Paclitaxel


title: ATAC_CD8T_6h_H2AZ-cKO_rep3

description:
Library name: ATAC_CD8T_6h_cKO3
ATAC_CD8T_6h_cKO.bw


title: K-562–Cas9, sgRosa26, rep1

description:
Library name: K562_control_rep1
countsMOLM13.csv


title: Col-0 whole seedling, 24h control, rep4, lane2

description:
Library name: 210421_Ath_SC_Ath_3do_Col_24control_4_2_10xRNA
10x Genomics


title: ATAC_CD8T_6h_H2AZ-cKO_rep2

description:
Library name: ATAC_CD8T_6h_cKO2
ATAC_CD8T_6h_cKO.bw


title: ATAC_A2780 TxR Rep1

description:
Library name: A2780 TxR Rep1
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_TxR_1


title: MOLM-13–Cas9, sgPTBP1+sgPTBP2, rep3

description:
Library name: MOLM13_PTBP1_PTBP2 DKO rep3
countsMOLM13.csv

value: acute myeloid leukemia


title: Col-0 whole seedling, 24h control, rep4, lane1

description:
Library name: 210421_Ath_SC_Ath_3do_Col_24control_4_1_10xRNA
10x Genomics


title: ATAC_CD8T_6h_H2AZ-cKO_rep1

description:
Library name: ATAC_CD8T_6h_cKO1
ATAC_CD8T_6h_cKO.bw


title: ATAC_A2780 CpR Rep2

description:
Library name: A2780 CpR Rep2
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_CpR_2

value: Cisplatin


title: MOLM-13–Cas9, sgPTBP1+sgPTBP2, rep2

description:
Library name: MOLM13_PTBP1_PTBP2 DKO rep2
countsMOLM13.csv

value: blood


title: ein2-5 seedling, 24h ethylene treated, rep5

description:
Library name: 210304_Ath_3do_ein2_24ethylene_5_1_10xRNA
10x Genomics

value: 24h ethylene


title: ATAC_CD8T_0h_WT_rep3

description:
Library name: ATAC_CD8T_0h_WT3
ATAC_CD8T_0h_WT.bw


title: ATAC_A2780 CpR Rep1

description:
Library name: A2780 CpR Rep1
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_CpR_1


title: MOLM-13–Cas9, sgPTBP1+sgPTBP2, rep1

description:
Library name: MOLM13_PTBP1_PTBP2 DKO rep1
countsMOLM13.csv


title: ATAC_CD8T_0h_WT_rep2

description:
Library name: ATAC_CD8T_0h_WT2
ATAC_CD8T_0h_WT.bw


title: ATAC_A2780 Control Rep2

description:
Library name: A2780 Control Rep2
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_Wt_2


title: ein2-5 seedling, 24h control, rep5

description:
Library name: 210304_Ath_3do_ein2_24control_5_1_10xRNA
10x Genomics


title: ATAC_A2780 Control Rep1

description:
Library name: A2780 Control Rep1
Column name in A2780_all_cpm_count_matrix.txt: A2780_ATAC_Wt_1


title: MOLM-13–Cas9, sgPTBP2, rep2

description:
Library name: MOLM13_PTBP2_KO_rep2
countsMOLM13.csv


title: ein2-5 seedling, 24h control, rep4

description:
Library name: 210304_Ath_3do_ein2_24control_4_1_10xRNA_reseq
10x Genomics


title: A2780 TxCpR Rep2

description:
Library name: A2780 TxCpR Rep2
Column name in A2780.txt: A2780_TxCpR_2

data_processing:
Paired-end RNA-seq reads were aligned to the human reference genome (hg38) using STAR (v2). Alignment parameters included: maximum of 20 multimapping reads (--outFilterMultimapNmax 20), minimum overhang for splice junctions of 8 bp (--alignSJoverhangMin 8), mismatch threshold set to 10% of read length (--outFilterMismatchNoverLmax 0.1), intron size limits of 20 bp to 1 Mb (--alignIntronMin 20, --alignIntronMax 1000000), and maximum mate gap of 1 Mb (--alignMatesGapMax 1000000). Additional filters were applied using --outFilterType BySJout, with minimum score and match thresholds scaled by read length (--outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33). Output files included unsorted BAM alignments (--outSAMtype BAM Unsorted), unmapped reads retained within the BAM (--outSAMunmapped Within), and gene-level read counts (--quantMode GeneCounts). Chimeric alignments were also enabled with minimum segment length 15 bp (--chimSegmentMin 15), minimum junction overhang 15 bp (--chimJunctionOverhangMin 15), and multiple output formats (--chimOutType Junctions SeparateSAMold WithinBAM SoftClip). Junctions were reported in format type 1 (--chimOutJunctionFormat 1) and limited to one main chimeric segment per read (--chimMainSegmentMultNmax 1). Alignment outputs included intron motif annotations (--outSAMstrandField intronMotif) and standard SAM attributes (NH, HI, AS, nM, NM, ch).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was isolated from A2780 cells using TRIzol reagent (Invitrogen) according to manufacturer’s recommendations.
The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations.


title: MOLM-13–Cas9, sgPTBP1, rep3

description:
Library name: MOLM13_PTBP1_KO_rep3
countsMOLM13.csv


title: Col-0 apical seedling tissue, 24h control, rep1

description:
Library name: 191015_Ath_SC_Ath_3do_hook_24control_1_1_10xRNA
10x Genomics

source_name: Apical seedling

value: Apical seedling


title: ATAC_CD8T_0h_H2AZ-cKO_rep2

description:
Library name: ATAC_CD8T_0h_cKO2
ATAC_CD8T_0h_cKO.bw


title: ATAC_CD8T_0h_H2AZ-cKO_rep1

description:
Library name: ATAC_CD8T_0h_cKO1
ATAC_CD8T_0h_cKO.bw


title: A2780 TxR Rep2

description:
Library name: A2780 TxR Rep2
Column name in A2780.txt: A2780_TxR_2


title: MOLM-13–Cas9, sgPTBP1, rep2

description:
Library name: MOLM13_PTBP1_KO_rep2
countsMOLM13.csv


title: Jurkat-H3K27ac-CUTandTag_WTvsH2AZKO_WT2

description: Library name: WTvsH2AZKO_Jurkat-H3K27ac-CUTandTag-WT2

extract_protocol:
Naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of  WT and H2AZ-cKO or WT and GABPa-cKO mice. Then the sorted naïve T cells were stimulated with anti-CD3 and anti-CD28 antibodies (Abs) for 24 h. Naive and activated T cells were collected for CUT&Tag assay. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z, GABPa and H3K27ac antibody in T cells. Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904). Moreover, CUT&Tag assay was performed in WT Jurkat cells and H2A.Z KO or GABPa KO Jurkat cells.
CUT&Tag libraries was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904), following the manufacturer’s instructions.

value: Jurkat

value: human T lymphocyte


title: Sunitinib3

city: beijing

first: zhouchen

last: zhang

address: Zhongguancun South Avenue No. 22

institute: Peking University School and Hospital of Stomatology

description:
Library name: sample6
fpkm_Sunitinib3

data_processing:
Raw reads were subjected to quality assessment and adapter trimming.
Clean reads were aligned to the zebrafish reference genome (GRCz11).
Gene expression was quantified and normalized.
Assembly: GRCz11 (Danio rerio)
Supplementary files format and content: tab-delimited text file containing normalized gene expression counts

organism: Danio rerio

source_name: tail fin

growth_protocol: Zebrafish (Danio rerio) AB strain and Tg(MPEG-GFP) transgenic line were maintained at 28.5°C under a 14-hour light/10-hour dark cycle. Embryos were obtained by natural spawning and cultured in E3 embryo medium until 2 days post-fertilization (dpf).

extract_protocol:
Total RNA was extracted from tail fin tissue samples using TRIzol reagent (15596026CN, Invitrogen, USA). Each biological replicate consisted of pooled tail fin tissue from >60 larvae. RNA quality was assessed before library construction.
Eukaryotic strand-specific RNA sequencing libraries were constructed. Briefly, mRNA was enriched from total RNA, fragmented, and reverse-transcribed into cDNA. After end repair, adapter ligation, and PCR amplification, paired-end 150 bp sequencing was performed on the Illumina NovaSeq 6000 platform.

treatment_protocol: Zebrafish larvae at 2 dpf were immersed in E3 embryo medium containing 8 μM sunitinib (S7781, Selleck, USA) or 0.1% DMSO (vehicle control) until 3 dpf. Following tail fin amputation at 3 dpf, larvae were maintained in respective treatment solutions until tissue collection at 6 hours post-amputation (hpa).

value: tail fin


title: A2780 TxR Rep1

description:
Library name: A2780 TxR Rep1
Column name in A2780.txt: A2780_TxR_1

value: WT


title: MOLM-13–Cas9, sgPTBP1, rep1

description:
Library name: MOLM13_PTBP1_KO_rep1
countsMOLM13.csv


title: Sunitinib2

description:
Library name: sample5
fpkm_Sunitinib2


title: MOLM-13–Cas9, sgRosa26, rep3

description:
Library name: MOLM13_control_rep3
countsMOLM13.csv


title: A2780 CpR Rep2

description:
Library name: A2780 CpR Rep2
Column name in A2780.txt: A2780_CpR_2


title: Jurkat-H3K27ac-CUTandTag_WTvsH2AZKO_KO2

description: Library name: WTvsH2AZKO_Jurkat-H3K27ac-CUTandTag-KO2


title: Sunitinib1

description:
Library name: sample4
fpkm_Sunitinib1


title: MOLM-13–Cas9, sgRosa26, rep2

description:
Library name: MOLM13_control_rep2
countsMOLM13.csv


title: DMSO3

description:
Library name: sample3
fpkm_DMSO3


title: A2780 CpR Rep1

description:
Library name: A2780 CpR Rep1
Column name in A2780.txt: A2780_CpR_1


title: Jurkat-H3K27ac-CUTandTag_WTvsH2AZKO_KO1

description: Library name: WTvsH2AZKO_Jurkat-H3K27ac-CUTandTag-KO1


title: MOLM-13–Cas9, sgRosa26, rep1

description:
Library name: MOLM13_control_rep1
countsMOLM13.csv


title: DMSO2

description:
Library name: sample2
fpkm_DMSO2


title: Jurkat-H2AZ-CUTandTag_WTvsH2AZKO_WT2

description: Library name: WTvsH2AZKO_Jurkat-H2AZ-CUTandTag-WT2


title: Enriched sample, rep3

city: Xiamen

first: chao

middle: jie

last: hao

state: Fujian

address: No. 422, Siming South Road

institute: Xiamen University

description: Library name: Sample 6

data_processing:
Reference genome index was built by Bowtie2(v2.5.1) and the de-duplicated Clean Reads were mapping to the reference genome using the miRDeep2(v2.0.0.8) software.
Unique Reads is annotated with known miRNAs first in the miRBase database (http://www.mirbase.org/) and then annotated with other non-coding RNAs. Sequences that are not annotated with any information use mireap(v0.2) for new miRNA prediction analysis. Organize the existing annotation results according to the known miRNA >piRNA> rRNA > tRNA > snRNA > snoRNA > novel miRNA priority to ensure that each small RNA has a unique annotation.
Assembly: human (GRCh38.p14)
Supplementary files format and content: gene expression matix in text file

source_name: breast

extract_protocol:
RNA was harvested using TRIzol (Labled).
RNA libraries for RNA-seg were prepared using VAHTS Small RNA Library Prep Kit for Illumina V2 following manufacturer's protocols.

value: breast

value: breast cancer cell

tag: sample group


title: DMSO1

description:
Library name: sample1
fpkm_DMSO1


title: Jurkat-H2AZ-CUTandTag_WTvsH2AZKO_WT1

description: Library name: WTvsH2AZKO_Jurkat-H2AZ-CUTandTag-WT1


title: MV4-11–Cas9,sgPTBP1_3

description:
Library name: MV411_PTBP1_KO_guide3
countsMV411.csv

value: chronic myeloid leukemia


title: ATAC_CD8T_0h_WT_rep1

description:
Library name: ATAC_CD8T_0h_WT1
ATAC_CD8T_0h_WT.bw

value: unstimulated


title: MOLM-13–Cas9, sgPTBP2, rep3

description:
Library name: MOLM13_PTBP2_KO_rep3
countsMOLM13.csv


title: ein2-5 seedling, 24h ethylene treated, rep4

description:
Library name: 210304_Ath_3do_ein2_24ethylene_4_1_10xRNA
10x Genomics

value: Whole seedling


title: Enriched sample, rep2

description: Library name: Sample 5


title: ci_wt_skm_4

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

description: Library name: 4

data_processing:
fastp v0.23.4, STAR v2.7.11a, RSEM v1.3.3
Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 (qualified_quality_phred=20, nqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30)
passing filter reads were mapped to the genome reference (Danio rerio GRCz11v113, Ensembl v113 ) using STAR v2.7.11a with standard parameters, except for the sjdbOverhang option set on read length
Genome and transcripts annotation provided as input were downloaded from Ensembl v113 repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix applying a dedicated RSEM command (rsem-generate-data-matrix).
Assembly: Danio rerio GRCz11v113, Ensembl v113
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: skeletal muscle

growth_protocol: Wild-type (wt) fish (AB) were maintained under standard conditions, in a circulating water system, under 14 h light/10 h dark cycle, at 28 ◦C.

extract_protocol:
Part of caudal peduncle around the cryoinjury (1-2 mm on both sides) was dissected out 7 days post-cryoinjury, and skin and bones were removed. The tissue was homogenized in TRIzol Reagent (Invitrogen, Thermo Fisher Scientific). Total RNA was extracted using RNA Clean and Concentrator Kit (ZYMO Research), following the manufacturer instructions.
cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, California, USA)

treatment_protocol: Cryoinjury of skeletal muscle of wt AB zebrafish was performed in the region of the caudal peduncle with the metal cryoprobe cooled in liquid nitrogen. After 7 days of recovery, zebrafish were euthanized.

value: skeletal muscle

value: wt

value: cryoinjury


title: Jurkat-H2AZ-CUTandTag_WTvsH2AZKO_KO2

description: Library name: WTvsH2AZKO_Jurkat-H2AZ-CUTandTag-KO2

value: spleen


title: MOLM-13–Cas9, sgPTBP2, rep1

description:
Library name: MOLM13_PTBP2_KO_rep1
countsMOLM13.csv

value: acute myeloid leukemia


title: ATAC_CD8T_0h_H2AZ-cKO_rep3

description:
Library name: ATAC_CD8T_0h_cKO3
ATAC_CD8T_0h_cKO.bw

value: naive CD8+ T cell


title: Enriched sample, rep1

description: Library name: Sample 4


title: MV4-11–Cas9,sgPTBP1_1

description:
Library name: MV411_PTBP1_KO_guide1
countsMV411.csv

value: blood


title: A2780 TxCpR Rep1

description:
Library name: A2780 TxCpR Rep1
Column name in A2780.txt: A2780_TxCpR_1

value: Ovarian cancer cells

value: Cisplatin/Paclitaxel


title: Jurkat-H2AZ-CUTandTag_WTvsH2AZKO_KO1

description: Library name: WTvsH2AZKO_Jurkat-H2AZ-CUTandTag-KO1

value: Jurkat

value: human T lymphocyte


title: ci_wt_skm_3

description: Library name: 3


title: Input sample, rep3

description: Library name: Sample 3

value: WT

value: input


title: MV4-11–Cas9,sgEMX1

description:
Library name: MV411_control2_EMX1
countsMV411.csv


title: ci_wt_skm_2

description: Library name: 2


title: Jurkat-GABPa-CUTandTag_WTvsH2AZKO_WT2

description: Library name: WTvsH2AZKO_Jurkat-GABPa-CUTandTag-WT2


title: Input sample, rep2

description: Library name: Sample 2

value: breast

value: breast cancer cell


title: ci_wt_skm_1

description: Library name: 1


title: MV4-11–Cas9,sgRosa26

description:
Library name: MV411_control1_Rosa26
countsMV411.csv

value: chronic myeloid leukemia


title: Jurkat-GABPa-CUTandTag_WTvsH2AZKO_WT1

description: Library name: WTvsH2AZKO_Jurkat-GABPa-CUTandTag-WT1


title: SiHa,TMEM30A KO,unsorted,14h

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

description:
Library name: SiHa_TMEM30A_KO_unsorted_14h
Whole genome library infected TMEM30A KO SiHA cells unsorted control

data_processing:
In-house customized pipeline for mapping and counting for sgRNAs
Assembly: GrCh38
Supplementary files format and content: Tab-delimited text files include guide count and clone count values for each sample
Supplementary files format and content: gene_symbol: gene_name
Supplementary files format and content: guide: gRNA
Supplementary files format and content: sample_counts: number of counts for a specific guide and barcode
Library strategy: CRISPR Screen

source_name: SiHa

growth_protocol: HCT116 and SiHa cells were grown in RPMI-1640 supplemented with 10% FBS. MC38 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For in vitro CRISPR screen, gDNAs were extracted from collected HCT116 or SiHA cell pellets using HSM 2.0 (promega) with The ReliaPrep™ Large Volume HT gDNA Isolation System. For in vivo samples, tumors were harvested when mean tumor volume for a single group reached 1,000 mm3 for gDNA isolation and subsequent analysis by next-generation sequencing (NGS).
sgRNA sequences were PCR amplified with primers forward: F: 5′AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNCTTGTGGAAAGGACGAAACACCG-3′ (where N sequence are stagger squence range from 6nt to 13nt to create diversity), reverse: R: 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′ (where N sequence are 8nt index for demultiplexing) and purified with Kapa Pure Beads (Roche, KK8802)

treatment_protocol: For in vitro CRISPR screen, HCT116 (RRID:CVCL_0291) and SiHa (RRID:CVCL_0032) cells with stable Cas9 expression were infected with lentivirus encoding sgRNA against TMEM30A and selected by hygromycin. Cells were then infected with a genome-wide CRISPR KO library and sorted for Annexin V-high and Annexin V-low  populations to represent PS high and PS low population. For in vivo CRISPR screening, we constructed an immune evasion context discovery library consisting of 20 essential genes as controls for KO efficiency, 18 IO control genes, and 471 tumor suppressor genes and genes associated with immune evasion. MC38 cells were first infected with lentivirus encoding enCas12a and a blasticidin resistance gene (BSD) flanked by LoxP sites. Stable cells were then infected with a CRISPR KO library encoding a puromycin resistance gene and RFP flanked by Lox2272 sites and two gRNA sequences outside the floxed region. Cells were then infected with an insertion-deficient lentivirus encoding Cre recombinase and EGFP (IDV-Cre) and cultured for an additional two weeks before injected subcutaneously into the right flank of C57BL/6 (RRID:MGI:2159769) (n = 50) or BALB/c-nude (RRID:IMSR_RJ:BALB-C-NUDE) BALB/c-nude (n = 15) mice (1.0 x 106 cells per mouse). A sub-population of cells was also maintained in culture for collecting gDNA on the day of inoculation and on the day tumors were harvested. C57BL/6 (RRID:MGI:2159769) C57BL/6 mice were randomized for anti-PD-1 (n = 30) or IgG2a (n = 20) treatment when mean tumor volume reached 50 mm3, as described above. Tumors were harvested when mean tumor volume for a single group reached 1,000 mm3 for gDNA isolation and subsequent analysis by next-generation sequencing (NGS).

value: SiHa

value: cervical squamous cell carcinoma cell line

value: TMEM30A KO,unsorted,14h


title: PDM250, 3

city: Guangzhou

first: liang

middle: liang

last: Bai

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital Sun Yat-Sen University

description: Library name: B_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Fastp (https://github.com/OpenGene/fastp,version: 0.23.0). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version: 2-2.1.0) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Life Invitrogen Qubit® 3.0 and NanoDrop™ One/OneC, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 200±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an DNBSEQ-T7 following the vendor's recommended protocol.

value: skin


title: SiHa,TMEM30A KO,PS,low,Sony,14h

description:
Library name: SiHa_TMEM30A_KO_PS_low_Sony_14h
Whole genome library infected TMEM30A KO SiHa cells sorted for PS low population using Sony sorter

value: TMEM30A KO,PS,low,Sony,14h


title: Jurkat-GABPa-CUTandTag_WTvsH2AZKO_KO2

description: Library name: WTvsH2AZKO_Jurkat-GABPa-CUTandTag-KO2

value: spleen


title: Input sample, rep1

description: Library name: Sample 1


title: 3D CULTURE 3

city: London

first: Stephen

last: Renaud

state: ON

address: 1151 Richmond Street

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

description:
Library name: Sample 6
3D_3

data_processing:
Partek Flow was used for all analyses.
Sequenced reads were trimmed for adaptor sequences, masked for low-quality sequences,  then mapped to hg38 genome using STAR (2.7.8a).
Counts Per Million (CPM) + 1.0 were calculated using Partek Flow.
Assembly: hg38 (release 110, ENSEMBL)
Supplementary files format and content: Matrix table with raw or nomalized gene counts for every gene and every sample.

source_name: Placenta

growth_protocol: Human trophoblast stem cells were cultured in trophoblast stem (cytotrophoblast) media.

extract_protocol:
RiboZol was used to extract RNA from cells. The aqueous layer was removed, diluted in 70% ethanol, placed on RNeasy columns, treated with DNase I, and RNA purified.
RNA libraries were prepared according to manufacturer's instructions using the NEBNEXT® Ultra™ Library Kit for Illumina®

treatment_protocol: Trophoblast stem cells were aggregated in microwells to form 3D cultures or plated in collagen-coated wells as 2D cultures.

value: Placenta

value: Human trophoblast stem cells

value: Placenta-derived trophoblasts

value: Wildtype

value: Spheroid


title: PDM250, 2

description: Library name: B_2


title: Jurkat-H3K27ac-CUTandTag_WTvsH2AZKO_WT1

description: Library name: WTvsH2AZKO_Jurkat-H3K27ac-CUTandTag-WT1

value: Jurkat

value: human T lymphocyte


title: Jurkat-GABPa-CUTandTag_WTvsH2AZKO_KO1

description: Library name: WTvsH2AZKO_Jurkat-GABPa-CUTandTag-KO1


title: SiHa,TMEM30A KO,PS,low,BD,14h

description:
Library name: SiHa_TMEM30A_KO_PS_low_BD_14h
Whole genome library infected TMEM30A KO SiHa cells sorted for PS low population using BD Aria sorter

value: TMEM30A KO,PS,low,BD,14h


title: 3D CULTURE 2

description:
Library name: Sample 5
3D_2


title: PDM250, 1

description: Library name: B_1


title: SiHa,TMEM30A KO,PS,high,Sony,14h

description:
Library name: SiHa_TMEM30A_KO_PS_high_Sony_14h
Whole genome library infected TMEM30A KO SiHa cells sorted for PS high population using Sony sorter

value: TMEM30A KO,PS,high,Sony,14h


title: Jurkat-H3K27ac-CUTandTag_WTvsGABPaKO_WT-rep2

description: Library name: WTvsGABPaKO_Jurkat_H3K27ac-CUTandTag_WT-2


title: 3D CULTURE 1

description:
Library name: Sample 4
3D_1


title: DMSO, 3

description: Library name: A_3

value: DMSO


title: Jurkat-H3K27ac-CUTandTag_WTvsGABPaKO_WT-rep1

description: Library name: WTvsGABPaKO_Jurkat_H3K27ac-CUTandTag_WT-1


title: A2780 Control Rep2

description:
Library name: A2780 Control Rep2
Column name in A2780.txt: A2780_Wt_2

value: Ovarian cancer cells

value: WT


title: SiHa,TMEM30A KO,PS,high,BD,14h

description:
Library name: SiHa_TMEM30A_KO_PS_high_BD_14h
Whole genome library infected TMEM30A KO SiHa cells sorted for PS high population using BD Aria sorter

value: SiHa

value: cervical squamous cell carcinoma cell line

value: TMEM30A KO,PS,high,BD,14h


title: 2D CULTURE 3

description:
Library name: Sample 3
2D_3

value: Monolayer


title: DMSO, 2

description: Library name: A_2

value: skin


title: HCT116,TMEM30A KO,unsorted,14h

description:
Library name: HCT116_TMEM30A_KO_unsorted_14h
Whole genome library infected TMEM30A KO HCT116 cells unsorted control

value: colorectal carcinoma cell line

value: TMEM30A KO,unsorted,14h


title: Jurkat-H3K27ac-CUTandTag_WTvsGABPaKO_KO-rep2

description: Library name: WTvsGABPaKO_Jurkat_H3K27ac-CUTandTag_KO-2

value: spleen


title: DMSO, 1

description: Library name: A_1


title: 2D CULTURE 2

description:
Library name: Sample 2
2D_2

value: Placenta

value: Human trophoblast stem cells

value: Placenta-derived trophoblasts

value: Wildtype


title: A2780 Control Rep1

description:
Library name: A2780 Control Rep1
Column name in A2780.txt: A2780_Wt_1


title: HCT116,TMEM30A KO,PS,low,14h

description:
Library name: HCT116_TMEM30A_KO_PS_low_14h
Whole genome library infected TMEM30A KO HCT116 cells sorted for PS low population

value: TMEM30A KO,PS,low,14h


title: ORv01, D10resection

city: Minneapolis

first: Grace

last: Walker

state: Minnesota

address: 425 East River Parkway

department: Masonic Cancer Center

institute: University of Minnesota

description:
Library name: V14F05-297_D1
fresh-frozen Visium v1 spatial transcriptomics sequencing

data_processing:
10x Genomics Visium v1 library FASTQs were aligned with Spaceranger v4.0.1 using the CanFam4 genome modified with the Y chromosome (ROS_Cfam_1.0 and NC_051844.1) and the mitochondrial genome taken from CanFam3.1. Spaceranger output files were processed downstream in Python (v3.12.12) and R (v4.4.3).
Assembly: canFam4 genome + Y chromosome from ROS_Cfam_1.0 (NC_051844.1) + MT chromosome from canFam3.1
Supplementary files format and content: Archived and compressed (.tar.gz) spaceranger folder containing spatial files and decomposed counts matrix files
Library strategy: Spatial Transcriptomics

organism: Canis lupus familiaris

source_name: Marginal zone lymphoma

growth_protocol: On day 10 of the study, a fully resected popliteal lymph node was cut into a 1 cm² piece and snap-frozen in dry-ice-cooled isopentane before transfer to -80°C storage. The sample was subsequently embedded in OCT compound and cryosectioned at 10 µm for direct placement onto Visium capture slides.

extract_protocol:
A 1cm2  section of freshly excised popliteal nodal tissue was flash-frozen in dry-ice-cooled isopentane and OCT embedded, cut into 10-µm sections, and mounted on Visium capture slides.
Spatial Transcriptomics sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression Reagent Kit v1 (poly(A)-based capture for fresh-frozen tissue) according to the manufacturer's protocol. Eluted cDNA was amplified, fragmented, end-repaired, and A-tailed before ligating Dual Index adapters to construct final Illumina-compatible libraries

treatment_protocol: On the first day of the trial (day 0, 10 days prior to spatial tissue extraction), the study dog received a single intravenous dose of 2 × 109 TCID50 / kg VSV.

value: Marginal zone lymphoma

tag: disease state

value: Tumor

tag: breed

value: Goldendoodle

tag: Sex

value: Male

tag: neuter status

value: Neutered

tag: age (yr)

value: VSV


title: Jurkat-H3K27ac-CUTandTag_WTvsGABPaKO_KO-rep1

description: Library name: WTvsGABPaKO_Jurkat_H3K27ac-CUTandTag_KO-1

value: Jurkat

value: human T lymphocyte


title: 2D CULTURE 1

description:
Library name: Sample 1
2D_1

value: Monolayer


title: HCT116,TMEM30A KO,PS,high,14h

description:
Library name: HCT116_TMEM30A_KO_PS_high_14h
Whole genome library infected TMEM30A KO HCT116 cells sorted for PS high population

value: colorectal carcinoma cell line

value: TMEM30A KO,PS,high,14h


title: Jurkat-H2AZ-CUTandTag_WTvsGABPaKO_WT-rep2

description: Library name: WTvsGABPaKO_Jurkat_H2AZ-CUTandTag_WT-2

value: spleen


title: skn-1b mutant male C. elegans, Day 1 adult biol rep 4

city: Canterbury

first: Jennifer

middle: M. A.

last: Tullet

state: Kent

address: Giles Lane

department: School of Natural Science

country: United Kingdom

institute: University of Kent

description: Library name: JT4BMX

data_processing:
Adapter trimming and filtering of low-quality reads were performed with Trimmomatic 0.40
Trimmed reads were mapped to the C. elegans genome using HISAT2 v. 2.2.1 with default settings
Read counts were quantified using featureCounts v. 2.0.1 with default settings
Assembly: WBCel235
Supplementary files format and content: Table (.csv) of read counts mapped to WBCel235

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
Approximately 2500 animals were pelleted with TRIzol, flash frozen in liquid nitrogen, and subject to 20-25 freeze-thaw cycles to break open the cuticle. Supernatants were transferred and RNA was extracted using a Direct-zol RNA Microprep Kit (Zymo Research) in accordance with the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Whole animal

value: skn-1b mutant


title: skn-1b mutant male C. elegans, Day 1 adult biol rep 3

description: Library name: JT3BMX


title: Jurkat-H2AZ-CUTandTag_WTvsGABPaKO_WT-rep1

description: Library name: WTvsGABPaKO_Jurkat_H2AZ-CUTandTag_WT-1


title: Sublingual Gland, donor J

city: Bethesda

first: Blake

middle: M

last: Warner

state: MD

address: 10 Center Drive, Room 1A01

institute: NIDCR

description: Library name: X31SLG

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to a custom GRCh38.v32 human genome that was modified to include ERCCs and SIRVs, using STAR v2.7.3a in single-pass mode with the --quantMode GeneCounts parameter.
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a GRCh38.v32 genome annotation GTF which included ERCCs and SIRVs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCh38.v32
Supplementary files format and content: RawCountFile.txt, raw gene counts in tab-delimited txt format.
Supplementary files format and content: RawCountFile_filtered.txt, filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: CPM_TMM_counts.txt, TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: SLG

extract_protocol:
RNA was extracted using Rneasy Plus Minikit
Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a NextSeq 2000 sequencer (Illumina) using 55x55bp paired-end  mode.

value: SLG

tag: condition

value: normal


title: day-8 + IAV bio rep 4

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

description: Library name: Flu_4

data_processing:
Sequence counts were trimmed, filtered and mapped with ProkSeq 2.0
featureCounts 1.4.5 was used to extract read counts per gene
Assembly: GCF_000006885.1
Supplementary files format and content: raw_counts.csv is a CSV file with raw read counts per gene

organism: Streptococcus pneumoniae

source_name: bacteria

growth_protocol: TIGR4 was grown in broth under static conditions at 37℃ to mid-log OD600=0.5. for In vivo samples bacteria was isolated from the upper respiratory tract at designated timepoints.

extract_protocol:
RNA was isolated using a modified phenol chloroform method.
Total RNA was used to prepare cDNA libraries using the Illumina® Stranded Total RNA Prep with Ribo‑Zero Plus Microbiome kit. Library preparation was performed according to Illumina’s recommended protocol.

value: bacteria

value: WT

value: in vivo_day 8 +IAV post infection


title: day-8 + IAV bio rep 3

description: Library name: Flu_3


title: Submandicular Gland, donor I

description: Library name: X31S9

source_name: SMG

value: SMG


title: Jurkat-H2AZ-CUTandTag_WTvsGABPaKO_KO-rep2

description: Library name: WTvsGABPaKO_Jurkat_H2AZ-CUTandTag_KO-2


title: day-8 + IAV bio rep 2

description: Library name: Flu_2


title: Jurkat-H2AZ-CUTandTag_WTvsGABPaKO_KO-rep1

description: Library name: WTvsGABPaKO_Jurkat_H2AZ-CUTandTag_KO-1


title: skn-1b mutant male C. elegans, Day 1 adult biol rep 2

description: Library name: JT2BMX

value: Male


title: Parotid Gland, donor H

description: Library name: X31S8

source_name: PG

value: PG


title: skn-1b mutant male C. elegans, Day 1 adult biol rep 1

description: Library name: JT1BMX


title: day-8 + IAV bio rep 1

description: Library name: Flu_1


title: Jurkat-GABPa-CUTandTag_WTvsGABPaKO_WT-rep2

description: Library name: WTvsGABPaKO_Jurkat_GABPa-CUTandTag_WT-2


title: Submandicular Gland, donor G

description: Library name: X31S7


title: skn-1b mutant hemaphrodite C. elegans, Day 1 adult biol rep 3

description: Library name: JT3BHX

value: Hermaphrodite


title: day-8 bio rep 4

description: Library name: PBS_4

value: in vivo_day 8 post infection


title: Jurkat-GABPa-CUTandTag_WTvsGABPaKO_WT-rep1

description: Library name: WTvsGABPaKO_Jurkat_GABPa-CUTandTag_WT-1

value: Jurkat

value: human T lymphocyte


title: Parotid Gland, donor F

description: Library name: X31S6a


title: skn-1b mutant hemaphrodite C. elegans, Day 1 adult biol rep 2

description: Library name: JT2BHX


title: day-8 bio rep 3

description: Library name: PBS_3


title: skn-1b mutant hemaphrodite C. elegans, Day 1 adult biol rep 1

description: Library name: JT1BHX


title: Jurkat-GABPa-CUTandTag_WTvsGABPaKO_KO-rep2

description: Library name: WTvsGABPaKO_Jurkat_GABPa-CUTandTag_KO-2


title: Submandicular Gland, donor E

description: Library name: X31S4


title: day-8 bio rep 2

description: Library name: PBS_2


title: Jurkat-GABPa-CUTandTag_WTvsGABPaKO_KO-rep1

description: Library name: WTvsGABPaKO_Jurkat_GABPa-CUTandTag_KO-1


title: Parotid Gland, donor D

description: Library name: X31S13


title: WT N2 male C. elegans, Day 1 adult biol rep 2

description: Library name: JT6NMMX


title: day-8 bio rep 1

description: Library name: PBS_1


title: Jurkat-WT-IgG

description: Library name: WT_Jurkat-IgG


title: WT N2 male C. elegans, Day 1 adult biol rep 1

description: Library name: JT5NMMX


title: day-1 bio rep 4

description: Library name: M5_Day5

value: in vivo_day 1 post infection


title: Submandicular Gland, donor B

description: Library name: X24S21


title: WT N2 Hermaphrodite C. elegans, Day 1 adult biol rep 2

description: Library name: JT6NMHX


title: day-1 bio rep 3

description: Library name: M4_Day5


title: Minor Salivary Gland, donor A

description: Library name: X24S10

source_name: MSG

value: MSG


title: H2AZ-CUTandTag_24h-WT2

description: Library name: H2AZ-CUTandTag_24h-WT2

source_name: spleen

value: spleen

value: naive CD8+ T cell


title: WT N2 Hermaphrodite C. elegans, Day 1 adult biol rep 1

description: Library name: JT5NMHX

value: Whole animal


title: H2AZ-CUTandTag_24h-WT1

description: Library name: H2AZ-CUTandTag_24h-WT1


title: day-1 bio rep 2

description: Library name: M2_Day5


title: Postmortem Sublingual Gland, donor 9

description: Library name: P9SG

value: SARS-CoV-2 infected


title: day-1 bio rep 1

description: Library name: M1_Day5


title: GABPa-24h_CD8T_WT_rep3

description:
Library name: GABPa-24hCD8WT3
GABPa-24hCD8WT3
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

data_processing:
Trim Galore (v0.6.7) and Trimmomatic (v0.39) was used to remove the low quality reads (parametrs- --quality 20 --stringency 3)
Bowtie2 (v2.5.1) was used to align reads to the mouse genome
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

growth_protocol: T cells were maintained in 1640 supplemented with 10% fetal bovine serum (BI), 10mM Hepes (Gibco), 1% NEAA (Gibco), 1% penicillin/streptomycin (Gibco), 50uM β-Mercaptoethanol (Gibco) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from 1 × 10⁶ naïve or activated T cells using TRIzol reagent (Invitrogen, 15596018).
RNA-seq libraries were constructed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with or without 2 µg/ml coated anti-CD3 antibody and 2 µg/ml soluble anti-CD28 antibody.

value: naive CD8 T cell


title: H2AZ-CUTandTag_24h-GABPa-KO2

description: Library name: H2AZ-CUTandTag_24h-GABPa-KO2


title: GABPa-24h_CD8T_WT_rep2

description:
Library name: GABPa-24hCD8WT2
GABPa-24hCD8WT2
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: SJRHB000026_X1_DYE8739_T0

description:
Library name: SJRHB000026_X1
2364123

source_name: Tumor

value: Tumor

value: RMS


title: SJRHB013757_X2_DYE8736_3D

description:
Library name: SJRHB013757_C2 Rep 2
2364120

source_name: Cells

value: Cells


title: SJRHB012_X_DYE8561_VT

description:
Library name: SJRHB000912_C9
2355612

value: VT


title: Postmortem Sublingual Gland, donor 8

description: Library name: P8SG


title: SJRHB013_X_DYE8562_VT

description:
Library name: SJRHB000913_C3
2355613


title: TSY, Ctrl-4

description: Library name: TSY_4

value: bacteria

value: WT


title: Postmortem Submandibular Gland, donor 7

description: Library name: P7SMG

value: SMG


title: GABPa-24h_CD8T_WT_rep1

description:
Library name: GABPa-24hCD8WT1
GABPa-24hCD8WT1
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: H2AZ-CUTandTag_24h-GABPa-KO1

description: Library name: H2AZ-CUTandTag_24h-GABPa-KO1


title: TSY, Ctrl-3

description: Library name: TSY_3


title: Pstmortem Sublingual Gland, donor 5

description: Library name: P5SG


title: H2AZ-CUTandTag_0h-WT2

description: Library name: H2AZ-CUTandTag_0h-WT2


title: Col-0 whole seedling, 24h control, rep4, lane3

description:
Library name: 210421_Ath_SC_Ath_3do_Col_24control_4_3_10xRNA
10x Genomics

data_processing:
Cell by gene matrices were generated with Cellranger v3.1.0
Assembly: TAIR10 genome; Araport 11 transcriptome
Supplementary files format and content: harmony.rds, Seurat object that contains the snRNA-seq dataset of whole seedlings
Supplementary files format and content: apical_clusters.rds, Seurat object that contains cells that compose the apical seedling
Supplementary files format and content: spatial_multiome_imputed_250825.rds, Seurat object that contains cells related to the spatial multi-modal integration
Supplementary files format and content: GA_subclust26_multiome_imputed_250825.rds, Seurat object that contains the AHR (cluster 26) cells

source_name: Whole seedling

extract_protocol:
1.5g pulverized frozen tissue was extracted in 10 mL nuclei purification buffer (NPB; 20 mM MOPS pH 7, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, 1X protease inhibitors (Sigma), 1:1000 SUPERase (Thermo), at 4 oC for 10 min with gentle agitation. The nuclei-containing extract was sequentially filtered through 70 µm (Fisher) and 30 µm (Miltenyi) filters at 4 oC. The filtered extract was then homogenized using a pre-chilled Dounce homogenizer with 10 loose pestle strokes followed by 10 tight pestle strokes. Nuclei were pelleted by centrifugation at 700 x g for 5 min at 4 °C and resuspended in 3 mL NPB. A discontinuous gradient of 15% / 45% optiprep was prepared by diluting 60% Optiprep (Sigma) to 50% with 120 mM Tris-Cl, pH 8.0, 150 mM KCl, 30 mM MgCl2, and further diluted to 15% or 45% with NPB containing 1:1000 SUPERase. The nuclear pellet was resuspended in 3 mL NPB, gently layered onto the 15%/45% OptiPrep gradient, and centrifuged at 1500 × g for 15 min at 4 oC. Following centrifugation, the nuclei were collected from the 15%/45% OptiPrep interface, washed with 10 mL of 1X PBS (Corning), and pelleted by centrifugation at 500 × g for 5 min at 4 oC. The nuclei were resuspended in 1 mL of PBS, stained with 3 µg of Hoechst 33342, placed on ice, and taken to the Flow Cytometry Core for Fluorescence-Activated Nuclei Sorting (FANS). A BD Influx sorter with a 100-μm nozzle was used to sort nuclei in 1x PBS with sheath fluid at 20 PSI; nuclei were kept at 4 °C during the purification process. Debris was excluded first by gating using forward and side scatter pulse area parameters (FSC-A and SSC-A in log scale), then exclusion of aggregates using pulse width parameters (FSC-W and SSC-W), and finally gating on Hoechst-positive nuclei. Hoechst was excited with a 405nm laser at 100mW and detected using the 460/50BP filter. The Hoechst-positive nuclei were sorted using the '1-drop pure' mode directly into 1.5mL Eppendorf tubes containing 1x PBS, 0.5% BSA, and 1:1,000 SUPERase.
Following FANS, nuclei were centrifuged at 500 × g for 5 min; the supernatant was aspirated, and the nuclei were resuspended in 50 µl of PBS, BSA, and RNase inhibitors and quantified using a hemocytometer (Incyto). 10,000 nuclei, or the total nucleus suspension if fewer than 10,000 nuclei were collected, were used as input for the 10x Genomics Single Cell 3’ Gene Expression v3 reagents. Sequencing libraries were constructed following the manufacturer’s instructions and were sequenced with the Illumina NovaSeq 6000.

value: Whole seedling

value: 24h control


title: GABPa-24h_CD8T_GABPa-cKO_rep3

description:
Library name: GABPa-24hCD8CKO3
GABPa-24hCD8CKO3
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

value: GABPa-cKO


title: H2AZ-CUTandTag_0h-WT1

description: Library name: H2AZ-CUTandTag_0h-WT1


title: TSY, Ctrl-2

description: Library name: TSY_2


title: GABPa-24h_CD8T_GABPa-cKO_rep2

description:
Library name: GABPa-24hCD8CKO2
GABPa-24hCD8CKO2
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: TSY, Ctrl-1

description: Library name: TSY_1


title: H2AZ-CUTandTag_0h-GABPa-KO2

description: Library name: H2AZ-CUTandTag_0h-GABPa-KO2


title: Pstmortem Sublingual Gland, donor 4

description: Library name: P4SG


title: Mature polyp

city: 三亚

first: Xin

last: Huang

address: 海南省三亚市崖州湾科技城用友产业园1号楼

institute: Ocean University of China

description:
Library name: csk3
GeneMind FASTASeq 300

data_processing:
Raw FASTQ files were processed using the standard BD Rhapsody Sequence Analysis Pipeline for read quality control, sequence alignment, and UMI counting.
Downstream filtering and integration were performed using Seurat v5 in R.
Assembly: NCBI Assembly Accession: GCA_948470475.1
Supplementary files format and content: Processed data are provided as filtered HDF5 (.h5) files containing unique molecular identifier (UMI) count matrices.

organism: Galaxea fascicularis

source_name: mature polyp

growth_protocol: Healthy colonies of Galaxea fascicularis were sampled across two distinct time points (August and September 2025)

extract_protocol:
Tissues were micro-dissected and enzymatically digested into single-cell suspensions. In-well cell lysis and mRNA hybridization were performed.
Libraries were prepared using the standard BD Whole Transcriptome Analysis protocol on the BD Rhapsody Express Single-Cell Analysis System.

value: mature polyp

tag: developmental stage

tag: sampling time


title: GABPa-24h_CD8T_GABPa-cKO_rep1

description:
Library name: GABPa-24hCD8CKO1
GABPa-24hCD8CKO1
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

tag: tissue


title: H2AZ-CUTandTag-0h-GABPa-KO1

description: Library name: H2AZ-CUTandTag-0h-GABPa-KO1

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag


title: Postmortem Parotid Gland, donor 20

description: Library name: P20PG

value: PG


title: Postmortem Minor Salivary Gland, donor 21

description: Library name: P21MSG

value: MSG


title: GABPa-CUTandTag-IgG-Ctr

description: Library name: GABPa-CUTandTag-IgG-Ctr

value: spleen

value: naive CD8+ T cell


title: Early polyp

address: 海南省三亚市崖州湾科技城用友产业园1号楼

description:
Library name: csk2-2
GeneMind FASTASeq 300

source_name: early polyp

value: early polyp


title: GABPa-0h_CD8T_WT_rep2

description:
Library name: GABPa-0hCD8WT2
GABPa-0hCD8WT2
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

value: naive CD8 T cell

tag: genotype

value: unstimulated


title: Postmortem Minor Salivary Gland, donor 20

description: Library name: P20MSG

value: SARS-CoV-2 infected


title: GABPa-CUTandTag-24h-WT2

description: Library name: GABPa-CUTandTag-24h-WT2


title: Budding tip

address: 海南省三亚市崖州湾科技城用友产业园1号楼

description:
Library name: csk2-1
GeneMind FASTASeq 300

source_name: active budding tip

value: active budding tip

value: budding tip


title: Postmortem Parotid Gland, donor 18

description: Library name: P18PG


title: GABPa-0h_CD8T_WT_rep1

description:
Library name: GABPa-0hCD8WT1
GABPa-0hCD8WT1
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

tag: treatment


title: Coenosarc replicate 2

address: 海南省三亚市崖州湾科技城用友产业园1号楼

description:
Library name: csk1-2
GeneMind FASTASeq 300

source_name: basal coenosarc

value: basal coenosarc

value: coenosarc


title: GABPa-CUTandTag-24h-WT1

description: Library name: GABPa-CUTandTag-24h-WT1

tag: cell line


title: Postmortem Minor Salivary Gland, donor 18

description: Library name: P18MSG


title: Coenosarc replicate 1

address: 海南省三亚市崖州湾科技城用友产业园1号楼

description:
Library name: csk1-1
GeneMind FASTASeq 300


title: GABPa-0h_CD8T_GABPa-cKO_rep3

description:
Library name: GABPa-0hCD8CKO3
GABPa-0hCD8CKO3
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt

tag: cell type


title: GABPa-CUTandTag-24h-H2AZ-KO2

description: Library name: GABPa-CUTandTag-24h-H2AZ-KO2


title: GABPa-0h_CD8T_GABPa-cKO_rep2

description:
Library name: GABPa-0hCD8CKO2
GABPa-0hCD8CKO2
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: Flpo TM Female2

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

institute: uiowa

description: Library name: 442

data_processing:
To quantify transcript-level abundances, we performed the quality control for RNA-seq reads and used the Salmon tool with mapping-based mode again the mouse reference transcriptome (mm10). After transcript quantification, the differential gene expression analysis between different groups was conducted with the DESeq2 package. Differential expression was defined as log 2 fc > 0.58 and FDRadjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: csv files include FPKM files for each sample

source_name: Liver

extract_protocol:
For RNA-seq, Trizol-purified RNAs were re-purified using RNeasy (QIAgen) and RNA integrity validated using NanoDrop.
Briefly, 2 μg/sample of RNA was used for sequencing using Illumina HiSeq 4000/75PE Sequencer. 23 million reads were generated for each sample.

value: Liver


title: Postmortem Minor Salivary Gland, donor 14

description: Library name: P14MSG


title: Postmortem Parotid Gland, donor 14

description: Library name: P14PG


title: GABPa-0h_CD8T_GABPa-cKO_rep1

description:
Library name: GABPa-0hCD8CKO1
GABPa-0hCD8CKO1
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: GABPa-CUTandTag-24h-H2AZ-KO1

description: Library name: GABPa-CUTandTag-24h-H2AZ-KO1


title: Flpo control Female2

description: Library name: 441


title: SJRHB030680_X1_DYE8558_VT

description:
Library name: SJRHB030680_C4
2355609

data_processing:
https://wiki.stjude.org/display/CAB/RNAseq+differential+gene+expression+analysis#RNAseqdifferentialgeneexpressionanalysis-1.WorkflowSummary
Assembly: hg38
Supplementary files format and content: gene counts

value: Tumor

value: VT

value: RMS

tag: batch


title: Postmortem Parotid Gland, donor 13

description: Library name: P13PG


title: Flpo TM Female1

description: Library name: 440


title: CD8T_24h-WT_rep3

description:
Library name: CD8_24h-WT2-3
24hCD8WT2-3
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: WT


title: GABPa-CUTandTag-0h-WT2

description: Library name: GABPa-CUTandTag-0h-WT2


title: GABPa-CUTandTag-0h-WT1

description: Library name: GABPa-CUTandTag-0h-WT1


title: Postmortem Minor Salivary Gland, donor 13

description: Library name: P13MSG


title: CD8T_24h-WT_rep2

description:
Library name: CD8_24h-WT2-2
24hCD8WT2-2
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: GABPa-CUTandTag-0h-H2AZ-KO2

description: Library name: GABPa-CUTandTag-0h-H2AZ-KO2


title: Flpo control Female1

description: Library name: 439


title: Flpo TM Male2

description: Library name: 438


title: CD8T_24h-WT_rep1

description:
Library name: CD8_24h-WT2-1
24hCD8WT2-1
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: GABPa-CUTandTag-0h-H2AZ-KO1

description: Library name: GABPa-CUTandTag-0h-H2AZ-KO1


title: Postmortem Submandibular Gland, donor 11

description: Library name: P11SMG

value: SMG


title: CD8T_24h-H2AZ-cKO_rep3

description:
Library name: CD8_24h-H2AZ-cKO2-3
24hCD8CKO2-3
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: hls1_region2_240912

type: RNA

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing: MERFISH images were processed according to the manufacturer's specifications (Vizgen). The resulting tables of spatial coordinates of single mRNA molecules are provided.

source_name: 3d-old control treated hls1 etiolated seedlings

growth_protocol: Arabidopsis seedlings were grown in complete darkness for 72h prior to embedding and flash freezing

extract_protocol: Embedded tissue blocks were acclimated to -18C in a pre-cooled cryostat chamber (Leica) for 1 h. Tissue blocks were trimmed until the tissue was entered, after which 10 µm sections were visually inspected until the region of interest was exposed. Sample mounting and preparation were performed according to the MERSCOPE user guide.

treatment_protocol: Seedlings were grown in control (zero grade air) or ethylene treatment conditions at a flow rate of 30mL / min

tag: treatmet

value: air

value: 3-day-old etiolated


title: Postmortem Parotid Gland, donor 11

description: Library name: P11PG

value: PG


title: Flpo TM Male1

description: Library name: 437


title: CD8T_24h-H2AZ-cKO_rep2

description:
Library name: CD8_24h-H2AZ-cKO2-2
24hCD8CKO2-2
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: spleen


title: hls1_region1_240912


title: Postmortem Minor Salivary Gland, donor 11

description: Library name: P11MSG

value: MSG


title: GFP TM Female2

description: Library name: 435


title: hls1_r3_240912


title: CD8T_0h-WT_rep3

description:
Library name: CD8_0h-WT3
0hCD8WT3
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: naive CD8 T cell

value: unstimulated


title: GFP TM Male2

description: Library name: 434


title: Postmortem Minor Salivary Gland, donor 10

description: Library name: P10MSG

value: SARS-CoV-2 infected


title: Postmortem Parotid Gland, donor 10

description: Library name: P10PG


title: CD8T_0h-WT_rep2

description:
Library name: CD8_0h-WT2
0hCD8WT2
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: hls1_air_section2_region2


title: TED orbital fibroblast_7

city: Rochester

first: Collynn

last: Woeller

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: Library name: TED_7

data_processing:
bcltofastq-2.19.0
Assembly: Human hg38, annotation H38
Supplementary files format and content: Supplementary files format and content: Tab delimited txt file contains raw count for each file

source_name: Orbital fibroblast

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion (RNase-Free DNase Set, Qiagen).
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina) at the University of Rochester Functional Genomics Core and sequenced on an Illumina NovaSeq 6000 (150-bp paired-end; ~30 million reads/sample).

treatment_protocol: Untreated

value: Orbital fibroblast

value: TED


title: CD8T_0h-WT_rep1

first: Mingzhao

last: Zhu

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: CD8_0h-WT1
0hCD8WT1
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: Flpo control Male1

description: Library name: 395


title: hls1_air_section2_region1


title: TED orbital fibroblast_6

description: Library name: TED_6


title: CD8T_0h-H2AZ-cKO_rep3

description:
Library name: CD8_0h-H2AZ-cKO3
0hCD8CKO3
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: GFP control Female2

description: Library name: 393


title: hls1_air_section2_region0


title: TED orbital fibroblast_5

description: Library name: TED_5


title: GABPa-0h_CD8T_WT_rep3

description:
Library name: GABPa-0hCD8WT3
GABPa-0hCD8WT3
GABPa-WTvscKO_CD8T_0-24h_fpkm.txt


title: CD8T_0h-H2AZ-cKO_rep2

description:
Library name: CD8_0h-H2AZ-cKO2
0hCD8CKO2
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: TED orbital fibroblast_4

description: Library name: TED_4


title: CD8T_0h-H2AZ-cKO_rep1

description:
Library name: CD8_0h-H2AZ-cKO1
0hCD8CKO1
CD8T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: Col_ET_section2_region2

source_name: 3d-old ethylene treated WT etiolated seedlings

value: Col

value: ethylene


title: GFP TM Male1

description: Library name: 370

value: Liver


title: TED orbital fibroblast_3

description: Library name: TED_3


title: CD4T_24h-WT_rep3

description:
Library name: CD4T_24h-WT-3
0h-WT-3
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: naive CD4 T cell


title: Col_ET_section2_region1


title: TED orbital fibroblast_2

description: Library name: TED_2


title: GFP control Male1

description: Library name: 368


title: Col_ET_section2_region0


title: CD4T_24h-WT_rep2

description:
Library name: CD4T_24h-WT-2
0h-WT-2
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: Col_ET_section1_region0


title: Non-TED orbital fibroblast_4

description: Library name: NonTED_4

value: Non-TED


title: CD4T_24h-H2AZ-cKO_rep3

description:
Library name: CD4T_24h-H2AZ-cKO-3
0h-cKO-3
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt


title: Day 42 IEL H2-Ab1^fl/fl biol rep 2

city: Birmingham

first: Casey

middle: T

last: Weaver

state: AL

address: 1900 University Blvd, THT Building

institute: University of Alabama at Birmingham

description:
Library name: D42ICpos2
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counts were made using Cell Ranger v8.0.1(https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Mid-distal colon

extract_protocol:
Three cellular compartments were isolated separately to capture spatial organization of immune responses. Intestinal epithelial cells (IECs) were isolated from 4 cm mid-distal colon tissue that was flushed with 1X PBS, opened longitudinally, and cut into 1 cm strips. Tissue pieces were incubated for 20 min at 37°C with 1 mM DTT, followed by 2 mM EDTA in H5H media (1X HBSS, 5% FBS, 20 mM HEPES, and 2.5 mM 2-β-ME). Tissue pieces were vortexed briefly after each 20 min incubation, followed by washing with H5H prior to centrifugation at 1750 rpm for 10 min at 4°C. IECs were then purified on a 40%/75% Percoll gradient by centrifugation for 20 min at 25°C and 2000 rpm with no brake. Intraepithelial lymphocytes (IELs) were obtained from the epithelial fraction during IEC isolation. Lamina propria lymphocytes (LPLs) were isolated from colonic tissue that was flushed with 1X PBS, opened longitudinally, cut into small pieces, and minced for 2-3 min before being transferred into complete R10 media (1X RPMI 1640, 10% FBS, 1X Pen/Strep, 1X NEAA, 1mM Sodium pyruvate, 2 mM L-glutamine, and 2.5 mM 2-β-ME) with collagenase IV (100 U/mL) and DNase I (20 μg/mL). Tissue was digested at 37°C for 40 min with stirring, filtered through a 70 μm filter, washed with complete R10 media, centrifuged at 1750 rpm at 4°C for 10 min, and then purified on a 40%/75% Percoll gradient. Following isolation, single-cell suspensions were stained and FACS-sorted to obtain live EpCAM⁺ IECs, live CD45⁺ IELs, and live CD45⁺ LPLs. B cells were depleted using anti-CD19 antibody during FACS to enrich for rare T cell populations. Post-sort viability was confirmed to be ≥90% by trypan blue exclusion, and sorted cells were collected directly into 5 μL PBS supplemented with 5% FBS and 0.1 mM EDTA.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3' Gene Expression Kit (10x Genomics) at the FCSC Core Facility (UAB) according to the manufacturer's protocol. For each sample, 10,000 live sorted cells were loaded onto the 10x Chromium Controller. All 52 libraries were pooled and sequenced on two Illumina NovaSeq 6000 S4 flow cells using 2×100 bp paired-end reads.

value: Mid-distal colon

value: EpCAM- CD45+

value: Wild-type


title: Day 42 IEC H2-Ab1^fl/fl biol rep 2

description:
Library name: D42ICneg2
10x Genomics

value: EpCAM+ CD45-


title: Male, Saline, IgG antibody, Replicate 4

city: New York

first: Molly

middle: S

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: M-sal-igg-4

data_processing:
The NGS-Data-Charmer pipeline was used for preprocessing, QC, and alignment of the dataset (https://github.com/shenlab-sinai/NGS-Data-Charmer). Peak calling was performed using MACS on deduplicated alignments (parameters: -f BAMPE -g mm -B -q 0.01), using IgG as background.
Assembly: mm10
Supplementary files format and content: Peak calls are provided as Narrowpeak files, generated by MACS.
Library strategy: CUT&Run

source_name: Nucleus accumbens

extract_protocol:
Nuclei were equally split for IGG and E2F3a and Cut&Run was performed using IGG (CellSignaling #2729; 1:100) or E2F3a (MilliporeSigma #HPA065012, 1:50) antibodies. DNA fragments were eluted by incubating the samples at 37˚C for 30 min with 500 RPM mixing (Eppendorf, Thermomixer). The samples were centrifuged at 16,000 RCF for 5 min at 4˚C and the supernatant was reserved for DNA clean-up via phenol-chloroform precipitation.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) with modifications.

treatment_protocol: Female and male mice were injected (i.p.) with saline or cocaine (20 mg/kg) for 7 consecutive days in their home-cages before brain collection for CUT&RUNseq. Nuclei were isolated from frozen tissue of bilateral  12G punches of the Nucleus accumbens) .

value: Nucleus accumbens

tag: antibody

value: IGG

value: Wildtype C57BL/6J

value: coc

value: Male


title: Col_air_section2_region0

source_name: 3d-old control treated WT etiolated seedlings

value: air

value: 3-day-old etiolated


title: CD4T_24h-H2AZ-cKO_rep2

city: Beijing

address: 15 Da Tun Rd, Chaoyang District

description:
Library name: CD4T_24h-H2AZ-cKO-2
0h-cKO-2
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: spleen


title: Non-TED orbital fibroblast_3

description: Library name: NonTED_3

value: Orbital fibroblast


title: Male, Cocaine, E2F3a antibody, Replicate 5

description: Library name: M-coc-5


title: Col_air_section1

value: Col


title: Non-TED orbital fibroblast_2

description: Library name: NonTED_2


title: GFP control Male2

description: Library name: 369

value: Liver


title: CD4T_24h-H2AZ-cKO_rep1

description:
Library name: CD4T_24h-H2AZ-cKO-1
0h-cKO-1
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: naive CD4 T cell


title: 27S Untreated Replicate 1

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

description:
Library name: Sample 6
23S rRNA from 27S

library_source: other

data_processing:
Base calls were performed uising Illumina RTA version 1.18. 54 or 3.4.4
The next generation sequencing reads were aligned to the rrlB and rrsB  genes of Bl21 (DE3)  E Coli and the mutations were counted using Shape-Mapper 1.2
Assembly: Escherichia coli BL21(DE3): B21_04498 (rrlB) ; Escherichia coli BL21(DE3): B21_04496 (rrsB)
Supplementary files format and content: *.csv files contain counted mutations per nucleotide position of RNA sequence of interest as output from Shape-Mapper 1.2

molecule: other

organism: Escherichia coli

source_name: BLR(DE3) Delta dbpA:  Kan, expressing R331A DbpA pET-3a

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME.
The NGS sequencing library was performed following the randomer workflow of the Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) protocol(Smola et al. 2015)

treatment_protocol: Some of the RNA samples were treated with KMnO4 for either 3 or 6 minutes followed by treatment with NaHCO3

value: Bacteria

value: BLR(DE3) Delta dbpA: Kan


title: Non-TED orbital fibroblast_1

description: Library name: NonTED_1

value: Non-TED


title: CD4T_0h-WT_rep3

description:
Library name: CD4T_0h-WT-3
24h-WT-3
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: WT

value: unstimulated


title: Male, Cocaine, E2F3a antibody, Replicate 4

description: Library name: M-coc-4

value: Nucleus accumbens


title: Male, Cocaine, IgG antibody, Replicate 3

description: Library name: M-coc-igg-3

value: IGG


title: CytoMix 10_T8 rep4

city: Lausanne

first: Aline

last: Roch

address: EPFL Innovation Park Building L

country: Switzerland

institute: DOPPL SA

description: Library name: S94

data_processing:
Aligned to hg19 genome using bowtie2 in --sensitive-local mode
Peak calling using epic
Assembly: hg19
Supplementary files format and content: csv files include raw counts for each sample

source_name: small intestine

extract_protocol:
Each well of the Gri3D® platform was collected individually on day T-2 or day T-8. 4 wells of the same condition were collected separately and analyzed as quadruplicates for transcriptome profiling. Samples were lysed using LBE lysis buffer (C39467, Beckman Coulter) and vortexed for 1 min. Lysates were stored at –80°C before performing RNA extraction and subsequent analysis. Total RNA was extracted from human organoid tissues using the Agencourt RNAdvance Tissue Kit (A32649, Beckman Coulter), following the manufacturer’s protocol. Tissue disruption and lysis were carried out using the FastPrep-24™ instrument (MP Biomedicals) at a speed setting of 6.0 for two cycles of 1 minute each. A total of 400 µL of lysate was processed per sample, and RNA was eluted in 50 µL of nuclease-free water. RNA concentration was quantified using the Quant-iT™ RiboGreen RNA Assay Kit (R11490, Invitrogen) on a SpectraMax® F1 Microplate Reader (Molecular Devices). Integrity was assessed with the Fragment Analyzer 96-capillary system (Agilent Technologies) using the Standard Sensitivity RNA Analysis Kit (DNF-471-0500). We consistently obtained high-quality RNA from all organoid samples, with an average yield of 0.36 µg per sample. Notably, all samples achieved an RNA integrity number (RIN) value of 10, indicating excellent RNA integrity.
A total of 300 ng of RNA per sample was used to generate sequencing libraries with the Illumina Stranded mRNA Library Prep Kit, following the manufacturer's protocol. The workflow includes a bead-based mRNA capture, followed by fragmentation, first- and second-strand synthesis, end repair, 3’ adenylation, and indexed linker ligation steps. The adapter-ligated cDNA library fragments were next enriched by PCR using 13 cycles of amplification. From the extracted total RNA, 90 individual barcoded stranded mRNASeq libraries were successfully prepared with an average yield of 35.4 ng/µL. Two equimolar pools of 78 and 12 unique dual (UD) indexed libraries were sequenced paired-end (PE) with 59 bases each read on four individual P3 100 NextSeq 2000 flow cells. The first dark cycle was introduced to the sequencing run to improve the flow-cell cluster detection. 5.0 billion PE reads passing the chastity filter (>Q30) were generated, with an average of 46.2 million reads per sample with a standard deviation of 11.8 million reads (26%).

treatment_protocol: On day 4, cytokines were introduced to the organoids to initiate Phase 1 of epithelial barrier disruption (T-0). Organoids were stimulated with CytoMix, a pro-inflammatory cytokine cocktail comprising TNF-α (300-01A, Thermo Fisher Scientific), IL-1β (200-01B, Thermo Fisher Scientific), and IFN-γ (300-02, Thermo Fisher Scientific), each administered at final concentrations of 5, 10, 20, or 50 ng/mL. In parallel, IFN-γ was applied as a single agent at identical concentrations. Cytokines were reconstituted at 100 µg/mL in PBS (10010056, Thermo Fisher Scientific) supplemented with 0.1% bovine serum albumin (BSA; 15260-037, Thermo Fisher Scientific). CytoMix was removed, and the cultures were washed by performing two successive medium replacements, marking the onset of the Phase 2 post-treatment recovery period (T–2). As part of the prevention protocol, organoids cultured in Gri3D® platform for 72 hours (day 3) were supplemented with the bioactive compounds’ dexamethasone (DEX - 1 µM; D4902, Sigma-Aldrich), niacinamide (NAM - 0.5 mM; 0429449, DSM-Firmenich), and β-hydroxybutyrate (BHB - 1 mM; 3HB-Mg, Osaka Gas). Following cytokine withdrawal and medium washout, bioactives were reintroduced into the culture at the same concentration on day T-2 and subsequently replenished at identical concentrations on days T-4 and T-6.

value: small intestine

value: primary intestinal epithelial cells

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL

tag: time

value: day 8 post cytokine treatment


title: CD4T_0h-WT_rep2

description:
Library name: CD4T_0h-WT-2
24h-WT-2
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

source_name: spleen


title: Male, Saline, IgG antibody, Replicate 3

description: Library name: M-sal-igg-3

value: Wildtype C57BL/6J

value: sal

value: Male


title: Caenorhabditis elegans with Jellyfish treatment_02

city: Shanghai

first: Zhou

last: Peng

address: 720 Xianxia Rd.

institute: Shanghai tongren hospital

description: Library name: I2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork(parameter-Qqality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLS genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM value for each sample
Supplementary files format and content: tab-delimited text files include Counts value for each sample

source_name: Whole organism

growth_protocol: Caenorhabditis elegans grown in NGM with OP50

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd.(Shanghai, China).

treatment_protocol: T5 stock peptide solutions 50 mg/mL diluted with OP50 suspension were added as 100 μL per plate. L4-stage worms were transformed onto these plates 24 h later for exposure.

value: Whole organism

value: Jellyfish peptide treated


title: CytoMix 10_T8 rep3

description: Library name: S93


title: Female, Saline, IgG antibody, Replicate 3

description: Library name: F-sal-igg-3

value: Female


title: CD4T_0h-H2AZ-cKO_rep3

description:
Library name: CD4T_0h-H2AZ-cKO-3
24h-cKO-3
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: spleen

value: naive CD4 T cell


title: Minor Salivary Gland, donor C

description: Library name: X24S7

source_name: MSG

value: MSG

value: normal


title: Caenorhabditis elegans with Jellyfish treatment_01

description: Library name: I1


title: Caenorhabditis elegans without Jellyfish treatment_03

description: Library name: T3


title: CytoMix 10_T8 rep1

description: Library name: S91


title: Male, Saline, IgG antibody, Replicate 2

description: Library name: M-sal-igg-2


title: Caenorhabditis elegans without Jellyfish treatment_02

description: Library name: T2


title: Control_T8 rep4

description: Library name: S90

value: Untreated


title: Female, Cocaine, IgG antibody, Replicate 2

description: Library name: F-coc-igg-2

value: Nucleus accumbens

value: coc


title: CD4T_0h-H2AZ-cKO_rep1

description:
Library name: CD4T_0h-H2AZ-cKO-1
24h-cKO-1
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

value: unstimulated


title: Caenorhabditis elegans without Jellyfish treatment_01

description: Library name: T1


title: Control_T8 rep3

description: Library name: S89

value: small intestine

value: primary intestinal epithelial cells


title: BCL-CD8T-24h-WT_rep3

description:
Library name: BCL-CD8T-24h-WT2-3
BCL-24h-WT2-3
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: naive CD8 T cell

value: WT


title: Control_T8 rep2

description: Library name: S88

value: day 8 post cytokine treatment


title: BCL-CD8T-24h-WT_rep2

description:
Library name: BCL-CD8T-24h-WT2-2
BCL-24h-WT2-2
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt


title: CAF18 transfected with ASO TERRA

city: Charlestown

first: Gian Paolo

last: Dotto

address: 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hsopital

description: Gene expression data from in vitro cultured CAFs derived from cutaneous SCC lesions and transfected with ASO targeting TERRA RNA

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data were processed using Transcriptome Analysis Console v4.0.3.14 with ASO_TERRA and ASO_SCR as comparison groups.

source_name: CAF18 transfected with ASO TERRA

label_protocol: RNA was not labeled.

growth_protocol: Cells are grown in DMEM with 10% FBS, 1% penicillin and 1% streptomycin in regular cell culture conditions.

extract_protocol: Total RNA was extracted using Zymo Direct-zol RNA Miniprep kit.

treatment_protocol: TERRA was silenced in CAFs using LNA-modified antisense oligonucleotides (ASOs) targeting the telomeric repeat sequence. Briefly, cells were transfected with 100 nM of TERRA-specific ASO or a scrambled control ASO using HiPerFect transfection reagent (Qiagen), according to the manufacturer’s protocol. ASOs and HiPerFect were incubated in serum-free medium for 10 minutes at room temperature to allow complex formation, then added dropwise to cells plated at 60–70% confluence in complete medium. Cells were collected 48 hours post-transfection for downstream analyses.


title: Male, Saline, E2F3a antibody, Replicate 2

description: Library name: M-sal-2

value: Wildtype C57BL/6J

value: sal

value: Male


title: Control_T8 rep1

description: Library name: S87


title: BCL-CD8T-24h-WT_rep1

description:
Library name: BCL-CD8T-24h-WT2-1
BCL-24h-WT2-1
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt


title: PFBS_placenta4_5um_female

city: San Diego

first: Elana

last: Elkin

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

description: Library name: PFBS_placenta4_5um_female

data_processing:
Reads were aligned to the human genome using STAR.
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than 100 across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the DeSeq2 package (version 4.1) for R statistical computing.
Assembly: hg38
Supplementary files format and content: tabular files

source_name: placenta

growth_protocol: HTR-8/SVneo cells: Cells were cultured between passages 25-75 and maintained in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37 °C in a 5% CO2 humidified incubator. Cells were split and passaged at 70-90% confluence prior to use for experiments. Villous Explants: Term trimester placental tissues (N = 7, 4 male, 3 female) were obtained from full-term, non-laboring elective cesarean sections performed at UC San Diego Medical Center under Institutional Review Board approval with written informed consent. Tissues were collected in collaboration with UC San Diego Center for Perinatal Discovery. Following collection, tissues were transported back to the lab in ice-cold media. Tissues were repeatedly washed in PBS and blood clots removed. Chorionic villous tissue was carefully dissected out to form explants. Explants were further dissected into approximately 5 mg (wet) pieces. Four to six explants were placed in each experimental well, yielding a total of approximately 25 mg per well. Explants were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% P/S and placed in experimental conditions immediately after dissections.

extract_protocol:
RNeasy Mini Kit (cells) miRNeasy Mini Kit (tissues)
TruSeq mRNA Library Prep Kit with poly(A) enrichment (Illumina, San Diego, CA, USA)

treatment_protocol: Explant Tissues: Immediately prior to each experiment 1M PFBS stock was quickly thawed in a 37°C water bath and diluted in complete RPMI 1640 medium (supplemented with 10% FBS and 1% P/S) to prepare a 1 mM intermediate working solution. The working solution was further diluted in RPMI 1640 medium to final concentrations of 100 nM-100 µM, depending on experiments. Final concentrations for RNA transcriptomic experiments were 0 and 5µM in cells, and 0, 5, and 20 µM PFBS in tissue explants.

value: placenta

value: male

value: Explants-various cells

tag: exposure time

value: 24 hours

tag: placental donor

tag: sequencing batch

value: batch 2026


title: PFBS_Placenta3_20um_male

description: Library name: PFBS_Placenta3_20um_male

tag: Sex

value: batch 2025


title: CytoMix + NAM 0.5mM_T8 rep4

description: Library name: S86

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL, Niacinamide 0.5mM


title: BCL-CD8T-24h-IL7R-cKO_rep3

description:
Library name: BCL-CD8T-24h-IL7R-cKO2-3
BCL-24h-CKO2-3
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: spleen


title: CAF7 transfected with ASO TERRA

source_name: CAF7 transfected with ASO TERRA


title: Female, Saline, E2F3a antibody, Replicate 2

description: Library name: F-sal-2

value: Nucleus accumbens

value: Female


title: CAF18 transfected with ASO SCR

description: Gene expression data from in vitro cultured CAFs derived from cutaneous SCC lesions and transfected with control ASO

source_name: CAF18 transfected with ASO SCR


title: BCL-CD8T-24h-IL7R-cKO_rep2

description:
Library name: BCL-CD8T-24h-IL7R-cKO2-2
BCL-24h-CKO2-2
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt


title: Male, Cocaine, IgG antibody, Replicate 1

description: Library name: M-coc-igg-1

value: IGG

value: coc


title: CAF15 transfected with ASO SCR

source_name: CAF15 transfected with ASO SCR


title: CytoMix + NAM 0.5mM_T8 rep2

description: Library name: S84

value: small intestine

value: primary intestinal epithelial cells


title: BCL-CD8T-24h-IL7R-cKO_rep1

description:
Library name: BCL-CD8T-24h-IL7R-cKO2-1
BCL-24h-CKO2-1
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: naive CD8 T cell


title: Male, Saline, IgG antibody, Replicate 1

description: Library name: M-sal-igg-1

value: Wildtype C57BL/6J

value: sal


title: CAF7 transfected with ASO SCR

source_name: CAF7 transfected with ASO SCR


title: CytoMix + NAM 0.5mM_T8 rep1

description: Library name: S83

value: day 8 post cytokine treatment


title: Female, Cocaine, IgG antibody, Replicate 1

description: Library name: F-coc-igg-1


title: CytoMix 10 +DEX 1µM_T8 rep4

description: Library name: S78

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL, Dexamethasone 1 µM


title: BCL-CD8T-0h-WT_rep2

description:
Library name: BCL-CD8T-0h-WT2
BCL-0h-WT2
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt

value: WT

value: unstimulated


title: Female, Saline, IgG antibody, Replicate 1

description: Library name: F-sal-igg-1


title: CytoMix 10 +DEX 1µM_T8 rep3

description: Library name: S77


title: Male, Cocaine, E2F3a antibody, Replicate 1

description: Library name: M-coc-1

value: Male


title: CAF24 transfected with siCTRL

data_processing: Data were processed using Transcriptome Analysis Console v4.0.3.14 with siNONO and siCTR as comparison groups.

source_name: CAF24 transfected with siCTRL

treatment_protocol: Cancer-associated fibroblasts (CAFs) were transfected with two independent siRNAs targeting NONO (siNONO#1(Mission siRNA  NM_007363 SASI_Hs02_00343477 and siNONO#2 (Mission siRNA  NM_007363 SASI_Hs02_00343479 or with a non-targeting control siRNA (MISSION siRNA Universal Negative Control #1 SIC001) at the concentration of 30nM using HiPerFect transfection reagent (Qiagen), according to the manufacturer’s instructions. Briefly, siRNAs and HiPerFect were mixed in serum-free medium and incubated for 10 minutes at room temperature to allow complex formation. The siRNA–HiPerFect complexes were then added dropwise to CAFs plated at 60–70% confluence in complete medium. Cells were harvested 72 hours post-transfection for downstream analyses.


title: CytoMix 10 +DEX 1µM_T8 rep2

description: Library name: S76


title: BCL-CD8T-0h-IL7R-cKO_rep3

description:
Library name: BCL-CD8T-0h-IL7R-cKO3
BCL-0h-CKO3
BCL2-WTvsIL7R-cKO_CD8T_0-24h_fpkm.txt


title: Male, Saline, E2F3a antibody, Replicate 1

description: Library name: M-sal-1


title: Male, Cocaine, E2F3a antibody, Replicate 3

description: Library name: M-coc-3


title: CAF19 transfected with siNONO2

source_name: CAF19 transfected with siNONO2


title: CytoMix 10 +DEX 1µM_T8 rep1

description: Library name: S75


title: Female, Cocaine, E2F3a antibody, Replicate 1

description: Library name: F-coc-1


title: Male, Cocaine, E2F3a antibody, Replicate 2

description: Library name: M-coc-2


title: CAF19 transfected with siNONO1

source_name: CAF19 transfected with siNONO1