title: U-251, anti-ZNF410, WT, rep2, ChIP

first: Siyuan

last: Xu

address: No.131, Dongan Road, Shanghai

institute: Fudan Unversity

data_processing:
ChIP-seq reads within FASTQ files were trimmed using trim_galore from 3’ end until the final base had a quality score > 25.
ChIP-seq reads were aligned to the human hg38 reference genome using Bowtie 2 version 2.2.5 with the default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format and removed PCR duplicates and unmapped reads.
The peak calling was done using MACS2 version 2.1.4 with the default parameters.
DeepTools version 3.5.1 was applied to transform BAM into the bigwig format, normalized using the counts per million (CPM).
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: IMDM, 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature, followed by quenching with glycine. After cell lysis, the chromatin was sonicated for 100-500 bp at 4°C.
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina from Vazyme. The purified DNA was end-repaired and then ligated with adapters. After purified by AMPure XP beads from Beckman, the DNA was amplified using 13 cycles with the PCR program.

value: human glioma

value: ZNF410 (Proteintech, #14529-1-AP)


title: U-251, anti-ZNF410, WT, rep1, ChIP

status: Public on Mar 22 2025

type: SRA

city: Shanghai

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: chip antibody


title: U-87, anti-ZNF410, WT, rep2, ChIP


title: SK-BR-3, anti-ZNF410, WT, rep2, ChIP

value: human breast cancer


title: U-87, anti-ZNF410, WT, rep1, ChIP


title: SK-BR-3, anti-ZNF410, WT, rep1, ChIP


title: BT-474, anti-ZNF410, WT, rep1, ChIP


title: K562, anti-H3K27ac, AU-15330-8h, rep2, ChIP

value: human myeloid leukemia

value: H3K27ac (Abcam, #ab4729)


title: K562, anti-H3K27ac, AU-15330-4h, rep1, ChIP


title: PHA_GD17_Ctrl_18-22_21a

status: Public on Mar 23 2025

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

library_source: transcriptomic

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Gévezé, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the rat reference transcriptome from the UCSC website (release rn6, downloaded August 2020) using BWA version 0.7.4.4 with the parameter “−l 24”
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,484 genes detected.

molecule: total RNA

organism: Rattus norvegicus

source_name: Control_Gestational Day 17

growth_protocol: Animals were housed in pairs (until GD17) or individually (GD17-21) under standard conditions with 12 h light/dark cycles in ScanTainers (Ventilated Cabinets from SCANBUR, Karlslunde, Denmark) with 50–60 air changes per hour at 22 °C ± 10 and humidity kept at 55% ± 5. High Temperature polysulfone cages with wood chip bedding, nesting material and a wooden shelter (Tapvei, Denmark). Animals were fed Altromin 1314 (Altromin GmbH, Lage, Germany, soy and alfalfa-free) and tap water was freely available in polysulfone bottles (84-ACBT0702SU Tecniplast, VA, Italy).

extract_protocol:
Dams were exposed 1 h ± 15 min before decapitation under CO2/O2-anesthesia on GD17 or 21. For gene expression analyses, the perineum including the genital tubercle (GT) was more finely dissected and placed in RNAlater. Total RNA was extracted (n = 11-12 samples/group) using an RNeasy Micro Kit (Qiagen, Germany) according to manufacturer’s instructions, including on-column DNase I digestion.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: Exposure was initiated at GD7 and continued until necropsy on GD17 or 21. Rats were weighed and gavaged each morning with vehicle (corn oil) or triticonazole (450 mg/kg bw/day) with a dosing volume of 2 ml/kg bw.

tag: strain

tag: tissue

value: Genital tubercle

tag: age

value: Gestational Day 17

tag: treatment

value: Control

value: wildtype


title: K562, anti-H3K27ac, AU-15330-8h, rep1, ChIP


title: K562, anti-H3K27ac, DMSO, rep2, ChIP


title: HeLa, Mid S, untreated, Rep2, Input

city: Bangalore

first: Radhakrishnan

last: Sabarinathan

state: Karnataka

address: GKVK, Kodigehalli

country: India

institute: National Centre for Biological Sciences- Tata Institute of Fundamental Research

description: Library name: Input_HeLa_Mid_S_Rep2

data_processing:
ChIP-seq data were analysed using the nfcore/ChIPseq pipeline version 20.10.0. Briefly, the pipeline trims the adapters (Trim Galore!), aligns the reads to reference genome (BWA), marks duplicates (picard), quality filters (SAMtools and BEDTools), performs alignment-level QC and library complexity estimation (picard, Preseq), creates normalised bigWig files (BEDTools, bedGraphToBigWig) and calls peaks (MACS2)
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Cervical

growth_protocol: HeLa cells were grown in DMEM with 10% FBS and 1% Penicillin/Streptomycin. Cells were cultured at 37 degree C at 5% CO2

extract_protocol:
Cells were cross-linked using 1% formaldehyde for 10 minutes and then were quenched with 125 mM glycine for 5 minutes at 60 rpm at RT. Cells were washed thrice with icecold PBS, scraped and pelleted down at 2000 rpm at 4°C for 5 minutes. The cell pellet was either stored at -80°C or directly used in further steps. First, the cells were lysed with L1A buffer (10 mM HEPES/KOH pH 7.9, 95 mM KCl, 1 mM EDTA pH 8 and 1% NP-40) for 10 minutes on ice and centrifuge at 3500 rpm for 5 minutes. Nuclei were obtained by adding a nuclear lysis buffer (L2) (50 mM Tris-HCl pH 7.4, 1% SDS and 10 mM EDTA pH 8) supplemented with 1x PIC, to the pellet for 10 minutes on ice. The chromatin was fragmented to an average size of 400-500 bp by 22 cycles of 30 seconds ON and 30 seconds OFF pulses using a Diagenode Bioruptor sonicator. Fragment size was 27 visualised by running the chromatin on 1% Agarose gel. The DNA concentration was checked in NanoDrop. Chromatin lysate was cleared by centrifugation at 12000 rpm at 4°C for 12 minutes. One hundred µg of chromatin lysate was diluted in the Dilution buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 2 mM EDTA pH 8 and 0.5% Triton X-100) in a 1:1.5 ratio and 10% of chromatin lysate was taken as input. The antibody was added and incubated overnight at 4°C with a constant rotation. Antibodies used are: CTCF (D31H2: Cell Signaling Technology, 1µg), RAD21 (ab992: Abcam, 1µg), MRE11 (ab208020: Abcam, 2µg), γH2AX (ab81299: Abcam, 2µg), H2AX (ab :Abcam, 2ug,), ATM (ab : Abcam, 2ug), FANCD2 (NB180, Novus Biologicals, 2ug) and RAD51 (ab176458: Abcam, 2µg). The next day, Protein A/G Dynabeads  which were blocked in 5% BSA for 1 hour, were added (15µl per tube) for 4 hours at 4°C at 12 rpm. This was followed by washes with wash buffer I (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 2 mM EDTA pH 8 and 1% Triton X-100), wash buffer II (20 mM Tris-HCl pH 7.4, 500 mM NaCl, 2 mM EDTA pH 8 and 1% Triton X-100), wash buffer III (20 mM Tris-HCl pH 7.4, 250 mM LiCl, 1% NP40, 1 mM EDTA pH 8 and 10% Sodium deoxycholate) and 1xTE buffer (10 mM Tris pH 8, 1 mM EDTA pH 8) in sequence for 5 minutes at 4°C. Flow through was discarded after each wash step. Then the proteinDNA complex was eluted in 200µl of Elution Buffer (100 mM NaHCO3, 1% SDS) at 37°C. Decrosslinking was performed by adding 14 µl of 5M NaCl to the eluate at 65°C overnight. The DNA was purified using the Phenol:Chloroform:IAA method followed by ethanol precipitation. Finally, the pellet was dissolved in water and the extracted DNA was used in a qPCR reaction to verify the ChIP and proceeded for sequencing
library preparation was done using NEBNext Ultra II DNA library Prep kit with Sample Purification Beads (E7103L).

treatment_protocol: To synchronize cells in Mid S phase, HeLa cells were treted with 2mM Thymidine for 16h and released for 4 hours. DNA damage was induced using 2mM HU or 25uM Etoposide for 3 hours in the Mid S phase. For prolonged DNA damage asynchronous HeLa cells were treted with 2mM HU for 16 hours

value: Cervical

value: HeLa

value: Epithelial


title: K562, anti-H3K27ac, DMSO, rep1, ChIP


title: K562, anti-ZNF410, AU-15330-8h, rep2, ChIP


title: K562, anti-ZNF410, AU-15330-8h, rep1, ChIP


title: K562, KO+FL, rep1, ATAC

data_processing:
ATAC-seq reads within FASTQ files were trimmed using trim_galore from 3’ end until the final base had a quality score > 25.
ATAC-seq reads were aligned to the human hg38 reference genome using Bowtie 2 version 2.2.5 with the default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format and removed PCR duplicates and unmapped reads.
DeepTools version 3.5.1 was applied to transform BAM into the bigwig format, normalized using the counts per million (CPM).
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: IMDM, 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured at 37°C with 5% (v/v) of CO2.

extract_protocol:
K562 cells were lysed with lysis buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin.
ATAC-seq libraries were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina from Vazyme. The purified DNA was end-repaired and then ligated with adapters. After purified by AMPure XP beads from Beckman, the DNA was amplified using 15 cycles with the PCR program.


title: K562, anti-ZNF410, AU-15330-4h, rep1, ChIP


title: K562, KO+ZNF, rep1, ATAC


title: K562, KO+ZNF, rep2, ATAC


title: K562, KO+ZNF-C, rep1, ATAC


title: K562, KO+FL, rep2, ATAC


title: K562, KO+N-ZNF, rep2, ATAC


title: K562, KO+N-ZNF, rep1, ATAC


title: K562, anti-ZNF410, DMSO, rep2, ChIP


title: K562, KO+ZNF-C, rep2, ATAC


title: K562, NC+EV, rep2, ATAC


title: K562, anti-ZNF410, DMSO, rep1, ChIP


title: K562, NC+EV, rep1, ATAC


title: K562, KO+EV, rep2, ATAC


title: K562, KO+EV, rep1, ATAC


title: K562, AU-15330-8h, rep2, ATAC


title: K562, AU-15330-8h, rep1, ATAC


title: BT-474, anti-ZNF410, WT, rep2, ChIP


title: HEK293T, STM2457, D14, Screen

city: Guangzhou

first: JianFei

last: Xi

address: 135 Xingang West Road

institute: Sun Yat-sen University

data_processing:
RNA-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). For differential expression analysis, we used DESeq2.
MERIP-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). M6A enriched region were detected by MACS2 software. For differential expression analysis, we used DESeq2.
CRISPR Screen: The MAGeCK pipeline was used to robustly estimate the log2fold change (FC) and significance of the enriched gRNA/genes from the cell death-based CRISPR screens.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tab-delimited text files include reads counts for each Sample.
Supplementary files format and content: MERIP-seq: bigwig files include peaks information.
Supplementary files format and content: CRISPR Screen: Tab-delimited text files include rank score for each gene.
Library strategy: CRISPR Screen

extract_protocol:
The total genomic DNA (gDNA) was isolated using FastPure® Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit.
To prepare the sgRNA library for NGS, we amplify the sgRNA target region with Illumina adaptor sequences primers.

value: Human embryonic kidney

tag: sgrna

value: sgRNA library targeting 18,360 protein-encoding genes

tag: time point


title: HEK293T, DMSO, D0, Screen

value: DMSO


title: HEK293T, DMSO, D14, Screen


title: K562, AU-15330-4h, rep1, ATAC


title: HEK293T, KO qualify, DNA-seq

data_processing:
RNA-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). For differential expression analysis, we used DESeq2.
MERIP-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). M6A enriched region were detected by MACS2 software. For differential expression analysis, we used DESeq2.
CRISPR Screen: The MAGeCK pipeline was used to robustly estimate the log2fold change (FC) and significance of the enriched gRNA/genes from the cell death-based CRISPR screens.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tab-delimited text files include reads counts for each Sample.
Supplementary files format and content: MERIP-seq: bigwig files include peaks information.
Supplementary files format and content: CRISPR Screen: Tab-delimited text files include rank score for each gene.
Library strategy: DNA-Seq

value: Dual sgRNAs for subset of genes


title: K562, anti-ZNF410, AU-15330-4h, rep2, ChIP


title: HEK293T, STM2457, biol rep2, MERIP-seq, Input

data_processing:
RNA-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). For differential expression analysis, we used DESeq2.
MERIP-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). M6A enriched region were detected by MACS2 software. For differential expression analysis, we used DESeq2.
CRISPR Screen: The MAGeCK pipeline was used to robustly estimate the log2fold change (FC) and significance of the enriched gRNA/genes from the cell death-based CRISPR screens.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tab-delimited text files include reads counts for each Sample.
Supplementary files format and content: MERIP-seq: bigwig files include peaks information.
Supplementary files format and content: CRISPR Screen: Tab-delimited text files include rank score for each gene.
Library strategy: MeRIP-Seq

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
rRNA was depleted by TransNGS rRNA Depletion Kit. The MeRIP-seq libraries were prepared by RNA fragmentation, 3' adapter ligation, sample pooling, m6A IP, 5' adapter ligation, cDNA synthesis and amplification.

tag: antibody


title: K562, DMSO, rep2, ATAC


title: HEK293T, STM2457, biol rep1, MERIP-seq, Ip


title: HEK293T, STM2457, biol rep1, RNA-seq

data_processing:
RNA-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). For differential expression analysis, we used DESeq2.
MERIP-seq: The cleaned reads were then aligned to the hg38 (Ensemble GRCh38 v100) reference genome using HISAT2 (v2.1.0). Read counts mapped to genes were quantified with FeatureCounts (v1.6.0). M6A enriched region were detected by MACS2 software. For differential expression analysis, we used DESeq2.
CRISPR Screen: The MAGeCK pipeline was used to robustly estimate the log2fold change (FC) and significance of the enriched gRNA/genes from the cell death-based CRISPR screens.
Assembly: hg38
Supplementary files format and content: RNA-seq: Tab-delimited text files include reads counts for each Sample.
Supplementary files format and content: MERIP-seq: bigwig files include peaks information.
Supplementary files format and content: CRISPR Screen: Tab-delimited text files include rank score for each gene.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed by NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S/L) according to the manufacturer's instructions.


title: HEK293T, STM2457, biol rep2, RNA-seq


title: K562, AU-15330-4h, rep2, ATAC


title: K562, DMSO, rep1, ATAC


title: HEK293T, DMSO, biol rep2, RNA-seq


title: HEK293T, DMSO, biol rep1, RNA-seq


title: K562, anti-H3K27ac, AU-15330-4h, rep2, ChIP


title: HEK293T, STM2457, biol rep1, MERIP-seq, Input


title: HEK293T, STM2457, biol rep2, MERIP-seq, Ip


title: HEK293T, DMSO, biol rep1, MERIP-seq, Ip


title: HEK293T, DMSO, biol rep2, MERIP-seq, Ip


title: HEK293T, DMSO, biol rep2, MERIP-seq, Input


title: K562, MT3_clone, rep2, ATAC

value: MT3 clone


title: K562, MT4_clone, rep1, ATAC

value: MT4 clone


title: K562, MT2_clone, rep1, ATAC

value: MT2 clone


title: K562, MT2_clone, rep2, ATAC


title: K562, MT1_clone, rep2, ATAC

value: MT1 clone


title: K562, MT3_clone, rep1, ATAC

value: human myeloid leukemia


title: K562, MT1_clone, rep1, ATAC


title: HEK293T, DMSO, biol rep1, MERIP-seq, Input


title: K562, WT_clone, rep2, ATAC

value: WT


title: K562, MT4_clone, rep2, ATAC


title: K562, ZNF410_KO, rep2, ATAC

value: ZNF410 KO


title: K562, ZNF410_KO, rep1, ATAC


title: K562, WT_clone, rep1, ATAC


title: K562, ZNF410_Neg2, rep2, ATAC


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-L-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-L-dis_rep2

value: ZNF410 (Proteintech, #14529-1-AP)


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-L-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-L-dis_rep1


title: K562, anti-H3K27ac, MT1_clone, rep2, ChIP-seq

value: H3K27ac (Abcam, #ab4729)


title: K562, ZNF410_Neg2, rep1, ATAC


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-I-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-I-dis_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-K-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-K-dis_rep2


title: K562, anti-H3K27ac, MT1_clone, rep1, ChIP-seq


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-J-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-J-dis_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-J-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-J-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-H-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-H-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-I-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-I-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-G-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-G-dis_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-G-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-G-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-F-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-F-prox_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgNeg2-dis_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-D-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-D-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-D-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-D-prox_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-E-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-E-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgNeg2-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-F-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-F-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-C-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-C-prox_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-K-dis, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-K-dis_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-H-dis, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-H-dis_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-C-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-C-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-B-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-B-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-B-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-B-prox_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-A-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-A-prox_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-A-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-A-prox_rep2


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgNeg2-prox_rep2


title: K562, anti-H3K4me3, enh-del_WT_clone, rep2, ChIP-seq

value: WT clone

value: H3K4me3 (Abcam, #ab8580)


title: K562, anti-H3K4me3, enh-del_WT_clone, rep1, ChIP-seq


title: K562, anti-H3K4me3, dis_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K4me3_dis_enh-del_clone_rep1


title: K562, anti-H3K4me3, prox_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K4me3_prox_enh-del_clone_rep1


title: K562, anti-H3K4me3, prox-dis_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K4me3_prox-dis_enh-del_clone_rep2


title: K562, anti-H3K27ac, prox-dis_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K27ac_prox-dis_enh-del_clone_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA-E-prox, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA-E-prox_rep2


title: K562, anti-H3K27ac, dis_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K27ac_dis_enh-del_clone_rep2


title: K562, anti-H3K27ac, prox_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K27ac_prox_enh-del_clone_rep2


title: K562, anti-H3K27ac, dis_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K27ac_dis_enh-del_clone_rep1


title: K562, anti-H3K27ac, prox-dis_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K27ac_prox-dis_enh-del_clone_rep2


title: K562, anti-H3K27ac, prox_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K27ac_prox_enh-del_clone_rep1


title: K562, anti-H3K4me3, prox_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K4me3_prox_enh-del_clone_rep2


title: CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin, H3K27me3

city: Oxford

first: Megan

middle: Rhonwen

last: Teh

address: John Radcliffe Hospital, Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: CM-mtc91-low-iron-2-H3K27me3_CM-mtc91-low-iron-2-H3K27me3

data_processing:
Fastq files were run through the seqnado analysis pipeline (https://github.com/alsmith151/SeqNado)
Assembly: mm39
Supplementary files format and content: bigWig files
Supplementary files format and content: bed files

organism: Mus musculus

source_name: CD8+ T-cells

growth_protocol: CD8+ T-cells were grown in RPMI 1640 + 1% penicillin/streptomycin + 1% glutamine + 10% iron free serum substitute (Pan Biotech, P04-95080).  Cells were activated on plates coated with 5μg/mL α-CD3 and provided with 50 μM β-mercaptoethanol, 1 μg/mL α-CD28 and 50 U/mL IL-2.  Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde.  Following lysis, chromatin was sheared using a Covaris unltrasonicator.  DNA was pulled down with anti-H3K27me3 antibody.
DNA fragments were tagged with Tn5 transposase.  Universal and index adaptor primers were added and DNA was amplified by PCR (NEBNext Ultra II Q5 MasterMix).  DNA was cleaned with Ampure XP beads.

treatment_protocol: Media was supplemented with either 0.625 mg/mL human holotransferrin or 0.001 mg/mL holotransferrin.  Additional apotransferrin was added to maintain a total transferrin concentration of 1.2 mg/mL.

value: CD8+ T-cells

value: OT-I

tag: treatment 1

value: 0.001 mg/mL holotransferrin

tag: chipmentation antibody

value: H3K27me3 (Sigma Aldrich, 07-449)

tag: time

value: day 2


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin, H3K27me3

description: Library name: CM-mtc91-low-iron-1-H3K27me3_CM-mtc91-low-iron-1-H3K27me3


title: K562, anti-H3K27ac, enh-del_WT_clone, rep2, ChIP-seq


title: CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin, H3K27me3

description: Library name: CM-mtc91-high-iron-3-H3K27me3_CM-mtc91-high-iron-3-H3K27me3

value: 0.625 mg/mL holotransferrin


title: CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin, H3K27me3

description: Library name: CM-mtc91-low-iron-3-H3K27me3_CM-mtc91-low-iron-3-H3K27me3


title: K562, anti-H3K4me3, dis_enh-del_clone, rep2, ChIP-seq

description: K562_anti-H3K4me3_dis_enh-del_clone_rep2


title: K562, anti-H3K4me3, prox-dis_enh-del_clone, rep1, ChIP-seq

description: K562_anti-H3K4me3_prox-dis_enh-del_clone_rep1


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2-prox, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgNeg2-prox_rep1


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin, H3K27me3

description: Library name: CM-mtc91-high-iron-1-H3K27me3_CM-mtc91-high-iron-1-H3K27me3


title: K562, anti-ZNF410, prox-dis_enh-del_clone, rep2, ChIP-seq

description: K562_anti-ZNF410_prox-dis_enh-del_clone_rep2


title: K562, anti-ZNF410, prox-dis_enh-del_clone, rep1, ChIP-seq

description: K562_anti-ZNF410_prox-dis_enh-del_clone_rep1


title: NB4_ATRA_4h_IRF1

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: JW-2

data_processing:
Sequencing reads were aligned to hg38 by Bowtie2 (version 2.2.9). The uniquely mapped and non-redundant reads were left to conduct peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-value cut off of 10e-10 or 10e-5.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. Peaks.xls files were generated using MACS v1.4.2.
Assembly: hg38
Supplementary files format and content: Peaks identified from the ChIP-seq

source_name: Bone. Marrow

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the pellets were then re-suspended in ChIP buffer (Active motif) containing 1 mM PMSF and proteinase inhibitor cocktail (Sigma). Chromatin shearing was performed using a Biorupter Pico ultrasonicator device (Diagenode) with 30s ON then 30s OFF for 30 cycles. Solubilized chromatin was used for immunoprecipitation by incubating overnight at 4 °C with chip antibodies. The immunoprecipitation reaction was transferred to the Protein G agarose Column (53039, Active Motif) and incubated for 2 hours at 4 °C, then each column was washed 4 times with 900 μL Wash Buffer AM1 (Active motif). The ChIPed sample was eluted using 100 μL 37 °C Elution Buffer AM4 (Active Motif). Cross-linking was reversed by adding 5 μL Proteinase K and the sample was incubated overnight at 65 °C. Input and ChIPed DNA were purified using a DNA purification column (Active Motif).
DNA libraries were prepared with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: NB4 cells were treated with DMSO or ATRA for 4 hours

value: Bone. Marrow

value: Leukemia


title: BM LSCs, CD37 KO, rep2

first: Lu

last: Jinyuan

address: 389 Xincun Rd.

institute: Tongji Hospital

description:
Library name: Sample 4
Column name in expression_FPKM.txt: CD37_KO2

data_processing:
2×150 bp paired-end sequencing (PE150) was conducted on the Illumina Novaseq™6000 (LC-Bio Technology) in accordance with the manufacturer's instructions.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (ver. 0.20.1)
Trimmed sequence reads were mapped to mm39 genome using STAR (ver. 2.7.7a)
Read count extraction and normalization were performed using FeatureCount (ver. 2.0.0)
Differential gene expression and functional enrichment analysis were performed using EdgeR and clusterProfiler (ver. 4.0.2)
Assembly: mm39
Supplementary files format and content: text file including FPKM values for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was purified from cells using TRIzol reagent (TransGen Biotech). 1 ug of total RNA was used for the construction of sequencing libraries.
The purity and concentration of each RNA sample were quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). RNA integrity was evaluated by Bioanalyzer 2100 (Agilent Technologies, California, USA). Poly(A) RNA was purified from total RNA using Dynabeads Oligo (dT) 25-61005 (Thermo Fisher Scientific) and fragmented into small pieces at 94°C for 5–7 minutes using the Magnesium RNA Fragmentation Module (NEB, e6150). Escherichia coli DNA polymerase I (NEB, m0209), RNase H (NEB, m0297), and dUTP solution (Thermo Fisher Scientific, R0133) were used for cDNA synthesis. Next, A base was added to the blunt end of each strand to prepare for ligation to the indexed adapter. Each adapter contains a T base overhang, which is used to ligate the adapter to the A-tailed fragmented DNA. The single-index or dual-index adapter was connected to the fragment and the size selection was performed using AMPureXP beads. After treating the U-labeled second-strand DNA with UDG enzyme (NEB, m0280), the ligated product was amplified by PCR under the following conditions: initial denaturation at 95°C for 3 minutes; 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, and extension at 72°C for 30 seconds; followed by extension at 72°C for 5 minutes. The average insert size of the final cDNA library was 300 ± 50 bp.

value: Bone marrow

value: Acute myeloid leukemia cells

tag: Sex

value: Male

value: 6 weeks after transplantation

tag: disease

value: Acute myeloid leukemia


title: NB4_Control_IRF1

description: Library name: JW-1


title: BM LSCs, CD37 KO, rep1

description:
Library name: Sample 3
Column name in expression_FPKM.txt: CD37_KO1


title: K562, anti-ZNF410, dis_enh-del_clone, rep2, ChIP-seq

value: human myeloid leukemia

value: ZNF410 (Proteintech, #14529-1-AP)


title: HeLa, Mid S, untreated, Rep2, RAD51, ChIP

description: Library name: RAD51_HeLa_Mid_S_Rep2

value: Cervical

value: HeLa

value: Epithelial

value: Anti-Rad51 antibody, ab176458, abcam


title: HeLa, Mid S, untreated, Rep1, RAD51, ChIP

description: Library name: RAD51_HeLa_Mid_S_Rep1


title: HeLa, Mid S, Etoposide treatment 3h, Rep2, RAD51, ChIP

description: Library name: RAD51_HeLa_Mid_S_ETO_3h_Rep2

value: 25uM Etoposide treatment for 3h


title: K562, anti-ZNF410, prox_enh-del_clone, rep2, ChIP-seq

description: K562_anti-ZNF410_prox_enh-del_clone_rep2


title: HeLa, Mid S, Etoposide treatment 3h, Rep1, RAD51, ChIP

description: Library name: RAD51_HeLa_Mid_S_ETO_3h_Rep1


title: BM LSCs, CD37 WT, rep2

description:
Library name: Sample 2
Column name in expression_FPKM.txt: CD37_WT2

value: CD37 fl/fl


title: K562, anti-ZNF410, prox_enh-del_clone, rep1, ChIP-seq

description: K562_anti-ZNF410_prox_enh-del_clone_rep1


title: BM LSCs, CD37 WT, rep1

description:
Library name: Sample 1
Column name in expression_FPKM.txt: CD37_WT1


title: HeLa, Asynchronous, HU treatment 16h, Rep1, RAD51, ChIP

description: Library name: RAD51_HeLa_HU_16h_Rep1

value: 2mM HU treatment for 16h


title: FLOX5

city: hangzhou

first: wei

last: wu

state: zhejiang

address: 2318 Yuhangtang Road, Yuhang District

department: School of Public Health

institute: Hangzhou Normal University

description:
Library name: sample 3
FPKM.FLOX5

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 Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: heart

growth_protocol: C57BL/6J mice were purchased from Shanghai Nanfang Model Biotechnology Co., LTD., and were raised in SPF experimental environment of Hangzhou Normal University

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 Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , 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 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: The model group was fed in SPF environment until 12 months, and the control group was fed in SPF environment until 8 weeks, without any intervention

value: heart

value: WT

value: no treatment

tag: batch

value: 12 monthes


title: HeLa, Mid S, untreated, Rep2, MRE11, ChIP

description: Library name: MRE11_HeLa_Mid_S_Rep2

tag: cell line

value: Anti-Mre11 antibody [EPR21027] - ChIP Grade, ab208020, abcam


title: K562, anti-ZNF410, enh-del_WT_clone, rep2, ChIP-seq

tag: cell type

value: WT clone


title: HeLa, Mid S, untreated, Rep1, RAD21, ChIP

description: Library name: RAD21_HeLa_Mid_S_Rep1

value: Anti-Rad21 antibody, ab992, abcam


title: FLOX6

description:
Library name: sample 4
FPKM.FLOX6

tag: genotype


title: K562, anti-ZNF410, enh-del_WT_clone, rep1, ChIP-seq

tag: chip antibody


title: HeLa, Mid S, HU treatment 3h, Rep1, MRE11, ChIP

description: Library name: MRE11_HeLa_Mid_S_HU_3h_Rep1

value: 2mM HU treatment for 3h


title: C5

description:
Library name: sample 2
FPKM.C5

value: 8 weeks


title: HeLa, Mid S, Etoposide treatment 3h, Rep2, MRE11, ChIP

description: Library name: MRE11_HeLa_Mid_S_ETO_3h_Rep2


title: K562, anti-ZNF410, MT4_clone, rep2, ChIP-seq

value: human myeloid leukemia

value: MT4 clone

value: ZNF410 (Proteintech, #14529-1-AP)


title: HeLa, Mid S, Etoposide treatment 3h, Rep1, MRE11, ChIP

description: Library name: MRE11_HeLa_Mid_S_ETO_3h_Rep1

value: Cervical

value: HeLa

value: Epithelial


title: K562, anti-ZNF410, dis_enh-del_clone, rep1, ChIP-seq


title: C4

description:
Library name: sample 1
FPKM.C4


title: K562, anti-ZNF410, MT4_clone, rep1, ChIP-seq


title: HeLa, Asynchronous, HU treatment 16h, Rep2, MRE11, ChIP

description: Library name: MRE11_HeLa_HU_16h_Rep2


title: HeLa, Mid S, untreated, Rep2, RAD21, ChIP

description: Library name: RAD21_HeLa_Mid_S_Rep2


title: HeLa, Asynchronous, HU treatment 16h, Rep1, MRE11, ChIP

description: Library name: MRE11_HeLa_HU_16h_Rep1


title: K562, anti-ZNF410, MT3_clone, rep2, ChIP-seq

value: MT3 clone


title: HeLa, Mid S, untreated, Rep1, Input

description: Library name: Input_HeLa_Mid_S_Rep1


title: emricasan treatment, 55, Week28

city: Kyotanabe

first: Taisuke

last: Numao

state: Kyoto

department: Department of Biomedical Engineering, Faculty of Life and Medical Sciences

country: Japan

institute: Doshisha University

description: Library name: Emricasan55

data_processing:
Raw fastq files were processed using fastp software (v0.20.4) to remove low-quality reads.
The processed reads were aligned to the mouse reference genome (GRCm39) using STAR (v2.7.10a).
Gene expression was quantified using RSEM (v1.3.1).
Differential expression analysis between the vehicle group (n=3) and the emricasan group (n=3) was performed using DESeq2 (v1.42.1).
Genes with P-value < 0.05 and absolute |Log₂ Fold Change| ≥ 1.0 were considered significantly differentially expressed.
Assembly: GRCm39

source_name: cornea

growth_protocol: Col8a2Q455K/Q455K mice were maintained at Doshisha University under standard conditions following institutional guidelines and ARVO Statement for the Use of Animals in Ophthalmic and Vision Research.

extract_protocol:
Mice were euthanized at 28 weeks of age, and eyes were enucleated and immersed in RNAlater. Under a microscope, corneas were isolated, and endothelial cells with Descemet membrane were carefully stripped from the corneas. Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol.
RNA sequencing libraries were prepared using the SMART-Seq HT Kit (Takara Bio Inc.) following the manufacturer's protocol. After full-length cDNA synthesis, Illumina libraries were prepared using NexteraXT (Illumina Inc.).

treatment_protocol: Col8a2Q455K/Q455K mice received twice-daily topical administration of 0.1% emricasan eye drops (treatment group) or vehicle eye drops (control group) from 8 to 28 weeks of age. At 28 weeks of age, mice were euthanized for tissue collection.

value: cornea

value: corneal endothelial cells

value: 0.1% emricasan eye drops


title: HeLa, Mid S, untreated, Rep2, H2AX, ChIP

description: Library name: H2AX_HeLa_Mid_S_Rep2

value: Anti-Histone H2A.X antibody - ChIP Grade, ab20669, abcam


title: K562, anti-ZNF410, MT3_clone, rep1, ChIP-seq


title: HeLa, Asynchronous, untreated, Rep1, Input

description: Library name: Input_HeLa_Asy_Rep1


title: emricasan treatment, 54, Week28

description: Library name: Emricasan54


title: emricasan treatment, 35, Week28

description: Library name: Emricasan35


title: HeLa, Mid S, untreated, Rep1, MRE11, ChIP

description: Library name: MRE11_HeLa_Mid_S_Rep1


title: HeLa, Mid S, untreated, Rep2, gH2AX, ChIP

description: Library name: gH2AX_HeLa_Mid_S_Rep2

value: Anti-gamma H2A.X (phospho S139) antibody [EP854(2)Y], ab81299, abcam


title: K562, anti-ZNF410, MT2_clone, rep2, ChIP-seq

value: MT2 clone


title: HeLa, Mid S, untreated, Rep1, gH2AX, ChIP

description: Library name: gH2AX_HeLa_Mid_S_Rep1


title: HeLa, Mid S, HU treatment 3h, Rep1, gH2AX, ChIP

description: Library name: gH2AX_HeLa_Mid_S_HU_3h_Rep1


title: HeLa, Mid S, Etoposide treatment 3h, Rep1, gH2AX, ChIP

description: Library name: gH2AX_HeLa_Mid_S_ETO_3h_Rep1

value: 25uM Etoposide treatment for 3h


title: vehicle treatment, 63, Week28

description: Library name: Vehicle63

value: vehicle eye drops


title: vehicle treatment, 44, Week28

description: Library name: Vehicle44


title: HeLa, Mid S, Etoposide treatment 3h, Rep2, gH2AX, ChIP

description: Library name: gH2AX_HeLa_Mid_S_ETO_3h_Rep2


title: K562, anti-ZNF410, MT2_clone, rep1, ChIP-seq


title: vehicle treatment, 45, Week28

description: Library name: Vehicle45


title: HeLa, Asynchronous, HU treatment 16h, Rep1, gH2AX, ChIP

description: Library name: gH2AX_HeLa_HU_16h_Rep1

value: 2mM HU treatment for 16h


title: HeLa, Mid S, untreated, Rep1, H2AX, ChIP

description: Library name: H2AX_HeLa_Mid_S_Rep1


title: K562, anti-ZNF410, MT1_clone, rep2, ChIP-seq

value: MT1 clone


title: HeLa, Mid S, untreated, Rep1, CTCF, ChIP

description: Library name: CTCF_HeLa_Mid_S_Rep1

value: Anti-CTCF antibody (D31H2), #3418, Cell SIgnaling Technology


title: HeLa, Asynchronous, untreated, Rep1, CTCF, ChIP

description: Library name: CTCF_HeLa_Asy_Rep1


title: BMDMs, M. bovis Δfrd, 12 hours, Replicate3

city: BEIJING

first: Yuhui

last: Dong

state: Select

address: HaiDian District, Mingyuanxilu No.2

department: College of Veterinary Medicine

institute: China Agricultural University

description:
Library name: Sample 6
KO3

data_processing:
CLC Genomics Workbench y 11.0.1
Sequence reads were trimmed r adaptor sequence/low-qality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mappedto GrCM38/mm10using CLC genomic benchwork (parameters-mismath cost:2insertion cost:3 deletin cost:3 length factin:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: macrophages

extract_protocol:
RNA was harvested using Rneasy miniplus kit (Qiagen).1.3 ug oftotal RNA was used for the cnstruction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: macrophages


title: K562, anti-ZNF410, MT_WT_clone, rep1, ChIP-seq

value: human myeloid leukemia

value: WT clone

value: ZNF410 (Proteintech, #14529-1-AP)


title: HeLa, Mid S, untreated, Rep2, CTCF, ChIP

description: Library name: CTCF_HeLa_Mid_S_Rep2

value: Cervical

value: HeLa

value: Epithelial


title: BMDMs, M. bovis Δfrd, 12 hours, Replicate1

description:
Library name: Sample 4
KO1


title: 10039567, HbAS, female, Unused_poor match

city: Dallas

first: Kabir

last: Olaniran

state: TX

address: 5939 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

description:
Library name: 10039567
a10039567(norm)
a10039567(raw)

data_processing:
Single-end sequencing 50bp was performed on an Illumina Hiseq 2500 at LC Sciences following the vendor's recommended protocol.
Raw reads were subjected to an in-house program, ACGT101-miR to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Unique sequences with length in 18-26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known microRNAs and novel 3p- and 5p- derived microRNAs.
Normalization of microRNA sequence counts in each sample was achieved by dividing the counts by a library size parameter of the corresponding sample.
Assembly: hg38
Supplementary files format and content: xlsx files including normalized (norm) and raw counts for each sample - ASvsAS_controls
Supplementary files format and content: xlsx files including normalized (norm) and raw counts for each sample - SSvsSS_controls
Supplementary files format and content: xlsx files including normalized (norm) and raw counts for each sample - All_data

source_name: plasma

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Approximately 1 ug of total RNA were used to prepare a small RNA library using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) following the manufacturer's protocol.

value: plasma

tag: subject status

value: HbAS

tag: gender

value: female

tag: sample group

value: Unused_poor match


title: K562, anti-ZNF410, MT1_clone, rep1, ChIP-seq


title: K562, anti-ZNF410, MT_WT_clone, rep2, ChIP-seq


title: 10093720, HbAA, male, AS_control

description:
Library name: 10093720
AS_control/a10093720(norm)
AS_control/a10093720(raw)
ASvsAS_control.xlsx

tag: tissue

value: HbAA

value: male


title: BMDMs, M. bovis Δfrd, 12 hours, Replicate2

description:
Library name: Sample 5
KO2


title: 10091027, HbAS, male

description:
Library name: 10091027
AS/a10091027(norm)
AS/a10091027(raw)
ASvsAS_control.xlsx


title: K562, anti-H3K4me3, dCas9-KRAB-sgRNA_BK, rep2, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgRNA_BK_rep2

value: H3K4me3 (Abcam, #ab8580)


title: 10103076, HbAA, female, SS_control

description:
Library name: 10103076
SS_control/a10103076(norm)
SS_control/a10103076(raw)
SSvsSS_control.xlsx


title: 10100385, HbAS, female

description:
Library name: 10100385
AS/a10100385(norm)
AS/a10100385(raw)
ASvsAS_control.xlsx


title: 10100762, HbSS, male

description:
Library name: 10100762
SS/a10100762(norm)
SS/a10100762(raw)
SSvsSS_control.xlsx

value: HbSS


title: BMDMs, wild-type M. bovis, 12 hours, Replicate2

description:
Library name: Sample 2
WT2


title: K562, anti-H3K4me3, dCas9-KRAB-sgRNA_BK, rep1, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgRNA_BK_rep1


title: 10098883, HbAA, female, AS_control

description:
Library name: 10098883
AS_control/a10098883(norm)
AS_control/a10098883(raw)
ASvsAS_control.xlsx


title: K562, anti-H3K4me3, dCas9-KRAB-sgRNA_AL, rep2, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgRNA_AL_rep2


title: 10084729, HbSS, female

description:
Library name: 10084729
SS/a10084729(norm)
SS/a10084729(raw)
SSvsSS_control.xlsx


title: BMDMs, wild-type M. bovis, 12 hours, Replicate1

description:
Library name: Sample 1
WT1


title: 10082963, HbAA, male, AS_control

description:
Library name: 10082963
AS_control/a10082963(norm)
AS_control/a10082963(raw)
ASvsAS_control.xlsx


title: K562, anti-H3K4me3, dCas9-KRAB-sgRNA_AL, rep1, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgRNA_AL_rep1


title: 10079692, HbAS, female

description:
Library name: 10079692
AS/a10079692(norm)
AS/a10079692(raw)
ASvsAS_control.xlsx


title: BMDMs, wild-type M. bovis, 12 hours, Replicate3

description:
Library name: Sample 3
WT3


title: 10079036, HbAA, male, SS_control, AS_control

description:
Library name: 10079036
SS_control/a10079036(norm)
SS_control/a10079036(raw)
AS_control/a10079036(norm)
AS_control/a10079036(raw)
SSvsSS_control.xlsx
ASvsAS_control.xlsx


title: Mouse liver, PS-MP sample, rep3

city: Taipei

first: Hui-Wen

last: Chiu

address: No.301, Yuantong Rd., Zhonghe Dist., New Taipei City

country: Taiwan

institute: Taipei medical university

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse liver

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six-week-old male C57BL/6 mice were orally dosed with 0.4 mg/day PS-MPs or water twice weekly for eight weeks.

value: mouse liver

tag: strain

tag: age

value: Six-week-old

tag: treatment

value: Six-week-old male C57BL/6 mice were orally dosed with 0.4 mg/day PS-MPs twice weekly for eight weeks.


title: 10078747, HbAA, female, AS_control

description:
Library name: 10078747
AS_control/a10078747(norm)
AS_control/a10078747(raw)
ASvsAS_control.xlsx


title: 10075413, HbAS, female

description:
Library name: 10075413
AS/a10075413(norm)
AS/a10075413(raw)
ASvsAS_control.xlsx


title: K562, anti-H3K4me3, dCas9-KRAB-sgNeg2, rep2, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgNeg2_rep2

value: human myeloid leukemia


title: K562, anti-H3K4me3, dCas9-KRAB-sgNeg2, rep1, ChIP-seq

description: K562_anti-H3K4me3_dCas9-KRAB_sgNeg2_rep1


title: Mouse liver, PS-MP sample, rep1


title: 10065159, HbAS, male

description:
Library name: 10065159
AS/a10065159(norm)
AS/a10065159(raw)
ASvsAS_control.xlsx


title: 10048999, HbAS, female

description:
Library name: 10048999
AS/a10048999(norm)
AS/a10048999(raw)
ASvsAS_control.xlsx


title: Mouse liver, normal sample, rep3

value: Six-week-old male C57BL/6 mice were orally with water twice weekly for eight weeks.


title: 10088703, HbSS, female

description:
Library name: 10088703
SS/a10088703(norm)
SS/a10088703(raw)
SSvsSS_control.xlsx


title: K562, anti-H3K9me3, dCas9-KRAB-sgRNA_BK, rep1, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgRNA_BK_rep1

value: H3K9me3 (Abcam, #ab8898)


title: 10048839, HbAA, female, AS_control

description:
Library name: 10048839
AS_control/a10048839(norm)
AS_control/a10048839(raw)
ASvsAS_control.xlsx


title: Mouse liver, normal sample, rep2


title: 10038363, HbAA, female, AS_control

description:
Library name: 10038363
AS_control/a10038363(norm)
AS_control/a10038363(raw)
ASvsAS_control.xlsx


title: Mouse liver, normal sample, rep1


title: 10037718, HbAA, female, AS_control

description:
Library name: 10037718
AS_control/a10037718(norm)
AS_control/a10037718(raw)
ASvsAS_control.xlsx


title: 10036338, HbAA, female, AS_control

description:
Library name: 10036338
AS_control/a10036338(norm)
AS_control/a10036338(raw)
ASvsAS_control.xlsx


title: K562, anti-H3K9me3, dCas9-KRAB-sgRNA_AL, rep1, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgRNA_AL_rep1


title: 10036617, HbAS, female

description:
Library name: 10036617
AS/a10036617(norm)
AS/a10036617(raw)
ASvsAS_control.xlsx


title: Mouse liver, PS-MP sample, rep2


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin, H3K4me3

extract_protocol:
Cells were fixed with 1% formaldehyde.  Following lysis, chromatin was sheared using a Covaris unltrasonicator.  DNA was pulled down with either an anti-H3K27ac or anti-H3K4me3 antibody.
DNA fragments were tagged with Tn5 transposase.  Universal and index adaptor primers were added and DNA was amplified by PCR (NEBNext Ultra II Q5 MasterMix).  DNA was cleaned with Ampure XP beads.

value: CD8+ T-cells

value: OT-I

tag: treatment 1

value: 0.001 mg/mL holotransferrin

value: H3K4me3 (Diagenode, C15410003)

value: day 2


title: K562, anti-H3K9me3, dCas9-KRAB-sgNeg2, rep2, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgNeg2_rep2


title: 10069346, HbAS, male

description:
Library name: 10069346
AS/a10069346(norm)
AS/a10069346(raw)
ASvsAS_control.xlsx

value: plasma

value: HbAS


title: 10027891, HbAA, female, SS_control

description:
Library name: 10027891
SS_control/a10027891(norm)
SS_control/a10027891(raw)
SSvsSS_control.xlsx

value: HbAA

value: female


title: K562, anti-H3K9me3, dCas9-KRAB-sgNeg2, rep1, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgNeg2_rep1


title: 10064169, HbAA, male, SS_control, AS_control

description:
Library name: 10064169
SS_control/a10064169(norm)
SS_control/a10064169(raw)
AS_control/a10064169(norm)
AS_control/a10064169(raw)
SSvsSS_control.xlsx
ASvsAS_control.xlsx

value: male


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin, H3K27ac

tag: chipmentation antibody

value: H3K27ac (Diagenode, C15410196)


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin, H3K4me3

value: 0.625 mg/mL holotransferrin

tag: time


title: 10028324, HbAA, female, SS_control

description:
Library name: 10028324
SS_control/a10028324(norm)
SS_control/a10028324(raw)
SSvsSS_control.xlsx


title: K562, anti-H3K27ac, dCas9-KRAB-sgRNA_BK, rep2, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgRNA_BK_rep2

value: H3K27ac (Abcam, #ab4729)


title: K562, anti-H3K9me3, dCas9-KRAB-sgRNA_BK, rep2, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgRNA_BK_rep2


title: 10041088, HbAA, female, SS_control

description:
Library name: 10041088
SS_control/a10041088(norm)
SS_control/a10041088(raw)
SSvsSS_control.xlsx


title: 10026826, HbAA, female, SS_control

description:
Library name: 10026826
SS_control/a10026826(norm)
SS_control/a10026826(raw)
SSvsSS_control.xlsx


title: 10021289, HbAS, female

description:
Library name: 10021289
AS/a10021289(norm)
AS/a10021289(raw)
ASvsAS_control.xlsx


title: 10068039, HbAA, female, Unused_control

description:
Library name: 10068039
a10068039(norm)
a10068039(raw)


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin, H3K27ac


title: K562, anti-H3K9me3, dCas9-KRAB-sgRNA_AL, rep2, ChIP-seq

description: K562_anti-H3K9me3_dCas9-KRAB_sgRNA_AL_rep2


title: 10014861, HbAA, female, SS_control

description:
Library name: 10014861
SS_control/a10014861(norm)
SS_control/a10014861(raw)
SSvsSS_control.xlsx


title: Ire

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

institute: NHRI

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence.
Supplementary files format and content: all.fpkm_anno.txt

source_name: NSCLC

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: NSCLC

value: epithelial cells

value: deletion of exon 19 in EGFR

value: Genfitnib resistant cell line


title: K562, anti-H3K27ac, dCas9-KRAB-sgRNA_AL, rep2, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgRNA_AL_rep2

data_processing:
ChIP-seq reads within FASTQ files were trimmed using trim_galore from 3’ end until the final base had a quality score > 25.
ChIP-seq reads were aligned to the human hg38 reference genome using Bowtie 2 version 2.2.5 with the default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format and removed PCR duplicates and unmapped reads.
The peak calling was done using MACS2 version 2.1.4 with the default parameters.
DeepTools version 3.5.1 was applied to transform BAM into the bigwig format, normalized using the counts per million (CPM).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature, followed by quenching with glycine. After cell lysis, the chromatin was sonicated for 100-500 bp at 4°C.
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina from Vazyme. The purified DNA was end-repaired and then ligated with adapters. After purified by AMPure XP beads from Beckman, the DNA was amplified using 13 cycles with the PCR program.

value: human myeloid leukemia


title: CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin + 40 mM aspartate

data_processing:
Read alignments were conducted using RNA-star to mm39
Aligned reads were annotated for features using FeatureCounts from the subread package
Differential gene expression analysis was completed using the EdgeR package
Assembly: mm39
Supplementary files format and content: comma separated file with RPKM values for each sample

molecule: polyA RNA

extract_protocol:
RNA was extracted from cell pellets with the Qiagen Rneasy plus minikit and treated on column with the Qiagen Rnase-free Dnase I set.
polyA enrichment and then library preparation by Novogene using the Novogene NGS RNA library prep set (PT042)

treatment_protocol: Media was supplemented with either 0.625 mg/mL human holotransferrin or 0.001 mg/mL holotransferrin.  Additional apotransferrin was added to maintain a total transferrin concentration of 1.2 mg/mL.  Media was also optionally supplemented with 40 mM aspartate.

value: CD8+ T-cells

value: OT-I

tag: treatment 2

value: 40 mM aspartate


title: K562, anti-H3K27ac, dCas9-KRAB-sgRNA_BK, rep1, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgRNA_BK_rep1


title: PE089


title: CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin

value: 0.001 mg/mL holotransferrin

value: 0 mM aspartate

value: day 2


title: 10014589, HbAA, female, AS_control

description:
Library name: 10014589
AS_control/a10014589(norm)
AS_control/a10014589(raw)
ASvsAS_control.xlsx

value: plasma

value: HbAA


title: K562, anti-H3K27ac, dCas9-KRAB-sgRNA_AL, rep1, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgRNA_AL_rep1


title: CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin + 40 mM aspartate


title: 10014059, HbAS, male

description:
Library name: 10014059
AS/a10014059(norm)
AS/a10014059(raw)
ASvsAS_control.xlsx

value: HbAS

value: male


title: 10026132, HbSS, female

description:
Library name: 10026132
SS/a10026132(norm)
SS/a10026132(raw)
SSvsSS_control.xlsx

value: HbSS

value: female


title: K562, anti-H3K27ac, dCas9-KRAB-sgNeg2, rep2, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgNeg2_rep2

value: H3K27ac (Abcam, #ab4729)


title: CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin

value: 0.625 mg/mL holotransferrin


title: Mac_WT_LPS_2

city: Worcester

first: Patipark

last: Kueanjinda

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

description: Library name: Mac-WT-plus-LPS-2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp module in galaxy (default parameters).
Trimmed sequence reads were mapped to GRCm39 using RNA STAR module in galaxy (default parameters).
BAM files were converted to fastq formats using SamToFastq module prior to quantification using Kallisto in galaxy platform (default parameters).
Read count extraction and normalization were performed using R.
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes log2-transformed of library size-normalized TPM values for each sample

source_name: WT macrophages, LPS 1 hr

growth_protocol: Bone marrow-derived macrophages from cGAS knockout mice were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified incubator with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from neutrophils using  RNeasy mini kit (Qiagen).
Approximately 300 ng of the total RNAs from each sample was used to create individually indexed strand-specific RNA-Seq libraries by using QIAseq Stranded mRNA Library kits (QIAGEN). The reactions were subjected to fragmentation and cDNA synthesis. QIAseq Beads (QIAGEN) were used to separate the cDNAs from the reaction mix. Indexing adapters were ligated to the cDNAs, and subsequently all cDNA libraries were inspected for quality by using Agilent 2100 Bioanalyzer (Agilent) and quantified with DeNovix fluorometer (DeNovix). The indexed sequencing libraries were pooled in equimolar quantity and subjected to cluster generation and paired end 150 nucleotide read sequencing on Illumina HiSeq sequencer.

treatment_protocol: Activation of BMDMs was induced with 100 ng/mL of LPS (E.coli 026:B6 from Sigma) or media control for 1 hours.

value: macrophage

value: wild-type

value: LPS, 1 hr


title: 10010065, HbAS, male

description:
Library name: 10010065
AS/a10010065(norm)
AS/a10010065(raw)
ASvsAS_control.xlsx


title: Mac_WT_LPS_3

description: Library name: Mac-WT-plus-LPS-3


title: K562, anti-H3K27ac, dCas9-KRAB-sgNeg2, rep1, ChIP-seq

description: K562_anti-H3K27ac_dCas9-KRAB_sgNeg2_rep1

value: human myeloid leukemia


title: CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin + 40 mM aspartate

value: CD8+ T-cells

value: OT-I


title: CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin

value: 0.001 mg/mL holotransferrin


title: 10005247, HbAS, female

description:
Library name: 10005247
AS/a10005247(norm)
AS/a10005247(raw)
ASvsAS_control.xlsx


title: Mac_WT_UT_3

description: Library name: Mac-WT-3

source_name: WT macrophages, untreated

value: media control


title: CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin, H3K27me3

description: Library name: CM-mtc91-high-iron-2-H3K27me3_CM-mtc91-high-iron-2-H3K27me3

value: H3K27me3 (Sigma Aldrich, 07-449)

value: day 2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA_BK, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA_BK_rep2

value: ZNF410 (Proteintech, #14529-1-AP)


title: 10004134, HbAA, female, SS_control

description:
Library name: 10004134
SS_control/a10004134(norm)
SS_control/a10004134(raw)
SSvsSS_control.xlsx

value: plasma

value: HbAA


title: Mac_WT_UT_2

description: Library name: Mac-WT-2


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA_BK, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA_BK_rep1


title: K562, anti-H3K27ac, enh-del_WT_clone, rep1, ChIP-seq

value: WT clone


title: CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin + 40 mM aspartate

value: 40 mM aspartate


title: 10002906, HbAA, female, SS_control

description:
Library name: 10002906
SS_control/a10002906(norm)
SS_control/a10002906(raw)
SSvsSS_control.xlsx

value: female


title: 10002543, HbAA, male, SS_control, AS_control

description:
Library name: 10002543
SS_control/a10002543(norm)
SS_control/a10002543(raw)
AS_control/a10002543(norm)
AS_control/a10002543(raw)
SSvsSS_control.xlsx
ASvsAS_control.xlsx

value: male


title: Mac_WT_UT_1

description: Library name: Mac-WT-1

value: macrophage


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA_AL, rep2, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA_AL_rep2


title: Mac_CGAS_LPS_3

description: Library name: Mac-CGAS-plus-LPS-3

source_name: cGAS KO macrophages, LPS 1 hr

value: cGAS knockout


title: K562, anti-ZNF410, dCas9-KRAB-sgRNA_AL, rep1, ChIP-seq

description: K562_anti-ZNF410_dCas9-KRAB_sgRNA_AL_rep1


title: Mac_CGAS_LPS_2

description: Library name: Mac-CGAS-plus-LPS-2

value: LPS, 1 hr


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin

value: 0 mM aspartate


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2, rep2, ChIP-seq

value: human myeloid leukemia


title: Mac_WT_LPS_1

description: Library name: Mac-WT-plus-LPS-1

value: wild-type


title: K562, anti-ZNF410, dCas9-KRAB-sgNeg2, rep1, ChIP-seq


title: Mac_CGAS_LPS_1

description: Library name: Mac-CGAS-plus-LPS-1


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin + 40 mM aspartate

value: CD8+ T-cells

value: OT-I

value: 0.625 mg/mL holotransferrin


title: K562, anti-H3K4me3, ZNF410-sgRNA, rep2, ChIP-seq

value: ZNF411 KO

value: H3K4me3 (Abcam, #ab8580)


title: Soleus skeletal muscle, subject 8, after 21-day dry immersion

city: Moscow

first: Roman

middle: O.

last: Bokov

state: Moscow

address: Khoroshevskoye shosse, 76A

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Quality control of RNA sequencing data for each library was performed using the FASTQC program (version 0.12.1).
The tool Trimmomatic (Galaxy Version 0.38.1) was used to trim adapter sequences and low-quality readings.
The tool RNA STAR (Galaxy Version 2.7.10b+galaxy3) was used to map sequences to the Homo sapiens reference genome (version GRCh38.p14).
The read counts files were processed in the R (version 4.3.1). Normalization and differential gene expression analysis were performed using the R package «DESeq2» (analysis of paired samples with Benjamini-Hochberg correction).
Assembly: GRCh38.p14
Supplementary files format and content: One tab-delimited text file includes per gene read counts for each Sample

source_name: Soleus skeletal muscle

extract_protocol:
Using the method of open-incision muscle biopsy under local anesthesia, samples of the soleus muscle were taken from all subjects 10-20 days before the start of the experiment (pre-immersion samples) and on the day of the end of the experiment (post-immersion samples). Soleus muscle samples were immediately frozen in liquid nitrogen and then stored in a low-temperature freezer at -80 °C. Total RNA was isolated from muscle tissue using the RNA isolation kit RNeasy Micro (Qiagen, Germany).
5 μg of purified total RNA from samples corresponding to 4 subjects (4 pre-DI samples and 4 post-DI samples) were concentrated in 5 μL of nuclease free water, using vacuum concentrator SpeedVac Savant SC210A (ThermoFisher Scientific, USA). Then this total RNA was used as a template for the synthesis of the first cDNA strand (nAnTiCAGE Library Preparation kit, DNAform, Japan and SuperScript III Reverse Transcriptase, Invitrogen, USA), which was then biotinylated at the 5’ end of using (nAnTiCAGE Library Preparation kit, DNAform, Japan). This allowed selection of 5’ cap contained RNAs using streptavidin beads (Dynabeads M270 Streptavidin, ThermoFisher Scientific, USA). At this stage, rRNA, truncated or not fully transcribed RNA was eliminated. For more efficient removal of nonspecific RNA strands, cDNA was treated by RNase I and H (nAnTiCAGE Library Preparation kit, DNAform, Japan) and then was purified using Agencourt AMPure XP (Beckman Coulter, USA). Next, linkers at the 5’and 3’ ends (nAnTiCAGE Library Preparation kit, DNAform, Japan) were sequentially ligated to the cap-trapped cDNA. The 5’ linker contains the XmaJI restriction endonuclease recognition and the MmeI class II restriction enzyme recognition site, as well as a barcode for multiplexing (nAnTiCAGE Library Preparation kit, DNAform, Japan). The 3’ linker contains an XbaI restriction enzyme recognition site. After treatment with restriction enzymes, short CAGE tags were obtained (nAnTiCAGE Library Preparation kit, DNAform, Japan). At the final stage, a second cDNA strand was synthesized (nAnTiCAGE Library Preparation kit, DNAform, Japan). The concentration of the libraries was validated using qPCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, South Africa) and sequenced on a HiSeq 2500 platform (Illumina, USA) using the HiSeq version 4 reagent kit (HiSeq SR Cluster Kit version 4 cBot and HiSeq SBS Kit version 4 50 cycles, Illumina, USA) in the 60 bp single end mode.

treatment_protocol: Under an immersion environment, the volunteer’s body is subjected to an impact of the buoyant force of water, and the support reactions are eliminated. The studies were carried out under standard conventional conditions, during which volunteer testers were placed one at a time in a pool measuring 200 x 100 x 100 cm, filled with water, in a horizontal position, the water temperature in the bath was maintained constant at +33 ± 0.5 °C. The daily routine in immersion was regulated by time intervals selected for examinations, preventive measures (if any), meals and sanitary and hygienic procedures. The daily routine was as close as possible to the onboard one, including 8 hours of sleep, 3 meals per day, a medical monitoring program and experimental studies. To carry out sanitary and hygienic measures, once a day the testers were removed from the bath for 15–20 minutes using a special lift.

value: Soleus skeletal muscle

tag: subject

tag: Sex

tag: time point

value: after

tag: unloading model

value: 21-day dry immersion


title: Soleus skeletal muscle, subject 6, after 21-day dry immersion


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin

tag: cell type

tag: genotype

value: day 2


title: CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin (day 2)

data_processing:
Read alignments were conducted using RNA-star to mm39
Aligned reads were annotated for features using FeatureCounts from the subread package
Differential gene expression analysis was completed using the EdgeR package
Assembly: mm39
Supplementary files format and content: csv file with RPKM values for each sample

value: 0.001 mg/mL holotransferrin


title: K562, anti-H3K4me3, ZNF410-sgNeg2, rep2, ChIP-seq

tag: cell line

value: WT

tag: chip antibody


title: CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin


title: Soleus skeletal muscle, subject 8, before 21-day dry immersion

value: male

value: before


title: K562, anti-H3K4me3, ZNF410-sgNeg2, rep1, ChIP-seq


title: CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin (day 2)


title: K562, anti-H3K4me3, ZNF410-sgRNA, rep1, ChIP-seq

value: ZNF410 KO


title: Mac_CGAS_UT_1

description: Library name: Mac-CGAS-1

source_name: cGAS KO macrophages, untreated

value: macrophage

value: cGAS knockout

value: media control


title: Mac_CGAS_UT_2

description: Library name: Mac-CGAS-2


title: Soleus skeletal muscle, subject 7, before 21-day dry immersion


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin + 40 mM aspartate

value: CD8+ T-cells

value: 40 mM aspartate


title: Blastocyst_Zn_rep3

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

data_processing:
>Basecalls were performed using NextSeq 500/550 RTA software, v. 2.11.3
>FASTQ files were generated using bcl2fastq, v. 2.20.0.422
>Raw sequence reads were trimmed to remove adapters and poor qualities using fastp, v. 0.20.0
>RNA-seq reads were aligned to the mm10 mouse genome assembly using STAR, v. 2.6.0
>Uniquely aligned reads on anotated genes or best matched reads on annotated TE loci were counted using HTSeq 0.10.0
>Read counts were normalized and TPM values using DESeq2 (v. 1.28.1) for differential expression analysis between Zn-treated and control embryos
>Ensembl gene annotation (mm10, 46078 genes) and TE annotation were used to calculate TPM values
Genome_build: mm10

source_name: Blastocyst

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Qiagen) accoring to manufacturer’s protocols.
RNA-seq libraries were prepared using the SMART-Seq HT Plus Kit (Takara Bio).

value: Wild type

value: Blastocyst

value: Embryonic day 3.5


title: 10000833, HbAA, female, SS_control

description:
Library name: 10000833
SS_control/a10000833(norm)
SS_control/a10000833(raw)
SSvsSS_control.xlsx

value: plasma

tag: subject status

value: HbAA

tag: gender

value: female

tag: sample group


title: K562, anti-H3K27ac, ZNF410-sgRNA, rep2, ChIP-seq

value: human myeloid leukemia

value: ZNF411 KO

value: H3K27ac (Abcam, #ab4729)


title: CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin (day 2)

value: OT-I

value: 0.625 mg/mL holotransferrin

value: day 2


title: K562, anti-H3K27ac, ZNF410-sgRNA, rep1, ChIP-seq

value: ZNF410 KO


title: Soleus skeletal muscle, subject 6, before 21-day dry immersion

tag: tissue

value: Soleus skeletal muscle

value: male

value: before

value: 21-day dry immersion


title: Mac_CGAS_UT_3

description: Library name: Mac-CGAS-3

value: macrophage

value: cGAS knockout

tag: treatment

value: media control


title: Blastocyst_Zn_rep2

tag: strain

value: Wild type

value: Blastocyst

tag: age

value: Embryonic day 3.5


title: Soleus skeletal muscle, subject 5, after 21-day dry immersion

value: after


title: CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin (day 2)

value: CD8+ T-cells

tag: time


title: K562, anti-H3K27ac, ZNF410-sgNeg2, rep2, ChIP-seq

value: human myeloid leukemia

value: WT

value: H3K27ac (Abcam, #ab4729)


title: CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin (day 2)

value: OT-I

value: 0.625 mg/mL holotransferrin

value: day 2


title: Blastocyst_Zn_rep4


title: CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin (day 2)

value: 0.001 mg/mL holotransferrin


title: Blastocyst_Zn_rep1


title: K562, anti-H3K27ac, ZNF410-sgNeg2, rep1, ChIP-seq


title: Soleus skeletal muscle, subject 5, before 21-day dry immersion

value: Soleus skeletal muscle

value: male

value: before


title: CD8+ T-cells, mouse 2, naïve (day 0)

value: Naive

value: day 0


title: IMR-90_NPC_siZCC_5

city: New York

first: Andrew

middle: F

last: Teich

state: NY

institute: Columbia University Irving Medical Center

data_processing:
HiSeq Control Software used for basecalling
Illumina's bcl2fastq 2.17 software used to convert bcl to fastq files and de-multiplex
Reads were aligned using STAR (v2.7.6a) in 2-pass mapping mode with standard ENCODE parameters
Gene counts were quantified from STAR-aligned BAM files using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited file with raw gene counts for every gene and every sample

source_name: human iPSC-derived neuron

extract_protocol:
lysed in Qiazol
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: neuron

value: ZCCHC17 siRNA


title: Blastocyst_Control_rep3

value: Wild type

value: Blastocyst

value: Embryonic day 3.5


title: IMR-90_NPC_siZCC_4


title: K562, anti-ZNF410, ZNF410-sgRNA, rep2, ChIP-seq

first: Siyuan

last: Xu

institute: Fudan Unversity

value: human myeloid leukemia

value: ZNF411 KO

value: ZNF410 (Proteintech, #14529-1-AP)


title: Blastocyst_Control_rep2


title: K562, anti-ZNF410, ZNF410-sgRNA, rep1, ChIP-seq

value: ZNF410 KO


title: CD8+ T-cells, mouse 1, naïve (day 0)

value: CD8+ T-cells

value: OT-I


title: IMR-90_NPC_siZCC_3


title: Blastocyst_Control_rep4


title: Blastocyst_Control_rep1


title: K562, anti-ZNF410, ZNF410-sgNeg2, rep2, ChIP-seq

value: WT


title: IMR-90_NPC_siZCC_2


title: Parietal, 2

city: Bethesda

first: Eva

last: Mezey

state: MD

address: 30 Convent Dr.

department: NIDCR

institute: NIH

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N4_Parietal

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
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: Custom mm10/GRCm38.vM11+ERCCs
Supplementary files format and content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Parietal bone

extract_protocol:
Osteocytes enriched bone fractions were isolated from frontal, parietal and femur and processed into total RNA.
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA). The multiplexed libraries were sequenced in an Illumina instrument in 37bp paired end mode.

value: Parietal bone

value: 12 weeks

value: osteocytes


title: K562, anti-ZNF410, ZNF410-sgNeg2, rep1, ChIP-seq


title: Twocell_Zn_rep4

source_name: Two-cell stage embryo

value: Two-cell stage embryo

value: 24 h post insemination (hpi)


title: Frontal, 3

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N4_Frontal

source_name: Frontal bone

value: Frontal bone


title: IMR-90_NPC_siZCC_1

value: neuron

value: ZCCHC17 siRNA


title: K562, input, ChIP-seq


title: Twocell_Zn_rep3

value: Wild type


title: IMR-90_NPC_siZCC_6


title: CD8+ T-cells, mouse 3, naïve (day 0)

source_name: CD8+ T-cells

value: Naive

value: day 0


title: Femur, 3

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N4_Femur

source_name: Femur bone

value: Femur bone


title: IMR-90_NPC_siNC_6

value: negative control siRNA


title: Twocell_Zn_rep2


title: IMR-90_NPC_siNC_5


title: K562, ZNF410_sgRNA#2_rep2, RNA-seq

data_processing:
RNA-seq reads within FASTQ files were trimmed using trim_galore with default parameters.
Trimmed reads were aligned to the human reference genome hg38 using HISAT2 version 2.2.1 with default parameters.
SAMtools version 1.9 was applied to transform SAM into the BAM format.
HT-seq version 0.6.1 was used to calculate the read counts of each transcript.
RSEM version 1.3.2 was used to calculate the expression levels of each transcript by FPKM.
DESeq2 package version 1.36.0 was used for differential expression analysis.
Assembly: hg38
Supplementary files format and content: Raw counts for each sample; tab-delimited text files.
Supplementary files format and content: FPKM and TPM for each sample; comma-separated text files.

extract_protocol:
RNA was harvested using RNeasy Mini Kit from QIAGEN. About 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s protocol.

value: human myeloid leukemia

value: ZNF410 KO


title: Twocell_Zn_rep1


title: K562, ZNF410_sgRNA#2_rep1, RNA-seq


title: Femur, 2

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N2_Femur


title: IMR-90_NPC_siNC_4


title: K562, ZNF410_sgRNA#1_rep2, RNA-seq


title: Frontal, 2

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N2_Frontal


title: IMR-90_NPC_siNC_2


title: Twocell_Control_rep4


title: K562, ZNF410_sgRNA#1_rep1, RNA-seq


title: IMR-90_NPC_siNC_3


title: Femur, 1

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N1_Femur


title: Twocell_Control_rep3


title: IMR-90_NPC_siNC_1


title: Frontal, 1

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N1_Frontal


title: K562, sgNeg2_rep1, RNA-seq


title: Twocell_Control_rep1


title: Parietal, 1

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt
N2_Parietal


title: KO

status: Public on Mar 21 2025

city: Columbia

first: Shamsun

last: Nahar

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

description: Library name: Knock-out

library_source: transcriptomic single cell

data_processing:
10× genomic workflow and the Seurat packages were used for analysis of the data on R studio.
Assembly: mm39
Supplementary files format and content: tab-separated value (.tsv) and matrix files for each data set

source_name: uterus

growth_protocol: Pgrcre/+Mig-6f/f female mice were generated by breeding Pgrcre/+ Mig-6f/f  male with Mig-6f/f females.

extract_protocol:
single cells were extrated using Trypsin digestion method. Blood cells were removed using Dead Cell Removal Kit (Miltenyi 130-048-801). Hhemocytometer was used to determine the final concentration of cells in 1X PBS + 0.04 % BSA.
10x Genomic sequencing

value: uterus

value: Female

tag: developmental stage

value: Gestational day 3.5


title: Cont

description: Library name: Control


title: Posterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 2

city: Vienna

first: Elly

last: Tanaka

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP (Research Institute of Molecular Pathology)

description:
Library name: PosteriorBlastema-lowerinput_biol rep 2
Column "PosteriorBlastemaLOW_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

data_processing:
Adaptors sequences were trimmed from the raw sequencing reads with Trimmomatic (version 0.39, Bolger et al. 2014), using parameters: ILLUMINACLIP:Adapters.fa:2:30:7 SLIDINGWINDOW:4:15 MINLEN:50.
Poly(A) tails were trimmed with BBDuk (JGI), using parameters: ref=polyA.fa.gz k=13 ktrim=r useshortkmers=t mink=5 minlength=60. polyA.fa.gz contained 18 A nucleotides.
Trimmed sequenced reads were mapped to axolotl genome AmexG_v6.0-DD with HISAT2 (Kim et al. 2019), using parameters: --no-unal --summary-file Output.log -k 5 --very-sensitive -x DBGenome -U Reads.fq.gz > Alignment.sam
featureCounts (Liao et al. 2014) was used to generate a read counts table.
Assembly: AmexG_v6.0-DD
Supplementary files format and content: Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes. Processed data file contains counts data for all libraries in this GEO accession.

organism: Ambystoma mexicanum

source_name: Limb blastema

growth_protocol: Limb amputations were performed at mid-zeugopod level.

extract_protocol:
Total RNA was extracted using an in-house magnetic beads-based RNA purification kit (Vienna Biocenter Core Facilities)
RNA libraries were prepared with QuantSeq 3’ mRNA-Seq V2 REV kit with unique dual indices (Lexogen), using the following RNA inputs: higher input libraries (45 ng), lower input libraries (4.5 ng), transplantation libraries (4.5 ng), Hand2/mCherry libraries (0.7 ng). Samples were multiplexed for sequencing, using dual i5/i7 indices in the Quantseq kit.

value: Limb blastema

value: CT-blastema (Alx4:mCherry- Hand2:EGFP+)

value: 15 dpa


title: Anterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 4

description:
Library name: AnteriorBlastema-lowerinput_biol rep 4
Column "AnteriorBlastemaLOW_Rep4" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

value: CT-blastema (Alx4:mCherry+ Hand2:EGFP-)


title: Posterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 3

description:
Library name: PosteriorBlastema-lowerinput_biol rep 3
Column "PosteriorBlastemaLOW_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 4

description:
Library name: PosteriorBlastema-lowerinput_biol rep 4
Column "PosteriorBlastemaLOW_Rep4" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 2

description:
Library name: AnteriorBlastema-lowerinput_biol rep 2
Column "AnteriorBlastemaLOW_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 3

description:
Library name: AnteriorBlastema-lowerinput_biol rep 3
Column "AnteriorBlastemaLOW_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 1

description:
Library name: PosteriorBlastema-lowerinput_biol rep 1
Column "PosteriorBlastemaLOW_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior cells in transplantation assay to posterior, replicate 2

description:
Library name: A-to-P-Transplant_biol rep 2
Column "Aptransplant_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

value: CT-blastema (EGFP+)

value: 12 dpa, 2nd blastema after transplantation


title: Anterior blastema, 11 cm axolotl, 15 dpa, lower input, replicate 1

description:
Library name: AnteriorBlastema-lowerinput_biol rep 1
Column "AnteriorBlastemaLOW_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Twocell_Control_rep2

value: Two-cell stage embryo

value: 24 h post insemination (hpi)


title: Anterior cells in transplantation assay to anterior, replicate 2

description:
Library name: A-to-A-Transplant_biol rep 2
Column "Aatransplant_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

value: CT-blastema (mCherry+)


title: Anterior cells in transplantation assay to anterior, replicate 1

description:
Library name: A-to-A-Transplant_biol rep 1
Column "Aatransplant_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema misexpressing mCherry only, 16 cm axolotl, 14 dpa, replicate 2

description:
Library name: Prrx1-mCherry-anterior_biol rep 2
Column "Prrx1-mCherry-A_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

value: 14 dpa


title: K562, sgNeg2_rep2, RNA-seq

city: Shanghai

address: No.131, Dongan Road, Shanghai

value: WT


title: Anterior blastema misexpressing mCherry-Hand2, 16 cm axolotl, 14 dpa, replicate 2

description:
Library name: Prrx1-mCherry-Hand2_biol rep 2
Column "Prrx1-Hand2_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 4

description:
Library name: PosteriorBlastema-higherinput_biol rep 4
Column "PosteriorBlastemaHI_Rep4" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema misexpressing mCherry-Hand2, 16 cm axolotl, 14 dpa, replicate 1

description:
Library name: Prrx1-mCherry-Hand2_biol rep 1
Column "Prrx1-Hand2_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema misexpressing mCherry-Hand2, 16 cm axolotl, 14 dpa, replicate 3

description:
Library name: Prrx1-mCherry-Hand2_biol rep 3
Column "Prrx1-Hand2_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema misexpressing mCherry only, 16 cm axolotl, 14 dpa, replicate 1

description:
Library name: Prrx1-mCherry-anterior_biol rep 1
Column "Prrx1-mCherry-A_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 4

description:
Library name: AnteriorBlastema-higherinput_biol rep 4
Column "AnteriorBlastemaHI_Rep4" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 2

description:
Library name: PosteriorBlastema-higherinput_biol rep 2
Column "PosteriorBlastemaHI_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 3

description:
Library name: PosteriorBlastema-higherinput_biol rep 3
Column "PosteriorBlastemaHI_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 2

description:
Library name: AnteriorBlastema-higherinput_biol rep 2
Column "AnteriorBlastemaHI_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Posterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 1

description:
Library name: PosteriorBlastema-higherinput_biol rep 1
Column "PosteriorBlastemaHI_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Anterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 1

description:
Library name: AnteriorBlastema-higherinput_biol rep 1
Column "AnteriorBlastemaHI_Rep1" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.


title: Batch 2 - ADT

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

description: 10x Feature Barcode

library_source: other

data_processing:
Cellranger 7.1 was run in multi mode and filtered matrices generated.
Assembly: mm10
Supplementary files format and content: Filtered H5 format matrices.

molecule: protein

source_name: Splenic GC B cells

extract_protocol:
Viable, CD19+CD38-GL-7+ GC B cells were sorted and labelled with Biolegend TotalSeq C HTOs (TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody = B-WT/Control diet; TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody = B-Asns/Control diet; TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody = B-WT/Asn-free diet; TotalSeq™-C0303 anti-mouse Hashtag 4 Antibody = B-Asns/Asn-free diet).
Approximately 10,000 cells per batch were loaded onto the 10X Genomics Chromium Controller (Chip K). Gene expression libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B).

value: Splenic GC B cells

value: Mixed (Mb1-cre x Asns flox or Mb1-cre x Asns WT)

tag: condition

value: Mixed (Asn-free diet or control diet)

tag: library type

value: HTO

tag: adt

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody = B-WT/Control diet; TotalSeq-C0302 anti-mouse Hashtag 2 Antibody = B-Asns/Control diet; TotalSeq-C0303 anti-mouse Hashtag 3 Antibody = B-WT/Asn-free diet; TotalSeq-C0303 anti-mouse Hashtag 4 Antibody = B-Asns/Asn-free diet)


title: Batch 3 - ADT

description: 10x Feature Barcode


title: Batch 1 - ADT

description: 10x Feature Barcode


title: Batch 2

description: 10x 5' Gex

value: mRNA


title: Batch 1

description: 10x 5' Gex


title: Batch 3

description: 10x 5' Gex


title: Anterior cells in transplantation assay to posterior, replicate 1

description:
Library name: A-to-P-Transplant_biol rep 1
Column "Aptransplant_Rep2" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.

value: Limb blastema


title: Anterior blastema, 11 cm axolotl, 15 dpa, higher input, replicate 3

description:
Library name: AnteriorBlastema-higherinput_biol rep 3
Column "AnteriorBlastemaHI_Rep3" in MatrixCounts.csv. Library was sequenced on two lanes of the same flow cell. Raw sequencing reads are provided separately for each lane. Processed data file contains combined counts from both lanes.