title: WT_CHD1_CHIP_1

description: Library name: WT_CHD1_CHIP_1


title: MLL4_DKO_rep_1

status: Public on Apr 09 2026

type: SRA

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

country: Japan

institute: Yokohama city university

description: Library name: MLL4_DKO_rep_1

library_source: genomic

data_processing:
Raw sequencing reads were quality-controlled and trimmed using Fastp
Sequence reads were aligned using bowtie2
Aligned reads were processed using SAMtools to generate BAM and index files
Peak calling was performed with MACS2 in narrowPeak mode using a q-value cutoff of < 0.05
MAnorm was used for comparison of ChIP peaks
For visualization, bamCoverage was used to generate BigWig files with counts per million normalization
ChIP tracks were visualized using the Integrative Genomics Viewer.
Heatmaps and aggregation plots were created using deepTools computeMatrix, followed by visualization with plotHeatmap and plotProfile.
De novo and known motif enrichment analyses were performed using HOMER
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: Embryonic cells

extract_protocol:
Cells were cross-linked with 2 mM disuccinimidyl glutarate in PBS/1 mM MgCl2 for 40 min at room temperature followed by 1% formaldehyde in PBS for 15 min at room temperature. The reaction was stopped by 125 mM glycine. The cells were washed with PBS and stored at –80°C prior to use. The cells were lysed in Lysis buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine) containing proteinase inhibitor cocktail (Roche). Sonication was conducted with the Handy sonicator UR-21P (Tomy) to generate DNA fragments of approximately 150-450 bp. The sonicated lysates from approximately 2 x 106 cells were diluted in ChIP dilution buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 1% IGEPAL-CA-630, 10% glycerol) containing proteinase inhibitor cocktail and incubated overnight at 4°C with 50 µl of protein G magnetic beads (Invitrogen) that were preincubated with ~2 µg of mouse Zscan4 antibodies. The precipitants were washed once with high salt wash buffer (20 mM Tris-HCl, pH8.0, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.2% Triton-X), three times with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% Na-deoxycholate) and once with 10 mM Tris-HCl, pH 8.0, 5 mM EDTA, 10 mM NaCl. Bound chromatin was eluted in elution buffer (90 mM NaHCO3, 1% SDS), followed by RNase treatment at 37°C for 30 min and crosslink reversal with decross-linking mixture (2 M NaCl, 0.1 M EDTA, 0.4 M Tris-HCl, pH 6.8) containing proteinase K at 65°C for 3 h. DNA was purified by a phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
ChIP DNA libraries were prepared with the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB)

tag: tissue

value: Embryonic cells

tag: cell line

value: ES cells (SEES3)

tag: cell type

value: Pluripotent stem cells


title: W131G_Input

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

country: USA

institute: MD Anderson Cancer Center

description: Library name: W131G_Input

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore (version 0.6.7) and cutadapt (version 4.1).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: ""--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 500 bp (less than 1% of the total) were excluded from subsequent analysis.
For bigWig files, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was normalized to 10M total number of fragments. These values were then averaged over a 10 bp resolution.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Prostate

growth_protocol: RPMI 1640 medium containing 10% (v/v) fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Cross-linking was quenched by glycine, followed by cell lysis. Chromatin was fragmented by sonication using ultrasonicator to obtain DNA fragments of appropriate size for downstream applications.
KAPA Hyper Prep Kit

value: Prostate

value: LNCaP

value: Human prostate cancer

tag: genotype

tag: treatment

tag: chip antibody


title: MLL4_hES_rep_1

description: Library name: MLL4_hES_rep_1


title: JH1O_53BP1_KO_JH1bait_12

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

description:
Library name: Sample 141
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using VDJ-HTGTS-Seq (Hu et al., 2016)

treatment_protocol: v-Abl transformed pro-B cell lines were cultured in R15 medium and stimulated with 3 uM STI-571 treated for 4 days.

value: v-Abl transformed pro-B cell line

value: 53BP1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Tim5

city: Freiburg

first: Philipp

last: Henneke

state: Baden-Württemberg

address: Breisacher Straße 115 B

department: Institute for Infection Prevention and Control (IIK)

country: Germany

institute: University Hospital Freiburg

description: Tim5 SW77

data_processing:
Data was preprocessed in Galaxy Europe. Adapters were trimmed with Cutadapt, the sequences aligned to mm10 via Bowtie2, and the reads filtered based on the phred scale scale ≥ 30 and proper pair alignment
Additionally, reads aligning to the mitochondrial chromosome were excluded, as well as further blacklist regions. Duplicates were removed with Picard’s MarkDuplicates function with a lenient validation stringency. Peaks were called using MACS2.
R studio (4.3.2) was used to analyse the data with DESeq2 for which a batch correction was performed. Genes with row sums below 10 were excluded.
Assembly: mm10
Supplementary files format and content: Processed bigwig files

source_name: liver

growth_protocol: SPF animal facility

extract_protocol:
Livers were isolated and digested 4 weeks after injection of PBS or BCG-BFP. Kupffer cells were sorted by flow cytometry.
Samples were subjected to the Tn5 Illumina Tagment DNA Enzyme and Buffer kit. Purification was performed with the MinElute Reaction Cleanup Kit (Qiagen), DNA amplified with NEBNext High-Fidelity 2x PCR MasterMix and 24 UDI for Tagmented libraries (8 cycles), and again subjected to the MinElute Reaction Cleanup Kit. Size selection was performed with the AMPure XP Bead-Based Reagent (Beckman Coulter) and verified with a Tapestation (Agilent)

treatment_protocol: Mice received either i.v. injection of BCG-BFP (10^7 cfu) or PBS in 100µl

value: liver

value: Kupffer cell

tag: time

value: 4 weeks post injection

tag: mouse

tag: antibody

value: tdTom+ Tim4-

value: BCG i.v.

tag: batch

value: batch 4


title: MCF7 with AdipoRON treatment No1

first: Shinya

last: Sato

address: 2-3-2, Nakao, Asahi-Ku

institute: Kanagawa Cancer Center Research Institute

description:
Library name: MCF7-A1
Takarabio

library_source: transcriptomic

data_processing:
For data cleaning, missing values were checked for each sample, and genes with high missing values were excluded. Data normalization was performed using the TPM (Transcripts Per Million) method. For filtering, genes with very low average expression levels (genes with expression levels less than 1 TPM) were excluded from the analysis. Differential gene expression analysis between conditions was performed using the DESeq2 package. Analysis was performed using the Takara analysis package to compare treated and untreated cases using heat maps.
Assembly: GRCh38.p14
Supplementary files format and content: Processed data files are provided in excel file containing count data normalized with TPM. Each row represents a unique gene, and each column corresponds to a sample.

molecule: total RNA

growth_protocol: All cell lines were incubated in RPMI1640 with 10%FBS and antibiotics

extract_protocol:
All RNAs of all samples were extracted using RNeasy mini (Qiagen) following their protocol.
Adapter sequences were added to both ends of the first strand cDNA using the SMART (Switching Mechanism At 5'End of RNA Template) method. PCR amplification was performed using a primer that recognized the added adapter sequence, and the PCR product obtained was purified using AMPure XP (Beckman Coulter) to obtain a double-stranded cDNA amplified product. Then, double-stranded cDNA was fragmented and adapter sequences were added to both ends by a tagmentation reaction using a transposon. PCR amplification was performed using indexed primers that recognized the adapter sequence and had a tag sequence that differed for each sample, and an indexed sequence library was created. The quality of the created sequence library was tested using an electrophoresis device. The reagents used for library creation are listed in the datasheet. The procedure was performed according to the manual that came with the reagent.

treatment_protocol: All cell lines were treated with AdipoRON or DMSO for 24 hours

value: breast cancer cell line

value: WT

value: AdipoRON treatment


title: SOX2_DKO_rep_2

description:
Library name: SOX2_DKO_rep_2
Replicates were merged and visualized as a single bigWig file.

value: Embryonic cells

value: ES cells (SEES3)


title: JH1O_HMGB1_KO_JH1bait_3

description:
Library name: Sample 140
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: HMGB1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: Low5

description: Low5 SW76

value: tdTom- Tim4+


title: High5

description: High5 SW75

value: tdTom+ Tim4+


title: W131G_CHD1_CHIP_1

description: Library name: W131G_CHD1_CHIP_1

value: Prostate

value: LNCaP

value: Human prostate cancer

value: CHD1 (4351S, Cell Signaling Technology)


title: W131G_CHD1_CHIP_2

description: Library name: W131G_CHD1_CHIP_2


title: SOX2_DKO_rep_1

description:
Library name: SOX2_DKO_rep_1
Replicates were merged and visualized as a single bigWig file.

value: Pluripotent stem cells


title: JH1O_HMGB1_KO_JH1bait_2

description:
Library name: Sample 139
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: SOX2_hES_rep_2

description:
Library name: SOX2_hES_rep_2
Replicates were merged and visualized as a single bigWig file.


title: PBS4

description: PBS4 SW73

value: liver

value: Kupffer cell

value: 4 weeks post injection

value: PBS i.v.

value: batch 3


title: SOX2_hES_rep_1

description:
Library name: SOX2_hES_rep_1
Replicates were merged and visualized as a single bigWig file.

value: Embryonic cells


title: JH1O_HMGB1_KO_JH1bait_1

description:
Library name: Sample 138
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Untreat_SP1_CHIP_2

description: Library name: Untreat_SP1_CHIP_2

value: SP1 (9389S, Cell Signaling Technology)


title: JH1O_JH1bait_17

description:
Library name: Sample 137
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Untreat_SP1_CHIP_1

description: Library name: Untreat_SP1_CHIP_1


title: Untreat_Input

description: Library name: Untreat_Input


title: Tim4

description: Tim4 SW72

value: tdTom+ Tim4-

value: BCG i.v.


title: OCT4_UTYKO_rep_2

description:
Library name: OCT4_UTYKO_rep_2
Replicates were merged and visualized as a single bigWig file.

value: ES cells (SEES3)


title: Treated_SP1_CHIP_2

description: Library name: Treated_SP1_CHIP_2

value: Prostate

value: LNCaP

value: Atorvastatin 10𝜇M 48hr


title: Low4

description: Low4 SW71

value: tdTom- Tim4+


title: OCT4_UTYKO_rep_1

description:
Library name: OCT4_UTYKO_rep_1
Replicates were merged and visualized as a single bigWig file.

value: Pluripotent stem cells


title: High4

description: High4  SW70

value: tdTom+ Tim4+


title: JH1O_JH1bait_16

description:
Library name: Sample 136
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: Treated_SP1_CHIP_1

description: Library name: Treated_SP1_CHIP_1

value: Human prostate cancer


title: OCT4_UTYKO_ctrl_rep_2

description:
Library name: OCT4_UTYKO_ctrl_rep_2
Replicates were merged and visualized as a single bigWig file.


title: JH1O_XRCC1_KO_JH1bait_3

description:
Library name: Sample 134
JH1 bait\, XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: XRCC1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: PBS3

description: PBS3 SW68

value: liver

value: Kupffer cell

value: 4 weeks post injection

value: PBS i.v.

value: batch 2


title: Treated_Input

description: Library name: Treated_Input


title: High3

description: High3 SW67

value: BCG i.v.


title: JH1O_JH1bait_15

description:
Library name: Sample 135
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: OCT4_DKO_rep_1

description:
Library name: OCT4_DKO_rep_1
Replicates were merged and visualized as a single bigWig file.

value: Embryonic cells

value: ES cells (SEES3)


title: JH1O_XRCC1_KO_JH1bait_2

description:
Library name: Sample 133
JH1 bait\, XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: EM-seq with Hifiv3, 10 pg input

city: Wuhan City

first: Zhiyuan

last: Hu

address: No. 115 East Lake Road (Donghu Road), Wuchang District

department: Medical Research Institute

institute: Wuhan University

description: Library name: Hifiv3_PCR_10pg

data_processing:
Adapter and quality filtering were performed with Trim Galore (v0.6.10). Parameters were applied specifically for each sample group: Converted HeLa were trimmed with default parameters, while methylc and fish samples were trimmed with -paired --length 35 --clip_R1 10 --clip_R2 15 --three_prime_clip_R 10 --three_prime_clip_R2 10. Trimmed reads were aligned to the human reference genome (GRCh38) or the zebrafish reference genome (GRCz11.114) with spike-in sequences included. Converted DNA libraries were aligned using Bismark (v0.24.2) with default parameters. Zebrafish samples were aligned using Bismark (v0.24.2) with --maxins 1000. PCR duplicates were removed using deduplicated_bismark. Methylation information was extracted from deduplicated BAM files using bismark_methylation_extractor with default settings.
Assembly: GRCh38, GRCz11.114
Supplementary files format and content: Supplementary_files_format_and_content: CpG modification bismark report in the bedGraph format
Library strategy: EM-seq

source_name: HeLa cell

growth_protocol: HeLa cells were cultured in a humidified incubator at 37°C with 5% CO₂. The cells were maintained in the DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin. Cells were seeded at a density of approximately 50,000 cells/cm² in T25 flasks and passaged upon reaching 80-90% confluency. Zebrafish were raised and maintained under standard conditions.

extract_protocol:
HeLa cells were detached, collected, and pelleted by centrifugation at 300 × g for 5 min. Genomic DNA was subsequently extracted using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme) according to the manufacturer’s protocol. Genomic DNA was fragmented to an average size of ~300  bp using a Covaris M220 Focused-ultrasonicator.  Embryos of zebrafish were collected at four developmental stages: 64-cell, 128-cell, 1k-cell, and Germ ring. Before DNA extraction, embryos were bleached with bleach solution (0.1 ml 5% NaClO in 170 ml system water) for 5 min and rinsed thoroughly with 1× PBS. Genomic DNA was isolated using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme), according to the manufacturer’s protocol. Genomic DNA from the embryos was fragmented to an average size of around 300 bp using the Bioruptor Pico sonication device (Diagenode). For the 128-cell, 1K-cell, and Germ-ring samples, an optimised sonication program was used, i.e., 15 s ON/30 s OFF, 4 cycles for the 50-μl sample volume. For the 64-cell-stage gDNA, 3 cycles of 15 s ON/30 s OFF were used instead.
End repair and A-tailing were performed for fragmented DNA using the VANTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) with EM-seq adapters (NEB) according to the manufacturer’s protocol. After adapter ligation, unmethylated cytosines in the DNA were enzymatically converted to uracil using the EpiArt DNA Enzymatic Methylation Kit (Vazyme), following the manufacturer’s protocol. For FINE-EM-seq libraries, FINE amplification was applied on converted DNA(including 1 ng, 100 pg, 1 pg HeLa gDNA and 1 ng of each stage's zebrafish gDNA), followed by a 3-cycle PCR to add full-length adapters for Illumina sequencing. For PCR methylation libraries, converted DNA was amplified using 2× Synthesis Mix (ABclonal) or HiFi V3 (Vazyme). PCR thermal cycling consisted of an initial denaturation at 98°C for 45 s; followed by 16 cycles (for 1 ng), 20 cycles (for 100 pg), or 23 cycles (for 10 pg) of 98°C for 15 s, 60°C for 30 s, and 72°C for 20 s; followed by a final extension at 72°C for 1 min and then hold at 12°C. The amplified DNA was purified twice using 0.8× VANTS DNA Clean Beads (Vazyme).

value: HeLa cell


title: OCT4_UTYKO_ctrl_rep_1

description:
Library name: OCT4_UTYKO_ctrl_rep_1
Replicates were merged and visualized as a single bigWig file.


title: JH1O_XRCC1_KO_JH1bait_1

description:
Library name: Sample 132
JH1 bait\, XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: OCT4_UTXKO_rep_2

description:
Library name: OCT4_UTXKO_rep_2
Replicates were merged and visualized as a single bigWig file.


title: EM-seq with Hifiv3, 100 pg input

description: Library name: Hifiv3_PCR_100pg


title: PBS2

description: PBS2 SW58

value: batch 1


title: PBS1

description: PBS1 SW57


title: OCT4_UTXKO_rep_1

description:
Library name: OCT4_UTXKO_rep_1
Replicates were merged and visualized as a single bigWig file.

value: Pluripotent stem cells


title: EM-seq with Hifiv3, 1 ng input

description: Library name: Hifiv3_PCR_1ng


title: OCT4_DKO_rep_2

description:
Library name: OCT4_DKO_rep_2
Replicates were merged and visualized as a single bigWig file.


title: Tim2

description: Tim2 SW56

value: tdTom+ Tim4-


title: JH1O_EXO1_KO_JH1bait_2

description:
Library name: Sample 130
JH1 bait\, EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: EXO1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: Low2

description: Low2 SW55

value: tdTom- Tim4+


title: JH1O_EXO1_KO_JH1bait_1

description:
Library name: Sample 129
JH1 bait\, EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_EXO1_KO_JH1bait_3

description:
Library name: Sample 131
JH1 bait\, EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: EM-seq with 2x syn, 100 pg input

description: Library name: 2xsyn_PCR_100pg


title: OCT4_hES_rep_2

description:
Library name: OCT4_hES_rep_2
Replicates were merged and visualized as a single bigWig file.


title: EM-seq with 2x syn, 10 pg input

description: Library name: 2xsyn_PCR_10pg


title: Tim1

description: Tim1 SW53

value: liver


title: JH1O_JH1bait_12

description:
Library name: Sample 126
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: EM-seq with 2x syn, 1 ng input

description: Library name: 2xsyn_PCR_1ng


title: JH1O_JH1bait_14

description:
Library name: Sample 128
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: FINE-EM-seq, 10 pg input

description: Library name: 2xsyn_FINE_10pg


title: High2

description: High2 SW54

value: Kupffer cell

value: tdTom+ Tim4+


title: OCT4_hES_rep_1

description:
Library name: OCT4_hES_rep_1
Replicates were merged and visualized as a single bigWig file.


title: Low1

description: Low1 SW52

value: 4 weeks post injection


title: FINE-EM-seq, 100 pg input

description: Library name: 2xsyn_FINE_100pg


title: JMJD3_Flag_Dif_rep_2

description: Library name: JMJD3_Flag_Dif_rep_2


title: JH1O_JH1bait_13

description:
Library name: Sample 127
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Flag_Dif_ctrl

description: Library name: Flag_Dif_ctrl


title: JH1O_PARP1i_JH1bait_3

description:
Library name: Sample 125
JH1 bait\, PARP1i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 1μM PARP1i on the second day


title: High1

description: High1 SW51

value: BCG i.v.


title: JMJD3_Flag_Dif_rep_1

description: Library name: JMJD3_Flag_Dif_rep_1


title: JH1O_PARP1i_JH1bait_2

description:
Library name: Sample 124
JH1 bait\, PARP1i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: FINE-EM-seq, 1 ng input

description: Library name: 2xsyn_FINE_1ng


title: A3023_plasmid_expression_input

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: A3023_plasmid_expression_input

data_processing:
ChIP-seq paired-end reads were trimmed and mapped to the E. coli MG1655 reference genome (GenBank accession NC_000913), the lambda phage genome(GenBank accession J02459 M17233 M24325 V00636 X00906), and the plasmid containg catalytically inactive Lamassu (Extended data table 2, ID MH134) using fastp (Chen et al., 2018) and Bowtie2 (Langmead et al., 2012) with default parameters, respectively.
Mapped reads were sorted and indexed using the SAMtools software package (Li et al., 2009) (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option).
Alignments were normalised by CPM (Counts Per Million) and converted to 1 bp-bin bigwig files using the deepTools2 (Ramirez et al., 2016) command bamCoverage (--normalizeUsing CPM -bs 1 parameters).
After normalization, genome-mapping reads were visualised in IGV (Robinson et al., 2011). The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) (Quinlan et al., 2010) and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously (Cooper et al., 2018).
Peaks were called on pre-normalised alignments using MACS3 (Zhang et al., 2008), with the parameters -g 4500000 --nomodel --extsize 400 -q 0.05 -B, with respect to a non-immunoprecipitated control sample of Eco_dTnpB (-n option). The peak summit coordinates in the MACS3 output summits.bed file were extended to encompass a 200-bp window using the following Bedtools command: bedtools slop -l 100 -r 99. Sequence motifs were identified using MEME ChIP (Bailey et al., 2009) with default parameters.
Assembly: NC_000913
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.

organism: Escherichia coli

source_name: Liquid cell culture

growth_protocol: For ChIP-seq, E. coli transformations were performed using a single plasmid encoding the catalytically inactive Lamassu system; LmuA (K57A), LmuC and LmuB. LmuB was 3xFLAG-tagged.  The E. coli growth protocol generally followed the ChIP-seq protocols that were previously described (Hoffmann, Kim, Beh et al. 2022; Meers et al. 2023; Wiegand et al. 2024) with exception for cells grown in liquid media instead of solid media. In brief, colonies were inoculated into 25 ml liquid LB media. At OD .1, cultures were induced with .02% arabinose and grown to OD .9 before lambda phage infection at MOI 5 for the period of time as described in the sample name. For plasmid expression of binding site, a separate plasmid was transformed into the E. coli strain expressing the Lamassu system, and cultures were grown to OD .6.

extract_protocol:
For ChIP-seq, liquid LB overnight E. coli cultures were made up to 40 ml of volume using LB media. Crosslinking and immunoprecipitation generally followed our previous ChIP-seq protocols (Hoffmann, Kim, Beh et al., 2022; Meers et al., 2023), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to the tubes containing 40 ml of overnight culture (~1% final concentration), and the solution was mixed immediately by inverting and vortexing. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD at 600 nm was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in paired-end mode with the Biosciences Aviti Cloudbreak Freestyle platform, or single end reads with the Illumina Miniseq.

treatment_protocol: For ChIP-seq, Lamassu systems were heterologously expressed in E. coli MG1655 using inducible promoters.

tag: strain

value: Liquid cell culture

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

value: induced expression, 4 h, 37°C

value: LmuB ectopic plasmid expression


title: A3060_plasmid_expression_IP

description: Library name: A3060_plasmid_expression_IP


title: UTY_Flag_Dif_rep_1

description: Library name: UTY_Flag_Dif_rep_1

value: Embryonic cells

value: ES cells (SEES3)

value: Pluripotent stem cells


title: UTX_Flag_Dif_rep_1

description: Library name: UTX_Flag_Dif_rep_1


title: Flag_hES_ctrl

description: Library name: Flag_hES_ctrl


title: JH1O_PARP1i_JH1bait_1

description:
Library name: Sample 123
JH1 bait\, PARP1i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: JH1O_DMSO_JH1bait_12

description:
Library name: Sample 121
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: UTY_Flag_hES_rep_3

description:
Library name: UTY_Flag_hES_rep_3
Replicates were merged and visualized as a single bigWig file.


title: JH1O_DMSO_JH1bait_13

description:
Library name: Sample 122
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Rh-LRG1 treatment with 100 ng/mL 3

type: RNA

city: Tlaxcala

first: Federico

last: Osorio Antonio

state: Puebla

address: 11 Pte av.

department: Faculty of biotechnology

country: Mexico

institute: Popular Autonomous University of the State of Pueb

description:
HCan_05_10.xls
Biological replicate 1 of 2. LRG1_2, Triple Negative Breast cancer cells MDA-MB-231 treated with RPMI medium control + 100 ng/mL of Rh_LRG1, harvested 24 hours after treatment.

hyb_protocol: standard protocol

scan_protocol: ScanArray 4000 system  (Packard BioChips, Billerica, MA, USA)

data_processing:
Microarray fluorescence data were normalized using the Z-score transformation method. Pathway and enrichment analyses were carried out in R software (v4.2.2) using RStudio, with the Bioconductor package clusterProfiler v4.9. Visualization and pathway mapping were performed using Pathview and Heatmapper. Additional functional enrichment of the top up- and down-regulated genes was performed using g:Profiler
Genes with a z-ratio > ±1.5 were considered significantly differentially expressed.

label: ALEXA 647

source_name: MDA-MB-231+ RPMI culture medium+Recombinant human LRG1 100 ng/ML

label_protocol: 5 μg of total RNA were reverse-transcribed into cDNA and labeled with Alexa Fluor 555 and Alexa Fluor 647 dyes

extract_protocol: cells were washed with PBS and total RNA was obtained using Trizol following manufacturer's instructions

treatment_protocol: MDA-MB-231 cells were grown in RPMI culture medium, suplemented with 10 % of FBS+L-glutamin + 100 ng/mL of recombinant human LRG1 protein

value: triple negtive cells from Breast Adenocarcinoma


title: 1DPA, Xenopus limb cultured in air liquid inteface

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

institute: The Max Planck Society for Biology

description: Library name: Xen_ALI

library_source: transcriptomic single cell

data_processing:
Mouse and Xenopus scRNA-seq samples were processed using Cell Ranger (version 8.0.1) with the GRCm39 (2024-A) mouse genome reference dataset provided by 10x Genomics Genomics (refdata-gex-GRCm39-2024-A) and the Xenopus laevis 10.1 (CRREF007_Xenopus_Laevis_v10.1_Genome), for Xenopus samples.
Assembly: GRCm39
Assembly: CRREF007_Xenopus_Laevis_v10.1_Genome
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: barcodes, genes, and matrix files.  barcodes_AERfactors.tsv (-1_1 = VehCtrl_96w, -1_2 = AER_96w, -1_3 = AER_ALI), barcodes_Mouse_ALI_vs_96w.tsv (-1_1 = ALI, -1_2 = 96w), barcodes_Xen_ALI_vs_96w.tsv (-1_1 = ALI, -1_2 = 96w).

organism: Xenopus laevis

source_name: limb explants

extract_protocol:
5 to 6 limb explants for 1 dpa were pooled in an Eppendorf tube and immediately processed for dissociation.
Single-cell Gene Expression libraries were then prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000268) following the manufacturer's instruction (protocol CG000315 Rev C).

treatment_protocol: 100 ng/mL BMP4 (PeproTech, 120-05ET), 100 ng/mL FGF10 (PeproTech, 100-26), 3 µM CHIR99021 (Calbiochem, 361559), and 100 ng/mL EGF (Thermo Scientific, AF-100-15). CHIR99021 was prepared in DMSO (Thermo Scientific, BP231-100) and recombinant proteins were prepared according to manufacturer’s recommendations. The vehicle control had the volume matched DMSO and according to the vehicle of the recombinant protein batches. All molecules were diluted in media and maintained throughout the duration of the experiment, with fresh cocktail added during media changes once every 2 days.

value: limb explants

value: Epithelial cells, Schwann cells, muscle,immune cells, chondrocytes,connective tissue, etc

value: WT Xenopus

value: No treatment


title: 1DPA, Xenopus limb cultured in 96 well plate

description: Library name: Xen_96w


title: Rh-LRG1 treatment with 100 ng/mL 2

description:
HCan_05_09 (2).xls
Biological replicate 1 of 2. LRG1_2, Triple Negative Breast cancer cells MDA-MB-231 treated with RPMI medium control + 100 ng/mL of Rh_LRG1, harvested 24 hours after treatment.

growth_protocol: MDA-MB-231 cells were grown in RPMI culture medium, suplemented with 10 % of FBS+L-glutamin

value: RPMI culture medium+Recombinant human LRG1 100 ng/ML


title: JH1O_DMSO_JH1bait_11

description:
Library name: Sample 120
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: UTY_Flag_hES_rep_2

description:
Library name: UTY_Flag_hES_rep_2
Replicates were merged and visualized as a single bigWig file.


title: A3163_20min_IP

description: Library name: A3163_20min_IP

value: induced expression, 4 h, 37°C, followed by 20 min phage infection

value: LmuB lambda infection


title: Control 3

description:
HCan_05_10.xls
Biological replicate 2 of 2. Control_3 Triple Negative Breast cancer cells MDA-MB-231 treated with RPMI medium, control, harvested 24 hours after treatment.

label: ALEXA 555

source_name: MDA-MB-231+ RPMI culture medium

value: RPMI culture medium


title: Control 2

description:
HCan_05_09 (2).xls
Biological replicate 1 of 2. Control_2 Triple Negative Breast cancer cells MDA-MB-231 treated with RPMI medium, control, harvested 24 hours after treatment.


title: PIP4K2A KD #2, Rep3

city: La Jolla

first: Brooke

middle: M.

last: Emerling

state: CA

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: PIP4K2A_KD2_Rep3

data_processing:
Raw sequencing reads were pre-processed to remove llumina Truseq adapters and polyA/polyT sequences using Cutadapt version 2.3. Trimmed reads were aligned against human genome version hg38 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene level estimated counts and transcripts per million (TPM) were obtained using RSEM version 1.3.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited RNA-seq transcripts per million (TPM) and counts

extract_protocol:
RNA was extracted from cell pellets washed with PBS using Directzol RNA MiniPrep (Zymo Research Corporation; Fisher Cat# 50-444-628). RNA yield and purity was tested using the Qubit 4 Fluorometer prior to analysis.
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001) with Elevate Long UDI Adapter Kit Set A (Element Biosciences, Cat: 830-00010). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Kit (Element Biosciences, Cat: 860-00004).

value: shPIP4K2B;shPIP4K2A shRNA


title: UTY_Flag_hES_rep_1

description:
Library name: UTY_Flag_hES_rep_1
Replicates were merged and visualized as a single bigWig file.


title: A3180_5min_IP

description: Library name: A3180_5min_IP

value: Liquid cell culture

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

value: induced expression, 4 h, 37°C, followed by 5 min phage infection


title: JH1O_Polqi_JH1bait_2

description:
Library name: Sample 118
JH1 bait\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 10μM Polqi on the second day


title: UTX_Flag_hES_rep_3

description:
Library name: UTX_Flag_hES_rep_3
Replicates were merged and visualized as a single bigWig file.

value: Embryonic cells

value: ES cells (SEES3)

value: Pluripotent stem cells


title: PIP4K2A KD #2, Rep1

description: Library name: PIP4K2A_KD2_Rep1


title: PIP4K2A KD #2, Rep2

description: Library name: PIP4K2A_KD2_Rep2


title: A3197_10min_IP

description: Library name: A3197_10min_IP

value: induced expression, 4 h, 37°C, followed by 10 min phage infection


title: A3109_20min_input

description: Library name: A3109_20min_input


title: JH1O_Polqi_JH1bait_3

description:
Library name: Sample 119
JH1 bait\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: UTX_Flag_hES_rep_1

description:
Library name: UTX_Flag_hES_rep_1
Replicates were merged and visualized as a single bigWig file.


title: JH1O_Polqi_JH1bait_1

description:
Library name: Sample 117
JH1 bait\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_DMSO_JH1bait_10

description:
Library name: Sample 116
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: PIP4K2A KD #1, Rep3

description: Library name: PIP4K2A_KD1_Rep3


title: UTX_Flag_hES_rep_2

description:
Library name: UTX_Flag_hES_rep_2
Replicates were merged and visualized as a single bigWig file.


title: A3123_10min_input

description: Library name: A3123_10min_input


title: JH1O_DMSO_JH1bait_9

description:
Library name: Sample 115
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: H3K27me3_DKO_rep_2

description:
Library name: H3K27me3_DKO_rep_2
rep_1 and rep_2 were merged and visualized as a single bigWig file.

data_processing:
Raw sequencing reads were quality-controlled and trimmed using Fastp
Sequence reads were aligned using bowtie2
Aligned reads were processed using SAMtools to generate BAM and index files
Peak calling was performed with MACS2 in narrowPeak mode using a q-value cutoff of < 0.05
MAnorm was used for comparison of ChIP peaks
For visualization, bamCoverage was used to generate BigWig files with counts per million normalization
ChIP tracks were visualized using the Integrative Genomics Viewer.
Heatmaps and aggregation plots were created using deepTools computeMatrix, followed by visualization with plotHeatmap and plotProfile.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were cross-linked with 1% formaldehyde in PBS for 15 min at room temperature, then quenched with 125 mM glycine. Cells were scraped, pelleted at 1,000 × g for 5 min at 4°C, and stored at –80°C. Protein G magnetic beads (40 µL/sample) were washed and incubated overnight at 4°C with 0.5% BSA/PBS and 1.5 µL anti-H3K27ac antibody. Cell pellets were lysed in buffer (1 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with protease inhibitors, and chromatin was sonicated (Handy Sonic UR-21P) to 150–450 bp. Beads were washed with ChIP dilution buffer and incubated overnight with chromatin at 4°C. Beads were washed with low salt, high salt, LiCl, and TE + NaCl buffers, then eluted in 1% SDS buffer at 65°C for 15 min. Cross-links were reversed at 65°C for at least 6 hours. Samples were treated with RNase A (0.15 mg/mL) at 37°C for 30 min and proteinase K (0.1 mg/mL) at 55°C for 1 h. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP DNA libraries were prepared with the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB)


title: H3K27me3_DKO_rep_1

description:
Library name: H3K27me3_DKO_rep_1
rep_1 and rep_2 were merged and visualized as a single bigWig file.


title: PIP4K2A KD #1, Rep1

description: Library name: PIP4K2A_KD1_Rep1


title: PIP4K2A KD #1, Rep2

description: Library name: PIP4K2A_KD1_Rep2


title: PA8835, 9 months, Baboon with Endometriosis, Sample 77

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

institute: Yale University

description:
Library name: Baboon-tRFs-Hugh Taylor_077
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 77

data_processing:
The differential analysis was performed using R (R version 4.5.0 (2025-04-11), RRID:SCR_001905). Raw tRF count data from serum samples were filtered to retain tRFs with a counts-per-million >1 in at least one sample. The raw count data were normalized using the trimmed mean of M-values (TMM) method implemented in edgeR (RRID:SCR_012802) to account for sequencing depth and compositional bias. Because repeated measurements were collected from the same animals, individual baboon identity was modeled as a fixed effect to adjust for individual baseline variation. Normalized counts were then transformed to log₂ counts per million and assigned precision weights using the voom method from the limma package (RRID:SCR_010943). A linear model was applied to the transformed dataset, and each post-induction timepoint (3, 6, 9, and 15 months) was statistically compared with the pre-induction baseline. Statistical comparisons were performed using limma's empirical Bayes moderated t-tests on voom-transformed expression values. Multiple testing correction was performed using the Benjamini-Hochberg procedure, with significance defined as FDR < 0.05. To assess robustness to within-animal correlation, we additionally re-estimated models using limma’s duplicateCorrelation framework, treating animal identity as a blocking factor. Internal validation was performed using leave-one-animal-out analyses restricted to candidate tRFs, assessing stability of effect sizes across folds. A fully annotated R script reproducing all preprocessing steps, statistical analyses, and figures is provided as Supplementary Material.
Supplementary files format and content: Both are csv files. One summarizes aligned counts for the tRFs, and the other summarizes aligned sequences for the tRFs.

organism: Papio anubis

source_name: Serum

extract_protocol:
RNAs were extracted using the MagMAX™ total RNA Isolation Kit. Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running Agilent Fragment Analyzer, which measures  the ratio of the ribosomal peaks.  Samples with RIN values of 7 or greater are used for library prep. RNA was normalized to a starting input between 1ng-500ng. Adapters were ligated sequentially to the 3’ and 5’ ends of miRNAs prior to cDNA synthesis with UMI assignment, cDNA cleanup, amplification, and final library cleanup
The library was run on the Agilent Tapestation and size selection was performed if there was excess adapter dimer. The library was then quantified by qRT-PCR using a commercially available kit (KAPA Biosystems). Sample concentrations were normalized to 2 nM and loaded onto an Illumina NovaSeq X flow cell at a concentration that yields 10-25 million passing filter clusters per sample.

value: Serum

tag: timepoint (months)

tag: serum volume

tag: baboon number

value: No treatment


title: Scrambled control, rep1

description: Library name: Scrambled_Rep1

value: Scrambled shRNA


title: Scrambled control, rep2

description: Library name: Scrambled_Rep2


title: PA8835, 0 months, Baboon with Endometriosis, Sample 71

description:
Library name: Baboon-tRFs-Hugh Taylor_071
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 71


title: JH1O_DNA2i_JH1bait_3

description:
Library name: Sample 113
JH1 bait\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 20μM DNA2i on the second day


title: PA8835, 6 months, Baboon with Endometriosis, Sample 75

description:
Library name: Baboon-tRFs-Hugh Taylor_075
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 75


title: JH1O_DMSO_JH1bait_8

description:
Library name: Sample 114
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: PA8835, 15 months, Baboon with Endometriosis, Sample 79

description:
Library name: Baboon-tRFs-Hugh Taylor_079
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 79


title: H3K27me3_hES_rep_1

description:
Library name: H3K27me3_hES_rep_1
rep_1 and rep_2 were merged and visualized as a single bigWig file.


title: Scrambled control, rep3

description: Library name: Scrambled_Rep3


title: RNAseq_Ecto-DKO1

description: Library name: Ecto-DKO1

data_processing:
Sequence reads were aligned to the human genome (GRCh38) using STAR
TPM and FPKM values were estimated using RSEM
Gene-level expression was also quantified using featureCounts based on the annotation file Homo_sapiens.GRCh38.105.gtf
Differential expression and PCA analyses were conducted using ExAtlas
GO term analysis was performed using ToppGene
Heatmap analysis was performed using Morpheus
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using TRIzol solution according to the manufacturer's instructions
The cDNA library was prepared from 500 ng of each total RNA sample for massive parallel sequencing using an NEBNext Poly(A) mRNA Magnetic Isolation Module and an Ultra Directional RNA Library Prep Kit for Illumina (NEB). The cDNA library produced ranged from 400 to 1000 bp, including the adaptor sequences


title: H3K27me3_hES_rep_2

description:
Library name: H3K27me3_hES_rep_2
rep_1 and rep_2 were merged and visualized as a single bigWig file.


title: H3K27ac_DKO_rep_1

description: Library name: H3K27ac_DKO_rep_1


title: PA8835, 3 months, Baboon with Endometriosis, Sample 73

description:
Library name: Baboon-tRFs-Hugh Taylor_073
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 73


title: RNAseq_Ecto-DKO2

description: Library name: Ecto-DKO2


title: JH1O_DNA2i_JH1bait_1

description:
Library name: Sample 111
JH1 bait\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: ExM-MOK20068P-D05, KO

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: ELK3_PTC_D05_NEW_GT25-02685_AACGTTCC-AGTACTCC_S142_L007
KOLF2.2J derived knockout cell line,ELK3 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

data_processing:
GRCh38 gencode.v44.primary assembly- Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon.
Assembly: GRCh38 gencode.v44.primary assembly
Supplementary files format and content: study12_featureCounts.csv study12_genesCounts.csv study12_genesRawCounts.csv study12_genesTPM.csv study12_stats.csv study12_txCounts.csv study12_txRawCounts.csv study12_txTPM.csv

extract_protocol:
RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) and Watchmaker RNA Library Prep Kit with Polaris™ Depletion Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

value: day 6

tag: model system

value: fibroblast of villous mesenchyme (CL:0002558)

tag: parental cell_line


title: A3131_5min_input

description: Library name: A3131_5min_input

tag: cell type

value: Liquid cell culture

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

value: induced expression, 4 h, 37°C, followed by 5 min phage infection

value: LmuB lambda infection


title: JH1O_DMSO_JH1bait_7

description:
Library name: Sample 110
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

tag: cell line

tag: genotype

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_DNA2i_JH1bait_2

description:
Library name: Sample 112
JH1 bait\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

tag: treatment


title: H3K27ac_hES_rep_1

description: Library name: H3K27ac_hES_rep_1

tag: tissue

value: Embryonic cells

value: ES cells (SEES3)

value: Pluripotent stem cells


title: PA8915, 15 months, Baboon with Endometriosis, Sample 69

description:
Library name: Baboon-tRFs-Hugh Taylor_069
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 69


title: JH1O_DMSO_JH1bait_6

description:
Library name: Sample 109
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: RNAseq_Ecto-YKO2

description: Library name: Ecto-YKO2


title: RNAseq_Ecto-YKO1

description: Library name: Ecto-YKO1


title: OCI-AML2 cell line DMSO treated rep 2

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

description: Library name: LIB191213BD_S11_aml2_d14_DMSO_2

data_processing:
*library strategy: CRISPR Screen
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample
Library strategy: CRISPR Screen

growth_protocol: OCI-AML2 human AML cell lines were obtained from the American Type Culture Collection (ATCC). Cells were cultured in RPMI-1640 medium supplemented with 20% fetal bovine serum, L-glutamine, penicillin-streptomycin, and amphotericin B. Cultures were maintained at 37 °C with 5% CO₂ and were routinely tested for mycoplasma contamination.

extract_protocol:
Genomic DNA was extracted.
Libraries amplified via PCR and sequenced on an Illumina HiSeq 2500 sequencer.

treatment_protocol: Loss-of-function screens were performed using the Y. Kosuke human genome-wide sgRNA library (Addgene #67989). Cells were treated with 30 nM AZD4320 or DMSO control for 14 days.

value: DMSO


title: OCI-AML2 cell line DMSO treated rep 1

description: Library name: LIB191213BD_S11_aml2_d14_DMSO_1


title: PA8915, 3 months, Baboon with Endometriosis, Sample 63

description:
Library name: Baboon-tRFs-Hugh Taylor_063
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 63

value: Serum

value: No treatment


title: PA8915, 0 months, Baboon with Endometriosis, Sample 61

description:
Library name: Baboon-tRFs-Hugh Taylor_061
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 61


title: RNAseq_Ecto-XKO2

description: Library name: Ecto-XKO2


title: PA8915, 9 months, Baboon with Endometriosis, Sample 67

description:
Library name: Baboon-tRFs-Hugh Taylor_067
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 67


title: RNAseq_Ecto-XKO1

description: Library name: Ecto-XKO1


title: PA8915, 6 months, Baboon with Endometriosis, Sample 65

description:
Library name: Baboon-tRFs-Hugh Taylor_065
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 65


title: JH1O_Mre11i_JH1bait_3

description:
Library name: Sample 108
JH1 bait\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 10μM Mre11i on the second day


title: JH1O_Mre11i_JH1bait_2

description:
Library name: Sample 107
JH1 bait\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: OCI-AML2 cell line AZD4320 treated rep 1

description: Library name: LIB191213BD_S11_aml2_d14_4320_1


title: JH1O_Mre11i_JH1bait_1

description:
Library name: Sample 106
JH1 bait\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: OCI-AML2 cell line AZD4320 treated rep 2

description: Library name: LIB191213BD_S11_aml2_d14_4320_2


title: Yusa Plasmid Untreated rep 1

description: Library name: LIB191213BD_S10_Yusa_plasmid_S10

value: Untreated


title: PA8914, 15 months, Baboon with Endometriosis, Sample 59

description:
Library name: Baboon-tRFs-Hugh Taylor_059
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 59


title: RNAseq_Ecto-WT1

description: Library name: Ecto-WT1


title: RNAseq_Ecto-WT2

description: Library name: Ecto-WT2


title: PA8914, 9 months, Baboon with Endometriosis, Sample 57

description:
Library name: Baboon-tRFs-Hugh Taylor_057
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 57


title: JH1O_DMSO_JH1bait_5

description:
Library name: Sample 105
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_Meso-DKO2

description: Library name: Meso-DKO2


title: JH1O_DMSO_JH1bait_4

description:
Library name: Sample 104
JH1 bait\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_XRCC1_DKO_JH1bait_3

description:
Library name: Sample 91
JH1 bait\, 53BP1 and XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: GES cells, 3

city: Nanjing

first: Han

last: Chen

state: Jiangsu

address: #300 Guzhou Road, Gulou District

institute: Nanjing Medical University

description:
Library name: sample12
GES cells, 3

data_processing: GLC genomics Workbench

source_name: GES

extract_protocol:
RNA was harvested using Rensay mini plus kit. total  TNA was used for the construction of sequenceing library
RNA library for RNA-seq was prepared using SMARTER mRNA-seq Library Prep kit following manufacturer‘s protocols.’

value: GES

value: normal cell

value: WT


title: GES cells, 2

description:
Library name: sample11
GES cells, 2


title: AGC cells, 3

description:
Library name: sample9
AGC cells, 3


title: RNAseq_Meso-YKO2

description: Library name: Meso-YKO2


title: RNAseq_Meso-YKO1

description: Library name: Meso-YKO1


title: PA8914, 0 months, Baboon with Endometriosis, Sample 51

description:
Library name: Baboon-tRFs-Hugh Taylor_051
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 51


title: JH1O_53BP1_KO_JH1bait_11

description:
Library name: Sample 88
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: RNAseq_Meso-XKO2

description: Library name: Meso-XKO2


title: PA8914, 3 months, Baboon with Endometriosis, Sample 53

description:
Library name: Baboon-tRFs-Hugh Taylor_053
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 53


title: JH1O_53BP1_XRCC1_DKO_JH1bait_2

description:
Library name: Sample 90
JH1 bait\, 53BP1 and XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_XRCC1_DKO_JH1bait_1

description:
Library name: Sample 89
JH1 bait\, 53BP1 and XRCC1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: PA8912, 9 months, Baboon with Endometriosis, Sample 47

description:
Library name: Baboon-tRFs-Hugh Taylor_047
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 47


title: PA8914, 6 months, Baboon with Endometriosis, Sample 55

description:
Library name: Baboon-tRFs-Hugh Taylor_055
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 55


title: PA8912, 15 months, Baboon with Endometriosis, Sample 49

description:
Library name: Baboon-tRFs-Hugh Taylor_049
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 49


title: JH1O_53BP1_KO_JH1bait_10

description:
Library name: Sample 87
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_Meso-DKO1

description: Library name: Meso-DKO1


title: JH1O_53BP1_PARP1_DKO_JH1bait_3

description:
Library name: Sample 86
JH1 bait\, 53BP1 and PARP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: AGC cells, control, 3

description:
Library name: sample6
AGC cells, control, 3

source_name: AGS

value: AGS

value: cancer cell


title: RNAseq_Meso-XKO1

description: Library name: Meso-XKO1

value: Embryonic cells


title: PA8912, 6 months, Baboon with Endometriosis, Sample 45

description:
Library name: Baboon-tRFs-Hugh Taylor_045
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 45


title: JH1O_53BP1_PARP1_DKO_JH1bait_2

description:
Library name: Sample 85
JH1 bait\, 53BP1 and PARP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: AGC cells, control, 2

description:
Library name: sample5
AGC cells, control, 2


title: RNAseq_Meso-WT2

description: Library name: Meso-WT2

value: ES cells (SEES3)


title: PA8912, 3 months, Baboon with Endometriosis, Sample 43

description:
Library name: Baboon-tRFs-Hugh Taylor_043
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 43


title: PA8912, 0 months, Baboon with Endometriosis, Sample 41

description:
Library name: Baboon-tRFs-Hugh Taylor_041
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 41


title: AGS cells, with  2-DG, 3

description:
Library name: sample3
AGS cells, with  2-DG, 3


title: RNAseq_Endo-DKO2

description: Library name: Endo-DKO2

value: Pluripotent stem cells


title: PA8873, 15 months, Baboon with Endometriosis, Sample 39

description:
Library name: Baboon-tRFs-Hugh Taylor_039
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 39


title: RNAseq_Meso-WT1

description: Library name: Meso-WT1


title: JH1O_53BP1_KO_JH1bait_9

description:
Library name: Sample 83
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: JH1O_53BP1_PARP1_DKO_JH1bait_1

description:
Library name: Sample 84
JH1 bait\, 53BP1 and PARP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: AGC cells, control, 1

description:
Library name: sample4
AGC cells, control, 1


title: AGS cells, with  2-DG, 2

description:
Library name: sample2
AGS cells, with  2-DG, 2


title: AGS cells, with  2-DG, 1

description:
Library name: sample1
AGS cells, with  2-DG, 1


title: JH1O_53BP1_KO_JH1bait_8

description:
Library name: Sample 82
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_Endo-DKO1

description: Library name: Endo-DKO1


title: PA8873, 6 months, Baboon with Endometriosis, Sample 35

description:
Library name: Baboon-tRFs-Hugh Taylor_035
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 35


title: JH1O_53BP1_EXO1_DKO_JH1bait_3

description:
Library name: Sample 80
JH1 bait\, 53BP1 and EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: GES cells, 1

description:
Library name: sample10
GES cells, 1


title: JH1O_53BP1_KO_JH1bait_7

description:
Library name: Sample 81
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_Endo-YKO1

description: Library name: Endo-YKO1


title: Intestine, nod2-/-, nod2-def, nod2ko,nod2-deficient

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: Library name: Nod2_ko

data_processing:
Raw base call files were demultiplexed and reads aligned to the Zebrafish reference genome (Ensemble GRCz11) using Cell Ranger v7.0.1
Assembly: Zebrafish reference genome (Ensemble GRCz11)
Supplementary files format and content: barcodes and features as TSV files
Supplementary files format and content: feature matrix as MTX file

organism: Danio rerio

source_name: Intestine

extract_protocol:
Intestinal tissue was dissociated enzymatically and mechanically followed by removal of debris and dead cells using OptiPrep™ Density Gradient Medium (Sigma).
single cell RNA libraries from freshly collected cells were prepared and barcoded with a 10X genomics Chromium Next GEM Single Cell 3' Reagents Kit v3.1.

value: Intestine

value: dissociated intestines


title: PA8873, 9 months, Baboon with Endometriosis, Sample 37

description:
Library name: Baboon-tRFs-Hugh Taylor_037
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 37

value: Serum


title: PA8873, 3 months, Baboon with Endometriosis, Sample 33

description:
Library name: Baboon-tRFs-Hugh Taylor_033
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 33

value: No treatment


title: JH1O_53BP1_EXO1_DKO_JH1bait_2

description:
Library name: Sample 79
JH1 bait\, 53BP1 and EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: AGC cells, 1

description:
Library name: sample7
AGC cells, 1


title: Intestine, WT TL, nod2+/+

description: Library name: WT


title: RNAseq_Endo-YKO2

description: Library name: Endo-YKO2


title: AGC cells, 2

description:
Library name: sample8
AGC cells, 2


title: RNAseq_Endo-XKO2

description: Library name: Endo-XKO2


title: PA8872, 15 months, Baboon with Endometriosis, Sample 29

description:
Library name: Baboon-tRFs-Hugh Taylor_029
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 29


title: JH1O_53BP1_EXO1_DKO_JH1bait_1

description:
Library name: Sample 78
JH1 bait\, 53BP1 and EXO1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: PA8872, 9 months, Baboon with Endometriosis, Sample 27

description:
Library name: Baboon-tRFs-Hugh Taylor_027
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 27


title: PA8873, 0 months, Baboon with Endometriosis, Sample 31

description:
Library name: Baboon-tRFs-Hugh Taylor_031
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 31


title: Plin2-Bleo 8wk Rep 2

city: Denver

first: Elizabeth

last: Redente

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

description: Library name: Sample26

data_processing:
raw sequencing reads were trimmed using skewer with parameters (end-quality=15, mean-quality=25, min=30). Trimmed reads were aligned to the mouse reference genome GRCm38 using Hisat2. Gene quantification was performed with htseq-count using GRCm38 ensembl v84 GTF. Differential expression analysis between groups was conducted with R package DESeq2.
Assembly: GPL24247
Supplementary files format and content: mapping.rate.cvs
Supplementary files format and content: QC and sequence counts.xlsx
Supplementary files format and content: Genecounts_pearson_correlation_Table.txt
Supplementary files format and content: demultiplex summar.cvs

source_name: Lung

extract_protocol:
TRIzol followed by purification of aqueious layer with Rneasy Micro Kit from Qiagen
Nugen mRNA kit was used with a total of 100ng of total RNA for library construction

treatment_protocol: Mice treated with saline (time 0) or bleomycin (3wk, 8wk)

value: Lung

value: Fibroblast

value: Cre+ TdTm+

value: Bleomyin


title: JH1O_53BP1_KO_JH1bait_5

description:
Library name: Sample 76
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: RNAseq_Endo-XKO1

description: Library name: Endo-XKO1


title: RNAseq_Endo-WT2

description: Library name: Endo-WT2


title: Plin2-Bleo 8wk Rep 1

description: Library name: Sample25


title: aSMA-Bleo 8wk Rep 3

description: Library name: Sample24


title: RNAseq_Endo-WT1

description: Library name: Endo-WT1


title: PA8872, 6 months, Baboon with Endometriosis, Sample 25

description:
Library name: Baboon-tRFs-Hugh Taylor_025
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 25


title: JH1O_53BP1_KO_JH1bait_6

description:
Library name: Sample 77
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_H9-UTXKO-4-2

description: Library name: H9-UTXKO-4-2

value: ES cells (H9)


title: RNAseq_H9-UTXKO-4-1

description: Library name: H9-UTXKO-4-1


title: PA8872, 0 months, Baboon with Endometriosis, Sample 21

description:
Library name: Baboon-tRFs-Hugh Taylor_021
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 21


title: JH1O_53BP1_Polqi_JH1bait_3

description:
Library name: Sample 74
JH1 bait\, 53BP1 knockout\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 10μM Polqi on the second day


title: JH1O_53BP1_Polqi_JH1bait_1

description:
Library name: Sample 72
JH1 bait\, 53BP1 knockout\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: RNAseq_H9-UTXKO-3-1

description: Library name: H9-UTXKO-3-1


title: Col1-Bleo 8wk Rep 3

description: Library name: Sample21


title: PA8003, 15 months, Baboon with Endometriosis, Sample 19

description:
Library name: Baboon-tRFs-Hugh Taylor_019
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 19


title: JH1O_53BP1_DMSO_JH1bait_8

description:
Library name: Sample 71
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: JH1O_53BP1_Polqi_JH1bait_2

description:
Library name: Sample 73
JH1 bait\, 53BP1 knockout\, Polqi\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Col1-Bleo 8wk Rep 1

description: Library name: Sample19


title: aSMA-Bleo 8wk Rep 2

description: Library name: Sample23


title: RNAseq_H9-WT2

description: Library name: H9-WT2

value: Embryonic cells


title: Plin2-Bleo 3wk Rep 3

description: Library name: Sample18


title: aSMA-Bleo 8wk Rep 1

description: Library name: Sample22


title: JH1O_53BP1_DMSO_JH1bait_7

description:
Library name: Sample 70
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: PA8872, 3 months, Baboon with Endometriosis, Sample 23

description:
Library name: Baboon-tRFs-Hugh Taylor_023
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 23


title: RNAseq_H9-UTXKO-3-2

description: Library name: H9-UTXKO-3-2


title: Col1-Bleo 8wk Rep 2

description: Library name: Sample20


title: PA8003, 3 months, Baboon with Endometriosis, Sample 13

description:
Library name: Baboon-tRFs-Hugh Taylor_013
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 13


title: PA8003, 6 months, Baboon with Endometriosis, Sample 15

description:
Library name: Baboon-tRFs-Hugh Taylor_015
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 15


title: JH1O_53BP1_KO_JH1bait_4

description:
Library name: Sample 75
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: Plin2-Bleo 3wk Rep 2

description: Library name: Sample17


title: JH1O_53BP1_DMSO_JH1bait_6

description:
Library name: Sample 69
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: PA8003, 9 months, Baboon with Endometriosis, Sample 17

description:
Library name: Baboon-tRFs-Hugh Taylor_017
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 17


title: RNAseq_H9-WT1

description: Library name: H9-WT1

value: Pluripotent stem cells


title: LTBP4-51

city: Shanghai

first: Jieyu

last: Guo

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

description:
Library name: Sample 4
LTBP4-CKO2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hista2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cufflinks
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: heart

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

treatment_protocol: Wild-type (WT) and LTBP4 cardiomyocyte-specific knockout  (LTBP4-CKO) mice aged 10-12 weeks underwent transaortic constriction (TAC) surgery. During the procedure, the transverse aorta was isolated and constricted using a 27-gauge needle and 7-0 silk suture, followed by layered closure of the chest wall.

value: heart

value: TAC


title: PA8003, 0 months, Baboon with Endometriosis, Sample 11

description:
Library name: Baboon-tRFs-Hugh Taylor_011
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 11


title: Plin2-Bleo 3wk Rep 1

description: Library name: Sample16


title: PA8001, 15 months, Baboon with Endometriosis, Sample 9

description:
Library name: Baboon-tRFs-Hugh Taylor_009
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 9


title: JH1O_53BP1_DNA2i_JH1bait_2

description:
Library name: Sample 67
JH1 bait\, 53BP1 knockout\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using VDJ-HTGTS-Seq (Hu et al., 2016)

value: v-Abl transformed pro-B cell line

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 20μM DNA2i on the second day


title: flox-5

description:
Library name: Sample 1
FLOX-1

value: WT


title: PA8001, 3 months, Baboon with Endometriosis, Sample 3

description:
Library name: Baboon-tRFs-Hugh Taylor_003
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 3

value: Serum

value: No treatment


title: JH1O_53BP1_DNA2i_JH1bait_1

description:
Library name: Sample 66
JH1 bait\, 53BP1 knockout\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_Mre11i_JH1bait_2

description:
Library name: Sample 62
JH1 bait\, 53BP1 knockout\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 10μM Mre11i on the second day


title: PA8001, 0 months, Baboon with Endometriosis, Sample 1

description:
Library name: Baboon-tRFs-Hugh Taylor_001
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 1


title: aSMA-Bleo 3wk Rep 1

description: Library name: Sample13

value: Lung

value: Fibroblast

value: Cre+ TdTm+

value: Bleomyin


title: LTBP4-5

description:
Library name: Sample 3
LTBP4-CKO1


title: JH1O_53BP1_DNA2i_JH1bait_3

description:
Library name: Sample 68
JH1 bait\, 53BP1 knockout\, DNA2i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Col1-Bleo 3wk Rep 2

description: Library name: Sample11


title: PA8001, 6 months, Baboon with Endometriosis, Sample 5

description:
Library name: Baboon-tRFs-Hugh Taylor_005
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 5


title: aSMA-Bleo 3wk Rep 2

description: Library name: Sample14


title: PA8001, 9 months, Baboon with Endometriosis, Sample 7

description:
Library name: Baboon-tRFs-Hugh Taylor_007
Differential expression of tRFs in Serum of Baboons with Endometriosis, Sample 7


title: Evs_1

city: Harbin

first: Yong

last: Fang

state: Hei longjiang

address: 157 Health Road, Nangang District, Harbin City

department: Department of Microbiology

institute: Harbin medical university

description:
Library name: Samples2
Evs

data_processing:
Data Quality Control
Reads mapping to the reference genome
Quantification of gene expression level
Differential expression analysis
GO and KEGG enrichment analysis of differentially expressed genes
Gene Set Enrichment Analysis
PPI analysis of differentially expressed genes
AS analysis
SNP analysis
Fusion Analysis
Weighted correlation network analysis
Tumor immune microenvironment analysis
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

growth_protocol: The oral cancer cell line CAL-27 were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), and 1% penicillin–streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent.RNA quality was assessed with an Agilent 2100 Bioanalyzer.
NEB library:Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand-specific library Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Streptococcus mutant derived extracellular vesicles(400μg/ml) were co cultured with CAL-27 cells for 48 hours.

value: Tumor

value: Human Oral Adenosquamous Carcinoma Cells

value: Evs


title: Sample 9 single cell for microglia sequenced with nextseq

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
Library name: samp9_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus

data_processing:
FASTQ files were processed with Cell Ranger v6.1.2, with the refdata-gex-mm10-2020-A Cell Ranger reference (10x Genomics) and with the expected number of cells set based on estimated loading
The downsampleReads command in DropletUtils v1.14.2 was used to downsample all samples to the same number of reads per cell, then the emptyDropsCellRanger command was used to remove empty droplets.
This count matrix was then loaded in R v4.0.3. A Seurat v4.0.0 object was created, cells with less than 200 genes were removed, and the data was LogNormalized with NormalizeData
Variable genes were extracted with FindVariableFeatures, data was scaled with ScaleData, and PCA was run with RunPCA with npcs=60. Dimensionality reduction was performed on the count data with scGBM v0.1.0, using the gbm.sc command with M=25 and subset=50,000, using just the variable genes
Clusters were calculated with the FindNeighbors and FindClusters commands using dims=1:25 and the scGBM reduction
Assembly: mm10
Supplementary files format and content: h5ad containing clustered object

source_name: Hippocampus

extract_protocol:
For single nuclei data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Nuclei were filtered, washed, and purified through sequential centrifugation steps. The final nuclei suspension was resuspended in RNase inhibitor-containing buffer, filtered, and counted prior to loading for single-nucleus RNA-seq. For single cell data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Cell suspensions were filtered, subjected to debris removal, and microglia were enriched using CD11b magnetic bead-based isolation. Purified cells were resuspended in RNase inhibitor-containing buffer and assessed for viability prior to scRNA-seq.
Single-nucleus and single-cell RNA-seq libraries were generated using the Chromium™ Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) following the manufacturer’s instructions, targeting recovery of up to 10,000 nuclei per sample. For single nucleus data, twenty-four libraries were pooled and sequenced on one NextSeq 500 flow cell and four NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1. For single cell data, twenty-four libraries from different animals were pooled based on molar concentrations and sequenced on one NextSeq 500 flow cell and two NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1.

value: Hippocampus

value: Microglia


title: Control_1

description:
Library name: Samples1
Contral

value: Contral

value: NO


title: flox-14

description:
Library name: Sample 2
FLOX-2

value: heart

value: TAC


title: Col1-Bleo 3wk Rep 3

description: Library name: Sample12


title: Col1-Bleo 3wk Rep 1

description: Library name: Sample10


title: JH1O_53BP1_DMSO_JH1bait_4

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description:
Library name: Sample 64
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with DMSO on the second day


title: aSMA-Bleo 3wk Rep 3

description: Library name: Sample15


first: Lei

last: Cui

address: 75 Ames st. room 8115b room 8115b

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 54
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone E12, replication 3

data_processing:
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases.
Trimmed reads were aligned to the ENSEMBL GRCh38 reference genome using STAR aligner (v2.5.2b), producing BAM files.
Unique gene-level counts were quantified using featureCounts from the Subread package (v1.5.2), restricted to uniquely mapped reads within annotated exon regions.
Differential gene expression analysis was performed with DESeq2 using the Wald test to calculate p-values and log2 fold-changes. Genes with adjusted p-values < 0.01 and absolute log2 fold-changes > 1 were considered differentially expressed.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: CSV file includes raw gene-level count values for each sample.

growth_protocol: iPSC-derived neurons were maintained in Neurobasal Medium supplemented with 1.5% v/v 20% glucose, Glutamax (1:100), MEM-NEAA (1:100), B27 Supplement (1:50), brain-derived neurotrophic factor (BDNF, 10 ng/mL), glial cell line-derived neurotrophic factor (GDNF, 10 ng/mL), and ciliary neurotrophic factor (CTNF, 10 ng/mL).

extract_protocol:
Total RNA was extracted from frozen cell pellets using the Qiagen RNeasy Plus Micro Kit following the manufacturer’s instructions. RNA concentration was measured with the Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was evaluated using the Agilent TapeStation 4200.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB) with poly(A) selection. mRNA was enriched with Oligod(T) beads and fragmented at 94°C for 15 minutes. First- and second-strand cDNA synthesis was followed by end repair, 3’ adenylation, adapter ligation, and PCR enrichment. Libraries were validated using the Agilent TapeStation and quantified via Qubit and qPCR (KAPA Biosystems) before sequencing on the Illumina NovaSeq platform (2×150 bp paired-end).

treatment_protocol: Human iPSCs were transduced with a doxycycline-inducible NGN2 expression construct via TALEN-mediated integration at the AAVS1 safe-harbor locus. Cells were cultured in Induction Medium composed of DMEM/F12, Glutamax (1:100), 1.5% v/v 20% glucose, N2 Supplement (1:100), LDN-193189 (200 nM), SB431542 (10 μM), XAV939 (2 μM), and doxycycline (2 μg/mL) to induce NGN2 expression. After 24 hours, the Induction Medium was refreshed to include zeocin (4 μg/mL) for selection. On Day 4, the medium was replaced with Neuron Medium.

value: iPSC-derived excitatory neurons

value: NGN2-induced differentiation

value: Day 56

value: batch 1


description:
Library name: Sample 53
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone E12, replication 2


title: JH1O_53BP1_Mre11i_JH1bait_3

description:
Library name: Sample 63
JH1 bait\, 53BP1 knockout\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days，treated with 10μM Mre11i on the second day


title: JH1O_53BP1_DMSO_JH1bait_5

description:
Library name: Sample 65
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 8 single cell for microglia sequenced with nextseq

description:
Library name: samp8_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 7 single cell for microglia sequenced with nextseq

description:
Library name: samp7_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Plin2-Sal2 Rep 2

description: Library name: Sample8

value: Lung

value: Fibroblast

value: Cre+ TdTm+

value: Saline


description:
Library name: Sample 51
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone B1, replication 3


title: Plin2-Sal3 Rep 3

description: Library name: Sample9


title: JH1O_53BP1_Mre11i_JH1bait_1

description:
Library name: Sample 61
JH1 bait\, 53BP1 knockout\, Mre11i\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_DMSO_JH1bait_3

description:
Library name: Sample 60
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Sample 6 single cell for microglia sequenced with nextseq

description:
Library name: samp6_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus

value: Hippocampus

value: Microglia


description:
Library name: Sample 52
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone E12, replication 1


title: aSMA-Sal3 Rep 3

description: Library name: Sample6


title: JH1O_53BP1_DMSO_JH1bait_1

description:
Library name: Sample 58
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 50
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone B1, replication 2


title: JH1O_53BP1_DMSO_JH1bait_2

description:
Library name: Sample 59
JH1 bait\, 53BP1 knockout\, DMSO\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 49
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7-/-, clone B1, replication 1


title: Sample 4 single cell for microglia sequenced with nextseq

description:
Library name: samp4_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Plin2-Sal1 Rep 1

description: Library name: Sample7


description:
Library name: Sample 48
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone D5, replication 3


title: JH1O_DNA_PKcs_KO_JH1bait_2

description:
Library name: Sample 56
JH1 bait\, DNA_PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: DNA_PKcs knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


description:
Library name: Sample 47
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone D5, replication 2


title: aSMA-Sal1 Rep 1

description: Library name: Sample4


title: Col1-Sal Rep 3

description: Library name: Sample3


title: Sample 2 single cell for microglia sequenced with nextseq

description:
Library name: samp2_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 3 single cell for microglia sequenced with nextseq

description:
Library name: samp3_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 5 single cell for microglia sequenced with nextseq

description:
Library name: samp5_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: Sample 24 single cell for microglia sequenced with nextseq

description:
Library name: samp24_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: aSMA-Sal2 Rep 2

description: Library name: Sample5


title: JH1O_DNA_PKcs_KO_JH1bait_1

description:
Library name: Sample 55
JH1 bait\, DNA_PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_SHLD2_KO_JH1bait_3

description:
Library name: Sample 54
JH1 bait\, SHLD2 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: Col1-Sal Rep 2

description: Library name: Sample2


title: Sample 23 single cell for microglia sequenced with nextseq

description:
Library name: samp23_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus


title: JH1O_SHLD2_KO_JH1bait_2

description:
Library name: Sample 53
JH1 bait\, SHLD2 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_DNA_PKcs_KO_JH1bait_3

description:
Library name: Sample 57
JH1 bait\, DNA_PKcs knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


description:
Library name: Sample 46
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone D5, replication 1


title: Col1-Sal Rep 1

description: Library name: Sample1


description:
Library name: Sample 44
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone A2, replication 2


description:
Library name: Sample 45
Column name in raw_counts_All_Samples.csv: iPSC-derived neurons, Day 56, XPO7+/-, clone A2, replication 3


title: Sample 22 single cell for microglia sequenced with nextseq

description:
Library name: samp22_SingleCell_nextseq
Single cell sequencing of microglia from the hippocampus