title: 10E_ap2hs_3xHA_plusCHO_rep2_in

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

description:
Library name: 10E_ap2hs_3xHA_plusCHO_rep2_in
10E_ap2hs_3xHA_plusCHO_rep2_in

data_processing:
ChIP-seq data analysis was carried out using custom scripts written in Python (v3.7.16), as previously described (Michel-Todó, L., 2023. PMID: 36515553). ChIP-seq reads were trimmed using the bbduk command from BBmap (v36.99) software. The 3' end was trimmed if it had a quality score < 6 and reads shorter than 10 bp after trimming were discarded. Quality control of raw reads was performed using FastQC (v0.11.9) and contamination with non-P. falciparum reads was checked with FastqScreen (v0.14.0).  Bowtie2 (v2.4.5) was used to align reads to the Plasmodium falciparum 3D7 reference genome (PlasmoDB v67) using the parameters: --very-sensitive --local -5 4 -3 4 -I 50 -X 2000, which are different from the default ones. SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads, from the alignment files. PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command. Normalized coverage (log₂-transformed enrichment of IP over input) was calculated at 10-bp resolution using the bamCompare function from DeepTools (v3.5.1), with the parameters: --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10. Normalized log₂(IP/input) coverage values were used to generate bedgraph tracks. For peak calling, alignment files were filtered using SAMtools view (v1.15) to retain only reads with mapping quality >30, and peak calling was performed as previously described (Michel-Todó, L., 2023. PMID: 36515553) but using MACS3 (v3.0.3). The FDR (q-value) was calculated from P values using the Benjamini-Hochberg method, and the MACS score was calculated as -10 × log10(q-value). Within each sample, significant peaks with overlapping genomic coordinates were identified using bedtools (v2.31.1), and only the peak with the highest MACS score was retained.
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Bedgraph tracks (.bdg): normalized log₂(IP/input) coverage values
Supplementary files format and content: Peak summits for AP2-HS ChIP-seq (.narrowPeak)

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ or O+ erythrocytes at a 3% hematocrit under standard conditions in RPMI-1640-based media, supplemented with 0.5% Albumax II (Gibco, 11021037) and 2 mM choline chloride (Sigma-Aldrich, C7527), and maintained in a shaking incubator with a 5% CO₂, 3% O₂, and balance N₂ atmosphere. All cultures were kept at 37ºC. Synchronization was achieved by sorbitol lysis (Sigma-Aldrich, S3889).

extract_protocol:
ChIP-seq was performed using cultures at late trophozoites or early schizont stage (not tightly synchronized). Chromatin was extracted from ~60 ml at ~3-4% parasitemia as previously described, with some modifications (Llorà-Batlle, O., 2020. PMID: 32577509). Briefly, after saponin lysis and formaldehyde cross-linking, chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies, 492024). All chromatin obtained was sonicated with a Bioruptor Plus sonicator (Diagenode) as previously described (Pérez-Cantero, A., 2025. PMID: 40455742) and used for the immunoprecipitation (diluted 1:5), except for a small fraction that was used to prepare input samples. For immunoprecipitation, the anti-HA antibody at 2 μg/ml (Roche, 11867423001) was used. An equal sample was processed in parallel as input, with no immunoprecipitation. Approximately half the volume of the DNAs obtained was used for library preparation (no Qubit quantification).
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).

treatment_protocol: Sexual conversion was induced by choline depletion. For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (after sorbitol lysis) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. A control condition was always kept in parallel until the end of the experiment.

value: ap2-hs 3xHA

value: control choline

tag: biological replicate

tag: chip antibody

tag: time

value: Late trophozoites/early schizonts


title: AAV2CBE, igg_ctrl, biol_rep1

status: Public on Jul 27 2026

type: SRA

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

country: USA

institute: University of Wisconsin

description: Library name: AAV2CBE sample 10

library_source: genomic

data_processing:
GitHub CUT&RUN pipeline doi: 10.5281/zenodo.5653535
genomes (human genome was excluded) using Bowtie2. Reads were sorted, and quality checked by samtools and picard before processed into coverage files (BEDtools) which were used for downstream processing. Genome coverage was computed from the aligned BAM files and scaled to sequencing depth using reads per million mapped reads (RPM).
Samples were then normalized to corresponding IgG control signal per bin across the genome. Normalized RPM signal was calculated by (Target RPM) – (IgG RPM). Negative values were set to zero and signal peaks over IgG levels were further processed. IgG normalization was performed by matching each target replicate to its corresponding IgG control replicate
Samples without a matching igg were normalized to each avalible igg for the biological condition independently then averaged between to produce a single normalized file.
Replicate normalized RPM peaks were averaged at each base pair
Assembly: Human genome (hg38)
Supplementary files format and content: bedgraph, RPM and RPM normalized to igg
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: Human embryonic kidney cells (HEK293T) in Dulbecco’s modified Eagle’s medium (DMEM, high glucose; Gibco) supplemented with 5% Serum Plus and 50 µg/ml gentamicin (Gibco). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
Cells were processed using the Epicypher kit (14-1048)
Libraries were prepped using the Epicypher kit (14-1001 and 14-1002)

treatment_protocol: 500,000 HEK293T cells infected for 24 hours were used per antibody reaction.

tag: tissue

value: Kidney

tag: cell line

value: HEK 293T

tag: cell type

value: Human Embryonic Kidney

tag: antibody


title: PilotPool_Sort2_Human PDL1_TechRep3

city: Bonn

first: Bianca

last: Broske

address: Venusberg-Campus 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

description:
Library name: Pilot Pool_Sort2_Sample5
NGS-Read-Counts_PilotPool.xlsx

data_processing:
Reads were filtered for a Q-Score > 30 and matched to AI-minibinder sequences using a self-written R script.
Assembly: Read alignment was performed against the designed sequences used for the respective oligo pool.
Supplementary files format and content: The processed data files contain all binder names and sequences present in the respective oligo pool. The target proteins used for staining are indicated in the sheet names, as well as in the header of the respective read column. Technical replicates (file names "*TechRepx") are already pooled and the different sorts indicate replicates of repeated experiments.

organism: synthetic construct

source_name: Transduced HEK293T cells

extract_protocol:
Sorted cells were lysed in direct lysis buffer (1 mM CaCl2, 3 mM MgCl2, 1 mM EDTA, 1% (v/v) Triton X-100, 10 mM Tris pH 7.5) with proteinase K at 65 °C for 10 minutes and 95 °C for 15 minutes.
After lysis, genomically integrated AI-minibinder sequences were PCR amplified using 2x NEBNext High-Fidelity MasterMix (NEB). After second barcoding PCR, product purification, and NanoDrop-based quantification, AI-minibinders were sequenced on Illumina MiSeq platforms.

treatment_protocol: HEK293T cells were lentivirally transduced with plasmid libraries encoding de novo generated minibinder proteins. The HEK293T AI-minibinder libraries were harvested and incubated with respective Fc-tagged recombinant target proteins at 10 µg/mL and secondary APC-labeled anti-human IgG Fc antibody at 250 ng/mL (clone M1310G05, Biolegend). Cells were sorted immediately after staining for distinct APC-signal using the fluorescence-activated cell sorter Sony MA900.

value: Transduced HEK293T cells

tag: treatment

value: Stained with recombinant human PD-L1


title: RNA-seq, pyramidal neurons, P0, Saline, rep9

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: P0_S_NN_01

library_source: transcriptomic

data_processing:
RNA-seq: Read quality was assessed using FastQC (Andrews, 2010). STAR (2.5.1b; Dobin et al., 2013) was used to map sequence reads and RSEM (version 1.2.31; Li and Dewey, 2011) was used to quantify gene expression.
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequencing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
RNA-seq: Batch correction in P0 samples was performed using ComBat-seq (Zhang et al., 2020). Mitochondrial and lowly expressed genes with fewer than 10 raw counts in all but one sample were removed before differential gene expression analysis. Differential expression analysis was conducted using DESeq2 (Love et al., 2014) with a false discovery rate 0.1. Enrichment analysis was performed by inputting differentially expressed genes into EnrichR (Kuleshov et al., 2016; Chen et al., 2013).
MethylC-seq: CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
Assembly: mm10
Supplementary files format and content: Tab-delimited file contains transcripts per million counts for each RNA-seq sample
Supplementary files format and content: Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosine Context, 5. methylated base call, 6. total mapped base call, 7. indicator of significant methylation (0: unmethylated; 1, methylated)

molecule: total RNA

organism: Mus musculus

source_name: brain (frontal cortex)

extract_protocol:
Cortex dissecxtion and nuclei isolation: The frontal cortex tissue was rapidly dissected from perinatal mice on ice. The INTACT method was used to label excitatory neurons and fluoreescence-activated nuclei sorting (FANS) was used to affinity purify GFP+ nuclei. RNA-seq: RNA was extracted by using the RNeasy Mini kit with DNAse I treatment (Qiagen, 74104) for whole frontal cortex, or by using Single-Cell RNA Purification Kit (Norgen, 51800) for nuclei. Bisulfite-Seq (MethylC-seq):  Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
RNA-seq: For whole tissue RNA, strand-specific cDNA libraries were constructed by selecting poly-adenylated mRNA transcripts using Truseq Stranded mRNA High Throughput Library Prep kit (Illumina, 20015963) with TruSeq RNA CD Indexes (Illumina, 20015949). Libraries were sequenced using Illumina NextSeq500, generating 20 million reads (75 bp, paired-end sequencing, whole cortex). INTACT-purified nuclear RNA (Norgen, 51800) was converted to cDNA and amplified with the Ovation RNA-seq System V2 (Nugen, 7102-A01) and libraries prepared with Kapa LTP library preparation kit (Illumina, KK8232) with TruSeq DNA Single Indexes (Illumina, 20015960), generating 40 million reads (150 bp, paired-end sequencing using Illumina HiSeq 4000 or NovaSeq 6000).
Bisulfite-Seq (MethylC-seq):  MethylC-seq libraries were constructed using the snmC-seq2 adapted for Bulk samples (https://dx.doi.org/10.17504/protocols.io.pjvdkn6). 40ng of DNA samples  were subjected to sodium bisulfite conversion using Zymo EZ DNA Methylation-Direct Kit (D5020, D5021), 0.5% of Lambda was added to each sample, resuspended in 9ul of EB buffer, 1ul of random primer was added to each of the samples, denature for 3 min at 95°C, put in ice for 3 min, then 10ul of Random primer was added and mixed, put in thermocycler with at 4°C 5 min,  25°C 5 min, 37°C 60 min. Exonuclease/SAP mix was added next put at 37°C 30min. Samples were subjected to one round of 0.8x SPRI beads clean up. Samples were resuspended in 10ul of EB and denature once again. Adaptase mix was added next, and put at 37°C 30min and 95°C 2min. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart, 1ul of P5 index primer (30uM), and 5ul of P7 index primer (10uM), for a final vol of 50ul. The reaction products were purified using SPRI beads. MethylC-seq libraries were sequenced on Illumina HiSeq 4000 or Novaseq 6000.

treatment_protocol: Dams received IP injection of 0.9% saline or 20 mg/kg polyriboinosinic–polyribocytidylic acid potassium salt (P9582, Lot number 095M4085V, Sigma-Aldrich, St. Louis, MO) in 0.9% saline on embryonic day 12.5.

value: brain (frontal cortex)

value: excitatory pyramidal neurons

tag: strain

tag: genotype

value: B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ. Strain 030952, Jackson laboratories

value: Saline

tag: age

value: Postnatal day 0

tag: Sex

value: male


title: PAT – CP7

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Library name: P28

data_processing:
Raw reads were aligned to the hg38 genome, with HISAT2 (2.2.1). FeatureCounts (2.0.6) was used to count the reads number mapped to each gene. The differentially expressed genes analyses between groups were performed using DESeq2 with the standard RNA-seq workflow, genes with counts <100 were filtered.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains fpkm data of all samples ("gene_fpkm")

source_name: Peripancreatic adipose tissue (PAT)

extract_protocol:
RNA was extracted from PAT snap frozen tissues of the 5 CTRL, 12 pancreatitis and 5 donors with T2D using the gentle MACS dissociator and the RNeasy lipid tissue kit (QIAGEN).
RNA-seq libraries were prepared and sequenced using standard Illumina protocols for a HiSeq 2500 instrument.

value: Peripancreatic adipose tissue (PAT)

tag: cell origin

value: adipose tissue

tag: condition

value: Chronic Pancreatitis (CP)


title: MZythdf2 6 hours post fertilization rep2

city: Farmington

first: Jean-Denis

last: Beaudoin

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health Center

description:
Library name: ythdf2KO_6hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset7_MZythdf2_perread_processed_pa_filtered.csv
SDataset11_per_read_MZythdf2WT_allsamples.csv

data_processing:
Master of Pores pipeline version 2 (MOP2):The mop_preprocess module was used to basecall the raw signal with Guppy v6.0.6 (Oxford Nanopore Technologies) using the m6A-aware basecalling model rna_r9.4.1_70bps_m6A_hac.cfg (m6Abasecaller).
The DeePlexiCon algorithm was used to demultiplex multiplexed reads.
ModPhred used to encode the modification probabilities and map reads to the GRCz11 genome with minimap2 2.17-r941 using the parameters “-ax map-ont -k13”.
Per-read gene and isoform annotation using the samtools flag “-F 3488”, with Isoquant v3.3.0 using parameters “--complete_genedb --data_type nanopore” and the zebrafish Ensembl annotation version 110. Poly(A) tail length estimation was performed using the mop_tail module of MoP2 with tailfindr v1.3.
m6AB_PerRead pipeline generated replicable m6A sites and per_read tables. For isoform-level and read-level analysis, reads were required to map uniquely to a single isoform that had at least 25 reads per replicate. Reads lacking a tailfindr poly(A) tail estimate (NaN values) were removed (pa_filtered files).
Assembly: GRCz11
Supplementary files format and content: SDataset5,6,7... .csv file of per_read tables produced by the m6AB_PerRead pipeline (m6Abasecaller_per_read_analysis) that has been filtered for isoform-level and read-level analysis. This includes isoform/gene assignment, m6A modification number and location, read length, poly(A) tail length, and relevant timepoint/treatment for each read.
Supplementary files format and content: SDataset8.. .tsv file of replicable m6A sites with information on their chromosome position, coverage, and modification frequency.
Supplementary files format and content: SDataset9,10,11... .csv file of pre_read tables produced by the m6AB_PerRead pipeline that includes m6A modification number and location, chromosomal alignment information, poly(A) tail length, isoform/gene assignment information, and sample for each read.

molecule: polyA RNA

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were maintained at 28 °C

extract_protocol:
RNA from frozen embryos was extracted using TRIzol (Invitrogen).  Poly(A)+ mRNAs were isolated with oligo d(T)25 magnetic beads (New England BioLabs) according to the manufacturer’s protocol and eluted in 30 µL of water.
RNA libraries were prepared using the direct RNA sequencing kit (SQK-RNA002), following ONT protocol version DRS_9080_v2_revI_14Aug2019 with half reactions of 250 ng of poly(A)+ RNA for each library up to the RNA Adapter (RMX) ligation step, with the following adaptations. Samples were ligated to pre-annealed custom RT adaptors (IDT) containing barcodes. For non-barcoded runs, the commercial RT adapter included in the SQK-RNA002 kit was used instead. Reverse transcription was then performed. Ligated products were purified using 1.8X Agencourt RNAClean XP beads (Fisher Scientific, NC0068576).For the final ligation, 50 ng of reverse-transcribed RNA from each reaction was pooled, and ligated with the RMX adapter. For non-barcoded runs, 200 ng of reverse-transcribed RNA was used for ligation with the RMX adapter. The ligated RNA:DNA hybrid was purified using 1X Agencourt RNAClean XP beads. Samples were run on a R9.4.1 flowcell on a MinION or PromethION device.

treatment_protocol: All injections into zebrafish embryos were performed on dechorionated one-cell stage embryos with 1 nL volumes. To inhibit RNA Polymerase II, embryos were injected with 0.2 ng of α-amanitin (Sigma-Aldrich, A2263) resuspended in nuclease-free water. To inhibit miR-430 activity, embryos were injected with 10 µM of tiny locked nucleic acid (tinyLNA), complementary to the seed region of miR-430 (5′-TAGCACTT-3′ (Exiqon)).

value: embryos

tag: sample group

value: MZythdf2 6 hours post fertilization


title: Control-1

city: Bengbu City, Anhui Province

first: Bohan

last: Li

address: 安徽省蚌埠市东海大道2600号

department: School of Pharmacy

country: China

institute: Bengbu Medical University

description: Library name: SAMPLES 1

library_source: other

data_processing:
Raw reads were filtered to remove adapter sequences and low‑quality reads using  fastp (0.23.0).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 （ Hierarchical Indexing for Spliced Alignment of Transcripts ）.
Gene expression levels were used HTSeq (0.10.0) for reads count calculation. HTSeq provides three overlap resolution modes — union, intersection_strict, and intersection_nonempty — to determine whether a read is assigned to a given gene..
Differentially expressed genes (DEGs) were identified using DESeq2 (1.18.1) with edegR (3.20.9)
KEGG and GO pathway enrichment analyses were performed using clusterProfiler (4.8.2) in R.
Assembly: hg38
Supplementary files format and content: Processed data files include a gene expression matrix (FPKM values) for all samples.
Supplementary files format and content: Raw count matrix and differential expression and enrichment results are also provided.

molecule: other

source_name: Cancer

growth_protocol: Triple-negative breast cancer cells were cultured inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS, Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco) in a humidified incubator with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted from cells using TRIzol® reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA purity and integrity were assessed using a NanoDrop™ One/OneC spectrophotometer and anAgilent 4200 TapeStation.
RNA‑seq libraries were constructed using theAMPure XP beads following the manufacturer’s protocol

treatment_protocol: Cells were treated with MAG (40 μM) for 24 h.

value: Cancer

value: TNBC

value: Control


title: PAT - HP1

description: Library name: P26

value: Resolved pancreatitis (HP)


title: PAT - HP2

description: Library name: P11


title: 10E_ap2hs_3xHA_plusCHO_rep1_in

description:
Library name: 10E_ap2hs_3xHA_plusCHO_rep1_in
10E_ap2hs_3xHA_plusCHO_rep1_in

value: ap2-hs 3xHA

value: control choline

value: Late trophozoites/early schizonts


title: PilotPool_Sort2_Human PDL1_TechRep2

description:
Library name: Pilot Pool_Sort2_Sample4
NGS-Read-Counts_PilotPool.xlsx

value: Transduced HEK293T cells

value: Stained with recombinant human PD-L1


title: PilotPool_Sort1_Human PDL1_TechRep6

description:
Library name: Pilot Pool_Sort1_Sample6
NGS-Read-Counts_PilotPool.xlsx


title: 10E_ap2hs_3xHA_minCHO_rep1_IP

description:
Library name: 10E_ap2hs_3xHA_minCHO_rep1_IP
10E_ap2hs_3xHA_minCHO_rep1_IP

value: choline depletion


title: 10E_ap2hs_3xHA_plusCHO_rep2_IP

description:
Library name: 10E_ap2hs_3xHA_plusCHO_rep2_IP
10E_ap2hs_3xHA_plusCHO_rep2_IP


title: AAV2CBE, H3K4me3, biol_rep1

description: Library name: AAV2CBE sample 6

value: Kidney

value: HEK 293T

value: Human Embryonic Kidney


title: AAV2CBE, H3K4me3, biol_rep2

description: Library name: AAV2CBE sample 7


title: 10E_ap2hs_3xHA_plusCHO_rep1_IP

description:
Library name: 10E_ap2hs_3xHA_plusCHO_rep1_IP
10E_ap2hs_3xHA_plusCHO_rep1_IP


title: 10E_ap2hs_3xHA_minCHO_rep2_IP

description:
Library name: 10E_ap2hs_3xHA_minCHO_rep2_IP
10E_ap2hs_3xHA_minCHO_rep2_IP


title: PAT – CP4

description: Library name: P7

value: Peripancreatic adipose tissue (PAT)

value: adipose tissue


title: Aβ42-treated forebrain organoid with maraviroc treatment and iPSC-derived microglia co-culture rep 2, oligo library

city: Shenzhen

first: Yilin

last: Feng

state: Please Choose

address: XILI Street

institute: Tsinghua University

description:
Library name: AD_mgL_mar_2_oligo
Oligo library generated from the same biological sample as AD_mgL_mar_2.

data_processing:
Raw sequencing data were processed using the DNBelab C-TaiM4 analysis pipeline to perform read demultiplexing, cell barcode identification, UMI extraction, and alignment to the human reference genome.
Gene-by-cell expression count matrices were generated for each biological sample after UMI deduplication.
Clean reads were aligned to the GRCh38 human reference genome using STAR (v2.7.11b).
Downstream quality control, normalization, dimensionality reduction, clustering, and data integration were performed using Seurat (v5) in R.
Assembly: GRCh38
Supplementary files format and content: integrated_SCT.rds

source_name: Forebrain organoid

growth_protocol: Human induced pluripotent stem cell (iPSC)-derived forebrain organoids were generated using a dorsal forebrain differentiation protocol and maintained under standard organoid culture conditions (37°C, 5% CO₂). Organoids were differentiated to Day 60 prior to experimental treatments. Mature human iPSC-derived microglia were generated separately using an established differentiation protocol.

extract_protocol:
Following completion of the experimental treatments, forebrain organoids were dissociated into single-cell suspensions using an enzymatic dissociation protocol. Cell suspensions were filtered through a 40-μm cell strainer, and cell viability was assessed prior to library preparation. Qualified single-cell suspensions were immediately processed for single-cell RNA sequencing.
Single-cell suspensions were processed using the MGI DNBelab C-TaiM4 platform. Individual cells were encapsulated with mRNA capture magnetic beads containing unique cell barcodes and unique molecular identifiers (UMIs) using a microfluidic droplet system. Cell lysis occurred within droplets, and poly(A)+ mRNA molecules were captured by Oligo(dT) primers on the magnetic beads and reverse transcribed to generate barcoded cDNA. The cDNA was purified, amplified, and ligated with sequencing adapters to construct sequencing libraries. Library quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Gene expression (cDNA) libraries and oligo libraries were sequenced on a DNBSEQ-T7 platform in paired-end 100-bp mode (PE100). Sequencing was performed by Hangzhou Astrocyte Technology Co., Ltd.

value: Forebrain organoid

value: WT

value: Aβ42 + maraviroc + iPSC-derived microglia co-culture

tag: batch


title: PilotPool_Sort1_Human PDL1_TechRep3

description:
Library name: Pilot Pool_Sort1_Sample3
NGS-Read-Counts_PilotPool.xlsx


title: AAV2CBE, H3K27ac, biol_rep2

description: Library name: AAV2CBE sample 4


title: PAT – CP3

description: Library name: P31

value: Chronic Pancreatitis (CP)


title: PilotPool_Sort1_Human PDL1_TechRep5

description:
Library name: Pilot Pool_Sort1_Sample5
NGS-Read-Counts_PilotPool.xlsx


title: PAT – CP5

description: Library name: P8


title: PAT – CP6

description: Library name: P9


title: PilotPool_Sort1_Human PDL1_TechRep4

description:
Library name: Pilot Pool_Sort1_Sample4
NGS-Read-Counts_PilotPool.xlsx


title: AAV2CBE, H3K27ac, biol_rep1

description: Library name: AAV2CBE sample 3


title: PilotPool_Sort1_Human PDL1_TechRep1

description:
Library name: Pilot Pool_Sort1_Sample1
NGS-Read-Counts_PilotPool.xlsx


title: Aβ42-treated forebrain organoid with maraviroc treatment and iPSC-derived microglia co-culture rep 2, cDNA library

description:
Library name: AD_mgL_mar_2_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids treated with maraviroc and co-cultured with mature human iPSC-derived microglia for 48 hours (3 organoids), biological replicate 2.


title: PAT - T2D_5

description: Library name: P25


title: AAV2CBE, H3K27ac, biol_rep3

description: Library name: AAV2CBE sample 5


title: AAV2CBE, CTCF, biol_rep3

description: Library name: AAV2CBE sample 2

value: CTCF


title: PAT – CP1

description: Library name: P5


title: Aβ42-treated forebrain organoid with maraviroc treatment and iPSC-derived microglia co-culture rep 1, cDNA library

description:
Library name: AD_mgL_mar_1_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids treated with maraviroc and co-cultured with mature human iPSC-derived microglia for 48 hours (3 organoids), biological replicate 1.


title: PAT – CP2

description: Library name: P6


title: PilotPool_Sort1_Human PDL1_TechRep2

description:
Library name: Pilot Pool_Sort1_Sample2
NGS-Read-Counts_PilotPool.xlsx


title: Soleus muscle, LCR, replicate 8

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: LCR8
23-24 months female

data_processing:
Raw reads were quality-controlled using FastQC and trimmed using Trim Galore (v0.6.10) in RRBS-specific and paired-end mode.
Cleaned reads were aligned to the Rattus norvegicus reference genome using Bismark with Bowtie2.
Assembly: rn7
Supplementary files format and content: bismark.cov.gz files containing methylation coverage and percentage for analyzed CpG sites.

organism: Rattus norvegicus

source_name: soleus muscle

growth_protocol: Selectively bred low- and high-running capacity rats (LCR and HCR; 44th generation) derived from genetically heterogeneous N:NIH stock were housed in temperature-controlled rooms under a 12:12-h light-dark cycle with ad libitum access to standard chow and water.

extract_protocol:
Left soleus muscle samples were snap-frozen and stored at -80°C. Total DNA extraction was performed with the PureLink Genomic DNA Mini Kit.
RRBS libraries were constructed using the Premium RRBS Kit V2 (Diagenode). 100 ng of genomic DNA underwent MspI digestion, followed by end-repair, adapter ligation, and size selection. Pools were subjected to bisulfite conversion and PCR amplification.

value: soleus muscle

value: low-running capacity


title: PAT – Control 5

description: Library name: P24

value: control (CTRL)


title: Soleus muscle, LCR, replicate 6

description:
Library name: LCR6
23-24 months female


title: AAV2, igg_ctrl, biol_rep4

description: Library name: AAV2 sample 12


title: Aβ42-treated forebrain organoid with iPSC-derived microglia co-culture rep 2, oligo library

description:
Library name: AD_mgL_2_oligo
Oligo library generated from the same biological sample as AD_mgL_2.

value: Aβ42 + iPSC-derived microglia co-culture


title: Aβ42-treated forebrain organoid with maraviroc treatment and iPSC-derived microglia co-culture rep 1, oligo library

description:
Library name: AD_mgL_mar_1_oligo
Oligo library generated from the same biological sample as AD_mgL_mar_1.


title: Soleus muscle, LCR, replicate 7

description:
Library name: LCR7
23-24 months female


title: AAV2, igg_ctrl, biol_rep3

description: Library name: AAV2 sample 11


title: Aβ42-treated forebrain organoid with iPSC-derived microglia co-culture rep 2, cDNA library

description:
Library name: AD_mgL_2_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids co-cultured with mature human iPSC-derived microglia for 48 hours (3 organoids), biological replicate 2.


title: PAT – Control 4

description: Library name: P20


title: AAV2CBE, CTCF, biol_rep1

description: Library name: AAV2CBE sample 1


title: PAT – Control 3

description: Library name: P22


title: Aβ42-treated forebrain organoid with iPSC-derived microglia co-culture rep 1, oligo library

description:
Library name: AD_mgL_1_oligo
Oligo library generated from the same biological sample as AD_mgL_1.


title: Soleus muscle, LCR, replicate 5

description:
Library name: LCR5
23-24 months female


title: Soleus muscle, LCR, replicate 4

description:
Library name: LCR4
23-24 months female


title: Aβ42-treated forebrain organoid with iPSC-derived microglia co-culture rep 1, cDNA library

description:
Library name: AD_mgL_1_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids co-cultured with mature human iPSC-derived microglia for 48 hours (3 organoids), biological replicate 1.


title: AAV2, igg_ctrl, biol_rep1

description: Library name: AAV2 sample 9


title: AAV2, igg_ctrl, biol_rep2

description: Library name: AAV2 sample 10


title: PAT – Control 2

description: Library name: P17


title: PAT – Control 1

description: Library name: P14


title: Aβ42-treated forebrain organoid rep 2, oligo library

description:
Library name: AD_2_oligo
Oligo library generated from the same biological sample as AD_2.


title: Soleus muscle, LCR, replicate 3

description:
Library name: LCR3
23-24 months female


title: AAV2, H3K27ac, biol_rep4

description: Library name: AAV2 sample 8


title: HiC, K562 cells, 3hrs rep2

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
Hi-C experiments were processed following the HiC-Pro (v2.11.1) with default parameters. The alignment of the reads was performed with Bowtie2 v2.3.4.1 against the hg19 human genome. The normalized ICE matrices were generated with same number of valid pairs and computed at 50kb resolution.
Assembly: hg19
Supplementary files format and content: Tabular separated data with chromatin interactions counts

extract_protocol:
HiC in nuclei were performed with 2x106 cells. The cells were fixed with formaldehyde 2%. Chromatin was digested with HindIII enzyme for 0.25, 1, 3 and 12 hours. The 5′ overhangs were filled with dCTP, dGTP, dTTP and Biotin-14-dATP and re-ligated in nuclei. DNA fragments were purified and sonicated in COVARIS S220. The DNA were selected using Ampure SPRI Beads to get 300-600bp fragments. The pull-down was performed with Dynabeads MyOne Streptavidine C1.
The libraries were marked with Illumina TrueSeq DNA Adapters and amplified using Taq Phusion NEB. The paired-end sequencing was performed in a HiSeq2500.


title: Soleus muscle, LCR, replicate 2

description:
Library name: LCR2
23-24 months female


title: HiC, K562 cells, 3hrs rep1


title: Aβ42-treated forebrain organoid rep 2, cDNA library

description:
Library name: AD_2_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids (3 organoids), biological replicate 2.


title: Soleus muscle, LCR, replicate 1

description:
Library name: LCR1
23-24 months female


title: Aβ42-treated forebrain organoid rep 1, oligo library

description:
Library name: AD_1_oligo
Oligo library generated from the same biological sample as AD_1.


title: Soleus muscle, HCR, replicate 6

description:
Library name: HCR6
23-24 months female

value: high-running capacity


title: AAV2, H3K27ac, biol_rep1

description: Library name: AAV2 sample 7


title: AAV2, H3K9me3, biol_rep2

description: Library name: AAV2 sample 6


title: HiC, K562 cells, 1hr rep2


title: HiC, K562 cells, 1hr rep1


title: Soleus muscle, HCR, replicate 5

description:
Library name: HCR5
23-24 months female


title: AAV2, H3K9me3, biol_rep1

description: Library name: AAV2 sample 5


title: Control forebrain organoid rep 2, oligo library

description:
Library name: CTR_2_oligo
Oligo library generated from the same biological sample as CTR_2.

value: Vehicle


title: Aβ42-treated forebrain organoid rep 1, cDNA library

description:
Library name: AD_1_cDNA
Gene expression (cDNA) library from pooled Day 60 Aβ42-treated forebrain organoids (3 organoids), biological replicate 1.


title: AAV2, H3K4me3, biol_rep2

description: Library name: AAV2 sample 4


title: HiC, K562 cells, 12hrs rep2


title: Control forebrain organoid rep 2, cDNA library

description:
Library name: CTR_2_cDNA
Gene expression (cDNA) library from pooled Day 60 control forebrain organoids (3 organoids), biological replicate 2.


title: AAV2, H3K4me3, biol_rep1

description: Library name: AAV2 sample 3


title: Soleus muscle, HCR, replicate 4

description:
Library name: HCR4
23-24 months female


title: Soleus muscle, HCR, replicate 3

description:
Library name: HCR3
23-24 months female


title: HiC, K562 cells, 12hrs rep1


title: Control forebrain organoid rep 1, oligo library

description:
Library name: CTR_1_oligo
Oligo library generated from the same biological sample as CTR_1.


title: AAV2, CTCF, biol_rep3

description: Library name: AAV2 sample 2


title: Soleus muscle, HCR, replicate 2

description:
Library name: HCR2
23-24 months female


title: HiC, K562 cells, 0.25hrs rep2


title: Control forebrain organoid rep 1, cDNA library

description:
Library name: CTR_1_cDNA
Gene expression (cDNA) library from pooled Day 60 control forebrain organoids (3 organoids), biological replicate 1.


title: AAV2, CTCF, biol_rep1

description: Library name: AAV2 sample 1


title: Mouse hepatocytes; Mito-TEMPO + FAC treated 3

status: Public on Jul 26 2026

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Library name: p22074-s012_MTposFAC3_S152

data_processing:
Reads aligned to GRCm38_102 by STAR S2.7.9a and quantified with STAR --quantMode
Assembly: GRCm38_102
Supplementary files format and content: Tab separated reads-per-gene table from STAR --quantMode, with Gene Symbols in first column and counts for Unstranded, Sense stranded and Anti-sense stranded interpretations of the alignments. Library prep was Unstranded

source_name: Liver

extract_protocol:
Cells were lysed in 350 L of Buffer RLT and then extracted using the RNeasy Micro kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions.
Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~35 million reads per sample on average.

value: Liver

value: Primary hepatocytes

value: MT+FAC


title: HiC, K562 cells, 0.25hrs rep1


title: Soleus muscle, HCR, replicate 1

description:
Library name: HCR1
23-24 months female


title: Mouse hepatocytes; Mito-TEMPO + FAC treated 1

description: Library name: p22074-s010_MTposFAC1_S150


title: Mouse hepatocytes; Mito-TEMPO + FAC treated 2

description: Library name: p22074-s011_MTposFAC2_S151


title: Mouse hepatocytes; liproxstatin-1 + FAC treated 3

description: Library name: p22074-s009_LiproxposFAC3_S149


title: Mouse hepatocytes; FAC treated 3

description: Library name: p22074-s006_FAC3_S146

value: FAC


title: Mouse hepatocytes; FAC treated 2

description: Library name: p22074-s005_FAC2_S145


title: Mouse hepatocytes; FAC treated 1

description: Library name: p22074-s004_FAC1_S144


title: Mouse hepatocytes; liproxstatin-1 + FAC treated 1

description: Library name: p22074-s007_LiproxposFAC1_S147


title: Mouse hepatocytes; liproxstatin-1 + FAC treated 2

description: Library name: p22074-s008_LiproxposFAC2_S148


title: Mouse hepatocytes; control 3

description: Library name: p22074-s003_Cont3_S143

value: Control


title: Mouse hepatocytes; control 1

description: Library name: p22074-s001_Cont1_S141


title: Mouse hepatocytes; control 2

description: Library name: p22074-s002_Cont2_S142


title: NaIO3-sc

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description: Library name: Sample2

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics, version 3.0.2) for single cell RNA sequencing.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of  barcodes
Supplementary files format and content: features.tsv.gz. list of genes
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

source_name: retina

extract_protocol:
Retinas from 6 mice per group were pooled together and cut into small pieces before incubated in Ames’ Medium containing 15 U/mL papain (Worthington) and 0.1 mg/mL DNase I (Sigma) at 34 ℃.Cell pellets from NaIO3 group were resuspended, incubated with CD11b MicroBeads (STEMCELL Technologies), and magnetically separated using an EasySep™ Magnet (STEMCELL Technologies) according to the manufacture instruction for single cell RNA-sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were injected intravenously with 20 mg/kg of NaIO3 (Sigma-Aldrich Corp., St. Louis, MO, USA), which was dissolved in phosphate-buffered saline (PBS). The mice receiving the same volume of PBS worked as controls.Seven days later, the mice were sacrificed by carbon dioxide euthanasia and the eyes were collected for further investigation.

value: retina

value: CD11b+ microglia

value: NaIO3 induced retinal degeneration mice


title: PBS-sc

description: Library name: Sample1

value: PBS treated control


title: RRBS Self-Administration Saline 4

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Library name: Sal 4

data_processing:
Single end 100 bp eRRBS sequencing, with a target of 100 million reads per sample, was performed on an Illumina NovaSeq6000 according to the manufacturer’s instructions.
Demultiplexed and converted to FASTQ files using the Illumina bcl2fastq software.
Alignment to the mm10 reference genome and methylation calling was performed using Bismark v22.1 using default settings
Bisulfite sequencing data using an in-house BisSeq pipeline (https://pubmed.ncbi.nlm.nih.gov/25742437/)
Assembly: mm10

source_name: Brain

extract_protocol:
dDG DGC layer was dissected from mouse brain and DNA extracted using Qiagen QIAamp DNA Micro Kit
Libraries were constructed by the Weill Cornell Epigenomics Core as previously described (https://pubmed.ncbi.nlm.nih.gov/25742437/)

value: Brain

value: male

value: dDG DGC

value: saline


title: RRBS Self-Administration Saline 3

description: Library name: Sal 3


title: RRBS Self-Administration Saline 1

description: Library name: Sal 1


title: RRBS Self-Administration Saline 2

description: Library name: Sal 2


title: RRBS Self-Administration Cocaine 3

description: Library name: Coc 3

value: cocaine


title: RRBS Self-Administration Cocaine 2

description: Library name: Coc 2


title: RRBS Self-Administration Cocaine 1

description: Library name: Coc 1


title: RRBS Self-Administration Cocaine 4

description: Library name: Coc 4


title: Self-Administration Saline 5

description: Library name: Sal 5

data_processing:
Sequencing reads were trimmed with cutadapt and aligned to the mm10 reference genome using STAR by the Weill Cornell Medicine Genomics core. Abundance of transcripts was measured with Cufflinks in Fragments per Kilobase of exon model per million mapped reads (FPKM). Read counts were counted using HT-seq program73.
Assembly: mm10
Supplementary files format and content: csv, matrix with column names for samples

extract_protocol:
dDG DGC layer was dissected from mouse brain and RNA extracted using Qiagen RNeasy Micro Kit
Library prep and sequencing was performed by the Weill Cornell Medicine Genomics Core. Library prep was done using NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module) according to manufacturer protocol


title: Self-Administration Saline 3

description: Library name: Sal 3


title: Self-Administration Saline 2

description: Library name: Sal 2


title: Self-Administration Saline 1

description: Library name: Sal 1


title: Self-Administration Cocaine 5

description: Library name: Coc 5


title: Self-Administration Cocaine 3

description: Library name: Coc 3


title: Self-Administration Cocaine 4

description: Library name: Coc 4


title: Self-Administration Saline 4

description: Library name: Sal 4


title: Self-Administration Cocaine 2

description: Library name: Coc 2


title: Self-Administration Cocaine 1

description: Library name: Coc 1


title: Hepa1-6 cells  P-Por-Os+US-3

city: chengdu

first: yinghao

last: lv

address: Guoxue Xiang

institute: Sichuan university

data_processing:
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on NovaSeq 6000 instrument (Illumina Inc) in PE150 mode.
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of Mus musculus from ftp://ftp.ensembl.org/pub/release-87/fasta/mus musculus/dna/ using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: GRCm38
Supplementary files format and content: processed data.xlsx

source_name: Hepa1-6 cells

growth_protocol: Hepa1-6 cells  were maintained in DMEM supplemented with 10% fetal bovine serum and with 5% CO2 at 37℃

extract_protocol:
RNA library preparation and high through-put sequencing and data analysis were conducted by Seqhealth Technology Co., LTD (Wuhan, China).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
1 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. N406, Vazyme) and KC-DigitalTM Stranded mRNA Library Prep Kit® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Hepa1-6 cells  were treated with P-Por-Os(25.57ug/mL) or P-Por-Os(25.57ug/mL) +US

value: Hepa1-6 cells

value: Mouse HepatocarcinomaCells

value: WT


title: Hepa1-6 cells  P-Por-Os+US-2


title: Hepa1-6 cells  P-Por-Os+US-1


title: Hepa1-6 cells  P-Por-Os-3


title: Hepa1-6 cells  P-Por-Os-2


title: Hepa1-6 cells  P-Por-Os-1


title: Hepa1-6 cells  NC-3


title: Hepa1-6 cells  NC-2


title: Hepa1-6 cells  NC-1


title: Aβ42-treated forebrain organoid rep3

description: Library name: ATO3

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Clean reads provided by BGI were used for downstream analyses.
Clean reads were aligned to the GRCh38 human reference genome using STAR (v2.7.11b).
Gene-level read counts were generated using featureCounts (v2.0.6)
Assembly: GRCh38
Supplementary files format and content: raw_counts_TPM.csv contains raw gene-level read counts and transcripts per million (TPM) values for all annotated genes across all biological samples. Each row represents a gene, and columns include raw read counts and TPM values for each sample.

growth_protocol: Human induced pluripotent stem cell (iPSC)-derived forebrain organoids were generated using a previously established dorsal forebrain differentiation protocol and maintained in organoid culture medium under standard conditions (37°C, 5% CO₂). Organoids were cultured until the designated experimental time point before treatment.

extract_protocol:
Total RNA was extracted from organoids using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions. RNA concentration and integrity were assessed prior to library preparation.
RNA library preparation and sequencing were performed by BGI Genomics. Poly(A)+ mRNA was enriched from total RNA, fragmented, and reverse-transcribed into cDNA. Libraries were prepared following BGI's standard stranded mRNA library preparation protocol, including end repair, adaptor ligation, PCR amplification, and library quality control prior to sequencing.

value: Forebrain organoid

value: IPSC


title: Aβ42-treated forebrain organoid rep2

description: Library name: ATO2


title: Aβ42-treated forebrain organoid rep1

description: Library name: ATO1


title: Control forebrain organoid rep3

description: Library name: CTO3

value: Vehicle


title: Control forebrain organoid rep1

description: Library name: CTO1


title: Control forebrain organoid rep2

description: Library name: CTO2


title: slender bsf, 8hrs after differentiation, replicate 2

city: Würzburg

first: Markus

last: Engstler

address: Am Hubland

department: Cell and Developmental Biology

institute: Universität Würzburg

description:
Library name: SL82
Sample5
slender bsf_8hrspostdiff_rep2

data_processing:
Read demultiplexing and quality control were performed with FASTQC (version 0.12.1, (Andrews, 2012)).
Adaptors were removed and reads were trimmed using Fastp (version 0.23.4, (Chen, 2023)).
Kallisto was used for read alignment, and genes with ≥ 3 counts per million (cpm) in at least two samples were retained for downstream analysis. Data normalization was performed using the EdgeR package in RStudio (Robinson et al., 2009; Team R.C., 2021).
Differentially expressed genes (DEGs) were identified using DESeq2, EdgeR, and Limma packages in RStudio (Love et al., 2014; Ritchie et al., 2015; Robinson et al., 2009; Team R.C., 2020)
The T. b. brucei TREU 972 reference genome was obtained from the Tritryp database (TritrypDB). rRNA was removed (Aslett et al., 2010), and, to remove redundancy, only one representative from each gene group was retained while others were masked. Gene groups were defined based on sequence similarity using CD-Hit software (Li & Godzik, 2006).
fastq files contain raw data
Assembly: HTML files contain read quality information
Supplementary files format and content: csv files contain gene-level read counts for each sample

organism: Trypanosoma brucei brucei

source_name: EATRO 1125 (serodome AnTAT1.1)

growth_protocol: Live cells were sorted using a FACS Aria III cytometer (BD Biosciences). 1000 cells per replicate were deposited into single wells of a 48 well-plate containing 2.6 µl of 1x lysis buffer (Takara) and 0.01 µl of RNase inhibitor (40 U/µl; Takara). Sorting was performed in triplicates for each timepoint, and plates were immediately placed on ice and stored at -80°C. Library preparation and sequencing were performed as previously described (Müller et al., 2018). Very briefly, lysates were supplemented with 0.2 µl ERCC Spike-in Control Mix 1 (Thermo Fisher Scientific) at a 1:20,000,000 dilution.

extract_protocol:
Cells were harvested from biological triplicates, resuspended in 1 ml pre-warmed PBS containing 10 % FCS. The cells were washed twice with pre-warmed PBS to remove FCS in 1 ml of pre-warmed PBS 15 min prior to sorting, Calcein-AM violet was added at a final concentration of 1 µM to label viable cells. Live cells were sorted using a FACS Aria III cytometer (BD Biosciences). 1000 cells per replicate were deposited into single wells of a 48 well-plate containing 2.6 µl of 1x lysis buffer (Takara) and 0.01 µl of RNase inhibitor (40 U/µl; Takara). Sorting was performed in triplicates for each timepoint, and plates were immediately placed on ice and stored at -80°C.
Bulk RNA-sequencing analysis was performed according to scripts and online resources published by Berry et al., 2021 using RStudio (version 4.02).

treatment_protocol: Libraries were prepared using the SMART-Seq v.4 Ultra Low Input RNA Kit (Takara), utilizing a quarter of the recommended reagent volumes.

value: EATRO 1125 (serodome AnTAT1.1)

value: unicellular protozoan parasite

value: cytoplasmic tdTomato protein, EP1 yellow fluorescent fusion protein, PAD1 green fluorescent stumpy marker

value: procyclic differentiation


title: slender bsf, 0hrs after differentiation, replicate 2

description:
Library name: SL02
Sample2
slender bsf_0hrspostdiff_rep2


title: slender bsf, 0hrs after differentiation, replicate 1

description:
Library name: SL01
Sample1
slender bsf_0hrspostdiff_rep1


title: slender bsf, 0hrs after differentiation, replicate 3

description:
Library name: SL03
Sample3
slender bsf_0hrspostdiff_rep3


title: slender bsf, 8hrs after differentiation, replicate 1

description:
Library name: SL81
Sample4
slender bsf_8hrspostdiff_rep1


title: stumpy bsf, 72hrs after differentiation, replicate 2

description:
Library name: ST722
Sample29
stumpy bsf_72hrspostdiff_rep2


title: stumpy bsf, 72hrs after differentiation, replicate 1

description:
Library name: ST721
Sample28
stumpy bsf_72hrspostdiff_rep1


title: stumpy bsf, 24hrs after differentiation, replicate 3

description:
Library name: ST243
Sample27
stumpy bsf_24hrspostdiff_rep3


title: stumpy bsf, 24hrs after differentiation, replicate 2

description:
Library name: ST242
Sample26
stumpy bsf_24hrspostdiff_rep2


title: stumpy bsf, 24hrs after differentiation, replicate 1

description:
Library name: ST241
Sample25
stumpy bsf_24hrspostdiff_rep1


title: stumpy bsf, 15hrs after differentiation, replicate 2

description:
Library name: ST152
Sample23
stumpy bsf_15hrspostdiff_rep2


title: stumpy bsf, 15hrs after differentiation, replicate 1

description:
Library name: ST151
Sample22
stumpy bsf_15hrspostdiff_rep1


title: stumpy bsf, 8hrs after differentiation, replicate 3

description:
Library name: ST83
Sample21
stumpy bsf_8hrspostdiff_rep3


title: stumpy bsf, 15hrs after differentiation, replicate 3

description:
Library name: ST153
Sample24
stumpy bsf_15hrspostdiff_rep3


title: stumpy bsf, 8hrs after differentiation, replicate 2

description:
Library name: ST82
Sample20
stumpy bsf_8hrspostdiff_rep2


title: stumpy bsf, 0hrs after differentiation, replicate 3

description:
Library name: ST03
Sample18
stumpy bsf_0hrspostdiff_rep3


title: stumpy bsf, 0hrs after differentiation, replicate 2

description:
Library name: ST02
Sample17
stumpy bsf_0hrspostdiff_rep2


title: stumpy bsf, 8hrs after differentiation, replicate 1

description:
Library name: ST81
Sample19
stumpy bsf_8hrspostdiff_rep1


title: stumpy bsf, 0hrs after differentiation, replicate 1

description:
Library name: ST01
Sample16
stumpy bsf_0hrspostdiff_rep1


title: slender bsf, 72hrs after differentiation, replicate 3

description:
Library name: SL723
Sample15
slender bsf_72hrspostdiff_rep3


title: slender bsf, 24hrs after differentiation, replicate 3

description:
Library name: SL243
Sample12
slender bsf_24hrspostdiff_rep3


title: slender bsf, 72hrs after differentiation, replicate 2

description:
Library name: SL722
Sample14
slender bsf_72hrspostdiff_rep2


title: slender bsf, 72hrs after differentiation, replicate 1

description:
Library name: SL721
Sample13
slender bsf_72hrspostdiff_rep1


title: slender bsf, 24hrs after differentiation, replicate 2

description:
Library name: SL242
Sample11
slender bsf_24hrspostdiff_rep2


title: slender bsf, 24hrs after differentiation, replicate 1

description:
Library name: SL241
Sample10
slender bsf_24hrspostdiff_rep1


title: stumpy bsf, 72hrs after differentiation, replicate 3

description:
Library name: ST723
Sample30
stumpy bsf_72hrspostdiff_rep3


title: slender bsf, 15hrs after differentiation, replicate 1

description:
Library name: SL151
Sample7
slender bsf_15hrspostdiff_rep1


title: Chicken embryo whole vestibular crista  500ng of totRNA

city: Pavia

first: Sergio

last: Masetto

address: Viale Golgi 19

department: Department of Brain and Behavioral Sciences

country: Italy

institute: University of Pavia

description: Library name: 2291_500pg

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.422 (Illumina)
Aligment and transcrips counts were performed using DRAGEN 4 (Illumina);
Illumina rna seq. alignment v2.0.0;
Assembly: bGalGal1.mat.broiler.GRCg7b.114(Gallus_gallus (UCSC galGal4)
Supplementary files format and content: 4I.counts.genes.geneinfo.txt ; Raw genes counts
Supplementary files format and content: 4I.quant.genes.sf.txt ; TPM normalized gene counts
Supplementary files format and content: 6II.counts.genes.geneinfo.txt; Raw genes counts
Supplementary files format and content: 6II.quant.genes.sf.txt; TPM normalized gene counts
Supplementary files format and content: 2291-500pg.counts.genes.geneinfo.txt; Raw genes counts
Supplementary files format and content: 2291-500pg.quant.genes.sf.txt; TPM normalized gene counts

organism: Gallus gallus

source_name: Chicken embryo whole vestibular crista

extract_protocol:
Collected cells were lysed according to the manufacturer's protocol, and cDNA was synthesized directly using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Ann Arbor, MI, USA), without prior RNA extraction.
SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Ann Arbor, MI)

treatment_protocol: Semicircular canal cristae were dissected, and vestibular hair cells were recorder by using the whole-cell patch-clamp technique in situ. After electrophysiological recordings were completed, the cytoplasmic contents of individual cells were collected using the same patch pipette and transferred into a collection tube containing lysis buffer.

value: Chicken embryo whole vestibular crista

value: ND

value: whole vestibular crista


title: slender bsf, 15hrs after differentiation, replicate 3

description:
Library name: SL153
Sample9
slender bsf_15hrspostdiff_rep3


title: slender bsf, 15hrs after differentiation, replicate 2

description:
Library name: SL152
Sample8
slender bsf_15hrspostdiff_rep2


title: Chicken embryo vestibular type II hair cell

description: Library name: 6II

source_name: embryonic vestibular apparatus

value: embryonic vestibular apparatus

value: vestibular type II hair cell


title: Chicken embryo vestibular type I hair cell

description: Library name: 4I

value: vestibular type I hair cell


title: GABPA_CT_mESC_dTAG_Truncated_rep1

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

description: Library name: GABPA_CT_mESC_dTAG_Truncated_rep1

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 and GABPA CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM. For PRO-seq, raw reads were trimmed by Trim Galore v0.6.7 and fastp v0.20.1, and ribosomal RNA reads were removed using Bowtie2 v2.4.4. Resulting reads were aligned to mm39 or dm6 genome using Bowtie2 v2.4.4, and PCR duplicates were removed by umi_tools v1.1.6. Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.13. Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.1 for single-base files with the following parameters: --Offset 1.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq, CUT&Tag and PRO-seq signals.
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: The B6 mESCs were maintained in DMEM supplemented with 15% foetal bovine serum (FBS), 100 U/mL penicillin-streptomycin, 2 mM L-Glutamine, 1 mM sodium pyruvate, 0.084 mM 2-mercaptoethanol, 1x MEM NEAA, 1,000 IU/mL LIF, 0.5 μM PD0325901, and 3 μM CHIR99021 at 37ºC with 5% CO2.

extract_protocol:
For RNA-seq and PRO-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads.
For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols. For PRO-seq, enriched RNA was ligated with RNA adapters. Reverse transcription was performed using the Superscript III enzyme. The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for 1, 2, 4 and12 hours, and the corresponding control cells were treated with DMSO. Nascent RNA was labeled with 500 μM 4-thiouridine for SLAM-seq.

value: cell line

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 3 hour


title: GABPA_CT_mESC_dTAG_Truncated_rep2

description: Library name: GABPA_CT_mESC_dTAG_Truncated_rep2


title: GABPA_CT_mESC_dTAG_WT_rep1

description: Library name: GABPA_CT_mESC_dTAG_WT_rep1


title: GABPA_CT_mESC_dTAG_WT_rep2

description: Library name: GABPA_CT_mESC_dTAG_WT_rep2


title: Single cell multiome, BM-MSCs, OSS,rep3,ATAC

city: Lund

first: Paul

last: Bourgine

state: Skane

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: D013_O_ATAC

library_source: genomic single cell

data_processing:
Demultiplexing and reference genome mapping using cellranger-ATC V2.1. reference genome Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: data.RDS : RDS file matrix with celltypes and annotations

source_name: Bone marrow

extract_protocol:
Tissues selected for multiomics sequencing were explanted from the mice and digested in Nattokinase (MedChemExpress #HY-P2373) as described 23.
Following isolation, cells were assessed for viability and lysed for nuclei isolation according to the 10X Genomics Demonstrated Protocol CG000365-Rev C. Library construction and sequencing were performed by the Centre for Translational Genomics (CTG Lund) using a 10X Multiome kit. Sequencing was performed on the NovaSeq X Series platform. Reference mapping and feature counting were performed  CellRanger-ARC.
10X genomics single nuclei multiome libraries

value: Bone marrow

value: primary BM-MSCs

value: MSCs

value: wt

value: Ossigel


title: Single cell multiome, BM-MSCs, OSS, rep2,ATAC

description: Library name: D009_O_ATAC


title: PRO_mESC_Gabpa_1h_dTAG_rep3

description: Library name: PRO_mESC_Gabpa_1h_dTAG_rep3

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM. For PRO-seq, raw reads were trimmed by Trim Galore v0.6.7 and fastp v0.20.1, and ribosomal RNA reads were removed using Bowtie2 v2.4.4. Resulting reads were aligned to mm39 or dm6 genome using Bowtie2 v2.4.4, and PCR duplicates were removed by umi_tools v1.1.6. Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.13. Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.1 for single-base files with the following parameters: --Offset 1.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq, CUT&Tag and PRO-seq signals.
Library strategy: PRO-Seq

value: treated with dTAG13 for 1 hour


title: PRO_mESC_Gabpa_1h_dTAG_rep2

description: Library name: PRO_mESC_Gabpa_1h_dTAG_rep2


title: Single cell multiome, BM-MSCs, In vitro,rep2,ATAC

description: Library name: D009_IV_ATAC

value: In vitro


title: PRO_mESC_Gabpa_1h_dTAG_rep1

description: Library name: PRO_mESC_Gabpa_1h_dTAG_rep1


title: Single cell multiome, BM-MSCs, Fibrin, rep2,ATAC

description: Library name: D009_F_ATAC

value: Fibrin


title: Single cell multiome, BM-MSCs, Fibrin,rep1, ATAC

description: Library name: D008_F_O_ATAC


title: PRO_mESC_Gabpa_1h_DMSO_rep2

description: Library name: PRO_mESC_Gabpa_1h_DMSO_rep2

value: treated with DMSO for 1 hour


title: PRO_mESC_Gabpa_1h_DMSO_rep1

description: Library name: PRO_mESC_Gabpa_1h_DMSO_rep1


title: Single cell multiome, BM-MSCs, OSS,rep3,GEX

description: Library name: D013_O_GEX


title: ATAC_mESC_Gabpa_4h_dTAG_rep2

description: Library name: ATAC_mESC_Gabpa_4h_dTAG_rep2

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM. For PRO-seq, raw reads were trimmed by Trim Galore v0.6.7 and fastp v0.20.1, and ribosomal RNA reads were removed using Bowtie2 v2.4.4. Resulting reads were aligned to mm39 or dm6 genome using Bowtie2 v2.4.4, and PCR duplicates were removed by umi_tools v1.1.6. Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.13. Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.1 for single-base files with the following parameters: --Offset 1.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq, CUT&Tag and PRO-seq signals.

value: treated with dTAG13 for 4 hour


title: Single cell multiome, BM-MSCs, Fibrin, rep2,GEX

description: Library name: D009_F_GEX


title: ATAC_mESC_Gabpa_4h_dTAG_rep1

description: Library name: ATAC_mESC_Gabpa_4h_dTAG_rep1


title: ATAC_mESC_Gabpa_4h_DMSO_rep2

description: Library name: ATAC_mESC_Gabpa_4h_DMSO_rep2

value: treated with DMSO for 4 hour


title: ATAC_mESC_Gabpa_4h_DMSO_rep1

description: Library name: ATAC_mESC_Gabpa_4h_DMSO_rep1


title: Single cell multiome, BM-MSCs, Fibrin,rep1, GEX

description: Library name: D008_F_O_GEX


title: ATAC_mESC_Gabpa_2h_dTAG_rep2

description: Library name: ATAC_mESC_Gabpa_2h_dTAG_rep2

value: treated with dTAG13 for 2 hour


title: ATAC_mESC_Gabpa_2h_dTAG_rep1

description: Library name: ATAC_mESC_Gabpa_2h_dTAG_rep1


title: ATAC_mESC_Gabpa_2h_DMSO_rep2

description: Library name: ATAC_mESC_Gabpa_2h_DMSO_rep2

value: treated with DMSO for 2 hour


title: CD4 T cell donor 3 replicate 3 micro C

city: Oxford

last: Hamley

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: cd4_don3_microc_3
Merged valid pairs file

data_processing:
Reads were aligned to gneome using BWA-mem with -5SP flag to support chimeric alignments.
The output was piped through the pairtools suitel alignments were parsed with a minimum mapping quality of 40, sorted, deduplicated and split to generate a valid apirs file.
Assembly: GRCh38
Supplementary files format and content: Valid pairs file

source_name: Blood

growth_protocol: Isolated CD4+ cells were cultured at 1x106 cells per ml in Immunocult-XF T cell expansion medium (Stemcell 10981) supplemented with 10ng/ml human IL-2 (Invitrogen X).

extract_protocol:
Dovetail Micro C kit
Dovetail Micro C kit

treatment_protocol: 25ul/ml of Immunocult Human CD3/CD28/CD2 T cell activator for 60 hours before collection.

value: Blood

value: CD4 T cell

value: WT

value: Activated


title: ATAC_mESC_Gabpa_2h_DMSO_rep1

description: Library name: ATAC_mESC_Gabpa_2h_DMSO_rep1

value: mESCs

value: GabpadTAG/dTAG


title: CD4 T cell donor 3 replicate 2 micro C

description:
Library name: cd4_don3_microc_2
Merged valid pairs file


title: CD4 T cell donor 3 replicate 1 micro C

description:
Library name: cd4_don3_microc_1
Merged valid pairs file


title: WT-CD36-negative cells-4

city: GuangZhou

first: Tian

last: Zhou

state: GuangDong

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description:
Library name: Sample9
CD36-NEG-7

data_processing:
Raw sequencing reads were first filtered using fastp (v0.18.0) to remove adapter contamination, reads containing more than 10% unknown nucleotides (N), and low-quality reads with >50% bases having a Q-value ≤20. Clean reads were then aligned to a ribosomal RNA (rRNA) database using Bowtie2 (v2.2.8) to remove rRNA-mapped reads. The remaining reads were mapped to the reference genome with HISAT2 (v2.1.0) using default parameters. For each sample, transcript assembly and quantification were performed with StringTie (v1.3.1) based on the reference annotation, and gene/transcript abundances were calculated as FPKM.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: isolated retinal cells

extract_protocol:
Retinal tissues were transferred into RPMI-1640 medium supplemented with HEPES buffer and mechanically dissociated by gentle trituration using wide-bore pipette tips. The resulting cell suspension was passed through a 70-μm cell strainer (BD Biosciences) to remove debris and cell aggregates. Cells were washed with phosphate-buffered saline (PBS) containing 1% fetal bovine serum (FBS) and incubated with fluorochrome-conjugated antibodies against CD45, CD11b, and CD36 and Live/Dead dye for 30 min at room temperature in the dark. Flow cytometric acquisition was performed using a BD flow cytometer (BD Biosciences) by sorting CD36+CD11b+CD45int live cells and CD36-CD11b+CD45int live cells
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: isolated retinal cells

value: CD45intCD11b+CD36-  microglia


title: BPAF2

city: Shanghai

first: jiaying

last: li

address: 99 Shangda Road, Baoshan District, Shanghai

institute: Shanghai University

description: Library name: Sample 5

data_processing:
FastQC and Cutadapt were used for raw read quality control and adapter sequence trimming.
Low-quality reads, reads containing ambiguous N bases and adapter-polluted reads were filtered out.
Clean reads were aligned to human GRCh38 primary assembly genome using HISAT2 software with default alignment parameters.
FeatureCounts was applied to extract raw gene read counts from aligned bam files.
Gene expression was normalized to TPM (Transcripts Per Million) values for cross-sample comparison.
Assembly: GRCh38 (human hg38 reference genome assembly)
Supplementary files format and content: Tab-delimited plain text file containing raw read counts of all genes across all samples (raw_counts_All_Samples.txt)
Supplementary files format and content: Comma-separated CSV file containing TPM normalized expression values of all genes across all samples (All_samples_TPM.csv)

source_name: Jurkat

growth_protocol: Human Jurkat T lymphocytes were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, maintained at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from cell pellets using TRIzol reagent combined with RNA purification kit. RNA integrity and concentration were detected, and qualified total RNA was reserved for library construction.
mRNA was enriched with oligo(dT) magnetic beads. Strand-specific paired-end mRNA-seq libraries were constructed following the manufacturer’s standard kit protocol, and sequenced on Illumina NovaSeq 6000 platform.

treatment_protocol: Cells were divided into two groups: vehicle control group (DMSO) and BPAF exposure group. Cells were treated for 24 h prior to RNA extraction.

value: Jurkat

value: T lymphocyte

value: Treated with 1 μM BPAF for 12 h


title: BPAF1

description: Library name: Sample 4


title: WT-CD36-negative cells-2

description:
Library name: Sample7
CD36-NEG-2


title: DMSO3

description: Library name: Sample 3

value: Treated with 0.1% DMSO for 12 h


title: DMSO2

description: Library name: Sample 2


title: DMSO1

description: Library name: Sample 1


title: WT-CD36-negative cells-1

description:
Library name: Sample6
CD36-NEG-1


title: WT-CD36 positive cells-4

description:
Library name: Sample4
CD36-POS-4

value: CD45intCD11b+CD36+  microglia


title: WT-CD36 positive cells-3

description:
Library name: Sample3
CD36-POS-3


title: CD4 T cell MCCu donor 3 replicate 4

first: Joseph

description:
Library name: cd4_don3_4_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt

data_processing:
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
The resulting fastq file is aligned to the genome using bowtie.
Assembly: hg38
Supplementary files format and content: BigWig of data from multiple viewpoints
Supplementary files format and content: Raw junction counts
Library strategy: Capture-C

growth_protocol: Jurkat cells, clone E6-1 (ATCC TIB-152) were culture in ATCC modified RPMI (Gibco A1049101) with 10% foetal bovine serum (Sigma) at 370C with 5% CO2, Isolated CD4+ cells were cultured at 1x106 cells per ml in Immunocult-XF T cell expansion medium (Stemcell 10981) supplemented with 10ng/ml human IL-2 (Invitrogen X). For edited T cell MCC samples, T cells were nucleofected post activation and allowed to cycle for 3 days before collection.

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction. CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.

value: CD4 T cell MCCu donor 3


title: CD4 T cell MCCu donor 3 replicate 3

description:
Library name: cd4_don3_3_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt


title: CD4 T cell MCCu donor 3 replicate 5

description:
Library name: cd4_don3_5_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt


title: WT-CD36 positive cells-1

description:
Library name: Sample1
CD36-POS-1


title: pSer2_CT_mESC_Gabpa_12h_dTAG_rep2

description: Library name: pSer2_CT_mESC_Gabpa_12h_dTAG_rep2

data_processing:
For RNA-seq, raw reads were trimmed with Trim Galore v0.6.7, followed by mapping to the mm39 genome using STAR v2.7.11a. Gene expression levels were calculated by RSEM v1.3.1, and differential expression analysis was performed using the DESeq2 R package v1.44.0.  For SLAM-seq, BCL files containing raw sequencing data were converted to FASTQ format. Adapters were trimmed from raw reads using Cutadapt v3.5 through Trim Galore v0.6.7. SLAM-seq analyses were performed using the SLAMdunk pipeline v0.4.3, which includes mapping, read filtering, SNP variant calling, conversion counts and rate calculation. The significantly differentially expressed genes were called using DESeq2 v1.44.0 with size factors estimated on corresponding total mRNA reads for global normalization. For ATAC-seq and CUT&Tag, the raw reads were first trimmed of the adaptors with Trim Galore v0.6.7 and then aligned to the mm39 genomes using Bowtie2 v2.4.4 with the following parameters: --no-unal --no-mixed --no-discordant. Low mapping quality reads, unmapped reads and duplicated reads were removed using Picard v2.21.4 and SAMtools v1.13. For the INTS11 CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length between 48 and 158 bp. For the histone modification CUT&Tag, the mapped reads were further filtered to retain only proper paired reads with fragment length at least 178 bp. Read coverages over the genome were estimated by bamCoverage from deepTools v3.5.1 with the following parameters: --binSize 20 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM.
Assembly: mm39
Supplementary files format and content: tab-delimited txt files contain gene-level reads counts for each sample; bigWig files contain ATAC-seq and CUT&Tag signals.
Library strategy: CUT&Tag

extract_protocol:
For RNA-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads.
For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols.

value: cell line

value: treated with dTAG13 for 12 hours


title: CD4 T cell MCCu donor 3 replicate 2

description:
Library name: cd4_don3_2_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt


title: slender bsf, 8hrs after differentiation, replicate 3

description:
Library name: SL83
Sample6
slender bsf_8hrspostdiff_rep3

value: EATRO 1125 (serodome AnTAT1.1)

value: unicellular protozoan parasite

value: cytoplasmic tdTomato protein, EP1 yellow fluorescent fusion protein, PAD1 green fluorescent stumpy marker

value: procyclic differentiation


title: CD4 T cell MCCu donor 3 replicate 1

description:
Library name: cd4_don3_1_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt

value: Blood

value: CD4 T cell

value: WT

value: Activated


title: pSer2_CT_mESC_Gabpa_12h_DMSO_rep2

description: Library name: pSer2_CT_mESC_Gabpa_12h_DMSO_rep2

value: mESCs

value: GabpadTAG/dTAG

value: treated with DMSO for 12 hours


title: pSer2_CT_mESC_Gabpa_12h_dTAG_rep1

description: Library name: pSer2_CT_mESC_Gabpa_12h_dTAG_rep1


title: CD4 T cell control donor 2 replicate 6

description:
Library name: cd4_don2_6_control
all_control_combined_chimeric.with_rsid.tsv

value: CD4 T cell control donor 2


title: pSer2_CT_mESC_Gabpa_12h_DMSO_rep1

description: Library name: pSer2_CT_mESC_Gabpa_12h_DMSO_rep1


title: CD4 T cell control donor 2 replicate 5

description:
Library name: cd4_don2_5_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer2_CT_mESC_Gabpa_1h_dTAG_rep2

description: Library name: pSer2_CT_mESC_Gabpa_1h_dTAG_rep2

value: treated with dTAG13 for 1 hour


title: PRO_mESC_Gabpa_1h_DMSO_rep3

description: Library name: PRO_mESC_Gabpa_1h_DMSO_rep3

value: treated with DMSO for 1 hour


title: CD4 T cell control donor 2 replicate 4

description:
Library name: cd4_don2_4_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer2_CT_mESC_Gabpa_1h_dTAG_rep1

description: Library name: pSer2_CT_mESC_Gabpa_1h_dTAG_rep1


title: CD4 T cell control donor 2 replicate 3

description:
Library name: cd4_don2_3_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer2_CT_mESC_Gabpa_1h_DMSO_rep2

description: Library name: pSer2_CT_mESC_Gabpa_1h_DMSO_rep2


title: Single cell multiome, BM-MSCs, In vitro,rep1, GEX

description: Library name: D008_IV_GEX

value: Bone marrow

value: primary BM-MSCs

value: MSCs

value: wt

value: In vitro


title: Single cell multiome, BM-MSCs, In vitro,rep2,GEX

description: Library name: D009_IV_GEX


title: CD4 T cell control donor 2 replicate 2

description:
Library name: cd4_don2_2_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer2_CT_mESC_Gabpa_1h_DMSO_rep1

description: Library name: pSer2_CT_mESC_Gabpa_1h_DMSO_rep1

value: cell line


title: CD4 T cell control donor 2 replicate 1

description:
Library name: cd4_don2_1_control
all_control_combined_chimeric.with_rsid.tsv


title: CD4 T cell control donor 1 replicate 6

description:
Library name: cd4_don1_6_control
all_control_combined_chimeric.with_rsid.tsv

value: CD4 T cell control donor 1


title: WT-CD36-negative cells-5

description:
Library name: Sample10
CD36-NEG-8

value: isolated retinal cells

value: CD45intCD11b+CD36-  microglia


title: BPAF3

description: Library name: Sample 6

value: Jurkat

value: T lymphocyte

value: WT

value: Treated with 1 μM BPAF for 12 h


title: pSer5_CT_mESC_Gabpa_12h_dTAG_rep2

description: Library name: pSer5_CT_mESC_Gabpa_12h_dTAG_rep2

value: mESCs

value: GabpadTAG/dTAG

value: treated with dTAG13 for 12 hours


title: pSer5_CT_mESC_Gabpa_12h_dTAG_rep1

description: Library name: pSer5_CT_mESC_Gabpa_12h_dTAG_rep1


title: CD4 T cell control donor 1 replicate 5

description:
Library name: cd4_don1_5_control
all_control_combined_chimeric.with_rsid.tsv

value: Blood

value: CD4 T cell

value: Activated


title: pSer5_CT_mESC_Gabpa_12h_DMSO_rep2

description: Library name: pSer5_CT_mESC_Gabpa_12h_DMSO_rep2

value: treated with DMSO for 12 hours


title: WT-CD36-negative cells-3

description:
Library name: Sample8
CD36-NEG-4


title: CD4 T cell control donor 1 replicate 4

description:
Library name: cd4_don1_4_control
all_control_combined_chimeric.with_rsid.tsv


title: CD4 T cell control donor 1 replicate 3

description:
Library name: cd4_don1_3_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer5_CT_mESC_Gabpa_12h_DMSO_rep1

description: Library name: pSer5_CT_mESC_Gabpa_12h_DMSO_rep1


title: pSer5_CT_mESC_Gabpa_1h_dTAG_rep2

description: Library name: pSer5_CT_mESC_Gabpa_1h_dTAG_rep2

value: treated with dTAG13 for 1 hour


title: CD4 T cell control donor 1 replicate 2

description:
Library name: cd4_don1_2_control
all_control_combined_chimeric.with_rsid.tsv


title: WT-CD36 positive cells-5

description:
Library name: Sample5
CD36-POS-7

value: CD45intCD11b+CD36+  microglia


title: CD4 T cell control donor 1 replicate 1

description:
Library name: cd4_don1_1_control
all_control_combined_chimeric.with_rsid.tsv


title: pSer5_CT_mESC_Gabpa_1h_DMSO_rep2

description: Library name: pSer5_CT_mESC_Gabpa_1h_DMSO_rep2

value: cell line

value: treated with DMSO for 1 hour


title: CD4 T cell donor 2 replicate 2 rna

description:
Library name: cd4_don2_rna_2
featurecounts - Geneid, Chr,Start,End,Strand, Length cd4_don1_minus_1_Aligned.sortedByCoord.out.bam  cd4_don1_minus_2_Aligned.sortedByCoord.out.bam  cd4_don2_minus_1_Aligned.sortedByCoord.out.bam  cd4_don2_minus_2_Aligned.sortedByCoord.out.bam  cd4_don3_minus_1_Aligned.sortedByCoord.out.bam  cd4_don3_minus_2_Aligned.sortedByCoord.out.bam

data_processing:
Reads were trimmed with Trimgalore before being aligned to the genome using STAR (V1.1.). Gene count tables were constructed using feature counts.
Assembly: hg38
Supplementary files format and content: featurecounts - Geneid, Chr,Start,End,Strand, Length cd4_don1_minus_1_Aligned.sortedByCoord.out.bam  cd4_don1_minus_2_Aligned.sortedByCoord.out.bam  cd4_don2_minus_1_Aligned.sortedByCoord.out.bam  cd4_don2_minus_2_Aligned.sortedByCoord.out.bam  cd4_don3_minus_1_Aligned.sortedByCoord.out.bam  cd4_don3_minus_2_Aligned.sortedByCoord.out.bam

extract_protocol:
RNA was extracted using the Zymo Direct-Zol RNA MiniPrep kit, followed by rRNA depletion with the RiboMinus Eukaryote Kit v2. The RNA was then partitioned into plus and minus libraries using the NEBNext Poly(A) mRNA magnetic isolation module.
Poly(A) minus libraries were prepped for NGS sequenicng using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.


title: pSer5_CT_mESC_Gabpa_1h_dTAG_rep1

description: Library name: pSer5_CT_mESC_Gabpa_1h_dTAG_rep1


title: CD4 T cell donor 2 replicate 1 rna

description:
Library name: cd4_don2_rna_1
featurecounts - Geneid, Chr,Start,End,Strand, Length cd4_don1_minus_1_Aligned.sortedByCoord.out.bam  cd4_don1_minus_2_Aligned.sortedByCoord.out.bam  cd4_don2_minus_1_Aligned.sortedByCoord.out.bam  cd4_don2_minus_2_Aligned.sortedByCoord.out.bam  cd4_don3_minus_1_Aligned.sortedByCoord.out.bam  cd4_don3_minus_2_Aligned.sortedByCoord.out.bam


title: pSer5_CT_mESC_Gabpa_1h_DMSO_rep1

description: Library name: pSer5_CT_mESC_Gabpa_1h_DMSO_rep1


title: H3K27ac_CT_mESC_Gabpa_12h_dTAG_rep2

description: Library name: H3K27ac_CT_mESC_Gabpa_12h_dTAG_rep2


title: H3K27ac_CT_mESC_Gabpa_12h_dTAG_rep1

description: Library name: H3K27ac_CT_mESC_Gabpa_12h_dTAG_rep1


title: CD4 T cell donor 3 replicate 2 ATAC

description:
Library name: cd4_don3_atac_2
Bigwig

data_processing:
ATAC and ChIP seq data, reads were trimmed with Trim galore (Babraham Institute), before being aligned with Bowtie2. Aligned BAMs were deduplicated with Picard before being converted to BigWigs using Deeptools BamCoverage and visualized on the UCSC genome browser. Peaks were called using Lanceotron27
Assembly: hg38
Supplementary files format and content: Bigwig

extract_protocol:
150,000 cells were harvested, centrifuged at 500g for 5 minutes before being resuspended in ATAC lysis buffer (10 mM Tris HCL, pH 7.5, 10 nM NaCl, 3mM MgCl2, 0.1 % Igepal CA-630) and immediately span at 40C for 10 minutes at 500g. the resulting nuclear pellets were PBS washed before being resuspended in a tagmentation buffer (20 mM Tris-HCl pH 7.5, 10mM MgCl2, 20 % Dimethyl Formamide) with Tn5 transposase (Illumina, 20034197). This reaction was incubated for 30 minutes at 370C. The reaction was quenched was buffer PB of the Qiagen MinElute DNA purification kit (Qiagen 28004) and DNA was purified following the manufacturer’s instructions.
The purified DNA was then amplified using the Q5 high-fidelity mastermix (NEB M0491S) with Illumina Nextera Sequencing primers. Capture enrihcment was performed using the Roche Hypercapture kit and reagents.


title: CD4 T cell donor 3 replicate 1 ATAC

description:
Library name: cd4_don3_atac_1
Bigwig


title: H3K27ac_CT_mESC_Gabpa_12h_DMSO_rep2

description: Library name: H3K27ac_CT_mESC_Gabpa_12h_DMSO_rep2


title: CD4 T cell MCCu donor 3 replicate 6

description:
Library name: cd4_don3_6_ultra
rs9526002_MCCu_combined_chimeric.txt
rs10950648_MCCu_combined_chimeric.txt

value: CD4 T cell MCCu donor 3


title: H3K27ac_CT_mESC_Gabpa_12h_DMSO_rep1

description: Library name: H3K27ac_CT_mESC_Gabpa_12h_DMSO_rep1


title: CD4 T cell donor 3 replicate 2 rna

description:
Library name: cd4_don3_rna_2
featurecounts - Geneid, Chr,Start,End,Strand, Length,cd4_don1_minus_1_Aligned.sortedByCoord.out.bam,cd4_don1_minus_2_Aligned.sortedByCoord.out.bam,cd4_don3_minus_1_Aligned.sortedByCoord.out.bam,cd4_don3_minus_2_Aligned.sortedByCoord.out.bam

data_processing:
Reads were trimmed with Trimgalore before being aligned to the genome using STAR (V1.1.). Gene count tables were constructed using feature counts.
Assembly: hg38
Supplementary files format and content: Merged featurecounts - cd4_don1_rna1, cd_don1_rna_2, cd4_don3_rna1, cd4_don3_rna_2


title: WT-CD36 positive cells-2

description:
Library name: Sample2
CD36-POS-2

value: isolated retinal cells


title: CD4 T cell donor 3 replicate 1 rna

description:
Library name: cd4_don3_rna_1
featurecounts - Geneid, Chr,Start,End,Strand, Length,cd4_don1_minus_1_Aligned.sortedByCoord.out.bam,cd4_don1_minus_2_Aligned.sortedByCoord.out.bam,cd4_don3_minus_1_Aligned.sortedByCoord.out.bam,cd4_don3_minus_2_Aligned.sortedByCoord.out.bam


title: H3K27ac_CT_mESC_Gabpa_1h_dTAG_rep2

description: Library name: H3K27ac_CT_mESC_Gabpa_1h_dTAG_rep2


title: CD4 T cell donor 1 replicate 2 rna

description:
Library name: cd4_don1_rna_2
featurecounts - Geneid, Chr,Start,End,Strand, Length,cd4_don1_minus_1_Aligned.sortedByCoord.out.bam,cd4_don1_minus_2_Aligned.sortedByCoord.out.bam,cd4_don3_minus_1_Aligned.sortedByCoord.out.bam,cd4_don3_minus_2_Aligned.sortedByCoord.out.bam


title: H3K27ac_CT_mESC_Gabpa_1h_dTAG_rep1

description: Library name: H3K27ac_CT_mESC_Gabpa_1h_dTAG_rep1


title: H3K27ac_CT_mESC_Gabpa_1h_DMSO_rep2

description: Library name: H3K27ac_CT_mESC_Gabpa_1h_DMSO_rep2


title: H3K27ac_CT_mESC_Gabpa_1h_DMSO_rep1

description: Library name: H3K27ac_CT_mESC_Gabpa_1h_DMSO_rep1


title: CD4 T cell donor 1 replicate 1 rna

description:
Library name: cd4_don1_rna_1
featurecounts - Geneid, Chr,Start,End,Strand, Length,cd4_don1_minus_1_Aligned.sortedByCoord.out.bam,cd4_don1_minus_2_Aligned.sortedByCoord.out.bam,cd4_don3_minus_1_Aligned.sortedByCoord.out.bam,cd4_don3_minus_2_Aligned.sortedByCoord.out.bam