title: SFN_micro_c_S077_ctcf_aid_witha

city: shenzhen

first: Chongren

last: Pei

state: guangdong

address: Gaoke Innovation Center, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

description: Library name: sample4

data_processing:
Micro-C data were processed using Microcket software (version 1.4) with default parameters. Raw contact maps were used for all downstream analyses without balancing. The resulting pair files were then converted to “. hic” format using Juicer Tools (versions 1.9.9 or 1.19.02). Subsequently, the .hic files were converted to “. cool” files at multiple resolutions using HiCexplorer (version 3.7).
Assembly: mm9
Supplementary files format and content: cool, hic and bigwig files of each individual biological replicate are provided.

source_name: erythroid

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium. The medium was supplemented with 15% fetal bovine serum, 2 penicillin‑streptomycin solution, 50 ng/ml mouse stem cell factor, 7.5 ng/ml Epogen, and 0.001% 1-Thioglycerol. All cell lines were routinely tested for mycoplasma contamination and maintained at 37 ℃ in a humidified atmosphere of 5% CO₂ (as described in Weiss et al., 1997).

extract_protocol:
MNase digestion
For each cell line, 100,000 cells were collected and cross-linked with 1% formaldehyde at room temperature. The reaction was quenched with glycine at a final concentration of 1 M, followed by one wash with PBS. The cells were then subjected to a second cross-linking step using 3 mM EGS crosslinker (MCE, HY-130458), which was again quenched with 1 M glycine. After a final PBS wash, the cells were lysed on ice with cell lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40) for 20 min and subsequently digested with MNase (Micrococcal Nuclease, NEB，M0247S) at a 1:500 dilutions in 30 min.
T4 ligase ligation
After chromatin fragmentation by MNase, a master mix was prepared containing T4 ligase buffer, biotin-dATP (Active-Motif, 14139), biotin-dCTP (MCE, HY-D1668), dGTP, dTTP, 100 mM ATP (Thermo, R1441), T4 PNK (T4 polynucleotide kinase, NEB, M0201L), Klenow fragment (NEB, M0210L), T4 DNA ligase (Thermo, EL0013), BSA, and EGTA. Cell pellets were resuspended in this mix and incubated first at 25 ℃ for 2 hours, then at 37 ℃ for 2 hours, followed by a final incubation at 16 ℃ for at least 8 hours to ensure efficient ligation. Following proximity ligation, unligated DNA ends were digested with Exonuclease III (NEB, M0206L) at 37℃ to reduce background noise in subsequent sequencing.
Reverse Cross-linking and DNA Extraction
The sample was normalized to a final volume of 100 μL with ddH₂O. The reaction was supplemented with 12.5 μL of Proteinase K (20 mg/mL), 12.5 μL of 10% SDS, and 1 μL of RNase A (10 mg/mL), yielding final concentrations of 2.5 mg/mL, 1.25%, and 0.1 mg/mL, respectively. Following incubation at 37℃ for 30 min, the samples were heated at 65℃ for at least 3 h to reverse cross-links. DNA was then purified using 0.8 volumes of DNA purification beads according to the manufacturer's instructions and eluted for library construction.
Biotin Pull-Down
15 μL of Dynabeads Myone Streptavidin C1 beads (Thermo, 65002) were placed on a magnetic stand and washed three times with BW buffer (Binding and Washing buffer, 5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). The beads were then resuspended in 50 μL of 2x BW buffer, followed by the addition of 50 μL of purified DNA. The mixture was incubated at room temperature for 25 minutes. After incubation, the beads were washed once with BW buffer and twice with 1xT4 ligase buffer. Finally, the beads were resuspended in 50 μL of DNase free water for subsequent library construction.
DNA Library Construction
A commercial DNA library construction kit (VAHTS Universal DNA Library Prep Kit for Illumina V4 (ND610)) was used for library preparation. The main procedure consisted of four stages: DNA end repair, adapter ligation, library amplification, and library purification. Following adapter ligation, beads were washed three times with BW buffer to reduce adapter-related background. Library amplification was typically performed for 9-10 cycles. Finally, the DNA library was purified using 0.9x DNA clean beads. To adapt to the MGI DNBSEQ‑T7 sequencing platform, all adapters and amplification primers were replaced with their MGI-compatible counterparts.
Micro-C, DNA libraries were prepared on-bead using the VAHTS Universal DNA Library Prep Kit (Vazyme), including end repair, dA-tailing, and adapter ligation. Libraries were PCR-amplified (9–11 cycles), size-selected with VAHTS DNA Clean Beads, and sequenced on Illumina NextSeq500 or MGI DNBSEQ-T7. Basecalling was performed using platform-specific software (NextSeq Control Software v2.2.0 or Basecall_T7_GPU_1.2.0.26_Centos).

treatment_protocol: For CTCF-AID-HaloTag cells. To degrade CTCF, 5-Ph-IAA (1 M) was added into the culture for 4 hours. Control cells treated without 5-Ph-IAA treatment were processed in parallel.

value: erythroid

value: G1E-ER4 cells

value: erythroblasts


title: D40_O-Torgs_rep1

status: Public on Mar 08 2026

type: SRA

city: Guangzhou

first: Qi

last: Li

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental biology

country: China

institute: Southern Medical University

description:
Library name: library5
Single-cell data of testicular organoids cultured with the optimized system on the fortieth day.

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed by Fastp (Chen et al., 2018a) to trim primer sequences and low-quality bases.
Seeksoul tools (Seekgene, v1.0.0) was used to process the resulting data, demultiplex cellular barcodes and map reads to the mouse mm10 reference genome (refdata-gex-mm10-2020-A downloaded from 10X Genomics) to generate a feature-barcode matrix for downstream analyses.
Assembly: mm10
Supplementary files format and content: rds file

molecule: polyA RNA

organism: Mus musculus

source_name: testis

extract_protocol:
After harvested, tissues were washed in ice-cold PBS (Hyclone SH30256.01) and dissociated using SeekMate Tissue Dissociation Kit C (SeekGene K01501-50) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using Fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent . Finally fresh cells were washed twice in the RPMI1640 (Gibco 11875119) and then resuspended at 1×106 cells per ml in RPMI1640 and 2% FBS (Gibco 10100147C).
The single-cell RNA-Seq library was prepared using the SeekOne® Digital Droplet Single Cell 3' library preparation kit (SeekGene catalog number: K00202). Briefly, an appropriate number of cells was mixed with reverse transcription reagents and then added to the sample wells of the SeekOne® Chip S3. Next, Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into the corresponding wells of the S3 chip, respectively. After droplet generation, reverse transcription was carried out at 42 °C for 90 min and inactivation was performed at 85 °C for 5 min. Subsequently, cDNAs were purified and used for PCR amplification. Then, the amplified cDNA products were cleaned, fragmented, subjected to end repair, and their tails were ligated to the sequencing adapters. Finally, the DNA of the 3' poly (A) portion of the genes were amplified by index PCR, which contains Cell Barcode and Unique Molecular Index. The sequencing library was cleaned up using VAHTS DNA Clean Beads (Vazyme N411-03) and analyzed using Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic Qsep400). The library was sequenced on the Illumina NovaSeq 6000 with a read length of PE150.

tag: tissue

value: testis

tag: treatment

value: optimized system


title: FSHD patient-derived primary myotubes (MB02), DUX4.6 siRNA, Replicate 4

city: San Diego

first: Barbora

last: Malecova

state: CA

address: 3020 Callan Rd

country: USA

institute: Avidity Biosciences

description: Library name: F1_B1_5

library_source: transcriptomic

data_processing:
Samples were sequenced on the Illumina NovaSeq instrument and using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).
RNA-seq reads were trimmed, and low-quality reads were removed using Trimgalore v0.6.3_dev with the “paired” parameter and length of 150 bps.
Trimmed fastq sequences were aligned to the human reference genome GRCh38 using STAR aligner v2.5.3a.
Raw read gene counts were obtained by using STAR aligner with options “—quantMode GeneCounts” and “--sjdbGTFfile” with gene models in GTF format obtained from human EnsEMBL release 83.
Alignment quality control and read mapping statistic were obtained from Picard tools using function “CollectMultipleMetrics”.
Raw counts were normalized to the total number of reads by calculating log2CPM (counts per million), and lowly expressed genes (average Log2CPM<-3) were eliminated before differential gene expression analysis.
Differential gene expression analysis was performed using the Limma 3.40.6 software.
Assembly: GRCh38
Supplementary files format and content: Gene expression values in the processed data file are in the unit of Log2(TPM+1)

organism: Homo sapiens

growth_protocol: FSHD and control primary myoblasts were grown in medium containing 80% Ham’s F-10 Nutrient Mix, 20% FBS, 10ng/ml rhFGF, 1µM Dexamethasone, and Penicillin and Streptomycin.

extract_protocol:
Myotubes were collected in Trizol and stored at -80°C until processing for RNA isolation using Direct-zol-96 RNA isolation kit (Zymo Research).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB), including enrichment of poly(A) transcripts using Oligod(T) beads.

treatment_protocol:
Myoblasts were seeded at 4000 cells/well on Matrigel-coated 96 well plates 24h prior to transfection. Next day, siRNAs (10nM) were formulated with Lipofectamine RNAiMAX (Life Technologies) and OptiMEM (Life Technologies) according to the manufacturer’s “forward transfection” instructions.
Myogenic differentiation was induced 24h post transfection with 15% KOSR-containing differentiation medium (85% DMEM/F-12, 15% KnockOutTM Serum Replacement -KOSR-, Penicillin and Streptomycin).

tag: cell line

tag: cell type

value: Primary myotubes

tag: disease state

value: FSHD

value: DUX4.6 siRNA

tag: replicate


title: D6_T-Torgs_rep2

description:
Library name: library4
Single-cell data of testicular organoids cultured with the traditional system on the sixth day.

value: traditional system


title: SFN_micro_c_S076_ctcf_aid_noa

description: Library name: sample3

library_source: genomic

molecule: genomic DNA


title: FSHD patient-derived primary myotubes (MB02), Non-targeting siRNA control, Replicate 4

description: Library name: F1_S_5

value: Non-targeting siRNA control


title: FSHD patient-derived primary myotubes (MB02), DUX4.6 siRNA, Replicate 2

description: Library name: F1_B1_2


title: FSHD patient-derived primary myotubes (MB02), DUX4.6 siRNA, Replicate 1

description: Library name: F1_B1_1


title: Embryo 5

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

description: Library name: S5

data_processing:
The fastq files were processed using the PIPsekerTM software for Single Cell Data Analysis, with alignment to the cattle genome (Bos_taurus.ARS-UCD2.0), and fragments counted based on the Bos_taurus.ARS-UCD2.0.114 annotation
Assembly: Bos_taurus.ARS-UCD2.0

molecule: total RNA

organism: Bos taurus

source_name: Day 16

growth_protocol: Embryos were produced using procedures described in Biase FH, Schettini G. Protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes. STAR Protoc. 2024 Mar 15;5(1):102940. doi: 10.1016/j.xpro.2024.102940. Ramos-Ibeas P, Perez-Gomez A, Gonzalez-Brusi L, Quiroga AC, Bermejo-Alvarez P. Pre-hatching exposure to N2B27 medium improves post-hatching development of bovine embryos in vitro. Theriogenology. 2023;205:73-8. 10.1016/j.theriogenology.2023.04.018. Ramos-Ibeas P, Lamas-Toranzo I, Martinez-Moro A, de Frutos C, Quiroga AC, Zurita E, et al. Embryonic disc formation following post-hatching bovine embryo development in vitro. Reproduction. 2020;160(4):579-89. 10.1530/REP-20-0243

extract_protocol: Llibraries were constructed using the PIP-seq protocl

value: Day 16


title: SFN_micro_c_S074_JC4

description: Library name: sample1


title: Embryo 4

description: Library name: S4

source_name: Day 12

value: Day 12


title: D6_T-Torgs_rep1

description:
Library name: library3
Single-cell data of testicular organoids cultured with the traditional system on the sixth day.


title: Embryo 3

description: Library name: S3


title: FSHD patient-derived primary myotubes (MB02), Non-targeting siRNA control, Replicate 3

description: Library name: F1_S_3


title: D6_O-Torgs_rep2

description:
Library name: library2
Single-cell data of testicular organoids cultured with the optimized system on the sixth day.


title: FSHD patient-derived primary myotubes (MB02), Non-targeting siRNA control, Replicate 2

description: Library name: F1_S_2


title: D6_O-Torgs_rep1

description:
Library name: library1
Single-cell data of testicular organoids cultured with the optimized system on the sixth day.


title: Embryo 2

description: Library name: S2


title: 832/13 cells, Kyono MPRA library, cDNA rep 3

city: Ann Arbor

first: Stephen

middle: CJ

last: Parker

state: Michigan

address: 1000 WALL ST, BREHM TOWER,RM 5474

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

description: Library name: Kyono MPRA library cDNA rep 3 from 832/13 INS-1 cell line

data_processing:
We processed MPRA sequencing data using a custom pipeline that quantifies barcode counts while accounting for possible sequencing errors. We extracted DNA barcodes from the first 16 bases of the R1 fastq file for the input DNA sample and clustered these at an edit distance of 0. We repeated this process for the cDNA barcode counts and used an added step to remove PCR-duplicated barcodes using the UMI information. The UMI sequence was the reverse complement of the first 6 bp in the R2 file. Finally, we used starcode to cluster and count barcodes.
Assembly: hg19
Supplementary files format and content: “library_counts.tsv” is a tab-delimited text file contained the barcode sequences, the RNA counts for the three replicates, the DNA counts for the input sample, the oligo ID, and the hg19 coordinates of each element tested in the MPRA library.

organism:
Rattus norvegicus
synthetic construct

source_name: Insulinoma

extract_protocol:
We electroporated 50 ug of plasmid into 25 million 832/13 rat insulinoma cells for each biological replicate and lysed cells with TRIzol 24 hours later. After phase separation, we used the Direct-zol RNA Miniprep Kit to isolate total RNA. We enriched for mature mRNA transcripts with fragment(dT) beads then treated 2 ug of mRNA with DNase I to remove plasmid or genomic DNA contamination. We reverse transcribed 1 ug of mRNA using SuperScript III with a custom primer containing a 6-bp unique molecular identifier (UMI) targeting transcripts derived from the MPRA plasmids (Supplemental Table 3). We treated cDNA samples with DpnI to eliminate any residual plasmid DNA.
MPRA amplicon library

value: Insulinoma


title: FSHD patient-derived primary myotubes (MB02), Non-targeting siRNA control, Replicate 1

description: Library name: F1_S_1


title: neuron;Sham16

status: Public on Mar 07 2026

city: SHANGHAI

first: Liting

last: Sun

state: SHANGHAI

address: 131 DONG'AN ROAD, XUHUI DISTRICT

institute: Fudan University

description: Library name: Sample42

data_processing:
Single-neuron RNA-seq raw data were pre-processed and analyzed. Briefly, initial quality assessment of concatenated replicate raw sequencing reads from each library was conducted using FastQC (Version 0.11.9) to ensure minimal PCR duplication and sequencing quality. Reads were aligned to the mouse mm10 genome using HISAT2 (Version 2.2.1). Multiple-aligned reads were discarded, and remaining transcript reads were counted using featureCounts (Version 2.1.1). Expression levels were normalized to Transcripts Per Million (TPM).Differential gene expression analysis was performed using the DESeq2(v1.48.1), excluding genes detected in fewer than two cells. Adjusted p value (i.e. false discovery rate, FDR) < 0.05 and Log2 (Fold Change) > 1 or Log2 (Fold Change) < -1 was set as the statistical threshold for significant DEGs.
Assembly: Mouse mm10
Supplementary files format and content: Tab-Separated Values file include raw counts for each Sample
Supplementary files format and content: csv files include Log2(TPM+1) values for each Sample

extract_protocol:
Superficial layers of Sp5C were collected and incubated in a choline chloride solution containing 20 U/mL papain (Worthington) and 100 U/mL DNase I (Worthington) for 15 min at 37°C, and this was followed by digestion with 1 mg/mL protease (Sigma) and dispase (Worthington) for 20 min at 25°C. Next, the post-digested tissues were gently triturated using fire-polished glass Pasteur pipettes to obtain single-cell suspensions. The single-cell suspensions were then centrifuged at 400 g, at 4°C for 5 min, and the supernatant was discarded. The cells were re-suspended with choline chloride solution containing 2% FBS (MACS).Fluorescence labeled cells were manually selected under a microscope and the cytosol of each single cell was transferred individually to a tube.
scRNA libraries for scRNA-seq were prepared using Smart-seq3 Protocol V.3 following manufacturer's protocols.(dx.doi.org/10.17504/protocols.io.bcq4ivyw)

treatment_protocol: To label the PBN-projecting Sp5C neurons for single-cell sequencing, AAV2/2Retro-hSyn-EGFP(-3Flag)-WPRE-pA virus was injected into the right PBN of wild type mice and cell collection was performed 3 weeks later.

value: neurons

tag: genotype

value: WT


title: neuron;Sham56

description: Library name: Sample48


title: neuron;Sham1

description: Library name: Sample43


title: neuron;Sham98

description: Library name: Sample51


title: neuron;Sham5

description: Library name: Sample49


title: neuron;Sham51

description: Library name: Sample46


title: 832/13 cells, Kyono MPRA library, cDNA rep 2

description: Library name: Kyono MPRA library cDNA rep 2 from 832/13 INS-1 cell line


title: neuron;Sham9

description: Library name: Sample52


title: neuron;Sham15

description: Library name: Sample41


title: neuron;Sham2

description: Library name: Sample44


title: neuron;Sham117

description: Library name: Sample39


title: neuron;Sham50

description: Library name: Sample45


title: neuron;Sham54

description: Library name: Sample47


title: neuron;Sham114

description: Library name: Sample36


title: neuron;Sham116

description: Library name: Sample38


title: neuron;Sham78

description: Library name: Sample50


title: neuron;Sham115

description: Library name: Sample37


title: 832/13 cells, Kyono MPRA library, cDNA rep 1

description: Library name: ATS0703_RNA


title: neuron;Sham112

description: Library name: Sample34


title: neuron;Sham10

description: Library name: Sample32


title: neuron;Sham110

description: Library name: Sample33


title: neuron;Sham107

description: Library name: Sample30


title: neuron;Sham105

description: Library name: Sample28


title: neuron;Sham109

description: Library name: Sample31


title: neuron;Sham100

description: Library name: Sample27


title: neuron;Sham14

description: Library name: Sample40


title: neuron;Sham113

description: Library name: Sample35


title: neuron;CION73

description: Library name: Sample26


title: neuron;Sham106

description: Library name: Sample29


title: neuron;CION67

description: Library name: Sample23


title: neuron;CION69

description: Library name: Sample22


title: neuron;CION71

description: Library name: Sample24


title: neuron;CION72

description: Library name: Sample25


title: neuron;CION68

description: Library name: Sample21


title: neuron;CION61

description: Library name: Sample19


title: neuron;CION58

description: Library name: Sample17


title: neuron;CION43

description: Library name: Sample16


title: Embryo 1

description: Library name: S1


title: neuron;CION38

description: Library name: Sample12


title: neuron;CION63

description: Library name: Sample20


title: neuron;CION59

description: Library name: Sample18


title: neuron;CION41

description: Library name: Sample14


title: neuron;CION31

description: Library name: Sample8


title: neuron;CION33

description: Library name: Sample9


title: neuron;CION35

description: Library name: Sample11


title: neuron;CION34

description: Library name: Sample10


title: neuron;CION27

description: Library name: Sample7


title: neuron;CION26

description: Library name: Sample6


title: neuron;CION151

description: Library name: Sample4


title: neuron;CION40

description: Library name: Sample13


title: neuron;CION23

description: Library name: Sample5


title: neuron;CION128

description: Library name: Sample2


title: B_85

city: Guiyang

first: Tao

last: Wang

state: Guizhou

address: #83 zhongshandong road

institute: Guizhou Provincial People's Hospital

description: Library name: SAMPLE155

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: breast carcinoma

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (Thermo Fisher, cat. no. 15596026) following the manufacturer's recommended protocol.
total RNA was used as input for RNA sequencing library preparation utilizing the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan, China), according to the manufacturer's instructions.

value: breast carcinoma


title: neuron;CION129

description: Library name: Sample3


title: neuron;CION127

description: Library name: Sample1


title: B_9

description: Library name: SAMPLE158


title: B_87

description: Library name: SAMPLE157


title: B_84

description: Library name: SAMPLE154


title: B_86

description: Library name: SAMPLE156


title: B_80

description: Library name: SAMPLE152


title: B_78

description: Library name: SAMPLE149


title: B_76

description: Library name: SAMPLE147


title: B_8

description: Library name: SAMPLE151


title: B_83

description: Library name: SAMPLE153


title: B_7

description: Library name: SAMPLE142


title: B_74

description: Library name: SAMPLE146


title: B_67

description: Library name: SAMPLE139


title: B_77

description: Library name: SAMPLE148


title: B_68

description: Library name: SAMPLE140


title: B_73

description: Library name: SAMPLE145


title: B_66

description: Library name: SAMPLE138


title: B_69

description: Library name: SAMPLE141


title: B_72

description: Library name: SAMPLE144


title: B_61

description: Library name: SAMPLE136


title: B_62

description: Library name: SAMPLE137


title: B_60

description: Library name: SAMPLE135


title: B_6

description: Library name: SAMPLE134


title: B_79

description: Library name: SAMPLE150


title: B_58

description: Library name: SAMPLE133


title: B_5

description: Library name: SAMPLE130


title: B_57

description: Library name: SAMPLE132


title: BV2 cells, NC, biol rep1

status: Public on Mar 11 2026

city: Suzhou

first: Lele

last: Liu

state: Jiangsu

address: No. 199, Ren'ai Road

department: college of pharmacy

institute: Soochow University

description: Library name: NC_1

data_processing:
Quality analysis: Dr.TOM II (v2)
Quality control: SOAPnuke (v2.2.1, proportion of N: 0.05, quality limit:0.2)
Alignment: Bowtie2 (v2.4.5) default parameters
Expression analysis: DESeq2 (v1.34.0)
Assembly: mm39
Supplementary files format and content: Microsoft Excel file include raw counts and FPKM values for each sample

source_name: Brain

growth_protocol: BV2 cells were maintained in DMEM supplement with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol Reagent (invitrogen). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: siRNA was mixed with RNAiMAX in OMEM and incubated for 30 minutes, following which the mixture was added to pre-inoculated cell culture plates for a 24-hour treatment. Subsequently, the medium was replaced with fresh DMEM supplement with 10% FBS and antibiotics, and the cells were cultured for an additional 24 hours.

value: Brain

value: BV2 cells

value: Microglia


title: B_49

description: Library name: SAMPLE129


title: B_43

description: Library name: SAMPLE125


title: B_54

description: Library name: SAMPLE131


title: B_71

description: Library name: SAMPLE143


title: B_47

description: Library name: SAMPLE128


title: B_44

description: Library name: SAMPLE126


title: B_42

description: Library name: SAMPLE124


title: B_34

description: Library name: SAMPLE117


title: neuron;CION42

description: Library name: Sample15


title: B_36

description: Library name: SAMPLE118


title: B_33

description: Library name: SAMPLE116


title: B_37

description: Library name: SAMPLE119


title: B_46

description: Library name: SAMPLE127


title: B_39

description: Library name: SAMPLE120


title: B_32

description: Library name: SAMPLE115


title: B_40

description: Library name: SAMPLE122


title: B_41

description: Library name: SAMPLE123


title: B_4

description: Library name: SAMPLE121


title: B_25

description: Library name: SAMPLE109


title: B_31

description: Library name: SAMPLE114


title: B_30

description: Library name: SAMPLE113


title: B_23

description: Library name: SAMPLE107


title: B_22

description: Library name: SAMPLE106


title: B_29

description: Library name: SAMPLE112


title: B_20

description: Library name: SAMPLE104


title: B_28

description: Library name: SAMPLE111


title: B_16

description: Library name: SAMPLE100


title: B_17

description: Library name: SAMPLE101


title: B_21

description: Library name: SAMPLE105


title: A_102

description: Library name: SAMPLE92


title: B_2

description: Library name: SAMPLE103


title: A_103

description: Library name: SAMPLE93


title: A_101

description: Library name: SAMPLE91


title: A_100

description: Library name: SAMPLE90


title: B_18

description: Library name: SAMPLE102


title: B_13

description: Library name: SAMPLE98


title: A_096

description: Library name: SAMPLE87


title: B_14

description: Library name: SAMPLE99


title: A_094

description: Library name: SAMPLE85


title: A_093

description: Library name: SAMPLE84


title: A_095

description: Library name: SAMPLE86


title: B_24

description: Library name: SAMPLE108


title: B_27

description: Library name: SAMPLE110


title: B_1

description: Library name: SAMPLE95


title: A_098

description: Library name: SAMPLE89


title: A_104

description: Library name: SAMPLE94


title: A_090

description: Library name: SAMPLE82


title: A_097

description: Library name: SAMPLE88


title: A_089

description: Library name: SAMPLE81


title: A_088

description: Library name: SAMPLE80


title: A_092

description: Library name: SAMPLE83


title: A_087

description: Library name: SAMPLE79


title: B_10

description: Library name: SAMPLE96


title: A_086

description: Library name: SAMPLE78


title: B_12

description: Library name: SAMPLE97


title: A_085

description: Library name: SAMPLE77


title: A_082

description: Library name: SAMPLE74


title: A_078

description: Library name: SAMPLE70


title: A_083

description: Library name: SAMPLE75


title: A_081

description: Library name: SAMPLE73


title: A_080

description: Library name: SAMPLE72


title: A_059

description: Library name: SAMPLE52


title: A_069

description: Library name: SAMPLE61


title: A_074

description: Library name: SAMPLE66


title: A_060

description: Library name: SAMPLE53


title: A_066

description: Library name: SAMPLE58


title: A_076

description: Library name: SAMPLE68


title: A_065

description: Library name: SAMPLE57


title: A_084

description: Library name: SAMPLE76


title: A_072

description: Library name: SAMPLE64


title: A_068

description: Library name: SAMPLE60


title: A_075

description: Library name: SAMPLE67


title: A_070

description: Library name: SAMPLE62


title: A_073

description: Library name: SAMPLE65


title: A_071

description: Library name: SAMPLE63


title: A_058

description: Library name: SAMPLE51


title: A_067

description: Library name: SAMPLE59


title: A_061

description: Library name: SAMPLE54


title: A_064

description: Library name: SAMPLE56


title: A_056

description: Library name: SAMPLE49


title: A_077

description: Library name: SAMPLE69


title: A_057

description: Library name: SAMPLE50


title: A_063

description: Library name: SAMPLE55


title: A_054

description: Library name: SAMPLE48


title: A_051

description: Library name: SAMPLE45


title: A_053

description: Library name: SAMPLE47


title: A_079

description: Library name: SAMPLE71


title: A_050

description: Library name: SAMPLE44


title: A_045

description: Library name: SAMPLE40


title: A_048

description: Library name: SAMPLE42


title: A_052

description: Library name: SAMPLE46


title: A_038

description: Library name: SAMPLE33


title: A_039

description: Library name: SAMPLE34


title: A_035

description: Library name: SAMPLE31


title: A_049

description: Library name: SAMPLE43


title: A_036

description: Library name: SAMPLE32


title: A_041

description: Library name: SAMPLE36


title: A_043

description: Library name: SAMPLE38


title: A_040

description: Library name: SAMPLE35


title: A_033

description: Library name: SAMPLE29


title: A_044

description: Library name: SAMPLE39


title: A_032

description: Library name: SAMPLE28


title: A_028

description: Library name: SAMPLE24


title: A_029

description: Library name: SAMPLE25


title: A_024

description: Library name: SAMPLE21


title: A_023

description: Library name: SAMPLE20


title: A_030

description: Library name: SAMPLE26


title: A_022

description: Library name: SAMPLE19


title: A_021

description: Library name: SAMPLE18


title: A_026

description: Library name: SAMPLE22


title: A_031

description: Library name: SAMPLE27


title: A_019

description: Library name: SAMPLE16


title: A_042

description: Library name: SAMPLE37


title: A_020

description: Library name: SAMPLE17


title: A_027

description: Library name: SAMPLE23


title: A_017

description: Library name: SAMPLE14


title: A_014

description: Library name: SAMPLE11


title: A_015

description: Library name: SAMPLE12


title: A_034

description: Library name: SAMPLE30


title: A_018

description: Library name: SAMPLE15


title: A_016

description: Library name: SAMPLE13


title: A_009

description: Library name: SAMPLE8


title: A_013

description: Library name: SAMPLE10


title: A_006

description: Library name: SAMPLE5


title: A_008

description: Library name: SAMPLE7


title: A_007

description: Library name: SAMPLE6


title: A_001

description: Library name: SAMPLE1


title: A_002

description: Library name: SAMPLE2


title: A_005

description: Library name: SAMPLE4


title: 4T1 NOS2 KO1 with cytokines IFNg, IL1b (20ug/ml), biol rep 1

city: Tucson

first: William

middle: R

last: Montfort

state: AZ

address: 1041 E Lowell St

institute: University of Arizona

description:
Library name: A2a
column name in mouse_counts.csv: A2a

data_processing:
Data were demultiplexed and adapter trimmed using Element's bases2fastq software version 2.2.0.1940753917.  Reads were aligned to the GRCh38/GRCm38 reference genome using STAR v2.7.3a and read counts produced using STAR's GeneCounts function. Genes were annotated using the biomaRt package.  Differential expression analysis was performed in R using edgeR exactTest.  Gene Set Enrichment Analysis (GSEA) was performed using Gene Ontology biological process terms.
Assembly: Genes were annotated using the biomaRt package.
Supplementary files format and content: csv files contain raw counts for each sample. Two files, mouse and human.

growth_protocol: Cells were cultured in Roswell Park Memorial Institute medium (RPMI 1640; Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S; Gibco).  Both cell lines were cultured at 37 °C in 5% CO2 with saturating humidity.  In general, 3x106 frozen cells were thawed and grown to ~80% confluency overnight.

extract_protocol:
1-1.5 million cells were grown under eight conditions in triplicate, pelleted, flash frozen, and stored at -80 °C.  Total RNA was extracted from thawed cell pellets with the PureLink RNA Mini Kit (Invitrogen).  RNA molecules were quantified on a Qubit 4 fluorometer using Qubit RNA Broad Range reagents (Invitrogen).  RNA quality was assessed on a Bioanalyzer 2100 using Agilent RNA 6000 Nano reagents (Agilent).
RNA libraries were prepared with a Watchmaker mRNA Library Prep Kit (Watchmaker Genomics) using 1000 ng total RNA input and indexed for multiplexing with xGen Stubby Adapter and UDI Primers for Element (IDT).  Libraries were quantified on a Qubit 4 fluorometer using Qubit 1X dsDNA HS reagents (Agilent).  Library size distributions were assessed on an AATI Fragment Analyzer using the HS NGS Fragment Kit (Agilent).  The libraries were pooled to equimolar concentration and a final round of QC was performed on the pool, as described for the individual libraries.  The final pool was sequenced on an AVITI24 instrument using an AVITI 2x75 Cloudbreak Freestyle High Output Sequencing Kit (Element Biosciences).

treatment_protocol: Cells were washed twice with 1X calcium and magnesium free PBS (CMF-PBS) and treated with or without murine (IFNγ and IL1β), or human (IFNγ, IL1β, and TNFα) cytokines for 18-24 h in the appropriate serum-free medium supplemented with 1% P/S.  For all experiments, murine cytokines were added at 20 ng/mL and human cytokines at 100 ng/mL.  When used, NOS2 inhibitor 1400W (Caymen Chemicals) was added from a DMSO stock solution (100 mM) to final concentration 20 mM.

value: triple negative breast cancer

value: Cytokine


title: 4T1 NOS2 KO1 w/o cytokine, biol rep 3

description:
Library name: A1c
column name in mouse_counts.csv: A1c

value: Vehicle


title: 4T1 NOS2 KO1 with cytokines IFNg, IL1b (20ug/ml), biol rep 2

description:
Library name: A2b
column name in mouse_counts.csv: A2b


title: A_003

description: Library name: SAMPLE3


title: A_012

description: Library name: SAMPLE9


title: 4T1 NOS2 KO1 w/o cytokine, biol rep 2

description:
Library name: A1b
column name in mouse_counts.csv: A1b


title: 4T1 NOS2 KO1 with cytokines IFNg, IL1b (20ug/ml), biol rep 3

description:
Library name: A2c
column name in mouse_counts.csv: A2c


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), plus NOS2 inhibitor 1400W, biol rep 1

description:
Library name: W3a
column name in mouse_counts.csv: W3a

value: Cytokine + NOS2i (1400W)


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), plus NOS2 inhibitor 1400W, biol rep 2

description:
Library name: W3b
column name in mouse_counts.csv: W3b


title: 4T1 NOS2 KO1 w/o cytokine, biol rep 1

description:
Library name: A1a
column name in mouse_counts.csv: A1a


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), biol rep 3

description:
Library name: W2c
column name in mouse_counts.csv: W2c


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), biol rep 2

description:
Library name: W2b
column name in mouse_counts.csv: W2b


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), biol rep 1

description:
Library name: W2a
column name in mouse_counts.csv: W2a


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), plus NOS2 inhibitor 1400W, biol rep 3

description:
Library name: D3c
column name in human_counts.csv: D3c

value: colorectal cancer


title: 4T1 wild type w/o cytokine, biol rep 2

description:
Library name: W1b
column name in mouse_counts.csv: W1b


title: 4T1 wild type w/o cytokine, biol rep 3

description:
Library name: W1c
column name in mouse_counts.csv: W1c


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), biol rep 3

description:
Library name: D2c
column name in human_counts.csv: D2c


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), plus NOS2 inhibitor 1400W, biol rep 1

description:
Library name: D3a
column name in human_counts.csv: D3a


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), biol rep 2

description:
Library name: D2b
column name in human_counts.csv: D2b


title: CMO multiplexing library on WT and Hox-/- gastruloids at 144h

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Library name: HoxLess_CellPlex_5_CMO

library_source: other

data_processing:
All scripts are in https://github.com/hrekaik/scriptsForRekaikEtAl2025.
Mapping and demultiplexing of cell barcode were performed using RNA STARSolo v2.7.10b against the mouse reference genome mm10 and a motified gtf file based on Ensembl 102 (doi:zenodo.org/doi/10.5281/zenodo.10079672) with the following parameters --soloBarcodeReadLength 1 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 -- soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_CR --soloUMIfiltering - --quantMode TranscriptomeSAM GeneCounts --outSAMattributes NH HI AS nM GX GN CB UB --outSAMtype BAM SortedByCoordinate --soloCellFilter None --soloOutFormatFeaturesGeneField3 'GeneExpression' --outSAMunmapped None --outSAMmapqUnique 60 --limitOutSJoneRead 1000 --limitOutSJcollapsed 1000000  --limitSjdbInsertNsj 1000000.Then the matrices have been filtered with DropletUtils version 1.10 (Method EmptyDrops, lower-bound threshold = 100, FDR threshold = 0.01).
Samples demultiplexing was performed using CITE-seq-Count v1.4.4 --cell_bacode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 --bc_collapsing_dist 1 --umi_collapsing_dist 2 --expected_cells 24000 --whitelist '3M-february-2018.txt' --max-error 2. Subsequently the cell barcodes were translated to match the one from the gene expression. Each gene–cell count matrix was then analyzed using Seurat v5.1.0. A Seurat object was generated by filtering out barcodes with less than 200 identified gene and genes identified in less than three cells. Then, the demultiplexing from the translated CMO matrices was performed: any cell barcode with less than 5 CMO UMI was excluded as well as any cell barcode absent from the Seurat object.  Sample attribution was performed with demuxmix using the total number of gene expression UMI per cell. Then, further filtering was applied to remove low-quality cells and doublets. For each dataset, the mean RNA count was used, and cells with either less than 40% of the mean or more than 2.5-fold of the mean were removed. In addition, cells with more than 8% or less than 0.05% mitochondrial counts were removed. Then, all individual datasets were merged into a single Seurat object. The combined dataset was then normalized and, the 2,000 most variable features were identified and data scaled and regressed by cell cycle score and percentage of mitochondrial reads. Principal component analysis (PCA) was computed using variable genes falling within the 5th and 80th percentile of expression and by excludinggenes included in the regions of the deletions of the 4 Hox clusters. UMAP and k-nearest neighbours were then computed using 30 principal components. Clusters were computed at a resolution of 1.5 in order to identify the NMP population. Clusters with similar identities (using known gene markers) were then manually grouped together. For the differential gene expression analysis, the function FindMarkers from Seurat was used and the thresholds were set to adjusted p-value below 0.01 and absolute log2 fold-change above 1.5. For RNA velocity, velocyto v0.17.17 was used to pre-processes datasets and generate loom files. scVelo v1.10.2 was used to estimate and project RNA velocity and compute the pseudotime. The velocity was computed once for the whole dataset in order to sort cells by pseudotime in the heatmap. In order to compare the dataset to a single-cell atlas, matrices from E6.5 to E9.5 were downloaded from https://tome.gs.washington.edu (REF TOME). The E9.5 sample was downsampled to get only 20'000 cells. All the mouse samples were merged with the Seurat object with the gastruloids and the gene labels were unified. The cells were splitted by study (Pijuan-Sala, Cheng, Mohammed, Tome, and our study) , normalized, 2500 variable features were identified. Genes included in the regions of the deletions of the 4 Hox clusters were excluded. Data was scaled and PCA was run with 50 components. Finally all cells from all studies were integrated with the IntegrateLayers function from Seurat with CCAIntegration, recursively: ((((Pijuan-Sala with Mohammed) with Cheng) with Tome) with our study). UMAP was computed using the 30 first component of the integrated cca.
Assembly: mm10
Supplementary files format and content: tar.gz: output of STARsolo or CITE-seq-Counts (translated) as output of cellranger (genes.tsv, barcodes.tsv, matrix.mtx)
Supplementary files format and content: loom: output of velocyto
Supplementary files format and content: CMO_samples.txt.gz: tabular separated text file with for each Library (first column), the different samples (second column), with their barcodes (third column). The Pool.96h.Rep4.5 refers to GSM7890936 and GSM7890954.
Supplementary files format and content: combined_AlltimewtvsBADC_96f83823.analyzed.scVelo.RDS: R object with the Seurat object with all wt and Hox-/- samples used in the study.
Supplementary files format and content: seurat.atlas.combined.E6.5-9.5.gastruloids.integrated.study.rds: R object with Seurat object with the integration of the Embryonic atlas and the samples used in this study.

molecule: other

source_name: Gastruloids

growth_protocol: For gastruloid differentiation, 300 mES cells were resuspended in 40μl of prewarmed N2B27 medium (50% DMEM/F12 and 50% Neurobasal supplemented with 0.5x N2 and 0.5x B27), and seeded into each well of a low-attachment, rounded-bottom 96-well plate. After 48h, 150µl of N2B27 medium supplemented with 3μM of GSK-3 inhibitor was added to each well. Medium was then replaced every 24h.

extract_protocol:
Control and Hox-/- gastruloid at 72h, 96h, 120h and 144h were collected, dissociated and processed.
Samples were processed following the manufacturer’s instructions of the 3' CellPlex Kit (10X Genomics). Cells were then pooled and subjected to single-cell RNA-seq using the 10x Genomics platform (V3.1 chemistry). cDNA preparations were performed according to 10X Genomics recommendations, amplified for 10–12 cycles and sequenced on a Novaseq 6000 or Element AVITI with the cbot2 chemistry.

value: Gastruloids

tag: Stage

value: wt and Hox-/-

tag: library type

value: CMO


title: 4T1 wild type w/o cytokine, biol rep 1

description:
Library name: W1a
column name in mouse_counts.csv: W1a


title: DLD1 wild type w/o cytokine, biol rep 3

description:
Library name: D1c
column name in human_counts.csv: D1c


title: 4T1 wild type with cytokines IFNg, IL1b (20ug/ml), plus NOS2 inhibitor 1400W, biol rep 3

description:
Library name: W3c
column name in mouse_counts.csv: W3c


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), biol rep 1

description:
Library name: D2a
column name in human_counts.csv: D2a


title: A_047

description: Library name: SAMPLE41


title: Cold_3 16° C for 7 days

city: Jiangsu Province

first: cunzhong

last: Fan

address: No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu, China.

institute: Southeast University

description: Library name: Cold_3

data_processing:
featureCounts v2.0.3
Assembly: GRCm39
Supplementary files format and content: A tab-delimited text file containing raw counts for each sample.

source_name: whole heart

extract_protocol:
Total RNA was extracted from heart tissues using TRIzol reagent
The enriched mRNA was then used for library preparation via fragmentation, cDNA synthesis, end repair, A-tailing, and adapter ligation.

value: whole heart


title: RT_3 Room temperature 22° C

description: Library name: RT_3


title: DLD1 wild type w/o cytokine, biol rep 2

description:
Library name: D1b
column name in human_counts.csv: D1b


title: RT_1 Room temperature 22° C

description: Library name: RT_1


title: Cold_2 16° C for 7 days

description: Library name: Cold_2


title: DLD1 wild type w/o cytokine, biol rep 1

description:
Library name: D1a
column name in human_counts.csv: D1a


title: Cold_1 16° C for 7 days

description: Library name: Cold_1


title: sgLkb1 (Lkb1 Mutant KP Tumor) Rep 3

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: Sample 6

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to GRCm38 (GENCODE M25) reference genome using STAR program with default parameters. Read counts, TPM and FPKM were calculated using RSEM program. Identification of differentially expressed genes (DEGs) between different genotype of KP tumor was performed using DESeq2 in R/Bioconductor.
Assembly: GRCm38
Supplementary files format and content: raw count in tab-delimintated text file

source_name: Lung

extract_protocol:
Mouse lung tissue was digested with Collagenase/DNAse in RPMI +10% FBS at 37 degrees for 35 minutes. Samples were washed and underwent RBC lysis. Samples were washed again and resuspended in FACS buffer, then stained for CD45 prior to sorting.  RNA was extracted usine an Invitrogen PureLink RNA extraction kit.
Sequencing libraries were prepared using Nextera XT DNA library preparation kit (Illumina) per manufacturer’s instruction

value: Lung

value: Lkb1 Mutant


title: DLD1 wild type with cytokines IFNg, IL1b, TNFa (100ug/ml), plus NOS2 inhibitor 1400W, biol rep 2

description:
Library name: D3b
column name in human_counts.csv: D3b


title: RT_2 Room temperature 22° C

description: Library name: RT_2


title: sgLkb1 (Lkb1 Mutant KP Tumor) Rep 2

description: Library name: Sample 5


title: Multiplexed scRNA-seq on WT and Hox-/- gastruloids at 144h

description: Library name: HoxLess_CellPlex_5_GEX

value: GEX


title: sgNeo (Lkb1 WT KP Tumor) Rep 2

description: Library name: Sample 2

value: Lkb1 Wildtype


title: sgLkb1 (Lkb1 Mutant KP Tumor) Rep 1

description: Library name: Sample 4


title: sgNeo (Lkb1 WT KP Tumor) Rep1

description: Library name: Sample 1


title: HEK293T GLO1 cells, MGO_4

first: Yael

last: David

state: NY

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample 6
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_MGO_rep4

data_processing:
RNA sequencing reads were 3’ trimmed for base quality >15 and adapter sequences using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and aligned to human assembly hg38 with STAR v2.4 using default parameters.
Data quality and transcript coverage were assessed using the Picard tool CollectRNASeqMetrics (http://broadinstitute.github.io/picard/).
Read count tables were generated with HTSeq v0.9.1.
Assembly: hg38
Supplementary files format and content: text file includes the raw counts of all samples.

source_name: HEK293T GLO1KO

growth_protocol: HEK293T cells were cultured in DMEM (4.5 g/L glucose) supplemented with 10% FBS, 2 mM L-glutamine and 500 U mL−1 penicillin and streptomycin. All cells were incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated from HEK293T GLO1-/- cells using the RNeasy Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 10 underwent polyA selection and library preparation using mRNA Library Prep Kit (Watchmaker catalog # 7BK0001) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq X in a PE100 run, using the NovaSeq X 10B Reagent Kit (Illumina).

treatment_protocol: Fresh stock of MGO was prepared by diluting MGO (~40% in H2O, Sigma, M0252) in PBS before treatment. 0.2 mM MGO was added to the media overnight.

value: HEK293T GLO1KO

value: embryonic kidney epithelial cell line

value: GLO1 KO

value: MGO


title: HEK293T GLO1 cells, Untreated_4

description:
Library name: Sample 3
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_NT_rep4

value: Untreated


title: HEK293T GLO1 cells, MGO_1

description:
Library name: Sample 4
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_MGO_rep1


title: HEK293T GLO1 cells, MGO_3

description:
Library name: Sample 5
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_MGO_rep3


title: HEK293T GLO1 cells, Untreated_2

description:
Library name: Sample 2
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_NT_rep2


title: sgNeo (Lkb1 WT KP Tumor) Rep 3

description: Library name: Sample 3


title: Inhibitor-H3K9me3-50mM-CUT-RUN-rep2

first: Dai

last: ranran

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou, Guangdong Province

institute: Sun Yat-Sen University

description: Library name: Sample 24

data_processing:
CUT&RUN data process pipline. High-confidence reads of CUT&RUN data obtained by using fastp (v0.20.0) with default parameters, were mapped to mouse genome mm9 by using Bowtie2 (v2.5.1)2 with parameters ‘--sensitive –p 24’, and PCR duplicated fragments were filtered by Picard (v2.22.8) (http://broadinstitute.github.io/picard). Then, the unmapped, multi-mapped reads were filtered, and the reads mapping to chrM were removed. Unique reads were filtered by MAPQ > 30. We used deepTools (v3.5.0) bamCoverage to generate bigWig file with RPKM normalization. SAM files were converted to BAM format for peak calling using SAMtools (v1.9). Peaks were identified by MACS2 (v2.2.4) callpeak pipeline.
Assembly: mm9
Supplementary files format and content: SAM files were converted to BAM format using SAMtools for each sample.
Supplementary files format and content: BedGraph files were generated using bamCoverage with normalized values for each sample.
Library strategy: CUT&RUN

source_name: Non-tissue samples

extract_protocol:
This part was performed according to the manufacturer's instructions of the Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme, HD102).
This part was performed according to the manufacturer's instructions of the Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme, HD102).

value: Non-tissue samples

value: ESC

value: embryonic stem cells


title: C4, Control, Normal_HTT

city: Oviedo

first: Sergio

middle: Pérez

last: Oliveira

state: Asturias

address: Avenida roma s/n

department: Investigación Clínica-Básica en Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)

description:
Library name: Sample C4
Column name in raw_counts.txt: C4

data_processing:
Raw sequencing data were obtained in FASTQ format and the quality control was performed using FastQC. Adaptor sequences were trimmed and miRTrace software was used to classify the types of RNA present in each sample, distinguish between miRNAs, rRNA, tRNA and artifacts. miRNA counts were generated using miRDeep.
Assembly: miRNA sequences were mapped to the human genome reference version hg38/GRCh38. Human miRNAs identification was performed using miRBase(v. 22).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: caudate

extract_protocol:
Total RNA was extracted using the mIRNeasy Micro Kit (Cat. No 74004, QIAGEN) following the manufacture´s protocol. 5 mg of tissue was used for RNA extraction.
Small RNA-Seq was performed by Seqplexing (Sequencing Multiplex S.L., Spain) using 200 ng of caudate nucleus total RNA per sample for miRNA library preparation. Library quality was assessed using the QIAxcel Advanced System (QIAGEN). Sequencing was performed on an Illumina NovaSeq X platform (Illumina, USA), generating paired-end reads (2 x 150bp). The sequencing depth ranged from 8.64 to 144 million reads per sample (median = 25.89 million).

value: caudate

tag: pathology

value: Control

tag: genotype htt

value: Normal HTT

tag: htt short_allele

tag: htt long_allele

tag: genotype apoe

tag: Sex

value: M

tag: death age


title: Inhibitor-H3K9me3-50mM-CUT-RUN-rep1

description: Library name: Sample 23


title: C6, Control, Normal_HTT

description:
Library name: Sample C6
Column name in raw_counts.txt: C6

value: F


title: C3, Control, Normal_HTT

description:
Library name: Sample C3
Column name in raw_counts.txt: C3


title: C5, Control, Normal_HTT

description:
Library name: Sample C5
Column name in raw_counts.txt: C5


title: C2, Control, Normal_HTT

description:
Library name: Sample C2
Column name in raw_counts.txt: C2


title: HEK293T GLO1 cells, Untreated_1

description:
Library name: Sample 1
Column name in Table_RNA_HEK293T_MGO_rawCounts.txt: RNA_GLO1KO_NT_rep1


title: Inhibitor-H3K9me3-25mM-CUT-RUN-rep2

description: Library name: Sample 20


title: Inhibitor-H3K9me3-25mM-CUT-RUN-rep1

description: Library name: Sample 19


title: B12, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B12
Column name in raw_counts.txt: B12

value: Late Onset Alzheimer's Disease

value: Intermediate allele HTT

tag: onset age

tag: braak stage

value: V


title: DMSO-H3K9me3-50mM-CUT-RUN-rep2

description: Library name: Sample 22

tag: tissue

tag: treatment

value: DMSO


title: B13, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B13
Column name in raw_counts.txt: B13


title: C1, Control, Normal_HTT

description:
Library name: Sample C1
Column name in raw_counts.txt: C1


title: B11, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B11
Column name in raw_counts.txt: B11


title: DMSO-H3K9me3-25mM-CUT-RUN-rep2

description: Library name: Sample 18

tag: cell line

tag: cell type


title: B7, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B7
Column name in raw_counts.txt: B7

value: VI


title: TMPO-MUT-LADs-CUT-RUN-rep2

description: Library name: Sample 16

value: MEF

value: mouse embryonic fibroblasts

value: TMPO-MUT


title: TMPO-MUT-LADs-CUT-RUN-rep1

description: Library name: Sample 15


title: DMSO-H3K9me3-50mM-CUT-RUN-rep1

description: Library name: Sample 21


title: DMSO-H3K9me3-25mM-CUT-RUN-rep1

description: Library name: Sample 17


title: B8, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B8
Column name in raw_counts.txt: B8


title: B4, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B4
Column name in raw_counts.txt: B4


title: B9, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B9
Column name in raw_counts.txt: B9


title: TMPO-WT-LADs-CUT-RUN-rep1

description: Library name: Sample 13

value: TMPO-WT


title: TMPO-WT-H3K9me3-CUT-RUN-rep1

description: Library name: Sample 9

value: Non-tissue samples


title: B10, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B10
Column name in raw_counts.txt: B10


title: B2, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B2
Column name in raw_counts.txt: B2


title: B3, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B3
Column name in raw_counts.txt: B3


title: B6, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B6
Column name in raw_counts.txt: B6


title: B5, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B5
Column name in raw_counts.txt: B5


title: TMPO-WT-H3K9me3-CUT-RUN-rep2

description: Library name: Sample 10


title: TMPO-MUT-H3K9me3-CUT-RUN-rep2

description: Library name: Sample 12


title: B1, LOAD, Intermediate_allele_HTT

description:
Library name: Sample B1
Column name in raw_counts.txt: B1

value: III


title: A11, LOAD, Normal_HTT

description:
Library name: Sample A11
Column name in raw_counts.txt: A11


title: Inhibitor-LADs-CUT-RUN-rep1

description: Library name: Sample 7


title: A10, LOAD, Normal_HTT

description:
Library name: Sample A10
Column name in raw_counts.txt: A10


title: DMSO-LADs-CUT-RUN-rep2

description: Library name: Sample 6


title: A13, LOAD, Normal_HTT

description:
Library name: Sample A13
Column name in raw_counts.txt: A13


title: Inhibitor-LADs-CUT-RUN-rep2

description: Library name: Sample 8


title: TMPO-WT-LADs-CUT-RUN-rep2

description: Library name: Sample 14


title: DMSO-LADs-CUT-RUN-rep1

description: Library name: Sample 5


title: A12, LOAD, Normal_HTT

description:
Library name: Sample A12
Column name in raw_counts.txt: A12


title: DMSO-H3K9me3-CUT-RUN-rep2

description: Library name: Sample 2


title: DMSO-H3K9me3-CUT-RUN-rep1

description: Library name: Sample 1


title: A14, LOAD, Normal_HTT

description:
Library name: Sample A14
Column name in raw_counts.txt: A14


title: A8, LOAD, Normal_HTT

description:
Library name: Sample A8
Column name in raw_counts.txt: A8


title: Inhibitor-H3K9me3-CUT-RUN-rep1

description: Library name: Sample 3


title: TMPO-MUT-H3K9me3-CUT-RUN-rep1

description: Library name: Sample 11


title: Group5 - subgroup12 #25

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
Library name: 105737-001-025
Mouse with FVB/NRJ background, control for C22-PMP22, 12 weeks old

data_processing:
RNAseq reads were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC.
FastQC (v0.11.9) was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with the default settings. RNAseq reads’ alignment was performed using STAR (v2.7.5a) on a customized mouse reference genome by adding human YAC locus sequence (GRCh38 chr17:14929773-15372292) to GRCm39.
UMI based alignment deduplication was performed using umi_tools (v1.1.1). The gene read quantification was performed using HTSeq-count (v0.12.4) with the Ensembl gene annotation version 110 including both all mouse genes and human genes presented in the YAC locus.
Assembly: GRCm39
Supplementary files format and content: TSV, raw gene count

source_name: Sciatic nerve

extract_protocol:
For RNA isolation, we pooled the sciatic nerves of 4 to 5 animals (males and females) per group per time point. We used a Trizol-2-propanol extraction. The RNA was purified using the NucleoSpin XS-kit (Macherey-Nagel, Düren, Germany) and the manufacturer protocol was followed without the optional filtrate step.
Libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, USA).The samples were poly(A) enriched and sequenced on a NovaSeq6000 sequencing.

treatment_protocol: There was no treatment for the mice in group 1, 2, 3, 4 and 5.

value: Sciatic nerve

value: FVB/NRJ

tag: batch


title: Group5 - subgroup9 #24

description:
Library name: 105737-001-024
Mouse with FVB/NRJ background, control for C22-PMP22, 9 weeks old

tag: genotype


title: A9, LOAD, Normal_HTT

description:
Library name: Sample A9
Column name in raw_counts.txt: A9

value: caudate


title: A4, LOAD, Normal_HTT

description:
Library name: Sample A4
Column name in raw_counts.txt: A4

value: Normal HTT


title: A7, LOAD, Normal_HTT

description:
Library name: Sample A7
Column name in raw_counts.txt: A7

value: M


title: A6, LOAD, Normal_HTT

description:
Library name: Sample A6
Column name in raw_counts.txt: A6

value: F


title: Inhibitor-H3K9me3-CUT-RUN-rep2

description: Library name: Sample 4


title: Group5 - subgroup3 #21

description:
Library name: 105737-001-021
Mouse with FVB/NRJ background, control for C22-PMP22, 3 weeks old


title: Group4 - subgroup9 #19

description:
Library name: 105737-001-019
Tg(pmp22)C22Clh, C22-PMP22, FVB/NRJ background, mouse model, 9 weeks old


title: P. maniculatus bairdii replicate 5

city: Cambridge, MA

first: KT

last: Tyssowski

state: Massachusetts

address: 16 Divinity Ave

institute: Harvard University

description:
Library name: BW6
Parse Evercode WT Mega kit

data_processing:
Data were demultiplexed using python-based pipelines from Parse and aligned to the P. maniculatus bairdii genome. To avoid confounds from mapping to the genome of one of the subspecies, before alignment, genomes were “personalized” to each subspecies, using a method similar to the generation of the P. polionotus genome (see Bendesky et al., PMID 28424518). Briefly, we aligned our data to the P. maniculatus bairdii genome using STAR aligner. Then we performed variant calling for the individuals we sequenced for each subspecies using GATK. We then incorporated variants back into the final genomes to which we mapped reads. We did the final alignment using STAR aligner as a part of the Parse pipeline. Cells that passed a UMI threshold determined automatically by the Parse preprocessing script were carried on to the next steps.
Data were analyzed as a cell x gene count matrix in Seurat version 4.3.0 Data were normalized with the SCTransform method and integrated across samples and subspecies using harmony. Data were then clustered using the default Seurat settings with the FindClusters and FindNeighbors functions. Data were then mapped to the BICNN mouse motor cortex dataset using Azimuth to identify cell types. Clusters with low prediction scores for the mapping (median prediction score < 0.75 out of 1.0) were further assessed by finding marker genes. If clusters showed markers of multiple larger cell types (e.g., neurons and oligodendrocytes) or if they appeared to be non-cortical cell types (e.g., from dissection error), they were removed from the dataset. After removing this contaminating signal, this alignment resulted in 96% of cells with a prediction score greater than 0.75 when mapping to gene classes. The remaining clusters were then re-normalized, re-integrated, and re-clustered.
Assembly: HU_Pman_2.1.3 (Peromyscus maniculatus bairdii)
Supplementary files format and content: RDS file with Seurat object. Genes x cells matrix with metadata labeling sample and cell type information

organism: Peromyscus maniculatus bairdii

source_name: frontal cortex

extract_protocol:
The anterior half of the cortex was extracted from both hemispheres for each animal (this includes all of sensorimotor cortex, as well as other areas) and flash-frozen in liquid nitrogen. Samples were stored at -70°C until further processing. Nuclei were extracted as described in Matson et al. (PMID 30371670) except that the high sucrose buffer had 1.2M sucrose. Nuclei were fixed using the Parse Evercode Fixation kit, according to the instructions of the manufacturer. Fixed nuclei were stored at -80C for up to 3 months.
Library construction was performed using the Parse Evercode WT Mega kit according to the instructions of the manufacturer. Samples from other projects were included in the run. The data here is de-multiplexed by sample, so as to include only the data for this project.

value: frontal cortex

tag: age

value: 3-6 months

value: female


title: A3, LOAD, Normal_HTT

description:
Library name: Sample A3
Column name in raw_counts.txt: A3

value: Late Onset Alzheimer's Disease

value: V


title: A2, LOAD, Normal_HTT

description:
Library name: Sample A2
Column name in raw_counts.txt: A2


title: P. maniculatus bairdii replicate 4

description:
Library name: BW5
Parse Evercode WT Mega kit

value: male


title: Group5 - subgroup5 #22

description:
Library name: 105737-001-022
Mouse with FVB/NRJ background, control for C22-PMP22, 5 weeks old


title: P. maniculatus bairdii replicate 1

description:
Library name: BW1
Parse Evercode WT Mega kit


title: Group5 - subgroup7 #23

description:
Library name: 105737-001-023
Mouse with FVB/NRJ background, control for C22-PMP22, 7 weeks old


title: PBMCs,Post-treatment,rep5

city: Fuzhou

first: si

last: ai

state: Fujian

address: No. 602 Middle 817 Road, Taijiang District

institute: The People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine

description:
Library name: Sample10
RB21001615-P210129-XR1-lnc-X-37

data_processing:
Filter:The raw data was handled by Skewer v0.2.2 (https://sourceforge.net/projects/skewer/files/?source=navbar) and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment: Clean reads were aligned to the human genome mm10 from ensembl using STAR (https://github.com/alexdobin/STAR), with one mismatch allowed.
Differential Gene Expression AnalysisStringTie (v1.3.1c) was used to generate gene expression data and differential gene expression was analysed by DESeq2 (v1.16.1) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) . The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2
Function Enrichment Analysis:Then DEGs were chosen for function and signaling pathway enrichment analysis using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KEGG database (https://www.genome.jp/kegg/pathway.html). The significantly enriched pathways were determined when P < 0.05
Assembly: GrCh39
Supplementary files format and content: Supplementary_file_format_and_content: processed data.xls

source_name: Blood

extract_protocol:
PBMCs from 3 mL whole blood; RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA wereused for the construction of sequencing libraries
RNA libraries were prepared using the NGS®Ultima Dual-mode mRNA Library Prep Kit (12309ES96, YEASEN)

value: Blood

value: PBMC

value: Post-treat,TCM


title: Group3 - subgroup9 #14

description:
Library name: 105737-001-014
Mouse with C57BL/6J background, control C3-PMP22, 9 weeks old


title: Group4 - subgroup12 #20

description:
Library name: 105737-001-020
Tg(pmp22)C22Clh, C22-PMP22, FVB/NRJ background, mouse model, 12 weeoks old


title: A1, LOAD, Normal_HTT

description:
Library name: Sample A1
Column name in raw_counts.txt: A1

value: VI


title: Group3 - subgroup3 #11

description:
Library name: 105737-001-011
Mouse with C57BL/6J background, control C3-PMP22, 3 weeks old


title: Group2 - subgroup12 #10

description:
Library name: 105737-001-010
B6.Cg-Tg(PMP22)C3Fbas/J, C3-PMP22, C57BL/6J background, mouse model, 12 weeks old


title: PBMCs,Post-treatment,rep2

description:
Library name: Sample7
RB21001615-P210129-XR1-lnc-X-3


title: PBMCs,Post-treatment,rep4

description:
Library name: Sample9
RB21001615-P210129-XR1-lnc-X-33


title: Group3 - subgroup12 #15

description:
Library name: 105737-001-015
Mouse with C57BL/6J background, control C3-PMP22, 12 weeks old


title: A5, LOAD, Normal_HTT

description:
Library name: Sample A5
Column name in raw_counts.txt: A5


title: Group3 - subgroup5 #12

description:
Library name: 105737-001-012
Mouse with C57BL/6J background, control C3-PMP22, 5 weeks old


title: Group4 - subgroup7 #18

description:
Library name: 105737-001-018
Tg(pmp22)C22Clh, C22-PMP22, FVB/NRJ background, mouse model, 7 weeks old


title: P. maniculatus bairdii replicate 2

description:
Library name: BW3
Parse Evercode WT Mega kit


title: Group4 - subgroup3 #16

description:
Library name: 105737-001-016
Tg(pmp22)C22Clh, C22-PMP22, FVB/NRJ background, mouse model, 3 weeks old


title: Group4 - subgroup5 #17

description:
Library name: 105737-001-017
Tg(pmp22)C22Clh, C22-PMP22, FVB/NRJ background, mouse model, 5 weeks old


title: Group2 - subgroup3 #6

description:
Library name: 105737-001-006
B6.Cg-Tg(PMP22)C3Fbas/J, C3-PMP22, C57BL/6J background, mouse model, 3 weeks old


title: Group3 - subgroup7 #13

description:
Library name: 105737-001-013
Mouse with C57BL/6J background, control C3-PMP22, 7 weeks old


title: PBMCs,Post-treatment,rep3

description:
Library name: Sample8
RB21001615-P210129-XR1-lnc-X-4


title: Group1 - subgroup12 #5

description:
Library name: 105737-001-005
C3-PMP22 c-JunP0Cre, Schwanncell specific knock out of c-Jun, 12 weeks old

value: C3-PMP22 c-JunP0Cre


title: PBMCs,Post-treatment,rep1

description:
Library name: Sample6
RB21001615-P210129-XR1-lnc-X-2


title: PBMCs,Pre-treatment,rep1

description:
Library name: Sample1
RB21001615-P210129-XR1-lnc-2-2

value: AR


title: Group1 - subgroup9 #4

description:
Library name: 105737-001-004
C3-PMP22 c-JunP0Cre, Schwanncell specific knock out of c-Jun, 9 weeks old

value: Sciatic nerve


title: VC3

city: Nantong

first: Yifu

last: Xiao

address: xisi Road

institute: Affiliated Hospital of Nantong University

description:
Library name: VC3
control group, replicate biosample 3

data_processing:
Raw reads were firstly processed using fastp (v0.22.0) and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2 (v2.1.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each samples

source_name: cell culture

extract_protocol:
total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA)。
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated

value: cell culture

value: wt


title: P. maniculatus bairdii replicate 3

description:
Library name: BW4
Parse Evercode WT Mega kit


title: Group2 - subgroup7 #8

description:
Library name: 105737-001-008
B6.Cg-Tg(PMP22)C3Fbas/J, C3-PMP22, C57BL/6J background, mouse model, 7 weeks old


title: PBMCs,Pre-treatment,rep2

description:
Library name: Sample2
RB21001615-P210129-XR1-lnc-3-2


title: PBMCs,Pre-treatment,rep3

description:
Library name: Sample3
RB21001615-P210129-XR1-lnc-4-2


title: WT-3

city: Jinan

first: Yuhan

last: Ren

address: 2 Wenbo Road, Zhangqiu District, Jinan, Shandong, P.R.China

department: School of Life Sciences

institute: Qilu Normal University

description: Library name: sample3

data_processing:
Base calling was performed using Illumina CASAVA software (v1.8.2) with default parameters. Raw FASTQ files were processed with in-house Perl scripts to remove reads containing adapter sequences, reads with >10% poly-N, and low-quality reads (Q-score < 20 in more than 50% of bases). Quality metrics (Q20, Q30, GC content, and sequence duplication levels) were calculated using FASTQC (v0.11.9).
Clean reads were aligned to the Homo sapiens reference genome (GRCh38) using HISAT2 (v2.0.5) with default parameters (--rna-strandness RF). Only reads with perfect matches or up to one mismatch were retained.
Transcripts were assembled and quantified using StringTie (v1.3.3) with default settings. Gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Assembly: GRCh38.112
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oryza sativa

source_name: root

growth_protocol: Five seedlings of wile type (WT) and mutant line (odmads61) of individual mutants or overexpressing plants were cultivated in a 8 L tank supplied with the modified IRRI nutrient solution (pH 5.5) (Wang et al., 2020) containing 2.5 mM nitrate as the high nitrate treatment.

extract_protocol:
Total RNA was extracted from 100 mg fully-grounded tissue using Trizol reagent (Thermo Fisher).
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: We performed RNA sequencing (RNA-seq) analysis of the roots collected from both WT and Osmads61 mutants grown in hydroponic solution containing 2.5 mM nitrate.

value: root


title: WT-1

description: Library name: sample1


title: OCI-AML5 cells, CEBPD-specific sgRNA, sgCEBPD 2

city: Charlottesville

first: Subhash

last: Prajapati

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
Library name: CEBPD8_1
Cells were transduced with CEBPD-specific lentiCRISPRv2-sgRNA 2 (sgCEBPD 2) lentiviral media

data_processing:
Qualtiy was assessed using FastQC and aligned to the hg38 human genome using hisat2. Differential expression analysis was conducted using DESeq2.
Assembly: hg38
Supplementary files format and content: Tab delimited file contains non-normalized raw read counts aligned to hg38

extract_protocol:
RNA was extracted using phenol-chloroform/Trizol
Libraries were prepared using Fast RNA-seq Lib Prep Kit V2 (Abclonal RK20306) by Novogene.

value: CEBPD-specific sgRNA 2 (sgCEBPD 2)


title: PBMCs,Pre-treatment,rep4

description:
Library name: Sample4
RB21001615-P210129-XR1-lnc-34-2


title: mads61-3-2

description: Library name: sample5


title: Group1 - subgroup3 #1

description:
Library name: 105737-001-001
C3-PMP22 c-JunP0Cre, Schwanncell specific knock out of c-Jun, 3 weeks old


title: mads61-3-1

description: Library name: sample4


title: mads61-3-3

description: Library name: sample6


title: Group2 - subgroup5 #7

description:
Library name: 105737-001-007
B6.Cg-Tg(PMP22)C3Fbas/J, C3-PMP22, C57BL/6J background, mouse model, 5 weeks old


title: Group2 - subgroup9 #9

description:
Library name: 105737-001-009
B6.Cg-Tg(PMP22)C3Fbas/J, C3-PMP22, C57BL/6J background, mouse model, 9 weeks old


title: TMPO-MUT-SETDB1-ChIP-seq-input

city: Guangzhou

data_processing:
ChIP-seq data process pipline. High-confidence reads of ChIP-seq data obtained by using fastp (v0.20.0) with default parameters, were mapped to mouse genome mm9 by using Bowtie2 (v2.5.1)2 with parameters ‘--sensitive –p 24’, and PCR duplicated fragments were filtered by Picard (v2.22.8) (http://broadinstitute.github.io/picard). Then, the unmapped, multi-mapped reads were filtered, and the reads mapping to chrM were removed. Unique reads were filtered by MAPQ > 30. We used deepTools (v3.5.0) bamCoverage to generate bigWig file with CPM normalization. SAM files were converted to BAM format for peak calling using SAMtools (v1.9). Peaks were identified by MACS2 (v2.2.4) callpeak pipeline.
RNA-seq data process pipline. Clean data were obtained by using trim_galore (v0.6.7) to remove reads containing adapter, reads containing ploy-N, and low quality reads from raw data. Clean reads with high quality were aligned to mm9 reference genome using STAR (v2.7.9a) with default parameters. The uniquely mapped reads were counted with HTSeq-count (v2.0.3). Raw counts were used as input to DESeq2 (v1.30.0) to generate differentially expressed genes as well as normalized count tables. Significantly differential expressed genes (DEGs) were identified when the adjusted p-value < 0.05 and the log2-fold change > 1.0.
Assembly: mm9
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

growth_protocol: The mouse ESC line R1 was cultured on gelatin-coated dishes with ESC medium. The ESC medium composition included DMEM (Hyclone, #SH30022.01), 15% (v/v) fetal bovine serum (FBS, Lonsera, #S712-012S), 0.1 mM β-mercaptoethanol (Sigma, #M6250), 2 mM L-glutamine (Thermo Fisher, #35050061), 0.1 mM nonessential amino acids (Thermo Fisher, #11140050), 1% (v/v) nucleoside mix, and LIF.

extract_protocol:
For RNA-seq: Total RNA was extracted from cell pellets using RNAzol reagent. For ChIP-seq: 1% formaldehyde in PBS was used to crosslink the cells. Antibody enrich DNA fragments overnight from Sonicated lysates.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols.

value: Non-tissue samples

value: ESC

value: embryonic stem cells

value: TMPO-MUT

tag: chip antibody


title: PBMCs,Pre-treatment,rep5

description:
Library name: Sample5
RB21001615-P210129-XR1-lnc-37-2


title: WT-2

description: Library name: sample2


title: Group1 - subgroup7 #3

description:
Library name: 105737-001-003
C3-PMP22 c-JunP0Cre, Schwanncell specific knock out of c-Jun, 7 weeks old


title: VC1

description:
Library name: VC1
control group, replicate biosample 1


title: OE3

description:
Library name: OE3
over-expression group, replicate biosample 3

value: over-expression


title: OCI-AML5 cells, CEBPD-specific sgRNA, sgCEBPD 3

description:
Library name: CEBPD9_1
Cells were transduced with CEBPD-specific lentiCRISPRv2-sgRNA 3 (sgCEBPD 3) lentiviral media

value: CEBPD-specific sgRNA 3 (sgCEBPD 3)


title: Group1 - subgroup5 #2

description:
Library name: 105737-001-002
C3-PMP22 c-JunP0Cre, Schwanncell specific knock out of c-Jun, 5 weeks old


title: OCI-AML5 cells, CEBPD-specific sgRNA, sgCEBPD 4

description:
Library name: CEBPD10_2
Cells were transduced with CEBPD-specific lentiCRISPRv2-sgRNA 4 (sgCEBPD 4) lentiviral media

value: CEBPD-specific sgRNA 4 (sgCEBPD 4)


title: VC2

description:
Library name: VC2
control group, replicate biosample 2


title: TMPO-MUT-SETDB1-ChIP-seq-rep2


title: OE2

description:
Library name: OE2
over-expression group, replicate biosample 2


title: OCI-AML5 cells, non-specific control sgRNA, sgControl 3

description:
Library name: NS9_1
Cells were transduced with non-specific control lentiCRISPRv2-sgRNA 3 (sgControl 3) lentiviral media

value: non-specific control sgRNA 3 (sgControl 3)


title: OE1

description:
Library name: OE1
over-expression group, replicate biosample 1


title: OCI-AML5 cells, non-specific control sgRNA, sgControl 4

description:
Library name: NS10_1
Cells were transduced with non-specific control lentiCRISPRv2-sgRNA 4 (sgControl 4) lentiviral media

value: non-specific control sgRNA 4 (sgControl 4)


title: OCI-AML5 cells, non-specific control sgRNA, sgControl 1

description:
Library name: NS7_2
Cells were transduced with non-specific control lentiCRISPRv2-sgRNA 1 (sgControl 1) lentiviral media

value: non-specific control sgRNA 1 (sgControl 1)


title: OCI-AML5 cells, non-specific control sgRNA, sgControl 2

description:
Library name: NS8_1
Cells were transduced with non-specific control lentiCRISPRv2-sgRNA 2 (sgControl 2) lentiviral media

value: non-specific control sgRNA 2 (sgControl 2)


title: TMPO-MUT-SETDB1-ChIP-seq-rep1


title: OCI-AML5 cells, CEBPD-specific sgRNA, sgCEBPD 1

description:
Library name: CEBPD7_1
Cells were transduced with CEBPD-specific lentiCRISPRv2-sgRNA 1 (sgCEBPD 1) lentiviral media

value: CEBPD-specific sgRNA 1 (sgCEBPD 1)


title: RNA-seq of Human breast cancer cells, Khellin-exp group, biol repl3

first: YINING

last: ZHENG

address: No. 280, Waihuan East Road

institute: Guangdong Pharmaceutical University

description: Library name: Khellin-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg39
Supplementary files format and content: xls file includes gene counts for all Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Human breast cancer cells


title: TMPO-WT-SETDB1-ChIP-seq-input

value: TMPO-WT


title: RNA-seq of Human breast cancer cells, Khellin-exp group, biol repl1

description: Library name: Khellin-1


title: TMPO-WT-SETDB1-ChIP-seq-rep2


title: RNA-seq of Human breast cancer cells, Khellin-exp group, biol repl2

description: Library name: Khellin-2


title: HEK293T GLO1KO cells, Untreated_KDM5B

description: Library name: Sample 4

data_processing:
ChIP-seq reads were trimmed and filtered for quality and library adapters using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to human assembly hg38 and additionally D. melanogaster assembly dm6 for ChIP samples with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools. To ascertain enriched regions, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 and run against input for ChIP data. A peak atlas was created by combining the superset of all peaks using the ‘merge’ function in the BEDTools suite v2.29.2. Read density profiles were created using deepTools 'bamCoverage’ v3.3.0 with read pileups extended to 200 bp. ChIP data was normalized using the external H2Av spike ins by scaling the signal to the inverse of the normalized dm6 counts. Version 1.6.1 of featureCounts (http://subread.sourceforge.net) was used to build a raw counts matrix and DESeq2 was used to calculate differential enrichment for all pairwise contrasts for experiments with replicates. For single sample data, MACS2 was run by swapping bams of different conditions to find differential regions. Peak-gene associations were created by assigning all intragenic peaks to that gene, while intergenic peaks were assigned using linear genomic distance to transcription start site. Composite and tornado plots were created using deepTools v3.3.0 by running computeMatrix and plotHeatmap on normalized bigwigs with average signal sampled in 25 bp windows and flanking region defined by the surrounding 2 kb.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
GLO1-/- HEK293T cells -/+ overnight 0.2 mM MGO were fixed with 1.5 mM EGS (ethylene glycol bis(succinimidyl succinate), Thermo Scientific, 21565) for 30 min, followed by 1% formaldehyde for 10 min, after which the reaction was quenched by the addition of glycine to a final concentration of 125 mM for 5 min. Fixed cells were washed twice with PBS, snap frozen and stored at -80℃. Frozen cell pellets were sent to the MSKCC Epigenetics Research Innovation Lab for processing. Cell pellets were resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spun down, resuspended in the immunoprecipitation buffer at 1 mL per 0.5 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail (Millipore Sigma, #11836170001) and processed on a Covaris LE220+ Focused-ultrasonicator to achieve an average fragment length of 200-300 bps with the following parameters: PIP=420, Duty Factor=30, CBP/Burst per sec=200, Time = 10min. Chromatin concentrations were estimated using the Pierce™ BCA Protein Assay Kit (ThermoFisher Scientific, 23227) according to the manufacturer’s instructions. The immunoprecipitation reactions were set up in 1mL of the immunoprecipitation buffer in Protein LoBind tubes (Eppendorf, 22431081) and pre-cleared with 50uL of Protein A/G magnetic beads (Cytiva, 9981922) for two hours at 4°C. After pre-clearing, the samples were transferred into new Protein LoBind tubes and incubated overnight at 4°C with the appropriate primary antibodies (Supplementary Table 1). For normalization purposes, 5 µL of drosophila Spike-in chromatin (Active Motif, 53083) and 2 µL of Spike-in antibody (Active Motif, 61686) were added to each reaction, as well as 2 µL of SNAP-ChIP K-MetStat Panel (Epicypher, 19-1100) to the H3K4me3 samples. The next day, 50 µL of BSA-blocked Protein A/G magnetic beads were added to the reactions and incubated for 2 hours at 4°C. The beads were then washed two times with low-salt washing buffer (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), two times with high-salt washing buffer (500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 20mM Tris-HCl pH 8.0), two times with LiCl wash buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1mM EDTA, 1% Na-Deoxycholate, 1% IGEPAL (CA-630) and one time with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The samples were then reverse-crosslinked overnight in the elution buffer (1% SDS, 0.1 M NaHCO3) and purified using the ChIP DNA Clean & Concentrator kit (Zymo Research, D5205) following the manufacturer’s instructions. The recovered DNA fragments were quantified using a Qubit Flex fluorometer (ThermoFisher Scientific) and sent to the MSKCC Integrated Genomics Operation core facility for library preparation and sequencing.
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA EvoPrep Kit (Roche, 10212250702) according to the manufacturer’s instructions with 0.2-5 ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina). An average of 20-30M paired reads were generated per sample.

value: HEK293T GLO1KO

value: embryonic kidney epithelial cell line

value: GLO1 KO

value: Untreated


title: HEK293T GLO1KO cells, Untreated_WDR5

description: Library name: Sample 3


title: TMPO-WT-SETDB1-ChIP-seq-rep1

value: Non-tissue samples

value: ESC


title: HEK293T GLO1KO cells, MGO_KDM5B

description: Library name: Sample 7

value: MGO


title: Inhibitor-SETDB1-ChIP-seq-input

value: embryonic stem cells


title: HEK293T GLO1 cells, MGO_H3R17MGH1_2

description: Library name: Sample 18

data_processing:
CUT&Tag reads were trimmed and filtered for quality and library adapters using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), with a quality setting of 15 and running cutadapt (v1.15) and FastQC (v0.11.5).
Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools.
To ascertain enriched regions, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 and run against a matched IgG control for each condition.
A peak atlas was created by combining the superset of all peaks using the ‘merge’ function in the BEDTools suite v2.29.2.
Read density profiles were created using deepTools 'bamCoverage’ v3.3.0, normalized to 10 million uniquely mapped reads and with read pileups extended to 200 bp. Version 1.6.1 of featureCounts (http://subread.sourceforge.net) was used to build a raw counts matrix and DESeq2 was used to calculate differential enrichment for all pairwise contrasts for experiments with replicates.
For single sample data, MACS2 was run by swapping bams of different conditions to find differential regions.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with HEK293T native nuclei (GLO1-/-) plus and minus MGO treatment (0.2 mM for GLO1-/-, overnight) using the EpiCypher CUTANA CUT&Tag Kit version 3 and following CUT&Tag protocol v3 with slight modifications. Briefly, for each reaction, 100K nuclei were immobilized to Concanavalin-A beads (ConA; EpiCypher, 21-1401) and incubated overnight (4 °C with gentle rocking) with 0.5 µg of primary antibodies listed in Supplementary Table 1.
Bead-bound nuclei were collected on a magnetic rack and resuspended in 50 µL Wash Buffer 1 with 0.5 µL of anti-rabbit immunoglobulin G (IgG) secondary antibody and incubated RT for 30 min on a nutator. After washes in Wash Buffer 1, bead-bound nuclei were resuspended in 50 µL of Wash Buffer 2 with 2.5 µL of pAG-Tn5 (EpiCypher, 15-1017) for 1 hour incubation at RT on a nutator. Bead-bound nuclei were washed a total of two times with Wash Buffer 2, resuspended in 50 µL cold Tagmentation Buffer and incubated 1 hour in a thermocycler set to 37°C. After tagmentation, chromatin-bound fragments were released with 5 µL of the SDS Release Buffer during an 1 hour thermocycler incubation at 58°C and quenched with 15 µL SDS Quench Buffer. For Library amplification, 2 µL of i5 unique index primer (10 µM), 2 µL of i7 unique index primer (10 µM), and 25 µL of Non-Hot Start 2X PCR Master Mix was added to each reaction and was subjected to PCR (58°C for 5 min; 72°C for 5 min; 98 °C  for 45s and for 14 cycles 98°C for 15 s, and 60°C for 10 s; 72°C for 1 min). To purify libraries 1.3 x volume of SPRIselect reagent (Beckman Coulter, B23317) was added to each reaction and incubated for 5 min RT. Libraries were twice washed with 85% EtOH and eluted in 17 µL 0.1X TE Buffer.


title: HEK293T GLO1KO cells, MGO_WDR5

description: Library name: Sample 6


title: HEK293T GLO1 cells, MGO_H3K4me3_2

description: Library name: Sample 17


title: HEK293T GLO1KO cells, Untreated_IgG

description: Library name: Sample 1


title: RNA-seq of Human breast cancer cells, control group, biol repl3

description: Library name: Control-3


title: RNA-seq of Human breast cancer cells, control group, biol repl2

description: Library name: Control-2


title: HEK293T GLO1KO cells, Untreated_H3K4me3

description: Library name: Sample 2


title: HEK293T GLO1 cells, MGO_H3R17MGH1_1

description: Library name: Sample 15


title: HEK293T GLO1 cells, MGO_IgG_2

description: Library name: Sample 16


title: RNA-seq of Human breast cancer cells, control group, biol repl1

description: Library name: Control-1


title: HEK293T GLO1 cells, MGO_H3K27me3_1

description: Library name: Sample 13


title: GEX_Z007

city: Rochester

first: Hu

last: Zeng

state: MN

address: 209 Third Ave SW

department: Rheumatology

institute: Mayo Clinic

description: Library name: Sample 19

data_processing:
Cell type annotation was conducted using the Azimuth package with the Human PBMC reference dataset.
To refine cell type classifications, we manually reviewed cluster-specific gene markers identified by Immunopipe and further annotated subpopulations of CD8 T cells. Gene set enrichment analysis was performed using the clusterProfiler package in R.
Additionally, ANOVA test was applied to compare gene expression scores across patient groups for selected genes involved in the CD8 T cell cytotoxicity pathway.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files

source_name: PBMC

growth_protocol: Blood samples were collected into sodium heparin tubes, and plasma was collected after centrifuging at 4 °C, 1300 rpm for 10 mins.

extract_protocol:
Specifically, 13 mL Ficoll-Paque™ PLUS density gradient media (GE Healthcare, Cat# 17-1440-02) were added to the bottom of 30 mL diluted peripheral blood, and centrifuged at 4 °C, 400 g for 25 min with the acceleration and deceleration at lower speed. The PBMC layer was collected and washed with wash buffer (1×PBS + 10 mM HEPES + 0.1% BSA + 2 mM EDTA), and PBMCs were aliquoted and cryopreserved in a liquid nitrogen tank.
FASTQ files generated from the Gene Expression and Feature Barcode libraries were processed using the 10x Genomics Cell Ranger multi pipeline to create expression matrices for downstream analysis.
Integrated single-cell analysis of gene expression and T cell receptor data was performed using the Immunopipe package.

treatment_protocol: Peripheral blood mononuclear cells were isolated from the peripheral blood using Ficoll-Paque gradient centrifugation.

value: PBMC

tag: sample group

value: immune-related adverse event (irAE)


title: HEK293T GLO1 cells, MGO_H3K9me3_1

description: Library name: Sample 12


title: DMSO-SETDB1-ChIP-seq-input

value: DMSO


title: Inhibitor-SETDB1-ChIP-seq-rep2


title: HEK293T GLO1KO cells, MGO_H3K4me3

description: Library name: Sample 5


title: HEK293T GLO1 cells, MGO_IgG_1

description: Library name: Sample 10


title: GEX_TZM035

description: Library name: Sample 18

value: rheumatoid arthritis control (RAC)


title: Inhibitor-SETDB1-ChIP-seq-rep1


title: HEK293T GLO1 cells, MGO_H3K4me3_1

description: Library name: Sample 11


title: GEX_TZ001

description: Library name: Sample 17


title: HEK293T GLO1 cells, Untreated_H3K4me3_2

description: Library name: Sample 8


title: DMSO-SETDB1-ChIP-seq-rep2


title: HEK293T GLO1 cells, MGO_H3K36me3_1

description: Library name: Sample 14


title: DMSO-SETDB1-ChIP-seq-rep1


title: HEK293T GLO1 cells, Untreated_H3R17MGH1_2

description: Library name: Sample 9


title: TMPO-MUT-H3K9me3-ChIP-seq-rep1

description:
TMPO-MUT-H3K9me3-ChIP-seq-rep1.bw
TMPO-MUT-H3K9me3-ChIP-seq-merge.bw

value: TMPO-MUT


title: HEK293T GLO1 cells, Untreated_H3K27me3_1

description: Library name: Sample 4


title: GEX_irAE04

description: Library name: Sample 14


title: GEX_irAE13

description: Library name: Sample 15


title: HEK293T GLO1 cells, Untreated_H3R17MGH1_1

description: Library name: Sample 6


title: GEX_RA12

description: Library name: Sample 16


title: TMPO-MUT-H3K9me3-ChIP-seq-rep2

description:
TMPO-MUT-H3K9me3-ChIP-seq-rep2.bw
TMPO-MUT-H3K9me3-ChIP-seq-merge.bw


title: Hnf4 RNAi Larval midgut, Day 4, rep 4

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

country: Germany

institute: University of Cologne

description: Library name: mex_Hnf4i_D4_rep4

data_processing:
The quality of the raw sequencing reads was checked using FastQC (v0.11.7) [1] and MultiQC (v.1.12) [2], and sequencing adaptor were trimmed using Trimmomatic (v0.39) [3]. No issues were detected.                         [1] http://www.bioinformatics.babraham.ac.uk/projects/fastqc, [2] https://doi.org/10.1093/bioinformatics/btw354 [3] https://github.com/usadellab/Trimmomatic
List of adapters is as follows: Read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; AGATCGGAAGAGCACACGTCTGAAC; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG Read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; AGATCGGAAGAGCGTCGTGTAGGGA; TGGAATTCTCGGGTGCCAAGG; AGATCGGAAGAGCACACGTCT; CTGTCTCTTATACACATCT; AGATGTGTATAAGAGACAG"
Reads were aligned to the Drosophila melanogaster reference genome BDGP6.54.114 with STAR (v2.7.10b) [4], A raw count matrix for all sample was then generated from STAR “ReadsPerGene.out.tab” outputs as described here: https://ucdavis-bioinformatics-training.github.io/2019_March_UCSF_mRNAseq_Workshop/data_reduction/counts.html [4] https://doi.org/10.1093/bioinformatics/bts635
Data were further analysed using R (v4.5.1). Filtering was performed for low-count genes (>1 read in all samples), retaining 9536 genes out of 24254. DESeq2 package (v1.49.3) [5] was used to carry out differential expression analysis. [5] https://doi.org/10.1186/s13059-014-0550-8
Assembly: D. melanogaster annotated transcripts (BDGP6.54.114)
Supplementary files format and content: The Excel file contains three spreadsheets. The "RAW" spreadsheet contains the read counts for each transcript in each sample, after alignment with STAR. The “CPM” spreadsheet contains Counts Per Million (CPM) read counts for each transcript in each sample. The “DEG” spreadsheet contains the log2 fold change (log2FC) and the adjusted p-value (padj) for each transcript following a comparison of two conditions using DESeq2, and after filtering out transcripts with low-counts, as described above. The following pairwise comparisons were made: - controls D4 vs controls D3 (attP40_D4_vs_attP40_D3) - Hnf4 RNAi D4 vs Hnf4 RNAi D3 (Hnf4i_D4_vs_Hnf4i_D3) - HNF4 RNAi D3 vs controls D3 (Hnf4i_D3_vs_attP40_D3) - Hnf4 RNAi D4 vs controls D4 (Hnf4i_D4_vs_attP40_D4). The Flybase ID and symbol are provided for each transcript.

organism: Drosophila melanogaster

source_name: Midgut

growth_protocol: The embryos were collected after an overnight egg-laying period and transferred in batches of 40 to polystyrene vials containing a yeast-only diet. These vials were then kept at 25°C under a 12-hour light/dark cycle. Larvae were collected on days three and four after egg laying for midgut dissection.

extract_protocol:
Total RNA was extracted using the Promega Reliaprep RNA Tissue Miniprep System
Libraries were prepared by the Cologne Center for Genomics using the Illumina Stranded Truseq RNA sample Preparation Kit

treatment_protocol: Hnf4 was silenced in ECs by driving the expression of a UAS-Hnf4 RNAi transgene wiht the EC-specific mex-GAL4 driver.

value: Midgut

tag: Stage

value: mex-GAL4 / UAS-Hnf4 RNAi

value: Yeast only diet


title: HEK293T GLO1 cells, Untreated_H3K4me3_1

description: Library name: Sample 2


title: TMPO-WT-H3K9me3-ChIP-seq-rep2

description:
TMPO-WT-H3K9me3-ChIP-seq-rep2.bw
TMPO-WT-H3K9me3-ChIP-seq-merge.bw

value: TMPO-WT


title: Hnf4 RNAi Larval midgut, Day 4, rep 3

description: Library name: mex_Hnf4i_D4_rep3


title: HEK293T GLO1 cells, Untreated_IgG_1

description: Library name: Sample 1

value: HEK293T GLO1KO


title: HEK293T GLO1 cells, Untreated_H3K9me3_1

description: Library name: Sample 3

value: embryonic kidney epithelial cell line


title: TMPO-WT-H3K9me3-ChIP-seq-rep1

description:
TMPO-WT-H3K9me3-ChIP-seq-rep1.bw
TMPO-WT-H3K9me3-ChIP-seq-merge.bw


title: GEX_ICI27

description: Library name: Sample 12

value: ICI control (ICI)


title: HEK293T GLO1 cells, Untreated_IgG_2

description: Library name: Sample 7

value: GLO1 KO

value: Untreated


title: Hnf4 RNAi Larval midgut, Day 4, rep 2

description: Library name: mex_Hnf4i_D4_rep2


title: Inhibitor-H3K9me3-ChIP-seq-rep2

description:
Inhibitor-H3K9me3-ChIP-seq-rep2.bw
Inhibitor-H3K9me3-ChIP-seq-merge.bw

value: Non-tissue samples

value: ESC


title: GEX_H052

description: Library name: Sample 11

value: healthy control (HC)


title: HEK293T GLO1 cells, Untreated_H3K36me3_1

description: Library name: Sample 5


title: GEX_ICI31

description: Library name: Sample 13

value: PBMC


title: Hnf4 RNAi Larval midgut, Day 4, rep 1

description: Library name: mex_Hnf4i_D4_rep1


title: GEX_H039

description: Library name: Sample 10