title: Left Ent-Pir Cx Pseudo-exposed-7

city: Paris

first: Michel

last: Mallat

address: Boulevard de l'Hôpital

institute: ICM

description: Library name: W-Ent-gauche-Pseudo

data_processing:
Quality of raw data was evaluated with FastQC. Poor quality sequences and adapters were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.6.3) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.  Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Following analysis were conducted with R software. Data were normalized with DESeq2 (v1.26.0) or/and edgeR (v3.28.0) bioconductor packages, prior to differential analysis with glm framework likelihood ratio test from edgeR package, and/or DESeq2 workflow. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
Assembly: mm10 reference genome and quantification with gencode vM25 annotation gtf file
Supplementary files format and content: Rdata file containing the matrices of not-normalized counts of both genes and isoforms, same file for all samples

source_name: Brain, left hemisphere, area in the entorhinal-piriform cortex

extract_protocol:
Tissue samples were extracted from a brain region covering adjacent area of the entorhinal and the piriform cortex (Ent-Pir Cx) of the right and the left hemispheres in 100 µm-thick coronal sections cut on a cryostat.Total RNA was extracted from the tissues samples  using RNeasy® Micro kit (QIAGEN). Quality of RNA was confirmed on Agilent TapeStation (RIN > 8).
RNA seq libraries were prepared using Illumina Stranded mRNA Prep kit (Illumina) and sequenced with Illumina NovaSeq 6000 platform (2 x 87 million reads with 100 nucleotides length per sample).

treatment_protocol: Mice were head exposed to a 5G-3.GHz electromagnetic field or pseudo- exposed  (5G signal generator turned off) 1h daily 5 days a week over 6 weeks. The animals were then euthanized under isoflurane anaestesia and whole brains were collected and frozen.

value: Male

value: Brain cells

value: WT

value: Pseudo-exposure

value: C57 BL/6J


title: R1881_48h, rep2

status: Public on Mar 28 2025

type: RNA

city: Vancouver

first: Anne

last: Haegert

state: BC

address: 2660 Oak Street

department: Genomics Core

country: Canada

institute: Vancouver Prostate Centre

description: DHT-treated 48h sample rep2

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID 072363)

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution

data_processing: Data was processed with Agilent Feature Extraction 11.0.1.1.  Processed signal was quantile normalized with Agilent GeneSpring 11.5.1.

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP cells

label_protocol: Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0. An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA

extract_protocol: Mirvana total RNA isolation kit from Ambion

tag: cell line

value: Immortalized cell line LNCaP

tag: silac

value: heavy amino acid-labeled

tag: treatment

value: DHT-treated 48h


title: R1881_24h, rep2

description: DHT-treated 24h sample rep2

value: medium animo acid-labeled

value: DHT-treated 24h


title: hnRNPC_Mut2

type: SRA

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

country: USA

institute: Case Western Reserve University

description: Library name: hnRNPC_Mut2

library_source: transcriptomic

data_processing:
Raw fastq files were used as an input for CLIPittyClip processing pipeline (PMID: 38658162)
Assembly: GRCh38. p14
Supplementary files format and content: tab-delimited text file containing peak coordinates
Library strategy: CLIP-seq

growth_protocol: HEK293 cell lines were grown and maintained at 37'C in DMEM media containing 5% FBS and 1% NEAA.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37'C with shaking at 1100RPM.  The lysates were then briefly treated with RNase I at 1:100 or 1:5000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4'C centrifuge for 10 minutes. V5 IP was performed overnight at 4'C with nutation. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revity)) and ran on SDS-PAGE. The SDS-PAGE was run in non-reducing conditions for hnRNPC and in reducing conditions for RBM25. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above the hnRNPC (32kDa) and RBM25 (100kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol: Expression of the exogenous proteins were induced by treating the cells with 1mg/mL doxycycline for 24 hours. Then, cellular media was replaced with ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80C until use.

tag: cell type

value: Human Embryonic Kidney

tag: genotype


title: Left Ent-Pir Cx Pseudo-exposed-6

country: France

description: Library name: V-Ent-gauche-Pseudo

molecule: polyA RNA

organism: Mus musculus

tag: tissue

value: Brain, left hemisphere, area in the entorhinal-piriform cortex

tag: Sex

tag: strain


title: CSS_ctrl, rep3

description: EtOH-treated ctrl sample rep3

value: light amino acid-labeled

value: EtOH-treated ctrl


title: R1881_48h, rep3

description: DHT-treated 48h sample rep3


title: placenta_PRYA290

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
For each sample 100 ng of total RNA were used for library preparation with the Illumina RNA Prep with Enrichment (L) Tagmentation kit (Illumina, cat # 20040536) following manufacturer’s instructions. Briefly, after the first and second strand cDNA synthesis, double-stranded DNA was subject to tagmentation, where the Transposomes simultaneously tagmented and added adapters to the double-stranded cDNA. After tagmentation, the fragments were purified and amplified to add index adapter sequences (IDT for Illumina DNA/RNA UD Indexes Set B, cat # 20027214) for dual indexing and P7 and P5 sequences for clustering. 200 ng of library were hybridized to enrichment oligos (Illumina Exome Panel cat # 20020183) with an overnight incubation at 58°C. The enriched libraries were amplified with 14 PCR cycles and cleaned up with Agencourt AMPure XP beads (Beckman Coulter cat # A63880). The libraries quality control was performed using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, cat # Q32850) and the Agilent D1000 ScreenTape assay (Agilent, cat # 5067-5582).
Demultiplexed .fastq files were trimmed using fastp (v0.23.1) with the following options: -w 8 -l 30 --trim_front1 10 --trim_front2 10, and specifying the Nextera adapter (CTGTCTCTTATACACATCT), followed by alignment to the human genome (GRCh38) and gene counts (to the Homo sapiens GRCh38.p10 gtf annotation) using STAR (2.7.9a) with default options. Counts were processed with DESeq2 (v1.40.2) to determine the differentially expressed genes (abs(log2FC) > 1 and adjusted p-value <0.05), with the following design formula: ~ Labor + Delivery + GestWeek + COVID19_positivity. Principal Component Analysis was performed using PCAtools (v2.12.0), correlation with the rcorr function in the Hmisc package (v5.1-0) and RcmdrMisc package (v2.7-2). Plots were generated in R with ggplot2 (v3.4.2) or ggpubr (v0.6.0), while volcano plots were generated using the R package EnhancedVolcano (v1.18.0).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw counts matrix for blood samples obtained with STAR RNA --quantMode GeneCounts option. Tab-separated values.
Supplementary files format and content: raw counts matrix for placenta samples obtained with STAR RNA --quantMode GeneCounts option. Tab-separated values.

source_name: placenta

extract_protocol:
Total RNA was extracted from placenta samples using the Qiagen Rneasy Mini kit cat #74104 and from blood samples using the Ribo kit Invitrogen AM1928
For each sample 100 ng of total RNA were used for library preparation with the Illumina RNA Prep with Enrichment (L) Tagmentation kit (Illumina, cat # 20040536) following manufacturer’s instructions. Briefly, after the first and second strand cDNA synthesis, double-stranded DNA was subject to tagmentation, where the Transposomes simultaneously tagmented and added adapters to the double-stranded cDNA. After tagmentation, the fragments were purified and amplified to add index adapter sequences (IDT for Illumina DNA/RNA UD Indexes Set B, cat # 20027214) for dual indexing and P7 and P5 sequences for clustering. 200 ng of library were hybridized to enrichment oligos (Illumina Exome Panel cat # 20020183) with an overnight incubation at 58°C. The enriched libraries were amplified with 14 PCR cycles and cleaned up with Agencourt AMPure XP beads (Beckman Coulter cat # A63880). The libraries quality control was performed using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, cat # Q32850) and the Agilent D1000 ScreenTape assay (Agilent, cat # 5067-5582). The libraries were pooled after quality control followed by sequencing on a NovaSeq 6000 SP lane as paired-end 100 bases.

treatment_protocol: Samples were preserved in RNA later solution right after delivery

value: placenta

value: placenta cells

tag: patient

value: control


title: Left Ent-Pir Cx Pseudo-exposed-5

description: Library name: H-Ent-gauche-Pseudo

value: Male


title: CSS_ctrl, rep1

description: EtOH-treated ctrl sample rep1


title: Left Ent-Pir Cx Pseudo-exposed-4

description: Library name: G-Ent-gauche-Pseudo

value: Brain cells


title: hnRNPC_Mut1

description: Library name: hnRNPC_Mut1


title: placenta_PRYA286


title: CSS_ctrl, rep2

description: EtOH-treated ctrl sample rep2


title: Left Ent-Pir Cx Pseudo-exposed-3

description: Library name: 8-Ent-gauche-Pseudo

value: WT


title: placenta_PRYA288


title: hnRNPC_WT4

description: Library name: hnRNPC_WT4


title: ENZA_48h, rep3

description: ENZA-treated 48h sample rep3

value: ENZA-treated 48h


title: hnRNPC_Mut4

description: Library name: hnRNPC_Mut4


title: ENZA_48h, rep2

description: ENZA-treated 48h sample rep2


title: placenta_PRYA187

value: mild/moderate COVID-19


title: ENZA_48h, rep1

description: ENZA-treated 48h sample rep1

value: Immortalized cell line LNCaP


title: Left Ent-Pir Cx Pseudo-exposed-2

description: Library name: B-Ent-gauche-Pseudo

value: Pseudo-exposure

value: C57 BL/6J


title: placenta_PRYA141

value: asymptomatic COVID-19


title: hnRNPC_WT3

description: Library name: hnRNPC_WT3


title: Left Ent-Pir Cx Exposed-7

description: Library name: 5-Ent-gauche-Expo

value: Exposure to 5G-3.5 GHz


title: placenta_PRYA49

value: critical/severe COVID-19


title: placenta_PRYA2000


title: hnRNPC_WT5

description: Library name: hnRNPC_WT5

value: Human Embryonic Kidney


title: hnRNPC_WT1

description: Library name: hnRNPC_WT1


title: placenta_PRYA190


title: TAZ KO F22 rep 2

city: Vienna

first: Martin

last: Knöfler

address: Währinger Gürtel 18-20, 5Q,

department: Department of Obstetrics and Gynaecology, Reproductive Biology Unit

country: Austria

institute: Medical University of Vienna

description:
Library name: F22-2
F22-2

data_processing:
Read qualities were checked with FastQC.
Reads were mapped to the GRCh38 human genome primary assembly and counted using STAR (version 2.7.5).
Differential gene expression analysis was done using DESeq2 (version 1.22.0).
Assembly: GRCh38.p13
Supplementary files format and content: TAZKO_counttable.tsv is a tab-separated values file containing read counts for all samples, for genes with Ensembl gene IDs and gene symbols (GRCh38.p13 build)

source_name: Placenta

growth_protocol: Cell lines are cultivated in DMEM/ 2mM L-glutamine/ 10% fetal bovine serum/ 0.5µg/mL Puromycin dihydrochloride/ 100 U/mL Penicillin Streptomycin.

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Illumina RNA-Seq Library Preparation stranded RNA with poly-A enrichment (NEB Next Ultra II Directional RNA Library Prep Kit for  Illumina).

treatment_protocol: TAZ/WWTR1 knockout was performed using CRISPR-Cas9 genome-editing.

value: Placenta

value: Choriocarcinoma

value: CRISPR/Cas9  GFP, puro  integrated in TAZ/WWTR1 locus (DC-HTN2622223-D01-B)

value: TAZ/WWTR1 knockout


title: ENZA_24h, rep2

description: ENZA-treated 24h sample rep2

value: medium animo acid-labeled

value: ENZA-treated 24h


title: Left Ent-Pir Cx Exposed-6

description: Library name: 7-Ent-gauche-Expo

value: Brain, left hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Brain cells


title: Left Ent-Pir Cx Pseudo-exposed-1

description: Library name: 2-Ent-gauche-Pseudo

value: WT


title: Left Ent-Pir Cx Exposed-5

description: Library name: J-Ent-gauche-Expo


title: TAZ KO F22 rep 1

description:
Library name: F22-1
F22-1


title: TAZ KO F10 rep 2

description:
Library name: F10-2
F10-2


title: placenta_PRYA146

value: placenta

value: placenta cells


title: ENZA_24h, rep1

description: ENZA-treated 24h sample rep1

value: Immortalized cell line LNCaP


title: DMSO_ctrl, rep3

description: DMSO-treated ctrl sample rep3

value: light amino acid-labeled

value: DMSO-treated ctrl


title: Left Ent-Pir Cx Exposed-4

description: Library name: D-Ent-gauche-Expo

value: Exposure to 5G-3.5 GHz

value: C57 BL/6J


title: DMSO_ctrl, rep1

description: DMSO-treated ctrl sample rep1


title: placenta_PRYA207

value: mild/moderate COVID-19


title: Left Ent-Pir Cx Exposed-3

description: Library name: A-Ent-gauche-Expo


title: DMSO_ctrl, rep2

description: DMSO-treated ctrl sample rep2


title: placenta_PRYA175-1

value: critical/severe COVID-19


title: TAZ KO F10 rep 1

description:
Library name: F10-1
F10-1

value: Placenta

value: Choriocarcinoma

value: CRISPR/Cas9  GFP, puro  integrated in TAZ/WWTR1 locus (DC-HTN2622223-D01-B)


title: ENZA-48h_rep3

description: ENZA-treated 48h sample rep3

value: ENZA-treated 48h


title: WT C5 rep 2

description:
Library name: C5-2
C5-2

value: CRISPR/Cas9 GFP, puro randomly integrated (DC-HTN2622223-D01-B)

value: wild-type


title: placenta_PRYA110/YA248

value: control


title: Left Ent-Pir Cx Exposed-2

description: Library name: O-Ent-gauche-Expo

value: Brain, left hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Brain cells

value: WT


title: placenta_PRYA148

value: placenta

value: placenta cells

value: asymptomatic COVID-19


title: ENZA-48h_rep2

description: ENZA-treated 48h sample rep2

value: Immortalized cell line LNCaP


title: Left Ent-Pir Cx Exposed-1

description: Library name: I-Ent-gauche-Expo

value: Exposure to 5G-3.5 GHz

value: C57 BL/6J


title: WT C5 rep 1

description:
Library name: C5-1
C5-1

value: Placenta


title: blood_PRYA49

source_name: whole blood

value: whole blood

value: blood cells

value: critical/severe COVID-19


title: Right Ent-Pir Cx Pseudo-exposed-8

description: Library name: W-Ent-droit-Pseudo

source_name: Brain, right hemisphere, area in the entorhinal-piriform cortex

value: Pseudo-exposure


title: ENZA-48h_rep1

description: ENZA-treated 48h sample rep1

value: ENZA-treated 48h


title: WT C4 rep 2

description:
Library name: C4-2
C4-2

value: Choriocarcinoma

value: CRISPR/Cas9 GFP, puro randomly integrated (DC-HTN2622223-D01-B)

value: wild-type


title: placenta_PRYA211

value: mild/moderate COVID-19


title: ENZA-24h_rep3

description: ENZA-treated 24h sample rep3

value: ENZA-treated 24h


title: Right Ent-Pir Cx Pseudo-exposed-6

description: Library name: H-Ent-droit-Pseudo

value: Brain, right hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Brain cells

value: WT


title: WT C4 rep 1

description:
Library name: C4-1
C4-1


title: Right Ent-Pir Cx Pseudo-exposed-5

description: Library name: K-Ent-droit-Pseudo


title: placenta_PRYA206/184-1

value: placenta

value: placenta cells


title: placenta_PRYA108/YA252

value: control


title: TAZsi treated, rep 3

description:
Library name: TAZsi_7
CC #7 2020-02-28, 16 #7, 72h, TAZ si

data_processing:
Read qualities were checked with FastQC.
Reads were mapped to the GRCh38 human genome primary assembly and counted using STAR (version 2.7.5).
Differential gene expression analysis was done using DESeq2 (version 1.22.0).
Assembly: GRCh38.p13
Supplementary files format and content: TAZsi_counttable.tsv is a tab-separated values file containing read counts for all samples, for genes with Ensembl gene IDs and gene symbols (GRCh38.p13 build)

growth_protocol: Trophoblast cells were seeded on fibronectin (20 µg/mL) coated cell culture dishes and were cultivated in DMEM/ Ham's F12 with GlutaMAX-I/ 10% fetal bovine serum/ 0.05 mg/mL gentamicin/ 0.5µg/mL fungizone.

treatment_protocol: For siRNA-mediated gene silencing Lipofectamine RNAiMAX (invitrogen) was used to transfect the trophoblasts with a mixture of four different siRNAs targeting TAZ (L-016083-00-0005; ON-TARGETplus SMARTpools; Dharmacon) or a nontargeting control pool (D-001810-10-20).

value: Placenta

value: Cell column cytotrophoblast

value: TAZ siRNA treated 72h

value: TAZ siRNA


title: control, rep 3

description:
Library name: ntcsi_7
CC #7 2020-02-28, 15 #7 ,72h, ntc si

value: ntc siRNA treated 72h

value: ntc siRNA


title: Right Ent-Pir Cx Pseudo-exposed-4

description: Library name: G-Ent-droit-Pseudo

value: Pseudo-exposure

value: C57 BL/6J


title: TAZsi treated, rep 2

description:
Library name: TAZsi_6
CC #6  2020-02-26, 10 #6  ,72h, TAZ si


title: placenta_PRYA176

value: asymptomatic COVID-19


title: placenta_PRYA209/133-1

value: critical/severe COVID-19


title: control, rep 2

description:
Library name: ntcsi_6
CC #6  2020-02-26, 9 #6, 72h ntc si


title: hnRNPC_WT2

description: Library name: hnRNPC_WT2

value: Human Embryonic Kidney


title: ENZA_24h, rep3

description: ENZA-treated 24h sample rep3

value: Immortalized cell line LNCaP

value: medium animo acid-labeled

value: ENZA-treated 24h


title: Right Ent-Pir Cx Pseudo-exposed-2

description: Library name: B-Ent-droit-Pseudo

value: Brain, right hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Brain cells

value: WT


title: placenta_PRYA132

value: placenta

value: placenta cells

value: control


title: Right Ent-Pir Cx Pseudo-exposed-7

description: Library name: V-Ent-droit-Pseudo


title: ENZA-12h_rep2

description: ENZA-treated 12h sample rep2

value: ENZA-treated 12h


title: ENZA-24h_rep2

description: ENZA-treated 24h sample rep2


title: Right Ent-Pir Cx Pseudo-exposed-1

description: Library name: 2-Ent-droit-Pseudo


title: ENZA-12h_rep3

description: ENZA-treated 12h sample rep3


title: ENZA-6h_rep3

description: ENZA-treated 6h sample rep3

value: ENZA-treated 6h


title: control, rep 1

description:
Library name: ntcsi_3
CC #3   2020-01-24, 9#3, 72h, ntc si

value: Placenta

value: Cell column cytotrophoblast

value: ntc siRNA treated 72h

value: ntc siRNA


title: ENZA-24h_rep1

description: ENZA-treated 24h sample rep1


title: placenta_PRYA186

value: mild/moderate COVID-19


title: ENZA-6h_rep2

description: ENZA-treated 6h sample rep2

value: Immortalized cell line LNCaP


title: placenta_PRYA215


title: ENZA-6h_rep1

description: ENZA-treated 6h sample rep1


title: DMSO_ctrl-rep3

description: DMSO-treated ctrl sample rep3

value: DMSO-treated ctrl


title: ENZA-12h_rep1

description: ENZA-treated 12h sample rep1


title: OMV-2

city: CHICAGO

first: Peng

middle: of

last: Xia

state: ILLINOIS

address: 929 E 57TH ST

department: chemistry

country: China

institute: University of chicago

data_processing:
CLC Genomics Workbench V 11.0.1
Assembly: GRCh38-hg38
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample

source_name: Colon26 cell mouse subcutaneous tumor

extract_protocol:
RNA was isolated
Total RNA was extracted by Trizol, and 1ug RNA was used for library construction.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: Colon26 cell mouse subcutaneous tumor

value: OMV


title: Right Ent-Pir Cx Exposed-6

description: Library name: 7-Ent-droit-Expo

value: Brain, right hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Exposure to 5G-3.5 GHz

value: C57 BL/6J


title: Right Ent-Pir Cx Exposed-5

description: Library name: J-Ent-droit-Expo

value: Brain cells

value: WT


title: OMV-1


title: OMV-3


title: MG63 Xenograft WT rep 2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

description:
MG63_Xeno_WT_199-5
xeno_os.raw_counts.tsv.gz

data_processing:
Trimmomatic (v0.32) was used to remove adaptor sequences and trim the reads with the cutoff phred33 >= 30 and length n >= 30.
Reads where aligned to the reference genome hg19 using STAR (v2.3.0e) and featureCounts (v1.4.4) was used to count reads uniquely mapped to the exon regions of genes from the ensGene Ensembl gene annotation (n = 60,234 genes).
Reads from xenograft tumors were aligned and counted using a custom hg19+mm10 reference. Downstream analysis only included reads uniquely aligned to hg19.
Assembly: hg19
Supplementary files format and content: tab-separated value files containing raw counts using the ensGene Ensembl gene hg19 reference. 1 column per sample.

source_name: Xenograft tumour

extract_protocol:
RNA was harvested using phenol-chloroform extraction
200-500 ng total RNA was submitted for sequencing. Poly-A mRNA enrichment as been used.

value: Xenograft tumour

value: Osteosarcoma


title: Right Ent-Pir Cx Exposed-4

description: Library name: D-Ent-droit-Expo


title: Right Ent-Pir Cx Exposed-7

description: Library name: 1-Ent-droit-Expo


title: MG63 Xenograft WT rep 1

description:
MG63_Xeno_WT_199-4
xeno_os.raw_counts.tsv.gz


title: Control group3

value: PBS


title: Right Ent-Pir Cx Exposed-3

description: Library name: A-Ent-droit-Expo


title: placenta_PRYA144-1

value: placenta

value: placenta cells

value: critical/severe COVID-19


title: MG63 Xenograft EZHIP over expression rep 3

description:
MG63_Xeno_EZHIP_201-4
xeno_os.raw_counts.tsv.gz

value: EZHIP


title: Control group1


title: Right Ent-Pir Cx Exposed-2

description: Library name: O-Ent-droit-Expo


title: DMSO_ctrl-rep2

description: DMSO-treated ctrl sample rep2

value: Immortalized cell line LNCaP


title: Right Ent-Pir Cx Exposed-1

description: Library name: I-Ent-droit-Expo


title: MG63 Xenograft EZHIP over expression rep 2

description:
MG63_Xeno_EZHIP_201-3
xeno_os.raw_counts.tsv.gz


title: DHT_48h_rep3

description: DHT-treated 48h sample rep3

value: DHT-treated 48h


title: WT_day21_rep1

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Assembly: GRCm38.96
Supplementary files format and content: Tab-delimited file including RAW counts for all samples

source_name: CD8+ T cells

extract_protocol:
To perform RNA-seq, we FACS-sorted brain CD8 GP33-41+ T cells from WT, MOG-GP, and IL-33 cKO MOG-GP mice at 21 days after rLCMV-GP33 infection. Each biological replicate (n = 3 for MOG-GP, n = 3 for IL-33 cKO MOG-GP and n = 1 pool of 4 WT mice) represents 104 sorted H-2Db-GP33-41-specific CD8+ T cells in RLT buffer with 1% ß-mercaptoethanol and processed with RNAeasy Micro Kit (Qiagen, 74004) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: CD8+ T cells

value: at 21 days after rLCMV-GP33 infection


title: DHT_48h_rep2

description: DHT-treated 48h sample rep2


title: MG63 Xenograft EZHIP over expression rep 1

description:
MG63_Xeno_EZHIP_200-3
xeno_os.raw_counts.tsv.gz


title: DHT_48h_rep1

description: DHT-treated 48h sample rep1


title: MOG-GP_day21_rep3


title: KHOS Xenograft WT rep 3

description:
KHOS_Xeno_WT_563-3
xeno_os.raw_counts.tsv.gz

value: KHOS


title: DHT_24h_rep3

description: DHT-treated 24h sample rep3

value: DHT-treated 24h


title: IL_33cKO

description: Library name: IL_33cKO

library_source: transcriptomic single cell

data_processing:
R1 reads were used to identify both cell barcodes and UMI using UMI-tools version 1.0.1 with the following settings: “--bc-pattern='(?P<cell_1>.{16})(?P<umi_1>.{12})' --extract-method=regex --knee-method=distance --method=umis --set-cell-number=15000 –ed-above-threshold=discard”
After read extraction and addition of cell barcodes and UMI to headers of R2 reads, fastq reads were mapped to the ENSEMBL reference genome using STAR version 2.7.1a with standard settings except that any reads mapping to more than one location in the genome (ambiguous reads) were discarded (m = 1)
All reads mapping in the proper orientation within exons and introns were reported using featureCounts version 1.6.4 UMI counts were calculated using UMI-tools with ‘--per gene --gene-tag=XT --assigned-status-tag=XS --per-cell’ arguments.
Assembly: GRCm38.96
Supplementary files format and content: Tab-separated table of gene counts per cell barcode

source_name: Brain

extract_protocol:
Freshly facs sorted CD45+ brain cells from MOG-GP and IL-33 cKO MOG-GP mice. Cells were adjusted to 5.5x105 cells/mL of PBS, 0.04% BSA before proceeding with droplet generation.
Library was performed according to the manufacter's instructions (single cell 3' V4 protocol, 10x Genomics; GC000731).

value: Brain

value: Lymphocyte

value: CD45+ cells

value: IL-33cKO MOG-GP


title: KHOS Xenograft WT rep 2

description:
KHOS_Xeno_WT_563-1
xeno_os.raw_counts.tsv.gz

value: Xenograft tumour

value: WT


title: Control group2

value: Colon26 cell mouse subcutaneous tumor

value: PBS


title: DMSO_ctrl-rep1

description: DMSO-treated ctrl sample rep1

value: DMSO-treated ctrl


title: KHOS Xenograft WT rep 1

description:
KHOS_Xeno_WT_563-10
xeno_os.raw_counts.tsv.gz

value: Osteosarcoma


title: KHOS Xenograft EZHIP over expression rep 3

description:
KHOS_Xeno_EZHIP_565-3
xeno_os.raw_counts.tsv.gz

value: EZHIP


title: CB3_2

city: Montreal

first: Christine

last: Vande Velde

state: QC

address: 900, rue Saint-Denis, R09.474

department: Neurosciences

institute: CRCHUM, Universite de Montreal

description: Library name: sample 7

data_processing:
RNA-seq
Aligner : STAR
QC : multiQC ; qualimap
Expression caller : Stringtie
DEG : R packages deseq2
Assembly: mm10
Supplementary files format and content: .txt files :  raw gene expression counts from Stringtie

extract_protocol:
Trizol
NEB rRNA-depleted (HMR) stranded library preparation

value: mouse erythroleukemia


title: CB3_3

description: Library name: sample 8


title: IL-33 cKO MOG-GP_day21_rep3


title: DHT_24h_rep2

description: DHT-treated 24h sample rep2

value: Immortalized cell line LNCaP


title: MOG_GP

description: Library name: MOG_GP

value: MOG-GP


title: CB3_1

description: Library name: sample 6


title: IL-33 cKO MOG-GP_day21_rep2

value: CD8+ T cells

value: at 21 days after rLCMV-GP33 infection


title: DHT_24h_rep1

description: DHT-treated 24h sample rep1

value: DHT-treated 24h


title: DHT_12h_rep2

description: DHT-treated 12h sample rep2

value: DHT-treated 12h


title: MOG-GP_day21_rep2


title: CB3_A1_3

description: Library name: sample 5


title: KHOS Xenograft EZHIP over expression rep 2

description:
KHOS_Xeno_EZHIP_565-2
xeno_os.raw_counts.tsv.gz

value: KHOS


title: IL-33 cKO MOG-GP_day21_rep1


title: DHT_6h_rep3

description: DHT-treated 6h sample rep3

value: DHT-treated 6h


title: KHOS Xenograft EZHIP over expression rep 1

description:
KHOS_Xeno_EZHIP_565-1
xeno_os.raw_counts.tsv.gz


title: DHT_12h_rep1

description: DHT-treated 12h sample rep1


title: CB3_A1_2

description: Library name: sample 4


title: MOG-GP_day21_rep1


title: U2OS cell line  EZHIP knock out rep 3

description:
U2OS_CL_EZHIP_KO_C54_C
cl_os.raw_counts.tsv.gz

value: EZHIP KO


title: CB3_A1_1

description: Library name: sample 3


title: MI_rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters
Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized.
Assembly: mm9
Supplementary files format and content: bigwig

source_name: MI oocytes

growth_protocol: Meiosis stage I oocytes were collected from mice

extract_protocol:
The total RNA of cells was extracted, followed the manufacturer’s instruction of Trizol Reagent (Invitrogen). KAPA HiFi HotStart DNA Polymerase (Roche) was used to amplify the cDNA.
The RNA-seq library was prepared using Nextera XT DNA Library Preparation Kit (Illumina), followed by the manufacturer’s instruction.

value: MI oocytes

tag: passages


title: DHT_6h_rep2

description: DHT-treated 6h sample rep2


title: CSS_ctrl_rep3

description: EtOH-treated ctrl sample rep3

value: EtOH-treated ctrl


title: CSS_ctrl_rep2

description: EtOH-treated ctrl sample rep2


title: U2OS cell line  EZHIP knock out rep 2

description:
U2OS_CL_EZHIP_KO_C54_B
cl_os.raw_counts.tsv.gz


title: MI_rep3


title: BVDV Transient Infection: 4 Months Postnatal PBMC DNA 2186

city: Fort Collins

first: Thomas

middle: R.

last: Hansen

state: Colorado

address: 3107 Rampart Road

department: Biomedical Sciences

institute: Colorado State University

description: Library name: Sample 10

library_source: genomic

data_processing:
Quality of reads were checked with fastqc 0.11.9, reads were trimmed with trimgalore 0.6.4_dev
Reads were mapped to the bosTau9 genome using bismark 0.22.3
Obtained bam files were analyzed with methylKit 1.24.0
Assembly: bosTau9
Supplementary files format and content: bedGraph files generated from bismark for each sample
Supplementary files format and content: comma-delimited files for diffrenetially methylated cytosines and regions

molecule: genomic DNA

organism: Bos taurus

source_name: PBMC

extract_protocol:
DNA was extracted from WBCs processed from whole blood using Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).
DNA samples were digested with 30 units of MspI, fragments purified with DNA Clean & Concentrator-5  and ligated to adapters with replacement of cytosine with 50-methyl-cytosine according to Illumina’s guidelines. Fragments greater than 50 base pairs were recovered and bisulfite treated using the EZ DNA Methylation-Lightning Kit . Samples were subjected to PCR with Illumina indices. Size and concentrations of purified products were confirmed with the Agilent 2200 TapeStation prior to sequencing on an Illumina platform

value: PBMC

value: White Blood Cells

value: BVDV Transient Infection


title: DHT_6h_rep1

description: DHT-treated 6h sample rep1


title: BVDV Transient Infection: 4 Months Postnatal PBMC DNA 2183

description: Library name: Sample 9


title: U2OS cell line parental EZHIP rep 2

description:
U2OS_CL_parental_C1_B
cl_os.raw_counts.tsv.gz

value: Osteosarcoma


title: U2OS cell line parental EZHIP rep 3

description:
U2OS_CL_parental_C1_C
cl_os.raw_counts.tsv.gz

value: EZHIP


title: CB3_A1B_2

description: Library name: sample 2

value: mouse erythroleukemia


title: ICF_RNA, WT-GSK-2

city: Kunming

first: meiqi

last: Lin

address: Kunming, Yunnan province

institute: LPBR

data_processing:
Raw data were filtered using fastp software (v 0.23.2), and reads were mapped to GRCm38 using HISAT2 (v 2.1.0), featureCounts (v 2.0.1) is used to count the reads mapped to each gene
Differential expression analysis between the two comparison sets was performed using DESeq2 software (1.40.2)
Analysis of transposon expression using Tetranscripts(v 2.2.3)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: mouse embryonic stem cells

growth_protocol: Mouse ES cells were cultured with the medium consist of DMEM (Gibco), 15% fetal bovine serum (FBS, Gibco (16000-004), 10ng/ml Recombinant Murine LIF, 0.1 mM non-essential amino acids (11146-050, Gibco), 0.1 mM PenStrep (15140-122, Gibco), 0.1 mM β-mercaptoethanol (21985-023, Gibco),1 mM GlutaMAX-1(35050-061, Gibco). The medium was changed daily, and cells were passaged every two days.

extract_protocol:
RNA extraction using the phenol/chloroform method,1 ug total RNA of each sample was used as the starting material to construct a transcriptome sequencing library
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02)

treatment_protocol: Stable cell lines were obtained. Mouse ESCs were cultured for 2 days then collected for RNA extractiona and RNA-seq.

value: mouse embryonic stem cells

value: WT


title: MI_rep1


title: U2OS cell line  EZHIP knock out rep 1

description:
U2OS_CL_EZHIP_KO_C54_A
cl_os.raw_counts.tsv.gz


title: CB3_A1B_1

description: Library name: sample 1


title: ICF_RNA, WT-GSK-1


title: MG63 cell line WT rep 3

description:
MG63_CL_WT_P19
cl_os.raw_counts.tsv.gz


title: BVDV Transient Infection: 4 Months Postnatal PBMC DNA 2106

description: Library name: Sample 7


title: BVDV Transient Infection: 4 Months Postnatal PBMC DNA 2169

description: Library name: Sample 8


title: HSJD-GBM01 WT 1

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Library name: HSJD_GBM01_WT_1

data_processing:
Data were mapped to the human genome (GRCh38) using gSNAP.
Expression (FPKM) was derived using Cufflinks.
Differential expression was analyzed with ANOVA in R.
Assembly: hg38
Supplementary files format and content: txt

growth_protocol: 1. HSJD-GBM01 cells were routinely generated by replating suspension cells typically 1.5-2x106 cells on a tissue culture flask in DMEM/F12 and Neurobasal-A media supplemented with 1% HEPES, 1% GlutaMAX-I, 1% Sodium Pyruvate, 1% AB/AM, 1% NEAA, 2% B-27 Supplement without Vitamin A, 20ng/mL hEGF, 20ng/mL hFGF, 10ng/mL hPDGF-AA, 10ng/mL hPDGF-BB and 2µg/mL Heparin. 2. SU-DIPG04 cells were routinely generated by replating adherent cells typically 1.5-2x106 cells on a tissue culture dish in DMEM/F12 and Neurobasal-A media supplemented with 1% HEPES, 1% GlutaMAX-I, 1% Sodium Pyruvate, 1% AB/AM, 1% NEAA, 2% B-27 Supplement without Vitamin A, 20ng/mL hEGF, 20ng/mL hFGF, 10ng/mL hPDGF-AA, 10ng/mL hPDGF-BB and 2µg/mL Heparin.

extract_protocol:
RNA-seq samples: Total RNA was extracted by ethanol precipitation in ddH2O using Qiagen miRNeasy Mini kit. 2µg of Total RNA was used.
RNA-seq

treatment_protocol: RNA-seq samples: 2x106 HSJD-GBM01 or SU-DIPG04 Cells were plated in a tissue culture dish on day 0 in triplicate for each group. Then, on day 1, cells were transduced with H3.3K27M or Empty Vector and shCD99 #1 and non-target control, respectively using 8ng/mL polybrene. On day 3, cells were treated with 2µg puromycin for selection. Cells were passaged regularly to maintain an MOI of 0.3. On day 7, Cells were collected in Qiazol and the total RNA was extracted. HSJD-GBM01 were collected in duplicates while SU-DIPG04 were collected as a single replicate.

value: Brain

value: glioblastoma

value: H3.3 WT

value: Puromycin selected

tag: batch


title: HSJD-GBM01 MT 2

description: Library name: HSJD_GBM01_MT_2

value: H3.3K27M Transduced


title: U2OS cell line parental EZHIP rep 1

description:
U2OS_CL_parental_C1_A
cl_os.raw_counts.tsv.gz


title: HSJD-GBM01 MT 1

description: Library name: HSJD_GBM01_MT_1


title: ICF_RNA, WT-DMSO-2


title: HSJD-GBM01 WT 2

description: Library name: HSJD_GBM01_WT_2


title: Hela cells, control, rep3

city: Temuco

first: Mauricio

middle: A.

last: Saez

address: Manuel Montt 56

country: Chile

institute: Universidad Catolica de Temuco

description: Library name: WT-3

data_processing:
Quality control was realized with fastqc,
adapter sequences and low-quality reads were removed with Trimgalore software.
Aligment was realized with STAR with GRCh38 as reference.
Counts on features was realized with HTseq-count
Differential expression was analyzed with Deseq2
Assembly: GRCh38
Supplementary files format and content: deseq2 count matrix

source_name: cell line

growth_protocol: Thermo Fisher, CA, USA) supplemented with 10% fetal bovine serum (FBS, Biological Industries, Israel) and 1% Penicillin 10,000 units/mL, streptomycin sulfate 100 mg/mL (P/S, SigmaAldrish, USA) at 37°C, 5% CO2 and 95% humidity. Stable transfections were performed using a pCAG-Cx46 vector, purchased from Vector Builder (Chicago, USA). Each transfection was performed using Lipofectamine 3000 (Invitrogen, Thermo Fisher, CA, USA) following the manufacturer's instructions and selection was made for 14 days by adding Blasticidin at a concentration of 10 µg/mL.

extract_protocol:
Total RNA from HeLa cells expressing pCAG-Connexin46 or untransfected was extracted with RNA-Solv® Reagent. 1 mL of RNA-Solv was added directly to the 3.5 cm culture plates with 80% confluence, it was pipetted to help with lysis and transferred to a tube where 200 µL of chloroform were added and vortexed for 15 seconds. It was incubated on ice for 10 min and centrifuged at 12,000 x g for 15 min. The aqueous phase was transferred to a new tube and 500 µL of isopropyl alcohol were added, the samples were incubated for 10 minutes and centrifuged at 12,000 x g for 10 minutes. The supernatant was discarded and the pellet was washed with 80% ethanol. Finally, it was centrifuged at 7500 x g for 5 minutes and the pellet was left to dry for 5 minutes. The pellet was suspended in nuclease-free water and quantified on a Nanoquant Plate in a TECAN infinite F200 equipment.
Total RNA extraction was digested with DNase I to avoid contamination with genomic DNA. RNA concentration was then measured with the Quant-iT™ RiboGreen® RNA Assay Kit and its integrity was determined with a Bioanalyzer 2100. RNA libraries were prepared with the IlluminaTruSeqTM RNA Kit (High Throughput Protocol) from according to the manufacturer's protocol. Briefly, 28S, 18S, 5.8S, and 5S rRNA were depleted from an initial 500 ng of total RNA from each sample type using the Ribo-Zero rRNA removal kit (human/mouse/rat). The rRNA depleted RNA was cleaved with divalent cations at elevated temperature. cDNA synthesis produced single-stranded DNA copies from the RNA fragmented by reverse transcription. After synthesis of the second strand cDNA, the ends were repaired and the 3' ends adenylated. Finally, the universal adapters were ligated to the cDNA fragments and PCR was performed to produce the final sequencing library.

value: cell line

value: Hela

value: Wild type


title: ICF_RNA, WT-DMSO-1


title: BVDV Transient Infection: 4 Months Postnatal PBMC DNA 2103

description: Library name: Sample 6


title: CSS_ctrl_rep1

description: EtOH-treated ctrl sample rep1

value: Immortalized cell line LNCaP

value: EtOH-treated ctrl


title: MG63 cell line WT rep 2

description:
MG63_CL_WT_P16
cl_os.raw_counts.tsv.gz


title: ICF_RNA, Cdca7-Dux-DKO-14-2

value: Cdca7/Dux double knockdown


title: MG63 cell line EZHIP over expression rep 3

description:
MG63_CL_EZHIP_P19
cl_os.raw_counts.tsv.gz


title: MG63 cell line WT rep 1

description:
MG63_CL_WT_P15
cl_os.raw_counts.tsv.gz


title: Hela cells, control, rep1

description: Library name: WT-1


title: ICF_RNA, Cdca7-KO-2-3

value: Cdca7 knockdown


title: ICF_RNA, Cdca7-Dux-DKO-14-1


title: Control: 4 Months Postnatal PMBC DNA 2156.

description: Library name: Sample 4

value: PBMC

value: White Blood Cells

value: control


title: Hela cells, Cx46 overexpression, rep3

description: Library name: Cx46-3

value: Cx46 over expression


title: MG63 cell line EZHIP over expression rep 2

description:
MG63_CL_EZHIP_P16
cl_os.raw_counts.tsv.gz

value: Osteosarcoma

value: EZHIP


title: MG63 cell line EZHIP over expression rep 1

description:
MG63_CL_EZHIP_P15
cl_os.raw_counts.tsv.gz


title: Control: 4 Months Postnatal PMBC DNA 2149.

description: Library name: Sample 3


title: Hela cells, Cx46 overexpression, rep2

description: Library name: Cx46-2


title: ICF_RNA, Cdca7-KO-2-2

value: mouse embryonic stem cells


title: Control: 4 Months Postnatal PMBC DNA 2147.

description: Library name: Sample 2


title: KHOS cell line WT rep 3

description:
KHOS_CL_WT_P188
cl_os.raw_counts.tsv.gz

source_name: KHOS

value: KHOS

value: WT


title: Hela cells, Cx46 overexpression, rep1

description: Library name: Cx46-1


title: ICF_RNA, Hells-Dux-DKO-21

value: Hells/Dux double knockdown


title: ICF_RNA, Hells-Dux-DKO-6


title: Control: 4 Months Postnatal PMBC DNA 2132.

description: Library name: Sample 1


title: KHOS cell line WT rep 2

description:
KHOS_CL_WT_P186
cl_os.raw_counts.tsv.gz


title: CUTTAG, BRD4, CBPKD, c14, repl2

city: Milan

first: Yinxiu

last: Zhan

address: via Adamello, 16

country: Italy

institute: European Institute of Oncology (IEO)

description: Library name: 230417_42_FRA_CUTTAG_fsh_715x174_nej-KD_st5_R2

data_processing:
The CUT&Tag data processing was done as in (Atinbayeva et al., 2024). Briefly, we used snakePipes version 2.4.0 (Bhardwaj et al., 2019) (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific Cut&Tag Bowtie2 alignment option  (--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700) was used. Since the Cut&Tag contains lambda phage spike-ins for reliable quantification of global effects, the libraries were mapped to a constructed hybrid genome of dm6 and lambda phage (NCBI GenBank ID: J02459.1). Macs2 was used to call Cut&Tag peaks using the following options: -g dm -q 0.05 --broad. Cut&Tag normalized signals were generated using bamCoverage from deepTools (v.2.5.7). More specifically, the relative dm6/lambda total number of reads was used as normalization factor to rescale each sample through the bamCompare option --scaleFactor. For samples with H3 Cut&Tag, the ratio between normalizations factors (H3 vs mark-specific Cut&Tag) was passed to bamCompare’s option –scaleFactor to account for differences in starting material. The coverage heatmaps were created using plotHeatmap from deepTools (v.2.5.7). To quantify the signal under the peaks, we integrated the normalized signal in a +/-1kb around each peak. Source code for data normalisation can be found https://github.com/zhanyinx/atinbayeva_paper_2023.
Assembly: dmel6
Supplementary files format and content: spike-in and H3 normalized bigwig file
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: The flies were reared under standard conditions (25 C) and transferred to cages to collect the embryos for further experiments.

extract_protocol:
CUT&Tag experiments were performed as described in Zenk, Cardamone et al., 2023 with small adaptations. Embryos were fixed with 1% of formaldehyde. Based on the developmental stage from before cycle 9 to cycle 14, 500, 150 or 50 hand-staged embryos were used for each antibody. To extract nuclei, embryos were lysed in 50 µL of Digitonin Wash Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 150 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.05% Digitonin (Millipore, #300410)). After lysis, nuclei were spin for 5 minutes at 600 g at 4 ºC and washed with 500 µL of Digitonin Wash Buffer to remove impurities. Following, 15 μL of BioMag ConcanavalinA beads (Polysciences, #86057-3) in Binding Buffer (20 mM HEPES (pH 7.5), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) were added to the sample and incubated on a wheel for 15 min at room temperature. For each condition, the pool of nuclei was split and histone H3 or another antibody was used, to use the same starting material for normalisation purposes. Next, the supernatant was removed by using a magnetic stand and beads were resuspended in 150 µL of Antibody Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 150 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.01% Digitonin (Millipore, #300410), 2 mM EDTA (ThermoScientific, #15575020) together with the respective antibody and incubated on a rocking platform at 4 ºC overnight. The following day, samples were mildly spin down and supernatant was removed with the help of a magnetic stand. Successively, the samples were washed twice with Antibody Wash Buffer, finally resuspended in 150 µL of Antibody Buffer supplemented with the secondary antibody and incubated for 1 hour at room temperature on a rocking platform. After two washes with Antibody Wash Buffer, the samples were resuspended in Digitonin Med Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 300 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 0.01% Digitonin (Millipore, #300410)) supplemented with the pA/G Tn5 (1:150) and incubated for 1 hour at room temperature on a rocking platform. The samples were mildly spin down and two washes were performed before starting the tagmentation reaction by adding 150 µL of Tagmentation Buffer (20 mM HEPES [pH 7.5] (Jena Bioscience, #CSS-511), 300 mM NaCl (Sigma Aldrich, #S6546), 0.5 mM Spermidine (Sigma Aldrich, #S0266), 5 mM sodium butyrate (Sigma Aldrich, #303410), Roche Protease Inhibitor (Sigma Aldrich, #11873580001), 10 mM MgCl2) and by incubating the reaction in a thermomixer for 1 hour at 37 ºC. The reaction was inhibited by adding 20 mM EDTA (final), 0.5% SDS (final) and 10 mg Proteinase K (final). The samples were incubated for 30 min at 55 ºC and another 20 min at 70 ºC. DNA purification was performed by using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205) following manufacturer instructions.
Libraries were prepared by supplementing the NEBNext HighFidelity 2x PCR Master Mix with 1 pg of Tn5-tagmented lambda DNA (New England Biolabs, #N3011S) spike-in as normalizer supplemented in the NEBNext HighFidelity 2x PCR Master Mix (New England Biolabs, #M0541S) for each sample. The indexing was performed using Illumina i5 and i7 (Buenrostro et al., 2015) through 15 cycles (1 x 5 min at 72 °C, 1 x 30 sec at 98°C, 13 x 10 s at 98 °C, 30 sec at 63 °C, 1 x 1 min at 72 °C, hold at 4 °C). The libraires were purified using Nucleomag NGS Clean-up and Size Select beads (Macherey-Nagel, #744970.50). Quality checks were done with Qbit DNA HS Assay (ThermoScientific, #Q32854) and Bioanalyser (Agilent, #5067-4626).  Finally, libaries were pooled and sent for next generation sequencing.

treatment_protocol: To induce RNAi mediated silencing of certain gene products, we employed the Gal4-UAS system. By crossing males of a Gal4 driver line (Bloomington #7063) to females of the fly RNAi collection TRiP1 we obtained an F1 generation depleted for E(z) (Bloomington #33695). For CBP, a homemade line was used (Ciabrelli et al., 2023). These females were crossed to siblings and produced embryos that were depleted of E(z) or CBP mRNA and protein. To enrich and collect exact stages of embryo development, the flies were allowed to lay eggs on apple juice agar plates in cages for one hour at 25 °C. Prior collection, egg laying of the flies was synchronized by changing plates for three consecutive times. After three pre-lays, the embryos were collected for one hours and aged 25 °C to reach the stage of interest.

value: embryos

tag: condition

value: CBP-KD

tag: Stage

value: cycle 14 (stage 5)

tag: antibody


title: Hela cells, Cx46 overexpression, ChIP Cx46

description: Library name: Cx46

data_processing:
Quality control was realized with fastqc,
adapter sequences and low-quality reads were removed with Trimgalore software.
Aligment was realized with bowtie2 with GRCh38 as reference.
ChIP-seq peak calling was done using MACS3 (q≤0.01)
Assembly: GRCh38
Supplementary files format and content: narrowPeak

source_name: Hela

extract_protocol:
Nuclear extracts were made from HeLa cells transfected with pCAG-Cx46, a total of 2e107 cells were washed with PBS and crosslinked with 1% Formaldehyde under gentle agitation at RT after 10 minutes glycine was added at a final concentration of 0.125M and incubated for an additional 10 minutes under agitation. The cells were washed with PBS 3 times and collected with the help of a cell scraper. Then the pellet was resuspended in 5 volumes of lysis buffer (50mM HEPES pH: 7.8, 3mM MgCl2, 20mM KCl, 0.1% NP-40, 2mM phenylmethylsulfonyl fluoride (PMSF), Aprotinin 2 µg/mL, Leupeptin 2 µg/mL and Pepstatin 1 µM) and incubated for 10 minutes on ice. Purified nuclei were obtained with a glass Dounce and verified by Trypan Blue. Nuclei were centrifuged and resuspended in Sonication Buffer (50 mM HEPES pH: 7.8, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% Sodium Dodecyl Sulfate, 2mM PMSF, Aprotinin 2 µg/mL, Leupeptin 2 µg/mL and Pepstatin 1 µM) and transferred to Bioruptor sonication tubes and sonicated for 50 minutes at 30 second intervals on a Bioruptor Pico sonication device. The degree of chromatin fragmentation was verified on a 1% agarose gel by decrosslinking an aliquot in a thermocycler at 95°C for 25 minutes, then 2 µg/mL of RNase A was added and incubated at 37°C for 15 minutes and finally Proteinase K 50 µg/mL was added and incubated for 15 minutes at 58°C. DNA was quantified using the Qubit dsDNA BR Assay Kit on a Qubit Fluorometer following the manufacturer's instructions
Libraries were prepared wit MicroPlex Library Preparation Kit v3  (Diagenode) unfer recommended protocol

value: Hela


title: Hela cells, control, rep2

description: Library name: WT-2

value: cell line

value: Wild type


title: Hela cells, Cx46 overexpression, Chromatin input

description: Library name: Input


title: CUTTAG, BRD4, CBPKD, c14, repl1

description: Library name: 230417_35_FRA_CUTTAG_fsh_715x174_nej-KD_st5_R1


title: KHOS cell line WT rep 1

description:
KHOS_CL_WT_P183
cl_os.raw_counts.tsv.gz


title: Control: 4 Months Postnatal PMBC DNA 2163.

description: Library name: Sample 5


title: FKH-1_input2ChIP

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

country: Germany

institute: Universitätsklinikum Halle

data_processing:
Adapters and low-quality bases  trimmed using Trimmomatic 0.38, alignment to a genome with bowtie2
Aligned reads filtered with samtools 1.9 (QV>30, concordantly aligned)
Duplicates removed with Picard 2.18.26
Assembly: hg38
Supplementary files format and content: TDF (generated from BAM files with: igvtools count -w 50 -z 5 -f mean --pairs)

growth_protocol: FKH-1 cells were grown in vitro in RPM1 supplemented with 20% FCS

extract_protocol:
Cells were fixed 5 minutes with 1% formaldehyde. After quenching with glycine and cell lysis, chromatin was sonicated with the Covaris S220
Illumina

treatment_protocol: cells were treated with vehicle (DMSO) or eltanexor 400 nM for 24h

value: acute myelocytic leukemia

tag: chip antibody

value: eltanexor 400 nM

tag: time


title: TAZsi treated, rep 1

description:
Library name: TAZsi_3
CC #3  2020-01-24, 10#3, 72h, TAZ si

value: Placenta

value: Cell column cytotrophoblast

value: TAZ siRNA treated 72h

value: TAZ siRNA


title: FKH-1_inputChIP

tag: cell line

value: DMSO


title: ICF_RNA, ZBTB24-Dux-DKO-23

value: mouse embryonic stem cells

value: ZBTB24/Dux double knockdown


title: CUTTAG, BRD4, WT, c14, repl1

description: Library name: 230417_07_FRA_CUTTAG_fsh_T180_WT_st5_R1

value: WT


title: CUTTAG, BRD4, WT, c14, repl2

description: Library name: 230417_14_FRA_CUTTAG_fsh_T180_WT_st5_R2


title: ICF_RNA, Hells-KO-2-2

value: Hells knockdown


title: FKH-1_eltanexor_NUP214ChIP


title: CUTTAG, RNAPII-S5P, CBPKD, c14, repl2

description: Library name: 20241030_16_FRA_CUTTAG_PolIIser5P_715x174_CBPKD_st5_R2

value: embryos


title: ICF_RNA, 2C-Cdca7-KO4

value: Cdca7 knockdown


title: FKH-1_eltanexor_XPO1ChIP


title: ICF_RNA, 2C-Cdca7-KO3


title: FKH-1_DMSO_NUP214ChIP


title: ICF_RNA, Hells-KO-2-3


title: hMSC cell line WT rep 3

description:
hMSC_CL_WT_rep3
cl_hMSC.raw_counts.tsv.gz

source_name: hMSC

value: hMSC

value: Human mesemchymal stem cells


title: hMSC cell line WT rep 2

description:
hMSC_CL_WT_rep2
cl_hMSC.raw_counts.tsv.gz


title: placenta_PRYA167-1

value: placenta

value: placenta cells

value: mild/moderate COVID-19


title: FKH-1_DMSO_XPO1ChIP

value: acute myelocytic leukemia


title: ICF_RNA, 2C-Cdca7-KO2


title: hMSC cell line WT rep 1

description:
hMSC_CL_WT_rep1
cl_hMSC.raw_counts.tsv.gz


title: Right Ent-Pir Cx Pseudo-exposed-3

description: Library name: 8-Ent-droit-Pseudo

data_processing:
Quality of raw data was evaluated with FastQC. Poor quality sequences and adapters were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.6.3) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.  Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Following analysis were conducted with R software. Data were normalized with DESeq2 (v1.26.0) or/and edgeR (v3.28.0) bioconductor packages, prior to differential analysis with glm framework likelihood ratio test from edgeR package, and/or DESeq2 workflow. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
Assembly: mm10 reference genome and quantification with gencode vM25 annotation gtf file
Supplementary files format and content: Rdata file containing the matrices of not-normalized counts of both genes and isoforms, same file for all samples

extract_protocol:
Tissue samples were extracted from a brain region covering adjacent area of the entorhinal and the piriform cortex (Ent-Pir Cx) of the right and the left hemispheres in 100 µm-thick coronal sections cut on a cryostat.Total RNA was extracted from the tissues samples  using RNeasy® Micro kit (QIAGEN). Quality of RNA was confirmed on Agilent TapeStation (RIN > 8).
RNA seq libraries were prepared using Illumina Stranded mRNA Prep kit (Illumina) and sequenced with Illumina NovaSeq 6000 platform (2 x 87 million reads with 100 nucleotides length per sample).

value: Brain, right hemisphere, area in the entorhinal-piriform cortex

value: Male

value: Brain cells

value: Pseudo-exposure

value: C57 BL/6J


title: 347956_exosomal_miRNA

city: Hefei

first: Qianqian

last: Tao

state: Anhui

address: Meishan Road, Shushan District, Hefei City, Anhui Province

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

data_processing:
filter the reads by removing the adapters at both ends, discarding reads with a fragment length <17 nt, and removing low-quality reads
Align the clean reads to the reference genome to obtain the distribution map of reads across the entire genome. Annotate the clean reads for non-coding RNA (ncRNA) classification.
Assembly: hg38
Supplementary files format and content: excel file include count value for each sample

source_name: plasma

extract_protocol:
The RNA from exosomes was extracted using a microRNA extraction kit, quantified, and used for subsequent sequencing.
The total RNA or purified small RNA fragments from the extracted samples were ligated with 3' and 5' adapters, reverse transcribed into cDNA, and then subjected to PCR amplification. The resulting libraries with the desired fragments were gel-purified, and the qualified libraries were sequenced.

treatment_protocol: Blood samples from liver cancer patients were collected before and after surgery for the isolation of plasma exosomes.

value: plasma

value: HCC

tag: disease state

value: HCC patient


title: CUTTAG, RNAPII-S2P, CBPKD, c14, repl1

description: Library name: 20241030_13_FRA_CUTTAG_PolIIser2P_715x174_CBPKD_st5_R1

value: CBP-KD

value: cycle 14 (stage 5)


title: ICF_RNA, 2C-Hells-KO2

value: mouse embryonic stem cells

value: Hells knockdown


title: KHOS cell line EZHIP over expression rep 3

description:
KHOS_CL_EZHIP_P188
cl_os.raw_counts.tsv.gz

value: KHOS

value: Osteosarcoma

value: EZHIP


title: CUTTAG, H3 RNAPII normalization, CBPKD, c14, repl2

description: Library name: 20241030_10_FRA_CUTTAG_H3_715x174_CBPKD_st5_R2

value: embryos


title: CUTTAG, H3 RNAPII normalization, CBPKD, c14, repl1

description: Library name: 20241030_09_FRA_CUTTAG_H3_715x174_CBPKD_st5_R1


title: KHOS cell line EZHIP over expression rep 2

description:
KHOS_CL_EZHIP_P186
cl_os.raw_counts.tsv.gz


title: hMSC cell line EZHIP over expression rep 3

description:
hMSC_CL_EZHIP_rep3
cl_hMSC.raw_counts.tsv.gz

value: hMSC

value: Human mesemchymal stem cells


title: ICF_RNA, ZBTB24-Dux-DKO-13

value: ZBTB24/Dux double knockdown


title: CUTTAG, RNAPII-S5P, CBPKD, c14, repl1

description: Library name: 20241030_15_FRA_CUTTAG_PolIIser5P_715x174_CBPKD_st5_R1


title: 349473_exosomal_miRNA

tag: treatment

value: Preoperative


title: KHOS cell line EZHIP over expression rep 1

description:
KHOS_CL_EZHIP_P183
cl_os.raw_counts.tsv.gz

tag: cell type


title: CUTTAG, RNAPII-S2P, CBPKD, c14, repl2

description: Library name: 20241030_14_FRA_CUTTAG_PolIIser2P_715x174_CBPKD_st5_R2


title: CUTTAG, RNAPII-S5P, WT, c14, repl1

description: Library name: 20241030_07_FRA_CUTTAG_PolIIser5P_T180_WT_st5_R1

value: WT


title: MB002-Cont3

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description: Biological replicate 3

data_processing:
nf-core/rnaseq v1.4.2
STAR Aligner was used to align trimmed reads
Aligned reads were annotated and quantified against the gencode comprehensive gene annotation release 38 (GRCh38.p13) using featureCounts of subread package v2.0.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include quantified reads from Subread package

growth_protocol: D425 cells were cultured in DMEM with 10% FBS and 1% P+S. MB002 cells were maintained in 1: 1 ratio of DMEM/F12 Glutamax and Neurobasal medium supplemented with B27 supplement, non-essential amino acids, 1 mM sodium pyruvate, 25 mM Hepes,  20 ng/ml epidermal growth factor (EGF), 20 ng/ml bFGF, 10 ng/ml LIF, 2 ng/ml heparin and 1% P+S.  CHLA01 and CHLA01R cells were cultured in DMEM/F12 with B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 1% P+S.

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell miniprep system (Promega). 600 ng of total RNA was used for the construction of sequencing libraries.
Library preparation was constructed using the TruSeq stranded total RNA Gold library preparation kit with RiboZero Gold treatment and unique dual indexes according to the manufacturer’s instructions
whole transcriptome RNA-seq with Ribosomal RNA depletion

treatment_protocol: Cells were treated either with BMP7 or LDN for 72 h. PBS and DMSO served as vehicles

value: Medulloblastoma-Group 3

tag: genotype

value: PBS


title: ICF_RNA, E14-2C-Dnmt3b-55

value: Dnmt3b knockdown


title: PBMC, LPVL, B6

city: Hurlingham

first: Hugo

last: Carignano

address: DR. NICOLAS REPETTO Y DE LOS RESEROS S/N

country: Argentina

institute: Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET)

data_processing:
Quality control (QC) and adapters trimming were performed with TrimGalore v0.6.4 using a q score > 20. Reads with length < 20 pb were discarded
QC-passed reads were mapped to the bovine reference genome ARS-UCD1.2 v100, using HISAT2 v2.2.0.
Genomic features (genes) were quantified using HTSeq-count v0.12.4 with the “union” mode, which counts only uniquely mapped reads and discards those overlapping with two or more genes.
Low-expressed genes were filter in edgeR (minimum count = 10 and minimum total count = 15). Differential expression analysis was conducted using the exact test based on the quantile-adjusted conditional maximum likelihood (qCML) method implemented in edgeR. Multiple comparisons were corrected using the Benjamini-Hochberg false discovery rate (q-value).
Assembly: ARS-UCD1.2 v100
Supplementary files format and content: Tab-delimited text files containing the following information for each sample: Ensembl Gene ID, Gene Symbol, Exon Number, and Raw Read Counts.
Supplementary files format and content: A comma-delimited file containing detailed information for each expressed gene, including: raw counts for each sample, gene location, log fold-change (logFC), log counts per million (logCPM), p-value, and q-value (adjusted p-value for multiple comparisons).

source_name: PBMCs

growth_protocol: Animals, which shared the same lactation period

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-Paque Plus (GE Healthcare, Uppsala, Sweden) density gradient centrifugation and resuspended in RNAlater® (Ambion, Austin, TX, USA). Total RNA was extracted with High Pure RNA Isolation Kit (Roche).
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA),

tag: tissue

value: PBMCs

value: Holstein

value: LPVL


title: PBMC, LPVL, B5


title: ICF_RNA, E14-2C-Dnmt3b-40

value: mouse embryonic stem cells


title: CUTTAG, RNAPII-S2P, WT, c14, repl1

description: Library name: 20241030_05_FRA_CUTTAG_PolIIser2P_T180_WT_st5_R1

value: cycle 14 (stage 5)


title: MB002-Cont2

description: Biological replicate 2


title: ICF_RNA, E14-2C-Dnmt3b-38


title: hMSC cell line EZHIP over expression rep 1

description:
hMSC_CL_EZHIP_rep1
cl_hMSC.raw_counts.tsv.gz


title: CUTTAG, RNAPII-S5P, WT, c14, repl2

description: Library name: 20241030_08_FRA_CUTTAG_PolIIser5P_T180_WT_st5_R2


title: CUTTAG, RNAPII-S2P, WT, c14, repl2

description: Library name: 20241030_06_FRA_CUTTAG_PolIIser2P_T180_WT_st5_R2


title: MB002-Cont1

description: Biological replicate 1


title: CUTTAG, H3 RNAPII normalization, WT, c14, repl2

description: Library name: 20241030_02_FRA_CUTTAG_H3_T180_WT_st5_R2


title: 349492_exosomal_miRNA

value: plasma

value: Postoperative

value: HCC patient


title: ICF_RNA, 2C-Hells-KO1

value: Hells knockdown


title: MB002-BMP3

description: Biological replicate 3

value: BMP7 ligand for 72 h


title: hMSC cell line EZHIP over expression rep 2

description:
hMSC_CL_EZHIP_rep2
cl_hMSC.raw_counts.tsv.gz

value: hMSC

value: Human mesemchymal stem cells

value: EZHIP


title: ICF_RNA, 2C-ZBTB24-KO1-2

value: ZBTB24 knockdown


title: PBMC, HPVL, A7

value: HPVL


title: ICF_RNA, 2C-WT-3

value: WT


title: PBMC, HPVL, A6


title: MB002-BMP2

description: Biological replicate 2

value: Medulloblastoma-Group 3


title: total, bulkRNAseq, E(z)-KD, c14, repl3

description: Library name: 220310_18_FRA_RNA_T09x174_EzKD_st5_rep3

data_processing:
RNA-seq data were processed using nf-core/rnaseq pipeline v 3.11.2 with default parameters.
Assembly: dmel6
Supplementary files format and content: raw gene count matrix, including all the samples.

molecule: nuclear RNA

extract_protocol:
Embryos were collected on apple juice agar plates. Embryos were submerged with halocarbon oil 27 (Sigma-Aldrich, #H8773) to allow hand-staging using a stereo-microscope. Embryos of the correct developmental stage were then transferred into 50 µl of Trizol (ThermoScientific, #15596026), dissociated with a tissue grinder and snap-frozen and stored at -80 °C until RNA extraction. The Trizol solution was defrosted and filled up to 500 µl supplemented with 1 µL of 1:1000 ERCC RNA spike-in (Ambion, #4456740). After the addition of 100 µl chloroform and mixing, the samples were spun down at 4 °C, 12.000 g for 15 min to separate the organic and aqueous phase. The aqueous phase was recovered and transferred into 300 µl of chloroform and the first step was repeated. Right after, the aqueous phase was transferred into isopropanol containing 20 µg of glycogen. The RNA was precipitated at -20 °C overnight and pelleted by centrifugation at 12.000 g for 60 min, 4 °C. The pellet was washed with 80% ethanol, air dried for 5 minutes and resuspended water. The RNA was quantified using Qubit RNA BR Assay kit (ThermoScientific, #Q10210) and integrity was assessed on agarose gels or the BioAnalyser (Agilent, #5067-4626).
Libraries were generated using the Illumina Stranded Total RNA-seq kit with Ribo-zero Plus (Illumina, #20072063) according to the manufacturer’s instructions followed by followed NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420). Libraries were pooled and sent for next generation sequencing.

value: embryos

value: EzKD

value: cycle 14


title: ICF_RNA, 2C-ZBTB24-KO1-1

value: mouse embryonic stem cells


title: ICF_RNA, E14-2C-Dnmt3b-5

value: Dnmt3b knockdown


title: CUTTAG, H3 RNAPII normalization, WT, c14, repl1

description: Library name: 20241030_01_FRA_CUTTAG_H3_T180_WT_st5_R1

value: cycle 14 (stage 5)


title: PBMC, LPVL, B7

value: PBMCs

value: Holstein

value: LPVL


title: MB002-BMP1

description: Biological replicate 1

value: BMP7 ligand for 72 h


title: PBMC, LPVL, B2


title: D425-Cont2

description: Biological replicate 2

value: PBS


title: total, bulkRNAseq, E(z)-KD, c14, repl1

description: Library name: 220310_16_FRA_RNA_T09x174_EzKD_st5_rep1


title: total, bulkRNAseq, E(z)-KD, c14, repl2

description: Library name: 220310_17_FRA_RNA_T09x174_EzKD_st5_rep2


title: 2C-Hells-KO2-1

data_processing:
Using FastQC and Trimmomatic for quality checking and quality control.
Employed Bowtie2 for genome indexing and reads mapping.
Utilized Samtools and grep for reads filtering and mitochondrial DNA removal.
Used Bedtools for BAM files intersection analysis.
Applied Samtools for BAM file indexing.
Employed bamCoverage for bigWig conversion and normalization.
Used computeMatrix and plotHeatmap for signal intensity matrix generation and visualization.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPGC values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
The sample used to perform ATAC-seq are prepared based on the commonly used method. AS for ATAC-seq, Cells were harvested and counted. Number of 50000~100000 cells were used for ATAC-seq.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stable cell lines were obtained. Mouse ESCs were cultured for 2 days then collected for DNA extractiona and Genome binding/occupancy profiling by high throughput sequencing.


title: ICF_RNA, 2C-WT-2


title: ICF_RNA, 2C-WT-1


title: total, bulkRNAseq, CBP-KD, c14, repl2

description: Library name: 220310_14_FRA_RNA_715x174_nejKD_st5_rep2

value: CBPKD


title: D425-Cont3

description: Biological replicate 3


title: PBMC, HPVL, A1


title: total, bulkRNAseq, CBP-KD, c14, repl1

description: Library name: 220310_13_FRA_RNA_715x174_nejKD_st5_rep1


title: D425-BMP3

description: Biological replicate 3


title: 2C-Cdca7-KO2-4


title: 2C-Cdca7-KO2-3


title: D425-BMP2

description: Biological replicate 2


title: total, bulkRNAseq, WT, c14, repl2

description: Library name: 220310_11_FRA_RNA_T180_WT_st5_rep2


title: D425-BMP1

description: Biological replicate 1


title: CHLA01R-LDN3

description: Biological replicate 3

value: Recurrent Medulloblastoma-Group 4

value: LDN


title: total, bulkRNAseq, WT, c14, repl3

description: Library name: 220310_12_FRA_RNA_T180_WT_st5_rep3


title: 2C-Cdca7-KO2-2


title: Primary differentiated adipocytes, Vehicle_8 Hrs, rep3

city: Indianapolis

first: Gabor

last: Varga

state: Indiana

address: Lilly Corporate Center

institute: Eli Lilly

hyb_protocol: Affymetrix protocol, ThermoFisher Human Clariom S Assay platform

scan_protocol: Affymetrix protocol

data_processing:
ProbeSummarizeEngine and GC-SST-RMA
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.mps

label: biotin

source_name: Human primary differentiated adipocytes

label_protocol: Affymetrix protocol

growth_protocol: Human primary differentiated adipocytes

extract_protocol: Flash frozen (500 mg) tissues were homogenized for 1-2 min in cold room. Total mRNA was prepared using miRNeasy Mini Kit (Qiagen Cat#1038703). cDNA was synthesized from 500 ng total RNA in a 20 µL reaction using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems Cat#4368814).

treatment_protocol: Adipocytes were differentiated as previously described and subsequently treated with insulin (100 nM), GIP (100 nM), insulin + GIP, or vehicle for 2, 8, and 24 h. RNA was collected and submitted for transcriptomic analysis utilizing the ThermoFisher Human Clariom S Assay platform.

value: primary differentiated adipocytes

value: Vehicle_8 Hrs


title: total, bulkRNAseq, CBP-KD, c14, repl3

description: Library name: 220310_15_FRA_RNA_715x174_nejKD_st5_rep3


title: Primary differentiated adipocytes, Vehicle_8 Hrs, rep2


title: 2C-Hells-KO2-2


title: D425-Cont1

description: Biological replicate 1

value: Medulloblastoma-Group 3

value: WT


title: Primary differentiated adipocytes, Vehicle_24 Hrs, rep3

value: Vehicle_24 Hrs


title: Primary differentiated adipocytes, Vehicle_24 Hrs, rep1


title: Primary differentiated adipocytes, Vehicle_24 Hrs, rep2


title: Primary differentiated adipocytes, Vehicle_2 Hrs, rep3

value: Vehicle_2 Hrs


title: 2C-ZBTB24-KO1-2

value: mouse embryonic stem cells


title: CHLA01R-LDN2

description: Biological replicate 2


title: total, bulkRNAseq, E(z)-KD, bfc9, repl3

description: Library name: 220310_09_FRA_RNA_T09x174_EzKD_0-1h_rep3

value: embryos

value: EzKD


title: E14-2C-1 embryonic stem cells


title: total, bulkRNAseq, WT, c14, repl1

description: Library name: 220310_10_FRA_RNA_T180_WT_st5_rep1

value: cycle 14


title: total, bulkRNAseq, E(z)-KD, bfc9, repl2

description: Library name: 220310_08_FRA_RNA_T09x174_EzKD_0-1h_rep2


title: Primary differentiated adipocytes, Vehicle_8 Hrs, rep1


title: E14-2C-2 embryonic stem cells


title: CHLA01R-LDN1

description: Biological replicate 1


title: total, bulkRNAseq, E(z)-KD, bfc9, repl1

description: Library name: 220310_07_FRA_RNA_T09x174_EzKD_0-1h_rep1


title: Primary differentiated adipocytes, Vehicle_2 Hrs, rep2


title: total, bulkRNAseq, CBP-KD, bfc9, repl3

description: Library name: 220310_06_FRA_RNA_715x174_nejKD_0-1h_rep3


title: CHLA01R-DMSO2

description: Biological replicate 2

value: DMSO


title: B cells, Th1 EAE model [Th1-CSP]

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

description:
10x genomics
2024.04.18_Th1-Th17.rds

data_processing:
To demultiplex samples, align the reads to the reference mouse mm10 genome, and process the raw data, we used the Cell Ranger Software (10X Genomics, v. 3.1.0). Following this, the unique molecule identifiers (UMIs) were summarized and the single-cells were filtered by the number of UMI counts identified. Then, we processed the gene matrices with R (v. 4.0.5) and the R package Seurat (v. 4.0.6 and 4.9.9) (56, 57). Cell hashing raw counts were normalized using centered log-ratio (CLR) transformation by comparing the counts of single cells to the geometric mean of the HTOs signal with subsequent logarithmic transformation. Cells with missing HTO signals or containing two different HTO-identifiers were removed from the further analysis. Further, the scRNA-seq count matrices were log-normalized and scaled by passing through only the cells containing more than 200 and less than 5000 genes with mitochondrial gene fractions below 5 %. Subsequently, the highly variable genes were identified with the vst method, and cells from each compartment were integrated using the canonical correlation analysis (CCA) method. The aligned BCR sequencing information was added into the metadata file of the Seurat object with subsequent removal of cells with missing BCR sequences. The cells were considered as expanded if at least 2 cells belonged to the same B cell clonotype. In the next step, 18413 cells were recovered and the corresponding PCA was computed using the previously identified highly variable genes. Based on the first 15 PCA dimensions, we constructed the Shared Nearest Neighbor (SNN) graph and clustered the cells by using the FindNeighbours and FindClusters functions of the Seurat R package. The following dimensional reduction was performed with the help of the Uniform Manifold Approximation and Projection (UMAP) method. One cluster, cluster 11, with markedly lower quality compared to the other clusters based on nFeature and nCount, was removed from further analysis. In addition, cluster 10 was identified as expressing macrophage/microglia markers and was therefore also excluded (based on AddModuleScore from Immgen Monocytes MHCIIhi blood vs Fo B cells spleen and Microglia CNS vs FoB form spleen). For identification of differentially upregulated genes per cluster, compartment, or expansion condition we used the FindMarkers function based on the log-transformed count matrices of each single cell by applying the Wilcoxon test and subsequent p-value adjustment with the Bonferroni correction, with logfc.threshold = 0.
Assembly: mm10
Supplementary files format and content: *.rds files countain the seurat object used for analysis with all the metadata, ClusterMarkers_Top50.csv countains the cluster markers and Signatures.xlsx the gene lists used for signature analysis

source_name: CNS

growth_protocol: Naïve MOG-specific CD4+ T cells, isolated from spleen and lymph nodes of 2D2 mice, were differentiated into Th1 or Th17 cells and restimulated with anti-CD3 and anti-CD28 antibodies. 48 h after restimulation, cells were collected and washed three times with PBS. In Th1-EAE, 1.7-3.2x106 IFNγ-producing cells were injected intraperitoneally (i.p.) into C57BL/6 recipients. In Th17-EAE, 4x106 IL-17A-producing cells were injected i.p. or intravenously (i.v.) into C57BL/6. Animals of both genders were used as donors, whereby male cells were injected only into male recipients. Clinical disease developed 8-15 days post transfer. Mice were monitored daily for the development of clinical signs of EAE, including classical and atypical disease signs, according to the following criteria: 0, no disease; 0.5, decreased tail tonus; 1, limp tail or mild balance defects; 1.5, limp tail and ataxia; 2, hind limb weakness, or severe balance defects that cause spontaneous falling over; 2.5, partial hind limb paralysis; 3, complete hind limb paralysis or very severe balance defects that prevent walking; 3.5, complete hind limb paralysis and partial front limb paralysis; 4, complete front and hind limb paralysis or inability to move body weight into a different position; 5, moribund state.

extract_protocol:
Recipient mice, which had been on a high score for several days to allow for continued immune cell infiltration, were sacrificed and perfused through the left cardiac ventricle with PBS. Brains were dissected by removing the skull using forceps and scissors, while spinal cords were flushed out from the bone column using a 21 gauge needle attached to a syringe filled with PBS. In addition, the vertebral column was opened to collect parts of meninges, which were still connected to the vertebrae. Then, brains and spinal cords were cut into pieces and digested for 30 min at 37 °C with DNase I (Sigma-Aldrich or Roche) at a concentration of 1 mg/ml and collagenase D (Roche) at a concentration of 3.75 mg/ml. Subsequently, the tissues were mashed and passed through a 70 μm cell strainer to prepare a single-cell suspension, followed by centrifugation at 350 g for 10 min at 4 °C. The cell pellet was resuspended in 5 ml 70 % Percoll (Cytiva), which was prepared by mixing 30 ml Percoll with 18 ml Percoll Mix Solution (mixture of 90 ml 10X PBS and 264 ml H2O). Then, the cell suspension was slowly and carefully overlaid with 5 ml 37 % Percoll, which was prepared by diluting the 70 % Percoll solution with 1X PBS, followed by centrifugation at 650 g for 30 min at 21 °C. Then, mononuclear cells were collected from the interface between the 70 % and 37 % layer and washed twice with T cell medium to remove residual Percoll. Finally, cells were either stimulated for intracellular cytokine staining or stained directly for flowcytometric analysis.
For each mouse, B cells from CNS, spleen and cLNs were pooled (90.000 B cells in total), centrifuged and, after a washing step, resuspended in PBS containing 0.04 % BSA at a concentration of 1000 cells/μl. The viability of cells was confirmed by staining with trypan blue solution. Further processing of samples was performed using the 10x Chromium Single Cell 5` Solution (Chromium Next GEM Single Cell V(D)J v1.1 with Feature Barcoding Technology for Cell Surface Protein, 10x Genomics) according to the manufacturer`s instructions. Prior to loading on the chip, 5000 cells of each compartment were labeled with anti-mouse hashtag oligonucleotide (HTO) antibodies (TotalSeq™-C0301/C0302/C0303, Biolegend) and pooled together. cDNA libraries were pooled and send for sequencing. scRNA-seq and scBCR-seq libraries were sequenced on NovaSeq S4 Flowcells using 150-bp paired-end reads and 8 bp for the i7 index, aiming for 50,000 reads per cell for gene expression and 5,000 reads per cell for BCR enrichment. Cell hashing libraries were sequenced on NovaSeq S1 Flowcells using 50-bp paired-end reads and 8 bp for the i7 index, aiming for 10,000 reads per cell.

value: CNS

value: CD45high CD11blow CD4- CD19+


title: B cells, Th1 EAE model [Th1-GEX]

description:
10x genomics
2024.04.18_Th1-Th17.rds


title: CHLA01R-DMSO1

description: Biological replicate 1


title: total, bulkRNAseq, CBP-KD, bfc9, repl2

description: Library name: 220310_05_FRA_RNA_715x174_nejKD_0-1h_rep2


title: Primary differentiated adipocytes, 100 nM Insulin_8 Hrs, rep3

value: 100 nM Insulin_8 Hrs


title: CHLA01R-Cont2

description: Biological replicate 2

value: PBS


title: B cells, Th17 EAE model, animal 3 [VDJ-A3]

description:
10x genomics
bcells_integrated_20220113_no11no10_reUMAP.rds
ClusterMarkers_Top50.csv
Signatures.xlsx

source_name: CNS, spleen, lymph nodes

value: CNS, spleen, lymph nodes


title: Primary differentiated adipocytes, Vehicle_2 Hrs, rep1


title: Primary differentiated adipocytes, 100 nM Insulin_8 Hrs, rep2


title: CHLA01R-Cont3

description: Biological replicate 3

value: Recurrent Medulloblastoma-Group 4


title: 2C-ZBTB24-KO1-1


title: CHLA01R-Cont1

description: Biological replicate 1


title: CHLA01R-DMSO3

description: Biological replicate 3


title: total, bulkRNAseq, WT, bfc9, repl2

description: Library name: 220310_02_FRA_RNA_T180_WT_0-1h_rep2


title: CHLA01R-BMP3

description: Biological replicate 3

value: BMP7 ligand for 72 h


title: Primary differentiated adipocytes, 100 nM Insulin_24 Hrs, rep3

value: primary differentiated adipocytes

value: 100 nM Insulin_24 Hrs


title: B cells, Th17 EAE model, animal 3 [CSP-A3]


title: B cells, Th17 EAE model, animal 2 [VDJ-A2]


title: total, bulkRNAseq, WT, bfc9, repl1

description: Library name: 220310_01_FRA_RNA_T180_WT_0-1h_rep1

value: WT


title: CHLA01R-BMP2

description: Biological replicate 2


title: Primary differentiated adipocytes, 100 nM Insulin_24 Hrs, rep1


title: Primary differentiated adipocytes, 100 nM Insulin_24 Hrs, rep2


title: CHLA01R-BMP1

description: Biological replicate 1


title: total, bulkRNAseq, CBP-KD, bfc9, repl1

description: Library name: 220310_04_FRA_RNA_715x174_nejKD_0-1h_rep1

value: CBPKD


title: total, bulkRNAseq, WT, bfc9, repl3

description: Library name: 220310_03_FRA_RNA_T180_WT_0-1h_rep3


title: B cells, Th17 EAE model, animal 2 [GEX-A2]


title: Multiome, scATACseq, EzKD, c14, rep1

data_processing:
Raw sequencing data were processed by Cell Ranger ARC v1 pipeline, using dmel6 as reference genome. Quality control and filtering were performed on RNA and ATAC data separately using Seurat version 4.3.0 (Hao et al.,2021), scanpy version 1.9.3 (Wolf, Angerer & Theis, 2018) and Signac version 1.10.0 (Stuart et al., 2021). For RNA sequencing assay, multiple datasets coming from different conditions were analysed together. Cells with less than 300 total counts, less than 200 detected genes, or more than 20% of counts originating from mitochondrial genes were discarded to retain high-quality cells. Putative doublets were identified and eliminated using doubletFinder_v3 (McGinnis et al., 2019). Following filtering, 22358 good quality cells were retained. Data was pre-processed applying Seurat NormalizeData() method.  To perform dataset integration, the anchor set was defined applying FindIntegrationAnchors() function on pre-selected features (obtained with SelectIntegrationFeatures() method). IntegrateData() function was further applied to compute the integration. To perform dimensionality reduction, 2000 high variable genes (HVGs) were identified using FindVariableFeatures() function and the PCA was computed on scaled data. UMAP visualization for the RNA assay was obtained with umap tool function from scanpy. For ATAC assay, the peak bed files from all replicates were imported into R, and a common set of peaks across datasets was generated using the reduce() function from GenomicRanges package version 1.52.1 (Lawrence et al.,2013). Low-quality peaks within the unified set were filtered out by retaining peaks with widths between 20 and 10000. For each dataset we quantified the unified peak set and quality control metrics were evaluated to exclude low-quality cells. Thresholds were selected individually for each replicate to ensure dataset-specific optimization. The filtered datasets were then merged to create a unique chromatin accessibility assay. ATAC counts matrix was normalised applying term frequency inverse document frequency (TF-IDF) method implemented in Signac. Dimensionality reduction was performed applying the Latent Semantic Indexing (LSI) technique using RunSVD() function and UMAP was computed utilizing 2 to 50 components from ‘lsi’ reduction, as the first dimension usually correlates with sequencing depth.  Single-cell profiling of gene expression and chromatin accessibility assays were combined in a unique Seurat object and cells passing QC in both modalities were retained. To represent RNA and ATAC modalities in the same UMAP space, we performed Weighted Nearest Neighbour (WNN) analysis. The co-embedding was computed on the WNN graph, constructed on a weighted combination of PCA and LSI obtained with FindMultiModalNeighbors() function.
Assembly: dmel6
Supplementary files format and content: rds file contains Seurat object obtained after filtering and data processing. It includes both modalities.

extract_protocol:
Control or KD embryos were independently collected for 1 hour on apple juice agar plates and aged at 25º C for 140 min to enrich cycle 14 timepoint. Dechorionation was performed for 2 min with 50% “bleach” solution: sodium hypochlorite (6-14% active chlorine). Embryos were collected in a 70-µm pore size sieve and washed with distilled water. Dechorionated embryos were transferred to 1.5 mL Wash Buffer (10 mM Tris-HCl [pH 7.4] (Sigma-Aldrich, # T2194), 10 mM NaCl (Sigma-Aldrich, #S6546), 3 mM MgCl2 (Sigma-Aldrich, #M1028), 1% BSA, 0.1% Tween-20 (Sigma-Aldrich, #P9416)). Hand-staging of cycle 14 embryos is performed on a cooling station under a microscope with transmitted light according to their morphology. Nuclei were isolated according to the protocol provided from 10X Genomics (demonstrated protocol CG000366, Rev A) with small adaptations. Around 100 embryos are immediately transferred into 50 μL of 0.1X Lysis Buffer composed by diluting 1X Lysis Buffer (10 mM Tris-HCl [pH 7.4] (Sigma-Aldrich, # T2194), 10 mM NaCl (Sigma-Aldrich, #S6546), 3 mM MgCl2 (Sigma-Aldrich, #M1028), 1% BSA (Sigma-Aldrich, #A9418), 0.1% Tween-20 (Sigma-Aldrich, #P9416), 0.1% NP-40 (Sigma-Aldrich, #CA630), 0.01% Digitonin (Millipore, #300410)) with Lysis Dilution Buffer (10 mM Tris-HCl [pH 7.4] (Sigma-Aldrich, #T2663), 10 mM NaCl (Sigma-Aldrich, #S6546), 3 mM MgCl2 (Sigma-Aldrich, #M1028), 1% BSA (Sigma-Aldrich, #A9418)) and supplemented with 1U/μL RiboLock RNAse inhibitor (ThermoScientific, #EO0381). The lysis is performed in a 0.5 mL glass douncer (Kimble, #885300-0000) by applying 5 strockes. The lysate is incubated 3 min on ice and the reaction is stopped by adding 100 μL of Wash Buffer. The nuclei suspension is transferred in a protein low-binding 1.5 mL tube containing 350 μL of Wash Buffer and immediately centrifuged at 600 g for 5 min at 4º C. The supernatant is removed and the pellet is resuspended in 1 mL of Wash Buffer and filtered through a 10-µm pore size sieve (Cell Strainer, # 43-10010-50). The flow-through is centrifuged at 600 g for 5 min at 4º C. Integrity and roundness of nuclei was checked by staining 10 μl of nuclei suspension with DAPI. Successively, nuclei were counted using a Trypan Blue assay (ThermoScientific, #T10282) on the automated cell counter Countess (ThermoScientific). Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338). Quality checks were done with Qbit DNA HS Assay (ThermoScientific, #Q32854) and Tapestation (Agilent, #5067-4626).  Finally, libaries were pooled and sent for next generation sequencing.
Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide, CG000338). Quality checks were done with Qbit DNA HS Assay (ThermoScientific, #Q32854) and Bioanalyser (Agilent, #5067-4626).  Finally, libaries were pooled and sent for next generation sequencing.
scMultiome

value: T09, Bloomington #33695

value: cycle 14 (stage 5)

tag: library type

value: ATAC


title: Primary differentiated adipocytes, 100 nM Insulin_8 Hrs, rep1


title: B cells, Th17 EAE model, animal 3 [GEX-A3]


title: CHLA01-Cont3

description: Biological replicate 3

value: Medulloblastoma-Group 4


title: Primary differentiated adipocytes, 100 nM Insulin_2 Hrs, rep3

value: 100 nM Insulin_2 Hrs


title: Multiome, scATACseq, EzKD, c14, rep2

value: embryos

value: EzKD


title: B cells, Th17 EAE model, animal 2 [CSP-A2]

value: CD45high CD11blow CD4- CD19+


title: Primary differentiated adipocytes, 100 nM Insulin_2 Hrs, rep2


title: CHLA01-Cont2

description: Biological replicate 2


title: B cells, Th17 EAE model, animal 1 [VDJ-A1]


title: Multiome, scATACseq, CBPKD, c14, rep2

value: V20 RNAi CBP attP2


title: Multiome, scATACseq, CBPKD, c14, rep1


title: B cells, Th17 EAE model, animal 1 [GEX-A1]


title: CHLA01-Cont1

description: Biological replicate 1

value: PBS


title: Multiome, scATACseq, WT, c14, rep2

value: T180, Bloomington #36303


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_8 Hrs, rep3

value: 100 nM Insulin + 100 nM hGIP_8 Hrs


title: CHLA01-BMP3

description: Biological replicate 3

value: BMP7 ligand for 72 h


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_8 Hrs, rep2

value: primary differentiated adipocytes


title: FLCNKO_old_F4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Transcriptome profile of control FlcnLiKO female mouse, 90- weeks of age, biological rep4

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files including raw counts

source_name: liver

extract_protocol:
For gene expression analyses, total RNA was extracted according to the manufacturer's instructions (RNeasy Mini Kit). Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: liver

tag: age

tag: Sex

value: Female

value: FlcnLiKO


title: CHLA01-BMP2

description: Biological replicate 2

value: WT


title: Primary differentiated adipocytes, 100 nM Insulin_2 Hrs, rep1


title: FLCNKO_old_F3

description: Transcriptome profile of control FlcnLiKO female mouse, 90- weeks of age, biological rep3


title: CHLA01-BMP1

description: Biological replicate 1


title: FLCNKO_old_F2

description: Transcriptome profile of control FlcnLiKO female mouse, 90- weeks of age, biological rep2


title: Multiome, scRNAseq, EzKD, c14, rep2

value: T09, Bloomington #33695

value: cycle 14 (stage 5)

value: mRNA


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_8 Hrs, rep1


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_24 Hrs, rep3

value: 100 nM Insulin + 100 nM hGIP_24 Hrs


title: Multiome, scRNAseq, EzKD, c14, rep1

value: embryos


title: Multiome, scRNAseq, CBPKD, c14, rep2

value: CBPKD


title: YBX1-IN2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: YBX1 size-matched input control

data_processing:
Following sequencing, raw reads were aligned to GRCh38 and analyzed following a previously published pipeline (Nostrand et al, 2016)
Consistent with the ENCODE standard 65, reads aligning to artifact-enriched or repetitive genomic regions were removed
Reproducible and significant peaks of aligned reads were defined as IDR cutoff of 0.01, P ≤ 0.001, and fold enrichment ≥8.
Genic regions of eCLIP peaks were annotated based on overlap with GENCODE v26 transcripts following the priority order consistent with the previous study
Assembly: GRCh38
Supplementary files format and content: wig files represent read covergae for plus and minus strands
Supplementary files format and content: peak files

source_name: Human iPSC cell lines CV-B (46, XY)

growth_protocol: 5 × 10^7 CVB hiPSC-derived motor neurons (Gift from Goldstein Lab) were differentiated on 15cm plates to synaptic maturity at Day 28. Subsequent protocol was followed as detailed in Markmiller et. Al, Cell Rep. 2021. One plate was used for each eCLIP replicate.

extract_protocol:
CVB motor neuron cultures were treated with 400mJ of UV using the CL-1000 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with NONO antibody-bound Dynabeads. Subsequent protocol was followed as detailed in Van Nostrand et al, Methods Mol Biol 2017. Sequencing was performed on Illumina Novaseq 6000 single-end reads and data processed through Dr. Yeo's seCLIP pipeline.
Libraries were constructed as per the (s)eCLIP protocol using Illumina 50x forward and 70x reverse primers.
seCLIP

treatment_protocol: No treatment

value: hiPSC-derived neuron

tag: strain

value: Motor Neuron


title: Multiome, scATACseq, WT, c14, rep1

value: ATAC


title: YBX1-IN1

description: YBX1 size-matched input control


title: YBX1-IP2

description: YBX1 IP

value: anti-YBX1 (eCLIP): Bethyl A303-230A


title: Multiome, scRNAseq, CBPKD, c14, rep1

value: V20 RNAi CBP attP2


title: B cells, Th17 EAE model, animal 1 [CSP-A1]

value: CNS, spleen, lymph nodes

value: CD45high CD11blow CD4- CD19+


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_24 Hrs, rep2

value: primary differentiated adipocytes


title: FLCNKO_old_F1

description: Transcriptome profile of control FlcnLiKO female mouse, 90- weeks of age, biological rep1

value: liver

value: Female


title: FLCNKO_old_M4

description: Transcriptome profile of control FlcnLiKO male mouse, 90- weeks of age, biological rep4

value: Male

value: FlcnLiKO


title: FLCNKO_old_M3

description: Transcriptome profile of control FlcnLiKO male mouse, 90- weeks of age, biological rep3


title: Multiome, scRNAseq, WT, c14, rep2

value: T180, Bloomington #36303

value: WT

value: cycle 14 (stage 5)


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_2 Hrs, rep3

value: 100 nM Insulin + 100 nM hGIP_2 Hrs


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_24 Hrs, rep1

value: 100 nM Insulin + 100 nM hGIP_24 Hrs


title: YBX1-IP1

description: YBX1 IP

value: hiPSC-derived neuron


title: FLCNKO_old_M2

description: Transcriptome profile of control FlcnLiKO male mouse, 90- weeks of age, biological rep2


title: DDX3X-IN2

description: DDX3X size-matched input control

value: Motor Neuron


title: Multiome, scRNAseq, WT, c14, rep1

value: embryos

value: mRNA


title: FLCNKO_old_M1

description: Transcriptome profile of control FlcnLiKO male mouse, 90- weeks of age, biological rep1


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_2 Hrs, rep2


title: Primary differentiated adipocytes, 100 nM hGIP_8 Hrs, rep3

value: 100 nM hGIP_8 Hrs


title: DDX3X-IN1

description: DDX3X size-matched input control


title: CUTTAG, GAF, CBPKD, c14, repl2

data_processing:
The CUT&Tag data processing was done as in (Atinbayeva et al., 2024). Briefly, we used snakePipes version 2.4.0 (Bhardwaj et al., 2019) (parameters: --trim --fastqc --properPairs –dedup --mapq 1) with specific Cut&Tag Bowtie2 alignment option  (--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700) was used. Since the Cut&Tag contains lambda phage spike-ins for reliable quantification of global effects, the libraries were mapped to a constructed hybrid genome of dm6 and lambda phage (NCBI GenBank ID: J02459.1). Macs2 was used to call Cut&Tag peaks using the following options: -g dm -q 0.05 --broad. Cut&Tag normalized signals were generated using bamCoverage from deepTools (v.2.5.7). More specifically, the relative dm6/lambda total number of reads was used as normalization factor to rescale each sample through the bamCompare option --scaleFactor.  For samples with H3 Cut&Tag, the ratio between normalizations factors (H3 vs mark-specific Cut&Tag) was passed to bamCompare’s option –scaleFactor to account for differences in starting material. The coverage heatmaps were created using plotHeatmap from deepTools (v.2.5.7). To quantify the signal under the peaks, we integrated the normalized signal in a +/-1kb around each peak. Source code for data normalisation can be found https://github.com/zhanyinx/atinbayeva_paper_2023.
Assembly: dmel6
Supplementary files format and content: spike-in and H3 normalized bigwig file
Library strategy: CUT&Tag

value: V20 RNAi CBP attP2

value: CBPKD

value: GAF


title: FLCNKO_young_F4

description: Transcriptome profile of control FlcnLiKO female mouse, 12- weeks of age, biological rep4

value: liver


title: DDX3X-IP2

description: DDX3X IP

value: anti-DDX3X (human iPSC ICC, rodent AP-MS, eCLIP):Bethyl Laboratories A300-474A; RRID:AB_451009


title: FLCNKO_young_F3

description: Transcriptome profile of control FlcnLiKO female mouse, 12- weeks of age, biological rep3

value: Female


title: DDX3X-IP1

description: DDX3X IP


title: CUTTAG, Zld, CBPKD, c14, repl2

value: Zld


title: CUTTAG, CBP, CBPKD, c14, repl2

value: CBP


title: CUTTAG, H3 cofactors normalization, CBPKD, c14, repl2


title: FPAH 46-e-cig

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

institute: University of Macau

description: SAMPLE 8

data_processing:
Hisat2
FeatureCounts
Assembly: hg38
Supplementary files format and content: Raw reads of genome-wide genes for RNA-seq.

source_name: iPSC-ECs

growth_protocol: iPSCs were differentiated into endothelial cells using a monolayer chemically-defined methods.

extract_protocol:
RNA was extrated using the a Direct-zol RNA Kit with DNA digestion, and collected total RNA was used for RNA-seq
RNA-seq construction protocol of Illumina.

treatment_protocol: iPSC-ECs were seeded into 6 well plates and once they reached 60-70% confluency, cells were treated with and without e-cigarette extraction for 24 hours.

value: FPAH

value: e-cig extract

value: iPSC-derived endothelial cells


title: Primary differentiated adipocytes, 100 nM hGIP_8 Hrs, rep2

value: primary differentiated adipocytes


title: FLCNKO_young_F2

description: Transcriptome profile of control FlcnLiKO female mouse, 12- weeks of age, biological rep2

value: FlcnLiKO


title: FPAH 46-untreated

description: SAMPLE 7

value: Vehicle


title: FLCNKO_young_F1

description: Transcriptome profile of control FlcnLiKO female mouse, 12- weeks of age, biological rep1


title: Primary differentiated adipocytes, 100 nM hGIP_8 Hrs, rep1


title: FLCNKO_young_M4

description: Transcriptome profile of control FlcnLiKO male mouse, 12- weeks of age, biological rep4

value: Male


title: CUTTAG, Zld, CBPKD, c14, repl1

value: embryos

value: cycle 14 (stage 5)


title: Primary differentiated adipocytes, 100 nM hGIP_24 Hrs, rep2

value: 100 nM hGIP_24 Hrs


title: Primary differentiated adipocytes, 100 nM Insulin + 100 nM hGIP_2 Hrs, rep1

value: 100 nM Insulin + 100 nM hGIP_2 Hrs


title: Primary differentiated adipocytes, 100 nM hGIP_24 Hrs, rep3


title: Primary differentiated adipocytes, 100 nM hGIP_24 Hrs, rep1


title: FPAH 29-e-cig

description: SAMPLE 6


title: CUTTAG, CBP, CBPKD, c14, repl1

value: V20 RNAi CBP attP2

value: CBPKD


title: CUTTAG, H3 cofactors normalization, CBPKD, c14, repl1


title: Primary differentiated adipocytes, 100 nM hGIP_2 Hrs, rep3

value: 100 nM hGIP_2 Hrs