title: KD-rescued with AKAP-WT-CHIP-Seq

city: Changsha

first: Bi

last: Shi

address: #2 Lushan South Road

institute: Hunan University

description:
Library name: AKAP_THP1_KD_rescue_AKAP_WT/ChIP-seq
ChIP-seq

data_processing:
For ChIP-seq, Reads were aligned to the human reference genome hg19 (GRCh37) using bowtie2 version 2.3.2. The ChIPseq peaks from each sample were called at P <10-4 with MACS2. Bigwig files were generated with Homer softwares. For Pro-seq, data were analyzed according to the protocol described in Mahat, D.et al. Nat Protoc 11, 1455–1476 (2016).
Assembly: hg19
Supplementary files format and content: bigwig for ChIP-seq and Pro-seq

growth_protocol: Hela cells were cultured in DMEM (Gibco) with 10% FBS and 100 ug/mL Pen/Strep.THP-1 cells were cultured in RPMI1640 (Gibco) with 10% FBS and 100 ug/mL Pen/Strep.

extract_protocol:
For Chip-seq, genomic DNA was pulled down by antibodies. For Pro-seq, nascentRNA was extracted according to the protocol described in Mahat, D.et al. Nat Protoc 11, 1455–1476 (2016).
For ChIP-seq, library was prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For Pro-seq, libraries were constructed according to the protocol described in Mahat, D.et al. Nat Protoc 11, 1455–1476 (2016).

value: Human monocytic cell line

value: wild-type with overexpression of AKAP-WT

value: AKAP-KD cells rescued with AKAP-WT


title: TSC_plus_DOX_2_input

status: Public on Nov 11 2025

type: SRA

city: Tianjin

first: Chunxiao

last: Chen

state: Tianjin

address: Xuefu Road

department: College of Life Science

country: China

institute: Nankai University

library_source: transcriptomic

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MeRIP-seq

molecule: total RNA

organism: Homo sapiens

extract_protocol:
For RNA-seq and MeRIP-seq, total RNA was extracted with TRIzol reagent. CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, 50,000 cells were collected and washed twice in pre-cold PBS without DNase. Nuclei were isolated, lysed, and incubated with Tn5 transposase according to the manufacturer’s protocol (Vazyme, TD501). Transposed DNA was isolated using a DNA Clean & Concentrator kit (Zymo).
For RNA-seq, Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). For MeRIP-seq, The NEBNext® Ultra™ II RNA Library Prep Kit (NEB, E7770) was used to construct libraries for both the input and IP samples. For CUT&Tag, Library preparation and amplification was followed by manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, Libraries were prepared by amplifying DNA for 12 cycles using the TruePrep DNA Library Prep Kit (Vazyme). After amplification, libraries were purified using VAHTS DNA Clean Beads (Vazyme).

tag: cell line

tag: cell type

value: trophoblast stem cell

tag: genotype

value: WT

tag: treatment

value: DOX


title: TSC_plus_DOX_1_input


title: OPC, Cortex, repeat-1

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

description: GABA Con1

data_processing:
Clean reads after filtering were aligned to the reference genome with HISAT.
Bowtie2 were used to align the clean reads to the reference genes.
Differential expression analysis was performed using DESeq2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xlsx file includes normalized read count.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Cortex

growth_protocol: For Cultured OPC, OPC were isolated and cultured in OPC proliferation medium for 2 days, followed by 200 uM GABA or 200 uM Glutamate treatment for 24 h, then subjected to RNA sample collection by Trizol.

extract_protocol:
For acute-isolated OPC, Mice were anesthetized and transcardially perfused with ice-cold HBSS. The brains were isolated with the meninges removed, followed by dissection of the cortex and hippocampus, which were then minced and digested by 1% papain. OPCs were isolated from the resulting cell suspension via immunopanning and directly lysed on the panning plate by Trizol.
Poly-A selected method was used to prepare the RNA-seq library. Sequencing was performed on the DNBSEQ platform with SE50 sequencing length

tag: tissue

value: Cortex

value: Cultured OPC

value: wild type


title: TSC_min_DOX_P3_1_IP

value: KO

value: wo DOX P3


title: TSC_min_DOX_P3_2_IP


title: KD-rescued with ZF-mut-CHIP-Seq

description:
Library name: AKAP_THP1_KD_rescue_ZF_mut/ChIP-seq
ChIP-seq

library_source: genomic

molecule: genomic DNA

value: wild-type with overexpression of ZF-mut

value: AKAP-KD cells rescued with ZF-mut


title: KD-rescued with PS-mut-CHIP-Seq

description:
Library name: AKAP_THP1_KD_rescue_PS_mut/ChIP-seq
ChIP-seq

value: wild-type with overexpression of PS-mut

value: AKAP-KD cells rescued with PS-mut


title: H3K27me3_CUT_Tag_TSCM_D3_noDOX

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CUT&Tag

value: embryonic stem cells

value: METTL3 inducible knockout


title: KD-rescued with vector control-CHIP-Seq

description:
Library name: AKAP_THP1_KD_rescue_control/ChIP-seq
ChIP-seq

value: Human monocytic cell line

value: wild-type

value: AKAP-KD cells rescued with vector control


title: THP1 OE of JD-PI95Scr-PRO-Seq

description:
Library name: THP1_OE_JD-PI95Scr/Pro-seq
Pro-seq

library_source: other

data_processing:
For ChIP-seq, Reads were aligned to the human reference genome hg19 (GRCh37) using bowtie2 version 2.3.2. The ChIPseq peaks from each sample were called at P <10-4 with MACS2. Bigwig files were generated with Homer softwares. For Pro-seq, data were analyzed according to the protocol described in Mahat, D.et al. Nat Protoc 11, 1455–1476 (2016).
Assembly: hg19
Supplementary files format and content: bigwig for ChIP-seq and Pro-seq
Library strategy: PRO-Seq

molecule: other

value: wild-type with overexpression of JD-PI95Scr

value: THP1 cells with overexpression of JD-PI95Scr


title: TSC_plus_DOX_1_IP

value: trophoblast stem cell

value: WT

value: DOX


title: TSC_plus_DOX_2_IP


title: THP1 OE of JD-PI95-PRO-Seq

description:
Library name: THP1_OE_JD-PI95/Pro-seq
Pro-seq

value: wild-type with overexpression of JD-PI95

value: THP1 cells with overexpression of JD-PI95


title: H3K27me3_CUT_Tag_TSCM_D3_DOX


title: ATAC_TSCMINDOXP2_2

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

value: KO

value: wo DOX P2


title: ATAC_TSCMINDOXP2_1


title: THP1 OE of vector-PRO-Seq

description:
Library name: THP1_OE_vector/Pro-seq
Pro-seq

value: THP1 cells with vector control


title: KD-rescued with ZF-mut-PRO-Seq

description:
Library name: Hela_KD_rescue_ZF_mut/Pro-seq
Pro-seq

source_name: Hela

value: Hela

value: cervical cancer cells

value: wild-type with overexpression of ZF-mut

value: AKAP-KD cells rescued with ZF-mut


title: ATAC_TSCPLUSDOX_2


title: KD-rescued with PS-mut-PRO-Seq

description:
Library name: Hela_KD_rescue_PS_mut/Pro-seq
Pro-seq

value: wild-type with overexpression of PS-mut

value: AKAP-KD cells rescued with PS-mut


title: ATAC_TSCPLUSDOX_1


title: KD-rescued with AKAP-WT-PRO-Seq

description:
Library name: Hela_KD_rescue_AKAP_WT/Pro-seq
Pro-seq

value: wild-type with overexpression of AKAP-WT

value: AKAP-KD cells rescued with AKAP-WT


title: JUND_P3_2


title: HUDEP-2_ASO12_ATAC

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

description: Library name: sample1

data_processing:
Adaptor sequence were trimmed from raw reads with Trim_Galore (v0.6.6) with the –nextera parameter.
The processed reads were mapped to human genome with Bowtie (v1.1.2) with parameter -k 1 and -m 1.
Duplicates were removed using MarkDuplicates with parameter --REMOVE_DUPLICATES true
To create the coverage track, bam file was converted to bed file with BEDTools (v2.25.0). The resulting BED files were converted to WIG format, followed by conversion to BigWig format using the wigToBigWig command from the UCSC Kent Utilities.
Assembly: hg38
Supplementary files format and content: bigWig format

source_name: cell line

extract_protocol:
ATAC-seq was performed using Zymo-Seq ATAC Library Kit (Zymo D5458) following manufacturer’s instructions.
Amplified DNA was collected with column and validated with Aligent Analyzer 4200.

value: cell line

value: human erythroid progenitor cells

value: E+58 ASO treated


title: JUND_P3_1

value: trophoblast stem cell


title: SCD_CD34_sg1617_ATAC

description: Library name: sample10

source_name: Bone marrow

value: Bone marrow

value: SCD CD34+ HSPCs

value: sg1617 edited


title: SCD_CD34_AAVS_ATAC

description: Library name: sample9

value: AAVS edited


title: JUND_P0_2

value: WT


title: HUDEP-2_E58_ASO23_H3K27me3 CUT&Run

description: Library name: sample33

data_processing:
Sequencing reads were processed by removing adapter sequences using Cutadapt (v4.4).
Processed FASTQ files were aligned to the human genome (hg38) using bowtie2 (v2.4.2).
Peaks calling was performed using MACS2 (v2.1.1) from BED files.
The resulting BED files were converted to WIG format, followed by conversion to BigWig format.
Assembly: hg38
Supplementary files format and content: bigWig format
Library strategy: CUT&Run

extract_protocol:
DNA from the pAG-MNase reaction was extracted using either SPRIselect beads or the DNA Clean & Concentrator-5 kit (ZYMO, D4014).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645L) amd size selected with SPRIselect beads for Illumina Nextseq2000 sequencing.


title: JUND_P0_1


title: HUDEP2_Ctrl_ASO_H3K27me3 CUT&Run

description: Library name: sample31

value: Control ASO treated


title: K27ac_P3_2

value: KO


title: HUDEP-2_E58_ASO12_H3K27me3 CUT&Run

description: Library name: sample32


title: K27ac_P3_1


title: HUDEP-2_C-12andC-7KO_H3K27me3_CUT&Run_rep2

description: Library name: sample30

value: C-12 and C-7 double knockout


title: K27ac_P0_1


title: K27me3_P3_2


title: HUDEP-2_C-12andC-7KO_H3K27me3_CUT&Run_rep1

description: Library name: sample29


title: liver, CuC, rep10

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

description: Library name: S12e

library_source: transcriptomic single cell

data_processing:
The count files in RDS format were acquired from fastq files using zUMIs.
Assembly: GRCh38 (mouse), GRCh38 (human), B73-NAM 5.0 (maize)
Supplementary files format and content: RDS for raw counts; h5ad for the filted barcodes and combined datasets.

molecule: nuclear RNA

organism: Mus musculus

source_name: liver

extract_protocol:
The cells were fixed directly with 10x volumes of methanol at -20°C. The murine tissues were lyzed by pestle in a pH3 citrate buffer or a lysis buffer contaning a RNase inhibitor. The maize roots and shoots were dissociated with dounce homogenizer (20 strokes) in spermidine- or divalent cation-containing buffers supplemented with the RNase inhibitor. The released nuclei from these tissues were filtered through 800-mesh-size nylon membrane, purified using iodixanol density-gradient centrifugation (30%), and fixed in a organic solvent as with the cells.
The barcoded cells/nuclei containing cDNA were lyzed. The cDNA were tailed with a PCR handle using TdT. Following second-strand systhesis and preamplification with KAPA HiFi, the cDNA were purified with carboxylic paramagnetic beads in a PEG/NaCl solution. The eluted DNA were tagmenmented with Tn5 and amplified with KAPA HiFi using primers containg P5 and P7 ends and multiplex indices. The amplified products were subjected to size selection, targeting libraries with peaks in the 450bp region.

value: liver

value: whole organ

value: mixed

value: one-pot lysis


title: HUDEP-2_sg1617_CTCF_15bp CUT&Run

description:
Library name: sample26
HUDEP-2_sg1617_CTCF_13bp_15bp_mean.bw

value: sg1617 edited -15bp INDEL


title: K27ac_P0_2


title: HUDEP-2_sg1617_CTCF_13bp CUT&Run

description:
Library name: sample25
HUDEP-2_sg1617_CTCF_13bp_15bp_mean.bw

value: cell line

value: sg1617 edited -13bp INDEL


title: HUDEP-2_C-12andC-7KO_CTCF_CUT&Run_rep2

description: Library name: sample28

value: human erythroid progenitor cells


title: HUDEP-2_C-12andC-7KO_CTCF_CUT&Run_rep1

description: Library name: sample27


title: K27me3_P0_2

value: trophoblast stem cell


title: liver, CuC, rep9

description: Library name: S12d


title: K27me3_P3_1


title: HUDEP-2_sg1617_CTCF_1bp CUT&Run

description: Library name: sample24

value: sg1617 edited +1bp INDEL


title: HUDEP-2_CTCF_CUT&Run_rep2

description:
Library name: sample23
HUDEP-2_CTCF_rep1_2_mean.bw

value: wild-type


title: HUDEP-2_NIPBL_CUT&Run_rep1

description: Library name: sample21


title: HUDEP-2_CTCF_CUT&Run_rep1

description:
Library name: sample22
HUDEP-2_CTCF_rep1_2_mean.bw


title: liver, CuC, rep8

description: Library name: S12c


title: RNA stability_KO_6h_2

value: wo DOX/ActD 6h


title: liver, CuC, rep7

description: Library name: S12b


title: K27me3_P0_1


title: liver, CuC, rep6

description: Library name: S12a


title: HUDEP-2_sg1617_SMC1_1bp CUT&Run

description: Library name: sample18


title: HUDEP-2_sg1617_SMC1_13bp CUT&Run

description:
Library name: sample19
HUDEP-2_sg1617_SMC1_13bp_15bp_mean.bw


title: HUDEP-2_sg1617_SMC1_15bp CUT&Run

description:
Library name: sample20
HUDEP-2_sg1617_SMC1_13bp_15bp_mean.bw


title: RNA stability_KO_6h_1


title: liver, CuC, rep5

description: Library name: S11e


title: RNA stability_KO_4h_2

value: wo DOX/ActD 4h


title: HUDEP-2_SMC1_CUT&Run_rep2

description:
Library name: sample17
HUDEP-2_SMC1_rep1_2_mean.bw


title: HUDEP-2_SMC1_CUT&Run_rep1

description:
Library name: sample16
HUDEP-2_SMC1_rep1_2_mean.bw


title: HUDEP-2_sg1617_H3K27me3_15bp CUT&Run

description:
Library name: sample15
HUDEP-2_sg1617_H3K27me3_13bp_15bp_mean.bw
HUDEP-2_sg1617_vs_WT_H3K27me3_log2.bw


title: HUDEP-2_sg1617_H3K27me3_13bp CUT&Run

description:
Library name: sample14
HUDEP-2_sg1617_H3K27me3_13bp_15bp_mean.bw
HUDEP-2_sg1617_vs_WT_H3K27me3_log2.bw


title: RNA stability_KO_4h_1


title: liver, CuC, rep4

description: Library name: S11d

value: WT


title: HUDEP-2_EnhKO_H3K27me3_CUT&Run_rep1

description:
Library name: sample11
HUDEP-2_EnhKO_H3K27me3_rep1_2_mean.bw
HUDEP-2_EnhKO_vs_WT_H3K27me3_log2.bw

value: enhancer knockout


title: liver, CuC, rep3

description: Library name: S11c


title: RNA stability_KO_2h_2

value: KO

value: wo DOX/ActD 2h


title: liver, CuC, rep2

description: Library name: S11b

value: liver


title: HUDEP-2_exon2mut_56_H3K27me3_CUT&Run_rep2

description:
Library name: sample10
HUDEP-2_exon2mut_H3K27me3_rep1_2_mean.bw
HUDEP-2_exon2mut_vs_WT_H3K27me3_log2.bw

value: exon2 mutant


title: HUDEP-2_exon2mut_51_H3K27me3_CUT&Run_rep1

description:
Library name: sample9
HUDEP-2_exon2mut_H3K27me3_rep1_2_mean.bw
HUDEP-2_exon2mut_vs_WT_H3K27me3_log2.bw


title: HUDEP-2_H3K27me3_CUT&Run_rep2

description:
Library name: sample8
HUDEP-2_H3K27me3_rep1_2_mean.bw


title: liver, CuC, rep1

description: Library name: S11a

value: whole organ

value: mixed


title: HUDEP-2_H3K27me3_CUT&Run_rep1

description:
Library name: sample7
HUDEP-2_H3K27me3_rep1_2_mean.bw


title: RNA stability_KO_2h_1


title: RNA stability_KO_0h_2

value: wo DOX/ActD 0h


title: pancreas, CuC, rep3

description: Library name: S10c

source_name: pancreas

value: pancreas

value: one-pot lysis


title: SCD_CD34_sg1617_H3K27me3 CUT&Run

description:
Library name: sample6
SCD_CD34_sg1617_vs_AAVS_H3K27me3_log2.bw

source_name: Bone Marrow

value: Bone Marrow

value: CD34+ HSPCs

value: sg1617 edited


title: RNA stability_KO_0h_1

value: trophoblast stem cell


title: SCD_CD34_AAVS_H3K27me3 CUT&Run

description:
Library name: sample5
SCD_CD34_sg1617_vs_AAVS_H3K27me3_log2.bw

value: AAVS edited


title: CD34_sg1617_H3K27me3_CUT&Run_rep2

description:
Library name: sample4
CD34_sg1617_H3K27me3_rep1_2_mean.bw
CD34_sg1617_vs_AAVS_H3K27me3_log2.bw


title: pancreas, CuC, rep2

description: Library name: S10b


title: RNA stability_DOX_6h_2

value: DOX/ActD 6h


title: HUDEP-2_sg1617_H3K27me3_1bp CUT&Run

description: Library name: sample13

value: cell line

value: human erythroid progenitor cells

value: sg1617 edited +1bp INDEL


title: pancreas, CuC, rep1

description: Library name: S10a

value: WT


title: CD34_AAVS_H3K27me3_CUT&Run_rep2

description:
Library name: sample2
CD34_AAVS_H3K27me3_rep1_2_mean.bw
CD34_sg1617_vs_AAVS_H3K27me3_log2.bw


title: RNA stability_DOX_6h_1


title: HUDEP-2_EnhKO_H3K27me3_CUT&Run_rep2

description:
Library name: sample12
HUDEP-2_EnhKO_H3K27me3_rep1_2_mean.bw
HUDEP-2_EnhKO_vs_WT_H3K27me3_log2.bw

value: enhancer knockout


title: CD34_AAVS_H3K27me3_CUT&Run_rep1

description:
Library name: sample1
CD34_AAVS_H3K27me3_rep1_2_mean.bw
CD34_sg1617_vs_AAVS_H3K27me3_log2.bw


title: CD34_sg1617_H3K27me3_CUT&Run_rep1

description:
Library name: sample3
CD34_sg1617_H3K27me3_rep1_2_mean.bw
CD34_sg1617_vs_AAVS_H3K27me3_log2.bw


title: RNA stability_DOX_4h_2

value: DOX/ActD 4h


title: HUDEP-2_sg1617_PROseq_15bp

description: Library name: sample5

data_processing:
Raw sequencing reads were aligned to the human genome (hg38) using BWA-MEM (v0.7.16a).
Duplicates reads were reomved using Duplicate reads were removed using the MarkDuplicates tool from the Picard suite (http://broadinstitute.github.io/picard/) with parameter --REMOVE_DUPLICATES true.
Forward and reverse strand reads were separated using the following SAMtools parameters: forward strand (-f 128 -F 16 and -f 80) and reverse strand (-f 144, -f 64 -F 16) using SAMtools (v1.17).
BigWig files were generated with a 1 bp bin size normalized with CPM (Counts Per Million) using deepTools (v3.5.4).
To identify transcriptional start site (TSS) from PRO-seq and PRO-cap data, the 5’ ends from bam files were separated into forward and reverse strands using SAMtools (v1.17) with the parameters -F 16 and -bg 5, and converted to BEDgraph files. TSS was then identified using the TSScall tool with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig Format and BED format
Library strategy: PRO-Seq

extract_protocol:
Nuclear RNA from run-on reactions with biotin-labeled CTP and UTP was extracted using the Total RNA Purification Kit (Norgen Biotek, 17200). Biotin-labeled newly transcribed RNA was captured on Dynabeads Streptavidin C1, followed by multiple on-bead processing steps, including adaptor ligation. The RNA was then purified using TRIzol reagent.
Reverse transcribed cDNA was amplified by UltraII Q5 polymerase and cleaned-up by SPRIselect beads and following Illumina Nextseq2000 sequencing.


title: HUDEP-2_sg1617_PROseq_13bp

description: Library name: sample4


title: MESC cells, Difluoromethylornithine and BENSpm, plate 8

city: Derio

first: Arkaitz

last: Carracedo

address: Bizkaia Science and Technology Park, building 801A

country: Spain

institute: CIC bioGUNE

description:
Library name: ESC_DFMO_BENSpm_24
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

data_processing:
RNA-seq  reads were aligned usig Vast-tools v2.5.1 to identify alternative splicing events.
Aligned reads from single and paired datasets were merged with Vast-tools v2.5.1.
Differentially spliced events were identified using Matt v.1.3.0 with a minimum abs(deltaPSI) > 10% and a Wilcoxon p-value < 0.01 after excluding events with PSIRANGE_ALL = NA and LENGTH= 0.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes PSI values for each sample

source_name: MESC

growth_protocol: DNEM, 15% fetal bovine serum, 2 mM glutamine, 1 x penicillin/streptomycin. Cells were cultured at 37C at 5% Coxigen.

extract_protocol:
RNA was extracted using NucleoSpin RNA isolation kit from Macherey-Nagel.
RNA libraries were prepared using Illumina Stranded mRNA Library Prep Kit following manufacture's protocol.

treatment_protocol: Mice in a mixed background were housed under controlled environmental conditions, such as time-controlled lighting on standard 12:12 light: dark cycles, controlled temperature at 22 ± 2ºC and 30-50% relative humidity. Mice were fed regular chow diet ad libitum and fasted for 6 h prior to tissue harvest (9 am-3 pm) to prevent metabolic alterations due to immediate food intake.

value: MESC

value: Mouse Embryonic Stem Cells

value: Difluoromethylornithine (50μM) and BENSpm (10μM) for 48 hours


title: MESC cells, Difluoromethylornithine and BENSpm, plate 7

description:
Library name: ESC_DFMO_BENSpm_17
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_sg1617_PROseq_1bp

description: Library name: sample3


title: RNA stability_DOX_4h_1


title: MESC cells, Difluoromethylornithine and BENSpm, plate 5

description:
Library name: ESC_DFMO_BENSpm_03
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_PROseq_rep2

description: Library name: sample2

value: wild-type


title: RNA stability_DOX_2h_2

value: DOX/ActD 2h


title: RNA stability_DOX_2h_1


title: HUDEP-2_E58_ASO23_NIPBL_CUT&Tag

description: Library name: sample28

data_processing:
Sequencing reads were processed by removing adapter sequences using Cutadapt (v4.4).
Processed FASTQ files were aligned to the human genome (hg38) using bowtie2 (v2.4.2).
Peaks calling was performed using MACS2 (v2.1.1) from BED files.
The resulting BED files were converted to WIG format, followed by conversion to BigWig format.
Assembly: hg38
Supplementary files format and content: bigWig format
Library strategy: CUT&Tag

extract_protocol:
After quenching the pAG-Tn5 reaction, DNA was directly amplified using non-hot start Q5 DNA polymerase.
DNA was amplified using Q5 High-Fidelity DNA Polymerase (NEB M0491) and purified with SPRIselect beads (Beckman B23318).

value: E+58 ASO treated


title: HUDEP-2_E58_ASO12_NIPBL_CUT&Tag

description: Library name: sample27


title: MESC cells, Difluoromethylornithine, plate 8

description:
Library name: ESC_DFMO_23
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: Difluoromethylornithine (50μM) for 48 hours


title: HUDEP-2_PROcap_rep2

description: Library name: sample2

data_processing:
Raw sequencing reads were aligned to the human genome (hg38) using BWA-MEM (v0.7.16a).
Duplicates reads were reomved using Duplicate reads were removed using the MarkDuplicates tool from the Picard suite (http://broadinstitute.github.io/picard/) with parameter --REMOVE_DUPLICATES true.
Forward and reverse strand reads were separated using the following SAMtools parameters: forward strand (-f 128 -F 16 and -f 80) and reverse strand (-f 144, -f 64 -F 16) using SAMtools (v1.17).
BigWig files were generated with a 1 bp bin size normalized with CPM (Counts Per Million) using deepTools (v3.5.4).
To identify transcriptional start site (TSS) from PRO-seq and PRO-cap data, the 5’ ends from bam files were separated into forward and reverse strands using SAMtools (v1.17) with the parameters -F 16 and -bg 5, and converted to BEDgraph files. TSS was then identified using the TSScall tool with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig Format, BED format
Library strategy: PRO-Seq

extract_protocol:
Nuclei RNAs from run-on reactions with four biotin-labeled NTPs were extracted using the Total RNA Purification Kit (Norgen Biotek, 17200). Biotin-labeled newly transcribed RNA was captured on Dynabeads Streptavidin C1, followed by multiple on-bead processing steps, including adaptor ligation. The RNAs were then purified using TRIzol reagent.
Reverse transcribed cDNA was amplified by UltraII Q5 polymerase and cleaned-up by SPRIselect beads and following Illumina Nextseq2000 sequencing.


title: HUDEP-2_Ctrl_ASO_NIPBL_CUT&Tag

description: Library name: sample26

value: Control ASO treated


title: RNA stability_DOX_0h_2

value: trophoblast stem cell

value: DOX/ActD 0h


title: MESC cells, Difluoromethylornithine, plate 7

description:
Library name: ESC_DFMO_16
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_sg1617_NIPBL_13bp_CUT&Tag

description:
Library name: sample24
HUDEP-2_sg1617_NIPBL_13bp_15bp_mean.bw

value: sg1617 edited -13bp INDEL


title: HUDEP-2_sg1617_NIPBL_1bp_CUT&Tag

description: Library name: sample23

value: cell line


title: HUDEP-2_NIPBL_CUT&Tag_rep2

description: Library name: sample22

value: human erythroid progenitor cells


title: MESC cells, Difluoromethylornithine, plate 5

description:
Library name: ESC_DFMO_02
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: MESC cells, Difluoromethylornithine, plate 6

description:
Library name: ESC_DFMO_09
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: CD34_sg1617_H3K27ac_CUT&Tag_rep2

description:
Library name: sample15
CD34_sg1617_H3K27ac_rep1_2_mean.bw

value: Bone marrow

value: CD34+ HSPCs

value: sg1617 edited


title: control_1

value: KO

value: wo DOX P3 control


title: MESC cells, SAM486A and BENSpm, plate 8

description:
Library name: ESC_SAM486A_BENSpm_27
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: MESC

value: Mouse Embryonic Stem Cells

value: SAM486A (0,5μM) and BENSpm (10μM) for 48 hours


title: HUDEP-2_PROseq_rep1

description: Library name: sample1

value: wild-type


title: A485_2

value: wo DOX P3+A485


title: MESC cells, Difluoromethylornithine and BENSpm, plate 6

description:
Library name: ESC_DFMO_BENSpm_10
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: Difluoromethylornithine (50μM) and BENSpm (10μM) for 48 hours


title: CD34_AAVS_H3K27ac_CUT&Tag_rep2

description:
Library name: sample13
CD34_AAVS_H3K27ac_rep1_2_mean.bw

value: AAVS edited


title: CD34_AAVS_H3K27ac_CUT&Tag_rep1

description:
Library name: sample12
CD34_AAVS_H3K27ac_rep1_2_mean.bw


title: A485_1

value: trophoblast stem cell


title: HUDEP-2_PROcap_rep1

description: Library name: sample1


title: HUDEP-2_C-12andC-7KO_H3K27ac_CUT&Tag_rep1

description: Library name: sample10

value: CTCF knockout


title: HUDEP-2_sg1617_NIPBL_15bp_CUT&Tag

description:
Library name: sample25
HUDEP-2_sg1617_NIPBL_13bp_15bp_mean.bw

value: sg1617 edited -15bp INDEL


title: HUDEP-2_sg1617_H3K27ac_15bp_CUT&Tag

description:
Library name: sample9
HUDEP-2_sg1617_H3K27ac_rep1_2_mean.bw

value: cell line


title: T4MINUSDOXP2_rep2

value: wo DOX P2


title: MESC cells, SAM486A and BENSpm, plate 5

description:
Library name: ESC_SAM486A_BENSpm_06
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: RNA stability_DOX_0h_1

value: WT

value: DOX/ActD 0h


title: T4MINUSDOXP2_rep1


title: HUDEP-2_EnhKO_H3K27ac_CUT&Tag_rep2

description:
Library name: sample6
HUDEP-2_EnhKO_H3K27ac_rep1_2_mean.bw

value: human erythroid progenitor cells

value: sg1617 edited


title: HUDEP-2_sg1617_H3K27ac_1bp_CUT&Tag

description: Library name: sample7


title: control_2

value: KO

value: wo DOX P3 control


title: CD34_sg1617_H3K27ac_CUT&Tag_rep1

description:
Library name: sample14
CD34_sg1617_H3K27ac_rep1_2_mean.bw

value: Bone marrow

value: CD34+ HSPCs


title: HUDEP-2_EnhKO_H3K27ac_CUT&Tag_rep1

description:
Library name: sample5
HUDEP-2_EnhKO_H3K27ac_rep1_2_mean.bw

value: enhancer knockout


title: T4MINUSDOXP1_rep2


title: HUDEP-2_exon2mut_51_H3K27ac_CUT&Tag_rep1

description:
Library name: sample3
HUDEP-2_exon2mut_H3K27ac_rep1_2_mean.bw

value: exon2 mutant


title: HUDEP-2_exon2mut_56_H3K27ac_CUT&Tag_rep2

description:
Library name: sample4
HUDEP-2_exon2mut_H3K27ac_rep1_2_mean.bw


title: MESC cells, SAM486A, plate 8

description:
Library name: ESC_SAM486A_26
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: MESC

value: Mouse Embryonic Stem Cells

value: SAM486A (0,5μM) for 48 hours


title: T4MINUSDOXP1_rep1

value: trophoblast stem cell


title: HUDEP-2_C-12andC-7KO_H3K27ac_CUT&Tag_rep2

description: Library name: sample11

value: CTCF knockout


title: MESC cells, SAM486A and BENSpm, plate 7

description:
Library name: ESC_SAM486A_BENSpm_20
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: SAM486A (0,5μM) and BENSpm (10μM) for 48 hours


title: MESC cells, SAM486A, plate 6

description:
Library name: ESC_SAM486A_12
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: MESC cells, SAM486A, plate 7

description:
Library name: ESC_SAM486A_19
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_H3K27ac_CUT&Tag_rep1

description:
Library name: sample1
HUDEP-2_H3K27ac_rep1_2_mean.bw

value: cell line

value: wild-type


title: HUDEP-2_H3K27ac_CUT&Tag_rep2

description:
Library name: sample2
HUDEP-2_H3K27ac_rep1_2_mean.bw


title: MESC cells, SAM486A, plate 5

description:
Library name: ESC_SAM486A_05
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: MESC cells, SAM486A and BENSpm, plate 6

description:
Library name: ESC_SAM486A_BENSpm_13
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: T4PLUSDOX_rep2

value: WT

value: DOX


title: HUDEP-2_CTCFAID_C16_2h

description: Library name: sample6

data_processing:
Sequencing reads were trimmed using Cutadapt (v4.4)and aligned to the hg38 reference genome with STAR (v2.5.2b) using the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM.
The resulting BAM files were converted to BED format using the bamtobed command from BEDtools (v2.30.0)
BED files were then normalized and transformed into wiggle format using a custom Python script. Finally, the normalized wiggle files were converted to bigWig format using wigToBigWig.
Assembly: hg38
Supplementary files format and content: bigWig format

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen 74134). For nascent RNA labeling, 2 μg of total RNA was subjected to a click reaction with biotin azide and CuSO₄.
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (NEB E7400X), and RNA library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770).

value: human erythroid progenitor cells

tag: time


title: T4PLUSDOX_rep1


title: HUDEP-2_CTCFAID_C16_4h

description: Library name: sample7


title: HUDEP-2_sg1617_H3K27ac_13bp_CUT&Tag

description:
Library name: sample8
HUDEP-2_sg1617_H3K27ac_rep1_2_mean.bw

value: sg1617 edited


title: MESC cells, EtOH, plate 7

description:
Library name: ESC_Veh_EtOH_25
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: Control for SAM486A


title: HUDEP-2_CTCFAID_C3_7h

description: Library name: sample4


title: MESC cells, EtOH, plate 6

description:
Library name: ESC_Veh_EtOH_18
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_CTCFAID_C3_4h

description: Library name: sample3


title: MESC cells, EtOH, plate 5

description:
Library name: ESC_Veh_EtOH_11
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_CTCFAID_C3_0h

description: Library name: sample1


title: MESC cells, EtOH, plate 4

description:
Library name: ESC_Veh_EtOH_04
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: T3MINUSDOXP1_rep2

value: KO

value: wo DOX P2


title: HUDEP-2_Ctrl_ASO_ATAC

description: Library name: sample11

value: Control ASO treated


title: CD34_sg1617_ATAC_rep2

description:
Library name: sample8
CD34_sg1617_ATAC_rep1_2_mean.bw

value: Bone marrow

value: CD34+ HSPCs


title: T3MINUSDOXP1_rep1


title: HUDEP-2_CTCFAID_C16_7h

description: Library name: sample8


title: MESC cells,  MetOH, plate 4

description:
Library name: ESC_Veh_MetOH_22
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab

value: MESC

value: Mouse Embryonic Stem Cells

value: Control for Difluoromethylornithine


title: CD34_AAVS_ATAC_rep2

description:
Library name: sample6
CD34_AAVS_ATAC_rep1_2_mean.bw

value: AAVS edited


title: MESC cells,  MetOH, plate 3

description:
Library name: ESC_Veh_MetOH_15
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: CD34_AAVS_ATAC_rep1

description:
Library name: sample5
CD34_AAVS_ATAC_rep1_2_mean.bw


title: T3PLUSDOX_rep2

value: trophoblast stem cell


title: HUDEP-2_sg1617_15bp_ATAC

description:
Library name: sample4
HUDEP-2_sg1617_ATAC_rep1_2_mean.bw

value: cell line


title: HUDEP-2_sg1617_13bp_ATAC

description:
Library name: sample3
HUDEP-2_sg1617_ATAC_rep1_2_mean.bw


title: HUDEP-2_CTCFAID_C16_0h

description: Library name: sample5


title: MESC cells,  MetOH, plate 2

description:
Library name: ESC_Veh_MetOH_08
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: T3MINUSDOXP2_rep2


title: HUDEP-2_ATAC_rep1

description:
Library name: sample1
HUDEP-2_ATAC_rep1_2_mean.bw

value: wild-type


title: F10121620_D

city: London

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

country: United Kingdom

institute: University College London

data_processing:
Spatial transcriptomics: Raw intensities files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger count". For fetal midbrain samples, the paths to the multiple FASTQ files generated from the library subdivisions were specified in the "--fastqs" argument.
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.

source_name: Fetal midbrain at 10, 12 PCW. Technical replicate 2

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell transcriptomics: samples were dissociated, treated with papain, equilibrated with 02:C02, minced, PBS wahed, dissociated again, triturated and finally pelleted
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell transcriptomics: single cell suspensions were prepared and processed using the Chromium Single Cell 3’ Reagent Kits v3

value: Fetal Midbrain

value: one foetus at PCW16 and PCW20 each


title: HUDEP-2_ATAC_rep2

description:
Library name: sample2
HUDEP-2_ATAC_rep1_2_mean.bw

value: human erythroid progenitor cells


title: F10121620_C

source_name: Fetal midbrain at 10, 12 PCW. Technical replicate 1


title: MESC cells, DFMO, plate 3

description:
Library name: MESC_DFMO_12
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: Difluoromethylornithine (50μM)  for 48 hours


title: NDRI7 RV

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Library name: FJ_MJ_NDRI_7RV

data_processing:
FASTQ files were aligned to human genome build hg38 using STAR (Dobin et al., 2013) (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.32.0).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: hg38
Supplementary files format and content: counts.txt: 60646 x 10 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 60646 x 10 matrix of variance-stabilizing-transformed (VST) expression values

source_name: heart tissue

extract_protocol: Following homogenization, RNA was isolated using the Qiagen RNeasy Fibrous Tissue Mini Kit.

treatment_protocol: Cardiac biosamples were transported in cardioplegic solution prior to flash freezing in liquid nitrogen.

value: heart tissue

tag: subject

tag: site

value: right ventricle

tag: disease

value: control


title: MESC cells,  MetOH, plate 1

description:
Library name: ESC_Veh_MetOH_01
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-24_ESC_SAM486A_DFMO.tab


title: HUDEP-2_CTCFAID_C3_2h

description: Library name: sample2


title: NDRI7 LV

description: Library name: FJ_MJ_NDRI_7LV

value: left ventricle


title: NDRI5 RV

description: Library name: FJ_MJ_NDRI_5RV

value: hypertension


title: F10121620_B

source_name: Fetal midbrain at 16, 20 PCW. Technical replicate 2

value: one foetus at PCW10 and PCW12 each


title: CD34_sg1617_ATAC_rep1

description:
Library name: sample7
CD34_sg1617_ATAC_rep1_2_mean.bw

value: Bone marrow

value: CD34+ HSPCs

value: sg1617 edited


title: NDRI5 LV

description: Library name: FJ_MJ_NDRI_5LV


title: MESC cells, DFMO, plate 2

description:
Library name: MESC_DFMO_8
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: MESC

value: Mouse Embryonic Stem Cells


title: NDRI4 RV

description: Library name: FJ_MJ_NDRI_4RV


title: MESC cells, DFMO, plate 1

description:
Library name: MESC_DFMO_4
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab


title: F10121620_A

source_name: Fetal midbrain at 16, 20 PCW. Technical replicate 1


title: T3PLUSDOX_rep1

value: trophoblast stem cell

value: WT

value: DOX


title: NDRI3 RV

description: Library name: FJ_MJ_NDRI_3RV


title: NDRI4 LV

description: Library name: FJ_MJ_NDRI_4LV


title: NDRI3 LV

description: Library name: FJ_MJ_NDRI_3LV


title: NDRI1 RV

description: Library name: FJ_MJ_NDRI_1RV


title: MESC cells, SAM486A, plate 2

description:
Library name: MESC_SAM486A_7
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: SAM486A (0,5μM) for 48 hours


title: NDRI1 LV

description: Library name: FJ_MJ_NDRI_1LV


title: OCT_BLOCK_4

data_processing:
Spatial transcriptomics: Raw intensities files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger count". For fetal midbrain samples, the paths to the multiple FASTQ files generated from the library subdivisions were specified in the "--fastqs" argument.
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.
Library strategy: Spatial Transcriptomics

source_name: Six midbrain-like organoids, set 4.

value: Organoids

value: Control 1, Control 2 (iPSCs)

value: Dopaminergic lineage


title: ZFmut_S2P_CHIP

description: ChIP-seq

data_processing:
For ChIP-seq, Reads were aligned to the human reference genome hg19 (GRCh37) using bowtie2 version 2.3.2. The ChIPseq peaks from each sample were called at P <10-4 with MACS2. Bigwig files were generated with Homer softwares.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Cell line

growth_protocol: Hela cells were cultured in DMEM (Gibco) with 10% FBS and 100 ug/mL Pen/Strep.

extract_protocol:
For Chip-seq, genomic DNA was pulled down by respective antibodies.
For ChIP-seq, library was prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: Cell line

value: Hela cells

value: Hela cell with an ZF domain mutated AKAP95 overexpression


title: OCT_BLOCK_2

source_name: Six midbrain-like organoids, set 2.


title: WT_S2P_CHIP

description: ChIP-seq

value: Hela cell with an empty vector overexpression


title: MESC cells, SAM486A, plate 1

description:
Library name: MESC_SAM486A_3
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab


title: ZFmut_PolII_CHIP

description: ChIP-seq


title: MESC cells, Ethanol, plate 3

description:
Library name: MESC_Veh_EtOH_10
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: Control for SAM486A


title: OCT_BLOCK_1

source_name: Six midbrain-like organoids, set 1.


title: WT_PolII_CHIP

description: ChIP-seq


title: PC_AGE_4_REP_3

source_name: Fetal midbrain at 17PCW. Spatial transcriptomics, biological rep 3.

value: Brain

value: Fetal Midbrain


title: PSmut_S2P_CHIP

description: ChIP-seq

value: Hela cell with an IDR region mutated AKAP95 overexpression


title: KO_H3K27Ac

description: ChIP-seq

value: AKAP95 knockout

value: ChIP with H3K27Ac antibody


title: MESC cells, Ethanol, plate 2

description:
Library name: MESC_Veh_EtOH_6
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: MESC

value: Mouse Embryonic Stem Cells


title: WT_H3K27Ac

description: ChIP-seq

value: wild-type


title: PC_AGE_4_REP_2

source_name: Fetal midbrain at 17PCW. Spatial transcriptomics, biological rep 2.


title: MESC cells, SAM486A, plate 3

description:
Library name: MESC_SAM486A_11
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: SAM486A (0,5μM) for 48 hours


title: KO_H3K4Me3

description: ChIP-seq

value: ChIP with H3K4Me3 antibody


title: WT_H3K4Me3

description: ChIP-seq


title: PSmut_PolII_CHIP

description: ChIP-seq


title: WT_H3K4Me1

description: ChIP-seq

value: ChIP with H3K4Me1 antibody


title: PC_AGE_4_REP_1

source_name: Fetal midbrain at 17PCW. Spatial transcriptomics, biological rep 1.


title: MESC cells,  Methanol, plate 3

description:
Library name: MESC_Veh_MetOH_9
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: Control for Difluoromethylornithine


title: OCT_BLOCK_3

source_name: Six midbrain-like organoids, set 3.

value: Organoids

value: Control 1, Control 2 (iPSCs)

value: Dopaminergic lineage


title: KO_H3K4Me1

description: ChIP-seq

value: Cell line

value: Hela cells


title: PC_AGE_3_REP_2

source_name: Fetal midbrain at 12PCW. Spatial transcriptomics, biological rep 2.

value: Brain


title: Leukocytes, endothelial cells and fibroblasts heterogeneity during MI transcriptome

city: Madrid

first: Alejandra

last: Aroca-Crevillén

address: C/ Melchor Fernández Almagro 3

institute: Spanish National Center for Cardiovascular Research Carlos III (CNIC)

description: Library name: cDNA

data_processing:
Rhapsody processing pipeline
Assembly: GRCm39
Supplementary files format and content: Seurat r object containing the raw counts and metadata

source_name: Mouse heart

growth_protocol: All experiments were performed on 7–16-week-old C57BL/6 male mice. Chow and water were available ad libitum.

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells.
Two separated indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomes, heart samples were procesed for obtention of single-cell solutions and these were sorted in a BD Aria/Fusion Cell Sorter as DAPI-CD45+, DAPI-CD45-CD31+ and DAPI-CD45-CD31-PDGFRa+ cells, and loaded into a BD Rhapsody cartridge

value: Mouse heart

value: Leukocyte, ECs and fibroblasts

tag: Sex

value: male

value: WT

tag: library type

value: mRNA


title: PC_AGE_3_REP_3

source_name: Fetal midbrain at 12PCW. Spatial transcriptomics, biological rep 3.

value: Fetal Midbrain


title: MESC cells,  Methanol, plate 2

description:
Library name: MESC_Veh_MetOH_5
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

source_name: MESC

value: MESC

value: Mouse Embryonic Stem Cells


title: KO_INPUT

description: ChIP-seq

value: AKAP95 knockout

value: Cell lysate


title: WT_INPUT

description: ChIP-seq

value: wild-type


title: MESC cells,  Methanol, plate 1

description:
Library name: MESC_Veh_MetOH_1
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: Control for Difluoromethylornithine


title: Leukocytes, endothelial cells and fibroblasts heterogeneity during MI sample tags

description: Library name: tags

value: Rhapsody tags


title: BRB-seq, NIH3T3, mix

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: Library name: n098_mix_01

data_processing:
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the mm10 reference using bowtie2 (ver. 2.3.5) for ATAC-seq data or hisat2 (ver. 2.2.1) for BRB-seq data.
ATAC-seq : Only uniquely mapped reads and paired reads were used for making bigwig file by deepTools bamCoverage.
BRB-seq : Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: mm10
Supplementary files format and content: BigWig format for storing continuous genomic data for genome browsers (.bw)
Supplementary files format and content: compressed tab separated files(.tsv.gz)

source_name: NIH3T3 TetOn3G/MyoD cells

extract_protocol:
After incubation, cells were collected and washed with PBS.
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.
ATAC libraries were prepared as previous report (Harada, Maehara, and Handa 2019).

value: NIH3T3 TetOn3G/MyoD cells

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.

value: MyoDminus:Cell were grown without doxyxycline. D0:Cell induced MyoD for 24 h after the addition of doxycycline. D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 72h (D72)


title: PC_AGE_2_REP_3

source_name: Fetal midbrain at 11PCW. Spatial transcriptomics, biological rep 3.

value: Brain


title: MESC cells, Ethanol, plate 1

description:
Library name: MESC_Veh_EtOH_2
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-12_MESC_SAM486A_DFMO.tab

value: Control for SAM486A


title: Mef_96D_dTS

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description:
Library name: Mef_96D_dTS
all.featurecounts.Mef.edger.tpm.anno.txt

data_processing:
Reads were mapped to the reference mouse genome (GRCm39) using STAR (v2.7.11b) [PMID: 23104886]. Gene-level read counts were obtained using featureCounts (v1.6.0) [PMID: 24227677] with Gencode M31 annotation [PMID: 36420896]. Differential expression analysis was performed using the edgeR package (v4.2.1) [PMID: 39844453].
Assembly: GRCm39
Supplementary files format and content: text files include CPM and log(foldchange) comparing Plagl1Δ322ts ; Lrrc58Δ503ts/Δ503ts to wildtype

source_name: Primary MEFs

growth_protocol: Mice were fed with standard diet. Primary MEFs were isolated from E14.5 mouse embryos as described in Tan et al (PMID: 30798523) MEFs were cultured in Dulbeccoʹs Modified Eagleʹs Medium (DMEM) (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Sigma) and 1×Antibiotic-Antimycotic (Invitrogen); primary MEFs were grown for less than 4 passages and were contact inhibited at harvest.

extract_protocol:
RNAseq: Total RNA was extracted using miRNeasy Kit (Qiagen)
RNA-seq libraries were constructed using the QuantSeq 3′ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set A1 and B1 (Lexogen, 192.24) using 500ng input RNA.

treatment_protocol: E18.5 tissues were flash frozen in liquid nitrogen until RNA extraction.

value: Primary MEFs

tag: strain

value: Plagl1del322ts; Lrrc58del503ts/del503ts

tag: developmental stage

value: Embryonic day 14.5


title: Mef_98D_dTS

description:
Library name: Mef_98D_dTS
all.featurecounts.Mef.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, MyoDminus, r3

description: Library name: NIH3T3_MyoDminus_3

value: Cell were grown without doxycycline.


title: Mef_86D_dTS

description:
Library name: Mef_86D_dTS
all.featurecounts.Mef.edger.tpm.anno.txt


title: PC_AGE_2_REP_2

source_name: Fetal midbrain at 11PCW. Spatial transcriptomics, biological rep 2.

value: Fetal Midbrain


title: Mef_101D_WTHet

description:
Library name: Mef_101D_WTHet
all.featurecounts.Mef.edger.tpm.anno.txt

value: Plagl1 wt ; Lrrc58wt/del503ts


title: Mef_87D_WT

description:
Library name: Mef_87D_WT
all.featurecounts.Mef.edger.tpm.anno.txt

value: wild type


title: Mef_99D_WTHet

description:
Library name: Mef_99D_WTHet
all.featurecounts.Mef.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, D72, r3

description: Library name: NIH3T3_D72_3

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 72h


title: ATAC-seq, NIH3T3, MyoDminus, r1

description: Library name: NIH3T3_MyoDminus_1


title: Lung_E80_dTS

description:
Library name: Lung_E80_dTS
all.featurecounts.Lung.edger.tpm.anno.txt

source_name: Lung

value: Lung

value: Embryonic day 18.5


title: PC_AGE_2_REP_1

source_name: Fetal midbrain at 11PCW. Spatial transcriptomics, biological rep 1.


title: Lung_E104_dTS

description:
Library name: Lung_E104_dTS
all.featurecounts.Lung.edger.tpm.anno.txt


title: PC_AGE_1_REP_3

source_name: Fetal midbrain at 7PCW. Spatial transcriptomics, biological rep 3.


title: PC_AGE_3_REP_1

source_name: Fetal midbrain at 12PCW. Spatial transcriptomics, biological rep 1.


title: Lung_E45_dTS

description:
Library name: Lung_E45_dTS
all.featurecounts.Lung.edger.tpm.anno.txt


title: Lung_E104_WT

description:
Library name: Lung_E104_WT
all.featurecounts.Lung.edger.tpm.anno.txt


title: Lung_E82_WT

description:
Library name: Lung_E82_WT
all.featurecounts.Lung.edger.tpm.anno.txt


title: PC_AGE_1_REP_2

source_name: Fetal midbrain at 7PCW. Spatial transcriptomics, biological rep 2.


title: ATAC-seq, NIH3T3, D72, r2

description: Library name: NIH3T3_D72_2


title: ATAC-seq, NIH3T3, D72, r1

description: Library name: NIH3T3_D72_1


title: Lung_E50_WT

description:
Library name: Lung_E50_WT
all.featurecounts.Lung.edger.tpm.anno.txt


title: PC_AGE_1_REP_1

source_name: Fetal midbrain at 7PCW. Spatial transcriptomics, biological rep 1.


title: Kidney_E104_dTS

description:
Library name: Kidney_E104_dTS
all.featurecounts.Kidney.edger.tpm.anno.txt

source_name: Kidney

value: Kidney


title: Kidney_E80_dTS

description:
Library name: Kidney_E80_dTS
all.featurecounts.Kidney.edger.tpm.anno.txt


title: PP_3

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean data were mapped to the reference genome of Homo sapiens from GRCh38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and logfold-change cutoff of 1 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample

source_name: AGS

growth_protocol: The generated sgPPFIA4-AGS cells and sgNC-AGS cells were cultured in complete RPMI 1640 medium supplemented with 10% FBS in a humidified environment containing 5% CO2 at 37 °C.

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).2 μg total RNAs were used for stranded RNA sequencing library
RNA libraries for RNA-seg were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02)  following manufacturer's protocols.

treatment_protocol: AGS cells were treated with PPFIA4 sgRNA or non-specific control sgRNA to generate sgPPFIA4-AGS cells and sgNC-AGS cells.

value: AGS

value: gastric epithelial cells

value: PPFIA4 sgRNA


title: Kidney_E45_dTS

description:
Library name: Kidney_E45_dTS
all.featurecounts.Kidney.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, MyoDminus, r2

description: Library name: NIH3T3_MyoDminus_2

value: NIH3T3 TetOn3G/MyoD cells

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.


title: ATAC-seq, NIH3T3, D24, r3

description: Library name: NIH3T3_D24_3

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 24h


title: PP_2


title: Kidney_E104_WT

description:
Library name: Kidney_E104_WT
all.featurecounts.Kidney.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, D24, r2

description: Library name: NIH3T3_D24_2


title: PP_1


title: Kidney_E50_WT

description:
Library name: Kidney_E50_WT
all.featurecounts.Kidney.edger.tpm.anno.txt


title: Kidney_E82_WT

description:
Library name: Kidney_E82_WT
all.featurecounts.Kidney.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, D24, r1

description: Library name: NIH3T3_D24_1


title: Intestine_E104_dTS

description:
Library name: Intestine_E104_dTS
all.featurecounts.Intestine.edger.tpm.anno.txt

source_name: Intestine

value: Intestine


title: AGS_3

value: non-specific control sgRNA


title: Intestine_E80_dTS

description:
Library name: Intestine_E80_dTS
all.featurecounts.Intestine.edger.tpm.anno.txt

value: Plagl1del322ts; Lrrc58del503ts/del503ts


title: ATAC-seq, NIH3T3, D0, r3

description: Library name: NIH3T3_D0_3

value: Cell induced MyoD for 24 h after the addition of doxycycline.


title: Intestine_E45_dTS

description:
Library name: Intestine_E45_dTS
all.featurecounts.Intestine.edger.tpm.anno.txt


title: Intestine_E104_WT

description:
Library name: Intestine_E104_WT
all.featurecounts.Intestine.edger.tpm.anno.txt


title: AGS_2


title: ATAC-seq, NIH3T3, D0, r2

description: Library name: NIH3T3_D0_2


title: Intestine_E50_WT

description:
Library name: Intestine_E50_WT
all.featurecounts.Intestine.edger.tpm.anno.txt


title: Intestine_E82_WT

description:
Library name: Intestine_E82_WT
all.featurecounts.Intestine.edger.tpm.anno.txt


title: ATAC-seq, NIH3T3, D0, r1

description: Library name: NIH3T3_D0_1


title: Liver_E45_dTS

description:
Library name: Liver_E45_dTS
all.featurecounts.Liver.edger.tpm.anno.txt

source_name: Liver

value: Liver


title: Liver_E37_dTS

description:
Library name: Liver_E37_dTS
all.featurecounts.Liver.edger.tpm.anno.txt


title: DU145 shAMD siF3A3 cells, DOX, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_DOX_4

growth_protocol: DNEM, 15% fetal bovine serum, 2 mM glutamine, 1 x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

value: Metastatic prostate cancer

value: Doxycycline (100 ng/mL) for 48 hours + 25 nM of siRNA


title: sci-ChIL-seq, NIH3T3-18, H3K4me3 (MyoDminus)

description: Library name: C18

data_processing:
The cell barcodes were made by modifing index sequences using seqkit (version 0.16.1)  and they were assigned to read sequences by umi_tools (version 1.1.1).
Adapter sequences were trimmed using Trim Galore (version 0.6.10) with the default options.
The paired-reads were mapped to the mm10 using bowtie2 (version 2.3.5.1) with the default options.
The reads uniquely mapped to autosome or sex chromosomes were extracted.
Duplicates were remove by R package GenomicRanges (version 1.54.1).
Assembly: mm10
Supplementary files format and content: The processed data fromat is BED. These indicate the position of unique fragments and column 3 indicates cell barcode.

extract_protocol:
Cell line were isolated with protease treatment.
A total of 10-30k biotinylated cells per well were combined in 96-well avidin-coated plates and stained with primary antibody (1st Ab) and sci-ChIL probe. Tn5 transposition via Tn5 transposase integrates the sci-ChIL probe’s indexed DNA into the genome around the primary antibody of the cell (cells are indexed with a unique sci-ChIL probe per well). The cells in the 96-well plate are then pooled, and 25 cells per well are added to another 96-well plate with a cell sorter, so that cells with different primary indexes are placed in the wells. The integrated regions are then amplified as RNA by in vitro transcription using T7 RNA polymerase. Transcribed RNA is purified and converted to cDNA for sequencing library preparation; a second index is added by PCR prior to sequencing. PCR is performed with a set of primers with unique i5 and i7 sequences per well. A library with a different primary index and the same secondary index was generated for each well. Overall, a library of approximately 2400 cells with different primary and secondary indices is produced. One single-target sequence includes one set of 96 sci-ChIL probes with T5 barcodes, and two sets of multi-target sequences is used.

value: Cell were grown without doxycycline.


title: AGS_1


title: Liver_E33_dTS

description:
Library name: Liver_E33_dTS
all.featurecounts.Liver.edger.tpm.anno.txt


title: Liver_E35_WT

description:
Library name: Liver_E35_WT
all.featurecounts.Liver.edger.tpm.anno.txt

value: wild type


title: Liver_E50_WT

description:
Library name: Liver_E50_WT
all.featurecounts.Liver.edger.tpm.anno.txt

value: Embryonic day 18.5


title: DU145 shAMD siF3A3 cells, DOX, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_DOX_3


title: Liver_E51_WT

description:
Library name: Liver_E51_WT
all.featurecounts.Liver.edger.tpm.anno.txt


title: Heart_E104_dTS

description:
Library name: Heart_E104_dTS
all.featurecounts.Heart.edger.tpm.anno.txt

source_name: Heart

value: Heart


title: Heart_E80_dTS

description:
Library name: Heart_E80_dTS
all.featurecounts.Heart.edger.tpm.anno.txt


title: sci-ChIL-seq, NIH3T3-17, RNAPolII (MyoDminus), sci-mtChIL-seq, H3K4me3-RNAPolII (MyoDminus),

description: Library name: C17


title: DU145 shAMD siF3A3 cells, DOX, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_DOX_1


title: sci-ChIL-seq, NIH3T3-16, H3K4me3, RNAPolII (MyoDminus)

description: Library name: C16


title: Heart_E45_dTS

description:
Library name: Heart_E45_dTS
all.featurecounts.Heart.edger.tpm.anno.txt


title: DU145 shAMD siF3A3 cells, noDOX, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_noDOX_4

value: Control


title: sci-mtChIL-seq, NIH3T3-15, PrimaryMinus-RNAPolII, H3K4me3-RNAPolII (MyoDminus)

description: Library name: C15


title: Heart_E82_WT

description:
Library name: Heart_E82_WT
all.featurecounts.Heart.edger.tpm.anno.txt


title: MEF cells, kiSF3A3 + SAM486A, plate2

description:
Library name: kiSF3A3_SAM486A_48
2x150 paired-end sequence reads

source_name: MEF

value: MEF

value: Mouse Embryonic Fibroblast

value: SF3A3 knock in  + SAM486A (2,5 μM)  for 24 hours


title: DU145 shAMD siF3A3 cells, noDOX, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_noDOX_3


title: Heart_E109_WT

description:
Library name: Heart_E109_WT
all.featurecounts.Heart.edger.tpm.anno.txt


title: DU145 shAMD siF3A3 cells, noDOX, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_noDOX_2


title: Brain_E45_dTS

description:
Library name: Brain_E45_dTS
all.featurecounts.Brain.edger.tpm.anno.txt

source_name: Brain

value: Brain


title: Brain_E37_dTS

description:
Library name: Brain_E37_dTS
all.featurecounts.Brain.edger.tpm.anno.txt


title: MEF cells, kiSF3A3 + SAM486A, plate1

description:
Library name: kiSF3A3_SAM486A_24
2x150 paired-end sequence reads


title: Brain_E33_dTS

description:
Library name: Brain_E33_dTS
all.featurecounts.Brain.edger.tpm.anno.txt


title: DU145 shAMD siF3A3 cells, noDOX, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_noDOX_1


title: Brain_E51_WT

description:
Library name: Brain_E51_WT
all.featurecounts.Brain.edger.tpm.anno.txt


title: DU145 shAMD siF3A3 cells, DOX, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siSF3A3_DOX_2


title: Brain_E50_WT

description:
Library name: Brain_E50_WT
all.featurecounts.Brain.edger.tpm.anno.txt


title: MEF cells, SAM486A, plate3

description:
Library name: WT_SAM486A_69
2x150 paired-end sequence reads

value: SAM486A (2,5 μM)  for 24 hours


title: Brain_E35_WT

description:
Library name: Brain_E35_WT
all.featurecounts.Brain.edger.tpm.anno.txt


title: MEF cells, SAM486A, plate2

description:
Library name: WT_SAM486A_45
2x150 paired-end sequence reads


description:
Library name: AGO-CLASH_ZSWIM8 KO_Lung-1024-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx

data_processing:
UMI barcodes were extracted from the reads using UMI-tools (v1.1.2) [PMID: 28100584]. ReadAdapter sequences were trimmed with Cutadapt (v3.1) [DOI:10.14806/ej.17.1.200s with base quality less than 30 at any position were dropped. Trimmed reads were aligned to mouse snoRNAs from snoRNA Atlas [PMID: 27174936] using Bowtie (v1.3.1) [PMID: 19261174], and all mapped reads were discarded. Mature miRNA sequences from the mouse genome were obtained from miRBase v22 [PMID: 30423142], and mapped to the remaining reads using Bowtie. Reads were filtered based on strand orientation and mismatch rate using chim-eCLIP (https://github.com/YeoLab/chim-eCLIP), which was also used to identify candidate chimeric reads. These reads were aligned to repetitive elements from the mouse genome (Repbase v27.07) using STAR (v2.7.1a), and mapped reads were excluded from downstream analysis.
Annotations were based on GENCODE M23. Conservation scores were calculated using phyloP-60way [PMID: 19858363], and the minimum free energy (MFE) between miRNA and target sequences was calculated using RNAhybrid [PMID: 15383676]. The remaining reads were aligned to the mouse reference genome (GRCm38) using Bowtie, and duplicate reads were removed using UMI-tools based on UMI barcodes. Enriched peak clusters were called using CLIPper (https://github.com/YeoLab/clipper), with peaks extended by 10 nt at the 5′ end.
Assembly: GRCm38
Supplementary files format and content: excel sheets of miRNA-target chimera counts from each sample individually
Supplementary files format and content: excel sheet of combined miRNA-target chimera counts from all enriched samples (miRNA.target.chimera)

growth_protocol: Mice were fed with standard diet.

extract_protocol:
AGO2 was Immunoprecipitated by AGO2 antibody (Santa cruz, EIFC2C2 4F9), RNA was extracted RNA Clean & Concentrator-5 columns (Cat R1016). RNAseq: Total RNA was extracted using miRNeasy Kit (Qiagen)
sequencing library was prepared as described by Manakov and Shishkin et al., 2022 (https://doi.org/10.1101/2022.02.13.480296) for illumina sequencing

treatment_protocol: AGO-CLASH: Frozen tissues were ground and UV cross-linked

value: Lung


title: DU145 shAMD siSCR cells, DOX, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_DOX_2

value: Doxycycline (100 ng/mL) for 48 hours


description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-1024-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-1024-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: Heart_E50_WT

description:
Library name: Heart_E50_WT
all.featurecounts.Heart.edger.tpm.anno.txt


title: MEF cells, kiSF3A3 + SAM486A, plate3

description:
Library name: kiSF3A3_SAM486A_25_72
2x150 paired-end sequence reads


title: MEF cells, SAM486A, plate1

description:
Library name: WT_SAM486A_21
2x150 paired-end sequence reads


title: DU145 shAMD siSCR cells, DOX, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_DOX_3


description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-1023-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: MEF cells, kiSF3A3 + noSAM486A, plate3

description:
Library name: kiSF3A3_noSAM486A_54
2x150 paired-end sequence reads

value: SF3A3 knock in


description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-1023-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: AGO-CLASH_WT_Lung-1024-enriched-2

description:
Library name: AGO-CLASH_WT_Lung-1024-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: DU145 shAMD siSCR cells, noDOX, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_noDOX_4


title: MEF cells, kiSF3A3 + noSAM486A, plate2

description:
Library name: kiSF3A3_noSAM486A_30
2x150 paired-end sequence reads


title: AGO-CLASH_WT_Lung-1024-enriched-1

description:
Library name: AGO-CLASH_WT_Lung-1024-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: AGO-CLASH_WT_Brain-1024-enriched-2

description:
Library name: AGO-CLASH_WT_Brain-1024-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: MEF cells, kiSF3A3 + noSAM486A, plate1

description:
Library name: kiSF3A3_noSAM486A_15
2x150 paired-end sequence reads


title: DU145 shAMD siSCR cells, noDOX, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_noDOX_3


title: AGO-CLASH_WT_Brain-1024-enriched-1

description:
Library name: AGO-CLASH_WT_Brain-1024-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: MEF cells, noSAM486A, plate 3

description:
Library name: WT_noSAM486A_51
2x150 paired-end sequence reads


title: DU145 shAMD siSCR cells, noDOX, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_noDOX_2


title: AGO-CLASH_WT_Brain-1023-enriched-1

description:
Library name: AGO-CLASH_WT_Brain-1023-enriched-1
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: MEF cells, noSAM486A, plate 2

description:
Library name: WT_noSAM486A_27
2x150 paired-end sequence reads


title: AGO-CLASH_WT_Brain-1023-enriched-2

description:
Library name: AGO-CLASH_WT_Brain-1023-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


description:
Library name: AGO-CLASH_ZSWIM8 KO_Lung-1024-enriched-2
small RNA-target transcript chimera
miRNA.target.chimera.xlsx


title: AGO-CLASH_ZSWIM8 KO_Lung-2

description:
Library name: AGO-CLASH_ZSWIM8 KO_Lung-2
small RNA-target transcript chimera


title: DU145 shAMD siSCR cells, noDOX, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_noDOX_1


title: AGO-CLASH_ZSWIM8 KO_Lung-1

description:
Library name: AGO-CLASH_ZSWIM8 KO_Lung-1
small RNA-target transcript chimera


title: MEF cells, noSAM486A, plate 1

description:
Library name: WT_noSAM486A_3
2x150 paired-end sequence reads


title: DU145 shAMD siSCR cells, DOX, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_DOX_1


title: AGO-CLASH_WT_Lung-2

description:
Library name: AGO-CLASH_WT_Lung-2
small RNA-target transcript chimera


title: DU145 shAMD1 cells, noDOX, plate 3 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_3


title: AGO-CLASH_ZSWIM8 KO_Brain-1

description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-1
small RNA-target transcript chimera


title: AGO-CLASH_ZSWIM8 KO_Brain-2

description:
Library name: AGO-CLASH_ZSWIM8 KO_Brain-2
small RNA-target transcript chimera


title: DU145 shAMD1 cells, noDOX, plate 4 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_4


title: AGO-CLASH_WT_Lung-1

description:
Library name: AGO-CLASH_WT_Lung-1
small RNA-target transcript chimera


title: Esrrg, replicate 2

first: Dogacan

last: Yucel

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

data_processing:
FASTQ files were mapped using mm10 assembly.
Reads were mapped and analyzed using BioJupies.
Assembly: mm10
Supplementary files format and content: processed data includes mapped raw counts.

extract_protocol:
Cardiac RNA was extracted using Zymogen Quick RNA Miniprep Plus Kit.
1 ug RNA per sample was used for library generation.

value: Cardiac cells

value: Wildtype

value: overexpressed Esrrg


title: Esrrg, replicate 3


title: AGO-CLASH_WT_Brain-2

description:
Library name: AGO-CLASH_WT_Brain-2
small RNA-target transcript chimera


title: Esrrg, replicate 1


title: DU145 shAMD1 cells, noDOX, plate 2 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_2

value: Metastatic prostate cancer


title: M2M3_WT_864130_SAN

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
Library name: DSP-1001660020554-A-E03
FFPE spatial transcriptome sequencing

data_processing:
FASTQ files were trimmed, stitched, aligned and deduplicated using the NanoString GeoMx NGS pipeline (version 2.3.3.10).
Generated DCC files were processed with the R GeoMxTools package (version 3.8.0).
Differential gene expression analysis was performed using Iimma (version 3.60.1) on quantile-normalized data.
Assembly: mm10
Supplementary files format and content: NS3 DE tables.xlsx (differential expression tables)
Library strategy: Spatial Transcriptomics

source_name: wild-type adult sinus node

extract_protocol:
Formalin-fixed paraffin embedded E17.5 fetusses were sectioned at 5 µm. The samples were prepared according to the GeoMx Manual Slide Preparation User Manual, MAN-10150-3 using rabbit-anti-HCN4 (Merck Millipore AB5805), goat-anti-cTnI (Hytest 4T21/2) and Sytox Green Nucleic Acid Stain (Thermo Fisher Scientific S7020) antibodies and the GeoMx Whole Transcriptome Atlas Mouse RNA Probes for NGS (Bruker Spatial Biology).
Spatial transcriptome sequence libraries were constructed and sequencing using the NextSeq2000 (P2.100).

value: wild-type adult sinus node

value: wild-type


title: M2M3_WT_864130_SCV

description:
Library name: DSP-1001660020554-A-E04
FFPE spatial transcriptome sequencing

source_name: wild-type adult superior caval vein

value: wild-type adult superior caval vein


title: DU145 shAMD1 cells, noDOX, plate 1 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_1


title: Dnmt3a, replicate 3

value: Heart

value: overexpressed Dnmt3a


title: M2M3_WT_864130_RA

description:
Library name: DSP-1001660020554-A-E02
FFPE spatial transcriptome sequencing

source_name: wild-type adult right atrium

value: wild-type adult right atrium


title: AGO-CLASH_WT_Brain-1

description:
Library name: AGO-CLASH_WT_Brain-1
small RNA-target transcript chimera

value: wild type

value: Embryonic day 18.5


title: DU145 shAMD siSCR cells, DOX, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-16_du145_shAMD_siSF3A3.txt
siCTR_DOX_4


title: M2M3_WT_864127_SCV

description:
Library name: DSP-1001660020554-A-E01
FFPE spatial transcriptome sequencing


title: Dnmt3a, replicate 2


title: DU145 shAMD1 cells, DOX 48 hours, plate 3 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_3


title: DU145 shAMD1 cells, DOX 48 hours, plate 4 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_4


title: Dnmt3a, replicate 1


title: M2M3_WT_864127_RA

description:
Library name: DSP-1001660020554-A-D11
FFPE spatial transcriptome sequencing


title: M2M3_WT_864126_SCV

description:
Library name: DSP-1001660020554-A-D10
FFPE spatial transcriptome sequencing


title: M2M3_WT_864127_SAN

description:
Library name: DSP-1001660020554-A-D12
FFPE spatial transcriptome sequencing


title: M2M3_WT_864126_SAN

description:
Library name: DSP-1001660020554-A-D09
FFPE spatial transcriptome sequencing


title: GFP, replicate 3

value: overexpressed control GFP


title: DU145 shAMD1 cells, DOX 48 hours, plate 2 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_2


title: M2M3_WT_864126_RA

description:
Library name: DSP-1001660020554-A-D08
FFPE spatial transcriptome sequencing


title: M2M3_HOM_884349_SCV

description:
Library name: DSP-1001660020554-A-D07
FFPE spatial transcriptome sequencing

source_name: delB/delB adult superior caval vein

value: delB/delB adult superior caval vein

value: homozygous mutant


title: DU145 shAMD1 cells, DOX 48 hours, plate 1 [single]

description:
50 single-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_1

value: Doxycycline (100 ng/mL) for 48 hours


title: GFP, replicate 2


title: M2M3_HOM_884349_SAN

description:
Library name: DSP-1001660020554-A-D06
FFPE spatial transcriptome sequencing

source_name: delB/delB adult sinus node

value: delB/delB adult sinus node


title: GFP, replicate 1

value: Cardiac cells


title: DU145 shAMD1 cells, noDOX, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_4

value: Control


title: M2M3_HOM_822321_SAN

description:
Library name: DSP-1001660020554-A-D04
FFPE spatial transcriptome sequencing


title: DU145 shAMD1 cells, noDOX, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_3


title: M2M3_HOM_822315_SCV

description:
Library name: DSP-1001660020554-A-D03
FFPE spatial transcriptome sequencing


title: 4mo-replicate2, ATAC

description:
ATAC library
atac_fragments.tsv.gz.tbi
atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Raw fastq files were processesd using cellranger ARC pipeline. The samples were associated with the following barcodes; 4-1 and -1, 4-2 and -2, 28-1 and -3, 28-2 and -4.
Output files  were further imported into R and analyzed using the Seurat/Signac pipeline
Assembly: mm10
Supplementary files format and content: processed data includes both 10x output files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz and h5 files)

extract_protocol:
Cardiac cell nuclei were isolated and FACS sorted.
10,000 nuclei were used to generate libraries according to 10x Genomics Next GEM Single Cell Multiome ATAC + Gene Expression Reagents Kit protocol.
scMulti-omics (concurrent scRNA+scATAC seq)

value: Wildtype


title: DU145 shAMD1 cells, noDOX, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_2

data_processing:
RNA-seq  reads were aligned usig Vast-tools v2.5.1 to identify alternative splicing events.
Aligned reads from single and paired datasets were merged with Vast-tools v2.5.1.
Differentially spliced events were identified using Matt v.1.3.0 with a minimum abs(deltaPSI) > 10% and a Wilcoxon p-value < 0.01 after excluding events with PSIRANGE_ALL = NA and LENGTH= 0.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes PSI values for each sample

value: Metastatic prostate cancer


title: M2M3_HOM_822315_RA

description:
Library name: DSP-1001660020554-A-D01
FFPE spatial transcriptome sequencing

source_name: delB/delB adult right atrium

value: delB/delB adult right atrium


title: 4mo-replicate1, ATAC


title: M2M3_HOM__822321_SCV

description:
Library name: DSP-1001660020554-A-C12
FFPE spatial transcriptome sequencing


title: DU145 shAMD1 cells, noDOX, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
noDOX_1


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep6

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

institute: Columbia University

description:
Library name: TetOMexHT_rep6_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
libraries were aligned with STAR, and bioinformatic steps were followed as described in Rahman et al. 2018 (PMID: 30013039)
sorted sam file was converted to a matrix using MySQL
perl script from PMID 30013039 used to identify editing sites compared to internal control RNA Seq samples with output of bedgraph
postprocessing using bedtools intersect to identify high confidence editing sites. Custom R script used to generate weighted average for given transcript across replicates
Assembly: mm10
Supplementary files format and content: csv with transcript per million data for each library

source_name: Main olfactory epithelium

growth_protocol: mice had access to food and water ad libitum

extract_protocol:
cells were isolated using papain enzymatic treatment (Worthington), RNA was extracted using TRIzol reagent, followed by standard 1-Bromo-3-chloropropane/isopropanol methods
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara) using 10ng of RNA as input

value: Main olfactory epithelium

value: sorted immature and mature OSN


title: 28mo-replicate2, ATAC

value: Heart


title: M2M3_HOM__822321_RA

description:
Library name: DSP-1001660020554-A-C11
FFPE spatial transcriptome sequencing


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep5

description:
Library name: TetOMexHT_rep5_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: 28mo-replicate1, ATAC


title: DU145 shAMD1 cells, DOX 48 hours, plate 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_4

extract_protocol:
RNA was extracted using NucleoSpin RNA isolation kit from Macherey-Nagel.
RNA libraries were prepared using Illumina Stranded mRNA Library Prep Kit following manufacture's protocol.


title: M2M3_HET_882322_SCV

description:
Library name: DSP-1001660020554-A-C10
FFPE spatial transcriptome sequencing

value: heterozygous mutant


title: DU145 shAMD1 cells, DOX 48 hours, plate 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_3


title: HyperTRIBE_InternalControl__Mex3a_gg8tTA_omptTA_rep5

description:
Library name: TetOMexHT_rep5_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: sorted mCherry- cells from Main olfactory epithelium


title: 4mo-replicate2, GEX

description:
GEX (3' mRNA library)
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz


title: DU145 shAMD1 cells, DOX 48 hours, plate 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_2


title: M2M3_HOM_884349_RA

description:
Library name: DSP-1001660020554-A-D05
FFPE spatial transcriptome sequencing


title: 4mo-replicate1, GEX


title: M2M3_HET_882322_SAN

description:
Library name: DSP-1001660020554-A-C09
FFPE spatial transcriptome sequencing

source_name: delB/+ adult sinus node

value: delB/+ adult sinus node


title: DU145 shAMD1 cells, DOX 48 hours, plate 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_DU145_shAMD.txt
DOX42H_1


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep4

description:
Library name: TetOMexHT_rep4_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: M2M3_HET_882322_RA

description:
Library name: DSP-1001660020554-A-C08
FFPE spatial transcriptome sequencing

source_name: delB/+ adult right atrium

value: delB/+ adult right atrium


title: HyperTRIBE_InternalControl__Mex3a_gg8tTA_omptTA_rep4

description:
Library name: TetOMexHT_rep4_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: 28mo-replicate2, GEX


title: M2M3_HET_862374_SCV

description:
Library name: DSP-1001660020554-A-C07
FFPE spatial transcriptome sequencing


title: dCas9-p300 I1417N, GDO

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

institute: Rice University

description:
Guide-derived oligonucleotide (GDO)
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads

data_processing:
Cell Ranger Count v7.1.0 was used to perform count matrix generation using default parameters. Human (GRCh38) 2020-A was used for the transcriptome reference. Cells with less than 10% mitochondrial reads and between 750 and 7000 genes detected were kept for analysis. Resulting processed matrices were used for all downstream analyses.
Each of the sequencing datasets was processed using Seurat. Cells with greater than 10% mitochondrial transcripts, or less than 4000 total RNA transcripts were removed. For each gRNA in the library, expression levels were gathered for all genes within 1Mb of the gRNA target site. For each gRNA-target gene pairing, the FindMarkers() function was used to calculate the log2() fold changes in expression using the following parameters: ident.1 = gRNA_Cells, ident.2 = Control_Cells, min.pct = 0, min.cells.feature = 0, min.cells.group = 0, features = target_gene, logfc.threshold = 0. Violin plots were created using Seurat on the top few hits by adjusted p-value for each dataset analyzed. To make the violin plots, cells were divided into those with the gRNA present and those without, and the resulting expression levels for the target gene for each set of cells were visualized.
SCEPTRE was implemented as described previously. Our processed count matrices were used along with single-cell metadata as covariates to fit the SCEPTRE model. We tested gRNA-response pairs for differential expression for all genes within 1MB upstream and 1Mb downstream of the gRNA of interest. SCEPTRE p-values were adjusted with the Benjamini-Hochberg procedure and target genes were identified if they were significantly below a threshold value of 10% FDR.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: individual files corresponding to each sample are outputs of 10X Genomics Cloud pipeline and SCEPTRE
Library strategy: Perturb-seq

growth_protocol: K562 (ATCC, CRL-243) were cultured in  ATCC-recommended RPMI media supplemented with 10% FBS (Sigma-Aldrich) and 1% pen/strep (100units/ mL penicillin, 100µg/ mL streptomycin; Gibco) at 37° C and 5% CO2.

extract_protocol:
Cells were harvested and prepared as per the 10X Genomics Single Cell Protocols Cell Preparation Guide. ~10,000 cells were captured per lane using a 10X Chromium device. One lane was used per construct (dCas9-p300 WT and dCas9-p300 I1417N). Cells were captured using a 10X Chromium chip using the Chromium Next GEM Single Cell 3’ Reagents Kit v.3 with Feature Barcoding Technology for CRISPR screening.
Final libraries were sequenced using a NovaSeq 6000 for each p300 screen. Gene expression and CRISPR Guide Capture transcript libraries were pooled at a 4:1 ratio for sequencing.

treatment_protocol: Monoclonal K562 cell lines expressing the construct of interest were generated by transducing cells (8ug/mL) at a range of %v/v and performing flow cytometry 2 days later. Wells receiving dilutions with ~40% mCherry+ were selected and plated for monoclonal lines by limiting dilution. Monoclonal lines were transduced (10ug/mL) with varying titers to assess viral copy number. Library transduction with a 1.5%v/v was selected for the scCRISPRa experiment. For this experiment, 500k cells were transduced with virus containing the gRNA library. Cells were spun out of polybrene-containing media and replaced with standard K562 culture media. At 2 days post-transduction, 1ug/mL puromycin was added to the culture. 9 days after transduction, cells were collected for scRNA-seq.

value: imortalized myelogenous leukemia cell line

value: GDO

value: Monoclonal line expressing dCas9-p300 WT transduced with lentiviral sgRNA at MOI ~20


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep3

description:
Library name: TetOMexHT_rep3_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: M2M3_HOM_822315_SAN

description:
Library name: DSP-1001660020554-A-D02
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: 28mo-replicate1, GEX


title: M2M3_HET_862374_SAN

description:
Library name: DSP-1001660020554-A-C06
FFPE spatial transcriptome sequencing


title: dCas9-p300 I1417N

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: 28-mo, male, replicate2

description: RRBS

data_processing:
FASTQ files were mapped using mm10 assembly.
Bam files were processed using bismark to identify differentially methylated regions between samples.
Assembly: mm10
Supplementary files format and content: processed data includes bismark coverage and BedGraph files.

extract_protocol:
Cardiomyocyte nuclei were isolated and purified using MACS.
250 ng of DNA was used to generate libraries according to Zymo-seq RRBS Library Kit.

value: Cardiomyocytes


title: M2M3_HET_862374_RA

description:
Library name: DSP-1001660020554-A-C05
FFPE spatial transcriptome sequencing