title: CasMINI_SM4_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 4 repeat 2


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

status: Public on Jun 22 2025

type: SRA

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: Indel_rates_of_gRNA_mismatch-NLRC4.txt.gz

library_source: genomic

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for indel rate for gRNA taget sites.
Library strategy: Deep-Seq

molecule: genomic DNA

organism: Homo sapiens

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 2

growth_protocol: MCF7 cells were maintained inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
Two round PCR were performed, the forward and reverse primers were used to amplify the target site of the first round of PCR, and then an equal amount of the first PCR product was mixed with primers containing P5 and p7 for a second round of PCR to generate the library.

treatment_protocol: In 24-well plates, MCF7 cells were transfected with 490ng gRNA plasmids and 10ng CasMINI or hpCasMINI or SpCas9 or LbCas12a plasmids.

tag: cell line

value: MCF7 cell line

tag: cell type

value: epithelial cell


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 2


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 3


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 3 repeat 1


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 5 repeat 3


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 2


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 1


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 3


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 2


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 1 repeat 1


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 2 repeat 3


title: CasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, complete gRNA repeat 2


title: CasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, complete gRNA repeat 1


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting NLRC4, repeat 2


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting NLRC4, repeat 1


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting NLRC4, repeat 3


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, single mismatch gRNA site 7 repeat 1


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate3

description: Indel_rates_of_enRhCas12f1_and_exoRhCas12f1.txt.gz

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoRhCas12f1 system targeting four different genomic sites, repeat 3


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoRhCas12f1 system targeting four different genomic sites, repeat 1


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the enRhCas12f1 system targeting four different genomic sites, repeat 3


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the enRhCas12f1 system targeting four different genomic sites, repeat 2


title: CasMINI_DM3_Deep-seq_gRNA-mismatch_NLRC4_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, double mismatch gRNA site 3 repeat 1


title: enRhCas12f1_Deep-seq_RhCas12f1_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the enRhCas12f1 system targeting four different genomic sites, repeat 1


title: Ctrl_Deep-seq_compare_Replicate3

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat3


title: Ctrl_Deep-seq_RhCas12f1_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the enRhCas12f1 or exoRhCas12f1 system targeting four different genomic sites, repeat 3


title: Ctrl_Deep-seq_compare_Replicate2

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat2


title: Ctrl_Deep-seq_RhCas12f1_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the enRhCas12f1 or exoRhCas12f1 system targeting four different genomic sites, repeat 2


title: S_acidocaldarius_WT_ChIPseq_rep2

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: Library name: sample 4

data_processing:
Miseq Illumina short reads (50 bp) were mapped to the S. acidocaldarius reference genome using Bowtie2 VN:2.5.3. Alignment parameteres used were: -D 15 -R 2 -N 1 -L 22 -i S,1,1.15.
ChIP-seq peaks were called usign MACS2 and further manually inspected using Artemis, and potential segB binding sites were discovered using MEME-ChIP.
ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Assembly: NC_007181.1
Supplementary files format and content: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Sulfolobus acidocaldarius DSM 639

source_name: Exponential Phase cells

growth_protocol: 100 mL or 200 mL cultures of each strain were grown in Brock media till log phase (0.4-0.5 OD) at 75°C

extract_protocol:
Cultures were cooled down at room temperature for 10-15 minutes before crosslinking with 1% formaldehyde (final concentration) at 37°C for 30 minutes followed by quenching with 250mM Glycine (final concentration). Cells were centrifuged, washed with PBS, lysed and sonicated using Soniprep 150 probe-type sonicator (15ON, 15OFF, 13 cycles, 8 Amp).
DNA was pulled down using anti-segB polyclonal antibodies and proteiun A beads. DNA was extracted from the beads and purified using a PCR purification kit (Qiagen). ChIP libraries were prepared using the NEXT Ultra II library preparation kit (NEB).

value: Exponential Phase cells

tag: genotype

value: wild type

tag: treatment

value: cells were grown to exponential phase before formadehyde were added to 1% (final concentration) to fix cells for ChIP-seq.


title: S_acidocaldarius_WT_ChIPseq_rep1

description: Library name: sample 3


title: Ctrl_Deep-seq_RhCas12f1_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the enRhCas12f1 or exoRhCas12f1 system targeting four different genomic sites, repeat 1


title: Ctrl_Deep-seq_compare_Replicate1

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat1


title: SpCas9_Deep-seq_compare_Replicate1

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat1


title: SpCas9_Deep-seq_compare_Replicate2

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat2


title: LbCas12a_Deep-seq_compare_Replicate3

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat3


title: S_acidocaldarius_delta_segB_ChIPseq_rep2

description: Library name: sample 2

value: delta segB


title: S_acidocaldarius_delta_segB_ChIPseq_rep1

description: Library name: sample 1


title: CasMINI_Full_Deep-seq_gRNA-mismatch_NLRC4_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting NLRC4, complete gRNA repeat 3


title: LbCas12a_Deep-seq_compare_Replicate1

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat1


title: exoRhCas12f1_Deep-seq_RhCas12f1_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoRhCas12f1 system targeting four different genomic sites, repeat 2


title: AC-5

city: Heifei

first: Gao

last: Li

address: Meishan Road

institute: The First Affiliated Hospital of Anhui Medical University

description: Library name: Sample6

library_source: transcriptomic

data_processing:
CLC Genomics Workbench
Assembly: GRCm39
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Renal cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit. 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit  following manufacturer's protocols.

tag: tissue

value: Renal cortex

tag: strain

tag: Sex

value: male

value: wt

tag: batch


title: exoCasMINI_Deep-seq_compare_Replicate3

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, exoCasMINI repeat3


title: AC-1

description: Library name: Sample4


title: AC-4

description: Library name: Sample5


title: NC-6

description: Library name: Sample3

value: Control


title: LbCas12a_Deep-seq_compare_Replicate2

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat2


title: NC-5

description: Library name: Sample2


title: exoCasMINI_Deep-seq_compare_Replicate2

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, exoCasMINI repeat2


title: exoCasMINI_Deep-seq_compare_Replicate1

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, exoCasMINI repeat1


title: MDA-MB-231-LM2_6h-3D-Normoxia_rep3

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

data_processing:
Basecalls were performed using bcl2fastq v2.20
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1, using minimum-length 18, error-rate 0.2, overlap 5.
Trimmed reads were mapped against the GRChr37/hg19 human reference genome, using the STAR spliced alignment algorithm (version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts).
Assembly: hg19
Supplementary files format and content: tab delimited raw STAR gene counts file for each file
Supplementary files format and content: tab delimited raw genecounts for each sample combined

molecule: polyA RNA

source_name: Human breast

growth_protocol: MDA-MB-231-LM2 breast cancer cells were cultured in DMEM supplemented with 10% Foetal bovine serum (FBS) and maintained in culture at 37°C, 5% CO2.

extract_protocol:
RNA was isolated using the mirVana ™ miRNA isolation kit (Ambion™, Life Technologies) as per the manufacturer's instructions.
RNA integrity was established with Bioanalyzer 2100 (Agilent) trace.

treatment_protocol: MDA-MB-231-LM2 cells were cultured under normoxic conditions (ambient 21% O2), either as 2-dimensional (2D; on tissue culture plastic (TCP)) (1.5x105 cells/well in an uncoated 24 well plate, 3 wells combined for each replicate) or 3-dimensional (3D; Matrigel (VM)) cultures (1.5x105 cells/well in 24 well plate coated with 150ul Matrigel diluted 1:1 in PBS, 3 wells combined for each replicate) and cells harvested over a time course of 2 and 6 hours. All samples were prepared in triplicate.

value: Human breast

value: Adenocarcinoma triple negative breast cancer

value: WT

value: 6h 3D Normoxia

tag: time

value: 6 hours


title: CasMINI_Deep-seq_compare_Replicate3

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, CasMINI repeat3


title: SpCas9_Deep-seq_compare_Replicate3

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat3


title: CasMINI_Deep-seq_compare_Replicate1

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, CasMINI repeat1


title: MDA-MB-231-LM2_6h-2D-Hypoxia_rep3

value: 6h 2D Hypoxia


title: MDA-MB-231-LM2_6h-2D-Normoxia_rep3

value: 6h 2D Normoxia


title: CasMINI_Deep-seq_compare_Replicate2

source_name: Evaluation of the editing efficiency of exoCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, CasMINI repeat2

value: MCF7 cell line


title: Ctrl_Deep-seq_Replicate3

description: Indel_rates_of_CasMINI_and_exoCasMINI.txt.gz

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting ten different genomic sites, repeat 3

value: epithelial cell


title: MDA-MB-231-LM2_2h-3D-Normoxia_rep3

value: 2h 3D Normoxia

value: 2 hours


title: Ctrl_Deep-seq_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting ten different genomic sites, repeat 2


title: Ctrl_Deep-seq_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or exoCasMINI system targeting ten different genomic sites, repeat 1


title: MDA-MB-231-LM2_2h-2D-Normoxia_rep3

value: 2h 2D Normoxia


title: exoCasMINI_Deep-seq_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting ten different genomic sites, repeat 3


title: MDA-MB-231-LM2_2h-2D-Hypoxia_rep3

value: 2h 2D Hypoxia


title: MDA-MB-231-LM2_Control_rep3

value: 0 hours


title: exoCasMINI_Deep-seq_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting ten different genomic sites, repeat 2


title: NC-4

description: Library name: Sample1

value: Renal cortex

value: male


title: MDA-MB-231-LM2_6h-3D-Hypoxia_rep2

value: 6h 3D Hypoxia


title: MDA-MB-231-LM2_6h-2D-Normoxia_rep2

value: Human breast


title: CasMINI_Deep-seq_Replicate3

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 3


title: LeLab_ParT_manuscript_sample2

data_processing:
For analysis of ChIP-seq data, a reference genome of S. coelicolor A3(2) SCP1+ SCP2+ ϕBT1::parT-flag was first constructed by concatenating the sequences of a linear chromosome (Genbank ID: AL645882.2) (with the sequence of pIJ10257::parT-flag plasmid inserted at the ϕBT1 locus), a linear plasmid SCP1 (Genbank ID:  AL589148.1), and a cicular plasmid SCP2 (Genbank ID: AL645771.1) together. Subsequently, Hiseq 2500 (50 bp) or NextSeq 550 Illumina (75 bp) short reads were mapped back to this reference genome using Bowtie 1 and the following command: bowtie -M 1 -n 1 –best –strata -p 4 –chunkmbs 512 A32-bowtie –sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools using the following command: bedtools genomecov -d -ibam output.sorted.bam -g A32.fna > coverage_output.txt. When necessary, MACS2 were employed to call peaks, for example, using the following command: macs2 callpeak -t ./exp/output.sorted.bam -c ./control/output.sorted.bam -f BAM -g 8e+6 --nomodel -n expvscontrol. ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) or number of reads per kb per million mapped reads (RPKPM) using custom R scripts.
Assembly: AL645882.2
Supplementary files format and content: text file
Supplementary files format and content: Files starting with LeLab_coverage_output_: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Streptomyces coelicolor A3(2)

source_name: mycelium

growth_protocol: S.coelicolorA3(2) strains harboring a FLAG-tagged or non-tagged parT alleles under the control of an ermE* promoter (Supp.Table3) were grown as liquid cultures as follows. Firstly, the spore stocks were diluted to the final OD450 nm of 0.25 in 5 mL of 0.05 M TES buffer and were incubated standing at 50°C for 10 min before adding 5 mL of 2x PG medium (1% (w/v) of yeast extract, 1% (w/v) of casamino acids and 10 mM of CaCl2). Then, the heat-shocked spores suspensions were incubated with shaking at 37°C for 3 hours and subsequently pelleted by centrifugation at 3000 rpm for 10 min at room temperature. The pelleted spores were resuspended in 0.5 mL of growth media comprising 40% (v/v) of YEME and 60% (v/v) TSB and then transferred to a 50 mL of the same media in a conical flask where a metal spring was fit in the bottom to facilitate a disperse growth of Streptomyces mycelium. The cultures were then grown overnight at 30°C with shaking. Formaldehyde (Merck;cat# F8775) was added to the cultures to the final concentration of 1%(v/v) and the cultures were incubated for 30min at 30°C with shaking to fix the cells. The crosslinking reaction was quenched by adding glycine (Fisher Scientific; cat# 10467963) to the final concentration of 0.1M, followed bya 10-min incubation at room temperature on a wheel rotator.

extract_protocol:
DNA was isolated using the Qiagen PCR purification columns and solutions. Detailed protocols are listed in the Supplementary Materials and Methods
Standard library construction for Illumina Hiseq2500 or NextSeq550 sequencing platform

value: mycelium

value: S. coelicolor A3(2)phiBT1::parT-flag

tag: antibody

value: anti-FLAG


title: LeLab_ParT_manuscript_sample1

value: S. coelicolor A3(2)phiBT1::parT


title: CasMINI_Deep-seq_Replicate2

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 2


title: MDA-MB-231-LM2_2h-3D-Normoxia_rep2

value: Adenocarcinoma triple negative breast cancer

value: WT


title: MDA-MB-231-LM2_6h-2D-Hypoxia_rep2

value: 6h 2D Hypoxia

value: 6 hours


title: MDA-MB-231-LM2_2h-3D-Hypoxia_rep2

value: 2h 3D Hypoxia


title: MDA-MB-231-LM2_6h-3D-Normoxia_rep2

value: 6h 3D Normoxia


title: exoCasMINI_Deep-seq_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the exoCasMINI system targeting ten different genomic sites, repeat 1

value: MCF7 cell line

value: epithelial cell


title: MDA-MB-231-LM2_6h-3D-Hypoxia_rep3


title: T, H3K27ac CUT&RUN

city: Saint Louis

first: Jing

state: MO

address: 600 S Euclid Ave

country: USA

institute: Washington University in St. Louis

description: Library name: T

data_processing:
The adaptor sequences were removed by Trimmomatic program. The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5. Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9). Data were visualized with the 'makeUCSCfile' of Homer. Peaking calling was performed with Homer software package.
Assembly: Genome_build: mm10
Supplementary files format and content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.
Library strategy: CUT&Run

source_name: BM MDP and CDP

extract_protocol:
0.5 million fresh cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg indicated antibodies overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.

value: BM MDP and CDP

value: wildtype

tag: cut&run antibody

value: H3K27ac (abcam4729)


title: MDA-MB-231-LM2_2h-2D-Normoxia_rep2

value: 2h 2D Normoxia

value: 2 hours


title: MDA-MB-231-LM2_2h-3D-Hypoxia_rep3

value: Human breast


title: IRF8KO, H3K27ac CUT&RUN

description: Library name: IRF8KO


title: MDA-MB-231-LM2_2h-2D-Hypoxia_rep2

value: 2h 2D Hypoxia


title: CasMINI_Deep-seq_Replicate1

source_name: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 1


title: MDA-MB-231-LM2_Control_rep2

value: 0 hours


title: Huh7_DDX21_ChIP

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
wig files were generated using deepTools.
Assembly: hg38
Supplementary files format and content: RNAseq_Huh7_NC_vs_FAM99B.xlsx
Supplementary files format and content: RNAseq_Huh7_siNC_vs_siDDX21.xlsx
Supplementary files format and content: Huh7-DDX21_vs_Input_peaks.loc.anno.gene.xlsx

source_name: liver

growth_protocol: Huh 7 was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.  Methods.2009;48:240-8)；
Total RNA extracted using TRIzol was used for library preparation with an Illumina mRNA sequencing (mRNAseq) sample preparation kit.  Quality control of the RNA sequencing libraries was performed using a Bioanalyzer 2100 (Agilent, CA, USA) prior to paired-end sequencing on the HiSeq 3000 platform (Illumina, CA, USA);  CUT&Tag was performed according to the manufacturer’s protocol (Novoprotein, Shanghai, China).

treatment_protocol: siRNAs targeting DDX21 and negative control siRNAs (siNCs) were procured from RiboBio (Guangzhou, China).  Cells were transfected with the specified targeted or control siRNA  using Lipofectamine RNAiMAX reagent (Invitrogen, CA, USA).  After 48 hours of transfection, the cells were collected for further experiments.Huh7 cells with stable overexpression of FAM99B and control cells were collected for further experiments.

value: liver

value: HCC cells


title: MDA-MB-231-LM2_6h-3D-Normoxia_rep1

source_name: Human breast

value: Adenocarcinoma triple negative breast cancer

value: WT


title: d12_2, H3K27ac CUT&RUN

description: Library name: d12_2


title: LeLab_ParT_manuscript_sample3

value: mycelium

value: S. coelicolor A3(2)phiBT1::flag-parT

value: anti-FLAG


title: Huh7_Input_ChIP

description: Huh7-DDX21_vs_Input_peaks.loc.anno.gene.xlsx


title: MDA-MB-231-LM2_6h-2D-Normoxia_rep1

value: 6h 2D Normoxia

value: 6 hours


title: d12_1, H3K27ac CUT&RUN

description: Library name: d12_1

value: BM MDP and CDP


title: MDA-MB-231-LM2_6h-2D-Hypoxia_rep1

value: 6h 2D Hypoxia


title: MDA-MB-231-LM2_2h-3D-Normoxia_rep1

value: 2h 3D Normoxia


title: d1_2, H3K27ac CUT&RUN

description: Library name: d1_2

value: H3K27ac (abcam4729)


title: Huh7_siNC

description:
siDDX21-1
RNAseq_Huh7_siNC_vs_siDDX21.xlsx

value: Huh7 cells transfected with siNC


title: d1_1, H3K27ac CUT&RUN

description: Library name: d1_1


title: MDA-MB-231-LM2_2h-3D-Hypoxia_rep1

value: Human breast

value: 2h 3D Hypoxia

value: 2 hours


title: MDA-MB-231-LM2_2h-2D-Normoxia_rep1

value: 2h 2D Normoxia


title: MDA-MB-231-LM2_2h-2D-Hypoxia_rep1

value: 2h 2D Hypoxia


title: Huh7_FAM99B

description:
L-99b-2
RNAseq_Huh7_NC_vs_FAM99B.xlsx

value: liver

value: HCC cells

value: FAM99B overexpression

value: Huh7 cells infected with pWPXL-FAM99B lentivirus


title: d1pm_2, H3K27ac CUT&RUN

description: Library name: d1pm_2


title: d1pm_1, H3K27ac CUT&RUN

description: Library name: d1pm_1


title: Lelab_ParT_manuscript_sample12

description: Library name: sample 12

data_processing:
For analysis of ChIP-seq data, a reference genome of S. coelicolor A3(2) SCP1- SCP2- i.e. M600 + ϕBT1::parT (WT or G87P)-flag was first constructed by concatenating the sequences of a linear chromosome (Genbank ID: AL645882.2) and the sequence of pIJ10257::parT-flag plasmid inserted at the ϕBT1 locus together. Subsequently, NextSeq 550 Illumina short reads were mapped back to this reference genome using Bowtie 1 and the following command: bowtie -M 1 -n 1 –best –strata -p 4 –chunkmbs 512 A32-bowtie –sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools using the following command: bedtools genomecov -d -ibam output.sorted.bam -g A32.fna > coverage_output.txt. When necessary, MACS2 were employed to call peaks, for example, using the following command: macs2 callpeak -t ./exp/output.sorted.bam -c ./control/output.sorted.bam -f BAM -g 8e+6 --nomodel -n expvscontrol. ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) or number of reads per kb per million mapped reads (RPKPM) using custom R scripts.
Assembly: AL645882.2
Supplementary files format and content: Files starting with LeLab_coverage_output_: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

source_name: mixed population, exponential phase, mycelium

growth_protocol: S. coelicolor A3(2) strains harboring a FLAG-tagged or non-tagged parT alleles under the control of an ermE* promoter were grown as liquid cultures as follows. Firstly, the spore stocks were diluted to the final OD450 nm of 0.25 in 5 mL of 0.05 M TES buffer and were incubated standing at 50°C for 10 min before adding 5 mL of 2x PG medium (1% (w/v) of yeast extract, 1% (w/v) of casamino acids and 10 mM of CaCl2). Then, the heat-shocked spores suspensions were incubated with shaking at 37°C for 3 hours and subsequently pelleted by centrifugation at 3000 rpm for 10 min at room temperature. The pelleted spores were resuspended in 0.5 mL of growth media comprising 40% (v/v) of YEME and 60% (v/v) TSB and then transferred to a 50 mL of the same media in a conical flask where a metal spring was fit in the bottom to facilitate a disperse growth of Streptomyces mycelium. The cultures were then grown overnight at 30°C with shaking. Formaldehyde (Merck; cat# F8775) was added to the cultures to the final concentration of 1% (v/v) and the cultures were incubated for 30 min at 30°C with shaking to fix the cells. The crosslinking reaction was quenched by adding glycine (Fisher Scientific; cat# 10467963) to the final concentration of 0.1 M, followed by a 10-min incubation at room temperature on a wheel rotator.

extract_protocol:
DNA was isolated using the Qiagen PCR purification columns and solutions. Detailed protocols are listed in the Supplementary Materials and Methods
Standard library construction for Illumina NextSeq550 sequencing platform

value: S. coelicolor M600 thetaBT1::parT (G87P)-flag

value: cells (mycelium) were grown to exponential phase from spores before formadehyde were added to 1% (final concentration) to fix cells for ChIP-seq.


title: Lelab_ParT_manuscript_sample10

description: Library name: sample 10

value: mixed population, exponential phase, mycelium

value: S. coelicolor M600 thetaBT1::parT-flag


title: Lelab_ParT_manuscript_sample11

description: Library name: sample 11


title: sample 1

city: Taizhou

first: Qingtao

last: Ni

state: State...

address: hailingnanlu No 399

institute: Jiangsu Taizhou People's Hospital

library_source: transcriptomic single cell

data_processing:
The BD Rhapsody WTA Analysis Pipeline (version 2.0) was employed for the generation of sequencing libraries from individual cell transcriptomes, without the specification of a targeted panel. Subsequent to sequencing, the analysis pipeline utilizes the FASTQ files, a reference genome file, and a transcriptome annotation file for sequence alignment. The unique molecular identifier (UMI) count matrix was processed using the R package Seurat (version 4.0.0)
Assembly: hg18
Supplementary files format and content: tab-delimited text files

source_name: plasma cell mastitis tissue

extract_protocol:
The cell suspension that had undergone digestion was passed through a BD 40μm cell sieve. Then, an equal volume of Red Blood Cell Lysis Solution (Miltenyi Biotec) was introduced and subjected to centrifugation for a duration of 5 minutes. The precipitate was subsequently washed using cold Sample Buffer (BD Rhapsody™ Cartridge Reagent Kit).
The resulting libraries were assessed for base balance and sequenced on the Illumina Nova 6000 platform

value: plasma cell

tag: disease state

value: Plasma cell mastitis

value: operation


title: Lelab_ParT_manuscript_sample9

description: Library name: sample 9

value: S. coelicolor M600 thetaBT1::parT


title: WT_2, H3K27ac CUT&RUN

description: Library name: WT_2

value: BM MDP and CDP

value: wildtype

value: H3K27ac (abcam4729)


title: MDA-MB-231-LM2_6h-3D-Hypoxia_rep1

value: Human breast

value: Adenocarcinoma triple negative breast cancer

value: WT

value: 6h 3D Hypoxia

value: 6 hours


title: Lelab_ParT_manuscript_sample8

description: Library name: sample 8


title: Lelab_ParT_manuscript_sample7

description: Library name: sample 7


title: WT_1, H3K27ac CUT&RUN

description: Library name: WT_1


title: 2_CORL88_TAS1440 [scRNA-seq]

city: Bethesda

first: Nitin

last: Roper

state: MD

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

description: 10x genomics

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.1.0 (STAR 2.7.2a).
Assembly: hg19 and mm10
Supplementary files format and content: H5 files

source_name: cell line

extract_protocol:
Single cells were collected for the COR-L88 cell line by trypsinization. For KP1, tumors were dissociated using the Tumor Dissociation Kit (Miltenyi #130-096-730) and mechanically separated using gentleMACS™ dissociators (Miltenyi #130-093-235) following the manufacturer’s protocol.
Single-cell libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5’v2 (Dual Index) kit, following the standard manufacturer’s protocols, with a single capture lane allocated per sample. The target recovery was set at 8000 cells per lane. Cells were partitioned, followed by reverse transcription of mRNA, and library preparation was carried out according to the user guide provided for the Chromium Connect system.

value: cell line

value: small cell lung cancer


title: Xist-Delm6A-11C_Dox24h

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

description:
Library name: Xist-Delm6A-11C_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)

library_source: other

data_processing:
The ChrRNA-seq data mapping pipeline used in this study was similar to our previous work (Pintacuda et al 2017; Nesterova et al 2019). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (mm10) with STAR using parameters (--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd) for all the sequencing libraries. Unique alignments were retained for further analysis. We made use of SNPs between Cast and 129S genomes and employed SNPsplit (v0.4.0dev, Babraham Institute, Cambridge, UK) to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) and the alignments were sorted by Samtools. Files of bigWig were generated by Bedtools and visualized by IGV or UCSC Genome Browser. Metagene profile and heatmap were generated by deepTools, as well as custom python scripts. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the R package of edgeR. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of Xi/(Xi+Xa) where Xi and Xa indicate inactive and active allele, respectively. Principal components analysis (PCA) was done using the prcomp function in R and plotted using the ggplot2 package. Allelic ratio of samples derived from SPEN KO or deletion of Xist B/C-repeat were taken from the previous studies, gene categories including initial X-linked gene expression level and promoter chromatin landscape were taken from Nesterova et al, 2019 and Pintacuda et al 2017, gene silencing kinetics data were taken from Bowness et al, 2022.
Assembly: mm10
Supplementary files format and content: text file with allelic ratio called for each X-linked genes (note: previously published WT cells [Neseterova et al Nature Comm 2019, GSE119602] and Xist_Delm6A_11C [Coker et al, Wellcoome Open Research 2020, GSE142270] data are used for comparion as well)

molecule: other

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

growth_protocol: ES cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1000U/mL Leukemia Inhibitory Factor (LIF) (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Chromatin RNA was extracted from one confluent T25 plates of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse.
Approximal 100 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by Qubit. The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours.

tag: strain background

value: Cast x 129S

value: mESC

tag: xist type

value: Endogenous Xist (exon1 m6A region 355bp deletion)


title: Xist-Delm6A-11C

description:
Library name: Xist-Delm6A-11C
RNA type: Chromatin-associated RNA (ChrRNA)

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: NoDox


title: Huh7_siDDX21

description:
siDDX21-2
RNAseq_Huh7_siNC_vs_siDDX21.xlsx

value: liver

value: HCC cells

value: DDX21 knockdown

value: Huh7 cells transfected with siDDX21


title: S3D3

first: Wang

last: tong

address: meilong road 130,Shanghai,China

institute: East China University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cervical

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Cervical

value: HeLa

value: Cervical cancer cells


title: ACE2KO5

city: Jining

first: Shuai

last: Xiao

address: No. 1068 Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District, Shenzhen, China University Town of Shenzhen, Xili Nanshan, Shenzhen 518055, P.R.China

institute: Jining First People's Hospital Affiliated to Shandong First Medical University

description: Library name: ACE2KO5

data_processing:
The raw paired-end fastq reads underwent filtering by Trimmomatic to eliminate adapters and low-quality bases.
The resulting clean reads were then aligned to the genome using hisat2, followed by reference-guided transcriptome assembly and gene expression quantification utilizing htseq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene_count values for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA)

value: Liver

value: Liver cells

value: knockout

value: male


title: Xist-Delm6A-7E_Dox24h

description:
Library name: Xist-Delm6A-7E_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)

value: Endogenous Xist (exon1 m6A region 355bp deletion and exon7 m6A region 153bp deletion)


title: 1_CORL88_DMSO [scRNA-seq]

description: 10x genomics

value: cell line

value: small cell lung cancer

value: DMSO


title: MDA-MB-231-LM2_Control_rep1

value: Human breast

value: Adenocarcinoma triple negative breast cancer

value: WT

value: 0 hours


title: Huh7_NC

description:
L-v-2
RNAseq_Huh7_NC_vs_FAM99B.xlsx

value: liver

value: HCC cells

value: Huh7 cells infected with pWPXL lentivirus


title: S3D2

value: Cervical

value: HeLa


title: ACE2KO3

description: Library name: ACE2KO3

value: Liver


title: ACE2KO4

description: Library name: ACE2KO4

value: Liver cells


title: S3D1

value: Cervical cancer cells


title: LARP-1::APEX2  IP-RNA-seq 2

city: Kunming City

first: Jiangyang Li

last: Jingyang Li

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

department: School of Life Science

institute: Yunnan Universiity

description:
Library name: Sample 5
LARP-1::APEX2  RNA-seq

data_processing:
RNA-seq raw reads were first processed using Trim Galore to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to a custom rRNA reference using Bowtie to remove rRNA contamination. Non-rRNA reads were subsequently mapped to the Caenorhabditis elegans genome (ce11) using STAR aligner with a genome index built from the ce11 genome assembly. Gene-level expression quantification was performed on the aligned BAM files using featureCounts, and normalized read counts were generated using DESeq2.
Assembly: The reference genome used for alignment and downstream analysis was the Caenorhabditis elegans genome assembly ce11, obtained from the UCSC Genome Browser. STAR genome indices were built based on this assembly.
Supplementary files format and content: The processed data includes:  BAM files: STAR-aligned reads to the ce11 genome.  Read count matrix (tab-delimited text): Raw and DESeq2-normalized gene expression counts generated by featureCounts and DESeq2. Each row in the count matrix corresponds to a gene, and each column corresponds to a sample, with values indicating raw or normalized counts.

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: C. elegans animals were cultured on NGM plates seeded with E. coli OP50 at 20 ℃

extract_protocol:
Total RNA was isolated by using TRIzol (Invitrogen)
Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Cat# 15596018), and genomic DNA was removed by DNase I treatment following the manufacturer's instructions (Thermo Scientific, Cat# EN0521). For library construction, ribo-depleted RNA-seq libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (Vazyme, Cat# NRM605-02). Library quality and fragment size distribution were assessed using a Bio-Fragment Analyzer.

treatment_protocol: Young adult animals from 150 10-cm plates were harvested and washed with M9T buffer (M9 buffer with 0.1% Tween 20). The animals were re-suspended in 950 μl of the labeling solutions (M9T buffer with 3.3 mM Biotin-aniline) for 2 h at 25 ℃ , and used for proximity labelling of RNAs.The proximity labeling of RNAs was achieved by adding 11 μl of H2O2 (100 mM) to the samples and incubating for 2 min, followed by adding 500 μl ice-cold quenching buffer (M9T containing 10 mM sodium azide, 10 mM sodium ascorbate and 5 mM Trolox). Samples were collected by centrifugation of 1,500 rpm at 4℃ and washed 4 times with 1 ml of quenching buffer.

value: Whole organism

value: LARP-1::APEX2 (yq637)


title: LARP-1::APEX2  IP-RNA-seq 3

description:
Library name: Sample 6
LARP-1::APEX2  RNA-seq


title: Xist-Delm6A-6F_Dox24h

description:
Library name: Xist-Delm6A-6F_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: mESC

value: Endogenous Xist (exon1 m6A region 355bp deletion)


title: 3_CORL88_TAS1440_GSI [scRNA-seq]

description: 10x genomics

value: cell line

value: small cell lung cancer


title: S2D3


title: Xist-Delm6A-6F

description:
Library name: Xist-Delm6A-6F
RNA type: Chromatin-associated RNA (ChrRNA)

value: NoDox


title: LARP-1::APEX2  IP-RNA-seq 1

description:
Library name: Sample 4
LARP-1::APEX2  RNA-seq


title: ACE2KO1

description: Library name: ACE2KO1

value: knockout

value: male


title: S2D2


title: LARP-1::GFP IP-RNA-seq 3

description:
Library name: Sample 3
LARP-1::GFP  RNA-seq

value: LARP-1::GFP (yq636)


title: S2D1

value: Cervical


title: LARP-1::GFP IP-RNA-seq 2

description:
Library name: Sample 2
LARP-1::GFP  RNA-seq


title: Xist-Delm6A-4E_Dox24h

description:
Library name: Xist-Delm6A-4E_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)

value: Endogenous Xist (exon7 m6A region 153bp deletion)


title: CK5

description: Library name: CK5

value: Liver

value: WT


title: CK4

description: Library name: CK4

value: Liver cells


title: Xist-Delm6A-4E

description:
Library name: Xist-Delm6A-4E
RNA type: Chromatin-associated RNA (ChrRNA)


title: LARP-1::GFP IP-RNA-seq 1

description:
Library name: Sample 1
LARP-1::GFP  RNA-seq

value: Whole organism


title: HT29 cells, shNFIB-991-miRNA

city: Chongqing

first: Li

last: Zhou

address: 1, Medical College Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

data_processing:
data evaluation of sRNA raw data mainly includes two aspects: 1) filtering of impurities; 2) Preliminary judgment of data quality.
The data quality statistics and length distribution statistics were carried out on the filtered data.
The species (represented by unique) and the total amount (represented by total) of common and endemic sequences between the two samples were counted.
The sRNA was located to the genome by SOAP, and the expression and distribution of tags on the genome were analyzed.
Comparing sRNA with miRBase database through blast. Expdiff method: log2-ratio and Scatter plot were respectively used to compare the differences in the expression levels of the mirnas co-expressed between the two samples.
Assembly: hg38
Supplementary files format and content: png and excel

growth_protocol: HT29 cells were maintained in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% FBS (Gibco, USA) and cultured in a 37°C incubator containing 5% CO2.

extract_protocol:
Total RNA from NFIB-knockdown HT29 or control cells was extracted and sequenced by Vazyme Corporation (Nanjing, China) to reveal differentially expressed mRNAs, lncRNAs, circRNAs, and small RNAs. After removing rRNA using the Ribo-Zero kit (Illumina, USA), the cDNA library was constructed using VAHTSTM DNA Clean Beads (Vazyme, China). The final libraries were quantified using an Agilent 2100 Bioanalyzer (Agilent, USA) and an ABI Step One Plus Real-Time PCR system.
The libraries were then sequenced on a HiSeq 2500 platform (Illumina, USA). For small RNA sequencing, small RNA was isolated from total RNA using 15% PAGE. The small RNA library was constructed using the TruSeq Small RNA Sample Preparation Kit (Illumina, USA). The libraries were then sequenced on a Hiseq 2500 platform (Illumina, USA) using a synthetic method.

treatment_protocol: Lentiviral particles containing shRNA sequences targeting NFIB (shRNA-991: GCCACATCATATCACAGTA; shRNA-993: CCAATTGGAGAAATCCCAA) or the NFIB coding sequence (NM_005596) were purchased from Obio (China). HT29 cells were seeded at 50-60% confluence and then they were transfected with lentivirus particles. Puromycin (Sigma-Aldrich, St Louis, MO, USA) was used to select stable clones 72 h after transfection. Knockdown efficiency was validated using qRT-PCR and western blotting.

value: Human colorectal cancer cell

value: NFIB knockdown


title: Xist-Delm6A-7E

description:
Library name: Xist-Delm6A-7E
RNA type: Chromatin-associated RNA (ChrRNA)

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: Endogenous Xist (exon1 m6A region 355bp deletion and exon7 m6A region 153bp deletion)


title: CK3

description: Library name: CK3


title: Xist-Delm6A-3B

description:
Library name: Xist-Delm6A-3B
RNA type: Chromatin-associated RNA (ChrRNA)

value: mESC


title: CK2

description: Library name: CK2


title: LeLab_ParT_manuscript_sample6

value: mycelium

value: S. coelicolor A3(2)phiBT1::flag-parT

value: anti-FLAG


title: LeLab_ParT_manuscript_sample5

value: S. coelicolor A3(2)phiBT1::parT-flag


title: Xist-Delm6A-2B_Dox24h

description:
Library name: Xist-Delm6A-2B_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)

value: Endogenous Xist (WT)


title: Xist-Delm6A-3B_Dox24h

description:
Library name: Xist-Delm6A-3B_Dox24h
RNA type: Chromatin-associated RNA (ChrRNA)


title: ACE2KO2

description: Library name: ACE2KO2

value: knockout

value: male


title: HT29 cells, GFP-miRNA


title: LeLab_ParT_manuscript_sample4

value: S. coelicolor A3(2)phiBT1::parT


title: SW620 cells, input, ChIP

data_processing:
Use Fastqc software to control the raw data.
The raw data is filtered using the software NGS QC Toolkit to filter out low-quality sequences (N<5%), sequences containing N, and sequences containing joints (> 30%).
Use the bowtie1 software to post the clean reads of each sample to the reference genome, mismatch=2, with specific parameters: -m1 and -best.
Peaks were called using MACS14 with the significance cut-off q-value<=10-5.
The R package (ChIPseeker) was used to analyze the peak sequence, such as related gene retrieval, genome component distribution, and a series of statistics. The related genes of peak were searched for the potential regulatory genes of the protein.
Assembly: hg38
Supplementary files format and content: bigWig, peakannostat (except for input sample)

growth_protocol: SW620 cells were maintained in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% FBS (Gibco, USA) and cultured in a 37°C incubator containing 5% CO2.

extract_protocol:
Cells were crosslinked with formaldehyde, and chromatin was fragmented by digestion with micrococcal nuclease and sonication.
The final libraries were quantified using an Agilent 2100 Bioanalyzer (Agilent, USA) and KAPA kit (Cat no. KK4602, UK). The libraries were then sequenced on a Hiseq 2500 platform (Illumina, USA). Peaking calling was performed based on the filtered sequence data. The peaks were further annotated according to the reference genome.

tag: chip antibody

value: input


title: PS mice, 24-weeks old, gene expression, pool of 4 mice

status: Public on Jun 21 2025

city: Toulouse

first: Rüçhan

last: Ekren

address: CHU Purpan – BP 3028 –  Toulouse Cedex, 3

department: INFINITY

country: France

institute: Inserm UMR 1291

description:
Library name: PS24gex
10x Genomics single cell Multiome ATAC + Gene Expression sequencing

data_processing:
ATAC reads and transcript reads were demultiplexed, and aligned to reference mouse genome (mm10 - GENCODE vM23/Ensembl 98) and quantified by the cellranger-arc-2.0.2
Seurat (v5.1.0) and Signac (v1.14) R packages  was preferred as a suite of analysis. Cells were retained if they exhibited high data quality, defined by RNA features ≥300 and RNA counts <5,000, ATAC counts between 100 and 20,000, mitochondrial RNA content <10%, a nucleosome signal <0.75, and TSS enrichment >2, ensuring the exclusion of low-quality cells, empty droplets, stressed or apoptotic cells, and potential doublets. After this QC-trimming, a total of 12499 cells (2130 cells from Control-week 8, 4094 cells from PS-week 8, 3767 cells from Control-week 24 and 2508 cells from PS-week 24) were retained for further analysis.
Assembly: mm10 - GENCODE vM23/Ensembl 98
Supplementary files format and content: h5 files of the filtered feature matrix of each sample and gzipped tsv files of atac_fragments, generated by Cell Ranger Arc (v2.0.2)
Library strategy: Multiome

molecule: nuclear RNA

source_name: Skin

growth_protocol: Mice were bred and housed in the local animal facilities of CREFRE (Toulouse, France) in pathogen-free sanitary conditions, with free access to water and food, and were submitted to alternating cycles of 12 hours of light and darkness at an ambient temperature of 22°C. Both age-matched male and female mice were used in experiments. All animal care and experimentation were conducted in France in compliance with the guidelines of the European Union (86/609/EEC) and the French Committee of Ethics (87/848) policies and with the specific approval from the local ministry-approved committee on ethics in animal experimentation (Ethics Committee UMS006 CEEA-122, project n°21938-2019090417341270v5).

extract_protocol:
Cell suspensions from adult mouse skin were obtained through mechanical dissociation and enzymatic digestion. Briefly, adult back skin from W8 or W24 mice was harvested in pre-digestion medium, finely minced and incubated at 37°C on a rotating plate to remove epithelial cells and other impurities. The samples were then digested for 45 minutes on a rotating plate with 1.25 mg of Liberase TM (Sigma) and 2.5 mg of DNAse I (Sigma) to disaggregate the tissue. Samples were further dissociated with the Miltenyi gentleMACS Dissociator and cells were then enriched with a Percoll gradient. Single cell suspensions were then magnetically sorted for CD45+ immune cells using Miltenyi CD45 microbeads.
Single nuclei were isolated following the 10X Genomics Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol (CG000365-Rev C). Briefly, approximately 150,000 single cells were lysed in chilled 0.025% IGEPAL Lysis Buffer (10X Genomics). The lysate was incubated on ice for 2 minutes, after which chilled Wash Buffer (10X Genomics) was added to quench lysis. The nuclei were then washed three times using Wash Buffer to remove cellular debris and residual lysis buffer components. Following the washes, the nuclei suspension was resuspended in Diluted Nuclei Buffer (10X Genomics) and filtered through a 40 μm strainer to remove aggregates and debris. Nuclei quality and concentration were assessed using Trypan Blue staining and quantified with a Countess 3 Automated Cell Counter (Thermo Fisher Scientific). Only preparations with greater than 80% intact nuclei and minimal debris were selected for downstream processing to ensure optimal sample integrity and sequencing efficiency. Nuclei were immediately treated using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338-Rev F). Nuclei were diluted to the optimal concentration (9000–10 000 nuclei/μL) and loaded into the Chromium Next GEM Chip J, followed by partitioning into Gel Bead-in-Emulsions (GEMs) using the Chromium X (10X Genomics). Reverse transcription and ATAC transposition were performed simultaneously within individual GEMs according to the manufacturer’s protocol. After GEM rupture, cDNA and transposed DNA fragments were purified using Dynabeads MyOne Silane (Thermo Fisher Scientific). Transposed DNA fragments underwent 7 PCR cycles amplification to generate chromatin accessibility libraries, while cDNA fragments were further processed through end-repair, adapter ligation, and 10 indexing PCR cycles to generate enrich gene expression libraries. The resulting gene expression and ATAC libraries were quantified using a Qubit Fluorometer (Thermofisher Scientific) and analyzed for fragment size distribution using an Agilent TapeStation before sequencing. The libraries were pooled at the recommended ratio and sequenced on an Illumina NovaSeq 6000 platform (Illumina) using paired-end reads (Read 1: 50 bp, Read 2: 49 bp, Index 1: 8 bp, Index 2: 24 bp), targeting a sequencing depth of ~25,000 read pairs per nucleus for ATAC ; and using paired-end reads (Read 1: 28 bp, Read 2: 90 bp, Index 1: 10 bp, Index 2: 10 bp), targeting a sequencing depth of ~50,000 read pairs per nucleus for gene expression to achieve a mean sequencing depth of 3350 median fragments per cell for a mean of 14946 cells post-aggregation.

treatment_protocol: Eight- to 10-week-old male and female mice were subjected to timed pregnancies. Pregnant dams were then subject to chronic restraint stress in transparent drilled 50-ml tubes, put under a bright light (200W), 3 times a day for 30 minutes each, from embryonic day (E)-13 until E-18. Control (CT) pregnant females were left undisturbed. After birth, all pups were kept in the same cage with their biological mother. Pups were then weaned at the age of 21 to 28 days in distinct gender groups in new cages and introduced to a new diet. Skin samples were collected from 8-week old (W8) and 24-week old (W24) control (CT) and PS offspring, and single Cell Multiome ATAC + Gene Expression sequencing of enriched CD45+ cells was conducted.

value: Skin

tag: age

value: 24-weeks old

value: CD45+ immune cells

tag: group

value: Prenatal stress offspring


title: SW620 cells, NFIB, ChIP

tag: cell line

value: Human colorectal cancer cell

value: NFIB


title: PS mice, 24-weeks old, ATAC, pool of 4 mice

description:
Library name: PS24atac
10x Genomics single cell Multiome ATAC + Gene Expression sequencing

tag: cell type


title: control mice, 24-weeks old, ATAC, pool of 4 mice

description:
Library name: C24atac
10x Genomics single cell Multiome ATAC + Gene Expression sequencing

tag: genotype

value: Control offspring


title: Xist-Delm6A-2B

description:
Library name: Xist-Delm6A-2B
RNA type: Chromatin-associated RNA (ChrRNA)

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (129 allele)

value: mESC

tag: treatment

value: NoDox


title: PS mice, 8-weeks old, gene expression, pool of 4 mice

description:
Library name: PS8gex
10x Genomics single cell Multiome ATAC + Gene Expression sequencing

tag: tissue

value: 8-weeks old


title: PS mice, 8-weeks old, ATAC, pool of 4 mice

description:
Library name: PS8atac
10x Genomics single cell Multiome ATAC + Gene Expression sequencing


title: control mice, 24-weeks old, gene expression, pool of 4 mice

description:
Library name: C24gex
10x Genomics single cell Multiome ATAC + Gene Expression sequencing


title: control mice, 8-weeks old, gene expression, pool of 4 mice

description:
Library name: C8gex
10x Genomics single cell Multiome ATAC + Gene Expression sequencing


title: wt_15_sed_8

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description: Library name: 0156_8

data_processing:
Reads were aligned to the mouse genome assembly (mm10) using STAR aligner
Transcripts were counted using featureCounts
Assembly: mm10
Supplementary files format and content: text file with raw counts per sample

source_name: gastrocnemius

growth_protocol: HIF1α flox mice were obtained from The Jackson Laboratory (RRID:IMSR_JAX:007561). Skeletal muscle-specific deletion of Hif1α was generated by crossing HIF1αflox homozygote mice with mice carrying the cre-recombinase driven by the human α-skeletal actin (HSA) promoter heterozygote males 28. Experimental animals were derived from crossing homozygote HIF1αflox females (HSA-Cre-/- and HIF1αfl/fl) with homozygote HIF1αflox and heterozygote HSA-cre males (HSA-Cre+/- and HIF1αfl/fl) (Figure 1A). Mice were bred on a C57BL/6JBomTac background for 2-9 generations before experimental use. All mice were group-housed with littermates of the same sex (2–7 in a cage) and maintained at 22 ± 1°C under a 12:12 hr light:dark cycle. Mice had ad libitum access to a chow diet (Altromin #1310) and water.

extract_protocol:
RNA was extracted from gastrocnemius muscle (~30mg). Tissue was homogenised in Trizol (1 mL) using a steel bead with the Qiagen TissueLyser II (3 x 90 sec at 30 Hz; 4°C). Chloroform (200 mL) was added to all the samples and mixed by 30 seconds of shaking prior to centrifugation for 15 minutes at 12,000 g at 4°C. The aqueous phase was combined with an equivalent volume of 70% ethanol and thereafter RNA extraction was performed according to the manufacturers’ instructions for the RNeasy Mini Kit (74,106, Qiagen).
Libraries were prepared uisng 500 ng of RNA and the TruSe Stranded mRNA Library Prep assay kit, according to manufacturers instructions.

treatment_protocol: Skeletal muscle specific HIF1α knock out and wild type mice were subjected to 60 min treadmill running (16 m/min, 5 % incline) or a sham treatment at zeitgeber time (ZT) 3 and ZT 15.

value: gastrocnemius

value: m

tag: zt

value: wt

value: sed


title: wt_15_sed_63

description: Library name: 0156_63

tag: Sex

value: f


title: control mice, 8-weeks old, ATAC, pool of 4 mice

description:
Library name: C8atac
10x Genomics single cell Multiome ATAC + Gene Expression sequencing

value: Skin


title: ko_15_sed_64

description: Library name: 0156_64

value: ko


title: wt_3_sed_62

description: Library name: 0156_62


title: ko_15_ex_61

description: Library name: 0156_61

value: ex


title: wt_3_sed_60

description: Library name: 0156_60


title: CK1

description: Library name: CK1

value: Liver

tag: strain

value: Liver cells

value: WT

value: male


title: ko_15_ex_59

description: Library name: 0156_59


title: ko_3_ex_58

description: Library name: 0156_58


title: wt_3_ex_57

description: Library name: 0156_57


title: wt_15_sed_56

description: Library name: 0156_56


title: ko_3_sed_55

description: Library name: 0156_55


title: wt_15_ex_52

description: Library name: 0156_52


title: ko_3_ex_53

description: Library name: 0156_53


title: ko_15_ex_51

description: Library name: 0156_51


title: wt_3_ex_50

description: Library name: 0156_50


title: wt_15_sed_49

description: Library name: 0156_49


title: wt_3_ex_48

description: Library name: 0156_48


title: ko_3_sed_45

description: Library name: 0156_45


title: ko_3_ex_44

description: Library name: 0156_44


title: wt_15_ex_46

description: Library name: 0156_46


title: ko_15_sed_43

description: Library name: 0156_43


title: wt_3_sed_5

description: Library name: 0156_5


title: ko_15_sed_42

description: Library name: 0156_42


title: ko_15_ex_9

description: Library name: 0156_9


title: wt_3_sed_7

description: Library name: 0156_7


title: wt_15_sed_41

description: Library name: 0156_41


title: wt_15_sed_40

description: Library name: 0156_40


title: wt_15_ex_39

description: Library name: 0156_39


title: wt_3_ex_6

description: Library name: 0156_6


title: wt_3_ex_36

description: Library name: 0156_36


title: wt_3_sed_38

description: Library name: 0156_38


title: ko_3_sed_35

description: Library name: 0156_35


title: wt_3_sed_54

description: Library name: 0156_54


title: ko_3_ex_34

description: Library name: 0156_34


title: ko_3_sed_33

description: Library name: 0156_33


title: ko_3_sed_30

description: Library name: 0156_30


title: wt_15_ex_31

description: Library name: 0156_31


title: ko_3_sed_32

description: Library name: 0156_32


title: ko_3_ex_3

description: Library name: 0156_3


title: ko_15_sed_29

description: Library name: 0156_29


title: ko_3_ex_28

description: Library name: 0156_28


title: ko_15_ex_47

description: Library name: 0156_47


title: ko_3_ex_23

description: Library name: 0156_23


title: wt_15_ex_26

description: Library name: 0156_26


title: ko_3_sed_21

description: Library name: 0156_21


title: ko_15_sed_25

description: Library name: 0156_25


title: ko_3_ex_20

description: Library name: 0156_20


title: ko_15_ex_24

description: Library name: 0156_24


title: wt_15_ex_37

description: Library name: 0156_37


title: wt_3_sed_22

description: Library name: 0156_22


title: ko_15_ex_4

description: Library name: 0156_4


title: ko_15_sed_15

description: Library name: 0156_15


title: ko_3_sed_16

description: Library name: 0156_16


title: wt_15_ex_19

description: Library name: 0156_19


title: wt_3_sed_18

description: Library name: 0156_18


title: wt_15_sed_14

description: Library name: 0156_14


title: wt_15_sed_17

description: Library name: 0156_17


title: wt_3_ex_12

description: Library name: 0156_12


title: wt_3_ex_13

description: Library name: 0156_13


title: Trim71 KO 6

city: Baltimore

first: Angelika

last: Doetzlhofer

address: 855 North Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

data_processing:
psuedoalignment and quantification using kallisto
QC and differential testing using Sleuth
Assembly: Ensembl v96 reference transcriptome
Supplementary files format and content: h5 abundance files

source_name: cochlear sensory epithelium

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen cat. 74004).
These samples were processed using Illumina's TruSeq stranded Total RNA kit, per manufacturer's recommendations, using the UDI indexes.  The samples were sequenced on the Illumina NovaSeq 6000, paired end, 2x50 bp reads

value: cochlear sensory epithelium

value: Trim71 KO


title: ko_15_sed_11

description: Library name: 0156_11


title: wt_15_ex_10

description: Library name: 0156_10


title: Trim71 KO 4


title: ko_15_sed_1

description: Library name: 0156_1


title: PS 8-weeks old,  exposed to prenatal stress, pool of 3 mice

description: 10x Genomics

data_processing:
Transcript reads were demultiplexed, aligned to reference mouse genome (mm10 - GENCODE vM23/Ensembl 98) and quantified by the Cell Ranger v(7.0.1)
Quantified gene counts of the samples were pre-processed to remove ambient RNA decontamination using the decontX function from the celda package (v1.6.0) The raw unfiltered matrix output of Cell Ranger-count of each sample was used as the respective background for the ambient RNA inference. Seurat package (v4.3.0) was preferred as a main suite of analysis. Cells having more than 10% of their reads assigned to mitochondrial genes, and cells having less than 100 detected genes were excluded from the dataset. After this QC-trimming, a total of 28015 cells (7211 cells from CT W8, 4474 cells from PS W8, 6812  cells from CT W24 and 9004 cells from PS W24) were retained for further analysis.
Assembly: mm10 - GENCODE vM23/Ensembl 98
Supplementary files format and content: h5 files of the filtered feature matrix of each sample by Cell Ranger v(7.0.1)

extract_protocol:
Cell suspensions from adult mouse skin were obtained through mechanical dissociation and enzymatic digestion. Briefly, adult back skin from W8 or W24 mice was harvested in pre-digestion medium, finely minced and incubated at 37°C on a rotating plate to remove epithelial cells and other impurities. The samples were then digested for 45 minutes on a rotating plate with 1.25 mg of Liberase TM (Sigma) and 2.5 mg of DNAse I (Sigma) to disaggregate the tissue. Samples were further dissociated with the Miltenyi gentleMACS Dissociator and cells were then enriched with a Percoll gradient. Cell suspensions from mouse skin were blocked with anti-mouse CD16/32 (S17011E, Biolegend) for 15 min at 4°C. Surface staining using CD45 was performed in FACS buffer for 1 hour at 4°C and CD45+ immune cells were sorted using FACS.
Approximately 16,000 cells per sample were encapsulated into droplets using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 according to manufacturer’s protocol (10× Genomics), Briefly, after generation of nanoliter-scale Gel bead-in-EMulsions (GEMs) using Next GEM Chip G, GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (BioRad) programed at 53°C for 45 min, 85°C for 5 min, and held at 4°C. After reverse transcription, single-cell droplets were broken and cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermofisher Scientific). cDNA was then amplified with a C1000 Touch Thermal Cycler programed at 98°C for 3 min, 12 cycles of (98°C for 15 s, 63°C for 20 s, 72°C for 1 min), 72°C for 1 min, and held at 4°C. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated, and cleaned with cleanup mix containing SPRIselect Reagent Kit (Beckman Coulter) in between steps. Post-ligation product was amplified and indexed with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 14 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and held at 4°C. The sequencing - ready libraries were cleaned up with SPRIselect beads. 10x libraries were pooled and charged with 1% PhiX on one SP lane of the NovaSeq 6000 instrument (Illumina) using the NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles), and the following sequencing parameters: 28 bp read 1 – 8 bp index 1 (i7) – 150 bp read 2. The SP lane generated a total of 434.10^6 reads.

treatment_protocol: Eight- to 10-week-old male and female mice were subjected to timed pregnancies. Pregnant dams were then subject to chronic restraint stress in transparent drilled 50-ml tubes, put under a bright light (200W), 3 times a day for 30 minutes each, from embryonic day (E)-13 until E-18. Control (CT) pregnant females were left undisturbed. After birth, all pups were kept in the same cage with their biological mother. Pups were then weaned at the age of 21 to 28 days in distinct gender groups in new cages and introduced to a new diet. Skin samples were collected from 8-week old (W8) and 24-week old (W24) control (CT) and PS offspring, and single-cell RNA sequencing of isolated CD45+ cells was conducted.

value: CD45+ immune cells

value: Prenatal stress offspring


title: Wild Type 1


title: ko_15_ex_27

description: Library name: 0156_27


title: DRG, PS128, exposed to prenatal stress, pool of 3 mice, biological replicate 3

description: TruSeq Stranded mRNA

data_processing:
Libraries quantification and sequencing were performed at the GeT-PlaGe core facility (INRAE, Toulouse, France). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche) to obtain an accurate quantification. Libraries were equimolarly pooled and RNA sequencing was then performed on one SP lane of the Illumina NovaSeq 6000 instrument (Illumina), using the NovaSeq 6000 SP v1 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy.
FastQC was performed on sequence reads to evaluate sequencing quality. Reads were then aligned on GRCm39 (mm10) as a reference genome using STAR aligner (v2.4) and counted with Htseq (v0.9.1), and a counting matrix was generated.
Assembly: GRCm39 (mm10)
Supplementary files format and content: mtx files, HTseq count output of each sample

source_name: DRG

extract_protocol:
DRG from adult mice were stored immediately in RNALater then dissociated in trizol with the Miltenyi gentleMACS Dissociator. Tissue RNA was extracted using the RNeasy Qiagen Mini Kit (Qiagen) according to the manufacturer’s guidelines.
RNA concentration and purity were determined using a ND-2000 Spectrophotometer (ThermoFisher Scientific). Integrity of RNA was checked with a Fragment Analyzer (Agilent Technologies), using the RNA Standard Sensitivity Kit. 260/280 purity ratios were all > 1.8. Integrity indices revealed acceptable and homogenous values for the RNA Integrity Number (8.2-8.6) and 28S/18S ratios (0.8-1.2). RNA-seq paired-end libraries were prepared at the GeT-Santé facility according to Illumina’s protocol with some adjustments, using the TruSeq Stranded mRNA library prep Kit (Illumina). Briefly, mRNAs were first selected from either 3000 ng (DRG sequencing) or 500 ng (sorted fetal MC sequencing) of total RNA using poly-T beads. Then, RNAs were fragmented for 2' and retrotranscribed to generate double stranded cDNA. Compatible adaptors were ligated, allowing the barcoding of the samples with unique single indices. 11 cycles of PCR were applied to amplify libraries, and an additional double-sized purification step allowed to obtain 280-1000 pb fragments. Libraries quality was assessed using the HS NGS kit on the Fragment Analyzer (Agilent Technologies).

treatment_protocol: Eight- to 10-week-old male and female mice were subjected to timed pregnancies. Pregnant dams were then subject to chronic restraint stress in transparent drilled 50-ml tubes, put under a bright light (200W), 3 times a day for 30 minutes each, from embryonic day (E)-13 until E-18. Control (CT) pregnant females were left undisturbed. After birth, all pups were kept in the same cage with their biological mother. Pups were then weaned at the age of 21 to 28 days in distinct gender groups in new cages and introduced to a new diet. Dorsal root ganglia (DRG) were collected from 8-week old (W8) control (CT) and PS offspring (3 mice per group), and bulk RNA sequencing was conducted.

value: DRG

value: 8-weeks old


title: PS 24-weeks old, exposed to prenatal stress, pool of 3 mice

description: 10x Genomics

value: 24-weeks old


title: CT 8-weeks old, control mice, pool of 3 mice

description: 10x Genomics

value: Control offspring


title: wt_3_ex_2

description: Library name: 0156_2

value: gastrocnemius

value: m

value: wt


title: DRG, CT46, control mice, pool of 3 mice, biological replicate 3

description: TruSeq Stranded mRNA


title: DRG, PS127, exposed to prenatal stress, pool of 3 mice, biological replicate 2

description: TruSeq Stranded mRNA


title: DRG, PS101, exposed to prenatal stress, pool of 3 mice, biological replicate 1

description: TruSeq Stranded mRNA


title: DRG, CT45, control mice, pool of 3 mice, biological replicate 2

description: TruSeq Stranded mRNA


title: CT 24-weeks old, control mice, pool of 3 mice

description: 10x Genomics

value: Skin


title: PS3, exposed to prenatal stress,  pool of 4 mice, biological replicate 3

description:
TruSeq Stranded mRNA
PS3_GCTTGTCA-GTATGTTC-AH37FJDRX2

data_processing:
FastQC was performed on sequence reads to evaluate sequencing quality. Reads were then aligned on GRCm39 (mm10) as a reference genome using STAR aligner (v2.4) and counted with HTseq (v0.9.1), and a counting matrix was generated.
Assembly: GRCm39 (mm10)
Supplementary files format and content: mtx files, HTseq count output of each sample

extract_protocol:
Cell suspensions from fetal mouse skin were obtained through mechanical dissociation and enzymatic digestion. Briefly, fetal skin from E18.5 embryos was harvested, finely minced and digested in RPMI medium containing 0.1 mg/ml DNAse I (Sigma), 400U/ml Collagenase I (Sigma), 0.1 mg/ml Liberase DL (Roche) and 1 mg/ml Dispase II (Roche) for 45 minutes on a rotating plate at 37°C. Digested tissue samples were filtered and single cell suspensions were used for flow cytometry. Cell suspensions from mouse skin were blocked with anti-mouse CD16/32 (S17011E, Biolegend) for 15 min at 4°C. Surface staining using CD45, F4/80, CD64, CD117 and ST2 was performed in FACS buffer for 1 hour at 4°C and mast cells (CD45+ F4/80- CD64- CD117+ ST2+) were sorted using FACS.
Samples quality control and libraries preparation were performed at the GeT-Santé facility (Toulouse, France, www.get.genotoul.fr). RNA concentration and purity were determined using a ND-2000 Spectrophotometer (ThermoFisher Scientific). Integrity of RNA was checked with a Fragment Analyzer (Agilent Technologies), using the RNA Standard Sensitivity Kit. 260/280 purity ratios were all > 1.8. Integrity indices revealed acceptable and homogenous values for the RNA Integrity Number (8.2-8.6) and 28S/18S ratios (0.8-1.2). RNA-seq paired-end libraries were prepared at the GeT-Santé facility according to Illumina’s protocol with some adjustments, using the TruSeq Stranded mRNA library prep Kit (Illumina). Briefly, mRNAs were first selected from either 3000 ng (DRG sequencing) or 500 ng (sorted fetal MC sequencing) of total RNA using poly-T beads. Then, RNAs were fragmented for 2' and retrotranscribed to generate double stranded cDNA. Compatible adaptors were ligated, allowing the barcoding of the samples with unique single indices. 11 cycles of PCR were applied to amplify libraries, and an additional double-sized purification step allowed to obtain 280-1000 pb fragments. Libraries quality was assessed using the HS NGS kit on the Fragment Analyzer (Agilent Technologies).Libraries quantification and sequencing were performed at the GeT-PlaGe core facility (INRAE, Toulouse, France). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche) to obtain an accurate quantification. Libraries were equimolarly pooled and RNA sequencing was then performed on one SP lane of the Illumina NovaSeq 6000 instrument (Illumina), using the NovaSeq 6000 SP v1 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy.

treatment_protocol: Eight- to 10-week-old male and female mice were subjected to timed pregnancies. Pregnant dams were then subject to chronic restraint stress in transparent drilled 50-ml tubes, put under a bright light (200W), 3 times a day for 30 minutes each, from embryonic day (E)-13 until E-18. Control (CT) pregnant females were left undisturbed. Skin samples were collected from E18.5 control (CT) and PS offspring, and bulk RNA sequencing of isolated fetal mast cells was conducted.

value: Embryonic day 18.5

value: Mast cells


title: PS2, exposed to prenatal stress,  pool of 4 mice, biological replicate 2

description:
TruSeq Stranded mRNA
PS2_ATCCACTG-ACGCACCT-AH37FJDRX2


title: CT3, control mice, pool of 4 mice, biological replicate 3

description:
TruSeq Stranded mRNA
CT3_GGACTTGG-CGTCTGCG-AH37FJDRX2


title: CT1, control mice, pool of 4 mice, biological replicate 1

description:
TruSeq Stranded mRNA
CT1_CCGCGGTT-CTAGCGCT-AH37FJDRX2


title: ATAC_EPI_WSB_AC635_20k40k

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files scaled by the size factors from DESeq2 normalization of the raw counts matrix.
Assembly: mm10
Supplementary files format and content: normalized bigwigs

growth_protocol: EpiSCs were cultured on irradiated MEFs and N2B27 containing 12.5 ng/mL hsFGF, 20 ng/mL Activin A, and 175 nM NVP-TNKS6561.  For DE, EpiSCs are plated at 110,000 cells/cm2 on laminin in chemically defined media (CDM) containing 0.7 ug/mL insulin, 1% KOSR, 2 uM thiazovivin, and the above hsFGF, Activin, and NVP. After 5 hours, the cells are washed and media replaced with CDM containing 3 uM CHIR and 40 ng/mL Activin A. After 16 hours, the cells are washed and media replaced with CDM supplemented with 100 ng/mL Activin A and 100 nM LDN-193189 for 24 additional hours. Definitive endoderm cells were dissociated in Accutase, washed in FACS buffer, counted, and resuspended with rat anti-mouse CD184/CXCR4 Alexa Fluor 647-conjugated antibody at a concentration of 1 µl/106 cells and incubated for 1 h at 4°C. Cells were then washed with FACS buffer, centrifuged (200 g for 3 min at 4°C) and resuspended in a solution composed by 80% FACS buffer and 20% anti-rat IgG MicroBeads (Miltenyi Biotec, 130-048-501). Cells were incubated in the mixture for 15 min at 4°C, then washed and resuspended in 500 µl buffer. The MS column was placed in an OctoMACS separator (Miltenyi Biotec, 130-048-501) on the MACS multistand. The cell suspension was added to the column and rinsed three times with buffer. Finally, the column was removed from the separator and the magnetically labeled cells were collected.

extract_protocol:
Briefly, cells were dissociated into single cells, filtered through a Flowmi cell strainer and the nuclei were isolated by incubation with lysis buffer [10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin and 1% bovine serum albumin (BSA)] for 5 min at 4°C; 20,000 and 40,000 nuclei were isolated. Two replicates of 20k and 40k nuclei were collected per biological sample.
Libraries were prepared for sequencing using standard Illumina protocols

value: epiblast stem cells

value: WSB/EiJ


title: ATAC_EPI_WSB_AC627_20k40k


title: ATAC_EPI_PWK_ALT_20k40k

value: PWK/PhJ


title: Wild Type 3

value: cochlear sensory epithelium

value: WT


title: ATAC_EPI_PWK_AC698_20k40k


title: ATAC_EPI_PWK_AC699_20k40k


title: ATAC_EPI_NZO_AC671_20k40k

value: NZO/HiLtJ


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL7 - dox

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: Library name: MUTZ3_1940_CEBPA_CL7_DOX_24HRS

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Transcript abundance was quantified using Salmon v0.3.1 for pseudoalignment against RefSeq gene transcripts of the hg38 human reference build
Assembly: hg38
Supplementary files format and content: quant.sf contain transcript abundance and transcripts per million (TPM) quantified by Salmon

source_name: Bone marrow

growth_protocol: MUTZ3 cells were cultured in Alpha mem medium supplemented with 20% supernatant of urinary bladder carcinoma cell line 5637, and 20% FCS. Medium used was supplemented with 50U/ml penicillin and 50 U/ml streptomycin.

extract_protocol:
Total RNA was isolated by phenol chloroform extraction followed by DNase digestion. The SuperScript II Reverse Transcriptase kit (Invitrogen) was used for synthesis of cDNA.
The cDNA was sheared with the Covaris device and further processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina)

treatment_protocol: MUTZ3 cells received one of the following treatments in order to interfere with MECOM function: 1) we targeted the MECOM RNA for degradation with short hairpin RNA (shRNA); 2) we prevented interaction of MECOM with its partner CTBP using a PLDLS peptide.

value: Bone marrow

value: acute myelomonocytic leukemia

value: dox

tag: timepoint


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL7 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL7_72HRS


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL7 - dox

description: Library name: MUTZ3_1940_CEBPA_CL7_DOX_72HRS


title: ATAC_EPI_NZO_AC653_20k40k


title: Wild Type 2


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL7 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL7_24HRS


title: CT2, control mice, pool of 4 mice, biological replicate 2

description:
TruSeq Stranded mRNA
CT2_TTATAACC-TCGATATC-AH37FJDRX2


title: ATAC_EPI_NOD_AC595_20k40k

value: NOD/ShiLtJ


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL5 - dox

description: Library name: MUTZ3_1940_CEBPA_CL5_DOX_24HRS


title: ATAC_EPI_NOD_AC576_20k40k


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL5 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL5_24HRS


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL5 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL5_72HRS


title: PS1, exposed to prenatal stress, pool of 4 mice, biological replicate 1

description:
TruSeq Stranded mRNA
PS1_AAGTCCAA-TACTCATA-AH37FJDRX2

value: Prenatal stress offspring


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL5 - dox

description: Library name: MUTZ3_1940_CEBPA_CL5_DOX_72HRS


title: ATAC_EPI_CAST_WM078_20k40k

value: CAST/EiJ


title: ATAC_EPI_CAST_WM080_20k40k


title: ATAC_EPI_C57B6_51_20k40k


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL22 - dox

description: Library name: MUTZ3_1940_CEBPA_CL22_DOX_72HRS


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL22 - dox

description: Library name: MUTZ3_1940_CEBPA_CL22_DOX_24HRS


title: ATAC_EPI_C57B6_44_S1S2


title: MUTZ3 - RNAseq - CEBPA overexpression - 72HRS - CL22 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL22_72HRS


title: ATAC_EPI_129_AC681_20k40k


title: MUTZ3 - RNAseq - CEBPA overexpression - 24HRS - CL22 - no_dox

description: Library name: MUTZ3_1940_CEBPA_CL22_24HRS


title: ATAC_EPI_C57B6_1_S1_S1S2


title: ATAC_EPI_129_AC630_20k40k


title: RNAi_3

city: tianjin

first: qiaoling

last: zhang

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description: Library name: Sample 6

data_processing:
2.1 Data Quality Control The image data measured by the high- throughput sequencer are converted into sequence data ( reads) by CASAVA base recognition. Raw data ( raw reads) of fastq format were firstly processed through in- house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
2.2 Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
2.3 Quantification of gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
2.4 Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/ groups ( two biological replicates per condition) was performed using the DESeq2 R package ( 1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P- values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj< =0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include FPKM values for each Sample

growth_protocol: HEC-1A cells were grown in Mc Coy’s 5A (Procell, China) supplemented with 10% fetal bovine serum (VivaCell, China) and cells were cultured at 37°C in a humidifed atmosphere of air containing 5% CO2.

extract_protocol:
RNA was harvested using TRIGene Reagent (Cat. #P118; Genstar, China) .400ng of total RNA was used forthe construction of sequencing libraries.
1. Library preparation for Transcriptome sequencing                                                                                Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly- T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 1 . 5 nM) to ensure the quality of the library.

value: C1orf106 knockdown


title: RNAi_2

description: Library name: Sample 5


title: RNAi_1

description: Library name: Sample 4


title: NC_3

description: Library name: Sample 3

value: Control


title: ATAC_DE_PWK_ALT_S1_20k

value: definitive endoderm


title: NC_2

description: Library name: Sample 2


title: NC_1

description: Library name: Sample 1


title: ATAC_DE_PWK_AC695_20k40k


title: ATAC_DE_NZO_AC671_20k40k


title: ATAC_DE_PWK_AC698_S1_20k


title: HCT116 cells,Knockdown,RBM25,repetition2

city: Dalian

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Txt file includes raw counts for each Sample
Supplementary files format and content: Txt file includes FPKM values for each Sample

source_name: colon

growth_protocol: HCT116 cells were maintained at standard culture conditions (37°C, 5% CO2) in McCoy’s 5A medium with 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: colon cancer cells

value: RBM25 sh


title: HCT116 cells,Knockdown,RBM25,repetition1


title: HCT116 cells,Knockdown,Control,repetition1

value: Control sh


title: HCT116 cells,Knockdown,Control,repetition2


title: ATAC_DE_NZO_AC653_S2_40k


title: MCF7 cells, knockdown1, RBM45

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: breast

growth_protocol: MCF7 cells were maintained at standard culture conditions (37°C, 5% CO2) in MEM (with 0.01mg/ml human insulin) medium with 10% FBS.

value: breast

value: breast cancer

value: RBM45 knockdown1


title: ATAC_DE_C57B6_4_20k40k


title: ATAC_DE_NOD_AC576_20k40k


title: ATAC_DE_C57B6_51_S1_20k


title: MCF7 cells, knockdown2, RBM45

value: RBM45 knockdown2


title: MCF7 cells, knockdown, control

value: control


title: ATAC_DE_C57B6_44_20k40k


title: FaDu cells, knockdown, ZCRB1_SH1

source_name: hypopharynx

growth_protocol: FaDu cells were maintained at standard culture conditions (37°C, 5% CO2) in MEM medium with 10% FBS, Sodium Pyruvate , Nonessential Amino Acids Solution .

value: hypopharynx

value: FaDu

value: Hypopharyngeal carcinoma

value: knockdown ZCRB1_SH1


title: FaDu cells, knockdown, HNRNPC_SH1

value: knockdown HNRNPC_SH1


title: ATAC_DE_129_AC630_20k40k


title: ATAC_DE_129_AC681_20k40k


title: FaDu cells, knockdown, SF3B3_SH1

value: knockdown SF3B3_SH1


title: ATAC_DE_WSB_AC627_20k40k

value: WSB/EiJ