title: MCM2-2A H3K9me3 D0 ESC CUT&Tag repeat 2

first: haiyun

last: gan

address: xueyuan lu 1068

extract_protocol:
CUT&Tag was performed as previously reported with modifications4,5. Cells (1-2×105) were washed twice in 1 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) at room temperature. Concanavalin-coated magnetic beads (Bangs Laboratories) were washed twice in 1 mL Binding Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were resuspended in 1 mL Wash Buffer and incubated with 10 μL pre-washed Concanavalin-coated magnetic beads at room temperature for 15 min. Beads (bound to cells) were incubated in Antibody Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells, 2 mM EDTA, 0.1% BSA, 1:100 dilution of the appropriate primary antibody) on a rotating platform overnight at 4°C. Prepare mixture of 1 μg appropriate secondary antibody (Table S1) and pAG-Tn5 adapter complex (Novoprotein) at 1:2 molar ratio at room temperature for 1 hour. Beads were washed once with 1 mL Dig-wash Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells) and nutated in 100 μL Dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1×Protease inhibitor cocktail, 0.01% Digitonin) added the secondary antibody bound pAG-Tn5 complex at room temperature for 1 hour. Beads were washed 3 times with 1 mL Dig-300 buffer and resuspended in Tagmentation Buffer (Dig-300 buffer, 10 mM MgCl2) at 37°C for 1 hour. Beads were washed once with 1 mL TAPS Wash Buffer (10mM TAPS, pH 7.5, 0.4 mM EDTA) and incubated in 250 µL Dig-300 buffer containing 15 mM EDTA, 0.1% SDS and 100 µg/mL Proteinase K at 37°C for 1 hour with shaking of 900rpm. Then CUT&Tag DNA was extracted by phenol-chloroform-isoamyl alcohol and purified again by DNA Clean & Concentrator-5 Kit (Zymo Research) to 20 µL EB buffer. CUT&Tag DNA was Incubated by RNase A (1/400) at 37°C for 10 min. To amplify libraries, 10 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, and 12 μL NEBNext 2× PCR mix, and run the following cycling conditions with lid heat on: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 10 °C. Post-PCR clean-up was performed by adding 1× volume of Ampure XP beads (24 μL) (Beckman Counter), and libraries were incubated with beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer. The libraries were used for paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq Xten platform by Annoroad Gene Technology Co. Ltd.
RNA-seq library preparation and deep sequencing were performed by Annoroad Gene Technology Co. Ltd.. Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit (10x Genomics).

value: ESC

tag: media

value: DMEM/F12 _serum

value: MCM2-2A mutant

tag: chip antibody

value: Anti-H3K9me3 Antibody (ab8898)


title: myoblasts_D0_chrRNA_rep1

status: Public on May 14 2023

type: SRA

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

library_source: transcriptomic

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_splicing_status_per_read.txt: text files containing the overall splicing status of each read
Supplementary files format and content: *_hg38_multi_introns_isoforms_counts.txt or hg38_multi_introns_counts.txt: text files containing the per-intron splicing status for each intron in each read
Supplementary files format and content: *_hg38_multi_exons_isoforms_counts.txt: text files containing the per-exon splicing status for each exon in each read

molecule: nuclear RNA

organism: Homo sapiens

source_name: myoblasts

extract_protocol:
Qiagen miRNeasy
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)

tag: cell line

value: myoblasts

tag: pcr-amplified gene


title: HeLa_chrRNA_rep2b

source_name: HeLa

extract_protocol:
Qiazol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)

value: HeLa


title: HeLa_CRISPR_IFRD2_ex6-int8C

tag: treatment

value: CRISPR-Cas9 sgRNAs IFRD2 exon6, intron8C


title: HeLa_CRISPR_IFRD2_ex6-int7

value: CRISPR-Cas9 sgRNAs IFRD2 exon6, intron7


title: HeLa_CRISPR_IFRD2_ex6-ex7

value: CRISPR-Cas9 sgRNAs IFRD2 exon6, exon7


title: HeLa_CRISPR_IFRD2_ex6-int6

value: CRISPR-Cas9 sgRNAs IFRD2 exon6, intron6


title: HeLa_CRISPR_IFRD2_ex5-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, intron8C


title: HeLa_CRISPR_IFRD2_ex5-int7

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, intron7


title: HeLa_CRISPR_non_targeting_clone

value: CRISPR-Cas9 non-targeting sgRNA


title: HeLa_ASO_MAF1_int3_rep2

molecule: total RNA

value: ASO MAF1 intron 3


title: HeLa_CRISPR_IFRD2_ex5-ex7

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, exon7


title: HeLa_CRISPR_IFRD2_ex5-ex6_rep1

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, exon6


title: HeLa_CRISPR_IFRD2_ex5-int6

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, intron6


title: HeLa_ASO_non_targeting_MAF1_rep2

value: ASO non-targeting


title: HeLa_CRISPR_IFRD2_int6-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 intron6, intron8C


title: HeLa_ASO_MAF1_int3_rep1


title: Isolated germ nuclei high salt prde-1(mj207)V input for H3 rep 1

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale University School of Medicine

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on prde-1(mj207)V
H3_highsalt_prde1_RPM.bw

library_source: genomic

data_processing:
Reads were aligned to ce11 with bowtie2.
Low-quality (q<30), duplicate reads and modENCODE-blacklisted reads were discarded.
Reads were normalized to RPM then custom R scripts were used for z-score values.
Replicates were used as input for peak calling with MACS2.
Assembly: ce11
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Isolated germ nuclei

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on peptone-enriched NGM plates seeded with OP50. For wild-type and prde-1(mj207)V strains, L1s were grown until young adult at 20˚C. Worms were harvested, washed with M9 and floated on sucrose to remove remaining bacteria.

extract_protocol:
For histone modification ChIP-seq, isolated germ cell nuclei were sonicated in a Misonix S-4000 water bath sonicator, and immunoprecipated overnight using 5 µg of anti-H3K27me3, anti-H3K36me3, or anti-H3K9me3 antibody. For each For histone modification ChIP-seq, isolated germ cell nuclei were sonicated in a Misonix S-4000 water bath sonicator, and immunoprecipated overnight using 5 µg of anti-H3K27me3, anti-H3K36me3, or anti-H3K9me3 antibody. For each IP, 90ng of Drosophila spike-in chromatin and 0.5 μg of Drosophila-specific H2Av antibody was added. The wash steps were performed as in previously described (Han et al 2019).    For Native ChIP-seq, 12 million nuclei were incubated with Lysis Buffer 1 (1 mM Tris–HCl pH7.5, 1 mM PMSF, 1 mM DTT, 0.1% Tween 20, 0.2% NP-40, 0.01% digitonin) for 10min. Then 10U of Mnase was added and digested at 37°C for 4 min and 30 sec. The reaction was stopped with 4 μL of 0.5M EDTA and spun for 17000g for 10 min at 4°C. Supernatant was collected and nuclei pellet was incubated with lysis buffer 2 (1 mM Tris–HCl pH7.5,1 mM PMSF, 1 mM DTT, 0.1% Tween 20, 1% Triton X-100 + 1x Complete Protease Inhibitor Cocktail) for 2 hours. Supernatants were combined and chromatin was pre-cleared with blocked beads. Chromatin was immunoprecipated overnight with 5 µg of anti-H3 antibody. For each IP, 10ng of Drosophila spike-in chromatin and 0.5 μg of Drosophila-specific H2Av antibody was added. After overnight incubation, , 40μL of pre-blocked beads were added and incubated 4°C for 2 hours. For the high salt wash, the ChIP samples with beads were washed 2 times with FA-150mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 150mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)) and 2 times with FA-500mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 500mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)). For the low salt wash, the ChIP samples were washed 2 times with FA-75mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 75mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)) and 2 times with FA-150mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 150mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)). DNA was eluted twice with elution buffer (100mM NaHCO3, 0.2% SDS, 5 mM DTT, 1x TE) at 65°C for 15 min. Samples were treated with RNAse, and incubated with proteinase K overnight at 55°C.
DNA was purified on Zymo ChIP DNA Clean & Concentrator kit (Zymo Research #D5205) and used for ChIP library preparation. Samples were sequenced on an Illumina NovaSeq using 100bp paired-end sequencing.

treatment_protocol: For Histone modification ChIP-seq samples, worms were crosslinked in 2% formaldehyde in M9 buffer for 28 minutes rotating at room temperature. Crosslinking was quenched with 1 M Tris pH 7.5, followed by two washes with M9. Wormed were washed For Histone modification ChIP-seq samples, worms were crosslinked in 2% formaldehyde in M9 buffer for 28 minutes rotating at room temperature. Crosslinking was quenched with 1 M Tris pH 7.5, followed by two washes with M9. Wormed were washed with NPB (50 mM HEPES pH 7.5, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.1% Tween 20, 0.2 mM DTT, 0.5 mM PMSF, 0.5 mM spermidine, 0.25 mM spermine, and 1x Complete Protease Inhibitor Cocktail) and resuspended in 6mL of NPB. Worms were dounced with fifteen loose strokes and 23 tight strokes. The sample was vortexed twice on medium-high speed for 30 s, followed by 5 min on ice. Worm debris was filtered with four 30μm strainers (MACS) and seven 20 μm strainers (Pluriselect). Dapi-stained nuclei were counted using a hemocytometer. The nuclei were transferred to a 1.5 ml tube and flash frozen in liquid nitrogen.    For Native ChIP-seq, worms were washed with NPB and resuspended in 6mL NPB. Worms were dounced with fifteen loose strokes and 23 tight strokes. The sample was vortexed twice on medium-high speed for 30 s, followed by 5 min on ice. Worm debris was filtered with four 30μm strainers (MACS) and seven 20 μm strainers (Pluriselect). Dapi-stained nuclei were counted using a hemocytometer. The nuclei were transferred to a 1.5 ml tube.

tag: tissue

value: Isolated germ nuclei

tag: developmental stage

value: Young adult

tag: antibody

tag: strain

tag: genotype

value: wild-type

value: high salt


title: Isolated germ nuclei high salt wild-type input for H3 rep 2

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on wild-type
H3_highsalt_WT_RPM.bw


title: Isolated germ nuclei high salt wild-type input for H3 rep 1


title: Isolated germ nuclei high salt prde-1(mj207)V input for H3 rep 2


title: Isolated germ nuclei high salt prde-1(mj207)V H3 rep 2

description:
Native-ChIP was performed with anti-H3 with high salt on prde-1(mj207)V isolated germ nuclei
H3_highsalt_prde1_RPM.bw


title: HeLa_CRISPR_non_targeting_pool_rep1

value: HeLa


title: HeLa_ASO_non_targeting_MAF1_rep1


title: HeLa_ASO_IFRD2_int4-9_rep2

value: ASO IFRD2 introns 4-9


title: HeLa_ASO_IFRD2_int4-5-9_rep2

value: ASO IFRD2 introns 4-5-9


title: Isolated germ nuclei high salt prde-1(mj207)V H3 rep 1


title: Isolated germ nuclei high salt wild-type H3 rep 2

description:
Native-ChIP was performed with anti-H3 with high salt was conditions on wild-type isolated germ nuclei
H3_highsalt_WT_RPM.bw


title: Isolated germ nuclei high salt wild-type H3 rep 1


title: Isolated germ nuclei low salt prde-1(mj207)V input for H3 rep 2

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on prde-1(mj207)V
H3_lowsalt_prde1_RPM.bw

value: low salt


title: HeLa_ASO_IFRD2_int4-5_rep2

value: ASO IFRD2 introns 4-5


title: HeLa_ASO_IFRD2_int5_rep2

value: ASO IFRD2 intron 5


title: HeLa_ASO_IFRD2_int9_rep2

value: ASO IFRD2 intron 9


title: Isolated germ nuclei low salt prde-1(mj207)V input for H3 rep 1


title: HeLa_ASO_IFRD2_int4_rep2

value: ASO IFRD2 intron 4


title: Isolated germ nuclei low salt wild-type input for H3 rep 2

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on wild-type
H3_lowsalt_WT_RPM.bw


title: Isolated germ nuclei low salt prde-1(mj207)V H3 rep 2

description:
Native-ChIP was performed with anti-H3 with low salt on prde-1(mj207)V isolated germ nuclei
H3_lowsalt_prde1_RPM.bw


title: HeLa_ASO_non_targeting_rep2


title: Isolated germ nuclei low salt prde-1(mj207)V H3 rep 1


title: HeLa_ASO_IFRD2_int4-5-9_rep1


title: HeLa_ASO_IFRD2_int5-9_rep1

value: ASO IFRD2 introns 5-9


title: HeLa_ASO_IFRD2_int4-9_rep1


title: Isolated germ nuclei low salt wild-type H3 rep 2

description:
Native-ChIP was performed with anti-H3 with low salt was conditions on wild-type isolated germ nuclei
H3_lowsalt_WT_RPM.bw


title: HeLa_ASO_IFRD2_int5-9_rep2


title: Isolated germ nuclei prde-1(mj207)V input for H3K9me3 rep 2

description:
A fraction of the input total chromatin that was used for H3K9me3 ChIP on prde-1(mj207)V
H3K9me3_prde1_zscore.bw


title: Isolated germ nuclei low salt wild-type H3 rep 1


title: Isolated germ nuclei prde-1(mj207)V input for H3K9me3 rep 1


title: HeLa_ASO_IFRD2_int4-5_rep1


title: 63Con-1

city: Shanghai

first: Dan

last: Yang

address: 355 Luding Road, Putuo District

country: China

institute: Shanghai Children's Hospital

data_processing:
Raw data were generated after sequencing, image analysis, base calling, and quality filtering on the Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase v22 plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by the edgeR approach.
Supplementary files format and content: The raw and normalized tag counts of the mature miRNA.

growth_protocol: MG63 and 143B cells were cultured in DMEM (Gibco, USA) supplement with 10% (vol/vol) fetal bovine serum (FBS, Gibco, USA), 100 μg/mL penicillin and streptomycin (Gibco, USA) at 37°C. The  hFOB1.19 cells were cultured in DMEM/F12 (Gibco, USA) supplement with 10% (vol/vol) FBS (Gibco, USA), 1% (vol/vol) nonessential amino acid solution (Gibco, USA), 0.3 mg/mL G418 and 100 μg/mL penicillin and streptomycin (Gibco, USA) at 33.5°C. Cells were cultured in an atmosphere of 5% CO2 and 90% relative humidity.

extract_protocol:
Exosomes were isolated from cell culture supernatant with the exoEasy Maxi Kit (Qiagen, No. 76046, USA) according to the manufacturer’s instructions. Total RNA was isolated from exosomes following the protocol of the exoRNeasy SerumKit (Qiagen, No. 77064, USA).
Extracted RNA was used to prepare the miRNA sequencing library with QIAseq miRNA Library Kit (Qiagen, No. 331505, USA).

tag: cell type

value: non-metastatic osteosarcoma  cell line

value: WT


title: 63test-2

value: IDO OE


title: 63Con-2


title: Isolated germ nuclei low salt wild-type input for H3 rep 1


title: HeLa_ASO_IFRD2_int5_rep1


title: HeLa_ASO_IFRD2_int4_rep1


title: Isolated germ nuclei wild-type input for H3K9me3 rep 1

description:
A fraction of the input total chromatin that was used for H3K9me3 ChIP on wild-type
H3K9me3_WT_zscore.bw


title: 63test-1


title: HeLa_U2_KD_chr_cDNA-PCR_rep2

value: U2 snRNA knockdown


title: Isolated germ nuclei wild-type input for H3K9me3 rep 2

value: Isolated germ nuclei


title: HeLa_control_KD_chr_cDNA-PCR_rep1

value: control knockdown


title: HeLa_control_KD_chr_cDNA-PCR_rep2


title: HeLa_U2_KD_chr_cDNA-PCR_rep1


title: Isolated germ nuclei prde-1(mj207)V H3K9me3 rep 2

description:
ChIP was performed with anti-H3K9me3 on prde-1(mj207)V isolated germ nuclei
H3K9me3_prde1_zscore.bw

value: Young adult


title: HeLa_ASO_non_targeting_rep1

value: ASO non-targeting


title: HeLa_ASO_IFRD2_int9_rep1

value: HeLa


title: 143B-test-1

value: metastatic osteosarcoma  cell line


title: 143B-test-2


title: MN_D14_chrRNA_rep3_Prom

source_name: iPSC-derived motor neurons

value: iPSC-derived motor neurons


title: HeLa_U2_KD_total_RNA


title: MN_D9_chrRNA_rep1_Prom

source_name: iPSC-derived motor neuron progenitors

value: iPSC-derived motor neuron progenitors


title: 143B-con-2


title: HeLa_control_KD_total_RNA


title: Isolated germ nuclei wild-type H3K9me3 rep 2

description:
ChIP was performed with anti-H3K9me3 on wild-type isolated germ nuclei
H3K9me3_WT_zscore.bw

value: wild-type


title: 143B-con-1

value: metastatic osteosarcoma cell line


title: Isolated germ nuclei wild-type H3K9me3 rep 1


title: 1.19test-2

value: non-tumorigenic immortalized osteoblastic cell


title: HeLa_U2_KD_nanoCOP_rep1


title: HeLa_control_KD_nanoCOP_rep2


title: Isolated germ nuclei prde-1(mj207)V input for H3K27me3 rep 1

description:
A fraction of the input total chromatin that was used for H3K27me3 ChIP on prde-1(mj207)V
H3K27me3_prde1_zscore.bw


title: Isolated germ nuclei wild-type input for H3K27me3 rep 2

description:
A fraction of the input total chromatin that was used for H3K27me3 ChIP on wild-type
H3K27me3_WT_zscore.bw


title: Isolated germ nuclei prde-1(mj207)V input for H3K27me3 rep 2


title: 1.19con-2


title: HeLa_control_KD_nanoCOP_rep1


title: MN_D14_chrRNA_rep2


title: 1.19con-1


title: Isolated germ nuclei wild-type input for H3K27me3 rep 1


title: Isolated germ nuclei prde-1(mj207)V H3K9me3 rep 1


title: HM6 S1P 3

city: St. Louis

first: Antonina

middle: I.

last: Frolova

state: MO

address: 660 S. Euclid Ave, CB 8064

department: OBGYN

institute: Washington University in St. Louis

description: Sample 11

data_processing:
Raw FASTQ files were used to perform analyses usingPartek®Flow®software, v10.0
RNA sequencing reads were aligned to the human hg38 primary assembly with STAR version 2.7.8a to generate BAM files.
Aligned reads were then quantified to the Ensembl transcript release 105 with STAR version 2.7.8a.
Gene counts were normalized with median ratio
Normalized counts were analyzed by DESeq2 to calculate differentially expressed genes (DEGs)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include median ratio (DESeq2) values for each Sample

source_name: Myometrium

growth_protocol: Both cell lines were cultured in DMEM/F12 medium without phenol red, supplemented with 10% FBS and 0.05% gentamicin (Life Technologies, MA, USA). Cells were serum starved in DMEM/F12 medium without phenol red, supplemented with 1% charcoal-stripped FBS overnight prior to all experiments.

extract_protocol:
Total RNA was isolated using the RNeasy/QIAshredder Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Human myometrial cell lines (hHM and HM6) were treated with 1 µM S1P or vehicle (4 µg/mL BSA) for 3 h

value: Myometrium

value: Immortalized human term pregnant myometrial smooth muscle cell

value: Sphingosin 1-phosphate (1uM)


title: MN_D9_chrRNA_rep2


title: HM6 S1P 2

description: Sample 10

value: WT


title: MN_D14_chrRNA_rep1


title: Isolated germ nuclei prde-1(mj207)V H3K27me3 rep 2

description:
ChIP was performed with anti-H3K27me3 on prde-1(mj207)V isolated germ nuclei
H3K27me3_prde1_zscore.bw


title: Isolated germ nuclei prde-1(mj207)V H3K27me3 rep 1


title: HeLa_U2_KD_nanoCOP_rep2


title: 1.19test-1

value: IDO OE


title: HM6 S1P 1

description: Sample 9


title: MN_D9_chrRNA_rep1


title: Isolated germ nuclei wild-type H3K27me3 rep 1

description:
ChIP was performed with anti-H3K27me3 on wild-type isolated germ nuclei
H3K27me3_WT_zscore.bw


title: Dsup-4 after 1000 Gy treatmet

type: RNA

city: Dubna

first: Mikhail

last: Zarubin

address: Russia, Moscow region, Dubna, Juliot Curie, 20

country: Russia

institute: Joint Institute for Nuclear Research

description: Gene expression data from  3-day-old adult D.melanogaster

hyb_protocol: Hybridisation was performed with GeneChip™ Hybridization, Wash and Stain Kit according to the manufacturers' instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G

data_processing: The data were analyzed using the Transcriptom analysis console software version 4.0.2.

label: biotin

organism: Drosophila melanogaster

source_name: Drosophila adult male fly

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (according GeneChip™ 3' IVT PLUS Reagent Kit Protocol)

growth_protocol: The strains were cultured on a standard cornmeal-molasses medium with antibiotic and maintained at 25 °C

value: Dsup-expressing

tag: age

value: 3 day adult

tag: Sex

value: male

value: whole bodies of 25 flies


title: Dsup-2 after 1000 Gy treatmet

extract_protocol: The strains were cultured on a standard cornmeal-molasses medium with antibiotic and maintained at 25 °C


title: Dsup-1 after 1000 Gy treatmet


title: Control after 1000 Gy treatmet,  biological rep3

value: Control


title: Isolated germ nuclei wild-type H3K27me3 rep 2

value: Isolated germ nuclei

value: Young adult


title: Isolated germ nuclei prde-1(mj207)V input for H3K36me3 rep 1

description:
A fraction of the input total chromatin that was used for H3K36me3 ChIP on prde-1(mj207)V
H3K36me3_prde1_zscore.bw


title: MN_D4_chrRNA_rep1

source_name: iPSC-derived neural progenitors

value: iPSC-derived neural progenitors


title: K562_EXOSC10_KD_nucRNA_rep2

extract_protocol:
Trizol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)

value: EXOSC10 knockdown


title: HM6 Vehicle 1

description: Sample 6

value: Vehicle (1 ug/mL BSA)


title: HM6 Vehicle 2

description: Sample 7


title: Dsup-3 after 1000 Gy treatmet


title: K562_EXOSC10_KD_nucRNA_rep1


title: HM6 Vehicle 3

description: Sample 8


title: Control after 1000 Gy treatmet,  biological rep2


title: Control after 1000 Gy treatmet,  biological rep1


title: Isolated germ nuclei wild-type input for H3K36me3 rep 1

description:
A fraction of the input total chromatin that was used for H3K36me3 ChIP on wild-type
H3K36me3_WT_zscore.bw

value: wild-type


title: hHM S1P 3

description: Sample 5

value: hTERT-HM

value: Immortalized human non-pregnant myometrial smooth muscle cell


title: K562_scrambled_nucRNA_rep2

value: control knockdown


title: Isolated germ nuclei prde-1(mj207)V H3K36me3 rep 1

description:
ChIP was performed with anti-H3K36me3 on prde-1(mj207)V isolated germ nuclei
H3K36me3_prde1_zscore.bw


title: Dsup-4, transgenic line

value: untreated


title: Dsup-1, transgenic line


title: Dsup-2, transgenic line


title: K562_scrambled_nucRNA_rep1


title: hHM S1P 2

description: Sample 4

value: Myometrium

value: WT

value: Sphingosin 1-phosphate (1uM)


title: Isolated germ nuclei wild-type H3K36me3 rep 1

description:
ChIP was performed with anti-H3K36me3 on wild-type isolated germ nuclei
H3K36me3_WT_zscore.bw


title: Dsup-3, transgenic line

value: Dsup-expressing

value: 3 day adult


title: hHM S1P 1

description: Sample 3


title: Control,  biological rep4

value: male

value: whole bodies of 25 flies


title: Isolated germ nuclei prde-1(mj207)V ATAC rep 3

description:
ATAC was performed on on prde-1(mj207)V isolated germ nuclei
peaks_ATAC_prde1.narrowPeak

data_processing:
Reads were trimmed with cutadapt and aligned to ce11 with bowtie2.
Low-quality (q<10), mitochondrial, duplicate reads and modENCODE-blacklisted reads were discarded.
Reads were normalized to RPM then custom R scripts were used for z-score values.
Replicates were used as input for peak calling with Genrich.
Assembly: ce11
Supplementary files format and content: narrowPeak

extract_protocol:
Worms were washed with Nuclei Purification Buffer (NPB) (50 mM HEPES pH 7.5, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.1% Tween 20, 0.2 mM DTT, 0.5 mM PMSF, 0.5 mM spermidine, 0.25 mM spermine, and 1x Complete Protease Inhibitor Cocktail), and resuspended in 6mL of NPB. Wormed were dounced with fifteen loose strokes were followed by 23 tight strokes. The sample was vortexed twice on medium-high speed for 30 s, followed by 5 min on ice. Worm debris was filtered with three 30μm strainers (MACS) and six 20 μm strainers (Pluriselect). Dapi-stained nuclei were counted using a hemocytometer. Fifty million nuclei were transferred to a 1.5 ml tube for ATAC-seq.
ATAC-seq library prepartion was performed as in (Corces et al. 2017). Nuclei was washed with ATAC-Resuspension Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, and 0.01% Digitonin) then spun at 2000rpm for 10 min. Nuclei were then washed with ATAC-Resuspension Wash Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween 20). Fifty million nuclei were resuspended in 50μl transposition mixture, incubated for 30 minutes at 37°C, and then tagmented DNA purified using a  Zymo ChIP DNA Clean & Concentrator kit (Zymo Research #D4014). Typically, libraries were amplified using 6–10 PCR cycles.

value: Isolated germ nuclei


title: K562_chr_rep3


title: Isolated germ nuclei prde-1(mj207)V ATAC rep 2

value: Young adult


title: hHM Vehicle 2

description: Sample 2


title: K562_chr_rep4


title: hHM Vehicle 1

description: Sample 1


title: Control,  biological rep3

value: Control


title: HeLa_U2_KD_NETseq_rep2

data_processing:
Adapter trimming (Cutadapt)
Alignment (STAR for RNAseq and NETseq, bowtie for DMS-MaPseq)
Differential splicing analysis with rMATS (RNAseq)
DREEM (DMS-MaPseq)
featureCounts (NETseq)
Assembly: GRCh38
Supplementary files format and content: RNAseq_control_vs_U2_KD_rMATS_stat_intron_retention.txt: intron-exon junction counts for every annotated intron in each RNAseq sample and statistical testing between control and U2 snRNA using rmats-stats
Supplementary files format and content: RNAseq_control_vs_U2_KD_SE.MATS.JC.txt: RNAseq rMATS output for skipped exons (SE) between all control and U2 snRNA knockdown replicates
Supplementary files format and content: *vienna.txt: DMS reactivities for every nucleotide in the in vitro transcribed RNAs used for DMS-MaPseq
Supplementary files format and content: *ER_counts.txt or *PR_counts.txt: featureCounts output from NET-seq data for the gene body region (ER, +300 nt from TSS to end of gene) or promoter region (PR -30 to + 300nt from TSS) of all genes
Library strategy: NET-seq

extract_protocol:
Qiagen miRNeasy kit (RNA-seq and NET-seq of U2 snRNA knockdown), Qiazol extraction (RNA-seq motor neurons),  Trizol extraction (DMS-MaPseq)
SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (RNA-seq motor neurons), KAPA mRNA HyperPrep kit (RNA-seq), NET-seq protocol (Mayer & Churchman Nature Protocols 2016) or xGen Broad-range RNA Library Prep Kit (DMS-MaPseq)

value: HeLa

value: U2 snRNA knockdown


title: Isolated germ nuclei prde-1(mj207)V ATAC rep 1


title: RHN434: hiPSC neural induction 6 d

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

description:
CountRHN424_434.txt
RHN434

data_processing:
Aligned using Array Sudio
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: keratinocytes were derived from the participants hair. The iPSC lines were reprogramed by introducing C-MYC, KLF4, OCT4 and SOX2 TF in a polycistronic excisable vector.

extract_protocol:
RNA was harvested by adding 1ml of Trizol reagent (Life technologies, 15596026), isolated with 100% chloroform, precipitated with 100% isopropanol follow by 80% ethanol and purified with Qiaquick RNA purification kit (Qiagen, 28106).
Libraries were prepared for RNA-seq using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, catalog no. RS-122-2303). Samples were sequenced at the Genome Institute Singapore (GIS) sequencing core on an Hiseq 2500 Sequencing System (Ilumina) generating paired-end, 100-bp reads with an average of 20-30 million reads per sample.

treatment_protocol: SB431542 (Sigma- Aldrich, S4317) 10μM and LDN193189 (Sigma-Aldrich, SML0559) were used for neural induction

value: hiPSC

value: dual SMAD inhibitors

tag: time

value: 6 day


title: Isolated germ nuclei wild-type ATAC rep 3

description:
ATAC was performed on wild-type isolated germ nuclei
peaks_ATAC_WT.narrowPeak

value: wild-type


title: RHN432: hiPSC neural induction 3 d

description:
CountRHN424_434.txt
RHN432

value: 3 day


title: HeLa_U2_KD_NETseq_rep1


title: HeLa_control_KD_NETseq_rep2

value: control knockdown


title: Isolated germ nuclei wild-type ATAC rep 2


title: Control,  biological rep2

value: untreated


title: HeLa_control_KD_NETseq_rep1


title: RHN431: hiPSC neural induction 2 d

description:
CountRHN424_434.txt
RHN431

value: WT

value: 2 day


title: Isolated germ nuclei wild-type ATAC rep 1


title: RHN430: hiPSC neural induction 1 d

description:
CountRHN424_434.txt
RHN430

value: 1 day


title: RHN429: hiPSC neural induction 8 d

description:
CountRHN424_434.txt
RHN429

value: dual SMAD and WNT inhibitors

value: 8 day


title: KO, I3C, hkSE activation, 20h, rep 4

city: Leipzig

first: Jörg

last: Lehmann

address: Perlickstr. 1

department: Preclinical Development and Validation

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

data_processing:
Reads were demultiplexed by Illumina’s bcl2fastq (v2.19.0.316).
Adapter sequences were removed from reads using adapter removal (v2.2.1a) using parameters –trimns, –trimqualities, –minquality ‘20’, and –minlength ‘30’).
Read alignment by HISAT2 (v2.1.0) with parameters –fr and rna-strandness: RF
Read counting by htseq-count (v0.9.1) using parameters –mode intersection-strict, –stranded reverse and –type exon
All steps were orchestrated by the workflow-manager uap
Assembly: mouse genome mm10 (GENCODE release M22)
Supplementary files format and content: htseq_counts.txt files contain raw reads per gene for a given sample
Supplementary files format and content: .csv file contains matrix table with vst normalized gene counts for every gene and every sample

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow cells were plated at a density of 4 x 10^5/ml into tissue culture dishes in RPMI 1640 medium without phenol red (20 % FBS, 2 mM L-glutamine, 10 mM HEPES, 100 U/ml penicillin, 100 µg/ml streptomycin, 50 μM β-mercaptoethanol) supplemented with 30 % macrophage colony-stimulating factor-enriched medium (culture supernatant from the fibroblastic cell line L929) prepared in-house. Fresh medium containing the same ingredients was added after 3 days. At day 6 of the myeloid differentiation process adherent cells were scraped off and tested for the surface expression of CD11b (Miltenyi Biotec, Bergisch-Gladbach, Germany) and F4/80 (Miltenyi Biotec) by flow cytometry (CytoFLEX, Beckman Coulter, Krefeld, Germany) in order to verify the differentiation to bone marrow-derived macrophages (BMMs).

extract_protocol:
Total RNA was isolated with TriReagent® according to manufacturer’s instructions (Sigma Aldrich). For subsequent RNA sequencing analyses 500 ng total RNA per sample was used.
Library preparation was conducted using TruSeq-Stranded mRNA Sample Prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: 1 x 10^6 BMMs/ml were cultured in complete RPMI 1640 medium without phenol red in the presence of 1 µM BaP, 10 µM I3C or 0.01 % (v/v) DMSO (vehicle control) for 6 h. Subsequently, the BMMs were activated for 3 h or 20 h by adding 1 x 10^7 heat-killed Salmonella enterica Serovar Enteritidis (hk S.E.)/ml to each culture. Hk S.E. that represent an excellent source of several PAMPs for broad-spectrum PRR activation were prepared from a S.E. vaccine strain that was kindly provided from IDT Biologika (Dessau-Roßlau, Germany).

value: bone marrow-derived macrophages

value: AhR-knockout

tag: prr activation

value: hkSE

value: 20h post administration


title: KO, BaP, hkSE activation, 20h, rep 4

value: BaP


title: RHN428: hiPSC neural induction 6 d

description:
CountRHN424_434.txt
RHN428

value: hiPSC


title: Control,  biological rep1

value: Control

value: 3 day adult

value: male

value: whole bodies of 25 flies


title: NF54 - Schizonts, rep3, periodate treated

city: Stockholm

first: Sherwin

last: Chan

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S3_periodate

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
UMI was extracted using UMI_tools v1.1.2.  Sequence reads were trimmed for adaptor sequence using fastx_toolkit v0.0.14
Trimmed reads were mapped to the reference using Bowtie2 v2.2.1 with sensitive local mode
UMI  deduplication was performed using UMI_tools v1.1.2. Read counts were then extracted from htseq-count v0.9.1
Assembly: In-house curated tRNA reference including both Plasmodium falciparum and homo sapiens tRNA sequences
Supplementary files format and content: tab-delimited text files (tabular) of raw count for each Sample

organism: Plasmodium falciparum

growth_protocol: infected red blooc cells were grown in RPMI 1640 supplemented with 10% pooled human serum, cultured at 37C at 5% CO2, 5% O2

extract_protocol:
MirVana miRNA isolation kit (invitrogen), small RNA purification according to manufacturer's instruction, for periodate treatment, the RNA was treated in 100 mM NaOAc/HOAc, pH 4.8 and freshly prepared 50 mM NaIO4 at room temperature for 30 mins and then column purified. The recovered RNA was treated again in 60 mM sodium borate, pH 9.5 at 45°C for 90 min before final column purification
library was constructed using TGIRT3 modular kit (InGex), 100ng small RNA was used as input
RNA-Seq, single-end 120 cycles

value: infected red blood cell

tag: time point

value: Schizont (40-44 hpi)

value: Standard culture condition


title: NF54 - Trophozoites, rep3, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T3_periodate

value: Trophozoite (24-28 hpi)


title: RHN433: hiPSC neural induction 4 d

description:
CountRHN424_434.txt
RHN433

value: WT

value: dual SMAD inhibitors

value: 4 day


title: KO, no ligand, hkSE activation, 20h, rep 4

value: bone marrow-derived macrophages

value: DMSO-control


title: RHN427: hiPSC neural induction 4 d

description:
CountRHN424_434.txt
RHN427

value: dual SMAD and WNT inhibitors


title: NF54 - ring, rep3, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R3_periodate

value: Ring (8-12 hpi)


title: RHN425: hiPSC neural induction 2 d

description:
CountRHN424_434.txt
RHN425

value: 2 day


title: KO, I3C, hkSE activation, 20h, rep 3

value: AhR-knockout

value: hkSE

value: 20h post administration


title: RHN426: hiPSC neural induction 3 d

description:
CountRHN424_434.txt
RHN426

value: hiPSC

value: 3 day


title: NF54 - Trophozoites, rep2, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T2_periodate

value: infected red blood cell


title: KO, no ligand, no activation, 20h, rep 4

value: DMSO control


title: NF54 - ring, rep2, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R2_periodate

value: Standard culture condition


title: NF54 - Trophozoites, rep1, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T1_periodate

value: Trophozoite (24-28 hpi)


title: KO, BaP, hkSE activation, 20h, rep 3

value: BaP


title: RHN115: hiPSC neural induction 30 H

description:
Count48hWNT.txt
RHN115

value: WT

value: 30 hour


title: NF54 - Schizonts, rep2, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S2_periodate

value: Schizont (40-44 hpi)


title: RHN424: hiPSC neural induction 1 d

description:
CountRHN424_434.txt
RHN424

value: 1 day


title: NF54 - Schizonts, rep1, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S1_periodate


title: NF54 - ring, rep1, periodate treated

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R1_periodate


title: KO, no ligand, no activation, 20h, rep 3

value: bone marrow-derived macrophages

value: DMSO-control


title: RHN114: hiPSC neural induction 24 H

description:
Count48hWNT.txt
RHN114

value: dual SMAD and WNT inhibitors

value: 24 hour


title: RHN116: hiPSC neural induction 48 H

description:
Count48hWNT.txt
RHN116

value: 48 hour


title: KO, no ligand, hkSE activation, 20h, rep 3

value: AhR-knockout

value: hkSE

value: 20h post administration


title: WTCHG_255090_212: hiPSC neural induction 8 d

description:
CountRHN200.txt
WTCHG_255090_212

value: hiPSC

value: dual SMAD inhibitors

value: 8 day


title: KO, BaP, hkSE activation, 20h, rep 2


title: KO, I3C, hkSE activation, 20h, rep 2


title: NF54 - Schizonts, rep3

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S3

value: infected red blood cell

value: Standard culture condition


title: RHN113: hiPSC neural induction 18 H

description:
Count48hWNT.txt
RHN113

value: WT

value: 18 hour


title: RHN112: hiPSC neural induction 8 H

description:
Count48hWNT.txt
RHN112

value: 8 hour


title: NF54 - Trophozoites, rep3

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T3

value: Trophozoite (24-28 hpi)


title: KO, no ligand, hkSE activation, 20h, rep 2

value: bone marrow-derived macrophages


title: RHN111: hiPSC neural induction 4 H

description:
Count48hWNT.txt
RHN111

value: 4 hour


title: WTCHG_255090_210: hiPSC neural induction 4 d

description:
CountRHN200.txt
WTCHG_255090_210

value: 4 day


title: WTCHG_255090_208: hiPSC neural induction 3 d

description:
CountRHN200.txt
WTCHG_255090_208

value: 3 day


title: KO, no ligand, no activation, 20h, rep 2

value: DMSO-control

value: DMSO control


title: KO, BaP, hkSE activation, 20h, rep 1

value: AhR-knockout

value: BaP

value: hkSE


title: NF54 - ring, rep3

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R3

value: Ring (8-12 hpi)


title: NF54 - Schizonts, rep2

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S2

value: Schizont (40-44 hpi)


title: WTCHG_255090_207: hiPSC neural induction 0 d

description:
CountRHN200.txt
WTCHG_255090_207

value: hiPSC

value: dual SMAD inhibitors

value: 0 day


title: RHN423

description: hiPSC neural induction 8 d

source_name: hiPSC

value: WT

tag: timepoint

value: 8 day


title: NF54 - ring, rep2

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R2

value: infected red blood cell

value: Standard culture condition


title: RHN422

description: hiPSC neural induction 6 d

value: 6 day


title: WTCHG_254732_212: hiPSC neural induction 8 d

description:
CountRHN200.txt
WTCHG_254732_212


title: KO, no ligand, no activation, 20h, rep 1

value: bone marrow-derived macrophages

value: 20h post administration


title: KO, I3C, hkSE activation, 20h, rep 1


title: NF54 - Schizonts, rep1

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA S1


title: WT, BaP, hkSE activation, 20h, rep 4

value: wildtype


title: KO, no ligand, hkSE activation, 20h, rep 1

value: DMSO-control


title: NF54 - Trophozoites, rep2

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T2

value: Trophozoite (24-28 hpi)


title: WTCHG_255090_204: hiPSC neural induction 0 d

description:
CountRHN200.txt
WTCHG_255090_204


title: RHN110: hiPSC neural induction 2 H

description:
Count48hWNT.txt
RHN110

value: dual SMAD and WNT inhibitors

value: 2 hour


title: RHN420

description: hiPSC neural induction 3 d

value: 3 day


title: WTCHG_254732_211: hiPSC neural induction 6 d

description:
CountRHN200.txt
WTCHG_254732_211


title: WTCHG_255090_211: hiPSC neural induction 6 d

description:
CountRHN200.txt
WTCHG_255090_211


title: RHN421

description: hiPSC neural induction 4 d

value: 4 day


title: WT, I3C, hkSE activation, 20h, rep 4

value: hkSE


title: RHN419

description: hiPSC neural induction 2 d

value: hiPSC

value: dual SMAD inhibitors

value: 2 day


title: NF54, amino acid depletion+halofuginone, rep3

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA halofuginone rep3

treatment_protocol: At the start of the experiment, infected cells were transferred to complete or amino acid deficient RPMI1640 (w/wo 70nM halofuginone) supplemented with 0.5% of Albumax2, the cells were cultured for another six hours.

value: 36hpi + 6h

value: amino acid depleted medium + 70nM halofuginone


title: WT, no ligand, hkSE activation, 20h, rep 4


title: WTCHG_254732_208: hiPSC neural induction 3 d

description:
CountRHN200.txt
WTCHG_254732_208

value: WT


title: WTCHG_255090_205: hiPSC neural induction 8 d

description:
CountRHN200.txt
WTCHG_255090_205

value: 8 day


title: RHN418

description: hiPSC neural induction 1 d

value: 1 day


title: NF54, amino acid depletion+halofuginone, rep2

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA halofuginone rep2

value: infected red blood cell


title: WTCHG_254732_207: hiPSC neural induction 0 d

description:
CountRHN200.txt
WTCHG_254732_207

value: 0 day


title: NF54 - Trophozoites, rep1

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA T1

value: Standard culture condition


title: RHN417

description: hiPSC neural induction 0 d


title: WT, no ligand, no activation, 20h, rep 4

value: bone marrow-derived macrophages

value: wildtype

value: DMSO-control

value: DMSO control

value: 20h post administration


title: RHN109

description: hiPSC neural induction 48 H

value: 48 hour


title: NF54, amino acid depletion+halofuginone, rep1

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA halofuginone rep1


title: WT, BaP, hkSE activation, 20h, rep 3

value: BaP

value: hkSE


title: RHN108

description: hiPSC neural induction 30 H

value: hiPSC

value: dual SMAD inhibitors

value: 30 hour


title: WT, I3C, hkSE activation, 20h, rep 3


title: RHN107

description: hiPSC neural induction 24 H

value: WT

value: 24 hour


title: NF54, amino acid depletion, rep2

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA AA depletion rep2

value: 36hpi + 6h

value: amino acid depleted medium


title: WT, no ligand, hkSE activation, 20h, rep 3


title: NF54, amino acid depletion, rep3

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA AA depletion rep3

value: infected red blood cell


title: NF54, amino acid depletion, rep1

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA AA depletion rep1


title: NF54 - ring, rep1

description:
small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA R1

value: Ring (8-12 hpi)

value: Standard culture condition


title: WT, no ligand, no activation, 20h, rep 3

value: bone marrow-derived macrophages

value: wildtype


title: NF54, complete medium, rep3

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA complete rep3

value: complete medium


title: WTCHG_254732_210: hiPSC neural induction 4 d

description:
CountRHN200.txt
WTCHG_254732_210

value: 4 day


title: RHN106

description: hiPSC neural induction 18 H

value: 18 hour


title: WT, BaP, hkSE activation, 20h, rep 2

value: BaP

value: 20h post administration


title: WTCHG_838864_72105282

description:
d7 + DOX Sample 1
OTX-D7-D1

value: hiPSC

value: OTX2 KD


title: WTCHG_838864_72115283

description:
d7 + DOX Sample 2
OTX-D7-D2

value: dual SMAD inhibitors


title: NF54, complete medium, rep2

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA complete rep2


title: RHN104

description: hiPSC neural induction 4 H

value: WT

value: 4 hour


title: WT, I3C, hkSE activation, 20h, rep 2

value: hkSE


title: RHN105

description: hiPSC neural induction 8 H

value: 8 hour


title: WTCHG_254732_205: hiPSC neural induction 8 d

description:
CountRHN200.txt
WTCHG_254732_205

value: 8 day


title: WTCHG_254732_204: hiPSC neural induction 0 d

description:
CountRHN200.txt
WTCHG_254732_204

value: 0 day


title: WTCHG_838864_72095281

description:
d7 - DOX Sample 3
OTX-D7-C3

value: Control


title: NF54, complete medium, rep1

description:
periodate treated small RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
tRNA complete rep1

value: infected red blood cell

value: 36hpi + 6h


title: WTCHG_838864_72125284

description:
d7 + DOX Sample 3
OTX-D7-D3


title: NF54, Schizonts, rep3

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
S3m

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with default setting
Trimmed reads were mapped to the genome using HISAT2 v2.2.1 with default parameters
Read counts on gene feature were extracted from htseq-count v0.9.1
Assembly: PlasmoDB-46_Pfalciparum3D7
Supplementary files format and content: tab-delimited text files of raw count for each Sample

extract_protocol:
Trizol reagent (sigma)
library was constructed using TruSeq Stranded mRNA library Prep kit, 100ng total RNA was used as input
PolyA enriched RNA-Seq, single-end 120 cycles

value: Schizont (40-44 hpi)

value: Standard culture condition


title: RHN102

description: hiPSC neural induction 0 H

value: 0 hour


title: WT, no ligand, hkSE activation, 20h, rep 2

value: bone marrow-derived macrophages

value: wildtype

value: DMSO-control


title: WTCHG_838864_72075279

description:
d7 - DOX Sample 1
OTX-D7-C1

value: hiPSC


title: WT, BaP, hkSE activation, 20h, rep 1

value: BaP

value: 20h post administration


title: WT, I3C, hkSE activation, 20h, rep 1


title: WTCHG_838864_72055277

description:
d2 + DOX Sample 2
OTX-D2-D2

value: WT

value: dual SMAD inhibitors

value: OTX2 KD


title: shZDHHC7_3_LNCaP

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Assembly: hg38
Supplementary files format and content: txt file of raw counts and RPKM/FPKM values for each Sample

source_name: prostate

growth_protocol: LNCaP and 22Rv1 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4824).using the Illumina provided protocol.
RNA-Seq samples were sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: LNCaP or 22Rv1 cells were infected with control empty vector (plvx) or ZDHHC7 overexpressing lentiviruses for 72 hours and selected for 72 hours.  shRNA (pLKO) or shRNA targeting ZDHHC7 (shZDHHC7) lentiviruses for 72 hours and selected for 72 hours.

value: LNCaP

value: prostate

tag: treatment/infection


title: NF54, Schizonts, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
S2m


title: NF54, ring, rep3

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R3m

value: Ring (8-12 hpi)


title: D0 SGBS, D0 3T3-L1 scRNAseq

city: Palo Alto

first: Christopher

middle: Ann

last: Jin

address: 3165 Porter Drive

institute: Stanford Medical School

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat was used to find the most variable features, find clusters of cells, find cell cluster markers, and perform dimensional reduction for PCA, UMAP, and tSNE plots.
Assembly: mm10, hg19
Supplementary files format and content: mtx
Supplementary files format and content: Rds files for the bioinformatics analysis in mice and human samples.
Supplementary files format and content: csv files for marker genes in mice and human samples.
Supplementary files format and content: html reports for quality control data for mice and human samples.

molecule: polyA RNA

source_name: Mus musculus

growth_protocol: The SGBS preadipocyte cell line was cultured and differentiated as previously described3. Cells were maintained in a humidified chamber at 37°C with 5% CO2, and the media was replaced every 2-3 days. The standard culture media used was composed of DMEM/Nutrient Mix F-12 (Invitrogen), supplemented with 33 uM biotin, 17 uM pantothenic acid, 10 % FBS and antibiotics (100 IU/ml penicillin and 100 ug/ml streptomycin). Differentiation was induced on D0, three days post-confluence, by the change of culture media to DMEM/F-12, 33 uM biotin, 17 uM pantothenic acid, 0.01 mg/ml human transferrin, 100 nM cortisol, 200 pM triiodothyronine, 20 nM human insulin (Sigma-Aldrich), 25 nM dexamethasone, 250 uM IBMX, 2 uM rosiglitazone, and antibiotics. After four days of differentiation, the medium was replaced with DMEM/F-12, 33 uM biotin, 17 uM pantothenic acid, 0.01 mg/ml human transferrin, 100 nM cortisol, 200 pM triiodothyronine, 20 nM human insulin and antibiotics. Cells were cultured for eight days after the induction of differentiation.   The 3T3-L1 preadipocyte cell line was maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher) with 10% Fetal Bovine Serum (GeminiBio), 100 units/ml penicillin and 100 µg/ml streptomycin, in a humidified 5% CO2 incubator. For adipogenic differentiation cells were grown to confluency. 48 h past confluency, at day 0 of differentiation, cells were stimulated with 1 µM dexamethasone, 0.5 mM IBMX, 10 µg/ml insulin in growth medium. After 48 h the medium was changed to growth medium with 10 µg/ml insulin in growth medium until day 5.

extract_protocol:
Freshly collected SGBS and 3T3-L1 cells were detached from culture plates using TrypLE Select Enzyme (Gibco), centrifuged at 300 x g for 5 min and resuspended in PBS with 0.04% Bovine Serum Albumin. Lack of staining with propidium iodine (PI) was used to sort live cells using Influx sorter (Beckman Dickinson). Equal numbers of SGBS and 3T3-L1 cells were mixed and subjected to single-cell capture on the 10X Chromium Controller device during which single cells were encapsulated with individual Gel Beads-in-emulsion (GEMs) using the Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics).
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3’ Library & Gel Bead Kit, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
scRNA-Seq - Single Cell 3' v2

value: Mus musculus

value: SGBS and 3T3-L1 co-cultured


title: D8 SGBS, D5 3T3-L1 scRNAseq

description: 10x Genomics

value: D8 and D5


title: NF54, Trophozoites, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
T2m

value: infected red blood cell

value: Trophozoite (24-28 hpi)

value: Standard culture condition


title: shZDHHC7_2_LNCaP


title: NF54, ring, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2m


title: WTCHG_838864_72035275

description:
d2 - DOX Sample 3
OTX-D2-C3

value: Control


title: RHN103

description: hiPSC neural induction 2 H

value: 2 hour


title: WTCHG_838864_72085280

description:
d7 - DOX Sample 2
OTX-D7-C2

value: hiPSC


title: WT, no ligand, no activation, 20h, rep 2

value: bone marrow-derived macrophages

value: wildtype

value: DMSO-control

value: DMSO control


title: shZDHHC7_1_LNCaP

value: WT


title: NF54, Schizonts, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
S1m

value: Schizont (40-44 hpi)


title: KO, BaP, hkSE activation, 3h, rep 4

value: AhR-knockout

value: BaP

value: hkSE

value: 3h post administration


title: NF54, Trophozoites, rep3

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
T3m


title: WTCHG_838864_72025274

description:
d2 - DOX Sample 2
OTX-D2-C2

value: dual SMAD inhibitors


title: PLKO_3_LNCaP

value: LNCaP

value: prostate

value: pLKO


title: WTCHG_838864_72015273

description:
d2 - DOX Sample 1
OTX-D2-C1

value: Control


title: KO, I3C, hkSE activation, 3h, rep 4


title: KO, no ligand, hkSE activation, 3h, rep 4


title: WTCHG_838864_72005272

description:
d1 + DOX Sample 3
OTX-D1-D3

value: OTX2 KD


title: WT, no ligand, hkSE activation, 20h, rep 1

value: 20h post administration


title: WTCHG_838864_72065278

description:
d2 + DOX Sample 3
OTX-D2-D3

value: hiPSC


title: WTCHG_838864_72045276

description:
d2 + DOX Sample 1
OTX-D2-D1


title: NF54, ring, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1m

value: infected red blood cell

value: Ring (8-12 hpi)

value: Standard culture condition


title: WT, no ligand, no activation, 20h, rep 1

value: bone marrow-derived macrophages

value: wildtype

value: DMSO-control

value: DMSO control


title: WTCHG_838864_71995271

description:
d1 + DOX Sample 2
OTX-D1-D2

value: WT


title: NF54, polysome, aa depletion, rep3

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_aa_depletion_3

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with default setting
Trimmed reads were mapped to the genome using HISAT2 v2.2.1 with default parameters
Read counts on gene feature were extracted from htseq-count v0.9.1
Assembly: PlasmoDB-46_Pfalciparum3D7
Supplementary files format and content: tab-delimited text (tabular) files of raw count for each Sample

extract_protocol:
Polysome purification was performed using 5-50% sucrose gradient. The total lysate before loading on the gradient was taken for total transcriptome, the fractions correposnding to the polysomes were pooled. Extraction was performed with Trizol reagent (sigma)
library was constructed using TruSeq Stranded mRNA library Prep kit, 100ng RNA was used as input
PolyA enriched RNA-Seq, single-end 150 cycles

treatment_protocol: At the start of the experiment, infected cells were magnetic enriched (MACS) and resuspended in complete or amino acid deficient RPMI1640 supplemented with 0.5% of Albumax2, the cells were cultured for another six hours

value: 36hpi + 6h

value: amino acid depleted medium


title: PLKO_1_LNCaP

value: LNCaP


title: WTCHG_838864_71985270

description:
d1 + DOX Sample 1
OTX-D1-D1

value: dual SMAD inhibitors


title: KO, BaP, hkSE activation, 3h, rep 3

value: AhR-knockout

value: BaP

value: hkSE

value: 3h post administration


title: shZDHHC7_2_22Rv1

value: prostate


title: KO, no ligand, hkSE activation, 3h, rep 3


title: NF54, total, aa depletion, rep3

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_aa_depletion_3

value: infected red blood cell

value: complete medium


title: KO, I3C, hkSE activation, 3h, rep 3


title: NF54, polysome, complete medium, rep3

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_control_3


title: NF54, Trophozoites, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
T1m

value: Trophozoite (24-28 hpi)

value: Standard culture condition


title: PLKO_2_LNCaP

value: pLKO


title: WTCHG_838864_71975269

description:
d1 - DOX Sample 3
OTX-D1-C3

value: hiPSC

value: Control


title: WTCHG_838864_71955267

description:
d1 - DOX Sample 1
OTX-D1-C1

value: WT


title: shZDHHC7_1_22Rv1


title: PLKO_3_22Rv1


title: NF54, total, complete medium, rep3

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_control_3

value: 36hpi + 6h


title: PLKO_2_22Rv1


title: KO, no ligand, no activation, 3h, rep 4

value: bone marrow-derived macrophages

value: DMSO-control

value: DMSO control


title: NF54, polysome, aa depletion, rep2

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_aa_depletion_2

value: amino acid depleted medium


title: WTCHG_838864_71965268

description:
d1 - DOX Sample 2
OTX-D1-C2

value: dual SMAD inhibitors


title: WTCHG_838864_71945266

description:
d0 + DOX Sample 3
OTX-D0-D3

value: OTX2 KD


title: NF54, total, aa depletion, rep2

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_aa_depletion_2


title: PLKO_1_22Rv1


title: shZDHHC7_3_22Rv1


title: NF54, polysome, complete medium, rep2

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_control_2


title: KO, no ligand, hkSE activation, 3h, rep 2

value: AhR-knockout

value: hkSE

value: 3h post administration


title: KO, I3C, hkSE activation, 3h, rep 2


title: WTCHG_838864_72885264

description:
d0 + DOX Sample 1
OTX-D0-D1


title: WTCHG_838864_71935265

description:
d0 + DOX Sample 2
OTX-D0-D2


title: ZDHHC7_3_22Rv1

value: prostate


title: NF54, total, complete medium, rep2

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_control_2

value: infected red blood cell

value: complete medium


title: KO, no ligand, no activation, 3h, rep 2


title: KO, BaP, hkSE activation, 3h, rep 2

value: BaP


title: ZDHHC7_1_22Rv1


title: KO, BaP, hkSE activation, 3h, rep 1


title: NF54, polysome, aa depletion, rep1

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_aa_depletion_1


title: KO, no ligand, no activation, 3h, rep 3


title: WTCHG_838864_72875263

description:
d0 - DOX Sample 3
OTX-D0-C3

value: hiPSC


title: WTCHG_838864_72865262

description:
d0 - DOX Sample 2
OTX-D0-C2

value: Control


title: NF54, total, aa depletion, rep1

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_aa_depletion_1


title: KO, I3C, hkSE activation, 3h, rep 1


title: WTCHG_838864_72855261

description:
d0 - DOX Sample 1
OTX-D0-C1

value: WT


title: plvx_3_22Rv1

value: plvx


title: KO, no ligand, hkSE activation, 3h, rep 1

value: bone marrow-derived macrophages


title: plvx_2_22Rv1


title: MN_D14_chr_polyA_rep2

data_processing:
Adapter trimming (Cutadapt)
Alignment (STAR for RNAseq and NETseq, bowtie for DMS-MaPseq)
Differential splicing analysis with rMATS (RNAseq)
DREEM (DMS-MaPseq)
featureCounts (NETseq)
Assembly: GRCh38
Supplementary files format and content: RNAseq_control_vs_U2_KD_rMATS_stat_intron_retention.txt: intron-exon junction counts for every annotated intron in each RNAseq sample and statistical testing between control and U2 snRNA using rmats-stats
Supplementary files format and content: RNAseq_control_vs_U2_KD_SE.MATS.JC.txt: RNAseq rMATS output for skipped exons (SE) between all control and U2 snRNA knockdown replicates
Supplementary files format and content: *vienna.txt: DMS reactivities for every nucleotide in the in vitro transcribed RNAs used for DMS-MaPseq
Supplementary files format and content: *ER_counts.txt or *PR_counts.txt: featureCounts output from NET-seq data for the gene body region (ER, +300 nt from TSS to end of gene) or promoter region (PR -30 to + 300nt from TSS) of all genes
Supplementary files format and content: *.splicingIndex.SE_intron_groups.txt: splicing index for introns flanking significant SE events (between Days 9 and 14) and their neighbors
Supplementary files format and content: MN_allSamples_SE_events_rMATS.txt: rMATS SE.JC output for every pairwise comparison between timepoints during motor neuron differentiation

extract_protocol:
Qiagen miRNeasy kit (RNA-seq and NET-seq  of U2 snRNA knockdown), Qiazol extraction (RNA-seq motor neurons), Trizol extraction (DMS-MaPseq)
SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (RNA-seq motor neurons), KAPA mRNA HyperPrep kit (RNA-seq U2 snRNA knockdown), NET-seq protocol (Mayer & Churchman Nature Protocols 2016) or xGen Broad-range RNA Library Prep Kit (DMS-MaPseq)

value: iPSC-derived motor neurons


title: NF54, polysome, complete medium, rep1

description:
polysome RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Polysome_control_1

value: 36hpi + 6h


title: NF54, total, complete medium, rep1

description:
total RNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file
Total_control_1


title: KO, no ligand, no activation, 3h, rep 1

value: DMSO-control

value: DMSO control


title: MN_D14_chr_polyA_rep1

description: MN_allSamples_SE_events_rMATS.txt: rMATS SE.JC output for every pairwise comparison between timepoints during motor neuron differentiation


title: ZDHHC7_3_LNCaP

value: LNCaP


title: WT, no ligand, no activation, 3h, rep 4

value: wildtype


title: MN_D9_chr_polyA_rep2

value: iPSC-derived motor neuron progenitors


title: WT, I3C, hkSE activation, 3h, rep 4

value: hkSE

value: 3h post administration


title: spo11D_2h_2

city: Beijing

first: Wei

last: Li

address: 1st Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Library strategy: DRIP-seq
Basecalls performed using CASAVA version 1.4.
Reads were aligned to the sacCer3 genome with Bowtie 2 using default settings.
All duplicates removed by Picard tools (http://broadinstitute.github.io/picard). The mapped reads (nonstranded R-loops) were divided into forward reads (wR-loops, representing an R-loop formation containing ssDNA on the Watson strand and an DNA:RNA hybrid on the Crick strand) and reverse reads (cR-loops) by using samtools.
MACS2 was used to identify peaks with default parameters.
Normalization was performed using bamCoverage from deepTools, with read coverage normalized to 1× sequencing depth (also known as reads per genomic content) with a re-normalization by shuffled peaks (total R-loop peaks were shuffled randomly, and the 95% mean of R-loop signal from each sample on shuffled peaks was used as denominator) to eliminate the disturbances from abnormally high-value regions.
Genome_build: sacCer3
Supplementary_files_format_and_content: *.bw: The aligned reads files (Binary Alignment Map [BAM]) were converted to normalized coverage files (bigWig) using bamCoverage from deepTools.
Supplementary_files_format_and_content: *_fwd.bw, *_rev.bw: These bigWig files are forward ssDRIP-seq (wR-loops, representing an R-loop formation containing ssDNA on the Watson strand) and reverse ssDRIP-seq (cR-loops, representing an R-loop formation containing ssDNA on the Crick strand) for each sample.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate (Sporulation medium, SPM) and sporulated at 30°C.

extract_protocol:
Nuclei were isolated from yeast cells by grind well in liquid nitrogen, followed by SDS (final concentration: 0.5%) /proteinase K (final concentration: 0.1 mg/ml) treatment at 37 °C overnight. Add 1/4 volume 5 M KAc, mix and place the tube on ice, 10~20 min. Genomic DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed at 37 °C overnight using endonucleases (Alu I, DdeI, MboI, MesI and Rsa I; New England Biolabs, Ipswich, MA, USA); the negative control was treated with RNase H (New England Biolabs) at 37 °C overnight before endonucleases treatment. DRIP was performed as described previously (Xu et al., 2017). Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody (ATCC, Manassas, VA, USA) in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonicated to 150 bp fragments.
The DRIPed DNA samples were sonicated to a set size of 250 bp with an M220 Focused-ultra sonicator (Covaris, Woburn, MA, USA). The sonicated DNA was denatured at 95 °C for 2 minutes and immediately placed on ice for 2 minutes to obtain ssDNA fragments. The first adapter (Adp1, GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(i7)ATCTCGTATGCCGTCTTCTGCTTG) was ligated to the 3’ end of the ssDNA using Adaptase (Swif Biosciences, Ann Arbor, MI, USA) via a highly efficient, proprietary reaction that tails only the 3’ ends of ssDNA and ligates the first truncated adapter to the 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter (Adp2, AATGATACGGCGACCACCGAGATCTACAC(i5)ACACTCTTTCCCTACACGACGCTCTTCCGATCT) to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified. The libraries were checked on an Agilent (Palo Alto, CA, USA) BioAnalyzer, followed by sequencing on an Illumina (San Diego, CA, USA) HiSeq X 10 system.

value: Incubated with SPM for 2h


title: spo11D_2h_1


title: ZDHHC7_2_22Rv1

value: prostate


title: MN_D9_chr_polyA_rep1


title: ZDHHC7_2_LNCaP


title: ZDHHC7_1_LNCaP


title: WT, BaP, hkSE activation, 3h, rep 4

value: BaP


title: MN_D14_chr_rep2


title: plvx_3_LNCaP


title: MN_D4_chr_polyA_rep1

value: iPSC-derived neural progenitors


title: WT, BaP, hkSE activation, 3h, rep 3


title: spo11D_05h_2

value: Incubated with SPM for 0.5h


title: WT, no ligand, hkSE activation, 3h, rep 4


title: spo11D_0h_2

value: Incubated with SPM for 0h


title: spo11D_05h_1


title: plvx_1_22Rv1

value: plvx

value: WT


title: MN_D14_chr_rep1

value: iPSC-derived motor neurons


title: WT, I3C, hkSE activation, 3h, rep 3

value: bone marrow-derived macrophages


title: plvx_2_LNCaP


title: spo11D_0h_1


title: MN_D9_chr_rep2


title: plvx_1_LNCaP


title: rnh1D_rnh201D_2h_2


title: MN_D9_chr_rep1


title: C4-2B_MDVr_P15_shCXCR7_3 [mr110]

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Assembly: hg38
Supplementary files format and content: txt file of RPKM/FPKM values for each Sample

source_name: Human prostate cancer cells

growth_protocol: LNCaP MDVr cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin / streptomycin and 2uM of enzalutamide, C4-2B MDVr cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin/streptomycin and 10uM enzalutamide.

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit,   according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp,   no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from   Illiumina (Kapa Biosystems, KK4603) using the Illumina provided protocol.  The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were   quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603) using the Illumina provided protocol.

treatment_protocol: LNCaP MDVr and C4-2B MDVr cells were infected with control shRNA (pLKO), shRNA targeting CXCR7 (shCXCR7) lentiviruses. Treated cells were subjected to total RNA isolation after 4 days post infection.


title: WT, no ligand, hkSE activation, 3h, rep 3

value: DMSO-control


title: C4-2B_MDVr_P15_shCXCR7_2 [mr109]


title: rnh1D_rnh201D_2h_1


title: MN_D4_chr_rep1


title: WT, no ligand, no activation, 3h, rep 3

value: DMSO control


title: WT, BaP, hkSE activation, 3h, rep 2


title: rnh1D_rnh201D_05h_2


title: MN_D0_chr_rep2

source_name: iPSC

value: iPSC


title: C4-2B_MDVr_P15_shCXCR7_1 [mr108]


title: WT, I3C, hkSE activation, 3h, rep 2

value: wildtype


title: rnh1D_rnh201D_05h_1


title: MN_D0_chr_rep1


title: rnh1D_rnh201D_0h_2


title: WT, no ligand, hkSE activation, 3h, rep 2


title: C4-2B_MDVr_P15_LKO_2 [mr106]

value: LKO


title: C4-2B_MDVr_P15_LKO_3 [mr107]


title: MLL7 PDX AZD1775 (Wee1i) scRNAseq

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: scRNAseq after AZD1775 (Wee1i) treatment,Chromium Single Cell 3ʹ Reagent Kits v3

data_processing:
PDX cell scRNA-seq data was processed and aligned with Cell Ranger (version 6.0.1) using GRCh38-2020-A genome as reference.
Cells were filtered with Cell Ranger 6.0.1 following alignment.
Utilization of R package Seurat (v3) enabled further analysis. MLL-7 data was filtered with the following cutoffs: cells had more than 1500 but less than 6000 UMIs and percentage of mitochondrial counts less than 10%
Assembly: GRCh38-2020-A
Supplementary files format and content: barcode annotation: filtered barcode annotation; feature annotation: filtered feature list; count matrix: filtered UMI count matrix

source_name: frozen bone marrow cells

growth_protocol: NSG mice of 8-9 weeks were sublethally irradiated (250cGy). 24 hours after 2000000 cells MLL-7 PDX were transplanted via tail vein injection.

extract_protocol:
Sample preparation for scRNA-sequencing was performed by thawing viably frozen bone marrow cells,  which were stained with Draq7 (BioLegend), hCD45 and hCD19, together with a PerCP/Cyanine5.5 anti-mouse CD45. Approximately 20.000 alive/mCD45neg/hCD45pos/hCD19pos cells were sorted into a PBS (GE Healthcare Life Sciences) + 2% FBS (Thermo Scientific) coated tube and prepared for sequencing using the 10x Genomics platform at the Center for Translational Genomics, Lund University
Chromium NEXT GEM Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index)

treatment_protocol: Mice were treated for 24 h with AZD1775 (Wee1i) (HY-10993 MedChemExpress) or DMSO (Sigma-Aldrich) when 1% of hCD45pos(BD Bioscience) hCD19pos (Biolengend) mCD45neg (Biolengend) cells were detected in peripheral blood. 4 hours after the second dose, mice were sacrificied by cervical dislocation and tibia, femur, and hip from both legs were collected and homogenized into single-cell suspensions by manual trituration and viably frozen in 10% DMSO (Sigma-Aldrich)

value: frozen bone marrow cells

tag: disease state

value: KMT2A-r acute lymphoblastic leukemia

value: KMT2A::AFF1;MEF2D::PTMA; KMT2A::PTPRC and clonal mutations in FLGE3292G; FLT3I836del; METL575I; CHEK1I465T; CSF1RS422C

tag: construct/treatment


title: MLL7 PDX Vehicle (DMSO) scRNAseq

description: scRNAseq in control, Chromium Single Cell 3ʹ Reagent Kits v3

value: DMSO


title: C4-2B_MDVr_P15_LKO_1 [mr105]

tag: cell line

value: prostate


title: LNCaP_MDVr_P23_shCXCR7_3 [mr104]

value: LNCaP


title: rnh1D_rnh201D_0h_1

tag: treatment


title: WT, no ligand, no activation, 3h, rep 2

value: 3h post administration


title: RS4.11 AZD1775 (Wee1i) scATAC-seq

description:
scATACseq after AZD1775(Wee1i) treatment, 10X Genomics multiome kit
RS411_Wee1i10h_atac_peak_annotation.tsv
RS411_Wee1i10h_atac_peaks.bed
RS411_Wee1i10h_raw_feature_bc_matrix.h5
RS411_Wee1i10h_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Data was aligned with Cell Ranger Single cell Multiome ATAC + Gene expression workflow cellranger-arc-2.0.1 to human reference (GRCh38) from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 2.0.1 following alignment.
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data raw and filtered CellRanger output in .h5 format. This data contains both the scRNA and scATAC count data.
Supplementary files format and content: Cellranger ATAC peak annotation in tsv format
Supplementary files format and content: Cellranger annotated ATAC peaks in bed format

growth_protocol: RS4;11 cell lines were maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM L-glutamine (Gibco, Thermo Fisher), 10mM HEPES (Lonza), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

extract_protocol:
Nuclei were then isolated with 10x Genomics Nuclei Isolation protocol for Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing user guide CG000365  Rev B.
scMultiome-seq was performed using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit and Next GEM Chip J, user guide CG000338 Rev E.
Chromium Single Cell ATAC and scRNA libraries

treatment_protocol: Cells were treated for 10 h with 1 micromolar AZD1775(Wee1i) or DMSO.

value: B-cell acute lymphoblastic leukemia

tag: agent


title: WT, BaP, hkSE activation, 3h, rep 1

value: BaP

value: hkSE


title: LNCaP_MDVr_P23_shCXCR7_2 [mr103]

tag: tissue


title: WT, I3C, hkSE activation, 3h, rep 1


title: Spo_AI_2

value: Incubated with SPM for 6h and added 1uM beta-estradiol for 2h


title: RS4.11 DMSO scATAC-seq

description:
scATACseq from vehicle treated cell line, 10X Genomics multiome kit
RS411_DMSO10h_atac_peak_annotation.tsv
RS411_DMSO10h_atac_peaks.bed
RS411_DMSO10h_raw_feature_bc_matrix.h5
RS411_DMSO10h_filtered_feature_bc_matrix.h5


title: Spo_MI_2

value: Incubated with SPM for 6h and added 1uM beta-estradiol for 1.5h


title: LNCaP_MDVr_P23_shCXCR7_1 [mr102]


title: WT, no ligand, no activation, 3h, rep 1

value: bone marrow-derived macrophages

value: DMSO-control


title: Spo_MI_1


title: LNCaP_MDVr_P23_LKO_3 [mr101]


title: RS4.11 AZD1775(Wee1i) scRNA-seq

description:
scRNAseq after AZD1775 (Wee1i) treatment, 10X Genomics multiome kit
RS411_Wee1i10h_raw_feature_bc_matrix.h5
RS411_Wee1i10h_filtered_feature_bc_matrix.h5


title: RS4.11 DMSO scRNA-seq

description:
scRNAseq from vehicle treated cell line, 10X Genomics multiome kit
RS411_DMSO10h_raw_feature_bc_matrix.h5
RS411_DMSO10h_filtered_feature_bc_matrix.h5


title: Spo_Pac_2

value: Incubated with SPM for 6h


title: RS4.11 AZD1775 24h GRO-seq biol rep2

description:
nascent RNA
GROseq after AZD1775 (Wee1i) treatment

data_processing:
Single-end sequencing (51-55bp) was performed with HiSeq 2000, according to the manufacturer instructions.
GRO-seq reads were quality controlled (FastQC). Reads were adapter trimmed using HOMER (version 4.9 (Heinz, Benner et al. 2010)) and filtered (min 95% of positions have a min phred quality score of 10) using the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads mapping to rRNA regions (AbundantSequences as annotated by iGenomes) were discarded.
The Bowtie software (version 1.1.2 Langmead et al., 2009) was then used for alignment of remaining reads to the hg19 genome version, allowing up to two mismatches and no more than three matching locations. The best alignment was reported. Reads corresponding with so-called blacklisted regions that include unusual low or high mappability as defined by ENCODE, ribosomal and small nucleolar RNA (snoRNA) loci from ENCODE and a custom collection of unusually high signal depth regions from GRO-seq was used to filter the data.
bigWig files were generated using the HOMER software http://biowhat.ucsd.edu/homer/. GRO-seq tagDirectories were generated from aligned reads with fragment length set to 75 and data visualized using makeMultiWigHub.pl with strand-specificity HOMER (version 4.9)
Assembly: hg19
Supplementary files format and content: bigWig GRO-seq signal files, separately for plus and minus strand
Library strategy: GRO-seq

growth_protocol: Cells were cultured in RPMI1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher) and 2 mM L-glutamine (Gibco, Thermo Fisher) and 10 mM HEPES (Gibco, Thermo Fisher).

extract_protocol:
Five million nuclei were collected from RS4;11 cells after 4, 10 and 24 h of 1 mircomolar AZD1775(Wee1i) or DMSO (vehicle) treatment. The nuclear run-on reaction buffer (496 mM KCl, 16.5 mM Tris-HCl, 8.25 mM MgCl2 and 1.65% Sarkosyl (Sigma-Aldrich, Steinheim, Germany) was supplemented with 1.5 mM DTT, 750 uM ATP, 750 uM GTP, 4.5 uM CTP, 750 uM Br-UTP (B7166,Sigma-Aldrich) and RNAse inhibitors (RNase Inhibitor (Thermo Fisher, Carlsbad, CA, USA, and RNasin Plus RNase Inhibitor Promega). To each 100 ul of nuclei samples 50 μl of the run-on reaction buffer was added and incubated for 5 min at 30C.
RNA was collected using Trizol LS, fragmented and run-on reaction products were immuno-purified two times using anti-Br-UTP antibody (ab-6326, Abcam) bound to 30 μl of magnetic beads (Protein G DynabeadsThermo Fisher Scientific) and washed with 300 μl of PBST wash buffer four times (refer to detailed protocol in Roberts et al. 2015). The cDNA template was PCR amplified (Illumina barcoding) for 12 cycles and size selected to 225–350 bp length. The ready libraries were sequenced with Illumina Hi-Seq2000 (GeneCore, EMBL Heidelberg, Germany).

treatment_protocol: Cells were treated with DMSO control or 1 micromolar AZD1775 (Wee1i) (MK-1775 / Adavosertib)  for  4 h, 10 h, or 24 h.

value: AZD1775 (Wee1i)

tag: replicate


title: RS4.11 AZD1775 24h GRO-seq biol rep1


title: LNCaP_MDVr_P23_LKO_1 [mr99]

value: LKO


title: Spo_Pac_1

tag: strain


title: RS4.11 AZD1775(Wee1i) scATAseq

description: scATACseq after AZD1775 (Wee1i) treatment, 10x Genomics ATAC-seq kit

data_processing:
Data was aligned with Cell Ranger atac workflow 1.2.0 to human+mouse combined reference (hg19 and mm10) from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 1.2.0  following alignment.
Mouse-human experiments: grep fragments corresponding to human analyzed. Selected only the human fragments, peak coordinates and cells.
Peaks detected from vehicle and AZD1775(Wee1i) treated cells were merged using bedtools (version 2.27.1), discardingsmaller than 10 bp wide peaks.
Data across treatments was combined by re-quantifying counts from the fragment files based on the merged peak regions. Peaks detected in over 1 percent of cells were kept for downstream analyses.
Seurat (version 3.1.1) package and Signac (version 0.1.6) were used for downstream analysis
Assembly: hg19
Supplementary files format and content: metadata annotation: 10x Genomics Cell Ranger filtered barcode list where selected only hg19 cells in tsv format
Supplementary files format and content: annotated hg19 peaks: filtered peak annotation in bed format
Supplementary files format and content: fragments: 10x Genomics Cell Ranger unique filtered hg19 fragments in tsv format

extract_protocol:
Excess dead cells were depleted from samples using bead-based Dead Cell Removal Kit (130-090-101, MACS miltenyi Biotech). Nuclei were then isolated with 10x Genomics Nuclei Isolation protocol for Single Cell ATAC Sequencing user guide CG000169 Rev D. Nuclei were mixed in 1:1 ratio with mouse nuclei (unrelated to this experiment) and loaded to the Chromium controller.
scATAC-seq was performed using Chromium Single Cell ATAC Library & Gel Bead and Chip E Single Cell ATAC Kit (10x Genomics), user guide CG000168 Rev C.
Chromium Single Cell ATAC Library

treatment_protocol: RS4;11 cells were treated for 24 h with 1 micromolar AZD1775 (Wee1i) or DMSO.

tag: genotype


title: RS4.11 DMSO 24h GRO-seq biol rep2

description:
nascent RNA
GROseq in control cell line


title: IVT_IFRD2_del_ex4-10_UT

library_source: other

data_processing:
Adapter trimming (Cutadapt)
Alignment (STAR for RNAseq and NETseq, bowtie for DMS-MaPseq)
Differential splicing analysis with rMATS (RNAseq)
DREEM (DMS-MaPseq)
featureCounts (NETseq)
Assembly: GRCh38
Supplementary files format and content: RNAseq_control_vs_U2_KD_rMATS_stat_intron_retention.txt: intron-exon junction counts for every annotated intron in each RNAseq sample and statistical testing between control and U2 snRNA using rmats-stats
Supplementary files format and content: RNAseq_control_vs_U2_KD_SE.MATS.JC.txt: RNAseq rMATS output for skipped exons (SE) between all control and U2 snRNA knockdown replicates
Supplementary files format and content: *vienna.txt: DMS reactivities for every nucleotide in the in vitro transcribed RNAs used for DMS-MaPseq
Supplementary files format and content: *ER_counts.txt or *PR_counts.txt: featureCounts output from NET-seq data for the gene body region (ER, +300 nt from TSS to end of gene) or promoter region (PR -30 to + 300nt from TSS) of all genes

molecule: other

organism: synthetic construct

source_name: In vitro transcription

value: In vitro transcription

value: untreated


title: Spo_AI_1


title: WT, no ligand, hkSE activation, 3h, rep 1

tag: cell type

value: wildtype


title: IVT_IFRD2_del_ex4-10_rep1

value: DMS


title: Spo_05h_2

value: WT

value: Incubated with SPM for 0.5h


title: RS4.11 DMSO scATACseq

description: scATACseq in control cell line, 10x Genomics ATAC-seq kit

value: DMSO


title: Spo_2h_1

value: Incubated with SPM for 2h


title: RS4;11 DMSO scRNAseq

description:
scRNAseq in control cell line
10x Genomics RNA-seq kit

data_processing:
Data was aligned with Cell Ranger 3.0.2 version to human+mouse combined reference (hg19 & mm10) from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 3.0.2 following alignment.
The mouse cells were left out by filtering cells which cellranger characterized as mouse or doublet cells or had more than 500 counts assigned to mouse genes.
The mouse genes were filtered out from the count matrix.
Assembly: hg19
Supplementary files format and content: barcode annotation: filtered barcode annotation; feature annotation: filtered feature list; count matrix: filtered UMI count matrix

growth_protocol: Nalm-6 (ACC-128, DSMZ, Germany) cell lines were maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM L-glutamine (Gibco, Thermo Fisher), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich). RS4;11 cell lines were maintained in RPMI 1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher), 2 mM L-glutamine (Gibco, Thermo Fisher), 10mM HEPES(Lonza), penicillin (100 U/ml), and streptomycin (100 mg/ml) (Sigma-Aldrich).

extract_protocol:
Excess dead cells were depleted from samples using bead-based Dead Cell Removal Kit (catalog number 130-090-101, MACS miltenyi Biotech). Cells were mixed in 1:1 ratio with mouse cells (unrelated to this experiment) and loaded to the Chromium controller.
scRNAseq: Cells were combined with reverse transcriptase Master Mix and partitioned into Gel Bead-In EMulsions (GEMs) using 10X GemCode Technology, where the poly-A transcripts are barcoded with an Illumina R1 sequence, a 16 bp 10X barcode and a 10 bp Unique Molecular Identifier (UMI). 11-12 cycles of PCR was used to amplify the cDNA.

treatment_protocol: Cells were treated for 24 h with 1 microM AZD1775 (Wee1i) or DMSO.

value: B-cell acute lymphoblastic leukemia


title: RS4.11 AZD1775 10h GRO-seq biol rep2


title: RS4;11 AZD1775(Wee1i) scRNAseq

description:
scRNAseq after AZD1775 (Wee1i) treatment
10x Genomics RNA-seq kit

value: AZD1775 (Wee1i) 1 microM


title: RS4.11 AZD1775 10h GRO-seq biol rep1


title: RS4.11 DMSO 24h GRO-seq biol rep1

description:
nascent RNA
GROseq in control cell line


title: Spo_05h_1


title: IVT_IFRD2_SE_ex4-10_UT


title: Nalm6 AZD1775(Wee1i) scRNAseq

description:
scRNAseq after AZD1775(Wee1i) treatment
10x Genomics

source_name: Nalm-6 B-cell acute lymphoblastic leukemia cell line

value: human near diploid karyotype - 46(43-47)<2n>XY, t(5;12)(q33.2;p13.2)


title: HeLa_U2_KD_RNAseq_rep3

description: RNAseq_control_vs_U2_KD_rMATS_stat_intron_retention.txt, RNAseq_control_vs_U2_KD_SE.MATS.JC.txt

source_name: HeLa

value: HeLa

value: U2 snRNA knockdown


title: Spo_0h_2

value: Incubated with SPM for 0h


title: RS4.11 DMSO 10h GRO-seq biol rep2

description:
nascent RNA
GROseq in control cell line


title: RS4.11 DMSO 10h GRO-seq biol rep1

description:
nascent RNA
GROseq in control cell line


title: IVT_IFRD2_SE_ex4-10_rep2


title: LNCaP_MDVr_P23_LKO_2 [mr100]

value: LNCaP

value: prostate


title: HeLa_U2_KD_RNAseq_rep2


title: Spo_0h_1


title: HeLa_U2_KD_RNAseq_rep1


title: Spo_2h_2


title: IVT_IFRD2_del_ex4-10_rep2


title: IVT_IFRD2_SE_ex4-10_rep1


title: RNaseH

value: Cultured with YPD, genomic DNA treated with RNase H


title: HeLa_control_KD_RNAseq_rep3

value: control knockdown


title: RS4.11 AZD1775 4h GRO-seq biol rep2

value: 4 h

value: AZD1775 (Wee1i)


title: RS4.11 AZD1775 4h GRO-seq biol rep1


title: IVT_IFRD2_WT_ex8-10_UT

value: In vitro transcription

value: untreated


title: YPD_2

value: WT

value: Cultured with YPD


title: HeLa_control_KD_RNAseq_rep2


title: RS4.11 DMSO 4h GRO-seq biol rep2

description:
nascent RNA
GROseq in control cell line

value: DMSO


title: IVT_IFRD2_WT_ex8-10_rep1

value: DMS


title: IVT_IFRD2_WT_ex8-10_rep2


title: HeLa_control_KD_RNAseq_rep1


title: YPD_1


title: RS4.11 DMSO 4h GRO-seq biol rep1

description:
nascent RNA
GROseq in control cell line

value: B-cell acute lymphoblastic leukemia


title: Vector-3

status: Public on May 13 2023

first: zhenzhen

last: zhang

state: Haidian Distinct

address: No.30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

data_processing:
Sequencing reads were mapped with Hisat2 v2.1.0.
Gene read counts were obtained with HTSeq v0.11.2.
The differential expression levels were estimated with R-package DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: Hematopoietic stem cell

extract_protocol:
HSCs were sorted into lysis buffer. RNA-Seq was performed according to Smart-seq2.
The RNA was reverse transcribed by SuperScript II reverse transcriptase (Invitrogen) and amplified to enrich the cDNA fragments. The cDNA was purified by VAHTS DNA Clean Beads (Vazyme). Tn5 transposase was used to tagment DNA, then stripped by 0.2% SDS. The DNA was amplified by Q5 High-Fidelity 2× Master Mix (NEB) followed by VAHTS DNA Clean Beads purification.

value: Hematopoietic stem cell

value: Vector


title: Pus10-OE-3


title: Pus10-OE-1


title: Vector-2


title: Pus10-OE-2


title: Vector-1


title: Sample 6_shRNA-S1PR2 3

city: Berkeley

first: Jen-Chywan

last: Wang

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

data_processing:
BGI's internal software SOAPnuke v1.5.2 was used to filter reads
reads with adaptors were removed, unknown bases >5% were removed.  Removed low quality reads (% of base which quality is more than 20 and lower than 15% in a read). BGI's SOAPnuke parameters: -n 0.001 -l 20 -q 0.4 -A 0.25
Reads were then mapped using HISAT2 to mm9. 94.84% were mapped. Clean reads were mapped to reference transcripts with Bowtie2
gene expression was caculated with RSEM (v1.2.12 parameters: default(, sequence saturation analysis was determined, reads coverage and distribution analysis of trascripts was calculated. DEseq2 and PossionDis algorithms to detect DEGs were used.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol:
Mouse livers were harvested and were snap frozen in liquid nitrogen. RNA was then extracted using the Zymogen RNA extraction microprep kit. RNA was eluted with RNAse free water and 1ug of RNA was used in constrution of the libraries.
DNB seq platform was used for sequncing

tag: strain background

value: mixed B6:sv129 background

tag: age

value: 7-12 weeks old

tag: genotype/variation

value: Liver


title: Sample 2_shRNA-Scramble 2

value: shRNA-Scramble


title: Sample 3_shRNA-Scramble 3


title: Sample 4_shRNA-S1PR2 1


title: Sample 1_shRNA-Scramble 1


title: Sample 5_shRNA-S1PR2 2


title: siRNA treatment rep2

first: Yinghao

last: Shen

address: 180 Fenlin Road

institute: Zhongshan Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

growth_protocol: The human Huh7 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of Huh7 HCCf cancer cells with different treatment was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Huh7 HCC  cells were transfected with control siRNA or METTL3 siRNA.

value: human Huh7 cells

tag: passage


title: Control rep2


title: Control rep3


title: Control rep1


title: siRNA treatment rep1


title: siRNA treatment rep3


title: ATDC5_5 kPa_2

city: Philadelphia

first: Grey

last: Hallstrom

state: Pennsylvania

address: 3450 Hamilton Walk

institute: University of Pennsylvania

data_processing:
paired-end reads were concatenated and aligned to the mouse reference genome mm10
files were converted to bam files
counts weres generated using feature counts
Deseq2 was used for differenital gene expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files after differential gene expression analysis

source_name: ATDC5 cells seeded on fibronectin coated 5 kPa polyacrylamide gels day 2

extract_protocol:
Trizol
TruSeq Stranded mRNA Library Prep

value: ATDC5 cells

value: Chondroprogenitor

tag: condition

value: chondrogenic differentiation


title: ATDC5_Glass_1

source_name: ATDC5 cells seeded on fibronectin coated glass day 2


title: ATDC5_55 kPa_2

source_name: ATDC5 cells seeded on fibronectin coated 55 kPa polyacrylamide gels day 2


title: ATDC5_Glass_2

value: seeded on fibronectin coated glass day 2


title: ATDC5_siYap1/Wwtr1_1

source_name: ATDC5 cells siRNA targetting Yap1 and Wwtr1 day 5 post-transfection


title: ATDC5_Scrmbl_3

source_name: ATDC5 cells non-targetting sirna control (scrmbl) day 5 post-transfection


title: ATDC5_siYap1/Wwtr1_2

value: siRNA targetting Yap1 and Wwtr1 day 5 post-transfection


title: ATDC5_Scrmbl_1

value: non-targetting sirna control (scrmbl) day 5 post-transfection


title: ATDC5_LPA_3

source_name: ATDC5 cells LPA treatment day 3

value: LPA treatment day 3


title: ATDC5_LPA_1


title: ATDC5_LPA_2


title: ATDC5_siYap1/Wwtr1_3


title: ATDC5_5 kPa_1

value: seeded on fibronectin coated 5 kPa polyacrylamide gels day 2


title: ATDC5_Scrmbl_2


title: ATDC5_C3_1

source_name: ATDC5 cells C3 treatment day 3

value: C3 treatment day 3


title: ATDC5_C3_3


title: ATDC5_C3_2


title: ATDC5_Ctrl_2

source_name: ATDC5 cells control day 3

value: control day 3


title: ATDC5_55 kPa_1

value: seeded on fibronectin coated 55 kPa polyacrylamide gels day 2


title: ATDC5_Ctrl_3


title: ATDC5_Ctrl_1