title: granulosa_old+lrp1low.biol rep 2

data_processing:
All of the RNA-Seq sequencing reads were processed using BBDuk (version 38.34) to remove adapters and low-quality reads.
The filted reads were mapped to the mouse reference genome using HISAT2 (version 2.2.1) with the default parameters.
Gene expression for each sample was quantified to FPKM using Stringtie (version 1.3.3b).
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include FPKM values for each transcript.

source_name: ovaries

extract_protocol:
Total oocyte and granulosa cell RNA was isolated using the Arcturus PicoPure RNA isolation kit (applied biosystems Cat.no. KIT0204).
The RNA sequencing libraries were generated using a KAPA Stranded RNA-Seq Kit Illumina platform (Cat.no.KK8440).

value: ovaries

value: granulosa

tag: developmental stage

value: old

tag: old mice with subgroups of uc-mscs


title: Differentiating cells Day 14 Control

status: Public on Mar 13 2024

type: SRA

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

country: USA

institute: The Ohio State University Wexner Medical Center

library_source: transcriptomic single cell

data_processing:
Samples were preprocessed using 10X Genomics Chromium Single Cell RNA v3 chemistry. Libraries were sequenced on an Illumina Novaseq instrument and counted with CellRanger v6.0.2 using hg38 reference genome.
Assembly: hg38
Supplementary files format and content: csv for count matrix, and metadata

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human induced pluripotent stem cells were cultured in Essential 8 medium (Thermo Fisher Scientific). Cardiac differentiation was performed by sequential modulation of WNT signaling by small molecules (CHIR99021 for 2 days and IWR-1 for 2 days) as we previously published (PMID: 33645570).

extract_protocol:
Single-cell suspension was processed and loaded into a Chromium Next GEM Chip G (10x Genomics) to generate single-cell gel bead in emulsions on a 10x Genomics Chromium Controller.
Single-cell RNA-seq libraries were constructed using a Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics).

treatment_protocol: Differentiating cells were collected on Day 5, Day 10, Day 14, and Day 30 during cardiac differentiation of healthy control and PA-IVS-1v iPSCs.

tag: cell type

value: Human iPSC

tag: disease state

value: Control

tag: time


title: mESC-Igf2_Igf2_inverted~dCTCFinICR-BS15283A

city: New York

first: Matthew

middle: T

last: Maurano

state: New York

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

library_source: genomic

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Payload and Targeted sequencing (Capture-seq)

treatment_protocol: Cells were engineered with different landing pads and payloads as described and were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript.

value: mESC

tag: strain

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: payload id

tag: genotype

tag: clone id

tag: seq method

value: Capture-seq


title: DLD-1 cells, oeTNFRSF12A, rep2

city: Guangzhou

first: Chuyue

address: Tianhe District, Guangzhou, Guangdong Province

country: China

institute: Sun Yat-Sen University

description: processed_counts.xlsx for all RNA-Seq samples

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.6.5) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean data were mapped to the GRCh38/hg38 by HISAT (v2.2.1) , then were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: GRCh38/hg38
Supplementary files format and content: xlsx format file includes raw counts for each sample

source_name: Large intestine; Colon

growth_protocol: DLD-1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). A certain amount of RNA was used for library construction
(1) Sample QC (2) mRNA Isolation by oligo (dT) -attached magnetic beads (3) mRNA Fragmentation (4) cDNA Synthesis (5) End Repair, Add A and Adaptor Ligation (6) PCR (7) Library QC

treatment_protocol: TNFRSF12A overexpression was induced by treatment with 0.1 μg/mL Doxycycline for 48 h

tag: tissue

value: Large intestine; Colon

tag: cell line

value: epithelial cell

value: TNFRSF12A overexpression

tag: treatment

value: Doxycycline treating 48 h


title: HCC827 cells-2

city: Chengdu

first: Jian

last: Zhang

state: Sichuan

address: Guoxuexiang Road

department: Westchina Hospital

institute: Sichuan University

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using bwa-mem
Mutations were identified following GATK best practice.
Duplicate reads were identified and removed by Picard, and Local Indel Realignment and Base Score Recalibration was applied to deduplicated reads using GATK
Somatic variants were called with Mutect2 and annotated by annovar.
Assembly: hg38
Supplementary files format and content: VCF file containing all mutations identified.
Library strategy: WES

source_name: lung

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were divided when they reached a high confluence, usually 3 days as an interval period.

extract_protocol:
We extract genomic DNA from the cultured cells following the manufacture's protocol (The QIAamp DNA Mini Kit (cat. nos. 51304 and 51306) ).
The exome sequences were efficiently enriched from 0.4 μg genomic DNA using Agilent liquidcapture system (Agilent SureSelect Human All Exon V6) according to the manufacturer’s protocol. Firstly, qualified genomic DNA was randomly fragmented to an average size of 180-280bp by Covaris S220 sonicator. Remaining overhangs were converted into blunt ends via exonuclease polymerase activities. Secondly, DNA fragments were end repaired and phosphorylated, followed by A-tailing and ligation at the 3’ends with paired-end adaptors. DNA fragments with ligated adapter molecules on both ends were selectively enriched in a PCR reaction. After PCR reaction, libraries hybridize with liquid phase with biotin labeled probe, then use magnetic beads with streptomycin to capture the exons of genes. Captured libraries were enriched in a PCR reaction to add index tags to prepare for sequencing. Products were purified using AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by NGS3K/Caliper and quantified by real-time PCR (3 nM). At last, DNA library were sequenced on Illumina for pairedend 150bp reads.

treatment_protocol: Cells were treated with or without the osimertinib with gradually increased concentration, the primary osimertinib concentration is 100nM.

value: lung

value: non-small cell lung cancer (NSCLC) cell line

value: WT


title: mESC-Igf2_Igf2_inverted~miICR-BS15281A


title: HCC827 cells-1


title: granulosa_old+lrp1high.biol rep 3

city: Shanghai

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

institute: Tongji University

molecule: polyA RNA


title: DLD-1 cells, oeTNFRSF12A, rep1


title: DLD-1 cells, oeControl, rep3

value: untreated


title: granulosa_old+lrp1high.biol rep 2


title: HCC827 cells, Osimertinib Resistance 2

data_processing:
RNAseq data was processed using a standard workflow, which includes quality assessment of fastq reads using FastQc. Raw sequence reads were trimmed adapters using Trimmomatic.
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR aligner. Expression counts was generated by HTSeq.
Differential expression analysis was performed by DESeq2 pipeline.
Assembly: hg38
Supplementary files format and content: file containing read counts for all genes

extract_protocol:
1. Homogenization 2. PHASE SEPARATION. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000xg for 15 minutes at 2 to 8°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 3. RNA PRECIPITATION. Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000xg for 10 minutes at 2 to 8°C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 4. RNA WASH. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500xg for 5 minutes at 2 to 8°C. 5. REDISSOLVING THE RNA. At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes).   6. samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.   In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: Osimertinib Resistance


title: granulosa_old+lrp1low.biol rep 1

value: ovaries


title: HCC827 cells, Osimertinib Resistance 3


title: DLD-1 cells, oeControl, rep2


title: mESC-Igf2_Igf2_inverted~miICR-BS15277A


title: mESC-Igf2_Igf2_inverted~miICR-BS15279A


title: DLD-1 cells, oeControl, rep1


title: HCC827 cells, Osimertinib Resistance 1


title: granulosa_old+lrp1high.biol rep 1

value: granulosa


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS15274A


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS15273A


title: granulosa_old.biol rep 2

value: old


title: HCC827 cells, 3

value: no treatment


title: MCF7_SETDB1_LMB_3

city: Nantong

first: Wenlin

last: Yang

address: No.30, Tongyang North Road, Tongzhou District, Nantong, Jiangsu 226006, P.R. China

department: Department of Pathology

institute: Nantong Tumor Hospital Affiliated to Nantong University

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping: The clean data were mapped  to UCSC_hg38 by HISAT (V2.2.1).
Reference gene mapping: Clean data to reference transcripts were mapped using Bowties (v2.4.5).
Assembly: UCSC_hg38
Supplementary files format and content: xls file includes FPKM vaules for each Sample

source_name: breast

extract_protocol:
Total RNA was extracted from cultures in triplicate using TRIzol Reagent (ThermoFisher Scientific) and Direct-zol™ RNA MiniPrep Kits (Zymo Research).
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit/BGI, LR00R96

value: breast

value: breast cancer cell line

value: SETDB1 overexpression

value: LMB


title: granulosa_old+all.biol rep 1

value: old+all


title: MCF7_SETDB1_LMB_2


title: granulosa_old.biol rep 1


title: HCC827 cells, 2


title: granulosa_young.biol rep 1

value: young


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS15270A

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: Capture-seq


title: MCF7_SETDB1_LMB_1


title: HCC827 cells, 1

value: lung

value: non-small cell lung cancer (NSCLC) cell line


title: PC9 cells, Osimertinib Resistance 2

description: JXQ.filtered.vcf

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.


title: mESC-Igf2_Igf2_dCTCFinICR-BS15267A


title: MCF7_SETDB1_DMSO_3

value: DMSO


title: PC9 cells, Osimertinib Resistance 1

description: JXQ.filtered.vcf

value: Osimertinib Resistance


title: oocyte_old+lrp1low.biol rep 2

value: ovaries

value: oocyte


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS13395A


title: MCF7_SETDB1_DMSO_2


title: PC9 cells 2

description: JX.filtered.vcf

value: WT


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS13394A


title: oocyte_old+lrp1high.biol rep 3

value: old


title: MCF7_NC_DMSO_3

value: breast


title: MCF7_NC_DMSO_2

value: breast cancer cell line


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS13390A


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS15271A


title: oocyte_old+lrp1high.biol rep 1


title: oocyte_old+lrp1high.biol rep 2


title: HCC827 cells, TET2 KO, 2

value: TET2 KO


title: HCC827 cells, TET2 KO, 3


title: HCC827 cells, TET2 KO, 1


title: oocyte_old+all.biol rep 2


title: MCF7_NC_DMSO_1


title: mESC-Igf2_Igf2_dCTCFinICR-BS13386A


title: oocyte_old+all.biol rep 1


title: KO_Polyribosome_rep3

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

description:
PolyA mRNA
Polyribosome_mRNA_expression.txt

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Fragments per kilo base per million mapped reads (FPKM) using edgeR.
For Ribo-Seq data analysis, adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases, respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Polyribosome_mRNA_expression.txt: Text file of RNA-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: Ribo-seq_reads.txt: Text file of Ribo-seq includes the FPKM values for every gene.
Supplementary_files_format_and_content: TRAC-seq_expression.txt: Text file of TRAC-seq represents the ratio and cleavage score for every tRNA in each sample.

source_name: Nasopharyngeal carcinoma 5-8F cells

growth_protocol: Human 5-8F cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: METTL1 was knocked out by sgRNA.

value: Nasopharyngeal carcinoma cell line

value: METTL1 knockout

tag: sample type

value: RNA-seq


title: mESC-Igf2_Igf2_dCTCFinICR-BS13385A

value: mESC


title: HCC827 cells 3


title: mESC-Igf2_Igf2_miICR~Igf2SV-BS13381A

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: oocyte_old+lrp1low.biol rep 1


title: MCF7_SETDB1_DMSO_1

value: SETDB1 overexpression


title: KO_Polyribosome_rep2


title: KO_Polyribosome_rep1


title: oocyte_old.biol rep 2


title: PC9 cells 1

description: JX.filtered.vcf

value: lung


title: HCC827 cells 2

value: non-small cell lung cancer (NSCLC) cell line


title: oocyte_old.biol rep 1


title: HCC827 cells 1


title: mESC-Igf2_Igf2_miICR~Igf2SV-BS13380A

value: Capture-seq


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS13389A


title: KO_Input_rep3


title: PC9 cells, Osimertinib Resistance, 3

value: Osimertinib Resistance


title: KO_Input_rep2


title: oocyte_young.biol rep 2

value: ovaries

value: young


title: mESC-Igf2_Igf2_Sox2DistalLCR~miICR-BS13349A


title: KO_Input_rep1


title: oocyte_young.biol rep 3

value: oocyte


title: oocyte_young.biol rep 1


title: mESC-Igf2_Igf2_Sox2DistalLCR~miICR-BS13346A


title: Vector_Polyribosome_rep3

value: Wild type


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS13393A


title: PC9 cells, Osimertinib Resistance, 2

value: WT


title: Sham cal res 16F

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava2.20 software used for basecalling.
Reads were aligned to UCSC mouse genome (mm10) using Tophat2 (2.1.1)
Gene-based read counts were performed using Rsubread from FeatureCounts
Assembly: UCSC mouse genome (mm10)
Supplementary files format and content: csv file includes Gene counts for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, stored at -80'C . RNA was extracted using Trizol reagent.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: Liver

tag: age

value: 21 weeks

tag: condition

value: diet-induced obesity (DIO)

tag: treatment group

value: Sham cal res (Sham-WM)


title: Vector_Polyribosome_rep2

value: Nasopharyngeal carcinoma cell line

value: RNA-seq


title: PC9 cells, 3

value: no treatment


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS13350A

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: PC9 cells, 1

value: lung

value: non-small cell lung cancer (NSCLC) cell line


title: Sham cal res 9F


title: PC9 cells, 2


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS12583A

value: Capture-seq


title: Vector_Polyribosome_rep1


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~dCTCFinICR-BS12582A


title: Vector_Input_rep2


title: Vector_Input_rep3


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~miICR-BS12581A


title: Sham cal res 15F


title: Sham cal res 2F


title: microRNA, PASI >10, severe4

city: Suwon

first: Eun-So

last: Lee

address: 164, Worldup-ro, Yeongtong-gu

department: Dermatology

country: South Korea

institute: Ajou University

data_processing:
Data filtering steps: Low quality bases or reads were trimmed or filtered using following criteria; bases with a quality score of less than 20 and read length with below 17bp were subject to trimming. The whole process was performed using the Cutadapt tool (Marcel Martin, 2011).
Sequence alignment: Filtered reads were mapped to the reference genome of the related species using the aligner Bowtie (Trapnell C. et al, 2009), followed by variant calling in the seed region of the miRNA has been done.  In order to find the expression estimation, mirdeep2 tool (Friedlander M. R. et al, 2011) was used.
Variant calling in the miRNA seed region: The variant calling was performed by the GATK (McKenna, A. et al, 2010) to search variants in the miRNA seed region. The dcov option was set to 1,000 for the max depth threshold in the region.
Expression estimation: The miRNA expression level was measured with mirdeep2 (Friedlander M. R. et al, 2011) using the gene annotation database of the species along with hairpin and mature miRNA sequence information which can be extracted from miBase (Kozomara, A., & Griffiths- Jones, S., 2013). All parameters were set to default values.
Differential Expressed (DE) miRNA analysis: For DE miRNA analysis, miRNA level count data were generated using mirdeep2 (Friedlander M. R. et al, 2011). Based on the calculated read count data, DE miRNAs were identified using the R package called TCC (Sun J. et al, 2013) where this package applies robust normalization strategies to compare tag count data. Normalization factors were calculated using the iterative DEGES/edgeR method. Q-value was calculated based on the p-value using the p.adjust function of R package with default parameter settings. The DE miRNAs were identified based on the q-value threshold less than 0.05 for correcting errors caused by multiple-testing (Benjamini Y., and Hochberg Y., 1995).
DE miRNA target gene identification: 14 websites containing information on miRNA and targeted gene of it were searched in order to identify the miRNA target genes.
Assembly: Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25

source_name: plasma exosomes

extract_protocol:
Namely, smallRNA molecules were isolated from 1μg of total RNA via the adapter ligation. The isolated smallRNAs were synthesized as single-stranded cDNAs through the RT (Reverse transcription) priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared through PCR (Polymerase Chain Reaction). And, the fragments around 150bp were extracted for sequencing through size selection by gel electrophoresis. Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA) followed by quantification with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s protocol. Following cluster amplification of denatured templates, sequencing was progressed using Illumina sequencing NovaSeq6000 S4 platform (Illumina, CA, USA).
The libraries were prepared for 50bp single-end sequencing using the NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific Corp.).

tag: subject status

value: patients with high psoriasis area and severity index (PASI) score (>10)

value: plasma exosomes

tag: molecule type

value: microRNA

value: Day 0


title: microRNA, PASI >10, severe5

tag: cell type


title: Sleeve gastrectomy 18F

value: Sleeve gastrectomy


title: Vector_Input_repl

value: Wild type


title: Sleeve gastrectomy 11F

value: Liver

value: 21 weeks


title: microRNA, PASI >10, severe3


title: mESC-Igf2_Igf2_Sox2DistalLCR~inverted~miICR-BS12579A


title: Sleeve gastrectomy  8F

value: diet-induced obesity (DIO)


title: microRNA, PASI >10, severe2


title: preterm_labor_without_PPROM_amnion_tissue_4

city: Providence

first: Alper

last: Uzun

state: RI

address: 69 Brown St

institute: Brown University

description: Amnion tissue from preterm labor with PPROM

data_processing:
Raw fastq files for all samples were checked for quality using FastQC v0.11.5 and did not require quality or adapter trimming.
Salmon v1.3.0 was used in mapping-based mode to align reads and quantify transcripts.
Assembly: Gencode v36 GRCh38.p13 genome and Gencode v36 transcriptome
Supplementary files format and content: Salmon quant files in quant.sf format.

source_name: amniotic membrane

extract_protocol:
Total RNA was extracted from each sample using a phenol-chloroform extraction protocol to produce mRNA. Total concentration of RNA was evaluated on an Agilent Bioanalyzer 2100 (Santa Clara, CA).
RNA-Seq library construction was conducted by BGI America. Double stranded PCR products were circularized by the splint oligo sequence, and the resulting single strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which has more than 300 copies of one molecule. The DNBs were loaded into a patterned nanoarray and single end 50 (pair end 100/150) base reads were generated by Probe-Anchor Synthesis (cPAS).
100bp paired-end

treatment_protocol: Chorioamnion was collected within 15 minutes of delivery from pregnancies complicated by preterm birth between the gestational ages of 24 to 37 weeks. The chorioamnion membrane was then separated into amnion and chorion and immediately frozen in liquid nitrogen, or placed in RNAlater solution, and stored at -80°C.

value: amniotic membrane


title: Sleeve gastrectomy 1F


title: mESC-LP300-BS12994A


title: preterm_labor_without_PPROM_chorion_tissue_3

description: Chorion tissue from preterm labor with PPROM

source_name: chorion

value: chorion


title: microRNA, PASI >10, severe1


title: preterm_labor_without_PPROM_chorion_tissue_4


title: mESC-Igf2_Igf2_Sox2DistalLCR~dCTCFinICR-BS12571A


title: preterm_labor_without_PPROM_amnion_tissue_3


title: mESC-Igf2_Igf2_Sox2DistalLCR~miICR-BS12570A


title: Sham Ad lib 10F

value: Sham Ad lib


title: mESC-Igf2_Igf2_Sox2DistalLCR~dCTCFinICR-BS12572A

value: mESC


title: microRNA, PASI <5, mild3

value: patients with high psoriasis area and  low PASI score (<5)


title: microRNA, PASI <5, mild2


title: mESC-Sox2_DistalLCR_H19enh~inverted-BS12007A

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: Sham Ad lib 6F


title: mESC-Sox2_DistalLCR_H19enh~inverted-BS12006A


title: preterm_labor_without_PPROM_chorion_tissue_2


title: microRNA, PASI <5, mild1


title: Sham Ad lib 4F


title: Day7 P hiPSCs, P3

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

description: P1, P2, P3 were the three replicates

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads. Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of at least two biological replicates per group was performed by using the edgeR_3.24.3. Genes with an adjusted P-value <0.05 were assigned as differentially expressed genes (DEGs).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Text file includes read counts for each Sample

source_name: P hiPSC-derived cardiac cells

growth_protocol: All hiPSCs were cultured in mTesR1 medium.

extract_protocol:
total RNAs were harvested using RNeasy Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations
Bulk RNA-seq

value: day 7

value: P hiPSC-derived cardiac cells

value: Trisomy 21


title: Day7 P hiPSCs, P2

description: P1, P2, P3 were the three replicates


title: preterm_labor_without_PPROM_amnion_tissue_2


title: Sham Ad lib 3F


title: mESC-Sox2_DistalLCR_H19enh-BS12004A

value: Capture-seq


title: preterm_labor_without_PPROM_amnion_tissue_1


title: mESC-Sox2_DistalLCR_H19enh-BS12003A


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS10037A


title: preterm_labor_without_PPROM_chorion_tissue_1


title: mESC-Sox2_DistalLCR_H19enh-BS12002A


title: preterm_labor_with_PPROM_chorion_tissue_4


title: preterm_labor_with_PPROM_amnion_tissue_4


title: Day7 P hiPSCs, P1

description: P1, P2, P3 were the three replicates


title: preterm_labor_with_PPROM_amnion_tissue_3


title: preterm_labor_with_PPROM_chorion_tissue_3


title: Day7 N hiPSCs, N1

description: N1, N2, N3 were the three replicates

source_name: N hiPSC-derived cardiac cells

value: N hiPSC-derived cardiac cells

value: isogenic normal


title: mESC-Sox2_DistalLCR_H19enh~inverted-BS12005A


title: Day7 N hiPSCs, N2

description: N1, N2, N3 were the three replicates


title: mESC-Igf2_Igf2_dEnh~dCTCFinICR-BS10036A


title: Day7 N hiPSCs, N3

description: N1, N2, N3 were the three replicates


title: hiPSCs with trisomy 21 (P hiPSCs), A12

description: A10, A11, A12 were the three replicates

source_name: hiPSCs

growth_protocol: All hESCs and hiPSCs were cultured in mTesR1 medium.

value: hiPSCs

value: trisomy 21

value: Calcitriol for 24 hours


title: preterm_labor_with_PPROM_chorion_tissue_2


title: mESC-Igf2_Igf2_dCTCFinICR-BS10031A


title: hiPSCs with trisomy 21 (P hiPSCs), A11

description: A10, A11, A12 were the three replicates


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS09214A


title: Pla2g3-/-, control, bronchial epithelial cells

type: RNA

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Whole Mouse Genome Microarray (4x44K, Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Mice were sensitized with intraperitoneal injections of OVA (Grade V, Merk-Sigma-Aldrich) (10 µg) as a antigen plus 1.3 mg of aluminum hydroxide (Alu-Gel-S suspension, SERVA) (alum adjuvant) in 0.2 ml of saline on days 0 and 14. On days 26, 27, and 28, the mice were challenged with 1% OVA aeroallergen for 30 min per day.

extract_protocol: Total RNA was extracted from cells and purified, and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 3 h after antigen challenge, lungs were harvested, and bronchial epithelial cells were isolated from lung tissues (reference to Kuroishi S et al. Respirology 14, 828-837, 2009) for microarray analysis.

value: bronchial epithelial cells

value: control


title: Pla2g3-/-, antigen challenged, bronchial epithelial cells

value: antigen challenged


title: preterm_labor_with_PPROM_amnion_tissue_2

value: amniotic membrane


title: Pla2g3+/+, antigen challenged, bronchial epithelial cells


title: Pla2g3+/+, control, bronchial epithelial cells


title: Pla2g3-/-, antigen challenged, lung

source_name: Pla2g3-/-, antigen challenged, lung

treatment_protocol: 48 h after antigen challenge, lungs were harvested for microarray analysis.

value: lung


title: hiPSCs with trisomy 21 (P hiPSCs), A10

description: A10, A11, A12 were the three replicates


title: preterm_labor_with_PPROM_chorion_tissue_1

value: chorion


title: mESC-Igf2_Igf2_dCTCFinICR-BS10033A

value: mESC


title: hiPSCs with trisomy 21 (P hiPSCs), A9

description: A7, A8, A9 were the three replicates

value: DMSO (Control) for 24 hours


title: mESC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS09212A

value: C57BL6/6J x CAST/EiJ F1 hybrid


title: mESC-Igf2_Igf2_miICR~Igf2SV-BS09210A


title: Pla2g3-/-, control, lung

source_name: Pla2g3-/-, control, lung


title: hoe-1(mpt67);glp-1(e2144)_atfs-1 RNAi_rep3

city: Nashville

first: Maulik

middle: R

last: Patel

address: 465 21st Ave S

institute: Vanderbilt University

data_processing:
Initial read quality was assessed with FastQC
Paired end reads were trimmed using Trimmomatic-0.39 [S4]. The universal Illumina adapter was removed, and reads were trimmed with a 4:15 sliding window
STAR 2.5.4 was used to align reads to the genome and transcriptome (WBcel.235) using default parameters
Salmon was used to generate transcript pseudo counts with the following options: --validateMappings --recoverOrphans --numBootstraps=30 --useVBOpt --seqBias --gcBias –writeUnmappedNames
Tximport was used to import data from the salmon files, including read abundance, length, counts, counts from abundance
DESeq2 was used to generate a contrast and determine significantly different transcript levels
DESeq2 was also used to normalize counts to account for variation in library size.
Assembly: WBcel.235
Supplementary files format and content: tab-delimited text file includes raw transcript pseudo counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal somatic

growth_protocol: All conditions were raised from embryo at 25°C for 72 hours

extract_protocol:
800 adult animals were collected for each replicate and transferred into 1 ml of M9 Buffer in a 1.5 mL microcentrifuge tube. Worms were pelleted at 500xg for 1 minute, supernatant removed and then washed once with 1 ml of fresh M9, and then once with 1 ml of M9 supplemented with 0.01% Tween-20 following the same spin and supernatant removal. After removing as much of the last supernatant as possible, 250 ul of Qiazol was added to each sample and snap-frozen in liquid nitrogen. Samples were then run through 3 freeze thaw cycles: 37°C bead bath for 2 min followed by liquid nitrogen for 1 minute. Following freeze thaw cycles, samples were completely thawed and incubated at room temperature for 5 minutes. 50 ul of chloroform was added to each sample, vigorously vortexed for 30 s and incubated at room temperature for 3 minutes. Then, samples were centrifuged at 4°C for 15 minutes at 12,000xg for 15 min. Following the spin, 125 ul of the upper aqueous phase was transferred to a fresh 1.5 ml tube. 187.5 ul of 100% molecular grade ethanol was then added to each sample and pipetted up and down to mix. Samples were then transferred to Qiagen RNeasy Mini Kit columns, centrifuged at 8,000xg for 30 seconds, and flow through discarded. Then, 700 ul of RW1 buffer was added to column, centrifuged at 8,000xg for 30 seconds, and flow through discarded. 500 ul RPE buffer added to column, centrifuged at 8,000xg for 30 seconds, and flow through discarded. Then again 500 ul of RPE buffer was added, centrifuged at 12,000xg for 2 min, and flow through discarded. Columns were then transferred to fresh collection tubes, centrifuged at 13,000xg for 1 minute with tube lids open to dry columns. Samples were then eluted from column with 20 ul of RNase free water into a fresh 1.5 ml microcentrifuge tube by centrifuging at 13,000xg for 1 min. Following RNA extraction, RNA samples were DNase treated with Turbo DNA-free Kit (Invitrogen #AM1907) following manufacturer’s directions. Briefly, 2 ul of 10x Turbo DNase Buffer and 1 ul of Turbo DNase were added to 20 ul RNA samples and gently mixed by pipetting up and down. Samples were then incubated in a 37°C bead bath for 20 min. Following incubation, 3 ul of resuspended Inactivation Reagent was added to each sample and mixed well by pipetting up and down. Samples were incubated at 25°C for 5 min. Then, samples were centrifuged at 10,000xg for 90 sec. The RNA containing supernatants were transferred to fresh tubes and stored at -80°C until RNA sequencing.
Stranded mRNA library preparation was conducted using NEBNext® Poly(A) selection following manufacturer's instructions.

treatment_protocol: Animals were grown on RNAi expressing bacteria (control or atfs-1) from embryo

value: whole animal somatic

value: wildtype strain N2

value: atfs-1 RNAi


title: mESC-Igf2_Igf2_miICR~Igf2SV-BS09209A

value: Capture-seq


title: Pla2g3+/+, control, lung

source_name: Pla2g3+/+, control, lung


title: VPM rep2

city: La Crosse

first: Kelly

last: Gorres

state: WI

address: 1725 State St, Cowley 4015

department: Chemistry & Biochemistry

institute: University of Wisconsin-La Crosse

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor and low-quality sequences using Trimmomatic Galaxy version 0.36.5.
Paired reads were mapped to an indexed hg38 transcriptome
Quantified was performed using Salmon v0.12.0 with parameter --validateMappings
Genome_build: hg38
Supplementary_files_format_and_content: Quantification files from Salmon (TPM)

source_name: HH514-16 P3HR-1-derived Epstein-Barr virus-positive Burkitt lymphoma cells

growth_protocol: Cells were maintained in 5% CO2 at 37°C in RPMI 1640 supplemented with 8% fetal calf serum. Cells were subcultured to 3-4 x 10^5 cells/mL 2 days prior to drug treatment.

extract_protocol:
Total RNA was extracted with the Qiagen Rneasy Mini kit.
Strand-specific sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol.

treatment_protocol: Cells at 1 x 10^6 cells/mL were treated with drugs for 6 hours.

tag: drug treatment

value: valpromide 10 mM

tag: treatment time

value: 6 hour


title: VPM+NaB rep1

value: valpromide 10 mM + sodium butyrate 3 mM


title: hiPSCs with trisomy 21 (P hiPSCs), A8

description: A7, A8, A9 were the three replicates

value: hiPSCs

value: trisomy 21


title: mESC-Igf2_Igf2_miICR~Igf2SV-BS09207A

source_name: mESC

tag: strain


title: VPM+NaB rep2


title: hiPSCs with trisomy 21 (P hiPSCs), A7

description: A7, A8, A9 were the three replicates


title: H9 hESCs, A6

description: A4, A5, A6 were the three replicates

source_name: hESCs

value: hESCs

value: normal

value: 5-OXO-ETE for 24 hours


title: hoe-1(mpt67);glp-1(e2144)_atfs-1 RNAi_rep2


title: VPM rep1


title: VPA+NaB rep2

value: valproic acid 10 mM + sodium butyrate 3 mM


title: hoe-1(mpt67);glp-1(e2144)_atfs-1 RNAi_rep1


title: H9 hESCs, A5

description: A4, A5, A6 were the three replicates


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08618A

tag: payload id


title: glp-1(e2144)_atfs-1 RNAi_rep3

tag: genotype


title: mESC-Igf2_Igf2_157kb~Igf2SV-BS09964A

tag: clone id


title: VPA+NaB rep1


title: H9 hESCs, A4

description: A4, A5, A6 were the three replicates


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08617A

tag: seq method


title: preterm_labor_with_PPROM_amnion_tissue_1

tag: tissue

value: amniotic membrane


title: glp-1(e2144)_atfs-1 RNAi_rep2

tag: cell line


title: VPA rep2

value: valproic acid 10 mM


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08616A

value: mESC


title: H9 hESCs, A3

description: A1, A2, A3 were the three replicates

tag: treatment

value: Ethanol (Control) for 24 hours


title: glp-1(e2144)_atfs-1 RNAi_rep1

value: whole animal somatic


title: PC9 cells, Osimertinib Resistance, 1

source_name: lung

value: lung

value: non-small cell lung cancer (NSCLC) cell line

value: WT

value: Osimertinib Resistance


title: VPA rep1

value: 6 hour


title: H9 hESCs, A2

description: A1, A2, A3 were the three replicates


title: mESC-Sox2_Sox2_143kb-BS08615A

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: Capture-seq


title: NaB rep2

value: sodium butyrate 3 mM


title: H9 hESCs, A1

description: A1, A2, A3 were the three replicates

value: hESCs


title: hoe-1(mpt67);glp-1(e2144)_control RNAi_rep2

value: wildtype strain N2

value: control RNAi


title: hiPSCs with trisomy 21 (P hiPSCs), B3

value: hiPSCs

value: trisomy 21


title: hoe-1(mpt67);glp-1(e2144)_control RNAi_rep1


title: Untreated rep2


title: hiPSCs with trisomy 21 (P hiPSCs), B2


title: glp-1(e2144)_control RNAi_rep3


title: Untreated rep1


title: hiPSCs with trisomy 21 (P hiPSCs), B1


title: NaB rep1


title: mESC-LP300-BS08269A


title: mESC-Sox2_Sox2_143kb-BS08611A


title: eif4g_clip_dep_6

first: Caryn

last: Hale

address: 1230 York Avenue

institute: Rockefeller University

description: eif4g CLIP in depolarized neurons, replicate 6

library_source: other

data_processing:
filtering and demultiplexing using fastq_filter.pl (CTK package, Zhang lab, min:0-15:20,mean:16-41:20)
trim 3' linker sequence using cutadapt (GTGTCAGTCACTTCCAGCGG)
collapse exact duplicates using fastq2collapse.pl (CTK package, Zhang lab)
trim 5' barcode and linker using stripBarcode.pl (CTK package, Zhang lab)
alignment with Rsubread to UCSC mm10 transcriptome
Assembly: mm10/TxDb.Mmusculus.UCSC.mm10.knownGene
Supplementary files format and content: tab-delimited text files include counts  that map to the 5'UTR of the longest transcript for each gene.

molecule: other

growth_protocol: Primary cortical neurons were grown in Neurobasal media supplemented with B27 and Glutamax.

extract_protocol:
UV cross-linked lysates were treated with DNase and RNase A (empirically determined concentration of RNase A for the cell type and IP’d protein), and cleared by centrifugation at 20,000g for 20 min at 4°C. The magnetic dynabeads (G for mouse and A for rabbit antibodies) were conjugated with the antibody (eIF4G2) and incubated with the lysates rotating overnight at 4°C. After washes and dephosphosphrylation, 3’pre-adenylated linker was ligated on to the RNAs overnight at 16°C. Ligated RNAs were then treated with T4 PNK to label them with radioactive P32.  Labeled RNA-protein complexes were then run on denaturing gels, transferred onto nitrocellulose membranes, and size selected to further digest with Proteinase K and release all the RNAs. RNAs were then purified using saturated phenol chloroform and heavy phase lock gel tubes and precipitated overnight at -20°C with linear acrylamide and ethanol.
Purified RNA was taken through reverse transcription using unique barcoded RT primers which allowed one to pool samples. Each replicate of resting and depolarized samples was pooled together after the reverse transcription step to increase yield. cDNA was then immunoprecipitated with BrdU antibody, circularized with CircLigase, and amplified with qPCR using the Kapa enzyme supplemented with SYBR and DP5-PE and SP3-PE Illumina primers. All samples were removed individually when they reached 200 RFU and purified using AMPure magnetic beads. Pooled libraries were sequenced on the Illumina MiSeq sequencer.

treatment_protocol: Depolarization was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 55 mM KCl addition for 1 hour, followed by resting for 30 minutes. Both resting and depolarized primary cortical neurons were treated with cycloheximide for 2 minutes before harvest.

value: primary neuronal culture (cortical)

value: Chx + KCl depolarization


title: mesendoderm-Igf2_Igf2_dCTCFinICR-CUT&RUN-CTCF-BS10389A

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences.
Illumina sequencing adapters were trimmed with Trimmomatic v0.39. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: GRCm38/mm10
Supplementary files format and content: bw
Library strategy: CUT&RUN

source_name: mesendodermal cells

growth_protocol: Differentiation to mesendodermal cells was adapted from a published protocol (Thomson et al. 2011). mESCs were seeded on plates coated with 0.1% gelatin (EMD Millipore ES006-B) in N2/B27 medium, containing a 1:1 mixture of DMEM/F12 (ThermoFisher 11330032) and Neuro-basal (ThermoFisher 21103049), supplemented with 0.5% N2 Supplement (ThermoFisher 17502048), 1% B27 Supplement (ThermoFisher 17504044), 1% glutamax (ThermoFisher 35050061), 1% Pen-Strep (ThermoFisher 15140122), 1% MEM nonessential amino acids (ThermoFisher 11140050), 100 μM sodium pyruvate (ThermoFisher 11360070), 0.1 mM 2-mercaptoethanol (Sigma M3148). The differentiation media was supplemented with 10 μM ROCK inhibitor Y-27632 (Cell Signaling 13264) the first 24 h after seeding the cells. For the next 3 days, 3 μM CHIR99021 (R&D Systems 4423) was added to the media, and replaced every 24 h. Four days after differentiation, plates were rinsed twice using PBS and cells were collected for further studies.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. CUT&RUN experiments were conducted using the CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assay kit (Cell Signaling Technology, #86652) following the manufacturer’s protocol. For each reaction, 5 million cells were used. The CTCF antibody (Cell Signaling Technology, #2899S) was used at a dilution of 1/50 for overnight incubation at 4°C. DNA fragments were purified using the DNA Clean & Concentrator-5 Kit (Zymo, D4014) according to the manufacturer’s procedures, and eluted in 15 µL. Up to 11.15 µL purified DNA was taken directly into end repair for library construction using the Illumina dsDNA protocol.
DNA fragments were end-repaired with T4 DNA polymerase (NEB M0203L), Klenow DNA polymerase (NEB M0210L), and T4 polynucleotide kinase (NEB M0201L), and A-tailed using Klenow (3′-5′ exo-; NEB M0212L). Illumina sequencing adapters were then ligated to DNA ends using Quick Ligase (NEB M2200L). The post-ligation product was purified using 18% Sera-Mag Magnetic Beads (Cytiva 65152105050250) in polyethylene glycol. DNA libraries were amplified with KAPA 2× Hi-Fi Hotstart Readymix (Roche 07958935001) and purified with 18% Sera-Mag Magnetic Beads in polyethylene glycol.

value: mesendodermal cells

tag: chip antibody

value: CTCF

value: Mesendoderm differentiation


title: isogenic normal hiPSCs (N hiPSCs), A3

value: normal


title: mesendoderm-Igf2_Igf2_miICR~Igf2SV-CUT&RUN-CTCF-BS10387A


title: glp-1(e2144)_control RNAi_rep2

value: whole animal somatic


title: isogenic normal hiPSCs (N hiPSCs), A2


title: eif4g_clip_dep_5

description: eif4g CLIP in depolarized neurons, replicate 5


title: hoe-1(mpt67);glp-1(e2144)_control RNAi_rep3


title: HDAC3miKO_tFCI_rep3 [ATAC-seq]

first: Yue

state: Shanghai

address: 131, Dong'an Road, Xuhui

department: Institute of Brain Science

institute: Fudan University

data_processing:
FastQC (v0.11.9) was first used for quality control assessment.
Paired-end clean data were aligned to the reference genome (M. musculus, UCSC mm10) using Bowtie2 (v2.2.5)(24).
Peaks were called using MACS2 v2.1.4 (--shift -100 --extsize 200 –nomodel).
BamCoverage from Deeptools was used to generate normalized bigwig files and visualized on IGV
Assembly: mm10
Supplementary files format and content: bigWig files were generated using BamCoverage from Deeptools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.1.4 (--shift -100 --extsize 200 –nomodel).

source_name: brain

extract_protocol:
Microglial nuclei were first extracted with lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAce2, 0.1 mM EDTA, 10 mM Tris-HCl, pH 8, 0.1% NP-40). Then ATAC-seq library was constructed using the reagents in TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-02). The experimental procedure was as follows: nuclei were treated with Tn5 at 37°C for 30 minutes. DNA was then purified with the MinElute Gel Extraction Kit (Qiagen, 28604) and eluted in 27ul EB buffer. 24ul of DNA samples, 10ul of 5XTAB, 5ul of PPM, 1ul of TAE, and selected aptamers (5ul of N5XX and 5ul of N7XX) (Vazyme, TD202) were mixed, followed by PCR amplification. Library DNA was purified and size-selected with SPRIselect beads (Beckman, B23318). Library quality was checked on a Qubit and Agilent 4200 Tapestation.
Library was sent to Novogene in China for paired-end sequencing on Illumina XTen (2 × 150bp read length).

treatment_protocol: The transient focal cerebral ischemia (tFCI) was induced by middle cerebral artery occlusion (MCAO) for 60 min. Briefly, mice were anesthetized with 1.5% isoflurane in a 30% O2/70% N2 mixture and placed on a temperature-adjustable heating pad to maintain the mouse rectal temperature at 37± 0.5°C during surgery. In MCAO mice, the left carotid artery was separated and exposed. The external carotid artery (ECA) was ligated and cut. The suture (diameter 0.10mm) wrapped with a silicone tip (0.21- 0.23mm, RWD, Shanghai, China) was inserted into the ECA and advanced along the internal carotid arteries until it meets resistance (occluding the middle cerebral artery). Sham-operated mice received the same anesthesia and arterial exposure, except that no MCAO procedure was performed.  FACS-purified microglia were applied to ATAC-seq. FACS was performed using a Beckman CytoFLEX SRT cell sorter powered by Kaluza analysis software. Fluorescence compensation was performed using single-stained OneComp eBeads according to the manufacturer's instructions. The antibodies used for sorting are as follows: CD45-eFluor 450 (48-0451-82, eBioscience, 1:50), CD11b-APC cy7 (47-0112-82, eBioscience, 1:200), CD11c-PerCP cy5.5(45-0114-82, eBioscience, 1:100), Ly6G(Gr1)-PE (12-9669-82, eBioscience, 1:200). Data were analyzed using FlowJo software to quantify positively stained cells.

value: brain

value: microglia

value: HDAC3 knockout

value: tMCAO-surgery

tag: batch


title: eif4g_clip_dep_4

description: eif4g CLIP in depolarized neurons, replicate 4


title: mESC-Sox2_Sox2_143kb-BS08612A

value: mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: Capture-seq


title: mesendoderm-Igf2_Igf2_157kb~Igf2SV-CUT&RUN-CTCF-BS10384A


title: isogenic normal hiPSCs (N hiPSCs), A1


title: mesendoderm-LP300-CUT&RUN-CTCF-BS10383A


title: eif4g_clip_dep_3

description: eif4g CLIP in depolarized neurons, replicate 3


title: P hiPSCs, P2

description: P1, P2 were the two replicates

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads. Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
For simulations of peaks called per input read, aligned andde-duplicated BAM files were used without any additional filtering.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: EXCEL file includes "P_vs_N_peak_compare_table" for each Sample.

extract_protocol:
ATAC-seq was performed based on previously reported protocols. Please see the citations 12and 53 in maunscript
Briefly, nuclei were extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 minutes. Equimolar Adapter1 and Adapter 2 were added after transposition, PCR was then performed to amplify the library.
After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to  the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

value: Trisomy 21


title: Pla2g3+/+, antigen challenged, lung

source_name: Pla2g3+/+, antigen challenged, lung

value: lung

value: antigen challenged


title: mesendoderm-dPiga-CUT&RUN-CTCF-BS10382A

value: Bl6/C dPiga_1_2_F2


title: HDAC3miKO_tFCI_rep2 [ATAC-seq]


title: P hiPSCs, P1

description: P1, P2 were the two replicates

value: hiPSCs


title: eif4g_clip_dep_2

description: eif4g CLIP in depolarized neurons, replicate 2

value: primary neuronal culture (cortical)

value: Chx + KCl depolarization


title: HDAC3miKO_tFCI_rep1 [ATAC-seq]


title: eif4g_clip_dep_1

description: eif4g CLIP in depolarized neurons, replicate 1


title: WT_tFCI_rep3 [ATAC-seq]

value: WT


title: WT_tFCI_rep2 [ATAC-seq]


title: N hiPSCs, N1

description: N1, N2 were the two replicates

value: isogenic normal


title: astrocytes, LA2

city: Hong Kong

first: Ying

last: Chen

address: No.21 Sassoon Road

country: Hong Kong

institute: the University of Hong Kong

data_processing:
Sequencing was performed on DNBSEQ platform developed by BGI Co.
4GB clean reads from each sample were obtained after filtering and the removal of low-quality reads and mapped to the reference genome and reference gene by using the HISAT and Bowtie databases separately.
The differential expression genes (DEGs) were defined by DEGseq with the settings: |log2 (foldchange)|≥1 and Q value ≤0.05
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: .txt table with raw gene counts for every different expression gene and every sample; summary.txt (average read counts and comparison)

source_name: hippocampus

extract_protocol:
hippocampus was extracted and dissolved by collogenase and DNAse I for 30 mins, debries and mylins were removed by percoll, single cell suspension was stained with GLAST- APC antibody fro 20min and DAPI for 10 min, GLAST+/DAPI- cells were collected by BD fusion as live astrocytes. total RNA was extrated by Qiagen RNeasy Micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: laparotomy mice were treated by abdominal surgery under sevoflurane anesthesia, control mice were treated by sevoflurane only

value: astrocytes

value: hippocampus

value: laparotomy


title: astrocytes, LA3


title: glp-1(e2144)_control RNAi_rep1

value: whole animal somatic

value: wildtype strain N2

value: control RNAi


title: eif4g_clip_rest_5

description: eif4g CLIP in resting neurons, replicate 5

value: Chx


title: Sample 3 ME180/C4.15.1/LV GAN 50, Lentiviral GAN gene transfected CRISPR-Cas9 clone

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

description:
raw_counts_all.csv
rpkm_counts_all.csv
DS9

data_processing:
Sequenced reads were trimmed for adaptor sequence
Read were aligned using STAR 2.7
readFilesCommand zcat  readMatesLengthsIn NotEqual  #outReadsUnmapped Fastx  outSAMmode Full  #outSAMtype BAM Unsorted SortedByCoordinate  outSAMtype BAM SortedByCoordinate  outSAMstrandField intronMotif  outSAMattributes All  outSAMunmapped None  outSAMorder Paired  outSAMprimaryFlag AllBestScore  outSJfilterReads All  outSJfilterCountUniqueMin 1 1 1 1  outSJfilterCountTotalMin 1 1 1 1  outSJfilterOverhangMin 30 10 10 10  outSJfilterDistToOtherSJmin 10 0 5 10  outSJfilterIntronMaxVsReadN 50000 100000 200000  outFilterType Normal  outFilterMultimapNmax 20  outFilterMultimapScoreRange 1  outFilterScoreMin 0  outFilterScoreMinOverLread 0.66  outFilterMatchNmin 0  outFilterMatchNminOverLread 0.75  outFilterMismatchNmax 999  outFilterMismatchNoverLmax 0.1  outFilterIntronMotifs None  scoreGap 0  scoreGapNoncan -200  scoreGapGCAG 0  scoreGapATAC 0  scoreStitchSJshift 0  alignIntronMin 21  alignIntronMax 100000  alignMatesGapMax 100000  alignSJoverhangMin 10  alignSJDBoverhangMin 1  alignSplicedMateMapLmin 0  alignSplicedMateMapLminOverLmate 0.66  sjdbScore 2  scoreGenomicLengthLog2scale -0.25  quantMode GeneCounts  #readNameSeparator -  outWigType bedGraph  outWigStrand Unstranded  alignSoftClipAtReferenceEnds No
Genome_build: GRCh38.primary.33
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: parental cell line ME 180

growth_protocol: Cell lines were grown in RPMI growth medium containing 10% FCS in tissue culture incubators at 37 deg for 48hrs. Cells were collected when there was 70% confluency..

extract_protocol:
RNA were extracted using respective Qiaigen isolation kits
RNAs were isolated from control or siRNA transfected cells using a pure Link RNA mini kit from Ambion (12183018A; Life Technologies, Inc., Carlsbad, CA) and the libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) according to the manufacturer recommendations. The final libraries were pooled at equimolar concentration and sequenced on an Illumina NovaSeq6000 sequencer (SP lane, 2x50bp).

treatment_protocol: RNA

value: cervical cancer cells


title: eif4g_clip_rest_4

description: eif4g CLIP in resting neurons, replicate 4


title: HDAC3miKO_Sham_rep3 [ATAC-seq]

value: brain

value: microglia

value: HDAC3 knockout

value: sham-surgery


title: Sample 3 ME180/C4.15.1/LV con 50, Control lentiviral transfected CRISPR-Cas9 clone

description:
raw_counts_all.csv
rpkm_counts_all.csv
DS6


title: astrocytes, LA1


title: Sample 2 ME180/C4.15.1, CRISPR-Cas9 clone 1

description:
raw_counts_all.csv
rpkm_counts_all.csv
DS8

value: ME180/C4.15.1, CRISPR-Cas9 clone 1


title: HDAC3miKO_Sham_rep2 [ATAC-seq]


title: astrocytes, SEV2

value: control


title: eif4g_clip_rest_2

description: eif4g CLIP in resting neurons, replicate 2

value: primary neuronal culture (cortical)


title: WT_Sham_rep3 [ATAC-seq]

value: WT


title: Sample 1 ME 180 parental cell line

description:
raw_counts_all.csv
rpkm_counts_all.csv
DS7

value: ME180 parental cell line


title: mESC-dPiga-CUT&RUN-CTCF-BS10373A

first: Matthew

address: 435 East 30th Street

institute: NYU Grossman School of Medicine

value: C57BL6/6J x CAST/EiJ F1 hybrid

value: Bl6/C dPiga_1_2_F2

value: CTCF


title: WT_Sham_rep2 [ATAC-seq]


title: N hiPSCs, N2

description: N1, N2 were the two replicates

value: hiPSCs

value: isogenic normal


title: K562 cells, SF3B1 K700E, 4 days, replicate 1 [LRSseq]

status: Public on Mar 12 2024

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

data_processing:
library strategy: LRS-seq
Porechop v0.2.4 was used to remove external adapters, Cutadapt for removing 3’ adapters and Prinseq-lite to remove PCR duplicates.
Minimap2 was used to align to hg38 build.
Custom scripts in Python and R were used to generate Co-SE and cumulative distribution of 3’ RNAPII position
Assembly: hg38
Supplementary files format and content: tab-delimited text files include average/median 3'RNAPII position (for each gene) and co-transcriptional splicing efficiency (CoSE) values (for introns genome-wide) for each sample

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
All extraction steps were performed on ice, and all buffers contained 25 uM α-amanitin, 40 U/ml RNase inhibitor, and protease inhibitor. Chromatin fractions were isolated from the cellular pellets using a previously published protocol. Chromatin was immediately dissolved in PBS and TRIzol Reagent. RNA was purified from chromatin using the RNeasy Mini kit according to the manufacturer’s protocol, including the on-column DNase I digestion. For genome-wide nascent RNA-seq, samples were depleted three times of polyA(+) RNA using the Magnetic mRNA isolation kit, each time keeping the supernatant, then depleted of ribosomal RNA using oligo probe-based rRNA depletion
A DNA adapter was ligated to 3′ ends of nascent RNA using the T4 RNA ligase kit by mixing adapter with nascent RNA. cDNA was generated from the adapter ligated RNA using the SMARTer PCR cDNA Synthesis Kit. cDNA was amplified by 15 cycles of PCR using the Advantage 2 PCR Kit with template switching custom oligo, cleaned up using a AMPure beads

treatment_protocol:
Modified allele expression induced with doxycycline (1ug/ml)
Cells (~20 million cells, per condition) were harvested at 4 days after doxycycline induction

value: Immortalized epithelial cells


title: eif4g_clip_rest_6

description: eif4g CLIP in resting neurons, replicate 6

value: Chx


title: K562 cells, SF3B1 K700E, 4 days, replicate 2 [LRSseq]


title: K562 cells, SF3B1 wild type, 4 days, replicate 2 [LRSseq]


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [LRSseq]


title: WT_tFCI_rep1 [ATAC-seq]

value: tMCAO-surgery


title: Compound 33 treated hTNFtg synovial fibroblasts REPLICATE 2

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens

data_processing:
FastQC 0.11.9 was used to check the quality of the raw data
Alignment was performed using Hisat2 v 2.2.1 with the following parameters:--score-min L,0,-0.36 -k 2 --max-seeds 20 --rna-strandness F
Summarization of aligned reads to gene count tables was performed with featureCounts v 2.0.3 using the following parameters:-t 'three_prime_utr' -g 'gene_name' --largestOverlap --readExtension3 500 --readExtension5 500 -s 1
Differential expression analysis was conducted between hTNFtg samples treated with compound33 versus samples treated with DMSO, using DESeq2
Assembly: mm10
Supplementary files format and content: Raw_counts_table.txt: contains gene raw counts for all samples as calculated by featureCounts
Supplementary files format and content: DESeq2-Condition_Tre_vs_Ctr.txt: contains the results of differential expression analysis performed with DESeq2

source_name: ankle joint

growth_protocol: Synovial fibroblasts isolated from ankle joints of hTNFtg mice were cultured for 3 passages

extract_protocol:
RNA was extracted using the Rneasy Mini kit from Qiagen according to manufacturer's protocol
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™V2 chips (ThermoFisher Scientific) on an Ion Proton™System, according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 10μΜ compound 33/ DMSO for 48 hours before isolating the RNA

value: ankle joint

value: primary cells

value: synovial fibroblasts

value: hTNFtg

value: compound 33


title: Compound 33 treated hTNFtg synovial fibroblasts REPLICATE 3


title: DMSO treated hTNFtg synovial fibroblasts REPLICATE 2

value: DMSO


title: DMSO treated hTNFtg synovial fibroblasts REPLICATE 3


title: DMSO treated hTNFtg synovial fibroblasts REPLICATE 1


title: astrocytes, SEV3

value: astrocytes

value: hippocampus

value: control


title: eif4g_clip_rest_3

description: eif4g CLIP in resting neurons, replicate 3

value: primary neuronal culture (cortical)


title: FADU_M_HiC

city: Maiami

first: Yuichiro

last: Nakata

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq).
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
HiC data fastq files were processed using the Juicer Pipeline from aidenlab (https://github.com/aidenlab/juicer).
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

source_name: Head and neck squamous cell carcinomas

growth_protocol: Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum, GlutaMAX and Penicillin-Streptomycin

extract_protocol:
Arima HiC-kit A510008
Arima HiC kit protocol followed by Library Preparation using NEBNext Ultra II DNA Library Prep Kit
See manuscript in method section
See manuscript in method section

tag: cell source

value: Homo sapiens

value: Head and neck squamous cell carcinomas

value: Lentiviraly expressed with histone H3.3K36 mutation

tag: genetic modification

value: genomic DNA


title: astrocytes, SEV1


title: eif4g_clip_rest_1

description: eif4g CLIP in resting neurons, replicate 1


title: FADU_WT_HiC

value: Lentiviraly expressed with histone H3.3


title: Transcriptomic profiling of HBG gene expression in HEK295T cell line rep1

city: Xianmen

first: Yuchen

address: Xiangan South Road

institute: Xianmen University

description: Circular

data_processing:
Base calling uses the software Bcl2fastq (v2.17.1.14) to analyze the original image of the sequencing result
Sequence reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequence using trim_galore (v0.6.7)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.9a)
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: human embryonic kidney

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested by addition of VeZol Reagent 3 days post transfection. And total RNA was extracted with RNA extraction auxiliary reagent.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. And then mRNA was mRNA was purified, fragmented, and used as the template for cDNA synthesis. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: In 12-well plates, HEK293T cells transfected with 32ng gRNA and 968ng pBluSKM vector plasmids.

value: human embryonic kidney

value: wild type

value: transfected plasmids encoding circular gRNAs targeting HBG


title: Transcriptomic profiling of HBG gene expression in HEK294T cell line rep3

description: Linear

value: transfected plasmids encoding  linear gRNAs targeting HBG


title: Transcriptomic profiling of HBG gene expression in HEK294T cell line rep1

description: Linear


title: Transcriptomic profiling of HBG gene expression in HEK295T cell line rep2

description: Circular


title: Transcriptomic profiling of HBG gene expression in HEK296T cell line rep3

description: NC

value: transfected plasmids encoding  gRNAs targeting  mNeonGreen


title: Transcriptomic profiling of HBG gene expression in HEK296T cell line rep2

description: NC


title: Transcriptomic profiling of HBG gene expression in HEK294T cell line rep2

description: Linear


title: Transcriptomic profiling of HBG gene expression in HEK295T cell line rep3

description: Circular


title: FCD2b_33

city: Brussels

first: Liesbeth

last: François

state: Brussels

address: Allée de la Recherche 60

country: Belgium

institute: UCB Pharma SA

data_processing:
The Decontamination Using Kmers (BBDuk) tool from the BBTools suite was used for adapter removal, quality trimming and removal of contaminant sequences (ribosomal or bacterial)60. A phred33 score of 20 was used to assess the quality of the read, with any read shorter than 31 nucleotides in length excluded from the downstream analysis. Reads were aligned directly to the human GRCh38 reference transcriptome (Gencode version 33)61 using Salmon v0.11.362. Transcript counts were summarized to the gene level and scaled using library size and average transcript length using the R package tximport63. Genes detected in less than 20% of the samples in any diagnosis cohort and with counts less than six across all samples were filtered out, resulting in 28,366 genes for downstream analysis. The gene counts were then normalized using the weighted trimmed mean of M-values method with the R package edgeR64. The normalized counts were then log2 transformed using the voom function from the R package limma65.
Assembly: GRCh38
Supplementary files format and content: Raw count matrix
Supplementary files format and content: Processed count matrix

source_name: Frontal

extract_protocol:
For RNA isolation, human tissue was homogenized in 700 µl Qiazol Lysis Reagent (Qiagen Benelux, Venlo, The Netherlands). Total RNA including the microRNA (miRNA) fraction was isolated using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands) according to the manufacturer’s instructions. The concentration and purity of RNA was determined at 260/280 nm using a Nanodrop spectrophotometer (Ocean Optics, Dunedin, FL, USA) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA integrity number (RIN) equal or greater than 6.0 were used for sequencing.
All library preparation and sequencing were performed by GenomeScan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) was used to process the samples. Sample preparation was performed according to the protocol NEBNext Ultra II Directional RNA Library prep Kit for Illumina (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of mRNA, cDNA synthesis was performed. Next, sequencing adapters were ligated to the cDNA fragments followed by polymerase chain reaction amplification. Clustering and DNA-sequencing was performed using the NovaSeq6000 (Illumina, Foster City, CA, USA) in accordance with manufacturers’ guidelines. All samples underwent paired-end sequencing of 150 nucleotides in length; the mean read depth per sample was 47 million reads.

value: Frontal

tag: Sex

value: Female

tag: age

tag: disease state

tag: seisure frequency


title: Compound 33 treated hTNFtg synovial fibroblasts REPLICATE 1

value: ankle joint

value: primary cells

tag: cell type

value: synovial fibroblasts

value: hTNFtg

value: compound 33


title: ControlHippocampus_11

source_name: Hippocampus

value: Hippocampus

value: Male

value: ControlHippocampus


title: ControlHippocampus_10


title: FCD2a_17


title: FCD2b_32


title: ControlHippocampus_13


title: TLE-HS_64

source_name: Temporal

value: Temporal

value: TLE-HS


title: Transcriptomic profiling of HBG gene expression in HEK296T cell line rep1

description: NC

value: human embryonic kidney


title: FCD2a_16


title: FCD2b_31


title: FCD2b_30


title: Transcriptomic profiling of HBG gene expression in HEK293T cell line rep3

value: wild type

value: transfected plasmids encoding U6 gRNAs targeting HBG


title: Transcriptomic profiling of HBG gene expression in HEK293T cell line rep2


title: FCD2b_29


title: Transcriptomic profiling of HBG gene expression in HEK293T cell line rep1


title: ControlHippocampus_12


title: TLE-HS_63


title: FCD2b_26


title: TSC_21

value: TSC


title: FCD2b_27


title: FCD2b_28


title: TLE-HS_61


title: TLE-HS_60


title: FCD2a_14


title: FCD2b_25

source_name: Parietal

value: Parietal


title: ControlHippocampus_9


title: TLE-HS_57


title: TLE-HS_58


title: TLE-HS_56


title: TLE-HS_55


title: ControlCortex_14

value: ControlCortex


title: FCD2a_15

value: Frontal


title: FCD2b_24


title: TLE-HS_54


title: TLE-HS_53

value: Female


title: TSC_20


title: TLE-HS_51


title: TLE-HS_49


title: FCD2a_13


title: TLE-HS_50


title: TLE-HS_52


title: FCD2b_23


title: ControlCortex_13


title: TLE-HS_46


title: Sample 33

city: Lund

first: Martin

last: Lauss

address: Barngatan 2B

department: Dept of Oncology

country: Sweden

institute: Lund University

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing:
The NanoString GeoMx Cancer Transcriptome Atlas assay was applied to the Regions of Interest according to the manufacturer’s instructions (Nanostring, Seattle, WA). The data were retreived as values that are scaled to the same 75% percentile across the regions.
The data underwent quantile-normalization and log-transformation as log2 (data+1).

label: not applicable

source_name: melanoma

label_protocol: Not applicable

extract_protocol: Tissue microarray cores were stained using immunofluorescence with CD3 (T-cell), CD20 (B-cell), PMEL/S100B (tumor cell) and DAPI antibodies, and tumor cell-containing regions of interest were selected based on these stainings.

tag: patient

tag: resistance


title: Sample 32


title: TLE-HS_47


title: Sample 31


title: Sample 29


title: TSC_19


title: TLE-HS_48


title: TLE-HS_45


title: Sample 27


title: Sample 26


title: Sample 28


title: FCD2b_22


title: FCD2a_11


title: TLE-HS_59


title: FCD2a_12

source_name: Occipital

value: Occipital


title: Sample 25


title: TLE-HS_43


title: TSC_18


title: TLE-HS_42


title: ENASIDENIB (2) -treated (120 h)

type: genomic

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

country: Spain

institute: Health Research Institute of Asturias (ISPA)

hyb_protocol: The processed DNA samples were then hybridised to Infinium MethylationEPIC v2.0 BeadChip following the Illumina Infinium HD Methylation Assay protocol.

scan_protocol: The arrays were scanned with iScan (Illumina) in accordance with the manufacturer's protocol.

data_processing: IDAT files were processed using the R/Bioconductor package minfi and differentially methylated probes were extracted with the R/Bioconductor package limma. Background correction was applied with the ssNOOB method. Probe signals were further corrected using the BMIQ algorithm. Sex chromosome, SNP-overlapping and multi-mapping probes were filtered out.

label: Cy3, Cy5

source_name: cell line

label_protocol: Labelling was performed automatically during the post-amplification xStain process and is achieved using Biotin and DNP labelled antibodies

growth_protocol: T-CDS17#1 chondrosarcoma cell line were growth in high glucose DMEM suplemented with 10% fetal bovine serum (FBS)

extract_protocol: Genomic DNA was extracted using the QIAmp DNA Mini Kit (Qiagen, Germany) following the manufacturing´s intructions.

treatment_protocol: T-CDS17#1 chondrosarcoma cell line was treated with 20 uM of enasidenib and DMSO (control) for 120 h

value: chondrosarcoma cells

tag: genotype

value: IDH2 mutant

value: ENASIDENIB 20 uM

tag: treatment time


title: TLE-HS_41


title: Sample 24


title: TLE-HS_44


title: ControlHippocampus_8

value: Hippocampus


title: Sample 30


title: DMSO (2) - control (120 h)

value: DMSO


title: DMSO (1) - control (120 h)


title: TLE-HS_38

value: Male


title: Sample 18


title: Sample 17


title: ENASIDENIB (3) -treated (120 h)


title: Sample 23


title: FCD2b_20


title: FCD2b_21


title: TLE-HS_40

value: Temporal


title: TLE-HS_37

value: TLE-HS


title: ENASIDENIB (1) -treated (120 h)


title: Sample 20


title: Sample 19


title: Sample 21


title: FCD2b_19


title: Sample 22


title: TLE-HS_39


title: TLE-HS_36


title: Sample 16


title: TLE-HS_34


title: Sample 12


title: ControlHippocampus_7

value: ControlHippocampus


title: TLE-HS_33


title: FCD2b_18


title: TLE-HS_35


title: TLE-HS_32


title: Sample 11


title: Sample 15


title: TLE-HS_62


title: Sample 9


title: TLE-HS_30


title: Sample 8


title: TSC_17


title: TLE-HS_31


title: Sample 14


title: ControlCortex_12


title: TSC_16


title: Sample 10


title: Sample 7


title: Sample 13


title: TLE-HS_29


title: Sample 4


title: Sample 6


title: Sample 5


title: Sample 1


title: Sample 2


title: Sample 3


title: TLE-HS_28


title: TLE-HS_27


title: FK866 plus succinate, replicate 1, CUT&Tag_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

data_processing:
library strategy: CUT&Tag
The raw reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using Bowtie2 (Version 2.5.0).
Assembly: mm10
Supplementary files format and content: bed

source_name: colon

extract_protocol:
Cultured-ILC2s were sorted by FACSMelody.
Cut & Tag libraries was generated and indexed using Hyperactive Universal CUT&Tag Assay Kit for Illumina and then TurePrep Index Kit for Illumina.

value: colon

value: FK866 plus succinate


title: FK866 plus succinate, replicate 2, CUT&Tag_seq


title: TLE-HS_25


title: FK866, replicate 1, CUT&Tag_seq


title: TLE-HS_26


title: Control, replicate 1, CUT&Tag_seq

value: Control


title: TLE-HS_24


title: TLE-HS_22


title: ControlHippocampus_6


title: gp61-sfGFP-1 IN

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
R1 data was processed using the single ended eCLIP pipeline and available at: http://github.com/yeolab/eclip.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (Pa_P01 + PhiPA3) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Assembly: PhiPA3
Assembly: Pa_PA01
Supplementary files format and content: compressed.bed files contain single replicate peaks (-log10 p-value, log2 fold enrichment above size-matched input in columns 4 and 5 respectively)
Supplementary files format and content: *vs* files contain reproducible peaks using IDR

organism: Pseudomonas aeruginosa

growth_protocol: Overnight bacterial cultures in LB media were diluted to OD600=0.1 and grown to OD600=0.5 at 30C. The cultures were diluted 1:10 into 50 mL total volume in 250 mL flasks and grown in LB supplemented with 0.2 mM CaCl2 and 0.1% Arabinose.

extract_protocol:
RNA isolation was performed with phenol/chloroform extraction and purified on spin columns (Zymo Research).
cDNAs were treated with ExoSAP-IT (Affymetrix) to remove the excess oligonucleotides. Second DNA adapters (containing 5 [N5] or 10 [N10] random bases at the 5′-end) were ligated to the 5′-end of the cDNA (T4 RNA Ligase, NEB). The DNA was amplified by PCR and purified with PippinPrep system (Sage Science) and sequenced with Illumina HiSeq 4000.

treatment_protocol: Each sample was treated with immunoprecipitation protocol with GFP-Trap beads. After the RNA-bound proteins were collected, cells were treated with FastAP (ThermoFisher) and T4 PNK (NEB), then barcoded RNA adapters were ligated to the 3′ end (T4 RNA Ligase, NEB).


title: FCD2b_17


title: gp61-sfGFP-2 IP


title: TLE-HS_21


title: TLE-HS_23


title: gp61-sfGFP-1 IP


title: sfGFP-2 IN

value: sfGFP


title: gp61-sfGFP-2 IN


title: FCD2b_15

value: Parietal


title: FCD2b_16

value: Frontal


title: sfGFP-1 IP


title: sfGFP-2 IP


title: TLE-HS_19


title: TLE-HS_20

value: Female


title: TLE-HS_18


title: sfGFP-1 IN


title: Sample 6, replicate 1, scRNAseq

city: New York

first: Nikhil

last: Sharma

state: NY

institute: Columbia University

description: 10x Genomics

data_processing:
Alignment, mapping, and quality control was performed using the 10x genomics cell ranger pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dorsal root ganglia

extract_protocol:
Sensory ganglia were dissociated in 40 units papain, 4 mg/ml collagenase, 10 mg/ml BSA, 1 mg/ml hyaluronidase, 0.6 mg/ml DNAse in DMEM:F12 + 1% pen/strep + 12.5 mM glucose for 25 min at 37C. Digestion was quenched using 20 mg/ml ovomucoid (trypsin inhibitor), 20 mg/ml BSA in DMEM:F12  + 1% pen/strep + 12.5 mM glucose. Ganglia were gently triturated with fire-polished glass pipettes. Neurons were then passed through a 70-micron filter to remove cell doublets and debris. Neurons were pelleted and washed 4x in 20 mg/ml ovomucoid (trypsin inhibitor) , 20 mg/ml BSA in DMEM:F12 + 1% pen/strep + 12.5 mM glucose followed by 2x washes with DMEM:F12 + 1% pen/strep + 12.5 mM glucose all at 4C. After washing, cells were resuspended in 45 microliters of DMEM:F12 + 1% pen/strep + 12.5 mM glucose.
library preparation were performed according to manufacturer's instructions (10x genomics chromium single cell kit, v3)

value: Dorsal root ganglia

value: sensory neuron

value: wild-type (C57/Bl6)


title: Sample 5, replicate 1, scRNAseq

description: 10x Genomics


title: Control, replicate 2, CUT&Tag_seq


title: FCD2b_14


title: Sample 4, replicate 1, scRNAseq

description: 10x Genomics


title: cumulus cells, Bl+ A13

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

description: cumulus cells associated to oocytes that developed to blastocysts

data_processing:
Paired-end read fastq files were quality checked with FastQC (Andrews, 2010) and preprocessed with fastp (Chen et al., 2018). Resulting files were pseudoaligned and quantified using kallisto (Bray et al., 2016) against the reference transcriptome of Bos taurus UCD1.2 (Ensembl release 104).
Assembly: Bos taurus UCD1.2 (Ensembl 104)
Supplementary files format and content: Tab-delimited text file with TPM normalized values for each Sample

organism: Bos taurus

source_name: cumulus cells

extract_protocol:
Total RNA was extracted using MagMAX mirVana Total Isolation Kit (Applied Biosystems) following the manufacturer's instruction with minor modifications. Briefly 200 µl of Lysis Binding Mix were added to the sample, followed by gentle pipetting and 5 min incubation at room temperature. Then 20 µl of Binding Beads Mix were added and shaken gently for 5 min. Beads‐mRNA complexes were washed once in each Wash Solution 1 and 2. Following the washing step, samples were treated with 50 µl of Turbo DNAse treatment, 50 µl of Rebinding Buffer and 100 µl of Isopropanol were added to the sample and mixed gently. Finally, following a double wash in Wash Solution 2, total RNA was eluted in 20 µl of Elution Buffer and stored at -80°C until analysis.
RNA‐seq libraries were prepared with KAPA Stranded mRNA‐Seq Illumina Platforms Kit (Roche) following the manufacturer's recommendations. Briefly, 50–100 ng of total RNA was used for the poly‐A fraction enrichment with oligo‐dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt‐end double stranded cDNA was 3′ adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on a HiSeq. 4000 system (Illumina) with a read length of 2 × 76 bp + 8 bp + 8 bp using the HiSeq. 4000 SBS kit (Illumina) obtaining >30 M reads/sample.

value: cumulus cells

tag: group

value: Bl+


title: Sample 3, replicate 1, scRNAseq

description: 10x Genomics

tag: tissue


title: cumulus cells, Bl+ A12


title: TLE-HS_17


title: Sample 2, replicate 1, scRNAseq

description: 10x Genomics


title: Sample 1, replicate 1, scRNAseq

description: 10x Genomics


title: cumulus cells, Bl+ A11


title: 1363.1_D169_4

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description:
21047R-30-39
30 million PE reads

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38)
We used FeatureCounts to assemble transcripts and generate raw count matrices. Following generation of raw count data, we used DESeq2 to normalize matrices and to determine differential gene expression statistics.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw expression values for each sample.

source_name: organoid

growth_protocol: hiPSCs were dissociated into single cells using Accutase (Innovate Cell Technologies, AT-104) and seeded into AggreWell plates (STEMCELL Technologies, 34815) at the density of 3 X 106 cells/well in Essential 8 medium (Life Technologies, A1517001) supplemented with 10 μ M Rock inhibitor Y-27632 (10 μ M, Selleckchem, S1049). Spheres formed the next day were collected and transferred to ultra-low-attachment 10 cm dishes (Corning, 3262). They were maintained in Essential 6 medium (Life Technologies, A1516401) supplemented with dual SMAD inhibitors SB-431542 (10 μ M, Tocris, 1614), dorsomorphin (2.5 μ M, Sigma-Aldrich, P5499) and Wnt pathway inhibitor XAV-939 (2.5 μ M, Tocris, 3748) for the first 6 days, with every day medium change. From Day 7, hCOs were cultured in Neurobasal A (Life Technologies, 10888) supplemented with B27 (Life Technologies, 12587), 20 ng ml–1 epidermal growth factor (R&D Systems, 236-EG) and 20 ng ml–1 basic fibroblast growth factor (R&D Systems, 233-FB), with every day medium change for another 8 days, and every other day medium change till Day 25. At this time point, hCOs were switched to neural basal medium supplemented with B27, 20 ng ml–1 brain-derived neurotrophic factor (BDNF; Peprotech, 450-02) and 20 ng ml–1 NT3 (Peprotech, 450-03) for another 20 days, with every other day medium change. From Day 45 onward, cells were maintained in Neurobasal A medium with B27, with medium change every 3-4 days.

extract_protocol:
RNA was harvested using RNAeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the NEB Next Ultra II kit using poly-A selection following manufacturer's protocols.

value: organoid

tag: cell line


title: TLE-HS_16


title: TSC_15

value: Male

value: TSC


title: 1363.1_D169_3

description:
21047R-30-38
30 million PE reads


title: 1363.1_D169_1

description:
21047R-30-36
30 million PE reads


title: cumulus cells, Bl+ A14


title: C49_D167_3

description:
21047R-30-31
30 million PE reads


title: C49_D167_2

description:
21047R-30-30
30 million PE reads


title: ControlHippocampus_5

value: Hippocampus


title: cumulus cells, Bl- A8

description: cumulus cells associated to oocytes that cleaved but didn’t develop to blastocysts

value: Bl-


title: C49_D167_1

description:
21047R-30-28
30 million PE reads


title: FK866, replicate 2, CUT&Tag_seq

value: colon

tag: treatment


title: FCD2b_13


title: cumulus cells, Bl- A7


title: C49_D95_3

description:
21047R-30-27
30 million PE reads


title: C49_D95_1

description:
21047R-30-26
30 million PE reads


title: C49_D95_2

description:
21047R-30-25
30 million PE reads


title: C1_D96_2

description:
21047R-30-11
30 million PE reads


title: TLE-HS_15

value: Temporal

value: TLE-HS


title: cumulus cells, Bl- A6


title: ControlHippocampus_4

value: ControlHippocampus


title: cumulus cells, Bl- A5


title: 8858.3_D169_2

description:
21047R-30-06
30 million PE reads

value: Control


title: 8858.3_D169_1

description:
21047R-30-05
30 million PE reads


title: 1363.1_D169_2

description:
21047R-30-37
30 million PE reads


title: cumulus cells, Cl- A4

description: cumulus cells associated to oocytes that did not cleave

value: Cl-


title: cumulus cells, Bl- A9


title: cumulus cells, Bl+ A10


title: cumulus cells, Cl- A3


title: TSC_14

value: Frontal


title: 8858.3_D95_2

description:
21047R-30-02
30 million PE reads


title: ControlCortex_11

value: ControlCortex


title: 8858.3_D95_3

description:
21047R-30-03
30 million PE reads


title: 8858.3_D95_4

description:
21047R-30-04
30 million PE reads


title: 8858.3_D95_1

description:
21047R-30-01
30 million PE reads


title: FCD2b_12

value: Female


title: FCD2a_10

value: Parietal


title: Liver organoids treated with Control mAb, Biol. Replicate 2

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

data_processing:
NGS reads were mapped to the Genome Reference Consortium GRCh38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR) utilising the “basic” Ensembl transcript annotation from version e100.
Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor GenomicAlignments package via the summarizeOverlaps function in Union mode.
Reads were normalized and differentially expressed genes were analyzed using DESeq2.
Supplementary files format and content: tsv file includes with raw gene counts for every gene and every sample
Supplementary files format and content: tsv file includes DESeq2 differential expression analysis mAB-vs-CTRL

source_name: Liver

growth_protocol: Liver organoids were cultured in 25 µl domes on 48 well plates and maintained in Organoid initiation medium (as described in Broutier L. et al. Nat. Protoc. 2016) supplemented with 10 µg/ml CLDN1 mAb or Control mAb at 37°C for 4 days.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen). 220 ng - 1.2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Liver organoids were treated with 10 µg/ml CLDN1 mAb or Control mAb for 4 days

value: Liver

value: Organoids

value: bile duct cells

value: wildtype

value: Control mAb


title: cumulus cells, Cl- A1

value: cumulus cells


title: cumulus cells, Cl- A2


title: Liver organoids treated with Control mAb, Biol. Replicate 3


title: Liver organoids treated with Control mAb, Biol. Replicate 1


title: 8858.3_D169_3

description:
21047R-30-07
30 million PE reads

value: organoid


title: Liver organoids treated with CLDN1 mAb, Biol. Replicate 2

value: CLDN1 mAb


title: Liver organoids treated with CLDN1 mAb, Biol. Replicate 3


title: FCD2a_9


title: TLE-HS_14

value: Temporal

value: Male


title: Liver organoids treated with CLDN1 mAb, Biol. Replicate 1


title: Hippocampus, Kat6a-cKO rep1

city: Baltimore

first: Yongqing

last: Liu

state: MARYLAND

address: 725 N Wolfe Street, WBSB 216

institute: Johns Hopkins University

data_processing:
Reads were aligned to the mm10 reference genome using the kb-python program (version 0.25.0). The data was then imported into R and low quality nuclei and “empty droplets” were filtered out using the barcodeRanks from the DropletUtils package. The data was analyzed using the Seurat R package (version 4.0.1) as described previously. Briefly, data normalization was performed using SCTransform function. The uwot package (https://github.com/jlmelville/uwot) was used for UMAP dimensional reduction. Seurat FindMarkers function was used for the analysis of differential gene expression and plotted using ggplot2 and the tidyverse collection of R packages in RStudio.
Assembly: mm10
Supplementary files format and content: txt file with barcodes or genes for all samples
Supplementary files format and content: mtx file with matrix for all samples
Supplementary files format and content: Excel file with differential expressed genes between two groups

molecule: nuclear RNA

extract_protocol:
Mouse hippocampal tissues were rapidly dissected in ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH=7.8). The tissue was homogenized using a loose-fitting pestle in 1.5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1×EDTA-free protease inhibitor (Roche), and 60 U/mL RNasin Plus RNase Inhibitor (Promega, N2611). A 6% IGEPAL CA-630 solution was added to bring the homogenate to 0.3% IGEPAL CA-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle. The sample was filtered through a 50 μm filter, underlayed with solutions of 30% and 40% iodixanol (Sigma, D1556) in homogenization buffer, and centrifuged at 10,000 g for 20 min in a swinging bucket centrifuge at 4 °C. Nuclei were collected at the 30-40% interface, diluted with two volumes of homogenization buffer and concentrated by centrifugation for 10 min at 500 g at 4 °C. These nuclei can be used for snRNA sequencing.
10x Genomics Chromium single cell kit
snRNA-seq

value: Hippocampus


title: Hippocampus, Control rep2


title: FCD2a_8