title: KO_iEsrrb_48_19

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

institute: CNR

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

growth_protocol: Mouse Embryonic Stem cells were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol) with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

treatment_protocol: For conditional Esrrb KO, cells were maintained with 2iL and DOX to stably express Esrrb and subsequently differentiated for 48 hours in the absence of 2iL and DOX, in order to generate a Esrrb conditional KO specifically at the time of activation of the formative program.

value: Mouse Embryonic stem cells

value: conditional KO

value: 48 hours differentiation

tag: time


title: Sri-6-1_S20

status: Public on Jan 25 2023

type: SRA

city: Oxford

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine, Oxford University

description:
Patient edited material
PCR and sequencing of base editing site

library_source: genomic

data_processing:
CIRCLE-seq data were analysed using the standard pipeling (https://github.com/tsailabSJ/circleseq)
Targetted capture NGS data were analysed with bowtie2 and samtools mpileup followed by custom scripts
Base editing data were analysed with CRISPRESSO
Assembly: Hg19
Supplementary files format and content: Processed data files are included in the manuscript

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood cells

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x105 cells were resuspended on day 0 in Phase I media at 2x105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x105 cells ml-1. Cells were counted on day 9 and diluted to 2x105 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

extract_protocol:
DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermofisher) following the manufacturer's protocol with no modifications
For sequencing of base edited sites, modified 2-PCR version of the NEBnext Ultra (NEB) library preparation protocol was followed. In the first PCR primer pairs with NEB adaptor sequences 5’ to the HBB exon 1-specific primer sequence were used for amplification using the Herculase II PCR kit (Agilent) in a 50μl reaction, ensuring the products had the adaptor sequences added by the end of the PCR. 5μl of this was used directly without clean-up for the indexing PCR. This added either single or dual end indices taken from a NEBNext Multiplex Oligos for Illumina kit (NEB).

tag: tissue

value: Blood cells

tag: cell type

value: Differentiated erythroid cells

tag: genotype

value: HbE/beta thalassaemia

tag: treatment

value: Control


title: Sham1_input

city: Hangzhou

first: Hao

last: Liu

address: 234 Gucui Road, Xihu District, Hangzhou City

country: China

institute: Tongde Hospital of Zhejiang Province

library_source: transcriptomic

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak2 (https://bioconductor.org/packages/exomePeak2), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using Annovar (https://bioconductor.org/packages/Annovar).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: text files include FPKM values and annotation for each Sample
Supplementary files format and content: text files include peak  information for each group

molecule: total RNA

organism: Mus musculus

source_name: brain tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: brain tissue

value: sham-operation


title: Acupuncture2_IP

value: acupuncture


title: ICH1_IP

value: autologous blood


title: MDS1079

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: read_counts

source_name: human BM Mononuclear cells

growth_protocol: not applicable

extract_protocol:
RNA was extracted from cells using the RNeasy Kit (Qiagen) following the instructions of the manufacturer. The purified RNA was used to prepare the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 mg) using oligo(dT)-coupled magnetic beads and fragmented into small pieces at elevated temperatures. First-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of doublestrand cDNA and adenylation on the 39 ends of DNA fragments, the adaptors were ligated and purified with the AMPure XP system (Beckman Coulter, Beverly, MA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system.
The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 system and a real-time polymerase chain reaction system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads generated by Genomics, BioSci & Tech Co. (New Taipei City, Taiwan).

treatment_protocol: not applicable

tag: disease state

value: MDS

tag: age

tag: Sex

value: F

value: BM

value: Mononuclear cells


title: MDS1059

value: M


title: Acupuncture1_input


title: Duplo_29ºC_1

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

country: Spain

institute: CBGP-INIA-UPM

description:
275_29_1
DUP29r1

data_processing:
Reads were mapped to rapeseed genome (AST_PRJEB5043_v1 (Chalhoub et al., 2014)) using HISAT2 (Kim et al., 2015).
Differential expression analysis of raw count data was performed using DESEQ2 (Love et al., 2014) in R.
Genome_build: AST_PRJEB5043_v1 (Chalhoub et al., 2014)
Supplementary_files_format_and_content: DESEQ2 output and raw counts

organism: Brassica napus

source_name: Duplo_29ºC_root tips

growth_protocol: Seeds were germinated in ¼ MS agar plates for 3 days and transferred to a pouch-and-wick system in nutrient solution (1/4MS) (Adapted from (Adu et al., 2014; Atkinson et al., 2015; Thomas et al., 2016)). Six seedlings per pouch were grown in a growth chamber set at constant temperature (21ºC/29ºC), 16h daylight and 40% RH.

extract_protocol:
Total RNA was extracted from 7 days’ root tips from pouch-and-wick grown seedlings using TRIzol reagent (Invitrogen) and total DNA free RNA was cleaned using RNeasy Plant Mini Kit purification columns (Qiagen).
Library preparation was performed using 1 μg of high-integrity total RNA (RIN>8) using the TruSeq Stranded mRNA library preparation kit.

treatment_protocol: optimal temperature (21ºC) vs warm temperature (29ºC)

value: Duplo

value: 7 days at 29ºC

value: root tips (1 cm)


title: E14_iEmpty_48_17

city: Pozzuoli

department: ISASI

country: Italy

extract_protocol:
Cells were harvested at the appropriate time point and RNA was purified by using "Total RNA extraction kit, Norgen".
NEGEDIA Digital mRNAseq - research grade.

tag: cell line

value: Mouse Embryonic stem cells

value: WT

value: 48 hours differentiation


title: N2 Ground Control Rep 3

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

country: USA

institute: University of Delaware

description: GC

data_processing:
Quality control was implemented on the raw sequence data with FASTQC software (version 0.11.2).
The raw reads were mapped to the reference genome (WBCel235), obtained from Ensembl along with the annotation file, by using TopHat.
The Tuxedo pipeline was employed to find differential gene expressions with default parameters.
Genome_build: WBCel235
Supplementary_files_format_and_content: format: cuffdiff; output: fold changes for the gene expressions among the conditions

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: After bleaching the adult worms, L1 worms were cultured in ground conditions in CeHR medium for three weeks. Then, the worms were exposed to clinostat-simulated microgravity for four days and the maintained impacts were observed at four, eight, and twelve days after placing the worms back to ground conditions All animals were grown at room temperature.

extract_protocol:
Total RNA from mixed stage C. elegans  were isolated with a modified TRIzol protocol and recovered by alcohol precipitation. Total RNA was further purified by PureLink ™ RNA Mini Kit (Life Technologies).
Two micrograms of total RNA were used for library preparations using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

tag: group

value: Ground Control

value: whole organism

tag: strain

tag: developmental stage

value: Mixed stage


title: ICH1_input

value: brain tissue


title: KO_iEsrrb_48_16

value: conditional KO


title: KO_iEsrrb_48_15


title: K-1_S11

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: Control


title: MDS1048

value: MDS

value: BM

value: Mononuclear cells


title: Duplo_29ºC_2

description:
275_29_2
DUP29r2

value: Duplo

value: 7 days at 29ºC


title: Sham3_IP

value: sham-operation


title: Sham2_IP


title: MDS1057

value: M


title: Sham1_IP


title: Duplo_21ºC_1

description:
275_21_1
DUP21r1

source_name: Duplo_21ºC_root tips

value: 7 days at 21ºC

value: root tips (1 cm)


title: small RNA-Seq TAC4

city: SHENZHEN

first: MINGYAO

last: GU

address: Xueyuan Avenue, Nanshan District

institute: Shenzhen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, unknown bases(N) are more than 10% and low-quality (Q-value≤20) sequence, removed reads without 3' ,5' adapters, and containing  3' and 5' adapters but no samll RNA fragment between them,and removed reads containing polyA in samll RNA fragment or shorter than 18 nt.
All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
All of the clean tags were then searched against miRBase database(Release 22) to identify known (Species studied) miRNAs (exist miRNAs)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with raw gene counts for every gene and every sample

source_name: cardiomyocytes

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction, RNA was harvested using TRIzol® reagent (Invitrogen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cardiomyocytes


title: KO_iEsrrb_48_20

value: Mouse Embryonic stem cells

value: 48 hours differentiation


title: E14_iEmpty_48_13

value: WT


title: MDS1021


title: KO_iEsrrb_48_12

value: conditional KO


title: Drakkar_29ºC_1

description:
238_29_1
DRK29r1

source_name: Drakkar_29ºC_root tips

value: Drakkar


title: E14_iEmpty_48_18


title: ICH2_IP

value: brain tissue

value: autologous blood


title: E14_iEmpty_48_14


title: Duplo_21ºC_2

description:
275_21_2
DUP21r2


title: E14_iEmpty_48_9


title: Drakkar_21ºC_3

description:
238_21_3
DRK21r3

source_name: Drakkar_21ºC_root tips


title: small RNA-Seq TAC2


title: small RNA-Seq Sham4


title: MDS1000

value: MDS


title: Duplo_21ºC_3

description:
275_21_3
DUP21r3


title: MDS1009

value: BM


title: KO_iEsrrb_48_11


title: MDS1016

value: Mononuclear cells


title: MDS1017


title: MDS1049

value: F


title: small RNA-Seq TAC1


title: E14_iEmpty_48_6


title: E14_iEmpty_48_10


title: E14_iEmpty_48_5


title: RNA-Seq TAC2

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, unknown bases(N) are more than 10% and low-quality (Q-value≤20) sequence
Trimmed sequence reads were mapped to  the reference genome using alignment tool Bowtie2 (version 2.2.8)
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample


title: KO_iEsrrb_48_4


title: PB-D0-1

city: Guangzhou

first: Jiaming

last: Gu

state: Guangdong

address: Kaiyuan Street

institute: Guangzhou Institutes of biomedicine and health, Chinese Academy of Sciences

description: shATG7-D7_mch-vs-SCR-D7_mch.diffgenes.TF.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Assembly: GRCh38/hg38
Supplementary files format and content: count

source_name: Peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood

value: Peripheral blood mobilized CD34+ cells

value: myeloid/granulocytes differentiation


title: SCR-D7_mch-2

value: Peripheral blood mobilized CD34+ cells derived myeloid/granulocytes

value: Scramble transduced


title: PB-D0-2


title: Drakkar_29ºC_2

description:
238_29_2
DRK29r2

value: 7 days at 29ºC

value: root tips (1 cm)


title: small RNA-Seq Sham3

value: cardiomyocytes


title: E14_iEmpty_48_2

value: Mouse Embryonic stem cells

value: WT

value: 48 hours differentiation


title: small RNA-Seq TAC3


title: Drakkar_29ºC_3

description:
238_29_3
DRK29r3

value: Drakkar


title: MDS1045


title: small RNA-Seq Sham1


title: E14_iEmpty_48_1


title: small RNA-Seq Sham2


title: Control_S8

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Sequencing data (fastq files) were uploaded to and analyzed on the Galaxy web platform (usegalaxy.eu) 38, as previously described 39-41. Quality control was performed with FastQC Galaxy Version 0.72 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ last access on 08/21/2021).
Reads were mapped to the human reference genome (Gencode, release 38, hg38) with RNA STAR Galaxy Version 2.7.8a 42 with default parameters using the Gencode annotation file (Gencode, release 38, https://www.gencodegenes.org/human/releases.html).
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 2.0.1 43 with default parameters using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (version 2022.02.0+443, R version 4.1.2). Gene symbols and gene types were determined based on ENSEMBL release 108 (Human genes, GRCh38.p12, download on 11/15/2022) 44.
T-distributed stochastic neighbor embedding (t-SNE) was applied to assess unsupervised clustering and to check for potential batch effects 45. Differential gene expression was analyzed using the R package DESeq2 Version 1.34.0 46 with default parameters (Benjamini-Hochberg adjusted p-values).
Assembly: human, Gencode, release 38, hg38
Supplementary files format and content: csv, normalized reads (DESeq2)

source_name: healthy conjunctiva

extract_protocol:
Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA).
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3’ RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.

value: healthy conjunctiva


title: KO_iEsrrb_48_8

value: conditional KO


title: SCR-D7_mch-1


title: shATG7-D7_mch-1

value: shATG7 transduced


title: Drakkar_21ºC_2

description:
238_21_2
DRK21r2

value: 7 days at 21ºC


title: KO_iEsrrb_48_3


title: RNA-Seq Sham2


title: Control_S3


title: RNA-Seq TAC1


title: RNA_ESC_Mll3KOMll4flox_rep2_D5XEN

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration - For ChIP-Seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); for ChIP-Seq of GATA6, MLL4 and T7 tag: Windows (50), Gaps (50), FDR (1e-10)
Paired-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Assembly: mm9
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM
Supplementary files format and content: tab-delimited text files include FPKM values for each gene

source_name: ES-derived ExEns

growth_protocol: Mouse ES cells were maintained on 0.1% gelatin and cultured in 2i+LIF medium (47.75% Advanced DMEM/F-12, 47.75%  Neurobasal, 0.5% N-2 supplement, 1% B-27 supplement minus Vitamin A, 1% GlutaMax, 1% Penicillin-Streptomycin, 1% EmbryoMax 2-mercaptoethanol supplemented with 1 µM MEK inhibitor PD0325901, 3 µM GSK3 inhibitor CHIR99021 HCl and 1,000 units/mL mouse LIF protein).

extract_protocol:
1 μg total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol:
For embryoid body (EB) differentiation, ESCs were suspended into 2,000 cells / 20 µL drop on the lid of tissue culture dishes. EBs were harvested 2 days later and then were transferred into ultra-low-attached dishes. EBs were cultured in suspension in medium without LIF but supplemented with 2% qualified ESC FBS to the indicated time points. Meidum was changed every other day.
For neural differentiation, aggregates were generated following EB differentiation protocol from day 0 to day 8 except that after day 4, 5 µM retinoic acid was added. At day 8, aggregates were dissociated and neural progentor cells (NPCs) were plated on PDL/laminin-coated dishes in N-2 medium. The N-2 medium was changed after 2 hours and again after 1 day. After 2 days, the medium was replaced by the B-27 medium to induce neurogenesis. Medium was changed every other day.
For extraembryonic endoderm (ExEn) differentiation, ESCs were seeded at a density of 2 x 104 / cm2 into gelatinized plates, and cultured for 5 days in ExEn medium (Advanced RPMI 1640 supplemented with 15% FBS, 1% GlutaMax, 1% EmbryoMax 2-mercaptoethanol, 0.1 μM retinoic acid and 10 ng/mL Activin A).
For trophectoderm (TE) differentiation, ESCs were infected with Doxycycline-inducible lentiviral pCW57.1 vector expressing T7-tagged CDX2 or EOMES. Cells were then seeded at a density of 1 x 104 / cm2 into gelatinized plates, and cultured for 6 days in TS medium (Advanced RPMI 1640 supplemented with 20% FBS, 1% GlutaMax and 1% EmbryoMax 2-mercaptoethanol) containing 70% MEF-conditioned TS medium and supplemented with 25 ng/mL FGF-4, 1 μg/mL Heparin and 1 μg/mL Doxycycline.

tag: stage of_differentiation

value: ES-derived ExEns

value: ExEn differentiation


title: Control_S5


title: Drakkar_21ºC_1

description:
238_21_1
DRK21r1


title: V5-ChIP-Seq,  HPC7 STAT3Y640F, replicate 3

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Alignment to genome version GRCm38 using STAR (RNA-seq) or BWA (ChIP-seq)
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
peak calling was done with MACS2
Assembly: GRCm38/mm10
Supplementary files format and content: count file (tab delimited)
Supplementary files format and content: bigWig file (CPM normalized)

source_name: Haematopoetic stem/Progenitor cells

growth_protocol: HPC7 and HPCLSK cells were cultured in IMDM culture media supplemented with  2% SCF (incl. 10% FCS, 50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin).HPCLSK were cultured on agarose coated plates.

extract_protocol: NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: no treatmend

value: Haematopoetic stem/Progenitor cells


title: V5-ChIP-Seq, HPC7 STAT3Y640F, replicate 1


title: Control_S2


title: KO_iEsrrb_48_7


title: input_DNA, HPC7, dsRed (empty vector)

value: dsRed (empty vector)


title: shATG7-D7_mch-2

value: Peripheral blood

value: Peripheral blood mobilized CD34+ cells derived myeloid/granulocytes

value: myeloid/granulocytes differentiation


title: RNA_ESC_Mll3KOMll4KI27_Cdx2C3xT7_D6TE

source_name: ES-derived TEs

value: ES-derived TEs

value: TE differentiation


title: RNA_ESC_Mll3KOMll4KI48_Cdx2C3xT7_D6TE


title: RNA_ESC_Mll3KOMll4flox_rep2_Cdx2C3xT7_D6TE


title: RNA_Mll34DKO65_neural_D8_STAR

source_name: ES-derived neural progenitor cells

value: ES-derived neural progenitor cells

value: Neural differentiation


title: Lymphoma_P8

source_name: conjunctival lymphoma

value: conjunctival lymphoma


title: Control_S7


title: RNA_ESC_Mll3KOMll4KI27_D5XEN


title: RNA-Seq Sham1

value: cardiomyocytes


title: V5-ChIP-Seq, HPC7, STAT3, replicate 3


title: RNA_ESC_Mll3KOMll4KI48_D5XEN


title: Control_S6

value: healthy conjunctiva


title: Lymphoma_P6_OS


title: input_DNA,HPC7, STAT3


title: V5-ChIP-Seq ,HPC7, STAT3, replicate 1


title: V5-ChIP-Seq, HPC7, dsRed (empty vector), replicate 1


title: RNA_ESC_Mll3KOMll4flox_rep1_D5XEN


title: V5-ChIP-Seq,  HPC7 STAT3Y640F, replicate 2


title: Control_S4


title: Control_S1


title: V5-ChIP-Seq, HPC7, STAT3, replicate 2


title: RNA_ESC_Mll3KOMll4flox_rep1_Cdx2C3xT7_D6TE


title: RNA_EmbryoE9_5_1114-9_KI

source_name: whole embryos

value: whole embryos


title: V5-ChIP-Seq, HPC7, dsRed (empty vector), replicate 2


title: Lymphoma_P7


title: RNA_EmbryoE9_5_1508-4_KI


title: input_DNA, HPC7, STAT3Y640F


title: RNA_EmbryoE9_5_1114-5_Ctr


title: RNA-Seq, HPCLSK, STAT3Y640F, replicate 2

extract_protocol:
QIAGEN RNeasy extraction kit
TruSeq Stranded mRNA LT sample preparation kit


title: RNA_EmbryoE9_5_1508-9_Ctr


title: Lymphoma_P6_OD


title: RNA_EmbryoE9_5_1114-12_KI


title: RNA-Seq, HPCLSK, STAT3, replicate 3


title: Lymphoma_P2


title: V5-ChIP-Seq, HPC7, dsRed (empty vector), replicate 3


title: Lymphoma_P9


title: Lymphoma_P1


title: RNA-Seq, HPCLSK, STAT3Y640F, replicate 3


title: RNA-Seq, HPCLSK, STAT3Y640F, replicate 1


title: Lymphoma_P3


title: RNA_EmbryoE8_5_1787-3_Ctr


title: RNA_EmbryoE8_5_1787-2_KI


title: Lymphoma_P5


title: RNA_EmbryoE8_5_1378-6_Ctr


title: RNA_EmbryoE8_5_1791-8_KI


title: RNA-Seq, HPCLSK, STAT3, replicate 2


title: RNA_EmbryoE8_5_1791-10_Ctr


title: RNA-Seq, HPCLSK, STAT3, replicate 1


title: RNA-Seq, HPCLSK, dsRed (empty vector), replicate 3


title: Lymphoma_P4


title: Liver_Healthy_Untreated_pool_9

type: RNA

city: Guadalajara

first: Carmen

middle: Magdalena

last: Gurrola-Díaz

state: Jalisco

address: Sierra Mojada 950

department: Departamento de Biología Molecular y Genómica

country: Mexico

institute: Universidad de Guadalajara

description:
Pool9-Healthy-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

hyb_protocol: Samples were hybridized with GeneChip Rat Transcriptome Array 1.0 (Affymetrix) and scanned at the Microarray Unit of the National Institute of Genomic Medicine (INMEGEN), Mexico Facility.

scan_protocol: Array scanning was performed in Affymetrix GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix).

data_processing: The gene expression files were processed and analyzed with the Applied Biosystem-sTM Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA). Gene expression data were RMA normalized, and differential expression determined with the following parameters: RMA+DABG (Rattus norvegicus) and expression analysis settings: Fold Change < -2 or > 2, p-value < 0.05, and ANOVA method: ebayes.

label: biotin

organism: Rattus norvegicus

source_name: Healthy-Untreated-Rat Liver Pool 9

label_protocol: RNA samples were processed using the protocol of GeneChip™ WT PLUS Reagent Kit. Single-stranded cDNA was generated from the amplified cRNA with the Kit RTA 1.0 AND WT PLUS (Affymetrix, ThermoFisher 902633) and then fragmented and labeled with the GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix, ThermoFisher 900720).

growth_protocol: Three biological replicates of liver total RNA pools were prepared for each experimental group: healthy untreated rat group, type 2 diabetic untreated group, and type 2 diabetic rats treated with 28 mg/kg BW Cγ + 20 mg/kg BW lupanine. Each pool consisted of the mixture of RNA isolated from three different animals.

extract_protocol: Total RNA was isolated from homogenized (30 mg of fresh liver tissue in 600 µl Buffer RLT in Healthy liver, or Trizol in T2D liver) with the RNeasy® Mini Kit (Qiagen, Germany), according to the manufacturer’s instructions.

treatment_protocol: Diabetic rats treated with the combination of 28 mg/kg BW Cγ + 20 mg/kg BW lupanine (both isolated from Lupinus albus), dissolved in vehicle (0,9% w/v NaCl), animals were daily administered by oral gavage during seven consecutive days at the same hour.

value: Healthy

value: Male

value: Liver


title: Mll3KOMll4KI_Neurod1-3xT7-1_D1_H3K4me1

source_name: Embryonic stem cells (ESCs)

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 30 million fixed cells were swelled in cold buffer containing 5mM PIPES (pH 8.0), 85mM KCl, 1% NP-40 and protease inhibitors for 20 min, and centrifuged at 2,000 g for 5 min at 4°C. Nuclei were resuspended with 3 mL TE buffer (pH 8.0), and subjected to sonication. Sheared chromatin was clarified by centrifugation at 4,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 150mM NaCl, 0.1% SDS, 1% Triton-X100 and protease inhibitors. 2% of the total material was set aside as input and 20 ng of spike-in chromatin (Active Motif, #53083) was added to each ChIP material. For each ChIP material, 2 - 8 µg of target antibodies and 1.5 μg of spike-in antibody (anti-H2Av, Active Motif, #61686) pre-bound with protein A Dynabeads (ThermoFisher) were added and incubated on a rotator at 4°C overnight. Beads were then collected on a magnetic rack and washed twice with 1 mL cold RIPA buffer, once with 1 mL cold RIPA buffer containing 500mM NaCl, twice with 1 mL cold LiCl buffer and once with 1 mL TE buffer. Finally, beads were eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 100 μg Proteinase K at 65°C overnight. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 50 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

value: Embryonic stem cells (ESCs)

value: Doxycycline

tag: chip antibody

value: H3K4me1 (EpiCypher, 13-0040)


title: RNA-Seq, HPCLSK, dsRed (empty vector), replicate 2

value: Haematopoetic stem/Progenitor cells

value: dsRed (empty vector)


title: Liver_Healthy_Untreated_pool_7

description:
Pool7-Healthy-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: Healthy-Untreated-Rat Liver Pool 7


title: Liver_Healthy_Untreated_pool_8

description:
Pool8-Healthy-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: Healthy-Untreated-Rat Liver Pool 8


title: RNA_EmbryoE9_5_1114-3_Ctr


title: Liver_T2D_Untreated_pool_5

description:
Pool5-T2D-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Untreated-Rat Liver Pool 5

value: Type 2 diabetes


title: RNA-Seq, HPC7, STAT3Y640F, replicate 3


title: RNA-Seq, HPC7, STAT3Y640F, replicate 2


title: RNA_EmbryoE8_5_1378-1_KI


title: Liver_T2D_Untreated_pool_6

description:
Pool6-T2D-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Untreated-Rat Liver Pool 6


title: RNA-Seq, HPC7, STAT3Y640F, replicate 1


title: S4plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

data_processing:
Base editing data were analysed with CRISPRESSO
RNA-seq data was aligned using STAR (2.7.3a) to hg19. Aberrant splicing of Poly-A negative RNA was detected using PySam (https://github.com/pysam-developers/pysam) find_introns method, considering position 5,248,159 of chromosome 11 (hg19) as the canonical splice site for exon 1 of the HBB gene. An RNA variant calling pipeline was established using GATK best practices. In keeping with the Broad Institutes recommendation for this tool, these data were realigned to hg38 using STAR two-pass alignment, followed by PCR duplicate removal and base score recalibration. GATK Haplotype Caller (4.0.11.0) was then used to call variants.
Assembly: Hg19
Supplementary files format and content: Base_Editing_Frequencies.txt
Supplementary files format and content: RNAseq_splicing.txt

source_name: RNA-seq (Poly A plus)

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x10^5 cells were resuspended on day 0 in Phase I media at 2x10^5 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x10^5 cells ml-1. Cells were counted on day 9 and diluted to 2x10^5 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: HbE gRNA V106W


title: RNA-Seq, HPCLSK, dsRed (empty vector), replicate 1


title: Mll3KOMll4flox_Neurod1-3xT7_D1_MLL4

value: MLL4 (homemade, #3)


title: Liver_T2D_Cy_lupanine_pool_3

description:
Pool3-T2D-Treated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Treated-Rat Liver Pool 3

value: Gamma conglutin + lupanine


title: Mll3KOMll4flox_Neurod1-3xT7_D1_T7

value: T7 tag (Cell Signaling Technology, 13246)


title: Liver_T2D_Cy_lupanine_pool_2

description:
Pool2-T2D-Treated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Treated-Rat Liver Pool 2


title: RNA-Seq, HPC7,dsRed (empty vector), replicate 2


title: S

city: Zhengzhou

first: Pingping

last: Zhu

address: 100 Kexue Road

institute: Zhengzhou University

description:
processed chrM-circRNA_allExp
processed circRNA_expression

data_processing:
library strategy: circRNA-Seq
TMM (trimmed mean of M-values) was used to normalize the gene expression
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Assembly: hg19
Supplementary files format and content: TMM values for each Sample
Supplementary files format and content: gene reads count for every gene and every sample

growth_protocol: Huh7 was cultured in sphere formation medium for TIC enrichment.

extract_protocol:
RNA  was extracted with Takara RNAiso Plus (Takara, Dalian, China)
The Total RNA was incubated for 30 min at 37 °C with 10 units RNase R (Geneseed) .Then，RNA-seq library was prepared with approximately 2μg of total RNA usingRNA-seq (H/M/R) Library Prep Kit for Illumina® (Geneseed). Briefly, ribosomal RNA was removed from the total RNA. and purified with VAHTS RNA Clean Beads. Next, the ribominus RNase R (+) RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.

treatment_protocol: TICs and non-TICs were used for mitchondria isolation and RNA extraction.

value: Liver cancer

tag: cell subtype

value: Stem cells

value: Mitchondria isolation and RNA extraction

tag: molecule subtype

value: mitochondrial RNA


title: Mll3KOMll4KI_Neurod1-3xT7_D1_MLL4

value: Embryonic stem cells (ESCs)


title: Mll3KOMll4flox_Neurod1-3xT7_D1_input

value: Doxycycline


title: S4plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: S2plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4KI_Neurod1-3xT7_D1_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: S4minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

source_name: RNA-seq (Poly A minus)


title: Mll3KOMll4KI_Neurod1-3xT7_D1_T7


title: aCD8CD4_rep3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw_counts.txt

source_name: P14 CD8+ TRM cells

extract_protocol:
To perform RNA-seq, we FACS-sorted P14 brain TRM cells from GP, αCD8α GFAP:GP and αCD4αCD8α GFAP:GP mice 7 days following tamoxifen administration. Each biological replicate (n = 3) represents 10E4 P14 TRM cells sorted in buffer RLT with 1% ß-mercaptoethanol and processed with RNAeasy Plus Micro Kit (Qiagen) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 7 days post tamoxifen

value: brain

value: Tissue-resident memory CD8+ T (Trm) cells

tag: facs-sorted p14 brain trm cells from

value: αCD4αCD8α GFAP:GP mice

tag: mouse recipient


title: Mll3KOMll4flox_Neurod1-3xT7-1_D1_H3K4me1

value: H3K4me1 (EpiCypher, 13-0040)


title: Liver_T2D_Untreated_pool_4

description:
Pool4-T2D-Untreated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Untreated-Rat Liver Pool 4

value: Type 2 diabetes

value: Male

tag: tissue

value: Liver


title: S2minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Blood cells

tag: cell type

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: HbE gRNA V106W


title: aCD8CD4_rep2

tag: time


title: RNA-Seq, HPC7, STAT3, replicate 2

source_name: Haematopoetic stem/Progenitor cells

value: Haematopoetic stem/Progenitor cells

tag: genotype


title: aCD8CD4_rep1


title: Liver_T2D_Cy_lupanine_pool_1

description:
Pool1-T2D-Treated-Rat
Gene Level - RMA expression value derived from Transcriptome Analysis Console 4.0.2 (TAC, ThermoFisher, CA, USA); Expression (Gene) analysis.

source_name: T2D-Treated-Rat Liver Pool 1

tag: disease state

tag: treatment

value: Gamma conglutin + lupanine


title: Mll3KOMll4KI_Neurod1-3xT7_D1_input

value: Embryonic stem cells (ESCs)


title: S2plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4flox_Neurod1-3xT7_D1_H3K27ac

value: Doxycycline


title: S1plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Control


title: Mll3KOMll4flox_Gata6-3xT7_D1_MLL4

value: MLL4 (homemade, #3)


title: RNA-Seq, HPC7, STAT3, replicate 3


title: Mll3KOMll4KI_Gata6-3xT7_D1_input


title: aCD8_rep1

tag: age

value: 7 days post tamoxifen

value: brain

value: αCD8α GFAP:GP mice


title: iso_rep3

value: Tissue-resident memory CD8+ T (Trm) cells

value: GP mice

value: GP


title: S4minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: HeLa, EGF, C7orf26, biol rep1

city: Philadelphia

first: Sarah

middle: R

last: Offley

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

description: C7orf26 ChIP-seq in serum-starved HeLa cells treated with 0.1ug/mL epidermal growth factor (EGF)

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM high glucose media, supplemented with 10%(v/v) super calf serum (GEMcell) and 2 mM of L-glutamine. HL-60 cells were maintained in RPMI high glucose media, supplemented with 10% (v/v) super calf serum and 2mM L-glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: WT HeLa cells were starved in DMEM media containing 0.3% super calf serum for 72 hours and then treated with 0.1ug/mL EGF for 15 minutes. HL-60 cells were differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours where noted. Where noted, HeLa cells were either infected with lentivirus containing shRNAs for Luciferase (control) or C7orf26, starved overnight in 0.3% serum containing-DMEM media and then treated with 0.1ug/mL EGF.

tag: cell line

value: HeLa

value: cervical epithelial

value: wt

value: Serum starved in DMEM media containing 0.3% serum for 72 hours and then treated with epidermal growth factor (EGF) for 15 minutes

value: C7orf26 (Sigma, HPA042899)


title: iso_rep2


title: RNA-Seq, HPC7, STAT3, replicate 1

value: Haematopoetic stem/Progenitor cells


title: S1plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

extract_protocol:
DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermofisher) following the manufacturer's protocol with no modifications
For sequencing of base edited sites, modified 2-PCR version of the NEBnext Ultra (NEB) library preparation protocol was followed. In the first PCR primer pairs with NEB adaptor sequences 5’ to the HBB exon 1-specific primer sequence were used for amplification using the Herculase II PCR kit (Agilent) in a 50μl reaction, ensuring the products had the adaptor sequences added by the end of the PCR. 5μl of this was used directly without clean-up for the indexing PCR. This added either single or dual end indices taken from a NEBNext Multiplex Oligos for Illumina kit (NEB).

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia


title: NS

value: Liver cancer

value: Non-stem cells

value: Mitchondria isolation and RNA extraction

value: mitochondrial RNA


title: S2minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: HbE gRNA V106W


title: RNA-Seq, HPC7, dsRed (empty vector), replicate 3

value: dsRed (empty vector)


title: iso_rep1

value: 7 days post tamoxifen

value: brain

value: Tissue-resident memory CD8+ T (Trm) cells

value: GP mice


title: Mll3KOMll4flox_Gata6-3xT7_D1_T7

value: Embryonic stem cells (ESCs)

value: Doxycycline

value: T7 tag (Cell Signaling Technology, 13246)


title: RNA-Seq, HPC7, dsRed (empty vector), replicate 1

value: Haematopoetic stem/Progenitor cells


title: HL-60, PMA, C7orf26, biol rep1

description: C7orf26 ChIP-seq in PMA-treated HL-60 cells

value: promyeloblast

value: wt

value: Differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours

value: C7orf26 (Sigma, HPA042899)


title: Mll3KOMll4KI_Gata6-3xT7_D1_H3K4me1

value: H3K4me1 (EpiCypher, 13-0040)


title: Mll3KOMll4KI_Gata6-3xT7_D1_T7


title: HeLa, shC7orf26, EGF, RNAPII, biol rep1

description: RNAPII ChIP-seq in C7orf26-KD, serum-starved HeLa cells treated with 0.1ug/mL EGF

value: HeLa

value: cervical epithelial

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: K9plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: Control


title: aCD8_rep2

value: 7 days post tamoxifen

value: brain

value: Tissue-resident memory CD8+ T (Trm) cells

value: αCD8α GFAP:GP mice


title: K9plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: aCD8_rep3


title: K9minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4KI27_neuralD8_H3K27ac

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER with following configuration - For ChIP-Seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); for ChIP-Seq of MLL4: Windows (50), Gaps (50), FDR (1e-10)
Single-end reads of RNA-seq are aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

source_name: Neural progenitor cells (NPCs)

value: ES-derived neural progenitor cells

tag: stage of differentiation

tag: antibodies

value: H3K27ac (Abcam, ab4729)


title: HeLa, shLUC, Ctrl, RNAPII, biol rep1

description: RNAPII ChIP-seq in shLuciferase(control), serum-starved HeLa cells

value: wt

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight


title: Mll3KOMll4flox_Gata6-3xT7_D1_H3K4me1

value: Embryonic stem cells (ESCs)

value: Doxycycline

value: H3K4me1 (EpiCypher, 13-0040)


title: HeLa, shLUC, EGF, RNAPII, biol rep1

description: RNAPII ChIP-seq in shLuciferase(Control), serum-starved HeLa cells treated with 0.1ug/mL EGF

value: HeLa

value: cervical epithelial

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: Mll3KOMll4KI_Gata6-3xT7_D1_H3K27ac


title: S1minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Blood cells

value: Differentiated erythroid cells


title: Mll3KOMll4KI_Gata6-3xT7_D1_MLL4

value: MLL4 (homemade, #3)


title: HeLa, Ctrl, C7orf26, biol rep1

description: C7orf26 ChIP-seq in serum-starved HeLa cells

value: Serum starved in DMEM media containing 0.3% serum for 72 hours

value: C7orf26 (Sigma, HPA042899)


title: Mll3KOMll4flox_Gata6-3xT7_D1_H3K27ac


title: Mll3KOMll4KI_D5ExEn_MLL4

source_name: ES-derived ExEns

value: ES-derived ExEns

value: ExEn differentiation


title: S1minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: HbE/beta thalassaemia

value: Control


title: HeLa, shC7orf26, Ctrl, RNAPII, biol rep1

description: RNAPII ChIP-seq in C7orf26-KD, serum-starved HeLa cells

value: wt

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: Mll3KOMll4flox_Gata6-3xT7_D1_input

value: Embryonic stem cells (ESCs)

value: Doxycycline


title: K9minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4KI27_neuralD8_H3K4me1

value: ES-derived neural progenitor cells

value: H3K4me1 (EpiCypher, 13-0040)


title: Mll3KOMll4flox_D5ExEn_MLL4


title: HeLa, shC7orf26, EGF, Biol rep 3

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq): BWA
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: HeLa cells were maintained in DMEM high glucose media, supplemented with 10%(v/v) super calf serum (GEMcell) and 2 mM of L-glutamine.

extract_protocol:
RNA was extracted using the Zymo RNA Miniprep kit, ribosome depleted with the NEBNext rRNA depletion kit (New England Biolabs) and then used to make sequencing libraries.
NEBNext Ultra Directional Strand specific RNA-Seq  Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: Where noted, HeLa cells were either infected with lentivirus containing shRNAs for Luciferase (control) or C7orf26, starved overnight in 0.3% serum containing-DMEM media and then treated with 0.1ug/mL EGF.

value: HeLa

value: cervical epithelial

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: K5plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Blood cells

value: Differentiated erythroid cells

value: HbE gRNA V106W


title: Mll3KOMll4KI_D5ExEn_input

value: ES-derived ExEns


title: Mll3KOMll4flox_neuralD8_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: HL-60, NT, C7orf26, biol rep1

description: C7orf26 ChIP-seq in untreated HL-60 cells

value: promyeloblast

value: No treatment

value: C7orf26 (Sigma, HPA042899)


title: HeLa, shLUC, EGF, Biol rep 3

value: WT (shLUC)

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: K5plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: HbE/beta thalassaemia


title: HeLa, shC7orf26, Control, Biol rep 3

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight


title: Mll3KOMll4flox_neuralD8_H3K4me1

value: ES-derived neural progenitor cells


title: K5minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4flox_D5ExEn_input

value: ExEn differentiation


title: Mll3KOMll4flox_neuralD8_MLL4

value: MLL4 (homemade, #3)


title: Mll3KOMll4KI_D5ExEn_H3K27ac


title: K5minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4KI27_neuralD8_MLL4


title: HeLa, shC7orf26, EGF, Biol rep 2

value: HeLa

value: cervical epithelial


title: Mll3KOMll4KI27_neuralD8_input


title: K4plus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Blood cells


title: K4plus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: Differentiated erythroid cells


title: HeLa, shLUC, EGF, Biol rep 2


title: Mll3KOMll4KI_D5ExEn_H3K4me1

value: H3K4me1 (EpiCypher, 13-0040)


title: Mll3KOMll4flox_neuralD8_input


title: Mll3KOMll4flox_D5ExEn_H3K27ac

value: ES-derived ExEns


title: Mll3KOMll4KI48_EBD10_RNA_3rd

source_name: Embryoid bodies (EBs)

treatment_protocol:
For embryoid body (EB) differentiation, ESCs were suspended into 2,000 cells / 20 µL drop on the lid of tissue culture dishes. EBs were harvested 2 days later and then were transferred into ultra-low-attached dishes. EBs were cultured in suspension in medium without LIF but supplemented with 2% qualified ESC FBS to the indicated time points. Meidum was changed every other day.
For neural differentiation, aggregates were generated following EB differentiation protocol from day 0 to day 8 except that after day 4, 5 µM retinoic acid was added. At day 8, aggregates were dissociated and neural progentor cells (NPCs) were plated on PDL/laminin-coated dishes in N-2 medium. The N-2 medium was changed after 2 hours and again after 1 day. After 2 days, the medium was replaced by the B-27 medium to induce neurogenesis. Medium was changed every other day.

value: ES-derived EBs


title: HeLa, shC7orf26, Control, Biol rep 2


title: HeLa ,shLUC, Control, Biol rep 3

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight


title: Mll3KOMll4flox_D5ExEn_H3K4me1


title: K4minus2_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt

value: HbE gRNA V106W


title: K4minus1_RNA-seq

description:
RNA-seq
RNAseq_splicing.txt


title: Mll3KOMll4KI48_EBD4_RNA_3rd


title: HeLa, shC7orf26, EGF, Biol rep 1

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: HeLa ,shLUC, Control, Biol rep 2

value: WT (shLUC)


title: Mll3KOMll4flox_D5ExEn_GATA6

value: GATA6 (R&D Systems, AF1700)


title: Mll3KOMll4KI_D5ExEn_GATA6


title: hCD45 cells, WT-MSC, rep 2

city: Madrid

first: Cristian

last: Suarez Cabrera

address: Av. Complutense 40

institute: CIEMAT

data_processing:
Sequencing of the samples was performed on a Illumina NovaSeq 6000 instrument producing 50bp pairedend reads running Control Software 1.7.0.
The sequenced reads were controlled for quality of sequencing with FastQC  and trimmed using Trim_Galore.
The cleaned reads were aligned to the reference genome using the STAR aligner version 2.7.0f and RNA abundance was estimated with featureCounts from the Subread package version 1.6.3.
Downstream analyses, including the identification of differentially expressed genes by pairwise comparison, were performed with the DESEQ2 R package version 1.26.0.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include total counts values for each sample and another file with all normalized counts (DeSeq2) together (named normalized_counts).

source_name: Spleen

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN).
Sequencing of the samples was performed by Diagenode

treatment_protocol: Human T-cells transplanted in mice untreated (Disease control; GvHD) or treated with 2 different mesenchymal stromal cell treatments (WT-MSC or modified CXCR4-IL10-MSC).

value: Spleen

value: CD45 positives cells

value: WT-MSCs


title: Mll3KOMll4KI_D4EB_input

source_name: ES-derived EBs

value: EB differentiation


title: HeLa, shLUC, EGF, Biol rep 1

value: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes


title: hCD45 cells, WT-MSC, rep 3


title: Mll3KOMll4KI48_D0_RNA_3rd

source_name: Embryonic stem cells (ESCs)

value: ESC


title: hCD45 cells, WT-MSC, rep 1


title: Mll3KOMll4flox_D4EB_input


title: Mll3KOMll4KI27_EBD4_RNA_3rd


title: Mll3KOMll4KI27_EBD10_RNA_3rd


title: HeLa ,shLUC, Control, Biol rep 1

value: HeLa

value: cervical epithelial


title: hCD45 cells, GvHD, rep 3

value: whitout treatment


title: Mll3KOMll4KI27_D0_RNA_3rd


title: hCD45 cells, GvHD, rep 2


title: WTSK-repl2

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

country: India

institute: CENTRAL UNIVERSITY OF PUNJAB

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line treated with WA 2 µM concentration replicate 2

data_processing:
Illumina genrated raw reads were filtered (Adaptor removal and length filtering) using trimgalore
High quality trimmed reads were alligned to human genome (GRCh38.p10) using Bowtie
Count expression for each miRNA condidate and sample was calculated using DESeq2 software
Count expression matrix for each miRNA condidate and sample was calculated using DESeq2 software
Genome_build: Human genome (GRCh38.p10)
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) count expression files (6) for each sample
Supplementary_files_format_and_content: Microsoft office excel worksheet (.xlsx) count expression matrix for every miRNA condidate and every sample

source_name: Breast mammary gland

growth_protocol: For this, Human breast TNBC (MDA-MB-231) cells were cultured in the Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) heat-inactivated FBS, 100 U/ml of penicillin, and 100 mg/ml of streptomycin and maintained in 5% CO2 at 37 OC in a humidified atmosphere of 95% air in CO2 incubator. A total of 1x105 MDA-MB-231 cells were seeded in 35mm treated culture dishes containing 1ml of DMEM culture media and sub-cultured at every 3–4 days.

extract_protocol: Small RNA was isolated from Withaferin A without treated (control group) and Withaferin A treated (experimenta group) MDA-MB-231 samples

treatment_protocol: The cultured MDA-MB-231 cells treated with WA (2 µM) concentration (experimental group) and without WA treated MDA-MB-231 cells (control group) incubated at 37 ºC under a 95 % humid environment in an incubator having 5% CO2 for 24 h.

value: WA 2 µM


title: Mll3KOMll4flox_D4EB_GATA6


title: Mll3KOMll4flox_EBD10_RNA_3rd


title: Mll3KOMll4flox_EBD4_RNA_3rd


title: hCD45 cells, CXCR4-IL10-MSC, rep 3


title: hCD45 cells, GvHD, rep 1


title: T34_KO3_2iL (RNAseq)

first: Margherita

last: Mutarelli

address: Via Campi Flegrei 34

institute: CNR

data_processing:
Alignment was performed with STAR (v. 2.7.6a); STAR parameters were set following Lexogen guidelines for data analysis.
Quantification was performed with Subread package featureCounts (v. 2.0.1); featureCounts was used with default parameters.
Assembly: Mus Musculus GRCm38 Ensembl release 102
Supplementary files format and content: normalized counts matrix

source_name: Mouse Embryonic Stem cells blastocyst derived

growth_protocol: E14 mouse Embryonic Stem cells were routinely cultured on 0.2% gelatin coated multiwell plates in N2B27 medium (DMEM-F12 Neurobasal at 1:1 ratio (Life Technologies), 1X N2 Supplement (Life Technologies), 1X B27 Supplement (Life Technologies), 2mM L-Glutamine (Life Technologies), 0.1mM 2-mercaptoethanol) with the addition of 2iL (3uM CHIR99021 (Axon), 1uM PD0325901 (Axon), 1uM LIF (Qkine)).

extract_protocol:
Cells were harvested at the appropriate time point and RNA was purified by using "Total RNA extraction kit, Norgen".
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) is used for library construction.

treatment_protocol: For Formative Stem (FS) cells generation, mouse ESCs were plated at standard density in fibronectin-coated well in N2B27 medium. The next day, medium was changed to AloXR (3 ng/ml of activin A, 2 µM XAV, 1.0 µM BMS439 in N2B27 medium). The next day cells were dissociated into clumps with Accutase and plated at higher density than established cultures (1/5 ratio). Medium was changed every day and cells split every other day.

value: embryonic stem cells

value: genetically depleted for Esrrb

value: untreated (2iL)


title: Mll3KOMll4KI_D4EB_GATA6

value: ES-derived EBs


title: Mll3KOMll4flox_D0_RNA_3rd


title: HeLa, shC7orf26, Control, Biol rep 1

value: shC7orf26, serum starved in DMEM media containin 0.3% serum overnight


title: WTSK-repl1

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line treated with WA 2 µM concentration replicate 1


title: T33_KO3_2iL (RNAseq)


title: SKWANT-repl3

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line without treated replicate 3

value: control


title: hCD45 cells, CXCR4-IL10-MSC, rep 2


title: Mll3KOMll4KI27_D0_ATAC

extract_protocol:
50,000 freshly collected cells were incubated in 50 µL of cold lysis buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) on ice for 3 min and was washed out with 1 mL of wash buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Nuclei were collected by centrifugation at 500 g for 10 min at 4°C, then resuspended in 50 µL of transposition reaction buffer (25 µL 2x Tagment DNA buffer, 2.5 µL Tn5 transposase (100nM final; Illumina), 16.5 µL PBS, 0.5 µL 1% digitonin, 0.5 µL 10% Tween-20, 5 µL H2O). The reaction was incubated at 37°C for 30 min with mixing (1000 rpm) and directly subjected to DNA purification using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer’s instructions.
DNA was amplified with PCR using Nextera i7-index primers for Illumina protocols


title: SKWANT-repl2

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line without treated replicate 2


title: WTSK-repl3

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line treated with WA 2 µM concentration replicate 3


title: T31_KO2_2iL (RNAseq)


title: T32_KO3_2iL (RNAseq)


title: SKWANT-repl1

description: Breast mammary gland epithelial MDA-MB-231 cancer cell line without treated replicate 1


title: hCD45 cells, CXCR4-IL10-MSC, rep 1


title: T30_KO2_2iL (RNAseq)


title: T29_KO2_2iL (RNAseq)


title: TEAD3_KD_2

city: Shanghai

first: Zhengyuan

last: Huo

state: Shanghai

address: 389 Xincun Road

department: Department of Neurosurgery

institute: Shanghai Tong Ji Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCH38
Supplementary files format and content: Matrix table for FPKM values for  each gene and each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: U251 cells

growth_protocol: Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% foetal bovine serum (ExCell Bio, Shanghai, China, 111323) and 1x penicillin/streptomycin was used to cultivate the human glioma cell lines U251 and U87.   all the cell lines were grown in an incubator at the temperature of 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Jima Gene (Shanghai, China) designed the plasmid vector for TEAD3.  In this study, transient transfection was used.  After the filtered siRNA was functional (approximately 36 h), the knockdown efficiency was measured by RT‒qPCR and Western blotting.

value: glioma

value: TEAD3 Knockdown


title: Tumor CD8s LCL161-Treated Replicate 3

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

data_processing:
Reads were trimmed for Illumina adapter sequences using cutadapt and aligned using STAR (v2.7.3a).
Feature counting was done in R using the package Rsubread allowing for fractional counting of multi-mapping reads.
Assembly: GRCm38
Supplementary files format and content: CSV matrix of raw (non-normalized) gene-level counts for each sample.

source_name: Tumor

extract_protocol:
CD45+ CD4+ or CD45+ CD8+ cells were sorted by FACS from orthotopic live passage M8 organoid pancreatic tumors implanted in TCRα-/- mice treated with vehicle or LCL161 for 12 days. Total RNA was prepared using Qiagen RNAeasy kit according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tumor

value: CD8 T cell

value: TCR alpha-/-


title: TEAD3_KD_3


title: Tumor CD8s LCL161-Treated Replicate 1


title: NC_3

value: Normal Control


title: Mll3KOMll4flox_D4_ATAC


title: Tumor CD8s LCL161-Treated Replicate 2


title: T27_PGG_2iL (RNAseq)

value: Esrrb WT


title: abx_2-2

first: Gary

middle: D

last: Wu

state: PA

address: 915 Biomedical Research Building, 421 Curie Blvd

department: Department of Medicine, Division of Gastroenterology

institute: University of Pennsylvania

data_processing:
Raw data was counted against transcripts described in gencode version M21 with salmon. Transcipt counts were summarized to gene-level with tximport in R.
Genome_build: GRCm38, gene models from gencode version M21
Supplementary_files_format_and_content: comma separated values, raw counts per gene, Ensembl gene IDs with version

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in RNALater on dry ice, and RNA was harvested using Trizol Reagent followed by RNA cleanup using Qiagen Rneasy Mini Kit.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) as per standard protocol

tag: strain

tag: antibiotics

value: yes

tag: diet


title: Tumor CD8s Vehicle-Treated Replicate 2

value: Vehicle


title: ctl_1-3

value: no


title: NC_1


title: Mll3KOMll4flox_D0_ATAC

value: ESC


title: T25_KO3_p3 (RNAseq)

value: embryonic stem cells

value: N2B27 for 1 day followed by AloXR medium for 5 days


title: abx_2-5


title: ctl_1-4


title: T26_PGG_2iL (RNAseq)

value: untreated (2iL)


title: NC_2


title: T28_PGG_2iL (RNAseq)


title: TEAD3_KD_1


title: Tumor CD8s Vehicle-Treated Replicate 3


title: Mll3KOMll4KI27_D4_ATAC

value: ES-derived EBs


title: Tumor CD4s LCL161-Treated Replicate 3

value: CD4 T cell


title: abx_2-1


title: TI-1309-Relapse-AS2896

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

institute: Instituto de Investigación Sanitaria La Fe

description: Liquidhope sample84

data_processing:
The libraries were sequenced on NovaSeq 6000 (Illumina) in paired-end with a read length of 2x151bp according to the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run are processed using the manufacturer’s software Real Time Analysis (RTA 3.3.3) and followed by generation of FASTQ sequence files.  The EMSEQ reads were processed using the gemBS pipeline v4.03 using as reference GRCh38[23]. Reads with MAPQ scores < 20 and read pairs mapping to the same start and end points on the genome were filtered out after the alignment step. The first 5 bases from each read were trimmed before the variant and methylation calling step to avoid artifacts due to end repair. For each sample, CpG sites were selected where both bases were called with a Phred score of at least 20, corresponding to an estimated genotype error level of <=1%, and where the total number of reads informative for methylation from both strands combined was >=6. Sites with >500x coverage depth were excluded to avoid centromeric/telomeric repetitive regions. Sequencing depth for the analysis of copy number was calculated using samtools v1.15.
Assembly: hg38
Library strategy: Methyl-Seq

source_name: Blood-derived plasma circulating cell-free DNA

extract_protocol:
Around 1 ml of blood-derived plasma obtained at diagnosis was used to isolate cfcDNA with the QIAamp circulating nucleic acids kit (QIAGEN).
NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, NEB), following manufacturer's recommendations
To prepare libraries for comprehensive methylome representation within a cfcDNA we used the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, NEB), following manufacturer's recommendations with minor modification that the cfcDNA was not sheared. The method utilizes 10 ng starting material of cfcDNA and relies on two step conversion of the cytosines. The first step uses TET2 oxidation of 5-methylcytosine that provides protection to the modified cytosines from conversion by APOBEC deamination, so only cytosines but not 5-methylcytosines are converted to uracil. Ultimately, cytosines are sequenced as thymines and 5-methylcytosines are sequenced as cytosines. The final 8 cycles of PCR library amplification were carried out using the NEB Unique dual index primer pairs (NEBNext multiplex oligos for Illumina).

value: High-risk neuroblastoma

tag: gender

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion

value: No


title: abx_2-3


title: Tumor CD4s LCL161-Treated Replicate 2

tag: tissue

value: Tumor

tag: cell type

tag: genotype

tag: treatment


title: T21_KO2_p3 (RNAseq)

tag: cell line

value: genetically depleted for Esrrb


title: TI-1309-Diagnosis-AS2895

description: Liquidhope sample83

value: Blood-derived plasma circulating cell-free DNA

tag: disease state


title: T24_KO3_p3 (RNAseq)


title: ctl_1-5

tag: strain

tag: antibiotics

tag: diet


title: T22_KO2_p3 (RNAseq)


title: T20_KO2_p3 (RNAseq)


title: TI-1264-Diagnosis-AS2893

description: Liquidhope sample82

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)


title: ctl_1-1


title: Tumor CD4s LCL161-Treated Replicate 1

value: TCR alpha-/-


title: Tumor CD8s Vehicle-Treated Replicate 1

value: CD8 T cell


title: Tumor CD4s Vehicle-Treated Replicate 2

value: Vehicle


title: Spleen CD8s LCL161-Treated Replicate 3

value: Spleen


title: Tumor CD4s Vehicle-Treated Replicate 1


title: Organoid, replicate 2, scRNAseq

city: New York

first: Shukti

last: Chakravarti

state: NY

address: 435 E 30th Street

department: Department of Ophthalmology and Pathology, Department of Ophthalmology

institute: NYU Grossman School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequence results were demultiplexed and converted to FASTQ format using the Illumina bcl2fastq software.
The 10X Genomics Cell Ranger Single-Cell Software Suite v7.0.0 was used for sample demultiplexing, barcode processing, single-cell 3’gene counting and mapping.
Meaningful reads were calculated using (1) valid barcodes; (2) valid unique molecular identifier (UMI); (3) associated with a cell barcode; and (4) confidently mapped to exons (72). Only confidently mapped, non-PCR duplicates with valid barcode and unique molecular identifiers were used to generate gene-cell-barcode matrices for the cornea and organoid samples (Table S2).
The Cell Ranger data output was analyzed using the Seurat R package v 4.0.4 (73, 74). Low-quality cells > 10000 and <1000 detected genes, as well as cells showing > 10% mitochondrial gene content were removed from the analysis. The data was normalized and scaled using the “LogNormalize” and the “ScaleData” Seurat functions.  Highly variable genes were selected using the “FindVariableFeatures” function for downstream analysis. PCA was performed and dataset dimensionality was reduced by selecting the first 20 principal components. Clusters of cells were identified for the cornea and the organoid using the “FindNeighbors” and “FindClusters” functions. We chose the resolution parameter of 0.2 which identified 12 and 16 biologically meaningful clusters in the cornea and the organoid, respectively. The cells and clusters were visualized in 2D using uniform manifold approximation and projection (UMAP) plots. DEGs were found for each cluster for both the cornea and the organoid dataset individually using the “FindAllMarkers” function. Clusters were manually marked and identified based on known markers of corneal structures. The cornea and organoid datasets were integrated by selecting the top scoring features from both datasets with the “SelectIntegrationFeatures” function, followed by “FindIntegrationAnchors” to find a set of anchors between the datasets that were used to finally integrate the objects using the “IntegrateData” function (74).
Assembly: Human References GRCh38-2020-A (July 7, 2020)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Organoid

extract_protocol:
The central region of the human corneas were cut into small pieces and digested in 2 ml of digestion mix: 2 mg/ml collagenase type 1 (#SCR103; EMD Millipore) in DMEM-F12 supplemented with 5% FBS (#10438026; Gibco), 1% antibiotic-antimycotic (#15240062; Gibco), 1mM L-ascorbic acid using rotatory nutator at 37oC for 6h at 5% CO2. The supernatant was collected by allowing the undigested tissue to settle under gravity every 2 hours (h) and this was repeated 2-3 times. The collected supernatant samples were stored on ice at all stages and pooled after a final 6h of digestion, and centrifuged at 500 g for 5 min.  The supernatant was discarded and the pellet resuspended in 5 ml of 1x Accutase and incubated at 37oC for 20 min in a 5% CO2 incubator.  Fresh 5 ml of DMEM-F12 with 5% FBS was added and passed through a 40 µm cell strainer and centrifuged at 500 g for 5 min/4oC. Supernatant was discarded and the pellet resuspended in PBS with 0.04% BSA or complete DMEM-F12 to make a single cell suspension. Live cells were counted by trypan-blue exclusion in a Countess® II automated cell counter.
A total 6 individual (3 organoids and 3 human corneas) cDNA libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) and sequenced using an Illumina HiSeq 4000 as 150-bp paired-end reads.

value: Organoid


title: T17_PGG_p3 (RNAseq)

city: Pozzuoli

value: embryonic stem cells

value: Esrrb WT


title: Tumor CD4s Vehicle-Treated Replicate 3


title: TI-1196-Diagnosis-AS2890

description: Liquidhope sample79

value: Female

tag: relapse

tag: efs (months)

tag: exitus

tag: os (months)


title: T18_PGG_p3 (RNAseq)

value: N2B27 for 1 day followed by AloXR medium for 5 days


title: ctl_1-2

value: no


title: T23_KO2_p3 (RNAseq)


title: TI-1257-Relapse-AS2892

description: Liquidhope sample81

tag: tissue

value: High-risk neuroblastoma

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: Organoid, replicate 3, scRNAseq

description: 10x Genomics


title: TI-1185-Diagnosis-AS2888

description: Liquidhope sample77


title: T19_PGG_p3 (RNAseq)

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Organoid, replicate 1, scRNAseq

description: 10x Genomics


title: TI-1257-Diagnosis-AS2891

description: Liquidhope sample80

tag: disease state


title: Spleen CD8s LCL161-Treated Replicate 2


title: TI-1161-Diagnosis-AS2886

description: Liquidhope sample75

tag: gender

value: Male


title: TI-1185-Relapse-AS2889

description: Liquidhope sample78

tag: year to_diagnosis

value: Yes

value: Normal

value: not evaluable


title: Cornea, replicate 3, scRNAseq

description: 10x Genomics

source_name: Cornea

value: Cornea


title: TI-1170-Diagnosis-AS2887

description: Liquidhope sample76

value: Blood-derived plasma circulating cell-free DNA

tag: year to_last_follow-up

value: No

value: Tumor


title: T16_PGG_p3 (RNAseq)


title: Spleen CD8s LCL161-Treated Replicate 1

value: CD8 T cell

value: TCR alpha-/-


title: T13_KO3_p2 (RNAseq)

value: genetically depleted for Esrrb

value: N2B27 for 1 day followed by AloXR medium for 3 days


title: TI-1156-Relapse-AS2885

description: Liquidhope sample74

tag: age at_diagnosis_(months)


title: Cornea, replicate 2, scRNAseq

description: 10x Genomics


title: Spleen CD8s Vehicle-Treated Replicate 3

value: Spleen

value: Vehicle


title: Spleen CD8s Vehicle-Treated Replicate 2


title: Spleen CD8s Vehicle-Treated Replicate 1


title: Cornea, replicate 1, scRNAseq

description: 10x Genomics


title: Spleen CD4s LCL161-Treated Replicate 3

value: CD4 T cell


title: Minimal change disease 12

city: Bergen

first: Oystein

last: Eikrem

address: Haukelandsveien 22

department: Department of Mecine

country: Norway

institute: Haukeland University Hospital

data_processing:
Base calling was performed by RTA 1.17.21.3.
FASTQ files were generated using CASAVA 1.8.2 (Illumina, Inc. San Diego, CA, USA).
Assembly: GRCh38
Supplementary files format and content: MNd_ncounts_annot.txt
Supplementary files format and content: Abundance measurements

source_name: kidney FFPE

extract_protocol:
RNA was extracted with the High Pure FFPET RNA Isolation Kit (Roche Diagnostics).
RNA libraries were prepared for sequencing using the Illumina Exome (Access) capture protocol.

value: kidney FFPE

value: glomeruli - LCM


title: T12_KO3_p2 (RNAseq)

value: embryonic stem cells


title: TI-1137-Diagnosis-AS2882

description: Liquidhope sample71

value: High-risk neuroblastoma

value: Female

tag: relapse

value: Yes


title: TI-1118-Diagnosis-AS2881

description: Liquidhope sample70

tag: efs (months)


title: TI-1145-Diagnosis-AS2883

description: Liquidhope sample72

value: Male

tag: exitus


title: T09_KO2_p2 (RNAseq)


title: TI-1112-Diagnosis-AS2880

description: Liquidhope sample69

value: Blood-derived plasma circulating cell-free DNA

tag: os (months)


title: Minimal change disease 10

tag: tissue


title: TI-1107-Diagnosis-AS2879

description: Liquidhope sample68

value: No

tag: cfdna (inferred_status)


title: Spleen CD4s LCL161-Treated Replicate 2


title: T07_PGG_p2 (RNAseq)

value: Esrrb WT


title: Minimal change disease 14


title: Minimal change disease 13


title: Spleen CD4s Vehicle-Treated Replicate 2


title: TI-1106-Diagnosis-AS2878

description: Liquidhope sample67

value: Normal

tag: mycn amplification

value: not evaluable


title: T10_KO2_p2 (RNAseq)

value: genetically depleted for Esrrb


title: Minimal change disease 11


title: Spleen CD4s LCL161-Treated Replicate 1

value: TCR alpha-/-


title: T08_KO2_p2 (RNAseq)

value: N2B27 for 1 day followed by AloXR medium for 3 days


title: T04_PGG_p2 (RNAseq)


title: TI-1088-Relapse-AS2877

description: Liquidhope sample66

value: Tumor

tag: 11q deletion


title: TI-1156-Diagnosis-AS2884

description: Liquidhope sample73


title: Minimal change disease 6


title: T06_PGG_p2 (RNAseq)

tag: cell line


title: Spleen CD4s Vehicle-Treated Replicate 3

value: Spleen

tag: cell type

value: CD4 T cell

value: Vehicle


title: Minimal change disease 9

value: kidney FFPE

value: glomeruli - LCM


title: T03_KO3_p1 (RNAseq)

value: embryonic stem cells

tag: genotype

value: N2B27 for 1 day followed by AloXR medium for 1 day


title: Minimal change disease 8


title: Spleen CD4s Vehicle-Treated Replicate 1

tag: treatment


title: ESC_H33KO_TWIST2_FLAG_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

tag: strain

tag: antibody

value: FLAG (2368, Cell Signaling)


title: T11_KO2_p2 (RNAseq)


title: ESC_H33WT_TWIST2_FLAG_rep2


title: ESC_H33KO_HAND2_FLAG_rep2

data_processing:
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The sequence length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag


title: Minimal change disease 4


title: Minimal change disease 7


title: Minimal change disease 2


title: ESC_H33WT_TWIST2_FLAG_rep1


title: Idiopathic membranous nephropathy 13

tag: phenotype


title: ESC_H33KO_TWIST2_FLAG_rep2


title: T05_PGG_p2 (RNAseq)


title: TI-1079-Diagnosis-AS2874

description: Liquidhope sample63

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

tag: gender

value: Male

tag: year to_diagnosis

tag: year to_last_follow-up

value: Yes


title: Minimal change disease 5


title: ESC_H33KO_HAND2_FLAG_rep1


title: ESC_H33WT_HAND2_FLAG_rep2


title: TI-1073-Relapse-AS2870

description: Liquidhope sample59

value: Female

tag: age at_diagnosis_(months)

tag: relapse

tag: efs (months)

tag: exitus

value: No


title: T02_KO3_p1 (RNAseq)

value: genetically depleted for Esrrb


title: Minimal change disease 3

tag: tissue


title: TI-1073-Diagnosis-AS2869

description: Liquidhope sample58

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: TI-1087-Diagnosis-AS2875

description: Liquidhope sample64


title: T01_KO3_p1 (RNAseq)

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: S98_KO2_p1 (RNAseq)


title: TI-1088-Diagnosis-AS2876

description: Liquidhope sample65

tag: disease state


title: Minimal change disease 1


title: ESC_H33KO_BHLHA15_FLAG_rep2

tag: strain

tag: antibody


title: S96_KO2_p1 (RNAseq)


title: ESC_H33WT_HAND2_FLAG_rep1


title: S94_PGG_p1 (RNAseq)

value: Esrrb WT


title: TI-1077-Diagnosis-AS2872

description: Liquidhope sample61

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

value: Tumor


title: Idiopathic membranous nephropathy 10

tag: phenotype


title: S93_PGG_p1 (RNAseq)


title: Idiopathic membranous nephropathy 9


title: TI-1076-Diagnosis-AS2871

description: Liquidhope sample60

tag: age at_diagnosis_(months)

tag: relapse

tag: efs (months)

tag: exitus


title: S91_PGG_p1 (RNAseq)


title: Idiopathic membranous nephropathy 7

tag: tissue


title: ESC_H33KO_SOX2_rep4

value: SOX2 (AF2018, R&D Systems)


title: TI-1041-Diagnosis-AS2868

description: Liquidhope sample57

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: Idiopathic membranous nephropathy 12

tag: cell type


title: TI-1033-Diagnosis-AQ4041

description: Liquidhope sample52

tag: disease state


title: TI-1078-Diagnosis-AS2873

description: Liquidhope sample62


title: Idiopathic membranous nephropathy 5


title: TI-1027-Diagnosis-AQ4040

description: Liquidhope sample51


title: Idiopathic membranous nephropathy 11


title: Idiopathic membranous nephropathy 4


title: TI-1035-Diagnosis-AQ4042

description: Liquidhope sample54


title: Yng-59J-T21

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Kallisto was used to map reads to the mouse reference genome (mm10) and to quantifying abundances of transcripts using default settings
Transcript-level abundances were imported into R and collapsed into gene counts using the tximport package
To estimate the effects of the experimental conditions, we used DESeq2 to fit the following model gene-wise model: count~ time + age + time:age, where the variable time denotes the effect of engraftment, the variable age denotes the effect of aging, and the interaction variable time:age represents the reprogramming effect on genes in the aged niche.
For the purposes of ranking and visualization, we use the apeglm shrinkage approach.
Assembly: mm10
Supplementary files format and content: *_abundance.tsv: reports abundances as “estimated counts” (est_counts) and in Transcripts Per Million (TPM).
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/

source_name: satellite cells

extract_protocol:
1000 GFP positive satellite cells from the donor mice were sorted by Fluorescence-Activated Cell Sorting (FACS) by gating for the GFP+/DAPI- cell population.  These cells were sorted directly into the SMART-Seq (Takara) reaction buffer composed of lysis buffer, water and RNAse inhibitors, these cells act as the T0 time point.
Concurrently, 10,000-20,000 GFP positive cells were sorted from the same donor mouse and transplanted into the tibialis anterior of the host mouse.  After 21 days, these cells were then reisolated by FACS directly into the SMART-Seq reaction buffer.
Sequencing ready libraries were generated using SMART-Seq HT kit (Takara, cat. #624456) and illumine adapters were added using Nextera XT (Illumina, cat. #FC-131-1024, FC-131-1001).

tag: age of donor/age of host

value: 5 weeks/ NA

tag: tag

value: skeletal muscle


title: Yng-62-T0


title: S99_KO3_p1 (RNAseq)

tag: cell line

tag: genotype

tag: treatment


title: TI-1017-Diagnosis-AS2864

description: Liquidhope sample50

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up


title: Yng-62B-T21

data_processing:
Kallisto was used to map reads to the mouse reference genome (mm10) and to quantifying abundances of transcripts using default settings
Transcript-level abundances were imported into R and collapsed into gene counts using the tximport package
To estimate the effects of the experimental conditions, we used DESeq2 to fit the following model gene-wise model: count~ time + age + time:age, where the variable time denotes the effect of engraftment, the variable age denotes the effect of aging, and the interaction variable time:age represents the reprogramming effect on genes in the aged niche.
For the purposes of ranking and visualization, we use the apeglm shrinkage approach.
Assembly: mm10
Supplementary files format and content: *_abundance.tsv: reports abundances as “estimated counts” (est_counts) and in Transcripts Per Million (TPM).
Project's Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/

extract_protocol:
1000 GFP positive satellite cells from the donor mice were sorted by Fluorescence-Activated Cell Sorting (FACS) by gating for the GFP+/DAPI- cell population.  These cells were sorted directly into the SMART-Seq (Takara) reaction buffer composed of lysis buffer, water and RNAse inhibitors, these cells act as the T0 time point.
Concurrently, 10,000-20,000 GFP positive cells were sorted from the same donor mouse and transplanted into the tibialis anterior of the host mouse.  After 21 days, these cells were then reisolated by FACS directly into the SMART-Seq reaction buffer.
Sequencing ready libraries were generated using SMART-Seq HT kit (Takara, cat. #624456) and illumine adapters were added using Nextera XT (Illumina, cat. #FC-131-1024, FC-131-1001)


title: ESC_H33WT_BHLHA15_FLAG_rep2

tag: strain

tag: antibody


title: S97_KO2_p1 (RNAseq)


title: S92_PGG_p1 (RNAseq)


title: ESC_H33WT_SOX2_rep4


title: TI-1035-Relapse-AS2866

description: Liquidhope sample55

tag: tissue

tag: age at_diagnosis_(months)

tag: relapse

tag: efs (months)

tag: exitus


title: ESC_H33WT_BHLHA15_FLAG_rep1


title: Yng-55-T21


title: Idiopathic membranous nephropathy 1

value: kidney FFPE

tag: phenotype

tag: cell type


title: TI-0987-Diagnosis-AS2862

description: Liquidhope sample47

tag: disease state

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion


title: Normal control 8

value: glomeruli - LCM


title: ESC_H33KO_BHLHA15_FLAG_rep1


title: ESC_H33WT_SOX2_rep3


title: ESC_H33WT_SOX2_rep2


title: ESC_H33WT_SOX2_rep1


title: Normal control 7


title: Aged-900-T21

tag: age of donor/age of host

value: 22 months/ NA

tag: tag


title: Idiopathic membranous nephropathy 8


title: S95_KO2_p1 (RNAseq)

tag: cell line

value: embryonic stem cells

tag: genotype

tag: treatment

value: N2B27 for 1 day followed by AloXR medium for 1 day


title: ESC_H33KO_KLF5_rep4

tag: strain

tag: antibody

value: KLF5 (61099, Active Motif)


title: TI-1036-Diagnosis-AS2867

description: Liquidhope sample56

tag: tissue

value: Blood-derived plasma circulating cell-free DNA

value: High-risk neuroblastoma

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up

tag: age at_diagnosis_(months)

tag: relapse


title: Aged-62-T0

value: 26 months/ NA


title: ESC_H33KO_SOX2_rep2


title: ESC_H33KO_KLF5_rep3


title: Aged-62-2-T21


title: TI-1015-Diagnosis-AS2863

description: Liquidhope sample49

tag: disease state

value: Female

value: Yes

tag: efs (months)

tag: exitus

tag: os (months)


title: TI-1033-Relapse-AS2865

description: Liquidhope sample53

value: No

tag: cfdna (inferred_status)

value: Normal

tag: mycn amplification

value: not evaluable

tag: 11q deletion


title: Normal control 4

tag: cell type


title: Normal control 3


title: Idiopathic membranous nephropathy 3

tag: phenotype


title: TI-0976-Diagnosis-AS2857

description: Liquidhope sample42

value: Tumor


title: ESC_H33WT_KLF5_rep4

tag: strain


title: Aged-58-T0

tag: age of donor/age of host

tag: tag


title: Normal control 2

tag: tissue


title: Idiopathic membranous nephropathy 2


title: ESC_H33KO_SOX2_rep3

tag: antibody

value: SOX2 (AF2018, R&D Systems)


title: Normal control 1


title: Yng-55-T0

value: 5 weeks/ NA

value: skeletal muscle


title: Normal control 5

value: kidney FFPE

value: glomeruli - LCM


title: ESC_H33KO_SOX2_rep1


title: Yng-59-T0


title: TI-0966-Diagnosis-AS2856

description: Liquidhope sample41

tag: gender

tag: year to_diagnosis

tag: year to_last_follow-up


title: ETX embryoid Day 5 mid

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

description: 10x Genomics

data_processing:
Cellranger mkref v6.0.0 was used to create a custom reference package containing the mm10 reference genome and the sequences of DSRED, GFP and EGP. The raw FASTQ files were processed using cellranger count based on the custom reference package. Cells with fewer than 500 counts, 250 detected genes and low complexity (log10 value of number of genes detected per count < 0.8) were removed. Genes with zero expression in all cells and that are expressed in less than 10 cells were removed.
Assembly: mm10
Supplementary files format and content: Tab-delimited file (tsv) with barcodes
Supplementary files format and content: Tab-delimited file (tsv) with genes
Supplementary files format and content: Matrix file (mtx) with expression values

source_name: Stem cell-derived ETX embryoid

extract_protocol:
ETX embryoids were collected on day 4, day 5 and day 6. ETX structures were selected on day 4 when they displayed a clear epiblast and a pro-amniotic cavity. Day-5 ETX embryoids were divided in a group displaying a morphology of early gastrulation and a group of ETX structures displaying signs of more advanced gastrulation. Selected day-6 ETX embryoids displayed a more developed phenotype with the apparent formation of an amnion, chorion and exocoelom. Per selected stage, 10 ETX structures were processed for 10x-sequencing as earlier described. Briefly, selected ETX embryoids were carefully removed from the wells and dissociated with TrypLE Express dissociation reagent (Life Technologies) at 37 °C for 5min and gently dissociated manually. Following inactivation with an equivalent amount of FBS, the single cells were filtered through a Flowmi Tip Strainer with 40 µm porosity (ThermoFisher Scientific, #136800040), washed and resuspended in PBS with 0.4% BSA.
Single cells were processed on the 10X Genomics Chromium Platform using the Chromium Next GEM Single Cell 3′ Reagent kit v3.1 with dual indexing (10X Genomics) following the manufacturer’s protocol. Briefly, 15,000 cells were loaded in each channel of a chip to be partitioned into gel beads in emulsion (GEMs). Within GEMs, cells were lysed followed by barcoded reverse transcription of RNA. Breaking of the GEMs was followed by amplification, fragmentation and addition of adapter and sample index. Libraries were pooled and sequenced 28-10-10-90 cycles on an Illumina NovaSeq6000 instrument aiming for a minimum coverage of 25,000 raw reads per cell.

value: Stem cell-derived ETX embryoid

value: Mixed

tag: genotype

value: Fgfr2-Gata6 transgenic PrE ESCs, Actin-GFP ESCs, X-GFP TS cells

tag: day


title: ESC_H33WT_KLF5_rep2

value: KLF5 (61099, Active Motif)


title: TI-0993-Diagnosis-AQ4039

description: Liquidhope sample48

value: Blood-derived plasma circulating cell-free DNA

tag: disease state

value: High-risk neuroblastoma

value: Male

tag: age at_diagnosis_(months)

tag: relapse

tag: efs (months)

tag: exitus


title: TI-0957-Diagnosis-AS2854

description: Liquidhope sample38

value: Female

tag: os (months)

tag: cfdna (inferred_status)

tag: mycn amplification

tag: 11q deletion

value: Yes


title: Aged-900-T0

tag: age of donor/age of host

value: 22 months/ NA

tag: tag


title: TI-0964-Diagnosis-AS2855

description: Liquidhope sample40

tag: tissue

value: No