title: CD8 Temra batch 2

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19-A1038

department: Department of Biomedicine

country: Estonia

institute: Institute of Biomedicine and Translational Medicine

data_processing:
The raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (version 6.1.2) with the GRCh38 reference. The scRNA-seq alignment and quantification were carried out on the Tartu University High Performance Computing Center Rocket cluster.
The samples were demultiplexed using the HTODemux function from the Seurat package.
Assembly: GRCh38

source_name: peripheral blood

extract_protocol:
PBMCs were isolated by Ficoll-Paque density gradient centrifugation method. CMV positivity was detected by LIPS method. Temra cells were sorted using Sony MA900 Cell Sorter (Sony Biotechnology). Cells were labeled simultaneously with TotalSeq-B Hashtags (BioLegend).
5000 Temra cells from 5-6 individuals with different barcodes were combined into one reaction and loaded onto the Chromium controller and cDNA was generated using Chromium Single Cell 3' Reagent Kit (v3.1 Chemistry Dual Index) and Chromium Next GEM Chip G Single Cell Kit (both from 10X Genomics) according to manufacturer’s instructions. Gene expression and hashtag libraries were paired-end sequenced on an Illumina NovaSeq 6000 instrument in Novogene.

value: peripheral blood

value: CD8 Temra


title: A3777_16

status: Public on Jan 23 2024

type: RNA

city: Beerse

first: Nádia

last: Conceição-Neto

address: Turnhoutseweg 30

country: Belgium

institute: Janssen R&D

description: mouse liver L7-4 treated with Compound JNJ-A_7 days post treatment

hyb_protocol: After fragmentation and end-labeling, the targets are hybridized to a multi-sample Clariom S plate array on a GeneTitan Multi-Channel Instrument (Thermo Fisher Scientific).

data_processing: Gene expression values were normalized by robust multiarray average normalization on the microarray probe-level data

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Transcriptome analysis was done using the Mouse Clariom S Assay (Thermo Fisher Scientific, 902930), in combination with the GeneChip WT PLUS Reagent kit (Thermo Fisher Scientific, 902280).

extract_protocol: RNA extraction on a QiaSymphony liquid handling system using the QIAsymphony RNA extraction kit

tag: agent

value: Compound JNJ-A

tag: time point

value: 7 days post treatment


title: HUVEC_shAmotL2_rep5

type: SRA

city: Stockholm

first: Lars

last: Holmgren

state: Stockholm

address: Solnavägen 30

department: Oncology Pathology

country: Sweden

institute: Karolinska Institute

description:
Data S1 HUVEC_shAmotL2_vs_V_shScr_peak_compare_table.tsv
Data S2 HUVEC_shAmotL2_vs_shScr_down_peak_related_genes.txt

library_source: genomic

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel -- keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering. distribution of peak over various functional areas is analysed by ChIPseeker software.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: *peak_compare_table (Data S1)
Supplementary files format and content: The first four columns refer to peak information
Supplementary files format and content: (1) Chromosome
Supplementary files format and content: (2) PeakStart
Supplementary files format and content: (3) PeakEnd
Supplementary files format and content: (4) oriSummitPos
Supplementary files format and content: (N) Count_*The number of reads to the peak was compared in each sample
Supplementary files format and content: (N) RPM_*   The proportion of 1M reads in each sample in peak
Supplementary files format and content: (N) FoldEnrich_*Enrichment of reads in each experimental group
Supplementary files format and content: (N) log2foldchange  log2?fold enrichment?
Supplementary files format and content: (N) In_*  Whether as the peak of this experiment
Supplementary files format and content: (N) Distance   Distance between peak and TSS
Supplementary files format and content: The five columns are information about the genes closest to TSS
Supplementary files format and content: (N) GeneStart
Supplementary files format and content: (N) GeneEnd
Supplementary files format and content: (N) ClosestTSS_ID
Supplementary files format and content: (N) Symbol
Supplementary files format and content: (N) Strand
Supplementary files format and content: Data S2 - peak related genelist

molecule: genomic DNA

organism: Homo sapiens

source_name: Endothelial

growth_protocol: Human umbilical vein endothelial cells (HUVEC, Promocell, Heidelberg, Germany) were cultured in Endothelial cell medium (ECM; ScienCell) supplemented with 5% foetal calf serum (FCS) (v/v), 1% endothelial cell growth supplement (ECGS) and 1% Pen/Strep antibiotic cocktail and were cultured on 0.2% gelatin (Sigma-Aldrich) (w/v in PBS)-coated plates. Human umbilical arterial endothelial cells (HUAEC, Promocell, Heidelberg, Germany)) were cultured as above in endothelial cell basal medium (ECBM) MV medium (Promocell) supplemented with 2% foetal calf serum (FCS) (v/v), 0.4% Endothelial Cell Growth Supplement, 0.1 ng/ml epidermal growth factor (recombinant human), 1 ng/ml basic fibroblast growth factor (recombinant human), 90 μg/ml heparin and 1 μg/ml hydrocortisone. Both HUVEC and HUAEC were grown to passage 4 or 5.

extract_protocol:
Using the ATAC-seq library preparation ATAC-seq library preparation kit (ActiveMotif) HUVEC and HUAEC cells were transduced with shScr and shAmotL2 for 72 h before cells were trypsinised and counted using Trypan blue. 100,000 cells were centrifuged, and nuclei was extracted using ice-cold ATAC-lysis buffer (according to the kit protocol; Active Motif) and the pellet resuspended in the Tn5 tagmentation master mix. The transposition reaction was incubated at 37°C for 30 min at 800 rpm using a thermomixer. Tagmented DNA was purified according to the protocol’s column purification step.
Tagmented DNA was purified according to the protocol’s column purification step, followed by PCR amplification of tagmented DNA for 10 cylces using Illumina’s Nextera indexed adapters.  After the PCR reaction, libraries were purified with the SPRI magnetic beads and library quality, and concentration was assessed with Qubit bioanalyzer. 4 independent experiments were prepared for ATAC-seq for both HUVEC and HUAEC, resulting in 16 libraries in total. Libraries were then sequenced with the Illumina Hiseq platform with a 150bp paired-end repeats protocol.

treatment_protocol: Lentiviral supernatants were produced in HEK293T cells following transfection using Lipofectamine 3000 (Invitrogen) transfection agent with 3rd generation packaging plasmids and either shScr (SHC332; Sigma), shAmotL2 (MXS19; Sigma), shAmotL2 #1 (GAACAAGATGGACAGTGAAAT) or shAmotL2 #2 (GAGAGATTGGAATCTGCAAAT) (VectorBuilder). HUVEC or HUAEC cells were transfected with the above lentiviral supernatants diluted (2:1) with ECMB supplemented media with polybrene (8μg/ml) (Sigma) overnight. The following day viral supernatants were removed and replaced with fresh supplemented media and cultured for 72-96h post transduction before downstream analysis.

tag: tissue

value: Endothelial

tag: cell line

value: HUVEC

tag: genotype

tag: treatment

value: Lentivirus


title: HUVEC_shAmotL2_rep4


title: CONTROL_NT#1

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
RNA was sequenced using Illumina NextSeq (HO) 150 cycle Sequencing.
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Reference and Annotation: GRCh38 from ENSEMBL
Assembly: GRCh38 from ENSEMBL
Supplementary files format and content: tab delimited text file of Raw counts of each smples  Generated using Bioconductor R package Rsubread and featureCounts function
Supplementary files format and content: tab delimited text file of counts per million of each smples

source_name: Blood

extract_protocol:
Cells were lysed with RLT Plus Buffer (QIAGEN, Cat. No. 1053393)followed by RNA purifcationusing RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to manufacturer’s protocol.
RNA-seq libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen; Cat. No. 015) with the UMI add-on kit.

treatment_protocol: PBMC from severe COVID-19 subjects (n = 3) and age-matched controls (n = 3) and stimulated them with the TLR4 ligand LPS (1 ug /ml for 2 hours).TLR ligand (LPS) were obtained from InvivoGen

value: Blood

tag: cell type

value: peripheral blood mononuclear cells

tag: group

tag: infection

value: control

value: No treatment


title: CD8 Temra batch 1

library_source: transcriptomic single cell

molecule: polyA RNA


title: E9.5F_119_Input

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw peaks were aligned to the mm10 mouse genome using the NGS Data Charmer pipeline with default settings (HISAT v.0.1.6b)
Peak calling was performed using macs2 (v.2.1.1) on individual files with default settings
Differential peaks using Diffbind package (v3.8.4)
Assembly: mm10
Supplementary files format and content: macs2 narrowPeak .xls file
Supplementary files format and content: bigWig file

source_name: placenta

growth_protocol: Embryonic placenta collections at designated time points

extract_protocol:
Chromatin from hemisected placental tissues were fixed with 1% formaldehyde rotated for 12 minutes at room temperature and was subsequently quenched using a final concentration of 125mM glycine. Samples were thoroughly homogenized and washed with ice cold PBS. Fixed chromatin was sonicated using a Covaris E220 for 30-60 minutes at 4°C with the following conditions: peak incident power, 140; duty factor, 10%; Cycles/burst, 200; Water level, 0. Equal amounts of chromatin per sample were rotated with select antibodies (2.5 μg antibody/sample of either H3K4me3Q5ser (MilliporeSigma ABE2580) or H3K4me3 (Active Motif 39159)) bound to M-280 Dynabeads at 4°C overnight. The next morning, samples were washed, eluted, and reverse-crosslinked at 65°C. Samples underwent RNA and protein digestion, and DNA was purified using QIAQuick MinElute Spin columns (Qiagen 28140). 1% inputs were removed prior to antibody incubation and purified in parallel with corresponding immunoprecipitates.
TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012)

value: placenta

tag: developmental stage

tag: Sex

value: F

value: WT

tag: chip antibody

value: Input


title: HUVEC_shScr_rep4

value: shScr


title: C6_D0_N3

city: London

first: Tegan

last: Gilmore

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: Francis Crick Institute

data_processing:
nf-core Nextflow RNAseq pipeline, revision 3.8.1 (https://github.com/nf-core/rnaseq), with STAR aligner and RSEM quantification
Assembly: GRCh38, release 95
Supplementary files format and content: Tab-delimited text file containing expected count, TPM and FPKM per detected gene

growth_protocol:
The mEGFP-tagged ACTN2 WTC hPSC line (AICS-0075-085; ACTN2-GFP-hPSC) was obtained from Allen Cell Collection (available through Coriell Institute) and maintained in essential 8 (E8) media (Life Technologies) on vitronectin peptide (Life Technologies) coated surfaces.
A CRISPR/Cas9 gene targeting strategy, previous described in detail[28], was used to generate a heterozygousHSPG2knockout hPSC line (HSPG2+/-).
WT andHSPG2+/-cells were differentiated towards left ventricle cardiomyocytes using a protocol developed in house (Dark et al., 2023;https://doi.org/10.1016/j.crmeth.2023.100456).

extract_protocol:
RNA was extracted from cells using Qiazol (Qiagen) following the manufacturers’ instructions.
Libraries were prepared using the polyA_KAPA_mRNA_Hyper_Prep kit (Roche) for sequencing on the Novaseq platform.

value: Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs)

value: HSPG2 +/-

tag: time

value: Day 0


title: A3777_33

description: mouse liver L82-4 treated with Vehicle_24 days post treatment

scan_protocol: on a GeneTitan Multi-Channel Instrument (Thermo Fisher Scientific).

value: Vehicle

value: 24 days post treatment


title: A3777_41

description: mouse liver L78-4 treated with Vehicle_23 days post treatment

value: 23 days post treatment


title: A3777_11

description: mouse liver L83-4 treated with Vehicle_24 days post treatment


title: A3777_74

description: mouse liver L84-4 treated with Vehicle_24 days post treatment


title: A3777_40

description: mouse liver L77-4 treated with Vehicle_23 days post treatment


title: E12.5M_67_Input

value: M


title: E12.5F_65_Dual


title: E12.5M_81_Input


title: A3777_32

description: mouse liver L76-4 treated with Vehicle_23 days post treatment


title: E12.5F_80_Input


title: HUVEC_shScr_rep2

value: Endothelial

value: HUVEC

value: Lentivirus


title: C6_D30_N3

value: Day 30


title: C6_D30_N1


title: HUVEC_shScr_rep3


title: HUAEC_shAmotL2_rep4

value: HUAEC


title: HUAEC_shAmotL2_rep3


title: E9.5M_118_Input

value: placenta


title: HUVEC_shScr_rep1


title: WT_D30_N3


title: A3777_46

description: mouse liver L72-4 treated with Vehicle_22 days post treatment

value: 22 days post treatment


title: C6_D30_N2


title: C6_D0_N2


title: E17.5M_44_Dual

value: WT


title: E17.5M_36_Dual


title: HUAEC_shAmotL2_rep2


title: WT_D30_N2


title: A3777_25

description: mouse liver L71-4 treated with Vehicle_22 days post treatment


title: A3777_07

description: mouse liver L65-4 treated with Vehicle_21 days post treatment

value: 21 days post treatment


title: E17.5F_34_Dual

value: F


title: HUAEC_shAmotL2_rep1


title: A3777_19

description: mouse liver L64-4 treated with Vehicle_21 days post treatment


title: WT_D30_N1

value: Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs)


title: A3777_02

description: mouse liver L70-4 treated with Vehicle_22 days post treatment


title: C6_D20_N3

value: HSPG2 +/-

value: Day 20


title: E9.5F_129_Dual


title: E17.5F_29_Dual


title: HUAEC_shScr_rep4

value: shScr


title: E9.5F_119_Dual


title: HUAEC_shScr_rep3


title: A3777_66

description: mouse liver L66-4 treated with Vehicle_21 days post treatment

value: Vehicle


title: HUAEC_shScr_rep2


title: E9.5M_122_Dual


title: C6_D20_N1


title: E9.5M_118_Dual


title: C6_D20_N2


title: DDX6-null replicate 2 for Ribo-seq

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

description: small RNA

data_processing:
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translation efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Assembly: hg19
Supplementary files format and content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimited file for translation efficiency analysis

growth_protocol: 6.4x10^6 cells of HEK293T WT or DDX6-null cells were plated on 15 cm dishes 24 hrs before harvesting.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: HUAEC_shScr_rep1


title: WT_D20_N3


title: A3777_62

description: mouse liver L60-4 treated with Vehicle_18 days post treatment

value: 18 days post treatment


title: DDX6-null replicate 1 for Ribo-seq

description: small RNA


title: WT_D20_N2


title: A3777_27

description: mouse liver L58-4 treated with Vehicle_18 days post treatment


title: E12.5M_81_Dual

value: M


title: A3777_63

description: mouse liver L59-4 treated with Vehicle_18 days post treatment


title: A3777_03

description: mouse liver L53-4 treated with Vehicle_16 days post treatment

value: 16 days post treatment


title: A3777_55

description: mouse liver L52-4 treated with Vehicle_16 days post treatment


title: C6_D0_N1

value: Day 0


title: Wild-type (DDX6-nul control) replicate 2 for Ribo-seq

description: small RNA


title: WT_D20_N1


title: E12.5F_80_Dual


title: E12.5M_67_Dual


title: Wild-type (DDX6-nul control) replicate 1 for Ribo-seq

description: small RNA


title: C6_D15_N3

value: Day 15


title: DDX6-null replicate 2 for RNA-seq

description: messenger RNA


title: Wild-type (DDX6-nul control) replicate 2 for RNA-seq

description: messenger RNA


title: A3777_81

description: mouse liver L54-4 treated with Vehicle_16 days post treatment


title: C6_D15_N2


title: C6_D15_N1


title: DDX6-null replicate 1 for RNA-seq

description: messenger RNA


title: snATACseq_CD31_P8MI_rep2

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: scATAC

library_source: genomic single cell

data_processing:
snATAC-seq: The 10x Genomics Cell Ranger software (cellranger-atac-1.2.0) was used to handle raw sequencing data. Reads were mapped to the mouse mm10 genome.
The peak outputs from each sample were aligned with cellranger-atac count and aggregated with cellranger-atac aggr (--nosecondary --normalize = none). MACS2 callpeak (v2.1.1.20160309) was used for initial clustering and per cluster and per sample peak calling (-f BAMPE -g mm -B -q 0.1). We then reaggregated samples with cellranger-atac aggr using a union set of peaks and imported them in Seurat for subsequent analysis.
Low-quality nuclei with <15% of fragments (reads) in peaks were removed. Nuclei with a minimum of 30 K (few reads) and a maximum of 1,500 K (doublets/nuclei clumps) peak region fragments were also removed.
To identify clusters in the snATAC-seq data, we transferred cluster labels from scRNA-seq data. To accomplish this, we first identified common correlation patterns in the gene activity matrix, which is the summation of fragments intersecting with the gene body and promoter region, from both datasets. Mapping of fragments of each cell to the 2-kb upstream region of gene coordinates is performed with the GeneActivity function in Seurat. The FindTransferAnchors function was used to identify patterns between the two experimental conditions for integration. Dimensionality reduction was performed with Harmony to correct principal component analysis embeddings. Each snATAC-seq nuclei was assigned scores on the basis of cluster labels from the scRNA-seq data.
Assembly: mm10

source_name: Heart

extract_protocol:
Atria and aorta were removed from the heart, and the remaining tissue was used for single cell digestion. Cells were harvested at either P5 or P12, from pools of 5 hearts subjected to MI at P1 or P8, respectively. Tissues were minced into small pieces in digestion buffer (HBSS, 1 mg/mL collagenase A) and incubated at 37ºC with agitation for 30 minutes. The suspension was triturated with a 5 mL pipette every 10 minutes. Proper digestion was verified by appearance of single cells under a microscope. The digestion was then diluted 1:1 with HBSS, and the resulting cell suspension was centrifuged at 300 rpm for 6 minutes to remove cardiomyocytes. Supernatant was passed through a 40-micron filter to remove tissue fragments and cardiomyocytes, and then centrifuged at 500 x g for 6 minutes. The cell pellet was resuspended in 1 mL of MACs buffer (PBS, 0.5 % BSA, 2 mM EDTA). The resuspended cells were centrifuged at 500 x g for 6 minutes to remove residual buffer and resuspended in a final volume of 80 uL for incubation with 20 uL of CD31 MACs beads (Miltenyi Biotech). MACs enrichment for CD31+ cells was performed according to the Miltenyi enrichment protocol. Live cells were quantified with Trypan Blue and inCyto C-Chip DHC-F01. For single-nuclei ATAC sequencing, nuclei were isolated from cells according to the 10x protocol. Live nuclei were quantified with DAPI and inCyto C-Chip DHC-F01.
scATAC-seq libraries were generated using the 10x Chromium Single Cell 3’ Library Kit v3 (10x Genomics) according to manufacturer’s instructions. We diluted cell suspensions for a target of 10,000 cells for each library.

treatment_protocol: Mouse were subjected to MI at P1 or P8

value: Heart

tag: enrichment

value: CD31+ enrichment

value: left anterior descending artery occlusion


title: snATACseq_CD31_P1MI_rep2

description: scATAC


title: snATACseq_CD31_P8MI_rep1

description: scATAC


title: A3777_93

description: mouse liver L47-4 treated with Vehicle_14 days post treatment

value: 14 days post treatment


title: WT_D15_N3

value: WT


title: WT_D0_N3


title: snATACseq_CD31_P1MI_rep1

description: scATAC


title: Wild-type (DDX6-nul control) replicate 1 for RNA-seq

description: messenger RNA


title: WT_D15_N2


title: snATACseq_WholeHeart_P8MI_rep3

description: scATAC

value: no enrichment


title: A3777_54

description: mouse liver L20-4 treated with Compound JNJ-A_9 days post treatment

value: Compound JNJ-A

value: 9 days post treatment


title: Mus musculus, Unlable_NC, RNA-seq, rep3

city: Xiamen

first: Guo

last: Ye

state: Fujian

address: 422 Siming South Road, Siming District

country: China

institute: Xiamen university

data_processing:
The barcoded processing,reads trimming using the Drop-seq pipeline (v2.4.0),
Trimmed sequence reads were mapped to GrCM38 using the STAR v2.7.3a workflow
Labeled and unlabeled transcripts were quantified using The scNT-seq pipline
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

extract_protocol:
The kidney tissue was dissociated into a single-cell suspension using Multi Tissue Dissociation Kit2(Miltenyi Biotec).
The cell suspension was introduced into the chip and paired with barcoded beads. After the mRNAs from the lysed cells were captured by the barcoded beads, recovered the beads from the chip. The mRNAs on the microspheres was then treated with 5mM iodoacetamide (IAA). Subsequently, reverse transcription was performed and the products were amplified by PCR. Finally, P5 and P7 junctions were added to both ends of the sequence by TruePrep DNA Library Prep Kit V2(Vazyme).

treatment_protocol: Initially, mice were anesthetized via intraperitoneal injection using 30 mg/mL pentobarbital sodium. Renal ischemia was induced by temporarily occluding the renal artery with a vascular clamp, thereby restricting blood flow to the kidney. Subsequently, reperfusion was facilitated by removing the vascular clamp. During the ischemic phase, the renal artery was clamped for durations of 30 min (two replicates) and 50 minutes, respectively. Following clamp removal, the injured kidney was promptly extracted to prepare a single-cell suspension. For the reperfusion phase, the renal artery underwent clamping for a duration of 50 minutes, after which the clamp was removed to restore bloodstream circulation in the kidney. Then, the injured kidney was collected at two distinct time points: 3 hours (two replicates) and 4.5 hours (two replicates) following the initiation of reperfusion.

value: Kidney

value: Normal renal cells

value: IAA treatment


title: snATACseq_WholeHeart_P8MI_rep2

description: scATAC


title: C6_D10_N3

value: Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs)

value: HSPG2 +/-

value: Day 10


title: Mus musculus, Unlable_NC, RNA-seq, rep2


title: Mus musculus, Lable_NC, RNA-seq, rep2


title: Mus musculus, Unlable_NC, RNA-seq, rep1


title: Mus musculus, Lable_NC, RNA-seq, rep1


title: A3777_69

description: mouse liver L41-4 treated with Vehicle_13 days post treatment

value: Vehicle

value: 13 days post treatment


title: Mus musculus, Ischemia-reperfusion_5.3h, RNA-seq, rep2

value: Injured renal cells


title: A3777_86

description: mouse liver L48-4 treated with Vehicle_14 days post treatment


title: Sca1- rep4

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
We used cutadapt version 1.16  to remove the adapter sequences from the reads and for quality trimming. We discarded all paired-end reads if one of the reads was shorter than 20 bases.
The reads were then aligned against the mouse genome (assembly GRCm38/mm10) using STAR version 2.5.3a
Assembly: mm10
Supplementary files format and content: row counts, comma separated; log2 normalized counts, tab separated

source_name: 4T1-Sca1- sorted from parental 4T1

extract_protocol:
4T1 tumor were stained for Sca1-PE and then sorted using MACS milteny columns
RNA was isolated using RNeasy plus mini (Qiagen) following manufacturer’s instructions. Isolated RNA sample quality was assessed by HS Total RNA 15nt on Fragment Analyzer (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
Trueseq RNA Libarary Prep kit V2 (RS-122-2001) as instructed by the manufacturer
NextSeq 500 sequencer Illumina using the Nextseq 500/550 HT reagent kit v2

tag: replicate

tag: facs sort


title: A3777_39

description: mouse liver L35-4 treated with Vehicle_12 days post treatment

value: 12 days post treatment


title: WT_D15_N1

value: Day 15


title: WT_D10_N2


title: WT_D10_N3


title: C6_D10_N1


title: C6_D10_N2


title: A3777_91

description: mouse liver L46-4 treated with Vehicle_14 days post treatment


title: snATACseq_WholeHeart_P1MI_rep2

description: scATAC

value: Heart

value: left anterior descending artery occlusion


title: snATACseq_WholeHeart_P1MI_rep1

description: scATAC


title: snATACseq_WholeHeart_P8MI_rep1

description: scATAC


title: WT_D0_N2

value: WT

value: Day 0


title: Sca1- rep1


title: WT_D10_N1


title: Sca1- rep3


title: Mus musculus, Ischemia-reperfusion_3.8h, RNA-seq, rep1


title: Mus musculus, Ischemia-reperfusion_5.3h, RNA-seq, rep1


title: Sca1+ rep4

source_name: 4T1-Sca1+ sorted from parental 4T1


title: A3777_15

description: mouse liver L34-4 treated with Vehicle_12 days post treatment


title: Mus musculus, Ischemia-reperfusion_3.8h, RNA-seq, rep2


title: Mus musculus, Ischemia_50min, RNA-seq


title: A3777_01

description: mouse liver L28-4 treated with Vehicle_11 days post treatment

value: 11 days post treatment


title: A3777_77

description: mouse liver L18-4 treated with Vehicle_9 days post treatment

value: 9 days post treatment


title: A3777_65

description: mouse liver L40-4 treated with Vehicle_13 days post treatment


title: A3777_04

description: mouse liver L24-4 treated with Vehicle_10 days post treatment

value: 10 days post treatment


title: Sca1+ rep3


title: A3777_92

description: mouse liver L36-4 treated with Vehicle_12 days post treatment


title: C6_D6_N3

value: Day 6


title: Sca1- rep2


title: C6_D6_N2


title: A3777_61

description: mouse liver L42-4 treated with Vehicle_13 days post treatment


title: Sca1+ rep2


title: C6_D6_N1


title: A3777_45

description: mouse liver L23-4 treated with Vehicle_10 days post treatment


title: A3777_60

description: mouse liver L22-4 treated with Vehicle_10 days post treatment


title: Mus musculus, Ischemia_30min, RNA-seq, rep1

value: Kidney

value: IAA treatment


title: Mus musculus, Fourthpart, RNA-seq

value: Normal renal cells


title: Sca1+ rep1


title: A3777_67

description: mouse liver L30-4 treated with Vehicle_11 days post treatment


title: Mus musculus, Secondpart, RNA-seq


title: WT_D6_N3

value: Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs)


title: WT_D6_N2


title: Mus musculus, Thirdpart, RNA-seq


title: Mus musculus, Ischemia_30min, RNA-seq, rep2


title: WT_D6_N1


title: WT_D0_N1


title: Mus musculus, Firstpart, RNA-seq


title: A3777_37

description: mouse liver L29-4 treated with Vehicle_11 days post treatment

value: Vehicle


title: A3777_73

description: mouse liver L12-4 treated with Vehicle_8 days post treatment

value: 8 days post treatment


title: MIM-Astrocytes

city: La Jolla

first: LEI

last: SHI

state: CA

address: 10010 N Torrey Pines  Rd, GEL-B

institute: Salk Institute for Biological Studies

data_processing:
Illumina  software used for basecalling.
10X GENOMICS CellRanger v3.0.2 software to align reads to the 10x Genomics pre-built mm10 reference genome(https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build) for astrocytes, MIM-astrocytes and NSCs(neural stem cells) datasets with default setting for de-multiplexing to generate feature-barcode matrix. The single cell analysis R package Seurat v3.1.1(Butler et al., 2018) was used to read and analyze feature-barcode matrix following the steps: First, we filtered the cells that have unique feature counts according to quality control matrix plots and after filtering,  we have astrocytes 9055 cells, MIM-astrocytes 14911 cells and NSCs 8985 cells;
Genome_build: mm10 (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build)

source_name: MIM-Astrocytes

growth_protocol: NSCs were derived from murine embryonic cortex at 14.5 embryonic days (vaginal plug considered 0.5 days). Single cell suspension was maintained in Neurobasal medium supplemented with 1X B27 and 20ng/mL of rh-EGF and h-FGF2. Primary neurospheres appeared after 6 days of culture and were used only during the first 3 passages. Cultures for NSCs were seeded at 200,000 cell/mL and maintained on standard conditions.Astrocyte cultures. Astrocytes were derived from cortical tissues postnatal or differentiated from dissociated neurospheres after a second or third passage, as described ahead. For postnatal astrocytes, cortices were isolated from P4 mice pups to get single cells and were plated as described by Schildge et al., (2013). After getting confluence the cultures were sorted with Anti-GLAST (ACSA-1) Microbead kit according manufacturer instructions. For inducing differentiation from NSCs, single cells derived from neurospheres were exposed to astrocyte media. In both cases, cells were plated over pre-treated Poly-L-Lysine plates or Poly-D-Lysine glass-coverslips using Astrocyte Differentiation Medium composed by DMEM-F12 with 10% heat inactivated FBS, 1X B27, and 1X Glutamax. Media was replaced every other day until reach a mature astrocytic phenotype corroborated by immunocytochemistry.  Neuronal cultures. Primary neurons were obtained from the cortex of E14.5 ICR mice brains. Brain dissection was performed in a cold solution of 2% glucose in PBS. Then, tissue was trypsinized and the suspension was transferred across a 40μm cell strainer to get a single cell suspension. Cells were plated in a ratio of 800,000 cells per each 22 mm poly-D-lysine coverslip with Neuron differentiation medium containing: Neurobasal media supplemented 1X B27 and 1X Glutamax. Cultures were maintained on standard conditions. Half volume of culture media was replaced every other day. In previous studies (Suzuki et al., 2016 and 2019), we tracked the disappearance of the proliferative neuronal progenitors present in the primary culture by 10μM EdU-pulses every day after plating and we found that 5 days after culture, the percentage of EdU+ cells was reduced to basal levels. We consider neurons at this time point as post-mitotic.  Primary cell cultures of adult brain tissues. Cerebella from 18.5 months old adults were dissociated and trypsinized and the cell suspension derived was filtered across 70μm cell strainer. Cells were plated in dishes coated with poly-L-lysine using Astrocyte Differentiation Media, as described for astrocyte cultures. Cells were passaged when they reached confluence of 90-100 % in a 1:3 ratio. Cultures were used at the passage 4 to 9.  Glioblastoma culture. Tumor cells obtained from mouse glioblastoma multiforme–like tumors (mice ID 005) were kindly donated by Mark Schmitt (Marumoto et al., 2009). The cells were grown in DMEM supplemented with 1X N2, 20ng/mL rhEGF, 20ng/uL FGF2. Cultures were maintained on standard conditions.

extract_protocol: Single-cell suspensions were collected by harvesting cell cultures by trypsinization. Cells were washed into 4°C PBS and pelleted by spinning at 300g; for 5 min at 4°C, the supernatant was discarded. This wash step was repeated two more times. After final washing 200 μL of cold PBS were added to 1x10^6 cells. For cell fixation20 800 μL of methanol were added dropwise and the samples were incubated for 30 min at -20 °C, then stored at -80 °C until further processing. Fixed cells were equilibrated on ice for 5 min and pelleted at 1,000g for 5 min 4°C. The supernatant was carefully removed, and cells were resuspended into 0.04 % BSA, 1 mM DTT, 0.2 U/mL RNase Inhibitor in 3X SSC buffer at approx 1000 cells/mL. Cells were processed for single-cell sequencing on a 10x genomics system according to the manufacturer's protocol. We use CellRanger v3.0.2 software to align reads to the 10x Genomics pre-built mm10 reference genome for astrocytes, MIM-astrocytes, and NSCs (Neural Stem Cells) datasets with the default setting for de-multiplexing to generate feature-barcode matrix.

treatment_protocol: Cell cultures seeded on adherent conditions were kept on their respective differentiation media until reach a mature phenotype. When cultures reached 80-90% confluence, the differentiation media was removed, cells were washed twice with PBS and the media was replaced with MIM. In all cases, from the same batch of each cell culture, a control culture was also washed with PBS but maintained with their own differentiation media along all the time of the treatment. Cells in this schema, were fed every other day. The composition of MIM includes up to 6 metabolites (details of the combinations used are specified in figure legends) including Methionine, Threonine, Glycine, Putrescine, S-adenosylmethionine and Cysteine, which are dissolved in a base medium (BM) composed by DMEM-F12 plus Neurobasal in ratio 1:1, supplemented with 1X B27, 1X N2. Due to the absence of serum, either the growth factor FGF2 (20ng/mL) or reduced concentrations of serum, were used according cell type (FGF2 was added in cultures of chondrocytes, astrocytes, neurons; while it didn’t support the viability in myoblasts, where 2% of serum was used instead. Similarly, in human fibroblasts the reduction of serum was enough without any added cytokine to keep viable cultures). Cells were daily monitored to attest the change on morphology. In all cases, cells were collected on or before the fifth day after starting the MIM treatment (indicated in each specific case in the figure legend) for further analyses. Viability of cultures before at the time of collection was measured by trypan blue, and all cases above 85% viable cells were processed.

tag: strain

value: cortex

tag: age


title: Astrocyte

source_name: Astrocytes


title: ChrMED7

status: Public on Jan 22 2024

city: Uxbridge

first: Annabelle

last: Lewis

address: Kingston Lane

institute: Brunel University London

data_processing:
RNA-seq data was perfomed using open-source software package Tuxedo Suite. Tophat2 and Bowtie2 were used to map paired end reads to the reference Homo sapiens genome build GRCh38. GENCODE38 was used as the reference human genome annotation.  Aligned reads were filtered for quality using Samtools with the minimum selection threshold of 30. Transcripts assembly and quantification was done through Cufflinks, and differential expression analysis was achieved through the use of Cuffdiff software. Differential expression was expressed in the form of log2 fold change between sample and control.
Assembly: GENCODE38
Supplementary files format and content: Excel-based file includes differential expression for each sample using CUFFDIFF open source software

growth_protocol: Cells were maintained in Gibco Dulbecco's Modified Eagle Medium supplemented with 10% foetal bovine serum (FBS) (Sigma-Aldrich), and 1% penicillin streptomycin (Sigma-Aldrich). Cells were grown in an humified atmosphere at 37◦c with 5% CO2.

extract_protocol:
RNA was extracted (RNeasy, QIAGEN)
RNA-seq was performed by the Oxford Genomic centre

treatment_protocol: CHRDL2 overepression was induced by treatment with doxycyline 0.1 μg/ml (low), 1 μg/ml  (Med) or 10 μg/ml (High)

value: epithelial cell

value: CHRDL2 overexpression

value: Doxycyline medium

value: 7 days


title: ChrHIGH3

value: Doxycyline high

value: 3 days


title: ChrMED3


title: ChrHIGH7


title: ChrLOW5

value: Doxycyline low

value: 5 days


title: ChrMED5


title: ChrHIGH5


title: ChrDMSO13

value: WT

value: DMSO


title: ChrDMSO15


title: ChrLOW3


title: ChrDMSO17


title: VCaP cells, R1881+Daro+Copa, 48h, rep2

city: Berlin

first: Bernard

last: Haendler

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing:
FASTQ reads were mapped via STAR aligner to the human genome GRCh38 and quantified with RSEM (v1.3.0; University of Wisconsin-Madison, Madison, WI, USA).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: VCaP

growth_protocol: Cells were routinely grown in the recommended medium in the presence of 10% (v/v) fetal bovine serum (Life Technologies, Carlsbad, CA) at 37°C and 5% CO2. Authentication was performed by the DSMZ using short tandem repeat DNA typing analysis.

extract_protocol:
Cells were lyzed and RNA was isolated using RNeasy columns with on-column DNA digestion, as described by the manufacturer
RNA library preparation was performed after mRNA purification using poly-T beads, as described by the manufacturer (TruSeq Stranded mRNA Kit; Illumina, San Diego, CA, USA).

treatment_protocol: Cells were stimulated with the synthetic androgen R1881 at a concentration of 0.1 nM after two days of starvation in medium supplemented with 10% charcoal-stripped fetal calf serum (cFCS). Combination treatments included 0.1 nM R1881 and 1 µM darolutamide, 0.1 nM R1881 and 100 nM copanlisib, or 0.1 nM R1881, 1 µM darolutamide and 100 nM copanlisib. RNA was extracted and profiled after treatment for 24 and 48 hours.

value: VCaP

value: human prostate cancer cell line


title: VCaP cells, R1881+Copa, 48h, rep1


title: VCaP cells, R1881+Daro+Copa, 48h, rep1


title: VCaP cells, R1881+Copa, 48h, rep3


title: VCaP cells, R1881+Copa, 48h, rep2


title: NSC

source_name: Neural Stem Cell


title: VCaP cells, R1881+Daro, 48h, rep1


title: VCaP cells, R1881, 48h, rep3


title: VCaP cells, R1881+Daro, 48h, rep2


title: VCaP cells, R1881+Daro, 48h, rep3


title: VCaP cells, R1881+Copa, 24h, rep3


title: VCaP cells, R1881+Copa, 24h, rep2


title: A3777_26

description: mouse liver L16-4 treated with Vehicle_9 days post treatment

tag: agent

tag: time point

value: 9 days post treatment


title: VCaP cells, R1881+Daro+Copa, 24h, rep1

tag: cell line


title: VCaP cells, R1881+Daro+Copa, 48h, rep3


title: VCaP cells, R1881, 48h, rep1


title: VCaP cells, DMSO, 48h, rep1


title: VCaP cells, R1881+Daro+Copa, 24h, rep2


title: VCaP cells, R1881+Daro+Copa, 24h, rep3


title: VCaP cells, DMSO, 48h, rep2


title: VCaP cells, DMSO, 48h, rep3


title: VCaP cells, R1881+Copa, 24h, rep1


title: VCaP cells, R1881+Daro, 24h, rep3


title: VCaP cells, R1881, 48h, rep2


title: VCaP cells, R1881+Daro, 24h, rep1


title: VCaP cells, R1881, 24h, rep3


title: VCaP cells, R1881+Daro, 24h, rep2


title: VCaP cells, DMSO, 24h, rep3


title: VCaP cells, DMSO, 24h, rep2


title: VCaP cells, DMSO, 24h, rep1


title: PSC043

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

institute: Christian-Albrechts Universität zu Kiel

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Pipeline rnaseq v1.3 https://zenodo.org/record/2610144
Alignment with STAR v2.6.1d
Feature counting with FeatureCounts from the subread package v1.6.4
for more details, see pipeline documentation
Assembly: GRCh37
Supplementary files format and content: csv: Comma-separated values of raw feature counts results

source_name: Whole blood

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in all samples. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

tag: tissue

value: Whole blood

tag: disease

value: PSC

value: female

tag: years since_psc_diagnosis

tag: sequencing plate


title: PSC042

value: male


title: VCaP cells, R1881, 24h, rep2

tag: cell type

tag: treatment


title: PSCUC176

value: PSCUC

tag: Sex


title: PSCUC177


title: VCaP cells, R1881, 24h, rep1


title: A3777_78

description: mouse liver L17-4 treated with Vehicle_9 days post treatment

value: Vehicle


title: A3777_59

description: mouse liver L5-4 treated with Vehicle_7 days post treatment

value: 7 days post treatment


title: A3777_72

description: mouse liver L10-4 treated with Vehicle_8 days post treatment

value: 8 days post treatment


title: Control317

value: Control


title: Control319


title: PSC039


title: Control320


title: PSCUC170


title: PSCUC168


title: Control316


title: PSCUC166


title: PSC041


title: PSC040


title: PSCUC175


title: PSCUC169


title: PSC038


title: PSCUC164


title: Control318


title: PSCUC173


title: PSCUC174


title: PSCUC172


title: A3777_09

description: mouse liver L11-4 treated with Vehicle_8 days post treatment


title: PSCUC163


title: PSCUC171


title: A3777_64

description: mouse liver L6-4 treated with Vehicle_7 days post treatment


title: PSCUC167


title: PSCUC165


title: PSCUC162


title: PSC036


title: PSCUC160


title: PSC035


title: PSCUC159


title: PSCUC158


title: PSCUC156


title: PSCUC153


title: PSC033


title: PSC034


title: PSCUC155


title: PSCUC154


title: Control311


title: Control309


title: Control314


title: PSC037


title: Control312


title: Control313


title: PSCUC152


title: PSCUC150


title: PSCUC149


title: PSCUC148


title: PSCUC161


title: PSC032


title: PSCUC147


title: PSCUC157


title: Control310


title: PSC031


title: PSCUC146


title: Control315


title: PSCUC151


title: PSC029


title: PSCUC145


title: PSC030


title: PSCUC144


title: PSCUC139


title: PSC028


title: PSCUC141


title: PSCUC140


title: PSCUC143


title: Control307


title: Control306


title: PSCUC135


title: PSCUC133


title: PSCUC136


title: PSCUC142


title: PSCUC138


title: Control304


title: PSCUC132


title: PSCUC131


title: Control305


title: PSC026


title: PSC027


title: PSCUC128


title: PSCUC129


title: PSCUC127


title: Control308


title: PSCUC126


title: PSCUC137


title: PSCUC124


title: PSCUC123


title: PSCUC121


title: PSCUC130


title: PSCUC120


title: PSC024


title: PSCUC119


title: Control303


title: Control302


title: PSCUC114


title: PSCUC112


title: PSCUC113


title: PSCUC117


title: PSCUC116


title: PSCUC118


title: PSCUC115


title: Control298


title: PSCUC110


title: Control297


title: Control300


title: Control296


title: PSCUC111


title: Control293


title: PSC025


title: Control294


title: Control301


title: PSC023


title: PSCUC109


title: Control292


title: PSCUC107


title: PSCUC105


title: PSCUC106


title: PSCUC103


title: PSCUC102


title: PSCUC104


title: PSCUC125


title: Control299


title: PSCUC095


title: PSCUC099


title: PSCUC098


title: PSCUC097


title: PSCUC101


title: PSCUC100


title: PSC021


title: PSCUC094


title: PSCUC092


title: PSCUC091


title: PSCUC088


title: Control291


title: PSCUC089


title: PSCUC090


title: PSCUC108


title: Control290


title: Control287


title: Control289


title: Control285


title: Control284


title: Control288


title: PSCUC093


title: PSC020


title: Control286


title: Control279


title: Control281


title: PSCUC086


title: Control283


title: PSC019


title: PSCUC085


title: Control280


title: Control295


title: PSCUC082


title: PSCUC081


title: PSCUC080


title: PSC017


title: PSC016


title: PSC015


title: Control282


title: PSCUC087


title: PSCUC079


title: PSCUC076


title: PSCUC077


title: PSCUC078


title: PSCUC075


title: PSC018


title: PSCUC074


title: PSCUC071


title: PSCUC084


title: PSCUC069


title: PSCUC073


title: PSCUC070


title: PSCUC068


title: PSCUC067


title: PSCUC066


title: PSCUC083


title: PSCUC065


title: ChrLOW7

value: epithelial cell

tag: genotype

value: CHRDL2 overexpression

value: 7 days


title: PSCUC063


title: PSCUC062


title: PSCUC064


title: PSC013


title: PSCUC072


title: PSCUC054


title: PSCUC059


title: PSCUC058


title: PSCUC060


title: PSCUC056


title: PSCUC055


title: PSCUC057


title: PSC014


title: PSCUC051


title: PSCUC050


title: PSCUC053


title: PSCUC052


title: Control277


title: PSCUC049


title: PSC012


title: Control278


title: PSCUC048


title: PSCUC061


title: PSC011


title: PSCUC046


title: PSCUC044


title: PSC010


title: PSCUC042


title: PSCUC043


title: Control271


title: Control275


title: Control273


title: Control274


title: Control276


title: PSCUC096


title: Control270


title: Control269


title: PSCUC122


title: PSCUC045


title: Control268


title: PSCUC047


title: PSCUC041


title: Control266


title: PSC009


title: PSCUC037


title: PSCUC039


title: PSCUC040


title: Control267


title: PSCUC038


title: PSCUC036


title: PSCUC035


title: PSC022


title: PSCUC034


title: PSCUC032


title: PSCUC031


title: PSCUC033


title: PSCUC029


title: PSC008


title: PSCUC030


title: PSCUC024


title: PSCUC027


title: PSCUC026


title: PSCUC025


title: PSCUC023


title: PSCUC017


title: PSC003


title: PSCUC022


title: PSC006


title: PSCUC019


title: PSCUC028


title: PSCUC021


title: PSC005


title: PSCUC018


title: PSCUC020


title: PSCUC015


title: 3BKO_k27me3_chip_rep_2_ChIPseq

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
All ChIP-seq experiments were processed previously described (Masalmeh et al., 2021, PMID: 33514701). Read quality was checked using FASTQC (v0.11.4, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), with low quality reads and adaptors removed using TrimGalore with default settings (v0.4.1). Reads were aligned to hg38 using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 --no-unal) (Langmead and Salzberg, 2012, PMID: 22388286). For paired end data, additional settings were used during alignment to remove discordant reads: --no-mixed –nodiscordant -X 1000. ChIP-Rx-seq reads were aligned to a combination of hg38 and dm6 genomes. Multimapping reads excluded using SAMtools (v1.6, with settings: -bq 10) (Li et al., 2009) and PCR duplicates excluded using SAMBAMBA (v0.5.9) (Tarasov et al., 2015, PMID: 25697820). For T7 ChIP-Rx-seq UMIs were used for de-duplication instead of SAMBAMBA. We first extracted UMIs from the appropriate read and placed them in the read FASTQ headers using UMI tools extract (v1.0.0 and setting: --bc-pattern=NNNNNNNNNNN). Then deduplication was performed using the UMI tools dedup function (v1.0.0 and setting: --paired). Tracks for visualisation of histone ChIP-seq were generated using Deeptools (v3.2.0) (Ramirez et al., 2016, PMID: 27079975). Counts per million normalised tracks were generated using the bamCoverage function (settings: --normalizeUsing CPM) with the default bin size of 50 bp. The mean of replicate tracks and normalisation over the input was calculated using the bigwigCompare function (settings: --operation mean). For the single-ended H3K36me3 ChIP-seq, the estimated fragment length of 150 bp was used. For the other paired-end experiments the actual fragment size was used.
Assembly: hg38
Supplementary files format and content: Processed data files are bigWig files generated by normalisation over input and from the mean of the two replicates as described under data processing.

source_name: HCT116 with knocked out DNMT3B

growth_protocol: HCT116 and DNMT3B cells were gifts from B. Vogelstein (Rhee et al 2002 PMID: 11932749). Cells were cultured in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Life technologies) and penicillin-streptomycin antibiotics at 140 and 400 µg/ml respectively.

extract_protocol:
ChIP-seq was performed as previously described (Masalmeh et al., 2021, PMID: 33514701). For T7-DNMT3B ChIP-Rx-seq experiments, 1×107 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS for 8 min at room temperature. Crosslinked cells were lysed for 10 min on ice in 50 μl of lysis buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500 μl. As prolonged sonication caused T7-DNMT3B degradation, chromatin was fragmented using Benzonase (Pchelintsev et al., 2016, PMID: 26821228): samples were sonicated on ice with Soniprep 150 twice for 30 s to break up nuclei; then 200 U of Benzonase Nuclease (Sigma) and MgCl2 (final concentration 2.5 mM) were added and samples were incubated on ice for 15 min. The reaction was blocked by adding 10 μl of 0.5 M EDTA pH 8. Following centrifugation for 30 min at 18,407 g at 4 °C, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A Dynabeads (Invitrogen) previously coupled with 10 μl of T7-Tag antibody per 1×107 cells in blocking solution (1x PBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 °C. Beads were then washed for 10 min at 4 °C with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1 M NaHCO3, 1% SDS) for 15 min at 37 °C. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300 mM respectively, and immunoprecipitations were incubated at 65 °C overnight. Samples were then incubated at 37 °C for 1 h after addition of 2 μl of RNase Cocktail Enzyme Mix (Ambion). Then 40 μg of Proteinase K (Roche) were added, followed by 2 h incubation at 55 °C. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN). For ChIP-Rx-seq of endogenous T7-DNMT3B and ectopic T7-DNMT3B expressed in DNMT3B KO cells, 20 μg of Spike-in chromatin (ActiveMotif 53083) was added to each sample after sonication. 2 μl of spike-in antibody per sample (ActiveMotif 61686) was also added in a ratio 1:5 versus the T7 antibody. A similar protocol was used for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq experiments, except: 0.5×107 cells were harvested and crosslinked with 1% methanol-free formaldehyde in PBS for 5 min at room temperature. For H3K36me3 ChIP-Rx-seq crosslinked Drosophila S2 cells were spiked into samples before sonication at a ratio of 20:1 human to Drosophila cells. Following nuclei rupture by sonication on ice with Soniprep 150, chromatin was fragmented using Bioruptor Plus sonicator (Diagenode) for 40 cycles (30 s on/30 s off on high setting at 4 °C). 2 μl /1×106 cells of the following antibodies were used for immunoprecipitations: H3K4me3 (EpiCypher 13-00041), H3K9me3 (Active Motif 39161), H3K27me3 (Cell Signaling Technology C36B11) and H3K36me3 (Abcam ab9050).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions. NEBNext Multiplex Oligos for Illumina (NEB) barcode adapters were used. Specifically, Illumina Index Primers Set 1 (E7335) for endogenous T7-DNMT3B and H3K36me3, and Unique Dual Index UMI Adaptors DNA Set 1 (E7395) for the other libraries.  For histone modifications ChIP-seq, adapter-ligated DNA was size selected for an insert size of 150 bp using Agencourt AMPure XP beads. Libraries were quantified using the Qubit dsDNA HS or BR assay kit and assessed for size and quality using the Agilent Bioanalyser. Endogenous T7-DNMT3B and H3K36me3 ChIP-Rx-seq libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75 bp paired end reads, DNMT3B or 75 bp single end reads, H3K36me3). The other ChIP-seq libraries were sequenced using the NextSeq 2000 P3 (50 bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed by the Edinburgh Clinical Research Facility.

tag: cell line_background

value: colorectal cancer cell line

value: DNMT3B KO

tag: chip antibody


title: PSCUC014


title: 3BKO_k27me3_chip_rep_1_ChIPseq

value: H3K27me3 (Cell Signaling Technology C36B11)


title: PSCUC013


title: Control265


title: PSC002


title: PSC007


title: 3BKO_k9me3_k27me3_input_rep_2_ChIPseq

description:
3BKO_k9me3_norm_mean_ChIPseq.bigWig
3BKO_k27me3_norm_mean_ChIPseq.bigWig

value: none (input)


title: PSCUC012


title: 3BKO_k9me3_chip_rep_2_ChIPseq

value: H3K9me3 (Active Motif 39161)


title: PSCUC016

value: Whole blood


title: PSC004

value: PSC


title: PSCUC010

value: female


title: PSCUC009

value: male


title: 3BKO_k9me3_k27me3_input_rep_1_ChIPseq


title: PSCUC011

value: PSCUC


title: Control264


title: PSCUC006


title: Control262


title: 3BKO_k9me3_chip_rep_1_ChIPseq


title: PSCUC008


title: Control263


title: Control260


title: 3BKO_k4me3_input_rep_1_ChIPseq


title: PSC001


title: 3BKO_k4me3_chip_rep_1_ChIPseq

value: H3K4me3 (EpiCypher 13-00041)


title: 3BKO_k4me3_input_rep_2_ChIPseq


title: 3BKO_k4me3_chip_rep_2_ChIPseq


title: Control261


title: Control257


title: Control256


title: Control258


title: PSCUC007


title: Control255


title: Control254


title: Control252


title: Control253


title: Control259


title: 9 NBW post bed rest

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

hyb_protocol: Hybridization was performed at Bioneer (Hørsholm, Denmark).Each labelled sample was hybridized to miRCURY LNA miRNA arrays v. 11 (lot numbers; 31004.01, 31004.04, 31060.03, 31060.04 and 31060.07; Exiqon, Vedbæk, Denmark) in a HS-400-Pro microarray hybridization station (Tecan, Grödig, Austria) according to the manufacturer’s instructions.

scan_protocol: Array scanning and image analysis including flagging of bad quality spots were done at Exiqon.

data_processing: Data was processed using Limma. Background correction was performed using norm exp with offset=0. Between array normalization was performed using quantile. Data was log2 transformed.

source_name: NBW_post bed rest

label_protocol: Labelling was performed at Bioneer (Hørsholm, Denmark). For each sample, total RNA was labelled with Hy3 using the miRCURY labelling kit (Exiqon, Vedbaek, Denmark).

extract_protocol: Biopsies were snap-frozen in liquid nitrogen and stored at −80°C subsequently. TRI reagent (Sigma-Aldrich, St. Louis, MO) was used for isolation of total RNA from the muscle biopsies. The quantity of RNA was measured by spectrophotometer, and the integrity of the RNA used for microarray analysis was assessed by the Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay Kit (Agilent Technologies, Wokingham, Berkshire, UK).

treatment_protocol:
Intervention protocol: 56 healthy young males were subjected to nine days of bed rest and subsequently four-weeks endurance-training program. Individuals were divided into three groups: normal birth weight (NBW, n=20) and two groups with predisposition to type 2 diabetes mellitus (T2DM); individuals born with low birth weight (LBW, n=19) and first degree relatives (REL, n=11) to patients with Type 2 Diabetes
Skeletal muscle biopsies from vastus lateralis were sampled with a Bergstrom needle using suction and local anaesthesia (1% lidocaine) at baseline, after bed rest and after retraining.

tag: subject status

value: healthy young male

tag: group

value: NBW

value: skeletal muscle

tag: visit

value: post bed rest


title: 7 LBW post bed rest

source_name: LBW_post bed rest

value: LBW


title: Control250

value: Control

tag: age


title: Control251


title: Control247


title: Control246


title: Control245


title: Control272


title: 47 LBW post bed rest


title: 48 LBW post bed rest


title: Control248


title: 48 LBW baseline

value: baseline


title: 5 NBW baseline


title: 7 LBW baseline


title: 46 LBW baseline


title: 5 NBW post bed rest


title: 46 LBW post bed rest


title: 6 NBW post bed rest


title: 6 NBW baseline


title: 5 NBW retraining

value: retraining


title: 47 LBW baseline


title: Control249


title: PSCUC005


title: PSCUC004


title: 45 LBW post bed rest


title: Control244


title: PSCUC003


title: 45 LBW baseline


title: PSCUC002


title: PSCUC001


title: UC494

value: UC


title: 44 LBW post bed rest


title: 43 LBW post bed rest


title: 44 LBW baseline


title: UC495


title: UC489


title: 43 LBW baseline


title: UC491


title: 42 NBW retraining


title: UC487


title: UC488


title: UC485


title: UC486


title: 42 NBW post bed rest


title: UC483


title: UC484


title: 4 NBW post bed rest


title: 4 NBW baseline


title: 39 LBW baseline


title: 38 LBW post bed rest


title: UC482


title: UC493


title: 38 LBW baseline


title: 36 NBW retraining


title: UC490


title: 40 LBW post bed rest


title: 42 NBW baseline


title: UC492


title: 40 LBW baseline


title: 39 LBW post bed rest


title: 36 NBW post bed rest


title: UC481


title: UC479


title: UC480


title: 36 NBW baseline


title: UC478


title: UC477


title: 35 NBW retraining


title: 35 NBW baseline


title: UC475


title: 35 NBW post bed rest


title: 34 NBW retraining


title: UC474


title: UC473


title: UC472


title: 32 NBW retraining

description:
This sample was initially included in the analysis, but was deemed to be an outlier after QC analysis (pca analyses). Data were analysed again without this sample
32_1_3


title: UC470


title: UC469


title: UC471


title: UC468


title: 32 NBW post bed rest

description:
This sample was initially included in the analysis, but was deemed to be an outlier after QC analysis (pca analyses). Data were analysed again without this sample
32_1_2


title: 34 NBW baseline


title: UC476


title: 34 NBW post bed rest


title: UC465


title: UC466


title: 30 NBW baseline


title: UC467


title: 3 NBW post bed rest


title: 31 NBW retraining


title: 30 NBW post bed rest


title: 31 NBW post bed rest


title: 31 NBW baseline


title: 30 NBW retraining


title: UC463


title: UC462


title: UC464


title: 32 NBW baseline

description:
This sample was initially included in the analysis, but was deemed to be an outlier after QC analysis (pca analyses). Data were analysed again without this sample
32_1_1


title: UC461


title: UC459


title: UC460


title: UC458


title: UC457


title: 28 NBW baseline


title: 3 NBW baseline


title: UC455


title: UC456


title: UC454


title: UC453


title: 27 NBW retraining


title: 28 NBW retraining


title: 28 NBW post bed rest


title: UC451


title: 27 NBW baseline


title: UC449


title: 26 NBW post bed rest


title: 26 NBW baseline


title: 24 NBW retraining


title: 23 NBW baseline


title: 23 NBW post bed rest


title: 24 NBW baseline


title: 23 NBW retraining


title: UC448


title: UC447


title: 27 NBW post bed rest


title: 26 NBW retraining


title: 22 LBW post bed rest


title: 21 NBW retraining


title: 24 NBW post bed rest


title: UC450


title: UC446


title: UC445


title: UC444


title: UC452


title: UC442


title: UC443


title: UC441


title: 21 NBW post bed rest


title: UC440


title: 20 LBW baseline


title: UC439


title: UC438


title: 22 LBW baseline


title: UC435


title: UC437


title: 2 NBW post bed rest


title: UC436


title: 20 LBW post bed rest


title: 21 NBW baseline


title: UC433


title: UC432


title: UC431


title: UC430


title: 17 LBW baseline


title: 18 LBW post bed rest


title: 17 LBW post bed rest


title: 19 LBW post bed rest


title: UC429


title: 15 LBW baseline


title: UC427


title: UC428


title: 13 LBW post bed rest


title: UC426


title: 16 LBW post bed rest


title: 2 NBW baseline


title: 18 LBW baseline


title: 19 LBW baseline


title: UC434


title: UC425


title: UC424


title: 111 REL post bed rest

source_name: REL_post bed rest

value: REL


title: 112 REL post bed rest


title: 12 LBW post bed rest


title: 113 REL post bed rest


title: 13 LBW baseline


title: 111 REL baseline


title: 16 LBW baseline


title: UC423


title: UC422


title: UC421


title: 110 REL post bed rest


title: UC420


title: UC419


title: UC417


title: UC416


title: UC418


title: UC415


title: 109 REL post bed rest


title: 109 REL baseline


title: UC414


title: UC413


title: 107 REL baseline


title: UC412


title: 110 REL baseline


title: 107 REL post bed rest


title: 108 REL post bed rest


title: UC410


title: UC411


title: 105 REL post bed rest


title: UC409


title: 102 REL post bed rest


title: 102 REL baseline


title: UC408


title: 101 REL baseline


title: 101 REL post bed rest


title: 108 REL baseline


title: 105 REL baseline


title: UC405


title: UC404


title: UC403


title: 10 LBW post bed rest


title: UC402


title: 1 NBW post bed rest


title: UC400


title: 1 NBW baseline


title: UC401


title: UC399


title: UC398


title: Cardiac leukocytes, UTY, scATAC

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

data_processing:
fastq files were generated by cellranger-arc mkfastq
sequencing results were aligned to the mm10 reference genome using cellranger-arc count
datasets from Control and UTYGT immune cells were combined using cellranger-arc aggr
Assembly: mm10
Supplementary files format and content: h5 data format for gene expression - cellranger-arc aggr output
Supplementary files format and content: fragments table for atac data - cellranger-arc aggr output

extract_protocol:
Nuclei were isolated from single cell suspensions by washing once in Cell Buffer (PBS with 0.4% BSA), pelleting and resuspending in Lysis Buffer (10 mM Tris-HCl pH 7.4, Sigma Cat. #T2194l; 10 mM NaCl, Sigma Cat. #59222C; MgCl2, Sigma Cat #M1028; 0.1% Tween-20; 0.1% Nonidet P40 Substitute, Sigma Cat. #74385; 0.01% Digitonin, Thermo Fisher Cat. #BN2006; 1% BSA, MACS Cat. #130-091-376; in nuclease-free water) for 3 min on ice, washed once in Wash Buffer (same as Lysis Buffer without Nonident P40 Substitute or Digitonin), and resuspended in Nuclei Buffer (10x Genomics, Cat. #PN-2000153).
Nuclei samples were processed for single-cell multiomics library preparation using the Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression Kit from 10X Genomics

value: Heart

value: Leukocytes

value: UTY BMT


title: Cardiac leukocytes, UTY, scRNA

molecule: nuclear RNA


title: UC397

value: Whole blood


title: Cardiac leukocytes, control, scATAC

value: CT BMT


title: UC407

value: male


title: PSCUC134

value: PSCUC


title: Cardiac leukocytes, control, scRNA


title: UC406


title: UC393

value: female


title: Hematopoietic stem cells, Fc-JAG1, embryo 3

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: RNA-seq

data_processing:
Sequence reads were trimmed to remove Clontech SMARTer IIA oligo (AAGCAGTGGTATCAACGCAGAGTAC) 5’ presence with cutadapt (v4.2). Default parameters were used except for a maximum 5% error rate and no indels allowed.
Trimmed reads were aligned to reference genome with STAR aligner tool (v2.7.8). STAR was executed with default parameters except for (i) the number of allowed mismatches was set to 1 and (ii) short reads consideration was relaxed to 50% of read length.
Uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software (v2.0.1) with gene as feature.
Raw counts matrix was imported into R Statistical software (v4.2.1). Prior to statistical analysis, those genes with less than 10 raw counts in at least two replicates from the same condition were removed.
For visualization purposes, counts were normalized by variance-stabilizing transformation method using local fit Type as implemented in DESeq2 R package (v1.38.3)
Assembly: mm10
Supplementary files format and content: Tab-separated value file: RNAseq_Raw_counts.txt: nascent RNAseq.Raw expression levels for each gene (55,487 rows) in each individual sample (7 columns) as calculated using featureCounts. This data is prior to conducting any pre-filtering step.
Supplementary files format and content: Tab-separated value file: RNAseq_Raw_Filtered_counts.txt: nascent RNAseq.Raw expression levels after pre-filtering low expressed genes (see processing steps). This matrix contains 10,311 genes (rows) per 7 columns (samples).
Supplementary files format and content: Tab-separated value file: RNAseq_Norm_Filtered_counts.txt. Normalized expression levels including the expression of 10,311 genes (rows) per 7 samples (columns). Normalization carried out with VST from DESeq2 (v1.38.3)

source_name: Hematopoietic stem cells

growth_protocol: 4 hrs in vitro culture in methyl-celluose with growth factors

extract_protocol:
Cells were processed with SuperScript™ IV Single Cell/Low Input cDNA PreAmp Kit for 14 cycles
RNA libraries for RNA-seq were prepared using Clontech SMARTer Library Prep Kit for low input material following manufacturer's protocols.

treatment_protocol:
AGM GFI1+IAHC (CD31+cKIT+GFI1+) was FACS purified and treated with 10mM of compound E (gamma-Secretase Inhibitor XXI,, Merk cat #565790) overnight.
The following morning, sample was washed, separated in sets of 300-400 cells and incubated for 4 hours in methylcellulose with the addition 0.3mM of EU (ethynyl Uridine,Thermo Fisher, cat #C10365) with 1ul DMSO,10mM of compound E or 4mg/ml of recombinant Fc-JAG1 (R&D Systems, Cat #599-JG).

tag: strain

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: Hematopoietic stem cells

tag: developmental stage

tag: time

value: 4hr treatment


title: UC395

tag: tissue


title: BALB/c wildtype_NT_1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression from WT mouse CXCL12-abundant reticular cells

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Mouse Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Brain microglia

label_protocol: We used the Applied Biosystems GeneChipTM 3' IVT Pico Kit (catlog n.: 902789) for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

growth_protocol: A20luc+GFP+ Cells were grown in RPMI-1640 media (10% FCS and 1% PenStrep) supplemented with 25µM Betamercaptoethanol.

extract_protocol: RNA was isolated using the picopure RNA Isolation kit according to the manufacturer's instructions

value: BALB/c

value: Microglia (CD11b+and CD45lo)

value: Brain

value: Wildtype

tag: protocol


title: UC396

tag: disease

value: UC


title: BALB/c wildtype_NT_4


title: Hematopoietic stem cells, Fc-JAG1, embryo 1

description: RNA-seq


title: Hematopoietic stem cells, CompE, embryo 2

description: RNA-seq

value: CompE


title: Hematopoietic stem cells, CompE, embryo 1

description: RNA-seq


title: UC391

tag: sequencing plate


title: BALB/c wildtype_ CAR Tc _4

tag: cell type

value: chimeric antigen receptor (CAR)


title: Hematopoietic stem cells, washed out, embryo 3

description: RNA-seq

tag: treatment

value: Washed out


title: UC389

tag: Sex


title: UC388


title: UC390


title: BALB/c wildtype_ CAR Tc _2

tag: genotype


title: Hematopoietic stem cells, washed out, embryo 1

description: RNA-seq


title: UC387


title: UC386


title: BALB/c wildtype_NT_3


title: UC394


title: UC385


title: UC384


title: Myofibers_scramble_3

city: San Diego

first: REYNA

last: HERNANDEZ-BENITEZ

state: California

address: 5510 MOREHOUSE DR, FLOOR 3

department: SDI

institute: ALTOS LABS INC.

data_processing:
Nextflow v 22.10.1 and nf-core/rnaseq v 3.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore v 0.6.7 in nf-core/rnaseq (parameter - Minimum number of trimmed reads below which samples are removed from further: 10000)
Trimmed sequence reads were mapped to GRCm39 using star v 2.7.10a and were quantified at the downstream BAM-level using salmon v 1.5.2 in nf-core/rnaseq (parameters - Minimum percentage of uniquely mapped reads below which samples are removed from further processing: 5)
The original BAM files generated by STAR/salmon were further processed with samtools v 1.15.1 to sort them by coordinate, for indexing, as well as to generate read mapping statistics in nf-core/rnaseq
picard v 2.27.4-SNAPSHOT were used to mark the duplicate reads identified amongst the alignments in nf-core/rnaseq
The sorted bam files were used transcript assembly and quantification using stringtie v 2.2.1
The nfcore/rnaseq created bigWig coverage files using bedtools v 2.30.0 and bedGraphToBigWig (ucsc v 377)
featureCounts (subread v 2.0.1) summarized the mapped read distribution over genomic features (parameters - group_type: gene_biotype, feature_type: exon) and then the nfcore/rnaseq used DESeq2 (bioconductor-deseq2 v 1.28.0) to normalize the read counts (parameters - Use vst transformation instead of rlog with DESeq2.)
Assembly: GRCm39
Supplementary files format and content: Binary version of a tab-delimited text file that contains sequence alignment data (BAM)

growth_protocol: C2C12 were differentiated in DMEM + 2% FBS

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

treatment_protocol:
In differentiated myofibers, the medium was supplemented with a combination of six metabolites related with 1C-network, named as 1C-MIM which stands for One-Carbon Metabolite Induced Medium
In differentiated myofibers, the medium was supplemented with a combination of six metabolites unrelated with 1C-network, named as scramble combination

tag: cell line

value: Myoblast differentiated

value: WT

value: Scramble-metabolite supplementation

value: Day 3


title: BALB/c wildtype_ CAR Tc _1


title: Myofibers_MIM_a_3

value: 1C-MIM supplementation


title: Myofibers_scramble_1


title: Myofibers_scramble_2


title: Myofibers_MIM_a_2


title: BALB/c wildtype_ CAR Tc _3


title: Myofibers_MIM_a_1


title: UC381

value: Whole blood

value: male


title: UC382


title: UC383


title: BALB/c wildtype_NT_2


title: Hematopoietic stem cells, washed out, embryo 2

description: RNA-seq

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: Hematopoietic stem cells


title: Myofibers_control_3

value: normal medium


title: UC380

value: female


title: Myofibers_control_2


title: Myofibers_control_1


title: UC377


title: UC379


title: 1C-MIM 4

data_processing:
Nextflow v 22.10.1 and nf-core/rnaseq v 3.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore v 0.6.7 in nf-core/rnaseq (parameter - Minimum number of trimmed reads below which samples are removed from further: 10000)
Trimmed sequence reads were mapped to GRCm39 using star v 2.7.10a and were quantified at the downstream BAM-level using salmon v 1.5.2 in nf-core/rnaseq  (parameters - Minimum percentage of uniquely mapped reads below which samples are removed from further processing: 5)
The original BAM files generated by STAR/salmon were further processed with samtools v 1.15.1 to sort them by coordinate, for indexing, as well as to generate read mapping statistics in nf-core/rnaseq
picard v 2.27.4-SNAPSHOT were used to mark the duplicate reads identified amongst the alignments in nf-core/rnaseq
The sorted bam files were used transcript assembly and quantification using stringtie v 2.2.1
The nfcore/rnaseq created bigWig coverage files using bedtools v 2.30.0 and bedGraphToBigWig (ucsc v 377)
featureCounts (subread v 2.0.1) summarized the mapped read distribution over genomic features (parameters - group_type: gene_biotype, feature_type: exon) and then the nfcore/rnaseq used DESeq2 (bioconductor-deseq2 v 1.28.0) to normalize the read counts (parameters - Use vst transformation instead of rlog with DESeq2.)
Assembly: GRCm39
Supplementary files format and content: Binary version of a tab-delimited text file that contains sequence alignment data (BAM)

source_name: Muscle

growth_protocol: C57BL mice were purchased from The Jackson Laboratory and the colony was maintained and expanded at both Salk Institute

extract_protocol:
RNA was harvested by Active Motif company
RNA libraries for RNA-seq were prepared by Active Motif company

treatment_protocol: Mice between 17-20-months-old for experiments for the old phenotype. All animals were weighed at the beginning and end of the intervention. The drinking solution was prepared from the stock of water provided by the animal facility, for both controls and supplemented animals. A volume of 150mL of water was provided every other day for each cage containing 5 mice maximum. The remaining volumes of control and supplemented water were measured every time before discarding the remaining volumes and the volume consumed was correlated to the number of mice present in each cage, to determine the drinking volume. The treated water supplementation was delivered in sterile red bottles for a period of one to three months. After these interventions, mice were habituated to walking around an open field test every other day for a week before the muscle injury in TA. But samples for RNA were collected from the same injured mice but from non-injured quadriceps.

value: Muscle


title: 1C-MIM 2


title: 1C-MIM 3


title: UC375


title: UC374


title: 1C-MIM 1


title: UC373


title: Control 5

value: control


title: UC371

value: UC


title: Control 4


title: UC372


title: Control 3


title: UC370


title: Control 2


title: Control 1


title: 1C-MIM 5


title: UC366


title: UC367


title: UC369


title: UC368


title: UC376


title: UC378


title: UC365


title: ATAC-seq_IMR90_Hypoxia_Raf_activated_rep1

city: Seoul

first: Insoo

last: Yoon

address: 163 Seoulsiripdaero, Dongdaemun-gu

department: Department of Life Science

country: South Korea

institute: University of Seoul

data_processing:
The qualities of ATAC-seq reads were checked using FastQC. Then the adapter sequences, low quality bases (base quality score <20) at the ends of the reads, and short reads (<20bp) were removed using Cutadapt.
The trimmed paired-end reads were aligned to the human reference genome (hg38) using Bowtie2. The maximum fragment length was extended to 1000bp and dovetailing of read pairs was allowed.
After the alignment, the mitochondrial DNA reads were removed and the properly paired reads of nuclear DNA were obtained with high mapping quality (MAPQ score 30) using Samtools. Duplicate reads were removed using Picard.
To visualize the read coverages, bigWig files were created using Deeptools bamCoverage with option --normalizeUsing RPKM.
Bam files were converted to BED format using Bedtools. Peaks were called using MACS2 with parameters --format BED --nomodel --shift -100 --extsize 200.
Assembly: hg38
Supplementary files format and content: bigWig (normalized ATAC-seq read coverage)
Supplementary files format and content: narrowPeak (Tn5 cutting site)

source_name: Lung

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin in humidified air containing 5% CO2 at 37ºC.

extract_protocol:
Cells were detached using trypsin and 100,000 cells were first harvested using hemocytometer. Cells were washed with 50 μl of cold PBS buffer, centrifuged 5 min at 500 × g, 4°C. Cell lysis was performed with 100 μl of cold lysis buffer, centrifuged 10 min at 500 × g, 4°C. 50,000 nuclei were counted and centrifuged 5 min at 500 × g, 4°C for the next analysis.
ATAC-seq libraries were prepared using a Tn5-Nextera DNA library prep kit. Transposed DNA was purified using the MinElute PCR Purification Kit. DNA fragments were then amplified by PCR using Nextera index primer 1 and 2 (Illumina) and tagmented DNA.

treatment_protocol:
Cells were incubated under hypoxic conditions in a Forma anaerobic incubator in an atmosphere of 5% CO2, 95% N2, and 0.5% O2.
IMR90 cells were infected with a retrovirus encoding △B-RAF:ER and treated with 4-hydroxy-tamoxifen (4-OHT).

value: Lung

value: fibroblast

value: Hypoxia, Raf-activated


title: ATAC-seq_IMR90_Hypoxia_Raf_activated_rep2


title: ATAC-seq_IMR90_Hypoxia_Raf_activated_rep3


title: ATAC-seq_IMR90_Hypoxia_Raf_activated_rep4


title: ATAC-seq_IMR90_Hypoxia_Raf_inactivated_rep4

value: Hypoxia, Raf-inactivated


title: UC363


title: ATAC-seq_IMR90_Hypoxia_Raf_inactivated_rep3


title: ATAC-seq_IMR90_Hypoxia_Raf_inactivated_rep2


title: UC362


title: ATAC-seq_IMR90_Hypoxia_Raf_inactivated_rep1


title: UC361


title: UC360


title: UC359


title: ATAC-seq_IMR90_Normoxia_Raf_activated_rep3

value: Normoxia, Raf-activated


title: ATAC-seq_IMR90_Normoxia_Raf_activated_rep4


title: UC358


title: ATAC-seq_IMR90_Normoxia_Raf_activated_rep2


title: UC356


title: ATAC-seq_IMR90_Normoxia_Raf_activated_rep1


title: UC364


title: ATAC-seq_IMR90_Normoxia_Raf_inactivated_rep2

value: Normoxia, Raf-inactivated


title: UC353


title: UC357


title: UC355


title: UC351


title: UC352


title: UC350


title: GL58_383_WN-S3-5_G23_Gfi1_pos_IAHC_S287

description:
SMART-Seq2
Not included in final analysis

data_processing:
Raw data was aligned to the reference mouse genome using STAR aligner tool (v2.7.3)
Gene counts were extracted from BAM files using HTSeq software (v0.9.1)
Python (v3.7.3) and scanpy (v1.4.4) for data pre-processing
As QC, cells with less than 2,500 expressed genes and less than 50,000 counts were discarded, and no more than 5% mitochondrial gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value file: scRNAseq_Cell_annotation.txt: cell sample metadata table. For each cell (row, 860 in total): cell full name, corresponding plate/well, embryo developmental stage, cell population, batch name, FACS index data for (in this order) DLL4, NOTCH2, CKIT, GFI1, CD41, NOTCH1, CD31, JAG1 and CD45. Additionally, for those cells passing the QC, UMAP coordinates and annotated cluster (Louvain method, see publication for details) are included.
Supplementary files format and content: Tab-separated value file: scRNAseq_Raw_counts.txt: full-length RNAseq (SMART-Seq2).Raw expression levels for each gene (46,170 rows) in each single cell (860 columns) as calculated using HTseq. This data is prior to conducting any QC.
Supplementary files format and content: Tab-separated value file: scRNAseq_Norm_counts_filtered.txt. Normalized expression levels after QC. Matrix comprises 30,362 rows (genes) per 775 columns (cells). Counts were normalized per cell with pp.normalize_total function from scanpy (target sum of 1e4) and values logarithmize with pp.log1p scanpy function.

source_name: AGM

growth_protocol: E10.5 and E11.5 AGMs were prepared for flow sorting

extract_protocol:
Single cells were sorted into well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol. Briefly, cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher).
Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems).

treatment_protocol: no treatments, only FACS staining

value: Hematopoietic cells

value: AGM

value: 6-8 weeks old

tag: population

tag: batch


title: GL58_384_WN-S3-5_H23_Gfi1_pos_IAHC_S288


title: GL58_381_WN-S3-5_G21_Gfi1_pos_IAHC_S285


title: ATAC-seq_IMR90_Normoxia_Raf_inactivated_rep1


title: UC349

value: Whole blood

value: male


title: GL58_382_WN-S3-5_J21_Gfi1_pos_IAHC_S286

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: ATAC-seq_IMR90_Normoxia_Raf_inactivated_rep3


title: GL58_380_WN-S3-5_I20_Gfi1_pos_IAHC_S284


title: GL58_379_WN-S3-5_H20_Gfi1_pos_IAHC_S283


title: UC348


title: GL58_378_WN-S3-5_G20_Gfi1_pos_IAHC_S282


title: UC346


title: UC345


title: UC344


title: GL58_377_WN-S3-5_F20_Gfi1_pos_IAHC_S281


title: ATAC-seq_IMR90_Normoxia_Raf_inactivated_rep4


title: 104 REL baseline

tag: subject status

value: healthy young male

tag: group

value: REL

value: skeletal muscle

value: baseline


title: UC354

value: UC

tag: age


title: GL58_376_WN-S3-5_J19_Gfi1_pos_IAHC_S280

tag: strain


title: UC343

value: female


title: UC342


title: GL58_373_WN-S3-5_G18_Gfi1_pos_IAHC_S277

tag: developmental stage


title: GL58_375_WN-S3-5_I19_Gfi1_pos_IAHC_S279


title: UC341


title: GL58_374_WN-S3-5_H19_Gfi1_pos_IAHC_S278


title: UC347


title: UC340


title: UC338


title: UC339


title: UC337


title: GL58_369_WN-S3-5_G08_Gfi1_pos_IAHC_S273


title: GL58_368_WN-S3-5_K07_Gfi1_pos_IAHC_S272


title: GL58_371_WN-S3-5_G11_Gfi1_pos_IAHC_S275


title: GL58_370_WN-S3-5_I08_Gfi1_pos_IAHC_S274


title: UC335


title: GL58_367_WN-S3-5_J07_Gfi1_pos_IAHC_S271


title: UC336


title: UC334


title: UC333


title: GL58_365_WN-S3-5_J06_Gfi1_pos_IAHC_S269


title: GL58_364_WN-S3-5_I03_Gfi1_pos_IAHC_S268


title: UC331


title: GL58_366_WN-S3-5_H07_Gfi1_pos_IAHC_S270


title: UC332


title: UC330


title: GL58_362_WN-S3-5_H01_Gfi1_pos_IAHC_S266


title: GL58_361_WN-S3-5_E23_Gfi1_HE_S265

value: Hemogenic endothelium cells


title: GL58_363_WN-S3-5_K02_Gfi1_pos_IAHC_S267


title: UC328


title: GL58_372_WN-S3-5_H12_Gfi1_pos_IAHC_S276


title: UC329


title: GL58_360_WN-S3-5_E05_Gfi1_HE_S264


title: GL58_359_WN-S3-5_F04_Gfi1_HE_S263


title: GL58_358_WN-S3-5_D04_Gfi1_HE_S262


title: UC392


title: GL58_356_WN-S3-5_F02_Gfi1_HE_S260


title: GL58_355_WN-S2-7_A22_Gfi1_HE_S259


title: UC324


title: GL58_354_WN-S2-6_B20_Gfi1_HE_S258


title: UC323


title: UC325


title: UC326


title: UC321


title: UC322


title: GL58_353_WN-S2-5_E19_Gfi1_HE_S257


title: GL58_352_WN-S2-4_D17_Gfi1_HE_S256


title: UC317


title: GL58_350_WN-S2-2_C15_Gfi1_HE_S254


title: GL58_351_WN-S2-3_C16_Gfi1_HE_S255


title: UC327


title: UC316


title: GL58_349_WN-S2-1_E14_Gfi1_HE_S253


title: UC315


title: GL58_191_WN-S3-5_J16_Gfi1_pos_IAHC_S383


title: UC319


title: UC318


title: UC314


title: GL58_192_WN-S3-5_I17_Gfi1_pos_IAHC_S384


title: GL58_190_WN-S3-5_I16_Gfi1_pos_IAHC_S382


title: UC313


title: GL58_189_WN-S3-5_H16_Gfi1_pos_IAHC_S381


title: GL58_357_WN-S3-5_C04_Gfi1_HE_S261


title: UC311


title: GL58_187_WN-S3-5_I15_Gfi1_pos_IAHC_S379


title: GL58_184_WN-S3-5_J13_Gfi1_pos_IAHC_S376


title: UC320


title: GL58_186_WN-S3-5_G15_Gfi1_pos_IAHC_S378


title: GL58_188_WN-S3-5_G16_Gfi1_pos_IAHC_S380


title: UC308


title: GL58_185_WN-S3-5_G14_Gfi1_pos_IAHC_S377


title: UC306


title: UC307


title: UC304


title: GL58_181_WN-S3-5_J12_Gfi1_pos_IAHC_S373


title: UC305


title: GL58_183_WN-S3-5_F13_Gfi1_pos_IAHC_S375


title: GL58_179_WN-S3-5_D22_Gfi1_HE_S371


title: GL58_180_WN-S3-5_C23_Gfi1_HE_S372


title: GL58_182_WN-S3-5_K12_Gfi1_pos_IAHC_S374


title: UC303


title: UC301


title: GL58_177_WN-S3-5_C16_Gfi1_HE_S369


title: UC300


title: UC312


title: GL58_176_WN-S3-5_A16_Gfi1_HE_S368


title: UC299


title: UC302


title: GL58_178_WN-S3-5_B20_Gfi1_HE_S370


title: UC298


title: GL58_174_WN-S3-5_B11_Gfi1_HE_S366


title: GL58_175_WN-S3-5_A12_Gfi1_HE_S367


title: UC309


title: UC310


title: UC297


title: UC296


title: UC295


title: GL58_171_WN-S3-5_F07_Gfi1_HE_S363


title: UC294


title: UC293


title: GL58_172_WN-S3-5_F09_Gfi1_HE_S364


title: UC292


title: UC291


title: UC290


title: GL58_167_WN-S2-1_C11_Gfi1_HE_S359


title: UC289


title: GL58_168_WN-S2-1_E13_Gfi1_HE_S360


title: GL58_165_WN-S2-1_F07_Gfi1_HE_S357


title: UC288


title: GL58_164_WN-S2-1_C07_Gfi1_HE_S356


title: UC287


title: GL58_162_WN-S2-1_D05_Gfi1_HE_S354


title: UC286


title: UC285


title: GL58_161_WN-S2-1_A04_Gfi1_HE_S353


title: GL58_173_WN-S3-5_B10_Gfi1_HE_S365


title: UC284


title: GL58_160_WN-S2-1_D02_Gfi1_HE_S352


title: UC283


title: GL58_170_WN-S3-5_E07_Gfi1_HE_S362


title: GL58_159_WN-S2-1_B02_Gfi1_HE_S351


title: UC281


title: GL58_158_WN-S2-1_D01_Gfi1_HE_S350


title: UC282


title: GL58_157_WN-S2-1_A01_Gfi1_HE_S349


title: GL58_166_WN-S2-1_D10_Gfi1_HE_S358


title: UC279


title: GL53_384_Plate1_c09_Gfi1_neg_IAHC_S192


title: UC277


title: GL53_381_Plate1_c15_Gfi1_neg_IAHC_S189


title: GL53_382_Plate1_c14_Gfi1_neg_IAHC_S190


title: GL53_380_Plate1_c19_Gfi1_neg_IAHC_S188


title: UC276


title: UC278


title: GL58_163_WN-S2-1_E05_Gfi1_HE_S355


title: UC274


title: GL53_378_Plate1_d08_Gfi1_neg_IAHC_S186


title: UC275


title: GL53_379_Plate1_d03_Gfi1_neg_IAHC_S187


title: UC273


title: UC272


title: UC280


title: GL53_376_Plate1_d21_Gfi1_neg_IAHC_S184


title: GL58_169_WN-S3-5_D07_Gfi1_HE_S361


title: UC270


title: GL53_375_Plate1_f02_Gfi1_neg_IAHC_S183


title: GL53_377_Plate1_d09_Gfi1_neg_IAHC_S185


title: UC271


title: GL53_373_Plate1_f05_Gfi1_neg_IAHC_S181


title: UC268


title: GL53_374_Plate1_f03_Gfi1_neg_IAHC_S182


title: UC269


title: GL53_383_Plate1_c13_Gfi1_neg_IAHC_S191


title: GL53_372_Plate4_a5_Gfi1_HE_S180


title: UC267


title: GL53_371_Plate4_a4_Gfi1_HE_S179


title: UC266


title: GL53_370_Plate4_a3_Gfi1_HE_S178


title: GL53_369_Plate4_a22_Gfi1_HE_S177


title: UC264


title: GL53_367_Plate4_l22_Gfi1_neg_IAHC_S175


title: GL53_368_Plate4_a18_Gfi1_HE_S176


title: UC262


title: UC261


title: GL53_366_Plate4_e14_Gfi1_HE_S174


title: GL53_365_Plate4_l21_Gfi1_neg_IAHC_S173


title: UC260


title: GL53_364_Plate4_l20_Gfi1_neg_IAHC_S172


title: GL53_363_Plate4_l17_Gfi1_neg_IAHC_S171


title: GL53_362_Plate4_l16_Gfi1_neg_IAHC_S170


title: UC259


title: UC257


title: UC255


title: GL53_359_Plate4_k22_Gfi1_neg_IAHC_S167


title: GL53_358_Plate4_l22_Gfi1_neg_IAHC_S166


title: GL53_361_Plate4_l14_Gfi1_neg_IAHC_S169


title: UC253


title: UC252


title: GL53_357_Plate4_c3_Gfi1_HE_S165


title: UC254


title: UC265


title: GL53_356_Plate4_l18_Gfi1_neg_IAHC_S164


title: UC263


title: GL53_354_Plate4_h2_Gfi1_pos_IAHC_S162


title: lib A NK

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The sequence reads were trimmed to remove a constant portion of the sgRNA sequences and mapped to the GeCKO v2 genome-wide CRISPR library with MAGeCK “count” module, which computes read counts for each sgRNA. We used MAGeCK “test” module to identify Daratumumab resistance regulators, for which targeting sgRNA were significantly enriched in the treated populations compared to the control untreated populations grown in parallel.
adaptor has been trimmed by flexbar
Assembly: hg19
Supplementary files format and content: The read count files returned from the MAGeCK
Library strategy: CRISPR screening

growth_protocol: H929 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
We extracted genomic DNA from each froup population by DNeasy Blood & Tissue Kits (Qiagen)
1 step PCR to construct the barcode-indexed sequencing library for each sample

treatment_protocol: No treatment

value: myeloma derived cell line

value: wildtype

value: NK+Daratumumab

tag: type

value: fastq


title: UC250

tag: tissue


title: GL53_353_Plate4_e2_Gfi1_HE_S161


title: PFG_DIP-seq_IP

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
DNBSEQ-G400RS sequencer
Sequence data were mapped onto P. berghei genome sequence (PlasmoDB, version 3) using BOWTIE2 software in default settings. Mapping data were analyzed using MACS2 peak-calling algorithm. Conditions for peak calling were FDR < 0.01.
Assembly: PlasmoDB, version 3
Supplementary files format and content: peak call
Library strategy: DIP-seq

organism: Plasmodium berghei

source_name: gametocyte

extract_protocol:
The recombinant AP2 domain of AP2-FG was prepared as a GST-fused protein. This recombinant GST-fused AP2 domain of AP2-FG and genomic DNA fragments were incubated at RT for 30 min in 100 μL of binding/washing buffer. The mixture was then incubated with 50 μL glutathione sepharose resin (Cytiva) at RT with rotation. Resin was washed three times with 150 μL of binding/washing buffer, and bound protein was eluted with 10 mM glutathione solution. Input genomic DNA fragments were also sequenced as a control.
Recovered DNA (5 ng) was used for library preparation.  Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems).

value: ANKA

value: wild type

tag: Stage

value: gametocyte

tag: fraction

value: IP


title: GL53_360_Plate4_k21_Gfi1_neg_IAHC_S168

value: Hematopoietic cells

value: AGM

value: 6-8 weeks old


title: UC256

value: Whole blood

tag: disease

value: male

tag: sequencing plate


title: GL53_352_Plate4_l1_Gfi1_neg_IAHC_S160

tag: cell type

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: lib_A baseline.

tag: treatment


title: PFG_DIP-seq_Input

tag: genotype

value: input


title: UC258

value: UC

tag: Sex

value: female


title: lib A control

tag: cell line

value: myeloma derived cell line

value: no treatment


title: GL53_351_Plate3_n23_Gfi1_neg_IAHC_S159

tag: population

tag: batch


title: UC251


title: shUBR5_DMSO_3

city: Guangzhou

first: Mei

last: Song

address: Zhongshan No.2 Road 1th, Nonglin Street

institute: Sun Yat-sen University

data_processing:
Base-calling was performed with the BGISEQ-500 software.
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were alignment to the reference genome, GRCh38.p13 using HISAT2 (v2.1.0).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: FPKM, TPM and read_count values for each sample and each gene

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (#RC112-01, Vazyme), according to manufacturer’s instructions.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads, then fragmented. Then cDNA were sythesized, added A and adaptor ligation, and put into PCR system. Finally, PCR products were circularized and single-stranded circle DNA molecules were replicated via rolling cycle amplificationa to generate a DNA nanoball (DNB), which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: UBR5 knockdown

value: DMSO


title: shUBR5_DMSO_1


title: shUBR5_Oxa_1

value: Oxaliplatin


title: H929 cells, sgKDM6A, bio rep2

data_processing:
The RNA-Seq data were processed following the VIPER pipeline
Raw reads were aligned to the human genome (hg38) by STAR
the differential gene expression analysis was performed by limma.
The differentially expressed genes (DEGs) were defined by the log of transformed fold change greater than 1 (log2(fold change)>1) and adjusted p value less than 0.05
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample …

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
1ug of RNA was used to make the libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: KDM6A KO


title: GL53_349_Plate3_l23_Gfi1_neg_IAHC_S157


title: H929 cells, sgKDM6A, bio rep1


title: shNC_Oxa_3

value: WT


title: GL53_350_Plate3_m23_Gfi1_neg_IAHC_S158


title: shUBR5_Oxa_2


title: shNC_Oxa_1


title: shUBR5_Oxa_3


title: GL53_355_Plate4_l7_Gfi1_neg_IAHC_S163


title: shUBR5_DMSO_2


title: shNC_Oxa_2


title: shNC_DMSO_3


title: GL53_348_Plate3_o22_Gfi1_neg_IAHC_S156


title: GL53_347_Plate3_m22_Gfi1_neg_IAHC_S155


title: shNC_DMSO_2


title: H929 cells, control, bio rep2

value: wildtype


title: H929 cells, control, bio rep1


title: GL53_346_Plate3_k22_Gfi1_neg_IAHC_S154

value: Hematopoietic cells


title: H929 cells, sgKDM6A, bio rep3


title: lib A_CD38_5%_low

data_processing:
The sequence reads were trimmed to remove a constant portion of the sgRNA sequences and mapped to the GeCKO v2 genome-wide CRISPR library with MAGeCK “count” module, which computes read counts for each sgRNA. We used MAGeCK “test” module to identify CD38 expression regulators, for which targeting sgRNA were significantly enriched in the sorted cell populations compared to the control unsorted populations grown in parallel.
Assembly: hg19
Supplementary files format and content: The read count files returned from the MAGeCK
Library strategy: CRISPR screening

value: 5% of cells with the lowest expression of CD38 were sorted


title: GL53_345_Plate3_j22_Gfi1_pos_IAHC_S153

value: AGM

value: 6-8 weeks old


title: GL53_344_Plate3_i22_Gfi1_pos_IAHC_S152


title: lib A_control


title: GL53_342_Plate3_g22_Gfi1_pos_IAHC_S150


title: CT-2

city: Chuo-ku, Kobe City, Hyogo

first: Kana

last: Uchiyama

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: gastrocnemius muscle

growth_protocol: Mice were maintained on a 12-hour light/dark cycle and allowed free access to food and water.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were subjected to restraint using 50 mL tubes for 3 hours every 4 days.

value: gastrocnemius muscle

value: muscle

value: wild type

value: Control_Day 4


title: R-3


title: R-1


title: GL53_343_Plate3_h22_Gfi1_pos_IAHC_S151

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: CT-1


title: R-2


title: GL53_341_Plate3_f22_Gfi1_pos_IAHC_S149