title: Pax7Low_f

city: Geneva

first: Thomas

last: Laumonier

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
The iGE3 Genomics Platform performed two independent analyses on each batch of samples. Reads were subjected to quality control using FastQC (Picard) and mapped using STAR program version 2.7.1b on the human gene (hg38). Sequences alignment and genes count were summarized using the Python software (HTSeq, v.0.9.1). Low-expressing genes were filtered independently and we then assemble the different sets of data from the analyzes of the different samples.
Unsupervised analyses by Principal Component Analysis (PCA) and Supervised analyses were conducted in R program version 4.0.2 on log2 transformed gene expression. Differential expression analysis was then performed with the R package edgeR. Data were processed with R language and graphs were produced with R language.
Data were analyzed using R program version 4.0.2 and are expressed as log2 fold change (Log2FC), adjusted p-value. The lists of genes differentially expressed between Pax7High and Pax7Low or Pax7High and myoblasts were obtained as follows. A cut-off at p<0.01 was applied with a Log2FC of 0,5. In addition, the Log2FC was required to be above 0.5 for a least 4 donors.
Pathway analysis was performed using the Reactome database and hypergeometric test to attest to enrichment p-value.
Assembly: hg38
Supplementary files format and content: assay_counts.tsv -Tab seperated value table with number of reads per gene
Supplementary files format and content: assay_cpm.tsv - Tab seperated value table with normalized number of reads per gene (DESeq2)
Supplementary files format and content: library_metadata.tsv - Tab seperated value table with library metadata

source_name: human myogenic cells

extract_protocol:
Human myoblasts and human MuRC were generated from six different biological replicates (N=6) and stained for Pax7 as previously described (Pax7 intra-cellular staining) in the presence of RNAse inhibitor (l/500, RNasin® Ribonuclease Inhibitors, Promega) in all buffers from the fixation step to the cell sorting step. Human myoblasts, MuRC-Pax7High and MuRC-Pax7Low subpopulations were then prepared for bulk RNA-sequencing according to the following steps: (1) flow cytometry cell sorting of human myoblasts Pax7+, of MuRC-Pax7High subpopulation and of MuRC-Pax7Low subpopulation (200,000 cells per condition) using a BD FACS Aria2 collected in FACS tube containing RNAse inhibitor and RNA later (2) RNA was extracted using either a high pure FFPE RNA Isolation Kit (Roche, cat#06650775001) or an RNeasy FFPE kit (Qiagen). Both kits were used following the manufacturer’s protocol and kept at -80°C until use (3) RNA concentrations were obtained using Qubit RNA assay (Life Technologies, New York, USA). The quality of the RNA (RNA integrity number) was determined on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). (4) Sequencing was performed on the HiSeq 4000 unit (Illumina, San Diego, CA) using Illumina TruSeq RNA Exome (previously known as the Illumina TruSeq RNA Access Library Prep). Samples were sequenced as single-end 75 bp, and an average of 21,769,230 reads were generated for each sample. RNA-seq experiments were performed at the iGE3 Genomics Platform of the University of Geneva (http://www.ige3.unige.ch/genomics-platform. php).
Illumina TruSeq RNA Exome

tag: donor

tag: batch

tag: condition

value: human myogenic cells

tag: cell subpopulation

value: MuRC Pax7 Low


title: Pax7Low_e

status: Public on Aug 25 2023

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type


title: BCAA-control, sham [Sham-b-Cont-H3K23Pr]

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave., MSB

department: Cell Biology and Molecular Medicine

country: USA

institute: Rutgers University

description:
Sham-b-Cont-H3K23Pr
00ZSRutgers_H3K23Pr_mergedregs.xlsx

library_source: genomic

data_processing:
Copied from Active Motif "The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed."
Copied from Active Motif "Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers."
Copied from Active Motif “Peak Finding: The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. MACS/MACS2 (Zhang et al., Genome Biology 2008, 9:R137) was used for peak calling. This method looks for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background)."
Copied from Active Motif "Standard Normalization: In the default analysis, the tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample. This normalization method works well for most assays and can detect site-specific as well as most global differences in target enrichments between samples."
Copied from Active Motif “Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Merged Region. The use of Merged Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples.”
Assembly: mm10
Supplementary files format and content: bigWig (BW). "To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers."
Supplementary files format and content: Excel (xlsx).  Merged Regions. Copied from Active Motif “Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Merged Region. The use of Merged Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples.”

molecule: genomic DNA

organism: Mus musculus

source_name: heart

extract_protocol: Active Motif

treatment_protocol: Mice were either maintained on a BCAA-control (all essential amino acids, incluing BCAA added in concnetration equivlarnt to those found in standard chow diets) or a BCAA-free diet, in which BCAA were completely elimnated). This was applied 4 days before the sham or TAC surgeries and continued throughout the survival period (1-wk after surgery).

tag: tissue

value: heart

tag: strain

tag: Sex

value: male

tag: age

tag: treatment

value: BCAA-control diet, sham surgery

tag: chip antibody


title: BJAB, parental, untreated, rep4

city: Parkville

first: Göksu

last: Avar

state: Victoria

address: 30 Flemington Road

department: Biochemistry and Pharmacology

country: Australia

institute: University of Melbourne

description:
S60
Sample_21L007060

data_processing:
151 kB paired-end RNA-Seq reads from Novaseq6000 sequencer (Illumina) were aligned to the human genome version GCF_000001405.39_GRCh38.p13 with STAR 2.7.9a
Aligned reads were converted into a count table by using Rsubread 2.8.1
The analysis focused on protein coding genes and the genes with TPM<1 in at least 50% of the samples were excluded from the analysis.
Differential expression analysis was performed with DESeq2 1.34.06 with default parameters, where the model was fitted to the 29 samples with 6 groups, which were the input for the design parameter.
Multiple hypothesis correction was performed with the Benjamini-Hochberg method.
Variance stabilizing transformation was applied for visualization of the results.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: rawtable.csv contains the count table before filtering
Supplementary files format and content: DESeq2_Counts.csv contains the filtered count matrix that was fed to DESeq2
Supplementary files format and content: coldata.csv contains a simple one-column metadata that was used for DESeq2
Supplementary files format and content: DESeq2_Object.RDS contains the DESeq2 R data object

molecule: total RNA

source_name: BJAB

extract_protocol:
3 – 5 x106 cells were harvested after inhibitor treatment or after adjusting the cells the day before to 0.7 x 106 cells/ml. RNA was isolated with the Qiagen RNeasy Mini Kit (Cat. No.: 74106) or Stratec InviTrap Spin Universal RNA Mini Kit (Cat. No.: 1060100300) following the manufacturer’s recommendation. For high quality RNA isolation, the RNA was harvested using Trizol (Cat. No. 15596018, Invitrogen) before further purification with the Qiagen RNeasy Mini Kit (Cat. No.: 74106). Therefore, 1x107 cells were washed once with PBS, resuspended in 600 μl Trizol and incubated at RT for 5 Min. 120 μl Chloroform (Cat. No.: 3313.4, Roth) were added to Trizol and mixed vigorously by hand for 15 s. The samples were incubated at RT for 3 Min before they were centrifuged at full speed for 5 Min at 4°C. To isolate the RNA the upper aqueous phase was transferred to a new tube and the RNA was isolated with the Qiagen RNeasy Mini Kit (Cat. No.: 74106) after addition of the same volume of 70% EtOH by adding the mixture to the column and proceeding according to the manufacturer’s recommendations.
RNA integrity number (RIN) of Trizol isolated RNA was measured using the Agilent 2100 Bioanalyzer system. RNAs with a RIN value > 7 were selected for mRNA sequencing (poly-A selected). The libraries were prepared using the TruSeq stranded mRNA Sample preparation kit (Illumina), following the instructions of the manufacturer. After a final QC, the libraries were sequenced in a paired-end mode (2x150 bases) in the Novaseq6000 sequencer (Illumina) with a depth of ≥ 30 Million reads per sample. The raw reads and MultiQC sequencing quality report were collected from the Helmholtz Center Munich Genomics Core.

value: B cell

tag: cell line

value: BJAB

tag: genotype

value: Wild-type-Parental


title: cortex, CPN_hemi4_AF

city: Cambridge

first: John

middle: Edward

last: Froberg

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

description:
JF132
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

data_processing:
Library strategy: Ribo-seq
To enable duplicate removal from these variable-length Ribo-seq sequences, we took advantage of the fact that we used paired-end sequencing, and that the first 12-nt of Read 2 of QiA-seq miRNA libraries is a 12-nt random barcode. We filtered for all reads with Read 2 > 12 reads (the vast majority), and extracted this random barcode using umi-tools: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNNNN.
To remove the QiASeq miRNA adapters from the 3’ ends of Read 1, we ran cutadapt v2.8.: cutadapt -a AACTGTAGGCACCATCAAT
We then aligned Read 1 to the reference mouse rRNA sequences using STAR v2.6: STAR --runMode alignReads --runThreadN 8 --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --outReadsUnmapped Fastx --outSAMmultNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 21.
We then used the *final.out files produced by STAR for accounting the number and fraction of reads aligned to rRNA. We then aligned the reads that failed to align to rRNA to the mm10 genome, and to the mm10 transcriptome for analysis of footprint length distribution, coverage over coding sequence, and producing gene-level raw counts. We aligned to the mm10 genome (GRCm38 build) using STAR v2.6 and the following parameters:STAR --sjdbGTFfile Mus_musculus.GRCm38.95_chrNamed_headFix.gtf --runMode alignReads --runThreadN 8 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --readFilesCommand gunzip -c --outSAMmultNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 21
We completed duplicate removal following mm10 alignment to collapse all reads with the same alignment coordinates and exactly matching barcode sequences using umi-tools: umi_tools dedup --method=unique
We used the duplicate-removed bamFiles produced by this alignment for visualization, and for all further analysis. We then obtained raw, gene level counts over UTRs, CDS, and non-coding sequence using subRead:featureCounts using the annotations in Mus_musculus.GRCm38.95.gtf. We calculated coverage over 5’, 3’ UTRs and CDS as reads per kilobase per million mapped in Excel. We used custom shell scripts (makeLengthDistrosOverFeatures.sh, makeLengthDistrosOverNonTrans.sh) to compute the length distributions of the aligned reads from the lengths of aligned sequences.
Genome_build: mm10
Supplementary_files_format_and_content: read_count_matrix: read_count matrix for reads mapping to gene CDS (CDS), 3'UTRs (three_utr), or 5' UTRs (five_utrs) obtained by subRead:featureCounts.  read_length_distribution: read length distributions computed by custom shell script for reads mapping to CDS, three_utrs, five_utrs, snRNAs, snoRNAs, and lncRNAs.  ORFs_collapsed.txt: text file with full information for all ORFs identified by RiboCode.  ORFs_collapsed.bed: mm10  .bed file for all ORFs annotated by RiboCode.

molecule: cytoplasmic RNA

source_name: Mouse cortex

growth_protocol: All animal experimental protocols were approved by the Harvard University Institutional Animal Care and Use Committee, and complied with all relevant ethical regulations regarding animal research. Mice received food and water ad libitum, and were housed on a 12-hour on/off light cycle.

extract_protocol:
alkaline fragmention: fragments between 20-60 nt were gel purified, then converted into libraries using the QiA-seq miRNA kit
We performed neuronal FACS using established approaches (Catapano et al., 2001), but with the addition of translational inhibitors to prevent ex vivo elongation. For the CPN sorts, all buffers contained 100 ug/mL cycloheximide to inhibit translational elongation. We dissected brain into HBSS buffer+CHX, visualized the labeled region of cortex using an epifluorescent dissection microscope, and dissected the labeled cortical region into Disassociation Solution (DS)+CHX. We washed cortex tissue pieces twice in DS+CHX, then enzymatically digested twice by incubation in Enzyme Solution (DS with cysteine and papain)+CHX for 15 minutes each time (with inversion every 5 minutes to keep tissue pieces mixed). We washed twice in Wash Solution (WS)+CHX, triturated 15-20 times in ~1 mL of WS+CHX using fire-polished glass pipettes. We diluted the cell suspension with 4 mL WS+CHX, spun down cells for 5 minutes at 1000g, triturated again in 1 mL WS+CHX, and passed the cell suspension through a strainer cap. We added 1:1000 SYTOX Blue to be able to screen out dead cells. We then FACS-sorted the red cells, and collected them in a DNA LoBind Eppendorf Tube containing 2X polysome buffer+CHX (25 mM HEPES pH=8.0, 200 mM KCl, 10 mM MgCl2, 4 mM CaCl2, 1% nonidet P-40, 100 ug/mL CHX). For the SCPN sort, we performed all steps as described above, except that we omitted CHX until the SCPN were sorted into 2X polysome buffer+CHX.

treatment_protocol: CPN: We performed electroporation of fluorescent constructs using CD-1 background animals at E14.5 or E15.5. Briefly, we exposed both uterine horns, and injected a solution of 5 ug/uL DNA + 0.1% FastGreen in 1X TE containing 5ug/uL plasmid encoding myristolated-TdTomato into one lateral ventricle in approximately ½ of embryos. We then electroporated per injected animal with 5 pulses of 500 ms each, 34 mV. We screened pups for red fluorescence in the cortex at P1 under an epifluorescent dissection scope. SCPN: We labeled SCPN by ultrasound-guided injection into the cerebral peduncle at P1 of B6SJL x CD-1 pups bred in-house. Briefly, we anaesthetized the pups by placing them on ice for 3 minutes, then securing to a solid surface. We then visualized the cerebral peduncle and placement of the injection needle via intracranial ultrasound. We injected   Alexa 555-Cholera Toxin B (CTB) into the cerebral peduncle, injecting 4 sites (at slightly different dorsal, ventral, medial and lateral sites to ensure coverage of the peduncle, with five 5 nl pulses per site), all into the left cerebral peduncle.

value: cortex

tag: input

value: 1.4k sorted CPN

tag: fragmentation

value: Alkaline Fragmentation (pH=9.2, 37 min at 95 deg C)

tag: Stage

value: Callosal Projection Neuron


title: cortex, CPN_hemi3_AF

description:
JF131
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: 0.8k sorted CPN


title: pooled-input [Pooled_Input]

description:
Pooled_Input
01XERutgers_H3K23Pr_mergedregs.xlsx

treatment_protocol: Mice were either maintained on a BCAA-control (all essential amino acids, incluing BCAA added in concnetration equivlarnt to those found in standard chow diets) or a BCAA-free diet, in which BCAA were completely elimnated, both diets were supplemented with 1% propionate. This was applied 4 days before the sham or TAC surgeries and continued throughout the survival period (1-wk after surgery).

value: pooled DNA from the BCAA-control and BCAA-free sham and tac treated mice


title: BJAB, TRAF6 KO and CARD11 mut, untreated, rep3

description:
S59
Sample_21L007059


title: 5dpi_INH, bio rep 3

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

country: Germany

institute: Biomedical Center (BMC),LMU - Munich

description: 10x Genomics, Single Cell 3’ Reagent kit V3.1 (Dual Index), cellranger v6.0.0

library_source: transcriptomic single cell

data_processing:
Primary processing of raw sequencing data to fastq files was carried out with the program bcl2fastq v2.20.0.422 (from Illumina).
Alignment was performed using Cell Ranger v3.0.2 or v6.0.0 (specified in description)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The lesioned grey matter of the somatosensory cortex of C57BL/6J male mice (8-12weeks old)  at 3dpi and 5dpi or the corresponding region of the noninjured cortex were isolated using a biopsy punch  ( ∅ 0.25cm ,6 cortical punches from 3 animals) and the cortical cells were dissociated at a single cell level using the Papain Dissociation System (Worthington, # LK003153) followed by the Dead Cell Removal kit (Miltenyi Biotec # 130-090-101), according to manufacturer’s instructions. Incubation with dissociating enzyme was performed for 60 min.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 or v3.1 protocol, 10x Genomics). Briefly, brain cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Animals received treatment by gavage feeding. Inhibitors mix: NBI 74330 (100 mg/kg, R&D Systems #4528) and CU CPT 22 (3 mg/kg, R&D Systems #4884) were dissolved in DMSO and diluted in corn oil. The vehicle solution consisted of DMSO diluted in corn oil and was administered to the control animals.

value: brain

value: multiple cell types

value: 8-12 weeks old

value: 4days Inhibitors mix

tag: timepoint

value: 5 dpi


title: cortex, CPN_hemi2_AF

description:
JF130
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: 3.0k sorted CPN


title: BJAB, TRAF6 KO, untreated, rep3

description:
S58
Sample_21L007058


title: BJAB, parental, untreated, rep5

description:
S64
Sample_21L007064


title: BCAA-free w prop,TAC [TAC-0BCAA-prop_H3K23Pr]

description:
TAC-0BCAA-prop_H3K23Pr
01XERutgers_H3K23Pr_mergedregs.xlsx

value: heart

value: male

value: BCAA-free diet with propionate, TAC surgery


title: Pax7Low_b

tag: donor

value: human myogenic cells

value: MuRC Pax7 Low


title: cortex, CPN_hemi1_AF

description:
JF129
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: cortex

value: 6.2k sorted CPN


title: 5dpi_CTRL, bio rep 2

description: 10x Genomics, Single Cell 3’ Reagent kit V2, cellranger v3.0.2

value: 4days DMSO


title: Pax7Low_a

tag: batch


title: BJAB, TRAF6 KO, untreated, rep4

description:
S62
Sample_21L007062

value: B cell

value: BJAB


title: BCAA-free w prop, sham [Sham-0BCAA-prop_H3K23Pr]

description:
Sham-0BCAA-prop_H3K23Pr
01XERutgers_H3K23Pr_mergedregs.xlsx

value: BCAA-free diet with propionate, sham surgery


title: BCAA-control w prop, TAC [TAC-control-prop_H3K23Pr]

description:
TAC-control-prop_H3K23Pr
01XERutgers_H3K23Pr_mergedregs.xlsx

value: BCAA-control diet with propionate, TAC surgery


title: BJAB, CARD11 mut, untreated, rep3

description:
S57
Sample_21L007057


title: cortex, CPN_hemi5_RP

description:
JF128
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

data_processing:
Library strategy: Ribo-seq
Library strategy: Ribo-seq
To enable duplicate removal from these variable-length Ribo-seq sequences, we took advantage of the fact that we used paired-end sequencing, and that the first 12-nt of Read 2 of QiA-seq miRNA libraries is a 12-nt random barcode. We filtered for all reads with Read 2 > 12 reads (the vast majority), and extracted this random barcode using umi-tools: umi_tools extract --extract-method=string --bc-pattern=NNNNNNNNNNNN.
To remove the QiASeq miRNA adapters from the 3’ ends of Read 1, we ran cutadapt v2.8.: cutadapt -a AACTGTAGGCACCATCAAT
We then aligned Read 1 to the reference mouse rRNA sequences using STAR v2.6: STAR --runMode alignReads --runThreadN 8 --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --outReadsUnmapped Fastx --outSAMmultNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 21.
We then used the *final.out files produced by STAR for accounting the number and fraction of reads aligned to rRNA. We then aligned the reads that failed to align to rRNA to the mm10 genome, and to the mm10 transcriptome for analysis of footprint length distribution, coverage over coding sequence, and producing gene-level raw counts. We aligned to the mm10 genome (GRCm38 build) using STAR v2.6 and the following parameters:STAR --sjdbGTFfile Mus_musculus.GRCm38.95_chrNamed_headFix.gtf --runMode alignReads --runThreadN 8 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --readFilesCommand gunzip -c --outSAMmultNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 21
We completed duplicate removal following mm10 alignment to collapse all reads with the same alignment coordinates and exactly matching barcode sequences using umi-tools: umi_tools dedup --method=unique
We used the duplicate-removed bamFiles produced by this alignment for visualization, and for all further analysis. We then obtained raw, gene level counts over UTRs, CDS, and non-coding sequence using subRead:featureCounts using the annotations in Mus_musculus.GRCm38.95.gtf. We calculated coverage over 5’, 3’ UTRs and CDS as reads per kilobase per million mapped in Excel. We used custom shell scripts (makeLengthDistrosOverFeatures.sh, makeLengthDistrosOverNonTrans.sh) to compute the length distributions of the aligned reads from the lengths of aligned sequences.
Genome_build: mm10
Supplementary_files_format_and_content: read_count_matrix: read_count matrix for reads mapping to gene CDS (CDS), 3'UTRs (three_utr), or 5' UTRs (five_utrs) obtained by subRead:featureCounts.  read_length_distribution: read length distributions computed by custom shell script for reads mapping to CDS, three_utrs, five_utrs, snRNAs, snoRNAs, and lncRNAs.  ORFs_collapsed.txt: text file with full information for all ORFs identified by RiboCode.  ORFs_collapsed.bed: mm10  .bed file for all ORFs annotated by RiboCode.

extract_protocol:
nanoRibo-seq: RPFs were gel purified, then converted into libraries using the QiA-seq miRNA kit.
We performed neuronal FACS using established approaches (Catapano et al., 2001), but with the addition of translational inhibitors to prevent ex vivo elongation. For the CPN sorts, all buffers contained 100 ug/mL cycloheximide to inhibit translational elongation. We dissected brain into HBSS buffer+CHX, visualized the labeled region of cortex using an epifluorescent dissection microscope, and dissected the labeled cortical region into Disassociation Solution (DS)+CHX. We washed cortex tissue pieces twice in DS+CHX, then enzymatically digested twice by incubation in Enzyme Solution (DS with cysteine and papain)+CHX for 15 minutes each time (with inversion every 5 minutes to keep tissue pieces mixed). We washed twice in Wash Solution (WS)+CHX, triturated 15-20 times in ~1 mL of WS+CHX using fire-polished glass pipettes. We diluted the cell suspension with 4 mL WS+CHX, spun down cells for 5 minutes at 1000g, triturated again in 1 mL WS+CHX, and passed the cell suspension through a strainer cap. We added 1:1000 SYTOX Blue to be able to screen out dead cells. We then FACS-sorted the red cells, and collected them in a DNA LoBind Eppendorf Tube containing 2X polysome buffer+CHX (25 mM HEPES pH=8.0, 200 mM KCl, 10 mM MgCl2, 4 mM CaCl2, 1% nonidet P-40, 100 ug/mL CHX). For the SCPN sort, we performed all steps as described above, except that we omitted CHX until the SCPN were sorted into 2X polysome buffer+CHX.

value: 9.9k sorted CPN

value: Rnase I 12.5 U/mL

value: Callosal Projection Neuron


title: Pax7High_f

tag: condition

value: MuRC Pax7 High


title: BJAB, parental, untreated, rep3

description:
S56
Sample_21L007056

value: Wild-type-Parental


title: Pax7Low_d

tag: cell subpopulation


title: BCAA-control w prop, sham [Sham-control-prop_H3K23Pr]

description:
Sham-control-prop_H3K23Pr
01XERutgers_H3K23Pr_mergedregs.xlsx

value: heart

value: BCAA-control diet with propionate, sham surgery


title: cortex, CPN_hemi4_RP

description:
JF127
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: 4.3k sorted CPN

tag: cell type


title: Pax7High_e

value: human myogenic cells


title: Pax7Low_c

value: MuRC Pax7 Low


title: Hypoxia-KO3

city: tsukuba

first: akiyama

last: tatsuya

address: amakubo

country: Japan

institute: university of tsukuba

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 10.1.1.Qiagen).
Reads were mapped to mouse reference genome (mm10) and quantified for 49585 genes.
Assembly: mm10
Supplementary files format and content: Microsoft Excel file format, containing expression and TPM, FPKM values for each Sample.

source_name: Lung

extract_protocol:
Lungs were removed, flash frozen in liquid nitrogen, and RNA was isolated using Trizol reagent(Invitrogen). RNA quality examined by RNA 6000 Pico kit (Agilent).
100 µg of total RNA was used for RNAseq library preparation using the NEBNext rRNA Depletion Kit and NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

tag: strain background

value: mixture of ICR and C57BL/6

tag: tissue

value: Lung

value: tdTomato potitive cells

value: Endothelial cells

value: Hypoxia


title: BJAB, TRAF6 KO, untreated, rep2

description:
S54
Sample_21L007054

value: B cell

value: BJAB


title: Pax7High_d


title: Hypoxia-KO2


title: cortex, CPN_hemi2_RP

description:
JF125
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: cortex

value: 9.1k sorted CPN


title: BJAB, CARD11 mut, untreated, rep2

description:
S53
Sample_21L007053


title: Pax7High_c


title: Hypoxia-KO1


title: cortex, CPN_hemi1_RP

description:
JF124
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: 20.8k sorted CPN

value: Rnase I 12.5 U/mL

value: Callosal Projection Neuron


title: Pax7High_b

value: MuRC Pax7 High


title: BJAB, parental, untreated, rep2

description:
S52
Sample_21L007052

value: Wild-type-Parental


title: cortex, 50kSCPN_12.5U_RP

description:
JF47
sorted_neurons_CDS_FC_matrix.csv
sorted_neurons_five_utr_FC_matrix.csv
sorted_neurons_three_utr_FC_matrix.csv
sorted_neurons_lengthDistro.csv

value: 50k sorted SCPN

value: Subcerebral Projection Neuron


title: BJAB, TRAF6 KO and CARD11 mut, untreated, rep1

description:
S51
Sample_21L007051


title: cortex, 17kCPN_12.5U_RP

description:
JF45
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
sorted_neurons_CDS_FC_matrix.csv
sorted_neurons_five_utr_FC_matrix.csv
sorted_neurons_three_utr_FC_matrix.csv
sorted_neurons_lengthDistro.csv

value: 17k sorted CPN


title: Hypoxia-Ctrl3

value: mixture of ICR and C57BL/6

value: control


title: Hypoxia-Ctrl2

value: Lung

value: tdTomato potitive cells


title: cortex, 50kCPN_2.5U_RP

description:
JF43
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
sorted_neurons_CDS_FC_matrix.csv
sorted_neurons_five_utr_FC_matrix.csv
sorted_neurons_three_utr_FC_matrix.csv
sorted_neurons_lengthDistro.csv

value: 50k sorted CPN

value: Rnase I 2.5 U/mL


title: cortex, CPN_hemi3_RP

description:
JF126
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
CPN_hemispheres_CDS_FC_matrix.csv
CPN_hemispheres_five_utr_FC_matrix.csv
CPN_hemispheres_three_utr_FC_matrix.csv
CPN_hemispheres_lengthDistro.csv

value: 2.5k sorted CPN


title: BJAB, TRAF6 KO and CARD11 mut, untreated, rep2

description:
S55
Sample_21L007055

value: B cell

value: BJAB


title: BJAB, CARD11 mut, untreated, rep1

description:
S49
Sample_21L007049


title: Hypoxia-Ctrl1

value: Endothelial cells

value: Hypoxia


title: MB_f

value: MPC

value: human myogenic cells

value: Myoblast


title: cortex, 50kCPN_12.5U_RP

description:
JF39
RiboCode_ORFs_collapsed.bed
RiboCode_ORFs_collapsed.txt
sorted_neurons_CDS_FC_matrix.csv
sorted_neurons_five_utr_FC_matrix.csv
sorted_neurons_three_utr_FC_matrix.csv
sorted_neurons_lengthDistro.csv

value: cortex

value: Rnase I 12.5 U/mL

value: Callosal Projection Neuron


title: BJAB, parental, untreated, rep1

description:
S48
Sample_21L007048

value: Wild-type-Parental


title: Normoxia-KO3

value: mixture of ICR and C57BL/6

value: Normoxia


title: MB_e


title: MB_d


title: MB_c


title: 143B cells, TPBC-PEG 3uM, 24h, rep3

city: shanghai

first: Junli

last: Chang

address: Wanping South Road 725

country: China

institute: Long hua Hospital

description:
TPBC-PEG-3-3
Experiment

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2
Count counting
Assembly: GRCh38 Ensembl100
Supplementary files format and content: All.counts.exp.txt: Tab-delimited text file contains counts for each sample.

growth_protocol: 143B cells were incubated with growth medium comprising FBS (10%), streptomycin (100 μg/ml) and penicillin (100 U/ml) in a 5% CO2-humidified incubator. The cells was cultured at 37 °C with DMEM culture media.

extract_protocol:
Total RNA was extracted from animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 143B cells were seeded in 6-well (15*10^4 cells/well) for 24 h at 37°C. Then the cells were treated with PBS and 300μM TPBC-PEG for 24h, respectively.

value: Osteosarcoma

value: TPBC-PEG 3uM, 24h


title: Normoxia-KO1

value: Lung

value: tdTomato potitive cells


title: Normoxia-KO2


title: 143B cells, TPBC-PEG 3uM, 24h, rep2

description:
TPBC-PEG-3-2
Experiment


title: Atg16l1 knockout CRC organoid cells

city: South San Francisco

first: Yasin

last: Senbabaoglu

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
Demultiplexing of raw data was performed with the CellRanger mkfastq software (10X Genomics).
Reads obtained from demultiplexing were provided as input to ‘cellranger count’ (CellRanger v6.0.1), which aligned the reads to the mouse reference genome GRCm38.p5 using STAR and collapsed to unique molecular identifier (UMI) counts.
Resulting gene-barcode matrices were filtered for background noise with 10X's cell-calling heuristic. Filtered gene-barcode matrices only included cells with at least 500 UMI counts
Subsequent data analysis was carried out in R 4.1.0 and the Seurat package (v4.0.4). Normalization was performed with the LogNormalize option in the NormalizeData function.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Barcode names, feature names (gene ID), and matrix of feature counts for all cells (before filtering out low quality cells). Separate Seurat objects for tumor and myeloid cells after removing low quality and contaminating cells.

source_name: Tumor-bearing liver in NSG mice

growth_protocol:
Animals were maintained in a pathogen-free animal facility under 12hr light/12hr dark cycle with access to a standard rodent chow and water ad libitum
AKPS CRC organoids were cultured in 50% matrigel 50% medium.

extract_protocol: Chromium Single Cell 3’ Library and Gel Bead Kit V3.1 (10X Genomics)

value: Liver

value: Tumor

value: Atg16l1 knockout

tag: library construction

value: 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit V3.1


title: Immune cells in Atg16l1 knockout group

value: Immune


title: Normoxia-Ctrl3

value: Endothelial cells

value: control


title: Pax7High_a

value: human myogenic cells

value: MuRC Pax7 High


title: 143B cells, TPBC-PEG 3uM, 24h, rep1

description:
TPBC-PEG-3-1
Experiment


title: BJAB, TRAF6 KO, untreated, rep1

description:
S50
Sample_21L007050

value: B cell

value: BJAB


title: RUNX1 KO, UCB1140

city: San Francisco

first: Amy

last: Fan

state: CA

address: 769 25th Ave

department: Pathology

institute: UCSF

data_processing:
fastp trimming
kallisto pseudoalignment
Assembly: hg38
Supplementary files format and content: RNA-seq raw counts aligned to genes

source_name: Cord blood

growth_protocol: StemSpan II + 20 ng/mL SCF, TPO, FLT3L, IL-6, 35nM UM-171

extract_protocol:
Qiagene RNeasy Micro Kit
mRNA was enriched using oligo(dT) coupled magnetic beads; first strand cDNA synthesis was performed using random hexamers, followed by second strand cDNA synthesis, terminal repair, 3’A-tailing, adapter ligation, size selection, and PCR amplification.

value: Cord blood

value: CD34+ hematopoietic stem and progenitor cells

value: RUNX1 KO


title: Atg16l1 wildtype CRC organoid cells

value: Atg16l1 wildtype


title: AAVS1 control, UCB1140


title: 143B cells, PBS, 24h, rep3

description:
con3
Control

value: Osteosarcoma

value: PBS, 24h


title: Immune cells in Atg16l1 wildtype group

value: Liver


title: 143B cells, PBS, 24h, rep2

description:
con2
Control


title: Atg16l1 knockout IFNg treated clone 2 rep 2

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie (Wu et al., 2016)(Pau and Reeder, 2012) as follows:
First, reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed.
The reads that passed were then aligned to the mouse reference genome GRCm38.p5 using GSNAP (Wu and Nacu, 2010) version ‘2013-10-10-v2’ with alignment parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000'.
Alignments of the reads that were reported by GSNAP as “uniquely mapping” were used for subsequent analysis.
Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor).
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: AKPS CRC organoids

growth_protocol: AKPS CRC organoids were cultured in 50% matrigel 50% medium.

extract_protocol:
Approximately 500,000 AKPS organoid cells were collected per condition and RNA was isolated according to manufacturer's protocol using Qiagen Rneasy Mini Kit 50. Standard input RNA sequencing was performed.
Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).
Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pair reads for each sample.

treatment_protocol: AKPS CRC organoids were treated overnight with IFNg 20 ng/ml.

value: Colon

tag: disease state

value: Tumor

tag: clone

value: IFN gamma


title: Normoxia-Ctrl2

value: mixture of ICR and C57BL/6

value: Lung

value: tdTomato potitive cells

tag: treatment

value: Normoxia


title: Normoxia-Ctrl1

tag: cell line

value: Endothelial cells

value: control


title: AAVS1 control, NYCB69

tag: genotype


title: Atg16l1 knockout IFNg treated clone 2 rep 1


title: Hypoxia day8_3

extract_protocol:
Lungs were removed, flash frozen in liquid nitrogen, and RNA was isolated using Trizol reagent(Invitrogen). RNA quality examined by RNA 6000 Pico kit (Agilent).
75 µg of total RNA was used for RNAseq library preparation using the NEBNext rRNA Depletion Kit and NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

value: ICR

value: Flk1 positive cells

value: Hypoxia

tag: time


title: cortex, AlkFrag_test

description:
JF44
sorted_neurons_CDS_FC_matrix.csv
sorted_neurons_five_utr_FC_matrix.csv
sorted_neurons_three_utr_FC_matrix.csv
sorted_neurons_lengthDistro.csv

value: cortex

tag: input

value: 7.5 ng extracted RNA

tag: fragmentation

value: Alkaline Fragmentation (pH=9.2, 37 min at 95 deg C)


title: 143B cells, PBS, 24h, rep1

description:
con1
Control

value: Osteosarcoma

value: PBS, 24h


title: RUNX1 KO, NYCB66

value: Cord blood

value: CD34+ hematopoietic stem and progenitor cells

value: RUNX1 KO


title: Atg16l1 knockout untreated clone 2 rep 2

value: Colon

value: Tumor


title: human blastoid

city: Dallas

first: Gary

last: Hon

address: 5323 Harry Hines Blvd.

department: Department of Obstetrics and Gynecology

institute: UT Southwestern

description: one library was sequenced multiple times

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 6.1.2).
Reads were processed to generate expression (UMI count) matrix using Cell Ranger pipeline (version 6.1.2) with default parameters, except the parameter of expected number of cells was set to 10000.
Assembly: GRCh38
Supplementary files format and content: Raw UMI count matrix representing gene expression values (comma-separated) was generated as described above. Each column represents a single cell, each row represents a single gene.
Supplementary files format and content: Raw UMI count matrix representing gene expression values were generated as described above in Apache Parquet format. Each column represents a single cell, each row represents a single gene.

source_name: blastoid

growth_protocol: 5iLA naive human PSCs were dissociated into single cells by incubation with Accumax (Stemcell technologies) for 3 min at 37 °C. Cells were centrifugated at 200g for 5 min and collected in 5iLA medium. Then, the cell suspension was incubated in a 0.1% gelatin-coated tissue culture dish for 30 min at 37 °C in 5% CO2 to remove MEF feeder cells. The supernatant containing naive human PSCs was collected and passed through a 40-μm cell strainer, and cells were counted. Meanwhile, the AggreWell-400 (STEMCELL Technologies) was prepared according to the manufacturer’s instructions. In brief, wells were rinsed with anti-adhesion rinsing solution (STEMCELL Technologies), centrifuged at max speed for 5 min, and then incubated at room temperature for 10 min. After incubation, wells were washed with eHDM once and 0.5 ml fresh eHDM was added. The corresponding number of cells (25 cells / microwell for WIBR3-hESCs, H9-hESCs. And 46XX-hESCs, 30 cells / microwell for RC-hiPSCs and JB-hiPSCs, and for other cell lines the starting number needs to be optimized) were resuspended in 1 ml eHDM and seeded into one well of a prepared AggreWell-400 24-well plate. The plate was centrifuged at 200g for 1 min and cultured at 37 °C in 5% CO2 and 5% O2, the day of cell plating was designated as day 0. The medium were half changed (remove 1 ml old medium were removed and 1ml fresh medium were added) with eHDM on day 1 and day 2. On day 3, carefully remove as much eHDM as possible, and then add 1.5 ml of eTDM. Repeat this step one additional time to help completely remove the remaining eHDM. On the remaining days, the fresh eTDM were half changed every two days. The human blastoids usually formed after around five to six days of culture in eTDM. All blastoids were manually isolated using a mouth pipette under a stereomicroscope for downstream experiments.

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Human blastoids were manually pooled using a mouth pipette, washed three times in PBS and then dissociated with trypsin-EDTA (0.25%) (Gibco) at 37 °C in 5% CO2 for 40 min with agitation.

value: blastoid


title: Hypoxia day8_1

value: Lung


title: AAVS1 control, NYCB66


title: Hypoxia day8_2

value: Endothelial cells


title: U2OS cells, siSETD2_HU_VE_R2

city: Oxford

first: Linda

last: van Bijsterveldt

state: non-US Resident

address: Old Road Campus

country: United Kingdom

institute: Oxford Institute for Radiation Oncology

data_processing:
Data QC using FastQC, and reads trimmed 22 from the left and 22 from the right (Illumina Adaptors)
Mapping to the hg38 genome was performed with STAR v2.6.1d (Parameter: mismatch = 2)
Quantification was performed with FeatureCounts v1.5.0-p3
Differential Analysis was performed using DESeq2 v1.26.0 (padj<=0.05)
Genome_build: hg38
Supplementary_files_format_and_content: fpkm matrix table for each condition

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle medium (GIBCO) with 10% fetal bovine serum (FBS) supplemented with penicillin and streptomycin (Invitrogen).

extract_protocol:
RNA was purified from cell pellets with the RNeasy mini kit (Qiagen)
Libraries were prepared according to the protocols of NEBNext® UltraTM RNA Library Prep Kit for Illumina

treatment_protocol: U2OS cells were treated with 2 mM of hydroxyurea (HU), or 2 µM VE-822 (VE), or with 2 mM HU and 2 µM VE for 4 hours, and siNT or siSETD2

tag: sirna transfection

value: SETD2 siRNA


title: Atg16l1 knockout untreated clone 2 rep 1


title: Hypoxia day1_3

value: ICR


title: U2OS cells, siSETD2_HU_VE_R1


title: Atg16l1 wildtype IFNg treated clone 2 rep 2

value: IFN gamma


title: RUNX1 KO, NYCB58


title: MB_b

tag: donor

value: MPC

value: human myogenic cells

value: Myoblast


title: U2OS cells, siSETD2_VE_R2


title: AAVS1 control, NYCB58


title: Hypoxia day1_2

value: Flk1 positive cells

value: Hypoxia


title: EOPE+FGR, S13, Villous Tissue

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

description: Illumina HiSeq 2500

data_processing:
Reads were subjected to adapter trimming using Trimmomatic v0.39.
Reads were mapped to the University of California Santa Cruz hg38 human genome assembly using TopHat2 version 2.0.14.
Raw read counts were generated using HTseq version 0.11.2 with the iGenomes (Illumina) Homo sapiens reference file .
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw feature count values for each sample.

source_name: placenta, villous tissue

extract_protocol:
RNA was isolated using TRIzol reagent (Life Technologies), then purified using the RNA Clean-Up and Concentration Kit (Norgen Biotek).
RNA libraries for RNA-seq were prepared using using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold following manufacturer's protocols (Illumina).

value: placenta, villous tissue

tag: clinical group

value: EOPE+FGR

tag: age of_mother_(years)

tag: birthweight interval_(grams)

tag: assigned neonatal_sex

value: Female

tag: maternal ethnicity

value: Non-Hispanic

tag: maternal race

value: White


title: Atg16l1 wildtype IFNg treated clone 2 rep 1

tag: tissue

value: Colon

value: Tumor


title: Hypoxia day1_1

tag: strain background

value: Lung

tag: cell type


title: RUNX1 KO, NYCB69

value: Cord blood

value: CD34+ hematopoietic stem and progenitor cells

value: RUNX1 KO


title: U2OS cells, siSETD2_VE_R1

value: SETD2 siRNA

tag: treatment


title: Vector-3

city: GUAGNZHOU

first: JIAYING

last: LI

state: GUAGNDONG

address: No. 1063, No. 1023, Shatai South Road, Baiyun District, Guangzhou

department: Gastrointerology

institute: Soutern Medical University

description: biol rep 3

data_processing:
Solexa pipeline version 1.8(Off-Line Base Caller software, version 1.8)
Sequence reads were trimmed for adaptor sequence using Cutadapt(verison 1.17) and the quality was assessed by FastQC.
Trimmed sequence reads were mapped to GRCh37 using Hisat2(verison 2.1.0)
Read count extraction and normalization were performed using StringTie and R software.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MKN-74 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:
RNA was harvested using TRIzol(Invitrogen). 1-2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit(Illumina) following manufacturer's protocols.

treatment_protocol: MKN-74 cells were infected with lentivirus with Vector and HOXD9 and puromycin(10μg/ml) were applied for more than 14 days to establish stable expression cell lines.

tag: cell line

value: epithelial-like cell

value: WT


title: Atg16l1 wildtype untreated clone 2 rep 2

tag: disease state

tag: clone

tag: genotype


title: U2OS cells, siSETD2_HU_R2

value: HU


title: Hypoxia day0_3

value: ICR

value: Flk1 positive cells

value: Endothelial cells

tag: time


title: Vector-2

description: biol rep 2


title: Atg16l1 wildtype untreated clone 2 rep 1


title: U2OS cells, siSETD2_HU_R1

tag: sirna transfection


title: HOXD9-3

description: biol rep 3

value: HOXD9 overexpressed


title: Hypoxia day0_2

value: Hypoxia


title: U2OS cells, siSETD2_Ctrl_R2

value: control


title: Hypoxia day0_1


title: Atg16l1 knockout IFNg treated clone 1 rep 2

value: IFN gamma


title: HOXD9-2

description: biol rep 2


title: Atg16l1 knockout IFNg treated clone 1 rep 1

value: Colon


title: E16 molar

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

institute: Tohoku University

description: 10x Genomics

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v2.0.0 pipeline using default settings.
Secondary analysis was performed using the Cell Ranger Single-Cell Software Suite v2. 1. 0.
Assembly: Custom mm10 with transgenes
Supplementary files format and content: CellRanger v2.0.0 gene counts matrices.

source_name: Tooth germ

extract_protocol:
Incisors were dissected with sharp tweezers from seven littermates of P7 Krt14-RFP mice. Single cell dissociation was essentially performed as previously described (Li et al. 2015). Briefly, dissected incisors were incubated in 4 mg/ml Dispase II (Roche) for 14 min at 37°C. Then incisors were placed in cold DMEM/F12 and dental epithelium and mesenchyme were separated under microscope. The tissues are then placed in Accutase (Sigma) for 30min at 37°C. After pipetting up and down using 1000 μm tips, single cell suspension was further produced through a 70 μm sterile cell strainer. The cells were resuspended with 0.04% BSA containing cold PBS.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: Tooth germ


title: forebrain, in_vitro_R>G

description:
JF31
RnaseTitration_CDS_FC_matrix.csv
RnaseTitration_five_utr_FC_matrix.csv
RnaseTitration_three_utr_FC_matrix.csv
RnaseTitration_lengthDistro.csv

source_name: Mouse forebrain lysate

value: forebrain

tag: input

value: 50 ng extracted RNA

tag: fragmentation

value: RNase I 0.05 U

tag: Stage


title: Atg16l1 knockout untreated clone 1 rep 2

value: Tumor


title: Atg16l1 knockout untreated clone 1 rep 1


title: HOXD9-1

description: biol rep 1


title: forebrain, 312.5U/mL_RP

description:
JF30
RnaseTitration_CDS_FC_matrix.csv
RnaseTitration_five_utr_FC_matrix.csv
RnaseTitration_three_utr_FC_matrix.csv
RnaseTitration_lengthDistro.csv

value: 30 ng RNA equiv. forebrain lysate

value: RNase I 312.5 U/mL


title: U2OS cells, siNT_HU_VE_R2

value: Non-targeting control siRNA


title: U2OS cells, siNT_HU_VE_R1


title: C50

city: Boston

first: Sean

last: Lawler

address: 75 Francis St

institute: Brigham and Women's Hospital

data_processing:
Fastq files were generated and demultiplexed using Illumina bcl2fastq v2.20
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1
Assembly: human samples were aligned to hg19 and mouse samples to mm10

source_name: control group

extract_protocol:
RNA of both in vitro and in vivo samples was isolated with an RNeasy mini kit (#74104, Qiagen)
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7

value: brain

value: glioblastoma


title: Atg16l1 wildtype IFNg treated clone 1 rep 2


title: U2OS cells, siNT_VE_R2


title: C5L


title: U2OS cells, siNT_VE_R1


title: Atg16l1 wildtype IFNg treated clone 1 rep 1


title: Vector-1

description: biol rep 1

value: epithelial-like cell

value: WT


title: forebrain, 12.5U/mL_RP

description:
JF28
RnaseTitration_CDS_FC_matrix.csv
RnaseTitration_five_utr_FC_matrix.csv
RnaseTitration_three_utr_FC_matrix.csv
RnaseTitration_lengthDistro.csv

value: RNase I 12.5 U/mL


title: Atg16l1 wildtype untreated clone 1 rep 2


title: U2OS cells, siNT_HU_R2

value: HU


title: C5R

value: control


title: U2OS cells, siSETD2_Ctrl_R1

value: SETD2 siRNA


title: T4RR

source_name: treatment group

value: CAN-2409 (previously called GMCI)


title: Atg16l1 wildtype untreated clone 1 rep 1

value: Colon


title: U2OS cells, siNT_HU_R1


title: forebrain, in_vitro_G>R

description:
JF21
BulkVs30ng_CDS_FC_matrix.csv
BulkVs30ng_five_utr_FC_matrix.csv
BulkVs30ng_three_utr_FC_matrix.csv
BulkVs30ng_lengthDistro.csv

value: forebrain

value: 30 ng extracted RNA


title: forebrain, bulk_RP

description:
JF20
BulkVs30ng_CDS_FC_matrix.csv
BulkVs30ng_five_utr_FC_matrix.csv
BulkVs30ng_three_utr_FC_matrix.csv
BulkVs30ng_lengthDistro.csv

value: 600 uL forebrain lysate (~100 ug RNA)

value: RNase I 2500 U/mL


title: U2OS cells, siNT_Ctrl_R2


title: T30


title: 3dpi_CTRL

description: 10x Genomics, Visium Spatial Gene Expression, spaceranger v1.2.2

data_processing:
Data demultiplexing was performed using the Je tool v1.2
Alignment was performed using Space Ranger v1.2.2
Tissue_hires_image.png images of brain sections were acquired on a Carl Zeiss Axio Imager.M2m microscope
Assembly: mm10
Supplementary files format and content: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5,: Tab-separated values files and matrix files
Supplementary files format and content: tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg: image files

extract_protocol:
Mouse brains were embedded and snap frozen in an isopentane/liquid nitrogen bath.  Two coronal sections (10µm) of the dorsal brain area were collected in each capture area and the tissue was enzymatically permeabelized according to the Visium Spatial Gene Expression from 10x Genomics.
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression , 10x Genomics).

tag: strain

tag: Sex

value: male

tag: age

value: 8-12 weeks old

value: 2days DMSO

tag: timepoint

value: 3 dpi


title: forebrain, 30ng_equiv

description:
JF19
BulkVs30ng_CDS_FC_matrix.csv
BulkVs30ng_five_utr_FC_matrix.csv
BulkVs30ng_three_utr_FC_matrix.csv
BulkVs30ng_lengthDistro.csv

tag: tissue

value: 30 ng RNA equiv. forebrain lysate

value: RNase I 2.5 U/mL


title: forebrain, 62.5U/mL_RP

description:
JF29
RnaseTitration_CDS_FC_matrix.csv
RnaseTitration_five_utr_FC_matrix.csv
RnaseTitration_three_utr_FC_matrix.csv
RnaseTitration_lengthDistro.csv

value: RNase I 62.5 U/mL


title: U2OS cells, siNT_Ctrl_R1

value: Non-targeting control siRNA


title: Th2cell, cKO3, RNAseq

status: Public on Aug 24 2023

city: ulsan

first: hansol

last: oh

address: 50, UNIST-gil, Ulsan 44919

country: South Korea

institute: UNIST

data_processing:
RNA seq) paired-end reads were mapped to reference mouse genome (mm10 assembly) using STAR aligner with default parameters.
The expression levels of genes in each sample were normalized by DESeq2. Read counts for edgeR analysis were obtained
with RSEM v1.3.3. After eliminating absent features (zero counts), the raw counts were normalized with edgeR, followed by differential expression analysis.
Significantly up or downregulated genes were defined as expressed genes with p-value adjusted for multiple testing (FDR) < 0.01 and
log2 fold-change of at least 1.5. To find the GO terms enriched in differentially regulated genes, we used the Gene Set Enrichment Analysis (GSEA) of MSigDB gene sets (Hallmark).
ATAC seq) For ATAC-seq analysis, sequenced reads were aligned to reference mouse genome (mm10 assembly)
using Bowtie2 v2.3.5.1 with default parameters, and clonal reads were removed from further analysis. We used the annotatePeaks.pl and
findMotifsGenome.pl commands from HOMER v4.11.
Assembly: mm10
Supplementary files format and content: RNA seq) normalizedcount
Supplementary files format and content: ATAC seq) bedgraph, Peaknumber

source_name: T cell

extract_protocol:
RNAseq) RNA was extracted using Quick-RNA microPrep kit (Zymo)
ATACseq) Fifty thousand cells were centrifuged at 500 × g for 5 min at 4 °C. Cell pellets were washed once with 1x PBS and cell pellets were resuspended in 50 μl of ATAC-RSB buffer
(10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween20 and 0.01% Digitonin, and incubate on ice for 5min.
Then, we washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but no NP-40 or digitonin and immediately centrifuged at 500 × g for 10 min at 4 °C.
RNAseq) RNA libraries for sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit following the manufacturer’s instructions.
ATACseq) The cell pellet was resuspended in the transposase reaction mix (25 μL 2 × TD buffer, 2.5 μL Illumina Tn5 transposase (100 nM final), 16.5 μL PBS, 0.5 ul 1% Digitonin,
0.5 ul 10% Tween-20, and 5 ul H2O). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition,
the sample was purified using a Zymo DNA Clean & Concentrator-5 Kit. Then, we amplified library fragments using NEBNext 2x PCR master mix and 25 uM of PCR primers,
using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.

value: T cell

value: cKO


title: Th2cell, cKO1, ATACseq


title: Th2cell, cKO2, RNAseq


title: Th2cell, cKO3, ATACseq


title: Th2cell, WT3, ATACseq

value: WT


title: Th2cell, cKO2, ATACseq


title: Th2cell, WT2, ATACseq


title: forebrain, 2.5U/mL_RP

description:
JF27
RnaseTitration_CDS_FC_matrix.csv
RnaseTitration_five_utr_FC_matrix.csv
RnaseTitration_three_utr_FC_matrix.csv
RnaseTitration_lengthDistro.csv


title: Th2cell, WT1, ATACseq


title: Th2cell, cKO1, RNAseq


title: Th2cell, WT1, RNAseq


title: Th2cell, WT3, RNAseq


title: Th2cell, WT2, RNAseq


title: Intact

value: brain

value: w/o treatment

value: Intact


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(DCRD1,2/DCRD1,2)_2

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
After sequencing, all reads that passed the Illumina quality filtering were considered for alignment. All samples were aligned to the mouse genome assembly version of December 2011 (GRCm38/mm10) (samples 111733-111741, 181421-181438), and mm9 (samples 12521-15072).
ChIP-Seq and ATAC-Seq reads were aligned with Bowtie 1.0.0 (Langmead, B. et al. ,2009). Read coverages were calculated with the BEDTool program version 2.27.1 (Quinlan, 2010), were normalized to reads per millions (RPM) using the SAMTools version 1.9 (Li, 2009) as well as the KentTools version 20190507 [Kuhn, 2013].
RNA-Seq reads were aligned with STAR 2.4.2a [Dobin, 2013] in transcriptome guided alignment mode (samples 111733-111741, 181421-181438), and tophat 1.4.1 (samples 12521-15072). Transcripts per million (TPMs) were calculated as described previously.
Assembly: mm9, mm10
Supplementary files format and content: bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: bone marrow

extract_protocol:
NebNext UltraII RNA Library Prep Kit
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: In vitro pro-B cell

tag: cell preparation

value: short term in vitro expansion

tag: chip antibody

value: anti-Pax5 (rabbit polyclonal Ab, detecting the paired domain (amino acids 17-145) (16); Busslinger laboratory)

tag: replicate number


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(DCRD1/DCRD1)_2

tag: cell type


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(DCRD1,2/DCRD1,2)_1


title: T40

tag: cell line

value: glioblastoma

tag: treatment

value: CAN-2409 (previously called GMCI)


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(+/+)_2

tag: genotype


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(+/+)_1


title: TDLN-H-B16-KOICB-CD8

city: London

first: Luca

last: Biasco

address: 30 Guilford St, Holborn

institute: UCL

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Tumor Draining Lymph node

extract_protocol:
scRNA-seq on tumor-infiltrating CD8+ TILs:Tcf7fl/fl (wildtype) and E8i-CRE+ x Tcf7fl/fl (TCF1 KO) mice were injected with 3.75x105 B16-OVA or 1x106 MC38-OVA cells subcutaneously in the right flank. On day 6 and 9, mice were randomized and treated intraperitoneally with a combination of anti-PD-L1 (10F.9G2, 200g per mouse) and anti-Tim-3 (RMT3-23, 200g per mouse) antibodies or control immunoglobulins (Rat IgG2a and Rat IgG2b). Two (for MC38-OVA tumors) or three (for B16-OVA tumors) days after the second dose, tumors were harvested (n=3-5 per group) dissociated to single cell suspensions prior to fluorescence-activated cell sorting. An equal amount of CD45+ TCRb+ CD8+ T cells were sorted from each mouse (10,000 cells/mouse) within each experimental group and then pooled together prior to scRNA sequencing. scRNA-seq on adoptively transferred OTI T cells from the TDLN: CD45.1 C57Bl/6 were injected with 3.75x105 B16-OVA or 1x106 MC38-OVA cells subcutaneously in the right flank. On day 5 post tumor implantation, mice were randomized by tumor size and given 1x106 TCF7 KO or WT OT-1 naïve T cells resuspended in PBS via tail vein injections. Mice were then treated on day 6 post tumor injection with one dose of ICB (PDL1 + Tim3, 200ug each) or control antibodies (Rat IgG2a and Rat IgG2b). On day 8 post tumor injection the inguinal tumor-draining lymph nodes (TDLN) were dissected and dissociated to single cell suspensions by passing tissue through a 70M filter prior to centrifugation and fluorescence-activated cell sorting. CD45.2+CD8+TCRVa2+ OTI T cells were purified from the TDLN of n=4-5 mice per group.
For the generation of single cell transcriptomes, 10^3 to 16x10^3 -  target cells from each sorted population were run using the Chromium Controller (10x Genomics) using Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries generated were then run on the NextSeq 550 Sequencing System (Illumina) using NextSeq 500/550 High Output v2.5 (150 cycles) Kit (Illumina).

value: CD8 T cells

value: Tumor Draining Lymph node

value: 8-9 weeks

value: TCF1 KO

tag: challenge

value: ICB


title: TDLN-G-B16-WTICB-CD8

description: 10x Genomics


title: TDLN-C-MC38-WTICB-CD8

description: 10x Genomics


title: TDLN-E-B16-WTISO-CD8

description: 10x Genomics

value: ISO


title: TDLN-D-MC38-KOICB-CD8

description: 10x Genomics


title: TDLN-F-B16-KOISO-CD8

description: 10x Genomics


title: TDLN-B-MC38-KOISO-CD8

description: 10x Genomics


title: TDLN-A-MC38-WTISO-CD8

description: 10x Genomics


title: Tumor-H-B16-KOICB-CD8

description: 10x Genomics

source_name: Tumor

value: Tumor

value: TCF1 KO (E8i-CRE+ x Tcf7fl/fl) and WT (E8i-CREneg x Tcf7fl/fl) mice, previously generated in our lab ( DOI:10.1016/j.immuni.2018.11.014).

value: 8-11 weeks


title: Tumor-A-MC38-WTISO-CD8

description: 10x Genomics

value: WT


title: Tumor-F-B16-KOISO-CD8

description: 10x Genomics


title: Tumor-G-B16-WTICB-CD8

description: 10x Genomics


title: Tumor-E-B16-WTISO-CD8

description: 10x Genomics


title: ChIP-Seq bone marrow In vitro pro-B cell Pax5(DCRD1/DCRD1)_1


title: DSE_PG_3.RNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

data_processing:
smrtlink (version 9.0, parameters) was used to perform primer removal, polyA tail removal, chimeric reads removal, and reads clustering on the long reads (LRs).
The clustered LRs were aligned to the susScr11 reference genome using GMAP (version 2018-07-04, parameters -t 10 -B 5 -A --nofails -f samse -n1). The aligned LRs with clipping region longer than 100-nt at either end were filtered out.
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: Long reads numbers mapped to each transcript have been summarized into Summary_PacBio.txt. Transcript TPM values were summarized into RNAseq_expression.tpm.txt. MiRNA RPM values were summarized into miRNAseq_expression.rpm.txt
Supplementary files format and content: PacBio's assembly file was tab-delimited.

organism: Sus scrofa

source_name: prostate gland

growth_protocol: All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
PacBio SMRTseq uses PacBio library construction protocol. Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA)

value: prostate gland


title: DSE_PG_1.RNAseq


title: BMI_BG_1.RNAseq

source_name: bulbourethral gland

value: bulbourethral gland


title: DSE_BG_3.RNAseq


title: DSE_VG_2.RNAseq

source_name: vesicular gland

value: vesicular gland


title: DSE_BG_1.RNAseq


title: BMI_BG_3.RNAseq


title: BMI_PG_3.RNAseq


title: DSE_BG_2.RNAseq


title: DSE_VG_1.RNAseq


title: DSE_VG_3.RNAseq


title: BMI_PG_2.RNAseq


title: BMI_PG_1.RNAseq


title: BMI_VG_2.RNAseq


title: DSE_Epi_3.RNAseq

source_name: epididymis

value: epididymis


title: DSE_Epi_2.RNAseq


title: DSE_Epi_1.RNAseq


title: BMI_BG_2.RNAseq


title: BMI_Epi_2.RNAseq


title: DSE_PG_2.RNAseq


title: DSE_Tes_3.RNAseq

source_name: testis

value: testis


title: DSE_Tes_1.RNAseq


title: DSE_Tes_2.RNAseq


title: BMI_Tes_2.RNAseq


title: BMI_VG_3.RNAseq


title: WISP3ko12wT

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
the Cell Ranger pipeline v3 was used to process the fastq files and generate the count matrix
Assembly: hg19

source_name: in vitro derived cartilage chrondrocytes, TGFb-treated, 12-weeks

growth_protocol: A detailed description of the protocol for generating chondrogenic cells and tissues from human pluripotent stem cells has been published (PMID: 25961409).

extract_protocol: RNA libraries were prepared using the 10x Chromium v2 3' kit following the manufacturer's protocols

value: F

tag: time

value: 12 weeks


title: WISP3ko6wT

source_name: in vitro derived cartilage chrondrocytes, TGFb-treated, 6-weeks

value: 6 weeks


title: BMI_Tes_1.RNAseq


title: 06wTi


title: 12wTi


title: H9_KO_T_rep1

description: H9WISP3KO hESC-derived articular chondrocytes, female

data_processing:
alignment to hg19: Star align version 2.7.3, default parameters for hg19 alignment
RNA-seq read mapping: Salmon version 1.2.1, salmon -l A --numBootstraps 100 --gcBias –validateMappings
Read abundance normalization: DESeq2 version 1.36.0
Assembly: hg19
Supplementary files format and content: Batch1-4_normalized_counts.xlsx : Normalized abundance counts across primary RNA-seq datasets generated

source_name: In-vitro TGF-beta treated sample

extract_protocol: TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Collagenase digestion

value: HESC-derived chondrocytes

value: female


title: H9_KO_T_rep3


title: H9_KO_T_rep2


title: BMI_VG_1.RNAseq


title: Control2

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw count and Differentially expressed gene list

source_name: Right ventricular

extract_protocol:
Total RNA was isolated using the miRNAeasy mini kit (Qiagen#217004) and used for RNA-sequencing.
A Illumina TruSeq kit  stranded total RNA  kit ( Ribo zero) was used in library preparation following the manufacturer's guidelines.

value: Right ventricular

tag: diseasse state


title: Control5


title: Control4


title: Control3


title: Patient2

value: endomyocardial


title: Patient1


title: Patient3


title: BMI_Epi_3.RNAseq


title: BMI_Tes_3.RNAseq


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP+, mecom -/-, 5dpf, scRNAseq

city: New York

first: Jeremy

last: Dasen

state: NY

address: 435 E 30th St

department: Neuroscience Institute

institute: New York University Grossman School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: build GRCz11
Supplementary files format and content: h5 files

organism: Danio rerio

source_name: tail

extract_protocol:
DsRed positive cells were isolated from 2 dpf or 5 dpf control, mecom mutant, or prdm16 mutant zebrafish embryos on an Tg(olig2:DsRed2) or Tg(prdm16::GFP);Tg(olig2:DsRed2) background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade, dissociated using papain, filtered, and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP-, DsRed2-, and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRanger(v5.0.1) pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome (build GRCz11).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: tail

value: olig2dsRed, mecom-/-, prdm16:gal4UASGFP

value: Spinal cord MNs


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP +, 5dpf, scRNAseq

description: 10x Genomics

value: olig2:dsRed, prdm16gal4:UASGFP


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP-, mecom -/-, 5dpf, scRNAseq

description: 10x Genomics


title: Joint sample, KBxN + 6F2-4

first: Jason

middle: A

last: Hackney

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the mouse genome assembly GRCm38.
Assembly: GRCm38
Supplementary files format and content: TSV count matrices

source_name: joint

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: disease state

value: K/BxN serum-induced arthritis model

value: anti-SIRPa

value: joint


title: Spinal cord MNs, olig2dsRed, 2dpf, scRNAseq

description: 10x Genomics


title: Joint sample, KBxN + 6F2-3


title: Joint sample, KBxN + 6F2-2


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP -, 5dpf, scRNAseq

description: 10x Genomics


title: Joint sample, Naive + aGP120-3

value: Naive


title: Joint sample, KBxN + aGP120-2


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP -, prdm16-/- 5dpf, scRNAseq

description: 10x Genomics


title: Joint sample, KBxN + aGP120-1


title: Joint sample, KBxN + aGP120-4


title: BMI_Epi_1.RNAseq

value: epididymis


title: Joint sample, KBxN + 6F2-1


title: Joint sample, Naive + aGP120-1


title: Joint sample, KBxN + aGP120-3


title: Joint sample, Naive + aGP120-4


title: single-nucleus Hi-C on mouse NPC - cell 186

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

data_processing:
The fastq files from scHi-C experiments have been mapped and preprocessed following the methods described in previous studies. In brief, the scHi-C read pairs were aligned to mm10 genome with BWA-MEM with the ‘-5’ option, to report the most 5′ end alignment as the primary alignment, and the ‘-P’ option to perform the Smith–Waterman algorithm to rescue chimeric reads. Only the primary alignments were used in the next steps. Then read pairs were deduplicated with the Picard tool to keep only one read pair at the exact same position. We further filtered the duplicated reads specific to scHiC datasets: (1) each chromosome was splitted into consecutive nonoverlapping 1-kb bins and only one contact was kept for each 1-kb bin pair, and (2) 1-kb bins that contact with more than ten other 1-kb bins were removed, since they are likely mapping artifacts.
Assembly: mm10
Supplementary files format and content: The ”valid_pairs.rm_hotspot.sorted.txt“ files contain the valid contacts for each single cell.

source_name: neuron progenitor cells

growth_protocol: The F1 Mus musculus castaneus × S129/SvJae mouse ESC (F123) line was a gift from Dr. Rudolf Jaenisch and was cultured in KSR medium as previously described. The detailed protocol can be found at 4DN data portal at: https://data.4dnucleome.org/protocols/1d39b581-9200-4494-8b24-3dc77d595bbb/. To differentiate F123 mESCs to mNPCs, we followed the previously published protocol: in brief, the F123 mESCs was first passaged once on 0.1% gelatin-coated feeder-free plates before formation of cellular aggregates (CAs). Then mESCs cells was then trypsinized and 4 million cells were plated onto Greiner Petri dishes in CA medium. After four days retinoic acid (RA) was added to CA medium at a final concentration 5μM and the CAs were cultured in CA medium with RA for another four days. After that the CAs were dissociated and the cells were plated on PORN/laminin-coated plates to allow differentiation of neuronal precursors in N2 medium for another two days before collection of NPCs.

extract_protocol:
F123 mESCs and NPCs were harvested by accutase treatment and fixed with 1% (v/v) methanol-free formaldehyde at room temperature for 10 minutes. scHi-C libraries were prepared using methods as previously described with slight modifications. In brief, 1-3 million crosslinked mESCs or NPCs were incubated overnight at 37 °C with 200 U MboI followed by proximity ligation at room temperature with slow rotation for 4 hours. Then the nuclei were stained with Hoechst and the single 2N nuclei were sorted by FACS into wells of 96-well plate. After overnight reverse crosslinking at 65 °C, the 3C-ligated DNA in each cell was amplified using GenomiPhi v2 DNA amplification kit (GE Healthcare) for 4-4.5 hours.
After purification with AMPure XP magnetic beads and quantification, 10ng WGA product was used to construct library with Tn5.
single-nucleus Hi-C

value: ES-derived neural progenitor cells

value: 129/Sv X Cast


title: Control6


title: single-nucleus Hi-C on mouse NPC - cell 188


title: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP +, prdm16-/- 5dpf, scRNAseq

description: 10x Genomics


title: single-nucleus Hi-C on mouse NPC - cell 185


title: single-nucleus Hi-C on mouse NPC - cell 187


title: single-nucleus Hi-C on mouse NPC - cell 183


title: single-nucleus Hi-C on mouse NPC - cell 182


title: single-nucleus Hi-C on mouse NPC - cell 181


title: single-nucleus Hi-C on mouse NPC - cell 180


title: single-nucleus Hi-C on mouse NPC - cell 177


title: single-nucleus Hi-C on mouse NPC - cell 178


title: single-nucleus Hi-C on mouse NPC - cell 179


title: single-nucleus Hi-C on mouse NPC - cell 175


title: single-nucleus Hi-C on mouse NPC - cell 176


title: single-nucleus Hi-C on mouse NPC - cell 172


title: single-nucleus Hi-C on mouse NPC - cell 170


title: single-nucleus Hi-C on mouse NPC - cell 174


title: single-nucleus Hi-C on mouse NPC - cell 167


title: single-nucleus Hi-C on mouse NPC - cell 165


title: single-nucleus Hi-C on mouse NPC - cell 171


title: single-nucleus Hi-C on mouse NPC - cell 173


title: single-nucleus Hi-C on mouse NPC - cell 166


title: single-nucleus Hi-C on mouse NPC - cell 164


title: single-nucleus Hi-C on mouse NPC - cell 184


title: single-nucleus Hi-C on mouse NPC - cell 163


title: single-nucleus Hi-C on mouse NPC - cell 162


title: single-nucleus Hi-C on mouse NPC - cell 160


title: single-nucleus Hi-C on mouse NPC - cell 161


title: single-nucleus Hi-C on mouse NPC - cell 159


title: single-nucleus Hi-C on mouse NPC - cell 156


title: single-nucleus Hi-C on mouse NPC - cell 158


title: single-nucleus Hi-C on mouse NPC - cell 154


title: single-nucleus Hi-C on mouse NPC - cell 150


title: single-nucleus Hi-C on mouse NPC - cell 148


title: single-nucleus Hi-C on mouse NPC - cell 168


title: single-nucleus Hi-C on mouse NPC - cell 149


title: single-nucleus Hi-C on mouse NPC - cell 147


title: single-nucleus Hi-C on mouse NPC - cell 143


title: single-nucleus Hi-C on mouse NPC - cell 145


title: single-nucleus Hi-C on mouse NPC - cell 146


title: single-nucleus Hi-C on mouse NPC - cell 140


title: single-nucleus Hi-C on mouse NPC - cell 139


title: single-nucleus Hi-C on mouse NPC - cell 141


title: single-nucleus Hi-C on mouse NPC - cell 142


title: single-nucleus Hi-C on mouse NPC - cell 138


title: single-nucleus Hi-C on mouse NPC - cell 137


title: single-nucleus Hi-C on mouse NPC - cell 135


title: single-nucleus Hi-C on mouse NPC - cell 136


title: single-nucleus Hi-C on mouse NPC - cell 134


title: single-nucleus Hi-C on mouse NPC - cell 155


title: Joint sample, Naive + aGP120-2


title: single-nucleus Hi-C on mouse NPC - cell 133


title: single-nucleus Hi-C on mouse NPC - cell 131


title: single-nucleus Hi-C on mouse NPC - cell 130


title: single-nucleus Hi-C on mouse NPC - cell 129


title: single-nucleus Hi-C on mouse NPC - cell 132


title: single-nucleus Hi-C on mouse NPC - cell 128


title: single-nucleus Hi-C on mouse NPC - cell 169


title: single-nucleus Hi-C on mouse NPC - cell 125


title: single-nucleus Hi-C on mouse NPC - cell 124


title: single-nucleus Hi-C on mouse NPC - cell 126


title: single-nucleus Hi-C on mouse NPC - cell 123


title: single-nucleus Hi-C on mouse NPC - cell 121


title: single-nucleus Hi-C on mouse NPC - cell 119


title: single-nucleus Hi-C on mouse NPC - cell 118


title: single-nucleus Hi-C on mouse NPC - cell 120


title: single-nucleus Hi-C on mouse NPC - cell 144


title: single-nucleus Hi-C on mouse NPC - cell 117


title: single-nucleus Hi-C on mouse NPC - cell 114


title: single-nucleus Hi-C on mouse NPC - cell 115


title: single-nucleus Hi-C on mouse NPC - cell 157


title: single-nucleus Hi-C on mouse NPC - cell 153


title: single-nucleus Hi-C on mouse NPC - cell 116


title: single-nucleus Hi-C on mouse NPC - cell 113


title: single-nucleus Hi-C on mouse NPC - cell 152


title: single-nucleus Hi-C on mouse NPC - cell 151


title: single-nucleus Hi-C on mouse NPC - cell 112


title: single-nucleus Hi-C on mouse NPC - cell 111


title: single-nucleus Hi-C on mouse NPC - cell 110


title: single-nucleus Hi-C on mouse NPC - cell 109


title: single-nucleus Hi-C on mouse NPC - cell 108


title: single-nucleus Hi-C on mouse NPC - cell 107


title: single-nucleus Hi-C on mouse NPC - cell 127


title: single-nucleus Hi-C on mouse NPC - cell 104


title: single-nucleus Hi-C on mouse NPC - cell 103


title: single-nucleus Hi-C on mouse NPC - cell 100


title: single-nucleus Hi-C on mouse NPC - cell 122


title: single-nucleus Hi-C on mouse NPC - cell 102


title: single-nucleus Hi-C on mouse NPC - cell 101


title: single-nucleus Hi-C on mouse NPC - cell 99


title: single-nucleus Hi-C on mouse NPC - cell 97


title: single-nucleus Hi-C on mouse NPC - cell 98


title: single-nucleus Hi-C on mouse NPC - cell 94


title: single-nucleus Hi-C on mouse NPC - cell 96


title: single-nucleus Hi-C on mouse NPC - cell 95


title: single-nucleus Hi-C on mouse NPC - cell 91


title: single-nucleus Hi-C on mouse NPC - cell 90


title: single-nucleus Hi-C on mouse NPC - cell 92


title: single-nucleus Hi-C on mouse NPC - cell 87


title: single-nucleus Hi-C on mouse NPC - cell 88


title: single-nucleus Hi-C on mouse NPC - cell 89


title: single-nucleus Hi-C on mouse NPC - cell 86


title: single-nucleus Hi-C on mouse NPC - cell 84


title: single-nucleus Hi-C on mouse NPC - cell 83


title: single-nucleus Hi-C on mouse NPC - cell 81


title: single-nucleus Hi-C on mouse NPC - cell 106


title: single-nucleus Hi-C on mouse NPC - cell 82


title: single-nucleus Hi-C on mouse NPC - cell 78


title: single-nucleus Hi-C on mouse NPC - cell 77


title: single-nucleus Hi-C on mouse NPC - cell 79


title: single-nucleus Hi-C on mouse NPC - cell 80


title: single-nucleus Hi-C on mouse NPC - cell 105


title: single-nucleus Hi-C on mouse NPC - cell 76


title: single-nucleus Hi-C on mouse NPC - cell 75


title: single-nucleus Hi-C on mouse NPC - cell 93


title: single-nucleus Hi-C on mouse NPC - cell 73


title: single-nucleus Hi-C on mouse NPC - cell 71


title: single-nucleus Hi-C on mouse NPC - cell 74


title: single-nucleus Hi-C on mouse NPC - cell 85


title: single-nucleus Hi-C on mouse NPC - cell 66


title: single-nucleus Hi-C on mouse NPC - cell 68


title: single-nucleus Hi-C on mouse NPC - cell 69


title: single-nucleus Hi-C on mouse NPC - cell 63


title: single-nucleus Hi-C on mouse NPC - cell 70


title: single-nucleus Hi-C on mouse NPC - cell 67


title: single-nucleus Hi-C on mouse NPC - cell 64


title: single-nucleus Hi-C on mouse NPC - cell 65


title: single-nucleus Hi-C on mouse NPC - cell 60


title: single-nucleus Hi-C on mouse NPC - cell 61


title: single-nucleus Hi-C on mouse NPC - cell 57


title: single-nucleus Hi-C on mouse NPC - cell 62


title: single-nucleus Hi-C on mouse NPC - cell 54


title: single-nucleus Hi-C on mouse NPC - cell 59


title: single-nucleus Hi-C on mouse NPC - cell 58


title: single-nucleus Hi-C on mouse NPC - cell 55


title: single-nucleus Hi-C on mouse NPC - cell 56


title: single-nucleus Hi-C on mouse NPC - cell 72


title: single-nucleus Hi-C on mouse NPC - cell 53


title: single-nucleus Hi-C on mouse NPC - cell 49


title: single-nucleus Hi-C on mouse NPC - cell 51


title: single-nucleus Hi-C on mouse NPC - cell 47


title: single-nucleus Hi-C on mouse NPC - cell 46


title: single-nucleus Hi-C on mouse NPC - cell 45


title: single-nucleus Hi-C on mouse NPC - cell 44


title: single-nucleus Hi-C on mouse NPC - cell 43


title: single-nucleus Hi-C on mouse NPC - cell 42


title: single-nucleus Hi-C on mouse NPC - cell 39


title: single-nucleus Hi-C on mouse NPC - cell 41


title: single-nucleus Hi-C on mouse NPC - cell 38


title: single-nucleus Hi-C on mouse NPC - cell 37


title: single-nucleus Hi-C on mouse NPC - cell 34


title: single-nucleus Hi-C on mouse NPC - cell 33


title: single-nucleus Hi-C on mouse NPC - cell 30


title: single-nucleus Hi-C on mouse NPC - cell 28


title: single-nucleus Hi-C on mouse NPC - cell 36


title: single-nucleus Hi-C on mouse NPC - cell 32


title: single-nucleus Hi-C on mouse NPC - cell 31


title: single-nucleus Hi-C on mouse NPC - cell 52


title: single-nucleus Hi-C on mouse NPC - cell 50


title: single-nucleus Hi-C on mouse NPC - cell 26


title: single-nucleus Hi-C on mouse NPC - cell 48


title: single-nucleus Hi-C on mouse NPC - cell 29


title: single-nucleus Hi-C on mouse NPC - cell 25


title: single-nucleus Hi-C on mouse NPC - cell 40


title: single-nucleus Hi-C on mouse NPC - cell 24


title: single-nucleus Hi-C on mouse NPC - cell 27


title: single-nucleus Hi-C on mouse NPC - cell 23


title: single-nucleus Hi-C on mouse NPC - cell 22


title: single-nucleus Hi-C on mouse NPC - cell 20


title: single-nucleus Hi-C on mouse NPC - cell 21


title: single-nucleus Hi-C on mouse NPC - cell 19


title: single-nucleus Hi-C on mouse NPC - cell 18


title: single-nucleus Hi-C on mouse NPC - cell 16


title: single-nucleus Hi-C on mouse NPC - cell 15


title: single-nucleus Hi-C on mouse NPC - cell 35


title: single-nucleus Hi-C on mouse NPC - cell 14


title: single-nucleus Hi-C on mouse NPC - cell 13


title: single-nucleus Hi-C on mouse NPC - cell 12


title: single-nucleus Hi-C on mouse ESC - cell 94

source_name: embryonic stem cells

value: embryonic stem cells


title: single-nucleus Hi-C on mouse NPC - cell 2


title: single-nucleus Hi-C on mouse NPC - cell 6


title: single-nucleus Hi-C on mouse NPC - cell 1


title: single-nucleus Hi-C on mouse NPC - cell 3


title: single-nucleus Hi-C on mouse NPC - cell 7


title: single-nucleus Hi-C on mouse NPC - cell 4


title: single-nucleus Hi-C on mouse NPC - cell 11


title: single-nucleus Hi-C on mouse ESC - cell 89


title: single-nucleus Hi-C on mouse NPC - cell 10


title: single-nucleus Hi-C on mouse ESC - cell 90


title: single-nucleus Hi-C on mouse NPC - cell 8


title: single-nucleus Hi-C on mouse NPC - cell 5


title: single-nucleus Hi-C on mouse NPC - cell 9


title: single-nucleus Hi-C on mouse ESC - cell 84


title: single-nucleus Hi-C on mouse ESC - cell 87


title: single-nucleus Hi-C on mouse ESC - cell 86


title: single-nucleus Hi-C on mouse ESC - cell 85


title: single-nucleus Hi-C on mouse NPC - cell 17


title: single-nucleus Hi-C on mouse ESC - cell 88


title: single-nucleus Hi-C on mouse ESC - cell 80


title: single-nucleus Hi-C on mouse ESC - cell 82


title: single-nucleus Hi-C on mouse ESC - cell 81


title: single-nucleus Hi-C on mouse ESC - cell 83


title: single-nucleus Hi-C on mouse ESC - cell 79


title: single-nucleus Hi-C on mouse ESC - cell 92


title: single-nucleus Hi-C on mouse ESC - cell 91


title: single-nucleus Hi-C on mouse ESC - cell 93


title: single-nucleus Hi-C on mouse ESC - cell 78


title: single-nucleus Hi-C on mouse ESC - cell 76


title: single-nucleus Hi-C on mouse ESC - cell 75


title: single-nucleus Hi-C on mouse ESC - cell 71


title: single-nucleus Hi-C on mouse ESC - cell 73


title: single-nucleus Hi-C on mouse ESC - cell 66


title: single-nucleus Hi-C on mouse ESC - cell 67


title: single-nucleus Hi-C on mouse ESC - cell 60


title: single-nucleus Hi-C on mouse ESC - cell 59


title: single-nucleus Hi-C on mouse ESC - cell 58


title: single-nucleus Hi-C on mouse ESC - cell 57


title: single-nucleus Hi-C on mouse ESC - cell 72


title: single-nucleus Hi-C on mouse ESC - cell 64


title: single-nucleus Hi-C on mouse ESC - cell 69


title: single-nucleus Hi-C on mouse ESC - cell 65


title: single-nucleus Hi-C on mouse ESC - cell 55


title: single-nucleus Hi-C on mouse ESC - cell 63


title: single-nucleus Hi-C on mouse ESC - cell 52


title: single-nucleus Hi-C on mouse ESC - cell 53


title: single-nucleus Hi-C on mouse ESC - cell 61


title: single-nucleus Hi-C on mouse ESC - cell 70


title: single-nucleus Hi-C on mouse ESC - cell 56


title: single-nucleus Hi-C on mouse ESC - cell 62


title: single-nucleus Hi-C on mouse ESC - cell 68


title: single-nucleus Hi-C on mouse ESC - cell 51


title: single-nucleus Hi-C on mouse ESC - cell 54


title: single-nucleus Hi-C on mouse ESC - cell 49


title: single-nucleus Hi-C on mouse ESC - cell 74


title: single-nucleus Hi-C on mouse ESC - cell 50


title: single-nucleus Hi-C on mouse ESC - cell 48


title: single-nucleus Hi-C on mouse ESC - cell 47


title: single-nucleus Hi-C on mouse ESC - cell 46


title: single-nucleus Hi-C on mouse ESC - cell 77


title: single-nucleus Hi-C on mouse ESC - cell 45


title: single-nucleus Hi-C on mouse ESC - cell 43


title: single-nucleus Hi-C on mouse ESC - cell 42


title: single-nucleus Hi-C on mouse ESC - cell 44


title: single-nucleus Hi-C on mouse ESC - cell 37


title: single-nucleus Hi-C on mouse ESC - cell 41


title: single-nucleus Hi-C on mouse ESC - cell 36


title: single-nucleus Hi-C on mouse ESC - cell 38


title: single-nucleus Hi-C on mouse ESC - cell 40


title: single-nucleus Hi-C on mouse ESC - cell 39


title: single-nucleus Hi-C on mouse ESC - cell 33


title: single-nucleus Hi-C on mouse ESC - cell 32


title: single-nucleus Hi-C on mouse ESC - cell 28


title: single-nucleus Hi-C on mouse ESC - cell 29


title: single-nucleus Hi-C on mouse ESC - cell 26


title: single-nucleus Hi-C on mouse ESC - cell 25


title: single-nucleus Hi-C on mouse ESC - cell 24


title: single-nucleus Hi-C on mouse ESC - cell 27


title: single-nucleus Hi-C on mouse ESC - cell 23


title: single-nucleus Hi-C on mouse ESC - cell 22


title: single-nucleus Hi-C on mouse ESC - cell 20


title: single-nucleus Hi-C on mouse ESC - cell 21


title: single-nucleus Hi-C on mouse ESC - cell 18


title: single-nucleus Hi-C on mouse ESC - cell 17


title: single-nucleus Hi-C on mouse ESC - cell 34


title: single-nucleus Hi-C on mouse ESC - cell 35


title: single-nucleus Hi-C on mouse ESC - cell 30


title: single-nucleus Hi-C on mouse ESC - cell 15


title: single-nucleus Hi-C on mouse ESC - cell 14


title: single-nucleus Hi-C on mouse ESC - cell 31


title: single-nucleus Hi-C on mouse ESC - cell 16


title: single-nucleus Hi-C on mouse ESC - cell 13


title: single-nucleus Hi-C on mouse ESC - cell 10


title: single-nucleus Hi-C on mouse ESC - cell 11


title: single-nucleus Hi-C on mouse ESC - cell 12


title: single-nucleus Hi-C on mouse ESC - cell 5


title: single-nucleus Hi-C on mouse ESC - cell 7


title: single-nucleus Hi-C on mouse ESC - cell 8


title: single-nucleus Hi-C on mouse ESC - cell 6


title: single-nucleus Hi-C on mouse ESC - cell 4


title: single-nucleus Hi-C on mouse ESC - cell 3


title: single-nucleus Hi-C on mouse ESC - cell 2


title: single-nucleus Hi-C on mouse ESC - cell 1


title: COX312A62_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

description:
RNA_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 genome and the GENCODE reference transcriptome version M22 with STAR software
Raw gene counts were retrieved using QoRTs software
Normalised read counts were retrieved using DeSeq2
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided  for RNA-seq data separated for both strands and normalised to RPKMs

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 3

extract_protocol:
RNA was extracted using the QIAShredder and RNeasy Mini Kit, or RNeasy Micro kit, both with on-column DNase digestion, according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were made with total RNA equally pooled from the technical triplicate wells within an independent biological experiment, using the Illumina Stranded TruSeq Library preparation kit V2 and unique multiplexing indexes, according to the manufacturer’s instructions (Illumina).

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: CD4+ T cells driven with IL-27

value: Day 3


title: COX312A58_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3

treatment_protocol: Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.


title: COX312A42_IL-27_prdm1 fl/fl maf fl/fl CD4-Cre_Day 3


title: single-nucleus Hi-C on mouse ESC - cell 19


title: COX312A54_IL-27_prdm1 fl/fl maf fl/fl_Day 3

description:
RNA_IL-27_prdm1 fl/fl maf fl/fl_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_DbKONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl maf fl/fl


title: COX312A46_IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: COX690A46_IL-27_prdm1 fl/fl CD4-Cre_Day 3

description:
RNA_IL-27_prdm1 fl/fl CD4-Cre_Day 3
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_Prdm1KONormCounts_invitro_GEO_11Feb2022.txt

value: prdm1 fl/fl CD4-Cre


title: COX690A38_IL-27_prdm1 fl/fl CD4-Cre_Day 3


title: COX312A38_IL-27_prdm1 fl/fl maf fl/fl_Day 3


title: single-nucleus Hi-C on mouse ESC - cell 9


title: COX312A18_IL-27_prdm1 fl/fl_Day 4

description:
RNA_IL-27_prdm1 fl/fl_Day 4
Spleens from 5-10 mice age-matched mice per genotype were homogenised and incubated with unconjugated rat anti-mouse antibodies against B220 (RA3.6B2, DNAX), MHC class-II (M5/114, eBioscience) and CD8 (C291.2.43, DNAX). CD4+ T cells were then negatively enriched using magnetic beads (BioMag, Qiagen). Live naïve CD4+CD62L+CD44loCD25- T cells were then sorted to over 95% purity using the following antibodies: CD4 (RM4-5, e450), CD8 (53-6.7, FITC), CD62L (MEL-14, PE-Cy7), CD44 (IM7, PE) and CD25 (PC61.5, APC) (all from eBioscience), and propidium iodide (final concentration 2µg/ml, Sigma) on either a MoFlo XDP or Influx flow cytometer (Beckman Coulter, Inc.). Sorted naïve CD4+ T cells were activated in vitro with anti-CD3 and anti-CD28 antibodies and differentiated in the presence of Medium (no cytokines), IL-12, IL-12+IL-27, or IL-27 until Day 4, with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 and Maf on Day 3.
RNA_KineticsNormCounts_invitro_GEO_11Feb2022.txt

source_name: In vitro differentiated CD4+ T cells differentiated in the presence of: IL-27 at Day 4

value: prdm1 fl/fl

value: Day 4