title: nanoRibo-seq_B_50000

city: Cambridge

first: John

middle: Edward

last: Froberg

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

description: Ribo-seq

data_processing:
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.
Assembly: mm10, hg38
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. TPM.csv: Transcripts per Million Mapped for genes passing filter

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:
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.

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.

tag: input

value: 50000 cells

tag: fragmentation

value: RNase I 12.5 U/mL


title: Urinary exosome, ultra-high speed centrifugation [P5]

status: Public on Aug 25 2023

type: SRA

city: Guangzhou

first: Wei

last: Zhu

address: No.1 Kangda Road, Haizhu District, Guangzhou City, Guangdong Province

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

library_source: other

data_processing:
*library strategy: exosome sRNA-seq
Illumina Bcl2FastQ software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Assembly: hg19
Supplementary files format and content: \06.know_miRNA_expression\*\*.miR.expre.xls
Supplementary files format and content: \11.differential_expression\*\**vs*.diff.xls

molecule: other

organism: Homo sapiens

source_name: Urinary exosome

extract_protocol:
Urine was mixed with RiboTM Exosome Isolation Reagent and exosome isolation was performed according to the manufacturer’s instructions (Ribobio, China). Exosomal RNA was extracted by HiPure Liquid miRNA Kit/HiPure Serum/Plasma miRNA Kit (Megan, China).
Exosomal RNA were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions

tag: tissue

value: Urinary exosome

tag: subject status

value: patients with renal calculi


title: nanoRibo-seq_B_1000

country: USA

description: Ribo-seq

library_source: transcriptomic

molecule: total RNA

value: 1000 cells

value: RNase I 2.5 U/mL

tag: cell type


title: Urinary exosome, ultra-high speed centrifugation [C9]

value: normal subjects


title: nanoRibo-seq_A_50000

description: Ribo-seq


title: H1, NAT10-KD, T1.5, rep2

city: Beijing

first: Yuan

last: Zhou

address: 38 college road

institute: Peking University

data_processing:
First, fastp software (v0.21.1) was used to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using HISAT2 software (v2.2.1), with the genome annotation from Ensembl (http://www.ensembl.org, version 107) as the reference gene model.
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
FeatureCounts (v2.0.3) software was used for gene expression quantification.
Absolute transcript concentrations per cell were computed by linear-fitting the RNA spike-in TPM values to attomoles.  RNA half-life measures were calculated as described in Wang et al. (Wang et al., 2014).
Assembly: hg38
Supplementary files format and content: Excel file includes half-life estimations based on attomole-transformed gene expression: All_samples.halflife_information.xlsx
Supplementary files format and content: Excel file includes includes raw read counts for all samples: All_samples.halflife_information.xlsx

molecule: polyA RNA

source_name: early embryo

growth_protocol: human ESC cell lines H1 (WiCell Research Institute) were cultivated in serum-free,defined Pluripotency Growth Master1 (PGM1) (Cellapy,Cat#CA1007500) and grown on plates coated with growth-factor-reduced Matrigel (CORNING,Cat#354248).

extract_protocol:
Total RNA was extracted from 18 samples using TRIzol Reagent (Invitrogen, cat. NO 15596026). RNA was purified and ERCC spike-in was added. A certain amount of RNA samples is denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
We used the BGISEQ platform for library construction. High-throughput sequencing was performed on each qualified library and the amount of data for each sample was guaranteed to meet the standard.

treatment_protocol: shRNA targeting sequences against NAT10 were designed, synthesized and subcloned into the GV112 vector. Cells transduced with NAT10 shRNA or negative control shRNA lentivirus with GFP (Genechem, Shanghai, China) were cultured for 48h. GFP+ cells then were enriched and expanded in TeSR-E8 medium with 0.5ug/ml puromycin. Transcription was inhibited by ActinomycinD and samples were collected at predetermined time intervels.

value: early embryo

tag: cell line

value: human embryonic stem cell

tag: genotype

value: NAT10 knockdown

tag: time


title: E18.5_ctrl1_cell19

city: Stockholm

first: Kasra

last: Nikouei

address: Solnav. 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
SmartSeq2
Munguba_Nikouei_E18.5_counts.txt
Munguba_Nikouei_E18.5_cell_annotation.txt

library_source: transcriptomic single cell

data_processing:
Fastq files demultiplexed by deindexer (https://github.com/ws6/deindexer) using the Nextera index adapters and the 384-well layout. Individual fastq files were then mapped to the genome assembly using the STAR aligner (Dobin et al. 2013; DOI:10.1093/bioinformatics/bts635) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads. The expression values were computed per gene as described in (Ramsköld et al. 2009; DOI: 10.1371/journal.pcbi.1000598 ), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013; DOI: 10.1371/journal.pone.0053822). The count matrix shows the individual counts aligning to each gene per cell.
genome build: mm10
Tab-delimited text format, in which cells make up the columns and genes the rows, with corresponding cell annotation file.

organism: Mus musculus

source_name: Neocortex

extract_protocol:
Embryonic day 18.5 (E18.5) pups were extracted after sacrificing SstCre/+::R26R CAG-boosted eGFP (RCE)/+::Sox6fl/± females with plugged pregnancies. The neocortices of the pups were dissected in ice-cold HBSS. Genotyping of the pups were done in parallel by using QuickExtract DNA Solution (Lucigen). The tissue was dissociated into a single cell suspension, as previously described (Muñoz-Manchado et al. 2018; DOI: 10.1016/j.celrep.2018.07.053). Briefly, the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Cell suspension obtained was filtered with 20 μm filter and kept in cold oxygenated Hank's balanced salt solution (HBSS) with 0.2% Bovine Serum Albumin (BSA). EGFP positive but DRAQ7 negative (dead cell marker, Invitrogen) cells were FACS sorted into 384-well plates containing lysis buffer and processed in large accordance with the Smartseq2 protocol (Picelli et al. 2014; DOI: 10.1038/nprot.2014.006).
The libraries were generated according to the Smartseq2 protocol (Picelli et al., 2014; DOI: 10.1038/nprot.2014.006). The single-cell transcriptome data was generated at the Eukaryotic Single-cell Genomics facility at Science for Life Laboratory in Stockholm, Sweden.

value: Neocortex

tag: age

value: Somatostatin interneuron

value: SstCre::RCE::Sox6 flox/+


title: H1, NAT10-KD, T1.5, rep3


title: E18.5_ctrl1_cell18


title: Urinary exosome, ultra-high speed centrifugation [C8]


title: H1, NAT10-KD, T3.5, rep3


title: E18.5_ctrl1_cell17


title: H1, NAT10-KD, T0, rep3


title: E18.5_ctrl1_cell16


title: E18.5_ctrl1_cell22


title: H1, NAT10-KD, T1.5, rep1


title: Urinary exosome, ultra-high speed centrifugation [C6]


title: Urinary exosome, ultra-high speed centrifugation [C7]


title: BJAB, Paracaspase and TRAF6 binding double-mutant MALT1, CARD11 mut, rep4

city: Parkville

first: Göksu

last: Avar

state: Victoria

address: 30 Flemington Road

department: Biochemistry and Pharmacology

country: Australia

institute: University of Melbourne

description:
S1546
Sample_23L001546

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. The three data tables (as described in the metadata) were handled separately. Observed batch effects were added to the "coldata". Where batch effects were observed, DESeq design was "~Batch+Genotype" (Rawtable2, Rawtable3), otherwise only "~Genotype" (rawtable1).
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 files contain the count tables before filtering
Supplementary files format and content: coldata#.csv files are the data tables that were used for DESeq2's "coldata" argument

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 for the RNAseq samples, 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

value: BJAB

tag: treatment


title: E18.5_ctrl1_cell20


title: nanoRibo-seq_A_1000

description: Ribo-seq


title: nanoRibo-seq_B_10000

description: Ribo-seq

value: 10000 cells


title: E18.5_ctrl1_cell15


title: E18.5_ctrl1_cell14


title: Urinary exosome, ultra-high speed centrifugation [C5]


title: H1, NAT10-KD, T0, rep1


title: H1, NAT10-KD, T0, rep2


title: nanoRibo-seq_A_10000

description: Ribo-seq


title: BJAB, Paracaspase mutant MALT1, CARD11 mut, rep4

description:
S1544
Sample_23L001544


title: Urinary exosome, ultra-high speed centrifugation [C4]


title: BJAB, MALT1 Wild type, CARD11 mut, rep4

description:
S1543
Sample_23L001543


title: H1, CTL, T3.5, rep3

value: sh control


title: H1, CTL, T3.5, rep2


title: E18.5_ctrl1_cell13


title: E18.5_ctrl1_cell12


title: Urinary exosome, ultra-high speed centrifugation [C3]


title: BJAB, MALT1 Knockout, CARD11 mut, rep4

description:
S1542
Sample_23L001542


title: Urinary exosome, ultra-high speed centrifugation [C2]


title: H1, CTL, T3.5, rep1


title: E18.5_ctrl1_cell11


title: BJAB, Paracaspase and TRAF6 binding double-mutant MALT1, CARD11 mut, rep3

description:
S1541
Sample_23L001541


title: E18.5_ctrl1_cell10


title: BJAB, TRAF6 binding mutant MALT1, CARD11 mut, rep3

description:
S1540
Sample_23L001540


title: Urinary exosome, ultra-high speed centrifugation [C1]


title: BJAB, TRAF6 binding mutant MALT1, CARD11 mut, rep4

description:
S1545
Sample_23L001545


title: E18.5_ctrl1_cell8


title: TB, S29, Decidua Basalis

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, decidua basalis

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, decidua basalis

tag: clinical group

value: TB

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: H1, CTL, T1.5, rep1


title: TB, S28, Decidua Basalis

description: Illumina HiSeq 2500


title: BJAB, Paracaspase mutant MALT1, CARD11 mut, rep3

description:
S1539
Sample_23L001539


title: BJAB, MALT1 Wild type, CARD11 mut, rep3

description:
S1538
Sample_23L001538


title: H1, CTL, T0, rep3


title: E18.5_ctrl1_cell7


title: BJAB, MALT1 Knockout, CARD11 mut, rep3

description:
S1537
Sample_23L001537


title: TB, S27, Decidua Basalis

description: Illumina HiSeq 2500

value: Male


title: E18.5_ctrl1_cell6


title: E18.5_ctrl1_cell5


title: BJAB, Paracaspase and TRAF6 binding double-mutant MALT1, CARD11 mut, rep2

description:
S1536
Sample_23L001536


title: H1, CTL, T0, rep2


title: H1, CTL, T0, rep1


title: TB, S26, Decidua Basalis

description: Illumina HiSeq 2500


title: E18.5_ctrl1_cell4


title: BJAB, TRAF6 binding mutant MALT1, CARD11 mut, rep2

description:
S1535
Sample_23L001535


title: H1, CTL, T1.5, rep2


title: BJAB, Paracaspase mutant MALT1, CARD11 mut, rep2

description:
S1534
Sample_23L001534


title: H1, NAT10-KD, rep4

data_processing:
First, fastp software (v0.21.1) was used to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using HISAT2 software (v2.2.1), with the genome annotation from Ensembl (http://www.ensembl.org, version 107) as the reference gene model.
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
FeatureCounts (v2.0.3) software was used for gene expression quantification. Differential gene detection was performed using DESeq2 (v1.26.0).
Assembly: hg38
Supplementary files format and content: Excel file includes read counts for all samples

extract_protocol:
Total RNA was extracted from control and NAT10 KD hESCs using TRIzol Reagent (Invitrogen, cat. NO 15596026). Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples is denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
We used the BGISEQ platform for library construction. High-throughput sequencing was performed on each qualified library and the amount of data for each sample was guaranteed to meet the standard.

treatment_protocol: shRNA targeting sequences against NAT10 were designed, synthesized and subcloned into the GV112 vector. Cells transduced with NAT10 shRNA or negative control shRNA lentivirus with GFP (Genechem, Shanghai, China) were cultured for 48h. GFP+ cells then were enriched and expanded in TeSR-E8 medium with 0.5ug/ml puromycin.


title: E18.5_ctrl1_cell9


title: EOPE+FGR, S25, Decidua Basalis

description: Illumina HiSeq 2500

value: EOPE+FGR


title: TB, S30, Decidua Basalis

description: Illumina HiSeq 2500

value: Hispanic


title: iPTB, S24, Decidua Basalis

description: Illumina HiSeq 2500

value: iPTB

value: Other


title: H1, NAT10-KD, rep3

value: early embryo

value: human embryonic stem cell

value: NAT10 knockdown


title: E18.5_ctrl1_cell3

value: Neocortex

value: Somatostatin interneuron

value: SstCre::RCE::Sox6 flox/+


title: H1, CTL, T1.5, rep3

value: sh control


title: iPTB, S23, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis


title: BJAB, MALT1 Wild type, CARD11 mut, rep2

description:
S1533
Sample_23L001533

value: B cell

value: BJAB


title: E18.5_ctrl1_cell2


title: EOPE, S22, Decidua Basalis

description: Illumina HiSeq 2500

value: EOPE

value: Female

value: Non-Hispanic


title: E18.5_ctrl1_cell1


title: H1, NAT10-KD, rep2


title: H1, NAT10-KD, rep1


title: EOPE, S21, Decidua Basalis

description: Illumina HiSeq 2500

value: Male

value: Black


title: H1, CTL, rep4


title: BJAB, MALT1 Knockout, CARD11 mut, rep2

description:
S1532
Sample_23L001532


title: BJAB, TRAF6 binding mutant MALT1, CARD11 mut, rep1

description:
S1530
Sample_23L001530


title: Rag1-/-Mom-VH81X pre-B nucRNA rep2

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were trimmed for poor quality and adaptor sequence using Trim galore and mapped to the GRCm38 mouse genome build with Hisat2.
Log2-transformed reads per million were calculated over 500 kb bins genome-wide using Seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Assembly: GRCm38
Supplementary files format and content: nucRNA_log2_reads_per_million.txt: tab-delimited text file containing coordinates of 500 kb bins and log2-transformed reads per million over these bins for each pro-B and pre-B cell replicate

molecule: nuclear RNA

source_name: Bone marrow

extract_protocol:
Single cell suspensions were prepared from bone marrow from femurs and tibias of 8-12-week old mice (6-11 mice pooled per sample), and pro- or pre-B cells were isolated by magnetic cell sorting using CD19 MACS beads (enrichment) for pro-B cells, or depletion of non-B cells using biotinylated antibodies against Ter119, Mac1, Gr1, Ly6c and Cd3e with streptavidin MACS beads for pre-B cells (Miltenyi), according to manufacturer's instructions, followed by FACS with the indicated markers. Nuclear RNA was isolated as previously described (Bolland et al., 2016; https://doi.org/10.1016/j.celrep.2016.05.020).
Nuclear RNA-Seq libraries were generated as previously described (Bolland et al., 2016; https://doi.org/10.1016/j.celrep.2016.05.020), and sequenced on paired end on Illumina HiSeq 2500 runs.

tag: strain

value: Bone marrow

value: Pre-B cells

value: 8-12 weeks

tag: Sex

value: pooled male and female

tag: facs markers


title: H1, CTL, rep3

tag: tissue

value: early embryo

value: human embryonic stem cell


title: Rag1-/-Mom-VH81X pre-B nucRNA rep1


title: Rag1-/-Mom pro-B nucRNA rep2

value: Pro-B cells


title: BJAB, Paracaspase mutant MALT1, CARD11 mut, rep1

description:
S1529
Sample_23L001529


title: H1, CTL, rep2


title: BJAB, MALT1 Knockout, CARD11 mut, rep1

description:
S1527
Sample_23L001527


title: H1, CTL, rep1


title: EOPE, S19, Decidua Basalis

description: Illumina HiSeq 2500


title: EOPE, S18, Decidua Basalis

description: Illumina HiSeq 2500

value: White


title: EOPE, S20, Decidua Basalis

description: Illumina HiSeq 2500


title: BJAB, MALT1 Wild type, CARD11 mut, rep1

description:
S1528
Sample_23L001528


title: EOPE+FGR, S17, Decidua Basalis

description: Illumina HiSeq 2500

value: EOPE+FGR

value: Other


title: Thymus CHi-C rep2

library_source: genomic

data_processing:
The Hi-C User Pipeline (HiCUP, version 0.7.2) (Wingett et al. 2015; https://doi.org/10.12688/f1000research.7334.1) was used to identify Hi-C ligation junctions, trim, map each of the paired reads separately to the GRCm38 mouse reference genome using Bowtie2 (version 2.3.2), filter out uninformative di-tags, de-duplicate and assess the cis:trans ratio in Hi-C and Capture Hi-C datasets.
CHi-C data from separate lanes were processed separately, before combining di-tags and further deduplicating.
For AB compartment analysis, the genome was binned into 500kb bins and the runHiCpca.pl function in HOMER was applied to Hi-C datasets (pre-capture) to identify the first principal component (PC1). A H3K4me3 ChIP-seq dataset (GSE80155) was used to determine the sign on the PC eigenvectors. Default parameters were used except -active H3K4me3.
HOMER (version 4.7) software (Lin et al. 2012; https://doi.org/10.1038/ni.2432) was used to produce raw and normalised interaction frequency matrices at 20kb resolution for the Igh locus in Rag-/-Mom and Rag-/-Bal pro-B cells, and thymocytes. A background model at 20kb resolution was generated and the analyzeHiC function was used to produce interaction matrices, using the -simpleNorm option to omit distance correction.
Virtual 4Cs were performed from each baited HindIII fragment in Seqmonk v1.47.1 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Other ends of reads mapping to each viewpoint were extracted and quantified in 500kb bins genome-wide, creating 4C-like datasets. The first 3Mb of every chromosome's centromeric end were omitted, as was 4.5Mb around the Vh81X transgene (chr16:81,000,000-85,500,000), and regions were screened against a blacklist. Modified z-score analysis was performed on inter-chromosomal read counts to identify the highest outlier bins with z-score>3.5, representing the most frequent interactions with the viewpoint. An interaction between the viewpoint and a 500kb bin was considered significant if z-score was greater than 3.5 in both biological replicates. For these, an average z-score was calculated. Note that finite z-scores for the Tcf3 baited region could not be calculated for Rag1-/-Mom pro-B CHi-C rep2; this viewpoint and ChrX_extra_region which was unintentionlly included due to BAC contamination were excluded from the trans analysis and are thus omitted from the transInteractions supplementary file.
Assembly: GRCm38
Supplementary files format and content: PC1.txt files: tab-delimited text files containing coordinates of 500kb bins and the scores of the first two principal components calculated from Hi-C (uncaptured) data.
Supplementary files format and content: HomerOutput.txt files: tab-delimited text files containing the raw interaction matrices obtained by HOMER analysis of CHi-C data for reads in which both ends map to the baited Igh region.
Supplementary files format and content: transInteractions.txt: tab-delimited text file containing coordinates and z-scores for trans interactions from each of the baited viewpoints in each replicate, showing all interactions that were significant (z-score > 3.5 in both replicates) for at least one cell type.

molecule: genomic DNA

source_name: Thymus

extract_protocol:
Single cell suspensions were prepared from bone marrow from femurs and tibias of 8-12-week old mice (5-11 mice pooled per sample), and pro- or pre-B cells were isolated by magnetic cell sorting using CD19 MACS beads (Miltenyi), according to manufacturer's instructions. Thymi from 4-6 mice were pooled per sample and mashed through a cell strainer to make a single cell suspension. 20-50x106 cells were cross-linked for 10min at room temperature (RT) in 37ml of DMEM supplemented with 10% FBS (Invitrogen) and containing a final concentration of 2% formaldehyde (Agar Scientific). The reaction was quenched with 1M glycine added to a final concentration of 0.125M.
Hi-C and corresponding CHi-C libraries were generated using HindIII, essentially as described (Schoenfelder et al. 2015; https://doi.org/10.1101/gr.185272.114), except that a custom bait system was used for CHi-C, to enrich for the following coordinates covering the indicated genes/loci: Igh (chr12:113074084-116172457); Igk (chr6:67551867-70946524); Igl (chr16:18988679-19399360); Pax5 (chr4:44520128-44726836); Foxo1 (chr3:52259656-52410291); Il7r (chr15:9383457-9554632); Rag1Rag2 (chr2:101453218-101668262); Hist1 (chr13:23435289-23662601); Vmrn (chr13:22567467-22766157); Hbb (chr7:103691846-103882170); Yy1 (chr12:108661004-108867386); Tcf3 (chr10:80376568-80590771); Ikzf1 (chr11:11620820-11820206); Nanog (chr6:122603111-122816854); p27kip (chr6:134790973-135002484); Ebf1 (chr11:44480841-44818451); Bach2 (chr4:32365899-32612758); Runx1 (chr16:92486288-92893397); Notch1 (chr2:26312447-26526297); ChrX_extra_region (chrX:151535649-151692794). Baits were generated from BACs covering the regions of interest, by digestion with HindIII, ligation of the T7 promoter sequence, sonication and in vitro transcription. Hi-C and Capture Hi-C libraries were sequenced as 100bp paired-end reads on Illumina HiSeq2500

value: Thymus

value: Total thymocytes

value: WT

tag: mouse model_source


title: EOPE, S16, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis

value: EOPE

value: Female


title: Rag1-/-Mom pro-B nucRNA rep1

tag: cell type


title: Cd4cre Nfe2l2fl/fl, scRNAseq

city: Incheon

first: Hye-Yeon

last: Ju

address: 119 Academy-ro Yeonsu-gu, Incheon Republic of Korea

country: South Korea

institute: Incheon National University

description: 10X Genomics

data_processing:
CellRanger v4.0.0 (10x Genomics) was used to perform single-cell 5’ gene counting using mouse genome GRCm38.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Mice were anesthetized with isoflurane and intranasally administrated with a mixture of 7 ug of PAO and 20 µg of Ova every other day for 9 days (day 0, 2, 4, 6, 8). In house dust mite (HDM)-induced lung inflammation experiments, mice were sensitized on day 0 by 1 µg of Der f 1 via intranasal route. After 1 week, mice were intranasally administered with 10 µg of Der f 1 every day for a total five times (day 7, 8, 9, 10, 11). Sixteen hours after the last administration, all mice were euthanized and bronchoalveolar lavage (BAL) fluid, lung, and mediastinal lymph node were obtained for further analysis. For mixed bone marrow transplantation experiment, donor bone marrow cells from WT control (CD45.1+/+) and Cd4creNfe2l2fl/fl (CD45.2+/+) mice were mixed at 1:1 ratio and adoptively transferred into irradiated recipient Rag1-/- mice. After 4-week reconstitution period, the recipients were intranasally injected with a mixture of PAO/Ova as previously described.
To generate single cell Gel Beads-in-Emulsion (GEMs), the 10x Genomics Chromium platform was used to capture and barcode the cells by following the manufacturer’s protocol (10x Genomics, Pleasanton, CA, USA). Cell suspensions were loaded on to 10x Genomics Chromium Next GEM Chip K along with the reverse transcription master mix. Along with gel beads coated with oligonucleotides, cells were divided into the GEMs. These oligonucleotides were used for mRNA capture inside the droplet by 13 bp oligo-dT after cell lysis. After reverse transcription, cDNAs with barcodes were amplified and qualified using BioAnalyzer 2100 (Agilent technologies, Santa Clara, CA, USA). The libraries were constructed from these DNA products with the Single Cell Reagent Kit (5’ v2 chemistry) for each sample. Adapters were ligated on to the cDNAs and amplified with indexing primer.

value: Lung

value: CD4+ cells

value: 8-15 weeks old


title: BJAB, Paracaspase and TRAF6 binding double-mutant MALT1, CARD11 mut, rep1

description:
S1531
Sample_23L001531

value: B cell

tag: cell line

value: BJAB


title: BJAB, TRAF6 binding mutant API2:MALT1 fusion protein expressing, rep5

description:
S1526
Sample_23L001526

tag: genotype


title: Nfe2l2fl/fl, scRNAseq

description: 10X Genomics


title: BJAB, Paracaspase mutant API2:MALT1 fusion protein expressing, rep5

description:
S1525
Sample_23L001525


title: FGR, S15, Decidua Basalis

description: Illumina HiSeq 2500

value: FGR

value: Male

value: Hispanic


title: BJAB, Wild type API2:MALT1 fusion protein expressing, rep5

description:
S1524
Sample_23L001524


title: Rag1-/-Mom-VH81X pre-B CHi-C rep2

value: Bone marrow

value: Pre-B cells

value: 8-12 weeks

value: pooled male and female


title: Thymus CHi-C rep1

value: Thymus

value: Total thymocytes


title: FGR, S14, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis

value: Non-Hispanic

value: White


title: Rag1-/-Mom-VH81X pre-B CHi-C rep1


title: EOPE+FGR, S13, Decidua Basalis

description: Illumina HiSeq 2500

value: EOPE+FGR

value: Female


title: BJAB, Mock for API2:MALT1 fusion data, untreated, rep5

description:
S1523
Sample_23L001523


title: BEC_2mos_vehicle_2

first: Sarah

middle: Elizabeth

last: Lutz

state: IL

address: 808 S. Wood St., Rm 578 MC 512, Anatomy Cell Biology Lutz Lab, Anatomy Cell Biology Lutz Lab

department: Anatomy and Cell Biology

institute: University of Illinois at Chicago

description: TruSEQ

data_processing:
STAR alignment to mm10
featureCounts
Assembly: mm10
Supplementary files format and content: featureCounts

source_name: brain

extract_protocol:
Brains were digested with papain, microvessels were isolated by differential centrifugation through 25%BSA gradient, microvessel fragments were digested to single cells with Collagenase, myelin was depleted, and cell suspension passed three times through column based CD31-positive selection to isolate endothelial cells.
RNA was extracted from purified brain endothelial cells using micro RNEasy kit (Qiagen). 1.5-3 ng of purified brain EC RNA was collected from each sample.
Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA-SEQ library protocol

value: brain

tag: chronological age

value: 2 months

value: male

value: microvascular endothelial

value: WT

value: Vehicle


title: BEC_2mos_vehicle_3

description: TruSEQ


title: Rag1-/-Bal pro-B CHi-C rep2

value: Bone marrow

value: Pro-B cells

value: Spanopoulou et al., 1994; https://doi.org/10.1101/gad.8.9.1030

tag: age


title: BEC_2mos_vehicle_1

description: TruSEQ

tag: treatment


title: BEC_12mos_MA10_4DPI_4

description: TruSEQ

value: 12 months

value: SARS-CoV-2 MA10 respiratory infection 4DPI


title: Rag1-/-Mom pro-B CHi-C rep2

value: 8-12 weeks

value: pooled male and female


title: BEC_12mos_MA10_4DPI_3

description: TruSEQ


title: BEC_2mos_vehicle_4

description: TruSEQ


title: BJAB, Wild type API2:MALT1 fusion protein expressing, rep4

description:
S1520
Sample_23L001520

value: B cell

value: BJAB


title: iPTB, S10, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis

tag: clinical group

value: iPTB

value: Non-Hispanic

value: Black


title: BEC_12mos_MA10_4DPI_2

description: TruSEQ

value: brain

value: male


title: Rag1-/-Mom pro-B CHi-C rep1


title: BJAB, Mock for API2:MALT1 fusion data, untreated, rep4

description:
S1519
Sample_23L001519


title: Thymus Hi-C rep2

value: Thymus

value: Total thymocytes

value: WT


title: iPTB, S09, Decidua Basalis

description: Illumina HiSeq 2500

tag: age of_mother_(years)

value: Male


title: FGR, S08, Decidua Basalis

description: Illumina HiSeq 2500

value: FGR

tag: birthweight interval_(grams)

value: Female

value: White


title: BEC_12mos_MA10_4DPI_1

description: TruSEQ

value: 12 months

value: microvascular endothelial

value: SARS-CoV-2 MA10 respiratory infection 4DPI


title: BEC_12mos_vehicle_4

description: TruSEQ

value: Vehicle


title: BJAB, Paracaspase mutant API2:MALT1 fusion protein expressing, rep3

description:
S1517
Sample_23L001517

value: B cell

value: BJAB


title: BJAB, TRAF6 binding mutant API2:MALT1 fusion protein expressing, rep3

description:
S1518
Sample_23L001518


title: Thymus Hi-C rep1

value: 8-12 weeks

value: pooled male and female


title: Rag1-/-Mom-VH81X pre-B Hi-C rep2

value: Bone marrow

value: Pre-B cells


title: EOPE, S07, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis

value: EOPE

tag: assigned neonatal_sex

value: Non-Hispanic

value: Black


title: BJAB, TRAF6 binding mutant API2:MALT1 fusion protein expressing, rep4

description:
S1522
Sample_23L001522


title: BJAB, Wild type API2:MALT1 fusion protein expressing, rep3

description:
S1516
Sample_23L001516


title: BJAB, Mock for API2:MALT1 fusion data, untreated, rep3

description:
S1515
Sample_23L001515


title: EOPE, S06, Decidua Basalis

description: Illumina HiSeq 2500

tag: maternal ethnicity


title: Rag1-/-Bal pro-B CHi-C rep1

value: Pro-B cells

value: Spanopoulou et al., 1994; https://doi.org/10.1101/gad.8.9.1030


title: BJAB, Paracaspase mutant API2:MALT1 fusion protein expressing, rep4

description:
S1521
Sample_23L001521


title: EOPE+FGR, S12, Decidua Basalis

description: Illumina HiSeq 2500

value: EOPE+FGR

value: Male

value: Hispanic

tag: maternal race

value: White


title: BEC_12mos_vehicle_3

description: TruSEQ

value: brain

value: 12 months

value: male

value: microvascular endothelial

value: WT

tag: strain

value: Vehicle


title: Rag1-/-Mom-VH81X pre-B Hi-C rep1

value: Bone marrow

value: Pre-B cells

value: 8-12 weeks

tag: Sex

value: pooled male and female


title: FGR, S11, Decidua Basalis

description: Illumina HiSeq 2500

value: placenta, decidua basalis

value: FGR


title: iPTB, S05, Decidua Basalis

description: Illumina HiSeq 2500

value: iPTB

value: Non-Hispanic


title: Rag1-/-Bal pro-B Hi-C rep2

value: Pro-B cells

value: Spanopoulou et al., 1994; https://doi.org/10.1101/gad.8.9.1030


title: BJAB, TRAF6 binding mutant API2:MALT1 fusion protein expressing, rep2

description:
S1514
Sample_23L001514

value: B cell

value: BJAB


title: BEC_12mos_vehicle_2

description: TruSEQ

value: brain

value: 12 months


title: FGR, S04, Decidua Basalis

description: Illumina HiSeq 2500

value: Male

value: Black


title: BEC_12mos_vehicle_1

description: TruSEQ

value: male

value: microvascular endothelial

value: WT

value: Vehicle


title: Rag1-/-Bal pro-B Hi-C rep1

value: Bone marrow

value: 8-12 weeks

value: pooled male and female


title: BJAB, Paracaspase mutant API2:MALT1 fusion protein expressing, rep2

description:
S1513
Sample_23L001513


title: TB, S30, Villous Tissue

description: Illumina HiSeq 2500

source_name: placenta, villous tissue

value: placenta, villous tissue

value: TB

value: Hispanic

value: White


title: TB, S29, Villous Tissue

description: Illumina HiSeq 2500

value: Female

value: Non-Hispanic


title: Mouse_Small_intestine_organoid_D1/2_scRNA

city: Daejeon

first: Bon-Kyoung

last: Koo

state: Yuseong-gu

address: Expo-ro 55

department: Center for genome engineering

institute: Institute for Basic Science

description: 10x Genomics scRNA-seq

data_processing:
To generate count matrices consist of both gene expression and chromatin peaks for each organoid sample such as Rnf43/Znrf3 double knock-out (RZ), and Kras activated RZ-DKO (RZK), cellranger-ARC count (v6.1.1) was utilized with default option and mouse reference (‘refdata-cellranger-arc-mm10-2020-A-2.0.0’) provided in 10x Genomics. Based on both Signac (v1.8.0) and Seurat (v4.1.0) pipelines, we generated analytic objects from ‘filtered_feature_bc_matrix’ and ‘atac_fragments.tsv.gz’ of cellranger based on mouse genome which is output from ‘GetGRangesFromEnsDb’ with ‘EnsDb.Mmusculus.79’ for annotations. We filtered out poor-quality cell nuclei with unique molecular identifiers (UMIs) for RNA less than 1,000 and more than 25,000, and for ATAC less than 1,000 and more than 100,000, percent mitochondrial genes more than 15%, and nucleosome signal more than 3 for both samples. Using the selected nulei, we sequentially conducted NormalizeData (lognormalization) and FindVariableFeatures (‘vst’ method, 2,000 features) functions for RNA expression profiles. We also implemented FindTopFeatures with min.cutoff is ‘q0’, RunTFIDF, and RunSVD for both ATAC and macs2 assays for peak profiles from Signac package.To generate count matrices for each organoid sample such as wildtype (‘WT_WENR’), Rnf43/Znrf3 double knock-out (RZ_WEN), and Daam1/Daam2 double knock-out (Daam_WEN), Cellranger (v6.1.1)37 was utilized with default option and mouse reference (‘refdata-gex-mm10-2020-A’) provided in 10X genomics. Based on Seurat pipeline (v4.1.0)38, we generated analytic objects from each gene-by-cell matrix from ‘filtered_feature_bc_matrix’ of cellranger, we firstly filtered-out poor-quality cells with less than 4,000 and more than 40,000 unique molecular identifiers (UMIs), more than 13% percent mitochondrial genes, and more than 4,000 detected genes for WT_WENR and RZ_WEN samples. Especially for Daam_WEN sample, we applied partially different criteria to discard poor-quality cells with more than 50,000 UMIs and more than 5,000 detected genes. After quality control step, we had 3,828 cells (WT_WENR), 4,342 cells (RZ_WEN), and 3,257 cells (Daam_WEN). Then, we sequentially conducted NormalizeData (log-normalization) and FindVariableFeatures (‘vst’ method, 2,000 features) functions of Seurat pipeline for each sample. In order to select singlet, DoubletFinder_v3, which is a recent version of DoubletFinder39, was conducted with default parameters. Using cell cycle markers derived from AnnotationHub R package (v3.4.0) with ‘Mus musculus’, ‘EnsDb’ for S and G2/M phases, we calculated cell cycle scores via CellCycleScoring function and regressed out based on the scores such as ‘S.Score’ and ‘G2M.Score’ on Seurat pipeline. After merging three count objects and storing each object to sample category, we performed PCA with RunPCA function to prepare harmonization which is one of batch reduction methods. The merged object was harmonized through RunHarmony function with ‘Sample’ as biological factor and 30 PCs40. Based on the dimensionally reduced object, we identified clusters through the sequential procedures such as RunUMAP, FindNeighbors (‘k.param’ is 25), and FindClusters (‘resolution’ is 0.75, Louvain algorithm) with 30 harmony PCs.
Assembly: mm10
Supplementary files format and content: hdf5: RNA
Supplementary files format and content: tsv: Tab separated files and matrices

source_name: Small intestine organoid

extract_protocol:
organoids were mechanically and chemically dissociated and prepared for library generation and sequencing by Vienna BioCenter Next Generation Sequencing Facility
Chromium Next GEM Gene Expression Reagent Kits

value: Small intestine organoid

value: multiple


title: Mouse_Small_intestine_organoid_RZ_scRNA

description: 10x Genomics scRNA-seq


title: BJAB, Mock for API2:MALT1 fusion data, untreated, rep2

description:
S1511
Sample_23L001511

value: B cell

value: BJAB


title: TB, S28, Villous Tissue

description: Illumina HiSeq 2500


title: Rag1-/-Mom pro-B Hi-C rep1

value: Pro-B cells


title: Mouse_Small_intestine_organoid_WT_scRNA

description: 10x Genomics scRNA-seq

value: Wildtype


title: Rag1-/-Mom pro-B Hi-C rep2


title: BJAB, Wild type API2:MALT1 fusion protein expressing, rep2

description:
S1512
Sample_23L001512


title: BJAB, Paracaspase mutant API2:MALT1 fusion protein expressing, rep1

description:
S1509
Sample_23L001509


title: BJAB, Wild type API2:MALT1 fusion protein expressing, rep1

description:
S1508
Sample_23L001508


title: TB, S26, Villous Tissue

description: Illumina HiSeq 2500

value: Male


title: EOPE+FGR, S25, Villous Tissue

description: Illumina HiSeq 2500

value: EOPE+FGR


title: BJAB, TRAF6 binding mutant API2:MALT1 fusion protein expressing, rep1

description:
S1510
Sample_23L001510


title: AF_SCPN_3600

description: Ribo-seq

source_name: sorted cortical neurons

tag: input

value: 3600 cells

tag: fragmentation

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

tag: Stage

value: Subcerebral Projection Neurons


title: AF_CPN_7500-2

description: Ribo-seq

value: 7500 cells

tag: cell type

value: Callosal Projection Neurons


title: BJAB, Mock for API2:MALT1 fusion data, untreated, rep1

description:
S1507
Sample_23L001507

tag: cell line


title: AF_CPN_7500-1

description: Ribo-seq


title: iPTB, S24, Villous Tissue

description: Illumina HiSeq 2500

tag: tissue

value: placenta, villous tissue

value: iPTB

value: Other


title: H1, NAT10-KD, IgG, acRIP-Seq rep2

data_processing:
First, fastp software (v0.21.1) was used to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using HISAT2 software (v2.2.1), with the genome annotation from Ensembl (http://www.ensembl.org, version 107) as the reference gene model.
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
Finally, the BAM-format reads for each paired IP + input (or IgG + input) samples were input to exomePeak2 software (http://bioconductor.org/packages/release/bioc/html/exomePeak2.html, v1.8.1) to identify significant acetylation peaks in each IP or IgG sample.
The exomePeak2 software was implemented with default parameter and the same Ensembl v107 reference gene model. To control false positive, any IP peak showing more than 10% coordinate overlap with the non-specific IgG peaks were removed by the subtract function of bedtools (v2.30.0). Moreover, less confident peaks whose sum of scores less than 20 and peaks that cannot be mapped to known genes were discarded.
Assembly: hg38
Supplementary files format and content: Excel file includes the ac4C acetylation sites information for each sample

extract_protocol:
Cells from WT and NAT10 KD hESCs were collected and total RNA was harvested with Trizol reagent (Invitrogen, cat. NO 15596026). Remove the rRNAs from the total RNA by using the Ribo-Zero rRNA Removal Kits (Illumina, USA). The RNA was randomly fragmented into fragments of about 200 nt. Protein A/G magnetic beads (Thermo Fisher Scientific, MA, United States) and ac4C antibody (ab252215, Abcam, Cambridge, United Kingdom) or control rabbit IgG antibodies (GS-ET-005, GenSeq, Shanghai, China) were rotated and incubated at room temperature for 1 hour to bind the antibody to the magnetic beads.
Then the RNA fragments and the antibody bound with magnetic beads were rotated and incubated at 4 ℃ for 4 hours. RNA/antibody complexes were eluted from magnetic beads by Protease K and RNA was extracted by phenol:chloroform method.
RNA sequencing libraries were constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (Thermo Fisher Scientific, MA, United States). The constructed libraries were quality-controlled with Agilent 2100 bioanalyzer and then sequenced on Illumina NovaSeq 6000 sequencer (Illumina, Inc., San Diego, CA, United States) for high-throughput sequencing.
ac4C-RIP-seq

treatment_protocol: shRNA targeting sequences against NAT10 were designed, synthesized and subcloned into the GV112 vector. Cells transduced with NAT10 shRNA lentivirus with GFP (Genechem, Shanghai, China) were cultured for 48h. GFP+ cells then were enriched and expanded in TeSR-E8 medium with 0.5ug/ml puromycin.

value: early embryo

value: human embryonic stem cell

tag: genotype

value: NAT10 knockdown


title: RP_SCPN_15800

description: Ribo-seq

value: 15800 cells

value: Rnase I 12.5 U/mL


title: iPTB, S23, Villous Tissue

description: Illumina HiSeq 2500

value: Female

value: Non-Hispanic

value: White


title: 10% MR, animal 30911

type: RNA

city: Dummerstorf

first: Anja

last: Baufeld

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Research Institute for Farm Animal Biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Raw data were processed with the Transcriptome Analysis Console 4.0 (V4.0.2; Affymetrix), where normalization, background reduction and a gene-level summary was done using the RMA method (Robust Multichip Average).

label: biotin

organism: Bos taurus

source_name: granulosa cells, 10% MR, isolated after slaughter

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: The 10% group received the whole milk replacer allowance for ten weeks followed by a two-week transition period from milk feeding to sole solid feeding. During the transition period, the daily milk allowance was gradually reduced. For the 20% group the transition period started already in week eight but lasted for four weeks. For both experimental groups milk feeding stopped at week 12. During the first 12 weeks of life, the calves of both groups were able to consume hay and calf starter ad libitum. Hay ad libitum feeding was continued until week 14. The calf starter was limited to 2 kg/day from week 12 to 14 and thereafter gradually reduced until week 16. From week ten onwards, all calves additionally received a total-mixed ration ad libitum. After week 16, the total-mixed ration was the sole feed offered for ad libitum intake in both groups until sampling.

extract_protocol: Total RNA was prepared using the RNeasy Kit (Qiagen).

treatment_protocol: In the 10% group, the calves were fed with a maximum of 10% milk replacer/kg bodyweight. In contrast, the calves of the 20% group received a maximum of 20% milk replacer/kg bodyweight (BERGIN Milch LC 50) per day from an automatic calf feeder (Kälbermama Lifestart, Urban GmbH & Co. KG, Hude/Wüsting, Germany). The milk allowance was adjusted weekly after weighing.

tag: age at slaughter

tag: follicle count

tag: rumen fistula

value: fistula


title: 10% MR, animal 36066


title: AF_SCPN_5200

description: Ribo-seq

value: 5200 cells


title: 10% MR, animal 67761


title: EOPE, S21, Villous Tissue

description: Illumina HiSeq 2500

tag: clinical group

value: EOPE

tag: age of_mother_(years)

value: Male

value: Black


title: RP_CPN_22500-2

description: Ribo-seq

value: 22500 cells

value: Callosal Projection Neurons


title: 10% MR, animal 18763

value: non fistula


title: EOPE, S22, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

tag: birthweight interval_(grams)

tag: assigned neonatal_sex


title: RP_SCPN_14400

description: Ribo-seq

value: 14400 cells

value: Subcerebral Projection Neurons


title: H1, NAT10-KD, IgG, acRIP-Seq rep1

value: early embryo

value: human embryonic stem cell

value: NAT10 knockdown

tag: treatment


title: H1, NAT10-KD, IP, acRIP-Seq rep2


title: H1, NAT10-KD, Input, acRIP-Seq rep2


title: H1, NAT10-KD, Input, acRIP-Seq rep1


title: AF_SCPN_3300

description: Ribo-seq

value: 3300 cells

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


title: RP_CPN_22500-1

description: Ribo-seq

value: Rnase I 12.5 U/mL


title: EOPE, S18, Villous Tissue

description: Illumina HiSeq 2500

value: Female

tag: maternal ethnicity

value: Non-Hispanic

tag: maternal race

value: White


title: EOPE, S19, Villous Tissue

description: Illumina HiSeq 2500

value: EOPE

value: Male


title: 20% MR, animal 67748

source_name: granulosa cells, 20% MR, isolated after slaughter


title: 20% MR, animal 67759

value: fistula


title: 10% MR, animal 18906


title: G9_pCDH_gmci2

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: treatment 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

value: CAN-2409 (previously called GMCI)


title: H1, WT, IgG, acRIP-Seq rep2

value: WT

value: wild type


title: AF_SCPN_3100

description: Ribo-seq

tag: input

value: 3100 cells

value: Subcerebral Projection Neurons


title: 20% MR, animal 36265


title: G9_pCDH_gmci3


title: 20% MR, animal 36051


title: EOPE, S16, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: Black


title: EOPE+FGR, S17, Villous Tissue

description: Illumina HiSeq 2500

value: EOPE+FGR

value: Other


title: AF_CPN_5000

description: Ribo-seq

value: 5000 cells

tag: fragmentation

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

value: Callosal Projection Neurons


title: H1, WT, IP, acRIP-Seq rep2

value: early embryo

value: human embryonic stem cell


title: H1, WT, Input, acRIP-Seq rep2


title: H1, WT, IgG, acRIP-Seq rep1


title: EOPE, S20, Villous Tissue

description: Illumina HiSeq 2500

value: EOPE

value: Female

value: Non-Hispanic


title: RP_SCPN_13200

description: Ribo-seq

value: 13200 cells

value: Rnase I 12.5 U/mL

tag: Stage


title: G9_pCDH_c3

source_name: control group

value: brain

tag: cell type

value: glioblastoma

value: control


title: 20% MR, animal 36163

value: non fistula


title: H1, NAT10-KD, IP, acRIP-Seq rep1

tag: cell line

value: NAT10 knockdown


title: RP_SCPN_13000

description: Ribo-seq

value: 13000 cells

value: Subcerebral Projection Neurons


title: G9_pCDH_c2

tag: tissue


title: AF_CPN_4600

description: Ribo-seq

value: 4600 cells


title: H1, WT, Input, acRIP-Seq rep1

tag: genotype

value: WT

value: wild type


title: G9_pCDH_gmci1

value: CAN-2409 (previously called GMCI)


title: FGR, S14, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: FGR

value: Male

value: White


title: G9_pCDH_c1


title: RP_CPN_13900

description: Ribo-seq

value: 13900 cells

value: Callosal Projection Neurons


title: H1, WT, IP, acRIP-Seq rep1

value: early embryo

value: human embryonic stem cell


title: SS4

city: Heraklion

first: Kriton

last: Kalantidis

state: Crete

address: Voutes University Campus

department: Biology

country: Greece

institute: University of Crete

data_processing:
Quality and adapter trimming was performed with BBDuk. Reads obtained after trimming were aligned to the indexed Niben101 genome using hisat2. Aligned reads were counted with htseq-count. Differential expression analysis of RNA-seq data was carried out using either the DESeq2 or edgeR workflows via the R package SARTools (more details in the DE_bioinfo_analysis.txt)
Assembly: The draft genome v1.0.1 of Nicotiana benthamiana obtained from https://solgenomics.net/organism/Nicotiana_benthamiana/genome
Supplementary files format and content: raw counts of sequencing reads for the features of interest, generated using htseq-count

organism: Nicotiana benthamiana

source_name: leaf tissue

growth_protocol: Wild type and transgenic GFP6.4 N. benthamiana seeds were sown in potting soil. The plantlets were grown in growth chambers under a 16-hour/8-hour light/dark photoperiod at 22oC and a photosynthetically active radiation of 90 µmol m-2 sec-1 provided by cool white fluorescent tubes.

extract_protocol:
500 mg of homogenized plant tissue were used per N. benthamiana leaf sample and RNA extraction buffer (38% saturated phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate) was added to each sample.
RNA libraries for RNA-seq were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit.

value: leaf tissue

value: GFP6.4 transgenic


title: TB, S27, Villous Tissue

description: Illumina HiSeq 2500

value: TB

value: Non-Hispanic


title: FGR, S15, Villous Tissue

description: Illumina HiSeq 2500

value: Hispanic


title: EOPE+FGR, S12, Villous Tissue

description: Illumina HiSeq 2500

value: EOPE+FGR


title: iPTB, S10, Villous Tissue

description: Illumina HiSeq 2500

value: iPTB

value: Female

value: Black


title: FGR, S11, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue


title: H1, NAT10-KD, Input, rep2

data_processing:
Low-quality reads and adaptor sequences were first trimmed by fastp (v0.21.1).
The in-house software of Seqhealth corporation (Wuhan, China) was used to eliminate duplicated reads according to UMI tags, and the UMI tag sequences were also trimmed by process.
Clean reads after duplication removal were then aligned to reference genome (hg38) by using STAR software (v2.7.8a), with the Ensembl v107 genome annotation as the reference gene model.
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12). The JACUSA software (Version 2.0.0-S-BETA-1) was used for detecting single nucleotide variant (SNV) sites and obtaining the corresponding pileups.
Finally, the standard algorithm code for ac4C-seq modification site identification (https://github.com/SchwartzLab/ac4c-seq) was utilized to identify the modification sites based on the significantly overrepresented SNV events at the ac4C sites.
Assembly: hg38
Supplementary files format and content: Excel file includes the ac4C acetylation sites information for sample

extract_protocol:
Total RNA was extracted from WT and NAT10 KD hESCs using TRIzol Reagent (Invitrogen, cat. NO 15596026). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by Qsep100 (bioptic) or Agilent5300 (Agilent).
30μg total RNA was used for mRNA capture using KAPA mRNA Capture Kit (KK8441) following the manufacturer’s instruction. Take a small amount of captured RNA as Input, and the remaining RNA was treated with NaCNBH3 at 25℃ for 20 minutes; RNA clean beads were used to retrieve the treated RNA.
KC Digital Stranded mRNA Library Prep Kit for Illumina（DR085-02）was used for library construction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Illumina Novaseq 6000 with PE150 model.
ac4C-seq (chemical ac4C sequencing)

value: NAT10 knockdown


title: NIH-3T3-MU-3

city: Shanghai

first: Wenqiang

last: Zheng

state: Shanghai

address: No. 320 Yueyang Road, Shanghai

institute: SIBCB

data_processing:
The total amount and integrity of RNA were assessed using an RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies). Two to four micrograms of total RNA were used as the starting material to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101, Illumina).
The size of the libraries was selected by using Agencourt AMPure XP beads (Beckman Coulter, A63882) at an average sample size of 400 bp. The libraries were sequenced using Illumina NovaSeq 6000 (pair-end 150 bp). Bioinformatic analysis of RNA-seq data: the feature Counts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Then, the log2-transformed gene expression values (FPKM) of each gene were calculated based on the length of the gene and the reads mapped to this gene. FPKM, the expected number of fragments per kilobase of transcript sequence per million base pairs sequenced, was determined on the basis of the effect of sequencing depth and gene length on the read count at the same time and is currently the most commonly used method for estimating gene expression levels. Sequencing quality was evaluated by FastQC v.0.11.4. All reads were mapped to the reference genome at Illumina iGenomes UCSC mm10 using HISAT2 v.2.05.0. A differential expression analysis was performed using the DESeq2 R package (1.20.0). DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. padj <= 0.05 & |log2(FoldChange)|> 0 was set as the threshold for identifying significantly different gene expressions. The FPKM values were normalized by subtracting the mean in every row and hierarchically clustering with a Pearson correlation algorithm.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: NIH-3T3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2-4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101, Illumina) following manufacturer's protocols.

value: embryonic fibroblast

value: Mutation

value: Cultural


title: H1, NAT10-KD, Treat, rep2


title: H1, NAT10-KD, Input, rep1


title: SS2


title: iPTB, S09, Villous Tissue

description: Illumina HiSeq 2500

value: Male


title: RP_CPN_15000

description: Ribo-seq

data_processing:
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.
Assembly: mm10, hg38
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. TPM.csv: Transcripts per Million Mapped for genes passing filter

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: 15000 cells

value: Rnase I 12.5 U/mL

value: Callosal Projection Neurons


title: H1, NAT10-KD, Treat, rep1

value: early embryo

value: human embryonic stem cell


title: FGR, S08, Villous Tissue

description: Illumina HiSeq 2500

value: FGR

value: Non-Hispanic

value: White


title: SS1

value: leaf tissue

value: GFP6.4 transgenic


title: NIH-3T3-WT-3

value: WT


title: OS5


title: H1, WT, Input, rep2

value: wild type


title: EOPE, S07, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: EOPE

value: Female

value: Black


title: NIH-3T3-MU-1

value: embryonic fibroblast

value: Mutation

value: Cultural


title: NIH-3T3-WT-2


title: OS3


title: SS3


title: H1, WT, Treat, rep2


title: EOPE, S06, Villous Tissue

description: Illumina HiSeq 2500


title: NIH-3T3-MU-2


title: NIH-3T3-WT-1


title: H1, WT, Input, rep1


title: OS2


title: BCAA-free, 2W-TAC, rep3

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave., MSB

department: Cell Biology and Molecular Medicine

institute: Rutgers University

description:
2W-BFT3
2W-BFT-vs-BFS.csv
2W-BFT-vs-BCT.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featuremCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between groups of samples was performed (as seen in the processed files). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: mm10
Supplementary files format and content: The processed data are provided in csv files. The files include the gene ID, log2 fold change, padj, p value, the normalized reads for each each detectable gene in each of the samples being compared, and gene name. The log2 fold change are for the TAC/sham with either diet, or TAC(BCAA-free)/TAC(BCAA-control), or sham(BCAA-free)/sham(BCAA-contro). The samples in each file are identified by the designated library names.

source_name: heart

extract_protocol:
Trizol extraction of total RNA followed by polyA selection
1. mRNA enrichment, mRNA fragmentation, random priming. 2. First and second strand synthesis. 3. End repair, 5'phosphorylation, and dA-Tailing. 4. Adaptor ligation, PCR enrichment, and sequencing.

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 (2-wk after surgery).

value: heart

tag: strain

tag: Sex

value: male

tag: age

value: BCAA-free diet, 2W-TAC surgery


title: iPTB, S05, Villous Tissue

description: Illumina HiSeq 2500

tag: clinical group

value: iPTB

value: Male


title: OS1


title: FGR, S04, Villous Tissue

description: Illumina HiSeq 2500

value: FGR

tag: age of_mother_(years)

value: Non-Hispanic


title: H1, WT, Treat, rep1

source_name: early embryo

value: early embryo

value: human embryonic stem cell


title: NS4

value: leaf tissue

value: GFP6.4 transgenic


title: BCAA-free, 2W-TAC, rep2

description:
2W-BFT2
2W-BFT-vs-BFS.csv
2W-BFT-vs-BCT.csv


title: BJAB, TRAF6 KO and CARD11 mut, MLT-748, rep5

description:
S77
Sample_21L007077

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

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

value: BJAB


title: EOPE+FGR, S03, Villous Tissue

description: Illumina HiSeq 2500

value: placenta, villous tissue

value: EOPE+FGR

tag: birthweight interval_(grams)

value: Female

value: Black


title: BCAA-free, 2W-TAC, rep1

description:
2W-BFT1
2W-BFT-vs-BFS.csv
2W-BFT-vs-BCT.csv

value: heart


title: NS3


title: BJAB, TRAF6 KO and CARD11 mut, DMSO, rep4

description:
S76
Sample_21L007076

value: DMSO


title: BCAA-free, 2W-sham, rep3

description:
2W-BFS3
2W-BFT-vs-BFS.csv
2W-BFS-vs-BCS.csv

value: male

value: BCAA-free diet, 2W-sham surgery


title: NS2


title: BJAB, TRAF6 KO and CARD11 mut, MLT-748, rep4

description:
S75
Sample_21L007075


title: EOPE+FGR, S01, Villous Tissue

description: Illumina HiSeq 2500

tag: assigned neonatal_sex

value: White


title: BCAA-free, 2W-sham, rep2

description:
2W-BFS2
2W-BFT-vs-BFS.csv
2W-BFS-vs-BCS.csv

tag: treatment


title: NS1


title: BCAA-free, 2W-sham, rep1

description:
2W-BFS1
2W-BFT-vs-BFS.csv
2W-BFS-vs-BCS.csv


title: WT4

value: WT


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

description:
S72
Sample_21L007072


title: BCAA-control, 2W-TAC, rep3

description:
2W-BCT3
2W-BCT-vs-BCS.csv
2W-BFT-vs-BCT.csv

value: BCAA-control diet, 2W-TAC surgery


title: BJAB, TRAF6 KO and CARD11 mut, MLT-748, rep3

description:
S73
Sample_21L007073


title: BJAB, TRAF6 KO and CARD11 mut, MLT-748, rep2

description:
S71
Sample_21L007071


title: WT2


title: Intact, bio rep 3

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

institute: Biomedical Center (BMC),LMU - Munich

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

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

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 DMSO

tag: timepoint

value: Intact


title: Intact, bio rep 4


title: BCAA-control, 2W-TAC, rep2

description:
2W-BCT2
2W-BCT-vs-BCS.csv
2W-BFT-vs-BCT.csv


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

description:
S70
Sample_21L007070

value: B cell

value: BJAB


title: 5dpi_INH, bio rep 2

value: 4days Inhibitors mix

value: 5 dpi


title: WT1

value: leaf tissue


title: BCAA-control, 2W-TAC, rep1

description:
2W-BCT1
2W-BCT-vs-BCS.csv
2W-BFT-vs-BCT.csv

value: heart


title: BJAB, TRAF6 KO and CARD11 mut, MLT-748, rep1

description:
S69
Sample_21L007069


title: heart, sham, TAC, pooled [5_Pooled_Input]

data_processing:
Copied from Active Motir "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.”

extract_protocol: Active Motif

value: sham, TAC, pooled

tag: chip antibody

value: Input


title: 5dpi_INH, bio rep 1

value: male


title: 5dpi_CTRL, bio rep 1


title: EOPE+FGR, S02, Villous Tissue

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.

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

value: EOPE+FGR

value: Male

tag: maternal ethnicity

value: Non-Hispanic

tag: maternal race

value: White


title: BCAA-control, 2W-sham, rep3

description:
2W-BCS3
2W-BCT-vs-BCS.csv
2W-BFS-vs-BCS.csv

value: BCAA-control diet, 2W-sham surgery


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

description:
S68
Sample_21L007068

value: DMSO


title: Intact, bio rep 2

value: brain

value: multiple cell types

value: 8-12 weeks old

value: 2days DMSO

value: Intact


title: BCAA-control, 2W-sham, rep2

description:
2W-BCS2
2W-BCT-vs-BCS.csv
2W-BFS-vs-BCS.csv


title: heart, BCAA-free, TAC [4_TAC-0BCAA-2W_H3K23Pr]

value: BCAA-control diet, TAC surgery


title: BCAA-control, 2W-sham, rep1

description:
2W-BCS1
2W-BCT-vs-BCS.csv
2W-BFS-vs-BCS.csv

value: heart


title: 3dpi_INH, bio rep 2

value: 2days Inhibitors mix

value: 3 dpi


title: BJAB, TRAF6 KO and CARD11 mut, untreated, rep5

description:
S67
Sample_21L007067

value: B cell

value: BJAB


title: WT3

value: leaf tissue

value: WT


title: heart, BCAA-free, sham [3_Sham-0BCAA-2W_H3K23Pr]

value: male

value: BCAA-control diet, sham surgery


title: BJAB, TRAF6 KO, untreated, rep5

description:
S66
Sample_21L007066


title: 3dpi_INH, bio rep 1


title: heart, BCAA-control, TAC [2_TAC-2W_H3K23Pr]


title: 3dpi_CTRL, bio rep 2


title: BJAB, CARD11 mut, untreated, rep5

description:
S65
Sample_21L007065


title: 3dpi_CTRL, bio rep 1


title: BCAA-free,TAC [TAC-BCAA-H3K23Pr]

description:
TAC-BCAA-H3K23Pr
00ZSRutgers_H3K23Pr_mergedregs.xlsx

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.”

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).

value: BCAA-free diet, TAC surgery


title: 5dpi_CTRL, bio rep 3

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

value: 4days DMSO

value: 5 dpi


title: BJAB, TRAF6 KO and CARD11 mut, untreated, rep4

description:
S63
Sample_21L007063


title: Intact, bio rep 5

value: brain

value: multiple cell types

value: w/o treatment


title: Intact, bio rep 1

value: 8-12 weeks old

value: 2days DMSO

value: Intact


title: heart, BCAA-control, sham [1_Sham-2W_H3K23Pr]

value: heart


title: cortex, CPN_hemi5_AF

description:
JF133
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

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.

value: cortex

tag: input

value: 3.2k sorted CPN

tag: fragmentation

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

tag: Stage

value: Callosal Projection Neuron


title: BCAA-control, TAC [TAC-b-Cont-H3K23Pr]

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

tag: tissue

value: BCAA-control diet, TAC surgery


title: BCAA-free, sham [Sham-BCAA-H3K23Pr]

description:
Sham-BCAA-H3K23Pr
00ZSRutgers_H3K23Pr_mergedregs.xlsx

value: male

value: BCAA-free diet, sham surgery


title: BJAB, CARD11 mut, untreated, rep4

description:
S61
Sample_21L007061

source_name: BJAB

tag: cell type

value: B cell

tag: cell line

value: BJAB

tag: genotype