title: 0731-066, NGN2, HCort, 0nM

description:
P1B3
RawCountMatrix_NGN2_Study1.txt


title: 0731-061, NGN2, HCort, 1000nM

status: Public on Nov 07 2022

type: SRA

city: New York

first: Carina

middle: of

last: Seah

state: New York

address: 1 Gustave L Levy Pl Fl 1

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
P1G6
RawCountMatrix_NGN2_Study1.txt

library_source: transcriptomic

data_processing:
Short reads with Illumina adapters were trimmed and low-quality reads were filtered using TrimGalore92 (–illumina option). All high-quality reads were then processed for alignment using the hg38 reference and the ultrafast universal RNA-seq aligner STAR with default parameters93. Mapped bam files were sorted using Samtools and short read data were quantified using featureCounts94 with the following parameters: -T 5, -t exon and -g gene_id.
Assembly: Hg38
Supplementary files format and content: Read count files

molecule: total RNA

organism: Homo sapiens

source_name: Neuron

extract_protocol: For NGN2-neurons, RNA was harvested with an RNeasy Plus Micro Kit (Qiagen). For PBMCs, RNA was extracted from TRIzol-lysed PBMCs using the miRNAeasy Mini Kit (Qiagen).

tag: tissue

value: Neuron

tag: cell type

tag: diagnosis

value: PTSD

tag: treatment

value: 1000 nM HCort


title: nasal_epithelial_cell [6c79_4493]

type: genomic

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
matrix processed value definition: SWAN normalized Beta values

label: cy3, cy5

molecule: genomic DNA

label_protocol: Standard Illumina protocol.

extract_protocol: Samples were spun through a Qiashredder column and then extracted using AllPrep DNA/RNA mini kits (Qiagen) following the manufacturer's protocol.

tag: plate

tag: array

tag: Sex

value: Male

tag: proportionpositiveskinpricktests

tag: percentciliatedepicells


title: nasal_epithelial_cell [e001_49ca]

value: Female


title: nasal_epithelial_cell [fd34_4c71]


title: 0731-061, NGN2, HCort, 100nM

description:
P1F6
RawCountMatrix_NGN2_Study1.txt

value: 100 nM HCort


title: nasal_epithelial_cell [925c_4863]


title: 0731-046, NGN2, HCort, 1000nM

description:
P1D2
RawCountMatrix_NGN2_Study1.txt

value: Control


title: 0731-069, NGN2, HCort, 0nM

description:
P1B4
RawCountMatrix_NGN2_Study1.txt

value: 0 nM HCort


title: nasal_epithelial_cell [11fb_4a49]


title: 0731-046, NGN2, HCort, 100nM

description:
P1C2
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [2ac4_41fa]


title: nasal_epithelial_cell [b563_48fa]


title: 0731-046, NGN2, HCort, 0nM

description:
P1B2
RawCountMatrix_NGN2_Study1.txt


title: 0731-040, NGN2, HCort, 1000nM

description:
P1G5
RawCountMatrix_NGN2_Study1.txt


title: 0731-040, NGN2, HCort, 100nM

description:
P1F5
RawCountMatrix_NGN2_Study1.txt


title: 0731-040, NGN2, HCort, 0nM

description:
P1E5
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [c513_4773]


title: 0731-032, NGN2, HCort, 1000nM

description:
P3D3
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [c897_4012]


title: nasal_epithelial_cell [9681_4fc0]


title: 0731-032, NGN2, HCort, 0nM

description:
P3B3
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [d39c_4ee4]


title: 0731-061, NGN2, HCort, 0nM

description:
P1E6
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [4cb1_4368]


title: nasal_epithelial_cell [d251_4dd9]


title: nasal_epithelial_cell [99e1_41b9]


title: 0731-017, NGN2, HCort, 0nM

description:
P1E4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [afd9_4a3c]


title: 0731-017, NGN2, HCort, 100nM

description:
P1F4
RawCountMatrix_NGN2_Study1.txt


title: 0731-037, NGN2, HCort, 1000nM

description:
P1G3
RawCountMatrix_NGN2_Study1.txt


title: 0731-037, NGN2, HCort, 100nM

description:
P1F3
RawCountMatrix_NGN2_Study1.txt


title: 0731-030, NGN2, HCort, 1000nM

description:
P3D6
RawCountMatrix_NGN2_Study1.txt


title: 0731-017, NGN2, HCort, 1000nM

description:
P1G4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [a183_4278]


title: 0731-037, NGN2, HCort, 0nM

description:
P1E3
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [55c8_4f16]


title: nasal_epithelial_cell [2794_48f9]


title: nasal_epithelial_cell [348c_4810]


title: nasal_epithelial_cell [30e4_4640]


title: 0731-018, NGN2, Hcort, 1000nM

description:
P1G2
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [cbc2_4320]


title: 0731-030, NGN2, HCort, 100nM

description:
P3C6
RawCountMatrix_NGN2_Study1.txt


title: PacBio Srsf10 KO-isolated_Sp

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
For bulk RNA-seq, after initial quality control, the clean reads were aligned to the mouse reference genome (mm 9) using Tophat v2.1.1 (TopHat: discovering splice junctions with RNA-Seq). Next, the gene expression was calculated by Cufflinks v2.2.1. And the normalization of the gene expression values was based on the fragments per kilobase of exon per million reads mapped (FPKM).
For Iso-seq, after running the Iso-Seq pipeline, sequence data were processed using the SMRTlink 5.0 software. A circular consensus sequence (CCS) was generated from subread BAM files.Differential splicing events of Iso-seq data were analyzed using SUPPA2 software with the standard protocol.  Additional nucleotide errors in consensus reads were corrected using the Illumina RNAseq data with the software LoRDEC. Then all the consensus reads were aligned to the mouse reference genome (mm 9) using Hisat2.
For Single-cell RNA-seq, raw data were processed using the Cell Ranger Software (version 4.0.0).
Genome_build: mm9
Supplementary_files_format_and_content: For bulk RNA-seq, the txt files for FPKM contain gene names and the FPKM value for samples. For Iso-seq, the  the txt files for the differential PSI value between control and Srsf10cKO.scRNA-Seq: UMI counts matrix with gene and barcode annotations

molecule: polyA RNA

organism: Mus musculus

source_name: P6 testes

growth_protocol: All mice were maintained under specific-pathogen-free (SPF) conditions in compliance with the guidelines of the Animal Care and Use Committee of the Institute of Zoology at the Chinese Academy of Sciences (CAS).

extract_protocol:
Total RNA was extracted from whole testes or enriched cells using RNAzol® RT (Molecular Research Center. Inc, RN 190) following the manufacturer’s instructions. The residual genomic DNA was removed with the DNase I Kit (Promega, M6101)
For Bulk RNA-seq,  a total amount of 1 ug of RNA per sample was used to prepare cDNA libraries generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations. For PacBio Isoform Sequencing (Iso-seq), 5 ug of total RNA per sample was used to prepare the Iso-Seq library using the Clontech SMARTer cDNA synthesis kit and the BluePippin Size Selection System protocol as described by Pacific Biosciences (PN 100-092-800-03). For Single-cell RNA-seq, Single cells were suspended in PBS containing 0.04% BSA and loaded onto the Chromium 3' v3 platform (10x Genomics) to generate single cell libraries according to the manufacturer’s protocol.

treatment_protocol: Testes samples were collected from control and Srsf10cKO mice at P3, P6 and P8, respectively. Isolated spermatogonia (THY1+ cells) for bulk RNA-seq and PacBio Isoform Sequencing (Iso-seq) were enriched from P6 control and Srsf10cKO testes using MACS method anti-THY1 antibody. Isolated spermatogonia for Single-cell RNA-seq  were enriched from P8 control and Srsf10cKO testes using MACS method anti-THY1 and anti-KIT antibody.

value: Testes

tag: genotype

value: isolated THY1+ cells


title: 0731-018, NGN2, Hcort, 100nM

description:
P1F2
RawCountMatrix_NGN2_Study1.txt


title: 0731-032, NGN2, HCort, 100nM

description:
P3C3
RawCountMatrix_NGN2_Study1.txt


title: 0731-018, NGN2, Hcort, 0nM

description:
P1E2
RawCountMatrix_NGN2_Study1.txt


title: 0731-107 PBMC, DEX, 50nM

description:
0731-107D7
RawCountMatrix_PBMC.txt

source_name: Blood

value: Blood

value: PBMC

value: 50 nM DEX


title: nasal_epithelial_cell [cf68_4ec1]


title: 0731-107 PBMC, DEX, 5nM

description:
0731-107D5
RawCountMatrix_PBMC.txt

value: 5 nM DEX


title: nasal_epithelial_cell [7f3a_4ad2]


title: nasal_epithelial_cell [a666_4d31]


title: 0731-107 PBMC, DEX, 2.5nM

description:
0731-107D4
RawCountMatrix_PBMC.txt

value: 2.5 nM DEX


title: 0731-107 PBMC, DEX, 0nM

description:
0731-107D1
RawCountMatrix_PBMC.txt

value: 0 nM DEX


title: 0731-108 PBMC, DEX, 50nM

description:
0731-108D7
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [0229_43b6]


title: testis Input control Monkey 4 (biol. Replicate 1)

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

library_source: genomic

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3 -5 10 -3 20
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were conversted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Assembly: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988
Supplementary files format and content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

organism: Macaca fascicularis

source_name: testis

extract_protocol:
Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through thwo mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrres C. A modified ChIP version named ChI-on-ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

value: testis

value: male dissected germline components

tag: chip antibody

value: untreated


title: tesis Input control Monkey 6 (biol. Replicate 2)


title: testis SMC3 ChIP Monkey 5 (biol. Replicate 1)

value: anti-SMC3 ab9263


title: 0731-108 PBMC, DEX, 0nM

description:
0731-108D1
RawCountMatrix_PBMC.txt


title: 0731-108 PBMC, DEX, 2.5nM

description:
0731-108D4
RawCountMatrix_PBMC.txt


title: 0731-030, NGN2, HCort, 0nM

description:
P3B6
RawCountMatrix_NGN2_Study1.txt

value: Neuron


title: 0731-108 PBMC, DEX, 5nM

description:
0731-108D5
RawCountMatrix_PBMC.txt


title: PacBio Ctrl-isolated_Sp


title: testis Input control Monkey 5 (biol. Replicate 1)


title: nasal_epithelial_cell [5636_4f30]

value: Female


title: testis SMC3 ChIP Monkey 4 (biol. Replicate 2)


title: 0731-097 PBMC, DEX, 50nM

description:
0731-097D7
RawCountMatrix_PBMC.txt


title: testis REC8* ChIP Monkey 6 (biol. Replicate 2)

value: proprietary mAb mix


title: nasal_epithelial_cell [90d2_46cd]

value: Male


title: 0731-097 PBMC, DEX, 5nM

description:
0731-097D5
RawCountMatrix_PBMC.txt

value: Control


title: 0731-097 PBMC, DEX, 2.5nM

description:
0731-097D4
RawCountMatrix_PBMC.txt


title: 0731-097 PBMC, DEX, 0nM

description:
0731-097D1
RawCountMatrix_PBMC.txt


title: 0731-101 PBMC, DEX, 50nM

description:
0731-101D7
RawCountMatrix_PBMC.txt

value: PTSD


title: nasal_epithelial_cell [459b_4030]


title: nasal_epithelial_cell [c003_4ac7]


title: 0731-101 PBMC, DEX, 2.5nM

description:
0731-101D4
RawCountMatrix_PBMC.txt


title: 0731-101 PBMC, DEX, 5nM

description:
0731-101D5
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [cd06_4d2c]


title: 0731-101 PBMC, DEX, 0nM

description:
0731-101D1
RawCountMatrix_PBMC.txt


title: MPNST-8

city: CINCINNATI

first: Lai Man

middle: (Natalie)

last: Wu

state: OH

address: 3333 Burnet Avenue, MLC7013,Lu lab, T6.525

institute: CCHMC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral nerve tumor

extract_protocol:
RNA of frozen neurofibroma and MPNST patient samples were extracted using TRIZOL (Life Technologies) followed by purification using a Direct-zol RNA MiniPrep Kit (Zymo Research). RNA-seq libraries were prepared and sequenced by a BGISEQ-500 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral nerve tumor

tag: age

tag: gender

value: M

tag: tumor type

value: MPNST


title: MPNST-11


title: nasal_epithelial_cell [4c2b_4543]


title: 0731-099 PBMC, DEX, 5nM

description:
0731-099D5
RawCountMatrix_PBMC.txt

value: Blood

value: PBMC


title: 0731-099 PBMC, DEX, 2.5nM

description:
0731-099D4
RawCountMatrix_PBMC.txt

value: 2.5 nM DEX


title: 0731-099 PBMC, DEX, 0nM

description:
0731-099D1
RawCountMatrix_PBMC.txt

value: 0 nM DEX


title: nasal_epithelial_cell [46fa_4aad]


title: nasal_epithelial_cell [7a4b_4bc0]


title: 0731-098 PBMC, DEX, 50nM

description:
0731-098D7
RawCountMatrix_PBMC.txt

value: 50 nM DEX


title: 0731-098 PBMC, DEX, 5nM

description:
0731-098D5
RawCountMatrix_PBMC.txt

value: 5 nM DEX


title: MPNST-5


title: MPNST-6


title: 0731-098 PBMC, DEX, 2.5nM

description:
0731-098D4
RawCountMatrix_PBMC.txt


title: 0731-098 PBMC, DEX, 0nM

description:
0731-098D1
RawCountMatrix_PBMC.txt


title: MPNST-4

value: F


title: 0731-059 PBMC, DEX, 50nM

description:
0731-059D7
RawCountMatrix_PBMC.txt


title: tesis REC8* ChIP Monkey 5 (biol. Replicate 1)

value: testis

value: male dissected germline components

value: untreated


title: 0731-059 PBMC, DEX, 5nM

description:
0731-059D5
RawCountMatrix_PBMC.txt


title: 0731-059 PBMC, DEX, 2.5nM

description:
0731-059D4
RawCountMatrix_PBMC.txt


title: MPNST-3


title: MPNST-12


title: nasal_epithelial_cell [29dc_4e34]

value: Female


title: 0731-099 PBMC, DEX, 50nM

description:
0731-099D7
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [f3e1_47fb]


title: 0731-059 PBMC, DEX, 0nM

description:
0731-059D1
RawCountMatrix_PBMC.txt


title: 0731-086 PBMC, DEX, 50nM

description:
0731-086D7
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [510c_4155]

value: Male


title: 0731-086 PBMC, DEX, 5nM

description:
0731-086D5
RawCountMatrix_PBMC.txt

value: Control


title: MPNST-2


title: nasal_epithelial_cell [747d_4031]


title: MPNST-7


title: nasal_epithelial_cell [7fea_4d2a]


title: 0731-086 PBMC, DEX, 2.5nM

description:
0731-086D4
RawCountMatrix_PBMC.txt


title: 0731-084 PBMC, DEX, 50nM

description:
0731-084D7
RawCountMatrix_PBMC.txt

value: PTSD


title: 0731-086 PBMC, DEX, 0nM

description:
0731-086D1
RawCountMatrix_PBMC.txt


title: NF1-15

value: Peripheral nerve tumor

value: benign NF


title: nasal_epithelial_cell [e519_4818]


title: 0731-084 PBMC, DEX, 5nM

description:
0731-084D5
RawCountMatrix_PBMC.txt


title: 0731-084 PBMC, DEX, 2.5nM

description:
0731-084D4
RawCountMatrix_PBMC.txt


title: 0731-084 PBMC, DEX, 0nM

description:
0731-084D1
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [9a54_426f]


title: 0731-072 PBMC, DEX, 50nM

description:
0731-072D7
RawCountMatrix_PBMC.txt


title: nasal_epithelial_cell [224e_4716]


title: NF1-12

value: M


title: 0731-072 PBMC, DEX, 2.5nM

description:
0731-072D4
RawCountMatrix_PBMC.txt

value: Blood


title: NF1-11


title: 0731-072 PBMC, DEX, 0nM

description:
0731-072D1
RawCountMatrix_PBMC.txt

value: PBMC


title: 0731-074 PBMC, DEX, 50nM

description:
0731-074D7
RawCountMatrix_PBMC.txt


title: 0731-074 PBMC, DEX, 5nM

description:
0731-074D5
RawCountMatrix_PBMC.txt


title: NF1-10


title: sox10:DsRed+ neural crest cells from 20 hpf wild-type embryos - biol rep 2

city: Cincinnati

first: Lindsey

last: Barske

address: 3333 Burnet Ave MLC 7016

institute: Cincinnati Children's Hospital Medical Center

description:
CON2
mRNA
Bulk RNA-seq

data_processing:
Illumina control software was used for base calling.
Sequences were pseudoaligned and quantified at TPM values using Kallisto.
Assembly: GRCz11
Supplementary files format and content: TPM_Barske2022.txt: Tab-delimited text file includes TPM values for each transcript.

organism: Danio rerio

source_name: sox10:DsRed+ neural crest cells

extract_protocol:
Total RNA was extracted from sorted cells using the RNeasy Micro kit (Qiagen).
The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse-transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input, and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters, assessed by Bioanalyzer, and quantified using the Kapa Library Quantification kit.

value: sox10:DsRed+ neural crest cells

value: wild-type

tag: developmental stage

value: 20 hpf


title: sox10:DsRed+ neural crest cells from 20 hpf wild-type embryos - biol rep 1

description:
CON1
mRNA
Bulk RNA-seq


title: NF1-8


title: NF1-16


title: 0731-074 PBMC, DEX, 0nM

description:
0731-074D1
RawCountMatrix_PBMC.txt

value: 0 nM DEX


title: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos - biol rep 2

description:
MUT2
mRNA
Bulk RNA-seq

value: nr2f2[unk]; nr2f5[mut]


title: NF1-6

value: F


title: 0731-071 PBMC, DEX, 50nM

description:
0731-071D7
RawCountMatrix_PBMC.txt

value: 50 nM DEX


title: 0731-071 PBMC, DEX, 5nM

description:
0731-071D5
RawCountMatrix_PBMC.txt

value: 5 nM DEX


title: NF1-14


title: 0731-071 PBMC, DEX, 0nM

description:
0731-071D1
RawCountMatrix_PBMC.txt


title: 0731-071 PBMC, DEX, 2.5nM

description:
0731-071D4
RawCountMatrix_PBMC.txt

value: 2.5 nM DEX


title: RNA_RG5

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Enterobacter cloacae

source_name: Intravenous Catheter

growth_protocol: isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

treatment_protocol: The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates

value: bacterial cells


title: Bulk BCR, Subject MuSK MG-1 at 68 months

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Single cell RNA-seq gene expression information from all subjects was processed using Seurat v4.1.1 in R v4.1.0.
All BCR repertoire sequence data were analyzed using the Immcantation (www.immcantation.org) framework.
Heavy and light chain BCR sequence data from 10X Genomics scRNA-seq + BCR sequencing began with the filtered V(D)J contigs from Cell Ranger version 3.1. To obtain V and J gene assignments, these contigs were aligned to the IMGT GENE-DB (v3.1.23, obtained August 3, 2019) human germline reference database using IgBlast v1.13.0. Preprocessing of NEBNext BCR sequences was performed using pRESTO v0.6.2.
Assembly: GRCh38
Supplementary files format and content: Compressed tar files contain output from CellRanger

source_name: Peripheral Blood

extract_protocol:
RNA was isolated from frozen PBMCs using the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions.
Bulk BCR libraries were either generated using the NEBNext Immune Sequencing Kit (NEB) or the SMARTer® Human BCR IgG IgM H/K/L Profiling Kit (Takara Bio USA, Inc.) using the primers targeting IgA, IgG and IgG-sub.   Single-cell libraries were generated from sorted B cells enriched from cryopreserved PBMCs, using the Chromium Single-cell 5′ Reagent Kit (10x Genomics; V 2.0) according to manufacturer’s instructions.

value: Peripheral Blood

value: B-Lymphocyte


title: Bulk BCR, Subject MuSK MG-1 at 70 months


title: 0731-072 PBMC, DEX, 5nM

description:
0731-072D5
RawCountMatrix_PBMC.txt

value: Control


title: 0731-069 PBMC, DEX, 0nM

description:
0731-069D1
RawCountMatrix_PBMC.txt


title: 0731-069 PBMC, DEX, 2.5nM

description:
0731-069D4
RawCountMatrix_PBMC.txt


title: 0731-069 PBMC, DEX, 50nM

description:
0731-069D7
RawCountMatrix_PBMC.txt


title: RNA_KP24

organism: Klebsiella pneumoniae

source_name: Tracheal Aspirate


title: Bulk BCR, Subject MuSK MG-4 at 0 months


title: 0731-069 PBMC, DEX, 5nM

description:
0731-069D5
RawCountMatrix_PBMC.txt


title: 0731-074 PBMC, DEX, 2.5nM

description:
0731-074D4
RawCountMatrix_PBMC.txt


title: RNA_KP15

source_name: Urine


title: 0731-067 PBMC, DEX, 2.5nM

description:
0731-067D4
RawCountMatrix_PBMC.txt

value: PTSD


title: RNA_RH3

source_name: Fliud Aspirate


title: 0731-067 PBMC, DEX, 50nM

description:
0731-067D7
RawCountMatrix_PBMC.txt


title: Bulk BCR, Subject MuSK MG-4 at 25 months


title: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos - biol rep 1

description:
MUT1
mRNA
Bulk RNA-seq


title: 0731-067 PBMC, DEX, 0nM

description:
0731-067D1
RawCountMatrix_PBMC.txt


title: 0731-066 PBMC, DEX, 50nM

description:
0731-066D7
RawCountMatrix_PBMC.txt


title: 0731-066 PBMC, DEX, 5nM

description:
0731-066D5
RawCountMatrix_PBMC.txt


title: RNA_KP14

source_name: Pus Aspirate


title: RNA_KP13

description: Processed data for this sample are included in files included on other samples.


title: 0731-066 PBMC, DEX, 2.5nM

description:
0731-066D4
RawCountMatrix_PBMC.txt


title: HD144_CD107a_negative

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
gRNA sequencing reads retrieved from this sequencing were demultiplexed and uploaded to PinAPL-py.ucsd.edu (Spahn et al., 2017). PinAPL-py was then used to align, control for quality, and count guides with the 5' adapter ATTTTAACTTGCTATTTCTAGCTCTAAAAC.
The STARS algorithm of the PinAPL-py platform was used with an alpha_g = 0.25 to generate gene rankings for both depletion and enrichment (run separately).
Supplementary_files_format_and_content: CRISPR_screen_annotated_PinAPLpy_GuideCounts_all_samples.txt: read counts for each guide RNA across samples
Supplementary_files_format_and_content: CRISPR_screen_PinAPLpy_STARS_enrichement_depletion_perGene_sorted.txt: gene ranking from the downstream analysis

source_name: NY-ESO-1 TCR transduced human healthy donor CD8 T cells

growth_protocol: Freshly isolated healthy donor CD8 T cells were stimulated as above. In addition, cells were co-transduced with LentiCRISPRv2-mCherry virus at an MOI of 0.5. For this purpose, non-treated 6-well polystyrene plates were coated with 2 mg/cm2 Retronectin (Takara) overnight in PBS at 4°C and then blocked using 2% BSA in PBS for 20 min at room temperature. The LentiCRISPRv2-mCherry virus was diluted according to the desired MOI in PBS with 0.1% BSA and added to the plates in 2ml per well. Plates were then centrifuged 90min at 2000 g at 32°C. Plates were then washed with 0.1% BSA in PBS, and CD8 T cells were added on top. Then the NY-ESO-1 TCR virus was added, and cells were incubated for 2 days. Fresh medium and 50 U/ml IL-2 was added every 2 days, and after 6 days, cells were sorted for live CD8+ TCR+ mCherry+ cells (co-transduction efficiency for the two donors was 0.57% and 0.99% respectively). Cells were then repetitively stimulated with NY-ESO-9V peptide, as described above.

extract_protocol:
Genomic DNA from these samples was extracted using the Qiagen Blood DNA mini kit, including a Proteinase K digestion step.
DNA was eluted in 5mM Tris-HCl (no EDTA), and a barcoded PCR amplification of gRNA sequences was performed as described (Wang et al., 2016) with PCR cycles: 95°C 2’; 35x: 98°C 10’, 60°C 15’’, 72°C 30’’; 72°C 5’. gRNA PCR product was isolated from a 2% agarose in Tris-Acetate-EDTA gel and eluted using Machery Nagel PCR cleanup kit and dried for 10 min at 56°C. DNA was eluted in 25 ml 5 mM Tris-HCl. This DNA library was loaded onto a 50 cycle MiSeq v2 Illumina Run on an Illumina MiSeq.

treatment_protocol: After four rounds of stimulation, cells were re-stimulated with NY-ESO-9V loaded T2 cells in the presence of an anti-CD107a-APC-H7 antibody. 4h later, cells were stained and sorted based on live CD8+ Vb13.1+ CD19- CD4- CD56- CD107a+/- fractions into 200ul PBS.

tag: donor

value: CD8+ T cells

tag: condition


title: RNA_KP4


title: 0731-066 PBMC, DEX, 0nM

description:
0731-066D1
RawCountMatrix_PBMC.txt

tag: tissue

value: Blood


title: HD144_CD107a_positive

tag: cell type


title: HD141_CD107a_negative


title: 0731-061 PBMC, DEX, 5nM

description:
0731-061D5
RawCountMatrix_PBMC.txt

value: PBMC

tag: diagnosis


title: 0731-061 PBMC, DEX, 50nM

description:
0731-061D7
RawCountMatrix_PBMC.txt

tag: treatment


title: 0731-061 PBMC, DEX, 2.5nM

description:
0731-061D4
RawCountMatrix_PBMC.txt


title: To Iron limitation N2

city: Seattle

first: Shiri

last: Graff van Creveld

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washingtom

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39,25 run in paired-end mode with cut adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1:true, Leading and Trailing thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Reads were mapped to the genome of T. pseudonana or T. oceanica using Hisat2-2.1.0. De-novo transcriptome assemblies were generated from RNA sequences extracted from isolate cultures of Amphora, Chaetoceros, and Cylindrotheca. Each species' quality-controlled RNA sequencing data was assembled using Trinity v2.12.0 using default settings and with sequences provided as un-merged paired end reads. The pre-assembly RNA sequencing reads were then mapped back to their respective assemblies as a quality control step, and at least 85% of the reads from all cultures successfully mapped onto the resulting assemblies. The assembly resulted in 53,401 contigs for Amphora, 37,507 contigs for Chaetoceros, and 73,553 contigs for Cylindrotheca
We calculated the number of T. pseudonana or T. oceanica reads that aligned to the gene models from resulting SAM alignment files with aligned sequences used in subsequent analyses.
Assembly: Thaps3 FilteredModels2 or ThaOc_1.0
Supplementary files format and content: csv files include TPM values for each sample,

organism: Thalassiosira oceanica

source_name: algal cell

growth_protocol: 16:8 hours light:dark cycles and a light intensity of about 100 μmol photons·m-2·sec-1. Specific growth conditions for each species marked under 'growth conditions' as: temprature (C), salts, nutrients, and day of harvest after initiating the experiment, in replete or no iron media. Hydrogen peroxide was added to replete cultures about 2 hours before harvest for RNA-Seq.

extract_protocol:
Total RNA was extracted from 0.2 µm membrane filters with the Zymo Direct-zol RNA MiniPrep Plus kit.
Poly-A-selection, library preparation and sequencing were performed at the Northwest Genomics Center (University of Washington) with standard Illumina NextSeq protocols

value: algal cell

tag: strain

value: iron limitation

tag: growth conditions

value: 20C, EASW, f/2, 6days


title: To Iron limitation N3


title: HD124_CD107a_negative


title: HD141_CD107a_positive


title: 0731-061 PBMC, DEX, 0nM

description:
0731-061D1
RawCountMatrix_PBMC.txt

value: 0 nM DEX


title: 0731-052 PBMC, DEX, 50nM

description:
0731-052-Dex7
Blood1_CountMatrix_final.txt


title: To Iron limitation N1


title: 0731-067 PBMC, DEX, 5nM

description:
0731-067D5
RawCountMatrix_PBMC.txt


title: HD124_CD107a_positive


title: 0731-052 PBMC, DEX, 5nM

description:
0731-052-Dex5
Blood1_CountMatrix_final.txt


title: 0731-052 PBMC, DEX, 0nM

description:
0731-052-Dex1
Blood1_CountMatrix_final.txt


title: 0731-047 PBMC, DEX, 50nM

description:
0731-047-Dex7
Blood1_CountMatrix_final.txt


title: HD122_CD107a_negative


title: To Hydrogren peroxide N3

value: Hydrogen peroxide treated


title: 0731-047 PBMC, DEX, 2.5nM

description:
0731-047-Dex4
Blood1_CountMatrix_final.txt


title: HD119_CD107a_negative


title: 0731-040 PBMC, DEX, 50nM

description:
0731-040D7
RawCountMatrix_PBMC.txt


title: HD122_CD107a_positive


title: To Control N3


title: 0731-052 PBMC, DEX, 2.5nM

description:
0731-052-Dex4
Blood1_CountMatrix_final.txt


title: To Hydrogren peroxide N1


title: To Hydrogren peroxide N2


title: HD119_CD107a_positive


title: 0731-040 PBMC, DEX, 0nM

description:
0731-040D1
RawCountMatrix_PBMC.txt


title: 0731-040 PBMC, DEX, 2.5nM

description:
0731-040D4
RawCountMatrix_PBMC.txt


title: 0731-040 PBMC, DEX, 5nM

description:
0731-040D5
RawCountMatrix_PBMC.txt


title: To Control N2


title: 0731-032 PBMC, DEX, 0nM

description:
0731-032-Dex1
Blood1_CountMatrix_final.txt


title: 0731-037 PBMC, DEX, 50nM

description:
0731-037D7
RawCountMatrix_PBMC.txt


title: 0731-037 PBMC, DEX, 5nM

description:
0731-037D5
RawCountMatrix_PBMC.txt


title: 0731-047 PBMC, DEX, 5nM

description:
0731-047-Dex5
Blood1_CountMatrix_final.txt


title: dCas9-VPR DF1, Mock control_A

city: University Park

first: Tae Hyun

last: Kim

state: PA

address: 317 AVBS

institute: Penn State University

data_processing:
Raw read quailty trimming and adaptor removal: TrimGalore (version 0.6.7)
Read alignment against bGalGal1.mat.broiler.GRCg7b (NCBI annotation release 106): STAR (version 2.7.10a)
Raw read count extraction from bam files: htseq-count (version 0.13.5)
Assembly: bGalGal1.mat.broiler.GRCg7b (NCBI annotation release 106)
Supplementary files format and content: csv, raw read counts of annotated genes in matrix format across all samples

organism: Gallus gallus

extract_protocol:
Total RNA was extracted using Zymo DirectZol mini
mRNA library preparation (poly A enrichment)

tag: cell line

value: Embryonic fibroblast

value: Mock control


title: FFLuc overexpression, donor 4

city: Houston

first: Leonid

middle: S

last: Metelitsa

state: TX

address: 1102 Bates Avenue

institute: Baylor College of Medicine

data_processing:
QC by FastQC (version 0.11.2)
Mapping and alignment by HISAT2 software (v2.1.0)
transcripts assembly by StringTie software (v1.3.5)
Generates raw read counts by prepDE.py (under stringtie software)
extracts coding genes by custom python scripts
Assembly: GRCh38.p13 assembly
Supplementary files format and content: gtf files including FPKM and TPM matrices for each sample
Supplementary files format and content: spreadsheet with gene raw counts

source_name: Peripheral blood

growth_protocol: Peripheral blood of healthy donors was purchased from Gulf Coast Regional Blood Center. PBMCs were isolated from buffy coats by density gradient centrifugation. NKTs were purified using anti-iNKT microbeads (Miltenyi Biotec), and the negative PBMC fraction was irradiated (40 Gy) and aliquoted. NKTs were stimulated with an aliquot of autologous PBMCs pulsed with αGalCer (100 ng/mL; Kyowa Hakko Kirin). The culture was supplemented every other day with recombinant IL-2 (200 U/mL; National Cancer Institute) in complete RPMI (RPMI 1640, 10% heat-inactivated FBS, 2 mM GlutaMAX-1). NKTs were expanded for 10 to 12 days and then restimulated with B-8-2 cells (irradiated with 100 Gy). Twenty four-well, non-tissue culture treated plates were coated with retronectin (Takara Bio) overnight. On  day 2 after restimulation, retronectin-coated plates were washed, inoculated with 1 ml of retroviral supernatant of GFP.LEF1 or GFP.FFLuc, and spun for 60 minutes at 4000 g. Viral supernatant was then removed, and stimulated NKTs were added to the wells in complete media and 200 U/ml IL-2. Cells were removed from the plate after 48 hours, washed, resuspended at 1 million cells/ml in complete RPMI with IL-2, and plated for continued expansion. NKT number was determined by trypan blue (Life Technologies) counting. At day 10 after secondary stimulation, transduced NKTs were FACS sorted according to GFP expression.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA library is formed by polyA capture and reverse transcription of cDNA. Illumine PE150 technology is employed to sequence the sample (Novogene).

value: Peripheral blood

value: Primary human NKTs

value: NKTs

value: FFLuc OE


title: FFLuc overexpression, donor 5


title: FFLuc overexpression, donor 6


title: FFLuc overexpression, donor 3


title: dCas9-VPR DF1, Mock control_B


title: 0731-037 PBMC, DEX, 2.5nM

description:
0731-037D4
RawCountMatrix_PBMC.txt

value: 2.5 nM DEX


title: dCas9-VPR DF1, CRISPRa IRF7 targeted activation_B

value: IRF7 overexpression


title: dCas9-VPR DF1, CRISPRa IRF7 targeted activation_A


title: 0731-037 PBMC, DEX, 0nM

description:
0731-037D1
RawCountMatrix_PBMC.txt

value: PTSD


title: FFLuc overexpression, donor 1


title: dCas9-KRAB DF1, Mock control_B


title: FFLuc overexpression, donor 2


title: 0731-047 PBMC, DEX, 0nM

description:
0731-047-Dex1
Blood1_CountMatrix_final.txt

value: Control


title: 0731-032 PBMC, DEX, 2.5nM

description:
0731-032-Dex4
Blood1_CountMatrix_final.txt

value: Blood


title: 0731-032 PBMC, DEX, 5nM

description:
0731-032-Dex5
Blood1_CountMatrix_final.txt

value: PBMC

value: 5 nM DEX


title: LEF1 overexpression, donor 6

value: LEF1 OE


title: 0731-032 PBMC, DEX, 50nM

description:
0731-032-Dex7
Blood1_CountMatrix_final.txt

value: 50 nM DEX


title: To Control N1

value: algal cell

value: 20C, EASW, f/2, 6days


title: dCas9-KRAB DF1, Mock control_A

value: Embryonic fibroblast


title: 0731-036 PBMC, DEX, 0nM

description:
0731-036-Dex1
Blood1_CountMatrix_final.txt

value: 0 nM DEX


title: 0731-035 PBMC, DEX, 5nM

description:
0731-035-Dex5
Blood1_CountMatrix_final.txt


title: 0731-036 PBMC, DEX, 50nM

description:
0731-036-Dex7
Blood1_CountMatrix_final.txt


title: 0731-036 PBMC, DEX, 5nM

description:
0731-036-Dex5
Blood1_CountMatrix_final.txt


title: 0731-036 PBMC, DEX, 2.5nM

description:
0731-036-Dex4
Blood1_CountMatrix_final.txt


title: 0731-035 PBMC, DEX, 50nM

description:
0731-035-Dex7
Blood1_CountMatrix_final.txt


title: LEF1 overexpression, donor 5

value: Peripheral blood


title: 0731-035 PBMC, DEX, 2.5nM

description:
0731-035-Dex4
Blood1_CountMatrix_final.txt


title: 0731-026 PBMC, DEX, 5nM

description:
0731-026-Dex5
Blood1_CountMatrix_final.txt


title: dCas9-KRAB DF1, CRISPRi IRF7 targted knockdown_A

value: IRF7 knockdown


title: dCas9-KRAB DF1, CRISPRi IRF7 targted knockdown_B


title: 0731-026 PBMC, DEX, 50nM

description:
0731-026-Dex7
Blood1_CountMatrix_final.txt


title: LEF1 overexpression, donor 4

value: Primary human NKTs

value: NKTs


title: 0731-035 PBMC, DEX, 0nM

description:
0731-035-Dex1
Blood1_CountMatrix_final.txt


title: 0731-026 PBMC, DEX, 0nM

description:
0731-026-Dex1
Blood1_CountMatrix_final.txt


title: RH3

data_processing:
All analysis was conducted within SMRTLINK v10.1
Library strategy: DNA-seq

value: bacterial cells


title: LEF1 overexpression, donor 3


title: 0731-026 PBMC, DEX, 2.5nM

description:
0731-026-Dex4
Blood1_CountMatrix_final.txt

value: 2.5 nM DEX


title: LEF1 overexpression, donor 2


title: 0731-021 PBMC, DEX, 50nM

description:
0731-021-Dex7
Blood1_CountMatrix_final.txt


title: KP24


title: 0731-021 PBMC, DEX, 2.5nM

description:
0731-021-Dex4
Blood1_CountMatrix_final.txt


title: 0731-024 PBMC, DEX, 50nM

description:
0731-024-Dex7
Blood1_CountMatrix_final.txt


title: LEF1 overexpression, donor 1


title: 0731-021 PBMC, DEX, 5nM

description:
0731-021-Dex5
Blood1_CountMatrix_final.txt


title: KP14


title: 0731-024 PBMC, DEX, 5nM

description:
0731-024-Dex5
Blood1_CountMatrix_final.txt


title: KP15


title: 0731-024 PBMC, DEX, 0nM

description:
0731-024-Dex1
Blood1_CountMatrix_final.txt


title: 0731-021 PBMC, DEX, 0nM

description:
0731-021-Dex1
Blood1_CountMatrix_final.txt


title: KP13


title: HeLa cells, IL-25 overexpressing, EV71 infected 2

city: Nanjing

first: Jing

address: Han Kou road 22#

institute: Nanjing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa cell

value: epithelial cell

value: IL-25 overexpression

value: EV71 infected

tag: timepoint


title: 0731-016 PBMC, DEX, 50nM

description:
0731-016-Dex7
Blood1_CountMatrix_final.txt

value: Blood

value: PBMC

value: Control


title: 0731-024 PBMC, DEX, 2.5nM

description:
0731-024-Dex4
Blood1_CountMatrix_final.txt


title: 0731-016 PBMC, DEX, 5nM

description:
0731-016-Dex5
Blood1_CountMatrix_final.txt

value: 5 nM DEX


title: HeLa cells, IL-25 overexpressing, EV71 infected 1


title: HeLa cells, Control,  EV71 infected 3

value: WT


title: 0731-016 PBMC, DEX, 0nM

description:
0731-016-Dex1
Blood1_CountMatrix_final.txt


title: 0731-018 PBMC, DEX, 50nM

description:
0731-018D7
RawCountMatrix_PBMC.txt

value: PTSD

value: 50 nM DEX


title: 0731-016 PBMC, DEX, 2.5nM

description:
0731-016-Dex4
Blood1_CountMatrix_final.txt


title: A41_C_2f (39-108 days post hatch dataset)

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4
Reads were mapped using TopHat2 v2.1.0 (--no-convert-bam --no-coverage-search -x 1 -g 1)
Counting of reads per gene was done using featureCounts v1.5.0 (-s 2)
Genome_build: genome v20150522 and annotation v20150922 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: xls file containing read counts/RPMs/RPKMs per gene

organism: Nothobranchius furzeri

source_name: whole brain

extract_protocol:
RNA was extracted with modified Trizol protocol, using Qiazol lysis reagent (Qiagen). In brief, samples were lysed in 1mL QIAzol and 0.2mL of Chloroform was added. Samples were mixed and centrifuged at 20000g for 20 minutes at 4°C in a tabletop centrifuge. After the centrifugation, the upper aqueous phase was withdrawn and mixed with 1.1 volumes (550µl) of isopropyl alcohol, 0.16 volumes (80µl) of 2M, pH 4.2 Sodium acetate and 1µL (10µg) of GlycoBlue to precipitate RNA. Samples were then centrifuged at 20000g for 30 minutes at 4°C, washed twice with 80% ethanol and centrifuged at 7500g for 5 minutes at 4°C. The resulting pellet was dried for no more than 5 minutes and dissolved in nuclease-free water.
Preparation of libraries was done using Illumina‘s TruSeq stranded mRNA kit according the manufacturer‘s description.

tag: Sex

value: female

value: 108 dph


title: HeLa cells, Control,  EV71 infected 1

tag: genotype


title: A41_B_11m (39-108 days post hatch dataset)

value: male

value: 73 dph


title: A41_B_12f (39-108 days post hatch dataset)


title: 0731-018 PBMC, DEX, 0nM

description:
0731-018D1
RawCountMatrix_PBMC.txt

value: 0 nM DEX


title: 0731-018 PBMC, DEX, 2.5nM

description:
0731-018D4
RawCountMatrix_PBMC.txt

value: 2.5 nM DEX


title: 0731-018 PBMC, DEX, 5nM

description:
0731-018D5
RawCountMatrix_PBMC.txt


title: HeLa cells, IL-25 overexpressing, EV71 infected 3

value: HeLa cell


title: 0731-013 PBMC, DEX, 50nM

description:
0731-013-Dex7
Blood1_CountMatrix_final.txt


title: A41_B_7m (39-108 days post hatch dataset)


title: A41_B_8f (39-108 days post hatch dataset)


title: 0731-013 PBMC, DEX, 5nM

description:
0731-013-Dex5
Blood1_CountMatrix_final.txt


title: 0731-013 PBMC, DEX, 2.5nM

description:
0731-013-Dex4
Blood1_CountMatrix_final.txt


title: HeLa cells, IL-25 overexpressing, 1

value: epithelial cell

value: unifected


title: 0731-013 PBMC, DEX, 0nM

description:
0731-013-Dex1
Blood1_CountMatrix_final.txt


title: KP4

value: bacterial cells


title: 0731-012 PBMC, DEX, 2.5nM

description:
0731-012-Dex4
Blood1_CountMatrix_final.txt

value: Blood


title: 0731-012 PBMC, DEX, 50nM

description:
0731-012-Dex7
Blood1_CountMatrix_final.txt

value: PBMC


title: HeLa cells, Control,  EV71 infected 2

value: EV71 infected


title: A41_B_6f (39-108 days post hatch dataset)


title: HeLa cells, Control, 1


title: A41_B_5m (39-108 days post hatch dataset)


title: 0731-011 PBMC, DEX, 50nM

description:
0731-011-Dex7
Blood1_CountMatrix_final.txt


title: 0731-012 PBMC, DEX, 5nM

description:
0731-012-Dex5
Blood1_CountMatrix_final.txt

value: Control

value: 5 nM DEX


title: A41_B_4f (39-108 days post hatch dataset)


title: Single-cell BCR, Subject MuSK MG-4 at 25 months

value: Peripheral Blood

value: B-Lymphocyte


title: 0731-012 PBMC, DEX, 0nM

description:
0731-012-Dex1
Blood1_CountMatrix_final.txt


title: HeLa cells, IL-25 overexpressing, 2

value: IL-25 overexpression


title: Single-cell GEX, Subject MuSK MG-4 at 25 months


title: 0731-011 PBMC, DEX, 2.5nM

description:
0731-011-Dex4
Blood1_CountMatrix_final.txt

value: PTSD


title: 0731-011 PBMC, DEX, 0nM

description:
0731-011-Dex1
Blood1_CountMatrix_final.txt


title: A41_B_1m (39-108 days post hatch dataset)

value: male


title: A41_A_12f (39-108 days post hatch dataset)

value: female

value: 39 dph


title: 0731-010 PBMC, DEX, 50nM

description:
0731-010-Dex7
Blood1_CountMatrix_final.txt

value: 50 nM DEX


title: Single-cell BCR, Subject MuSK MG-1 at 70 months


title: 0731-010 PBMC, DEX, 5nM

description:
0731-010-Dex5
Blood1_CountMatrix_final.txt


title: 0731-010 PBMC, DEX, 2.5nM

description:
0731-010-Dex4
Blood1_CountMatrix_final.txt

value: 2.5 nM DEX


title: HeLa cells, Control, 2

value: HeLa cell

value: epithelial cell

value: WT


title: A41_A_11m (39-108 days post hatch dataset)


title: 0731-006 PBMC, DEX, 50nM

description:
0731-006-Dex7
Blood1_CountMatrix_final.txt

value: Blood


title: A41_A_10f (39-108 days post hatch dataset)


title: 0731-006 PBMC, DEX, 2.5nM

description:
0731-006-Dex4
Blood1_CountMatrix_final.txt

value: PBMC


title: TMD8, DMSO, 24h

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

description: Sequencing performed by Novogene Co., Ltd.

data_processing:
Sequenced reads of mRNA were aligned against the human transcriptome using HISAT2 [D. Kim, B. Langmead and S.L. Salzberg, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, vol. 12, no. 4, pp. 357–360, 2015.]
Gene and transcript annotations were used from RefSeq (GCF_000001405.38_GRCh38.p12_genomic.fna from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference)
Aligned sequence counts were then aggregated for genes using RSEM [B. Li and C.N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol. 12, p. 323, Aug. 2011.]
Assembly: GRCh38.p12
Supplementary files format and content: RSEM aggregation results on gene level are provided as text files with 7 columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, and FPKM.

source_name: diffuse large B-cell lymphoma

growth_protocol: RPMI-1640, 10% FCS, Pen/Strep, beta-Mercaptoethanol, sodium pyruvate

extract_protocol:
NucleoSpin RNA Plus kit (Macherey-Nagel, Germany)
RNA library was prepared for sequencing on the Illumina platform according to the manufacturers’ protocol

treatment_protocol: DMSO (control); 0.5µM AZD8186

value: diffuse large B-cell lymphoma

value: activated B-cell-like

value: DMSO

tag: time point

value: 24 hours


title: TMD8, DMSO, 18h

value: 18 hours


title: 0731-011 PBMC, DEX, 5nM

description:
0731-011-Dex5
Blood1_CountMatrix_final.txt

value: 5 nM DEX


title: A41_A_8f (39-108 days post hatch dataset)

tag: age


title: 0731-006 PBMC, DEX, 0nM

description:
0731-006-Dex1
Blood1_CountMatrix_final.txt

value: PTSD

value: 0 nM DEX


title: A41_A_7m (39-108 days post hatch dataset)

value: male


title: TMD8, AZD8186, 24h


title: 0731-005 PBMC, DEX, 5nM

description:
0731-005-Dex5
Blood1_CountMatrix_final.txt


title: 0731-005 PBMC, DEX, 2.5nM

description:
0731-005-Dex4
Blood1_CountMatrix_final.txt


title: A41_A_5m (39-108 days post hatch dataset)

value: 39 dph


title: 0731-005 PBMC, DEX, 50nM

description:
0731-005-Dex7
Blood1_CountMatrix_final.txt

value: 50 nM DEX


title: 0731-005 PBMC, DEX, 0nM

description:
0731-005-Dex1
Blood1_CountMatrix_final.txt


title: A41_A_3m (39-108 days post hatch dataset)


title: 0731-004 PBMC, DEX, 0nM

description:
018-011-Dex1
Blood1_CountMatrix_final.txt


title: 0731-004 PBMC, DEX, 5nM

description:
018-011-Dex5
Blood1_CountMatrix_final.txt


title: 0731-004 PBMC, DEX, 2.5nM

description:
018-011-Dex4
Blood1_CountMatrix_final.txt

value: 2.5 nM DEX


title: A41_A_4f (39-108 days post hatch dataset)

value: female


title: Single-cell GEX, Subject MuSK MG-1 at 70 months

value: Peripheral Blood

value: B-Lymphocyte


title: TMD8, AZD8186, 6h

value: 6 hours


title: 0731-010 PBMC, DEX, 0nM

description:
0731-010-Dex1
Blood1_CountMatrix_final.txt

value: Blood

value: PBMC


title: 0731-006 PBMC, DEX, 5nM

description:
0731-006-Dex5
Blood1_CountMatrix_final.txt


title: 0731-003 PBMC, DEX, 50nM

description:
018-006-Dex7
Blood1_CountMatrix_final.txt


title: A41_C_11m (39-108 days post hatch dataset)

value: 108 dph


title: Ly10, DMSO, 24h

value: diffuse large B-cell lymphoma

value: activated B-cell-like

value: DMSO


title: 0731-003 PBMC, DEX, 5nM

description:
018-006-Dex5
Blood1_CountMatrix_final.txt

value: 5 nM DEX


title: A41_C_10f (39-108 days post hatch dataset)


title: TMD8, DMSO, 6h


title: 0731-003 PBMC, DEX, 0nM

description:
018-006-Dex1
Blood1_CountMatrix_final.txt

value: PTSD


title: 0731-003 PBMC, DEX, 2.5nM

description:
018-006-Dex4
Blood1_CountMatrix_final.txt


title: 0731-002 PBMC, DEX, 50nM

description:
0731-002-Dex7
Blood1_CountMatrix_final.txt


title: 0731-002 PBMC, DEX, 5nM

description:
0731-002-Dex5
Blood1_CountMatrix_final.txt


title: Ly10, DMSO, 18h

description: Sequencing performed by Novogene Co., Ltd.

value: 18 hours


title: 0731-002 PBMC, DEX, 0nM

description:
0731-002-Dex1
Blood1_CountMatrix_final.txt

value: 0 nM DEX


title: TMD8, AZD8186, 18h


title: 0731-002 PBMC, DEX, 2.5nM

description:
0731-002-Dex4
Blood1_CountMatrix_final.txt


title: 0731-004 PBMC, DEX, 50nM

description:
018-011-Dex7
Blood1_CountMatrix_final.txt


title: Ly10, AZD8186, 24h

value: 24 hours


title: Ly10, DMSO, 6h


title: Ly10, DMSO, 12h

value: 12 hours


title: 0731-001 PBMC, DEX, 50nM

description:
0731-001-Dex7
Blood1_CountMatrix_final.txt

value: 50 nM DEX


title: 0731-001 PBMC, DEX, 5nM

description:
0731-001-Dex5
Blood1_CountMatrix_final.txt


title: A41_C_6f (39-108 days post hatch dataset)

value: female


title: 0731-001 PBMC, DEX, 0nM

description:
0731-001-Dex1
Blood1_CountMatrix_final.txt


title: A41_C_8f (39-108 days post hatch dataset)


title: 0731-001 PBMC, DEX, 2.5nM

description:
0731-001-Dex4
Blood1_CountMatrix_final.txt

value: 2.5 nM DEX


title: Ly10, AZD8186, 18h


title: A41_C_5m (39-108 days post hatch dataset)

value: male


title: A41_C_3m (39-108 days post hatch dataset)


title: Ly10, AZD8186, 6h

value: 6 hours


title: DAP5-2_Ribo: DAP5-null replicate 2 for Ribo-seq

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

institute: University of Zurich

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

growth_protocol: 6.4x10^6 cells of HEK293T WT or DAP5-null cells were plated on 15 cm dishes 24 hrs before harvesting.

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


title: A41_C_9m (39-108 days post hatch dataset)


title: NC_7

first: Liu

middle: xue

last: ting

address: Dongzhimen

institute: China Academy of Chinese Medical Science

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads)
Use Hisat2 software to compare Clean Reads with reference genes (the reference genome version is GRnor_6.0.100)
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate FPKM (Fragments PerKilobase Million) value of each gene
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package
Assembly: GRnor_6.0.100
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: muscle

extract_protocol:
RNA was harvested using RNeasy Mini Kit （250） Qiagen#74106.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: muscle

value: Sprague Dawley

value: NC


title: DAP5-1_Ribo: DAP5-null replicate 1 for Ribo-seq


title: NC_6


title: NC_4


title: M_11

value: MPS


title: M_10


title: NC_5


title: K422, DMSO, 24h

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like


title: control-2_Ribo: Wild-type replicate 2 for Ribo-seq


title: K422, DMSO, 18h

value: DMSO


title: K422, DMSO, 12h


title: drug_27

value: TZG


title: drug_43


title: drug_26

value: Sprague dawley


title: Ly10, AZD8186, 12h

value: activated B-cell-like


title: control-1_Ribo: Wild-type replicate 1 for Ribo-seq


title: K422, AZD8186, 24h

value: 24 hours


title: K422, DMSO, 6h


title: DAP5-2_RNA: DAP5-null replicate 2 for RNA-seq

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


title: K422, AZD8186, 18h

value: 18 hours


title: H9 hESC, cNPCs (hindbrain), Day 11, rep.1

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
The RNA-seq data were quality controlled (Phred score 20) and adapter trimmed using trim_galore (v0.3.3). Filtered data were mapped to the human genome (hg19) using TopHat2 and mRNA quantification was done using featureCounts, a part of the Subread package (v1.6.1) using Ensembl release 71 gene annotations. CircRNAs were quantified using a stringent version of the find_circ pipeline and the CIRCexplorer pipeline.
Assembly: hg19
Supplementary files format and content: For circRNA detection using findcirc and CIRCexplorer algorithms, tab delimeted text files are produced. These show genomic coordinated (hg19) for each circRNA and number of reads for each sample.
Supplementary files format and content: For mRNA detection using featurecounts a tab delimited text file is produced with the output from featurecounts. The text file shows Geneid, Chr, Start, End, Strand, Length for each mRNA followed by number of reads detected in each sample.

growth_protocol: H9 hESCs were transferred to 4-well plates in N2B27 medium (1:1 mix of neurobasal medium and DMEM/F12 medium, 1% insulin/transferrin/selenium, 1x N2 supplement, 1x retinol-free B27 supplement, 0.3% glucose, and 1% p/s (all components are from Gibco, Thermo Fisher Scientific)) for 11 days of differentiation. For rostral NPC differentiation, SB431542 (SB, 10 μM; Tocris, Bristol, UK) and LDN193189 (LDN, 0.1uM; STEMCELL Technologies, BC, Canada) was added to the media for four days. The cells were further cultured with SB, LDN, and FGF2 (20 ng/ml; STEMCELL Technologies) until day seven. Between day 7 and 11, the cell media was only supplemented with FGF2 (20 ng/ml). For caudal NPC differentiation, SB431542 (10 μM) and CHIR99021 (CHIR; 3 μM; STEMCELL Technologies) was added to the media from days zero to four. The cells were further cultured from days 4 to 11 in the absence of SB and CHIR, but with FGF2 (20 ng/ml).

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines.
Total RNA was depleted for ribosomal RNA (rRNA) using the Ribo-Zero rRNA Removal Kit (Human, Mouse, Rat) (Epi-centre, WI, USA), and the sequencing libraries generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre). The libraries were quality controlled on the 2100 Bioanalyzer (Agilent Technologies) and quantified using the KAPA library quantification kit (Kapa Biosystems, MA, USA). RNA-Seq was performed on the HiSeq 4000 system (Illumina, San Diego, CA, USA) using the 100 bp paired-end sequencing protocol.

tag: cell type_source

value: human embryonic stem cells (hESCs)

value: cNPCs (hindbrain)

value: Day 11


title: DAP5-1_RNA: DAP5-null replicate 1 for RNA-seq


title: H9 hESC, cNPCs (hindbrain), Day 11, rep.3


title: control-2_RNA: Wild-type replicate 2 for RNA-seq


title: H9 hESC, rNPCs (forebrain), Day 11, rep.3

value: rNPCs (forebrain)


title: H9 hESC, rNPCs (forebrain), Day 11, rep.2


title: H9 hESC, rNPCs (forebrain), Day 11, rep.1


title: M_14


title: K422, AZD8186, 12h

value: 12 hours


title: H9 hESC, NMPs (hindbrain), Day 4, rep. 3

value: NMPs (hindbrain)

value: Day 4


title: control-1_RNA: Wild-type replicate 1 for RNA-seq


title: H9 hESC, NMPs (hindbrain), Day 4, rep. 2


title: RG3

organism: Enterobacter bugandensis

source_name: Rectal Swab

value: bacterial cells


title: HT, DMSO, 24h

value: HT


title: EU-Seq_RPAC1_IAA_rep2

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

description:
TELP libraries
cDNA

data_processing:
Ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC (v4.0.0) separately, clean reads were then aligned to the concatenated mm10+dm6 genome using bowtie2 with default options (Wang et al., 2012).
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section using featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: For EU-seq, Pol III and RPAC1 degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
After EU labeling, the cells are lysed, and total RNA was extracted using TRIzol reagent and fragmented by base hydrolysis. The nascent RNA labeled by Biotin were enriched with streptavidin beads and extracted using TRIzol reagent again. Biotin is conjugated to EU-labeled RNAs as described (Palozola KC et al., 2017).
The enriched RNA was reverse transcribed into first-strand DNA using SuperScript IV reverse transcriptase kit (Invitrogen, 18090010) with N9 random primer. And RNA was eliminated by adding 2μl 1M NaOH and heating at 98℃ for 20min. DNA was purified with Phenol/Chloroform and precipitated with Ethanol. Finally, the DNA samples were subjected to TELP library construction (Peng et al., 2015). 200bp-400bp DNA libraries were gel-selected, purified, and subjected to HiSeq X-ten PE150 sequencing.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 h to induce OsTir1 expression, then treated with or without 500 uM IAA for 1 h to induce target protein degradation. 5-ethynyluridine (EU), is added to the culture medium with 1 mM concentration for 10 min to allow in vivo labeling of nascent transcripts according to the protocol of Palozola et al. (Palozola KC et al., 2017), and 10% of the total cell number of Drosophila S2 cells were treated similarly and used as spike-in control.

value: RPAC1 degron 1h mESCs


title: RB2

organism: Acinetobacter baumannii

source_name: Fluid Aspirate


title: K422, AZD8186, 6h

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like

value: 6 hours


title: H9 hESC, NMPs (hindbrain), Day 4, rep. 1


title: H9 hESC, cNPCs (hindbrain), Day 11, rep.2


title: HT, DMSO, 18h

value: DMSO


title: EU-Seq_RPAC1_IAA_rep1

description:
TELP libraries
cDNA


title: Pooled bulk BCR sample (MuSK MG-1 70mo, MuSK MG-2 105mo, MuSK MG-4 25mo, MuSK MG-5 48mo)

value: Peripheral Blood

value: B-Lymphocyte


title: RA5

organism: Enterobacter asburiae

source_name: Catheter Urine


title: H9 hESC, NEPs (forebrain), Day 4, rep. 2

value: NEPs (forebrain)


title: Pooled bulk BCR sample (MuSK MG-1 61mo, MuSK MG-5 0mo, MuSK MG-4 0mo, MuSK MG-1 68mo)


title: EU-Seq_RPAC1_Untreated_rep2

description:
TELP libraries
cDNA

value: RPAC1 untreated mESCs


title: HT, DMSO, 12h


title: EU-Seq_RPAC1_Untreated_rep1

description:
TELP libraries
cDNA


title: H9 hESC, NEPs (forebrain), Day 4, rep. 1

value: human embryonic stem cells (hESCs)


title: Pooled bulk BCR sample (HC_A, HC_B, HC_C, HD_D)


title: H9 hESC, undifferentiated, Day 0, rep. 3

value: undifferentiated

value: Day 0


title: EU-Seq_Pol_III_IAA_rep1

description:
TELP libraries
cDNA

value: Pol III degron 1h mESCs


title: Pooled bulk BCR sample (MuSK MG-4 0mo, MuSK MG-1 68mo, MuSK MG-1 70mo, MuSK MG-4 25mo)


title: HT, AZD8186, 24h

value: 24 hours


title: HT, AZD8186, 18h

value: 18 hours


title: H9 hESC, undifferentiated, Day 0, rep. 2


title: Pooled bulk BCR sample (HC_A, HC_B, HC_C, HC_D)


title: EU-Seq_Pol_III_Untreated_rep2

description:
TELP libraries
cDNA

value: Pol III untreated mESCs


title: HT, AZD8186, 12h

value: HT

value: 12 hours


title: H9 hESC, undifferentiated, Day 0, rep. 1


title: Pooled bulk BCR sample (MuSK MG-1 61mo, MuSK MG-1 70mo, MuSK MG-2 105mo, MuSK MG-4 25mo)


title: HT, AZD8186, 6h

value: diffuse large B-cell lymphoma


title: EU-Seq_Pol_III_Untreated_rep1

description:
TELP libraries
cDNA


title: Pooled bulk BCR sample (MuSK MG-5 0mo, MuSK MG-4 0mo, MuSK MG-1 68mo, MuSK MG-5 48mo)


title: CD28_P1_PMA [primary CD4+ T cells]

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

data_processing:
The RSeQC package (Wang et al., Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356) (http://rseqc.sourceforge.net) was used for quality evaluation of the raw high throughput sequence data.
Raw RNA -seq reads were aligned with UCSC human genome assembly version hg38 using STAR (Dobin et al., Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635) (https://github.com/alexdobin/STAR/releases).
HTseq-count (Anders et al., Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638) (https://htseq.readthedocs.io/en/master) was used to count the reads mapping to each gene feature.
Genome_build: hg38
Supplementary_files_format_and_content: Log2 normalized read count

source_name: primary CD4+ T cells

growth_protocol: Frozen PBMCs were thawed and negatively-sorted naive CD4+ T cells were rested overnight in X-VIVO 20 medium prior to stimulation.

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro Kit (QIAGEN), according to the manufacturer’s instructions.
cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation. We used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively, for idexing with low DNA input requirements.

treatment_protocol: The naïve CD4+ T cells were stimulated for two hours with beads coated with the indicated combination of anti-CD2, anti-CD3 and anti-CD28 mAbs (Miltenyi Biotec), or were left untreated.

tag: disease

value: RLTPR deficiency Patient

value: PMA


title: CD28_P1_CD3+CD28 [primary CD4+ T cells]


title: RNA-Seq_Pol_III_96h_rep1

description:
TELP libraries
cDNA

data_processing:
Cutadapt V1.18 (Martin, 2011) was used to remove the adaptors (TELP libraries adaptor) and low-quality reads from the paired-end sequencing reads, then the filtered reads were mapped to the mm10 genome with bowtie2 (--very-sensitive-local) (Langmead and Salzberg, 2012).
In order to obtain the more reliable nascent RNA signals, the duplicate, discordant and multi-mapping reads were removed, rRNA reads were also removed with split_bam.py from RseQC V 2.6.6 (Wang et al., 2012).
The remaining reads were adapter trimmed and aligned against the concatenated genome of mm10 and dm6 using the STAR aligner (Dobin et al., 2013) with default parameters, and then subsequently separated into the mouse and fly bins. Finally, non-redundant reads were determined by samtools.
To display the information of the plus and minus chains at the same time, bamCoverage (Ramirez et al., 2014) was used to make the tracks for plus and minus chains separately with parameters –filterRNAstrand forward/reverse and –scaleFactor.
The uniquely aligned reads were counted over the Gencode annotated genes (M23) using featureCounts, and the output files from two replicates of each group were subsequently analyzed with a custom R script utilizing the DESeq2 package (Love et al., 2014), which incorporates spike-in calibration for data normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq_counts_DESeq2.txt: RNA-seq raw read counts per sample per replicate in tab-delimited text format.

growth_protocol: For RNA-Seq, Pol III degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature and was used as spike-in.

extract_protocol:
Total RNA was isolated using TRIzol following manufacturer’s recommendations.
Sequencing libraries were generated by Novogene corporation with standard Illumina protocols.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 hr to induce OsTIR1 expression, then treated with or without 500 μM IAA for different time points to induce Pol III degradation.

value: Pol III degron 96h mESCs


title: EU-Seq_Pol_III_IAA_rep2

description:
TELP libraries
cDNA


title: HD287_Teff

data_processing:
Primary data analysis was performed with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.
Reads were mapped to the human hg38 genome assembly with STAR (version 2.7.9a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Gene expression was quantified with featureCounts from the Subread package (v2.0.1) using gene annotation from Ensembl release 105, and options "-O -M --read2pos=5 --primary -s 2 -p -B"
Assembly: hg38
Supplementary files format and content: An R .rds file including an edgeR DGElist class object. Read counts matrix is accessible in the dge$counts slot. Information about samples is in the dge$samples slot. Information about genes is in the dge$genes slot.

source_name: Human CD8+ T cells

growth_protocol: Four human healhy donor CD8+ T cells  were isolated, transduced with an NY-ESO-1 TCR lentivirus construct. Cells were cultured in RPMI1640 (Sigma)  supplemented with 8% heat-inactivated (56°C 30min) human AB+ male serum, 100 ng/ml penicillin/streptomycin (Sigma), 2 mM L-Glutamine (Sigma), 1 mM Sodium Pyruvate (Sigma),1% MEM non-essential amino acids (Sigma), 50 nmol/l beta-mercaptoethanol (Thermo Fisher) and 10mM HEPES (Sigma). Cells received 50 U/ml recombinant human IL2 every 3 days.

extract_protocol:
Total RNA were purified using the kit Direct-Zol RNA Miniprep (Zymo-Research, Cat# R2050). The purified RNA was quality-checked on the Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Pico Chip (Agilent, Cat# 5067-1513). RNA was quantified by Fluorometry using the QuantiFluor RNA System (Cat# E3310, Promega, Madison, WI, USA).
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and IDT TruSeq RNA UD Indexes. Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical). Libraries were sequenced as paired ends PE51 (in addition: 8 bases for index 1 and 8 bases for index 2) using an Illumina NovaSeq 600.

treatment_protocol: Cells were stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. INY-ESO-1 TCR specific T cells were plated at 0.125 mio/ml specific cells.  T2 tumor cells were irradiated with 3000 rad gamma rays using a GammaCell irradiator. Irradiated cells were mixed with the indicated dose (1 M) of NY-ESO-1 9V peptide and added to the T cells at an effector to target ratio of 1:3 in the presence of 50 U/ml IL-2. This procedure was repeated (with IL-2 stimulation at each stimulation) according to the scheme in  Extended Data Fig. 1A. At each stimulation, 75% of the medium was replaced. The cells were expanded 1:2 on the day of the second stimulation with tumor cells and peptide. Ttumor were treated identically, but without the addition of NY-ESO-1 9V peptide. For Trest, we only exchanged 75% of the medium every three days replenishing IL2. Acute stimulation controls were only cultured as Trest with IL2 on days 0, 3, 6, and with tumor cells + peptide + IL2 on day 9 after plating. After 12 days (thus 3 days after last stimulation), cells were stained and analyzed by flow cytometry. Functional assays were performed the same or the next day normalized to cell numbers.. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells.

value: Teff


title: Pool of myeloid cells from ILC2-proficient mice and epithelial cells from ILC2-deficient mice

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: myeloid cells from ILC2-proficient mice and epithelial cells from ILC-deficient mice

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single Cell Software Suite 5.0.0 was used in default parameter settings to perform sample demultiplexing, barcode processing, and single cell 5’ gene counting for transcriptome wirh refdata-cellranger-mm10-1.2.0 as reference and expected-cells number of 3000 for each sample.
Assembly: mm10
Supplementary files format and content: h5: aggregated gene count matrix in hdf5 format.

source_name: lung and trachea

extract_protocol:
Lung tissue was digested using Liberase TM and DNaseI to obtain single-cell suspensions. Cells were subsequently incubated with fluorochrome-conjugated antibodies and epithelial cells were sorted by FACS as live CD45lo/- EpCAM+ cells, myeloid cells were sorted as live CD45+ (CD11b and/or CD11c)+. Epithelial cells from ILC2-proficient mice were pooled with myeloid cells from ILC2-deficient mice and vice versa. These cells were then applied to the 10X Genomics platform using the Chromium™ Single Cell 5’ Library & Gel Bead Kit v2 (10x Genomics) following the manufacturer’s instructions.
The purified cDNA was amplified using 12 cycles of PCR and then used for 5’ gene expression (GEX). Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 5’ GEX was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).The sequencing was performed on a NextSeq2000 device (Illumina) with the recommended sequencing conditions for 5’ GEX libraries (read1: 26nt, read2: 90nt, index1: 10nt, index2:10).

value: lung and trachea

value: male

value: epithelial and myeloid cells

value: cKO:Nmur1Cre (tg), Id2 fl/fl, ctrl:Id2fl/fl or Id2 fl/wt

value: untreated


title: HD287_Ttumor

value: Ttumor


title: HD287_Tex

value: Tex


title: CD28_P1_CD28 [primary CD4+ T cells]


title: RNA-Seq_Pol_III_48h_rep2

city: Beijing

description:
TELP libraries
cDNA

value: Pol III degron 48h mESCs


title: CD28_P1_CD3 [primary CD4+ T cells]


title: HT, DMSO, 6h

value: germinal center B-cell-like

value: DMSO

value: 6 hours


title: HD287_Trest

value: Trest


title: RNA-Seq_Pol_III_24h_rep2

description:
TELP libraries
cDNA

value: Pol III degron 24h mESCs


title: RNA-Seq_Pol_III_48h_rep1

description:
TELP libraries
cDNA


title: CD28_P1_NS [primary CD4+ T cells]

value: RLTPR deficiency Patient

value: unstimulated


title: HD286_Tex


title: RLTPR_KM_PMA [primary CD4+ T cells]

value: PMA


title: RNA-Seq_Pol_III_24h_rep1

description:
TELP libraries
cDNA


title: RNA-Seq_Pol_III_96h_rep2

description:
TELP libraries
cDNA

value: Pol III degron 96h mESCs


title: HD286_Teff

value: Teff


title: RLTPR_KM_CD3+CD28 [primary CD4+ T cells]


title: Pool of myeloid cells from ILC2-deficient mice and epithelial cells from ILC2-proficient mice

description: myeloid cells from ILC2-deficient mice and epithelial cells from ILC-proficient mice

value: lung and trachea

value: male


title: RLTPR_KM_CD28 [primary CD4+ T cells]


title: HD286_Ttumor


title: HD286_Trest


title: RNA-Seq_Pol_III_0h_rep1

description:
TELP libraries
cDNA

value: Pol III degron 0h mESCs


title: HD280_Tex


title: RLTPR_KM_CD3 [primary CD4+ T cells]


title: RLTPR_KM_NS [primary CD4+ T cells]


title: PRO-Seq_Pol_III_IAA_rep1

description:
TELP libraries
PRO-Seq_Pol_III_IAA_plus.bw
PRO-Seq_Pol_III_IAA_minus.bw

data_processing:
Library strategy: PRO-Seq
Ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC (v4.0.0) separately, clean reads were then aligned to the concatenated mm10+dm6 genome using bowtie2 with default options (Wang et al., 2012).
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section using featureCounts (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

growth_protocol: For PRO-Seq, Pol I, Pol II and Pol III degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
1-Biotin run-on was applied according to the protocol of Dig et al. (Dig et al., 2016). Total RNA was extracted using TRIzol reagent and fragmented by base hydrolysis. The nascent RNA labeled by Biotin were enriched with streptavidin beads and extracted using TRIzol reagent again.
The enriched RNA was reverse transcribed into first-strand DNA using SuperScript IV reverse transcriptase kit (Invitrogen, 18090010) with N9 random primer. And RNA was eliminated by adding 2μl 1M NaOH and heating at 98℃ for 20min. DNA was purified with Phenol/Chloroform and precipitated with Ethanol. Finally, the DNA samples were subjected to TELP library construction (Peng et al., 2015). 200bp-400bp DNA libraries were gel-selected, purified, and subjected to HiSeq X-ten PE150 sequencing.

treatment_protocol: Cells were treated with 2 μg/ml Doxycycline for 12 h to induce OsTir1 expression, then treated with or without 500 uM IAA for 1 h to induce target protein degradation. Cell nuclei were isolated according to the protocol of Dig et al. (Dig et al., 2016), and 5% S2 cells were added during the cell permeabilization.

value: Pol III degron 1h mESCs


title: HD280_Teff


title: RLTPR_EM_PMA [primary CD4+ T cells]


title: HMEC-FL2 - laminin-521 3

city: Helsinki

first: Pekka

last: Katajisto

state: helsinki

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

data_processing:
Base-calling and demultiplexing was performed using CASAVA software with default settings generating Fastq files
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v1.8.4 program
STAR v2.5.2b (Dobin et al., 2013) was used to index the human reference genome (hg38) and align the resulting fastq files
Mapped reads were then counted in annotated exons using featureCounts v1.5.1 (Liao et al., 2014)
The entrez gene annotations and reference genome were obtained from UCSC. The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR (Robinson et al., 2009) package and its general linear models pipeline
Genome_build: hg38
Supplementary_files_format_and_content: count text file

source_name: Human mammary epithelial cell line

growth_protocol: HMECs were grown on laminin-111, -421 or -521 coated (50 ug/ml) 6-well plates  in mammary epithelial basal medium (MEGM; Lonza) for 48 hours. Cells were lysed directly on plates with RNAeasy Kit lysis buffer.

extract_protocol:
RNeasy Kit (Qiagen) was used for RNA extraction following the manufacturer’s instructions. RNA was stored at -80 until further processing.
To construct libraries suitable for Illumina sequencing the Illumina TruSeq Stranded mRNA Sample preparation protocol which includes cDNA synthesis, ligation of adapters and amplification of indexed libraries was used
Illumina HiSeq 2000 for a 50-cycle v3 sequencing run generating 50 bp single-end reads

value: Cultured on laminin-521 coated plate


title: HMEC-FL2 - laminin-521 2


title: HD280_Trest


title: RLTPR_EM_CD3+CD28 [primary CD4+ T cells]


title: RNA-Seq_Pol_III_0h_rep2

description:
TELP libraries
cDNA


title: RLTPR_EM_CD28 [primary CD4+ T cells]


title: HMEC-FL2 - laminin-521 1


title: PRO-Seq_Pol_III_IAA_rep2


title: HD276_Tex

value: Tex


title: PRO-Seq_Pol_III_Untreated_rep2

description:
TELP libraries
PRO-Seq_Pol_III_Untreated_plus.bw
PRO-Seq_Pol_III_Untreated_minus.bw

value: Pol III untreated mESCs


title: PRO-Seq_Pol_II_NTD_IAA_rep2

description:
TELP libraries
PRO-Seq_Pol_II_NTD_IAA_plus.bw
PRO-Seq_Pol_II_NTD_IAA_minus.bw

value: Pol II N-terminal degron 1h mESCs


title: HMEC-FL2 - laminin-521 4


title: PRO-Seq_Pol_III_Untreated_rep1


title: RLTPR_EM_CD3 [primary CD4+ T cells]


title: PRO-Seq_Pol_II_NTD_IAA_rep1


title: HD276_Teff


title: FZH_CQ

type: RNA

city: Jinan

first: lina

last: wang

address: North Park Street 247

institute: Second Hospital of Shandong University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarray data were extracted and visualized using the Feature Extraction software 10.7(Agilent Technologies), and the resulting raw data were subjected to quantile normalization using the limma package in R. Data analysis was performed according to by Agilent Technologies at Sinotech Genomics Corporation. Differentially expressed circRNAs were identified using a fold change cutoff of 2 and a P value of 0.05.

source_name: plasma samples of GDM women before delivery

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: RNA from the three paired samples was extracted with RNeasy Mini Kit (Qiagen, Germany) per the manufacturer’s instructions. RNA from the other 44 samples was extracted using Sparkzol Reagent (SparkJade Science Co., Ltd., China), chloroform, and isopropanol precipitation.

tag: subject status

value: pregnant women with GDM

tag: gender

value: female

value: plasma

value: before delivery


title: RLTPR_EM_NS [primary CD4+ T cells]

value: RLTPR deficiency Patient


title: FZH_CH

source_name: plasma samples of GDM women  48 h after delivery

value: 48 h after delivery


title: ZCL_CH


title: XYC_CH


title: XYC_CQ


title: HD280_Ttumor

tag: donor

tag: condition

value: Ttumor


title: ZCL_CQ

tag: tissue


title: HD276_Ttumor


title: Ctl5_PMA [primary CD4+ T cells]

value: healthy Control

value: PMA


title: Ctl5_CD3+CD28 [primary CD4+ T cells]


title: HMEC-FL2 - laminin-421 3

value: Cultured on laminin-421 coated plate


title: HMEC-FL2 - laminin-421 2


title: PRO-Seq_Pol_II_IAA_rep2

description:
TELP libraries
PRO-Seq_Pol_II_IAA_plus.bw
PRO-Seq_Pol_II_IAA_minus.bw

value: Pol II degron 1h mESCs


title: PRO-Seq_Pol_II_NTD_Untreated_rep2

description:
TELP libraries
PRO-Seq_Pol_II_NTD_Untreated_plus.bw
PRO-Seq_Pol_II_NTD_Untreated_minus.bw

value: Pol II N-terminal untreated mESCs


title: PRO-Seq_Pol_II_NTD_Untreated_rep1


title: rNPCs_11_circRMST_b8_rep4 [20200617_38_N286_22]

data_processing:
Raw reads were filtered and trimmed using trim_galore (version 0.6.5dev, using parameters: -a AAAAAAAAAAAA --clip_R1 12).  The filtered QuantSeq 3’ mRNA-Seq reads were mapped to the human reference genome (hg19) using STAR (version 2.7.3a) with default setting. Read mapping results per gene were then quantified using the tool featureCounts with gene annotation from Gencode (version 28). All samples used for downstream analysis in the corresponding manuscript "A circular RNA expressed from the FAT3 locus regulates neural development " are indicated in the column "Samples used for downstream analysis".
Assembly: hg19
Supplementary files format and content: FeatureCounts output file with mRNA expression as raw reads for each sample. Tab delimited text file

source_name: H9 hESCs

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines.
RNA quality was controlled using the RNA 6000 Nano Kit (Agilent Technologies, CA, USA) on a Bioanalyzer 2100 (Agilent Technologies), and RNA quantity determined using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). The TURBO DNA-free Kit (Thermo Fisher Scientific) was used for DNA removal and followed by an additional RNA precipitation step.  For library generation, the QuantSeq 3’mRNA-Seq Library Kit (Lexogen, Vienna, Austria) was utilized according to the manufacturer’s instructions.

value: H9 hESCs

tag: batch

value: circRMST KD

tag: treatment/time point

value: rNPCs; Day 11

tag: samples used_for_downstream_analysis

value: yes


title: Ctl5_CD28 [primary CD4+ T cells]

tag: treatment


title: HD276_Trest

value: Trest


title: HMEC-FL2 - laminin-421 4

tag: cell line


title: HMEC-FL2 - laminin-421 1


title: PRO-Seq_Pol_II_IAA_rep1


title: rNPCs_11_circRMST_b7_rep3 [20200617_35_N286_19]


title: Ctl5_CD3 [primary CD4+ T cells]


title: H9 hESC, NEPs (forebrain), Day 4, rep. 3

value: human embryonic stem cells (hESCs)

tag: cell type

value: NEPs (forebrain)

value: Day 4


title: HMEC-FL2 - laminin-111 4

value: Cultured on laminin-111 coated plate


title: PRO-Seq_Pol_II_Untreated_rep2

description:
TELP libraries
PRO-Seq_Pol_II_Untreated_plus.bw
PRO-Seq_Pol_II_Untreated_minus.bw

value: Pol II untreated mESCs


title: HMEC-FL2 - laminin-111 3


title: Ctl5_NS [primary CD4+ T cells]

value: unstimulated


title: HMEC-FL2 - laminin-111 2


title: rNPCs_11_circRMST_b6_rep2 [20200617_32_N286_46]


title: PRO-Seq_Pol_II_Untreated_rep1


title: Ctl3_CD3+CD28 [primary CD4+ T cells]


title: PRO-Seq_Pol_I_IAA_rep2

description:
TELP libraries
PRO-Seq_Pol_I_IAA_plus.bw
PRO-Seq_Pol_I_IAA_minus.bw

value: Pol I degron 1h mESCs


title: HMEC-FL2 - laminin-111 1


title: rNPCs_11_circRMST_b5_rep1 [20200617_28_N286_16]


title: PRO-Seq_Pol_I_IAA_rep1


title: HMEC-FL2 - uncoated 4

value: Cultured on uncoated plate


title: Ctl3_PMA [primary CD4+ T cells]

value: healthy Control

value: PMA


title: PRO-Seq_Pol_I_Untreated_rep1

description:
TELP libraries
PRO-Seq_Pol_I_Untreated_plus.bw
PRO-Seq_Pol_I_Untreated_minus.bw

value: Pol I untreated mESCs


title: PRO-Seq_Pol_I_Untreated_rep2


title: Ctl3_CD3 [primary CD4+ T cells]


title: rNPCs_11_circFAT3_b8_rep4b [20200617_56_N286_28]

value: circFAT3 KD


title: rNPCs_11_circFAT3_b6_rep2 [20200617_30_N286_44]

value: H9 hESCs


title: rNPCs_11_circFAT3_b5_rep1 [20200617_26_N286_14]


title: Ctl3_NS [primary CD4+ T cells]


title: ChIP_Seq_Pol_II_CTD_IAA_anti_NTD_rep1

description: ChIP_Seq_Pol_II_CTD_IAA_anti_NTD_merged.bw

data_processing:
Adapters were trimmed with cutadapt (v2.10) in paired-end mode with the following parameters: -q 15,15 –minimum-length 18 -a CCCCCCCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT. Trimmed reads were first aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1) with default options
SAMtools (v 0.1.19) and sambamba (v0.7.0) were used to filter unmapped reads, multiple mapped reads, and potential PCR duplicates.
Only uniquely aligned reads were retained before calling peaks with MACS2 (v2.2.5) (Zhang et al., 2008). High-confidence peaks shared across two biological replicates with irreproducible discovery rate (IDR) < 0.05 were selected for each condition.
For visualization, bam files of individual replicates for each condition were combined and then converted to bigwig files, binned (10 bp), and normalized to 1x depth of reads per genome coverage (RPGC) using the bamCoverage from the deepTools suite (v3.4.3) with parameters “–normalizeUsingRPGC –bs 10” (Ramirez et al., 2014).
Downstream analyses such as TSS plots, metagene plots, and heatmaps were also performed using deepTools with a bin size of 50 bp.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

growth_protocol: For ChIP-Seq, WT, Pol I, Pol II Pol III and RPAC1 degron mouse embryonic stem cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) with MEF and maintained at 37℃ cell incubator with 5% CO2. After two passages of MEF feeders, cells were harvested for experiment.

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40U MNase (NEB, M0247), followed by sonication as previously described (Jiang et al., 2020). 1μg antibodies and 30μl Protein G beads (Thermo Fisher, 10004D) were used for each replicate..
ChIP DNA were subjected to TELP library construction (Peng et al., 2015). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: Cells were treated with 1 μg/ml Doxycycline for 12 hr to induce OsTIR1 expression, then treated with or without 500 μM IAA for 1 hr to induce targeted proteins degradation. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.

value: Pol II_degron mESCs IAA 1hr

tag: antibody

value: RPB1 NTD(CST, Cat#D8L4Y, lot#4)


title: ChIP_Seq_Pol_II_CTD_IAA_anti_NTD_rep2


title: HMEC-FL2 - uncoated 3


title: rNPCs_11_circFAT3_b7_rep3b [20200617_55_N286_27]

tag: genotype

value: rNPCs; Day 11

value: yes


title: Ctl2_CD3+CD28 [primary CD4+ T cells]

tag: time point


title: Sense2 Small RNA

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Florida

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: N/A
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

source_name: Primary Hippocampal neurons

growth_protocol: Hippocampi were cultured from P0 mice for generating RNA at DIV 16.

extract_protocol:
RNA was extracted using DirectZol RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DIV 16 neurons from P0 pups


title: Ctl3_CD28 [primary CD4+ T cells]


title: Ctl2_CD28 [primary CD4+ T cells]


title: ChIP_Seq_Pol_II_CTD_Untreated_anti_NTD_rep2

description: ChIP_Seq_Pol_II_CTD_Untreated_anti_NTD_merged.bw

value: Pol II_degron mESCs untreated


title: ChIP_Seq_Pol_II_CTD_Untreated_anti_NTD_rep1


title: Ctl2_CD3 [primary CD4+ T cells]


title: ChIP_Seq_Pol_II_CTD_Input

value: Pol II_degron mESCs input


title: rNPCs_11_ciRS7_b6_rep2 [20200617_31_N286_45]

value: ciRS-7 KD


title: Sense1 Small RNA


title: Antisense3 Small RNA


title: rNPCs_11_ciRS7_b5_rep1 [20200617_27_N286_15]


title: rNPCs_11_CTRL_b8_rep4b [20200617_58_N286_30]

value: CTRL


title: ChIP_Seq_Pol_III_IAA_anti_SSRP1_rep2

description: ChIP_Seq_Pol_III_IAA_anti_SSRP1_merged.bw

value: Pol III_degron mESCs IAA 1hr


title: rNPCs_11_CTRL_b8_rep4 [20200617_36_N286_20]


title: Antisense2 Small RNA


title: Ctl2_NS [primary CD4+ T cells]

value: unstimulated


title: Ctl1_PMA [primary CD4+ T cells]


title: rNPCs_11_ciRS7_b8_rep4 [20200617_37_N286_21]


title: HMEC-FL2 - uncoated 1

value: Cultured on uncoated plate


title: ChIP_Seq_Pol_III_IAA_anti_SSRP1_rep1


title: Sense3 Small RNA


title: rNPCs_11_CTRL_b7_rep3b [20200617_57_N286_29]


title: rNPCs_11_ciRS7_b7_rep3 [20200617_34_N286_18]


title: Ctl1_CD3+CD28 [primary CD4+ T cells]

value: healthy Control


title: Antisense1 Small RNA


title: ChIP_Seq_Pol_III_Untreated_anti_SSRP1_rep1

description: ChIP_Seq_Pol_III_Untreated_anti_SSRP1_merged.bw

value: Pol III_degron mESCs untreated


title: rNPCs_11_CTRL_b7_rep3 [20200617_33_N286_17]


title: Ctl1_CD28 [primary CD4+ T cells]


title: Ctl1_CD3 [primary CD4+ T cells]


title: rNPCs_11_CTRL_b6_rep2 [20200617_29_N286_43]


title: ChIP_Seq_Pol_III_IAA_anti_INTS3_rep2

description: ChIP_Seq_Pol_III_IAA_anti_INTS3_merged.bw


title: rNPCs_11_CTRL_b5_rep1 [20200617_25_N286_13]


title: FSK_miRNA_6

data_processing:
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes

extract_protocol:
RNA was extracted using traditional Trizol/chloroform extraction method
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Sample Prep

value: DIV 16 neurons

tag: developmental stage

value: P0 pups

tag: agent

value: FSK


title: FSK_miRNA_4


title: FSK_miRNA_5


title: Ctl1_NS [primary CD4+ T cells]

tag: disease


title: hESCs_0_circRMST_b9_rep7 [20200617_62_N286_62]

value: H9 hESCs

value: circRMST KD

value: undifferentiated; Day 0

value: no


title: ChIP_Seq_Pol_III_Untreated_anti_INTS3_rep2

description: ChIP_Seq_Pol_III_Untreated_anti_INTS3_merged.bw


title: hESCs_0_circRMST_b6_rep6 [20200617_4_N286_35]

value: yes


title: ChIP_Seq_Pol_III_Untreated_anti_INTS3_rep1


title: FSK_miRNA_3


title: ChIP_Seq_Pol_III_IAA_anti_INTS3_rep1


title: FSK_miRNA_2


title: ChIP_Seq_Pol_III_IAA_anti_TBP_rep2