title: SMPAT_WT+NAA_Replicate_3

source_name: W303 PMY1 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1)

growth_protocol: Yeast cells pre-cultured in liquid YPD medium at 30°C for 3h and thereafter NAA was added to a final concentration of 1mM and growth was continued for 6h.


title: SMPAT_WT+NAA_Replicate_2

status: Public on Mar 19 2025

type: SRA

city: Bethesda

first: Poonam

last: Poonia

state: MD

address: 6 Center Drive, Bldg 6, Room 240

department: NICHD

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For SMPAT-Seq: Sequencing reads from the Sequel instrument come in the form of continuous reads around a “rolling circle.” The insert is read over multiple passes in each direction. These insert passes are referred to as subreads. Multiple passes gives circular consensus sequences (CCS; also referred to as HiFi). CCS reads were demultiplexed to individual samples using the program “lima” (v2.6 or above) using the appropriate sample barcodes utilized during library construction. Samtools was used to convert demultiplexed sample CCS reads to fastq format for further processing and alignment. CCS read IDs are assigned to transcripts through the use of PacBio minimap2 to align reads to Ensembl Saccharomyces cerevisiae.R64-1-1 release 109. To determine and assign a poly(A) tail length to a CCS ID, reads are evaluated in either direction for a poly(A) stretch abutting the adapter utilized in library construction. A one base mismatch is tolerated for the adapter sequence pattern matching.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples. For CAGE-sequencing the file contains three columns providing: Chromosome (Chr), Position of detected TSS (pos), strand information (strand) and 14 columns with read counts for different samples. For SMPAT-Seq, report.txt file contains multiple columns providing: Gene name (#Gene), Counts for each gene (Counts), mean poly(A) tail lengths (MeanPolyA), Standard error (STDERR), Minimum poly(A) tail length (Min), Quartile1 (Q1), median poly(A) tail lengths (Median), Quartile 3rd (Q3), Maximun poly(A) tail lengths (Max) and ListOfValues.
Library strategy: SMPAT-seq

molecule: total RNA

organism: Saccharomyces cerevisiae

extract_protocol: SM-PAT sequencing was conducted on the same total RNA samples described above that were subjected to RNA-Seq and Ribo-Seq. SM-PAT libraries were constructed from  total RNA for each sample as previously described in "Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform. Iben et al., 2024, Methods Mol Biol, 2723, 285-301.

tag: cell type

value: Yeast whole cells

tag: treatment

value: 1mM 1-Napthaleneacetic acid (NAA)


title: con-3-30-11

city: Shang Hai Shi

first: Bowen

last: Zhu

state: Shang Hai Shi

address: Pu Dong Xin Qu Hua Tuo Lu 88Hao, Gao Ke Yuan18-604

country: China

institute: Interdisciplinary Research Center on Biology and Chemistry

library_source: genomic

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) using bismark (v0.24.1) with default parameters. Uniquely mapped read pairs were extracted using samtools (v1.17) Methylation level was extracted by bismark.
After extracting the methylation data using bismark to obtain the raw data, we found that there were many invalid site data with all values of 0 or NA in the data, so we used two conditions to screen for valid methylation sites: 1. Since we designed five pairs of PCR primers to be amplified and then sequenced, only the CpG sites located within these five sequences could be valid sites. 2. Methylation ratio screening, we considered that only sites with a methylation rate greater than 0 in 70% of the population were valid sites, and the final results of the screening can be found in the file I uploaded, 'methylation_whole_1.csv'.
Assembly: GRCh38
Supplementary files format and content: csv table with methylation site at row and samples at column; the proportion of methylation at the specific locus for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Genomic DNA was extracted and purified using MagPure Uninversal DNA Kit B (Magen, catalog: D6310-03B) and RNase A (ABclonal, Catalog: RM29870)
Converted DNA libraries were prepared using Bisulfite Conversion Kit(Singlera, catalog: EP110192) and PCR

tag: tissue

value: Blood

tag: Sex

value: F

tag: age


title: SMPAT_WT+NAA_Replicate_1


title: con-YY230330-39


title: SMPAT_dcp2∆pab1-AID+NAA_Replicate_3

source_name: W303 PRY1 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 dcp2∆::HIS3 lys2:: PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)

growth_protocol: Yeast cells were cultured in YPD at 30°C for one division and thereafter NAA was added to a final concentration of 1mM and growth was continued for 6h.


title: SMPAT_pab1-AID+NAA_Replicate_1

source_name: W303 PMY2 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)


title: con-YY230330-38


title: pre-metastatic niches,replicate 2,scRNAseq

city: Guangzhou

first: Yue

last: Jiang

state: Guangdong

address: No. 26, Erheng Road, Yuancun

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

description:
Library name: PMN2
BD Rhapsody system

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8, Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: liver

extract_protocol:
Liver single cell suspension preparation was performed by the laboratory staff of NovelBio Biopharmaceutical Technologies Ltd. Liver lysis was performed as described previously, whole mouse livers were removed, cut into small pieces on ice, and then enzymatically lysed with 1 mg/mL Collagenase II (Worthington) for 30 min on a shaker at 37°C. 70-micron cell filters were sieved and then erythrocytes were lysed in erythrocyte lysis buffer (Miltenyi Biotec), rinsed twice with PBS, and then the MACS Dead Cell Removal Kit (Miltenyi Biotec) was used to further enrich the single cell suspension.
Single cell capture was realized using the BD Rhapsody system. Whole transcriptome libraries were prepared according to the BD Rhapsody Single Cell Whole Transcriptome Amplification Workflow and 150 bp paired-end sequencing was performed using the Illumina (Illumina, San Diego, California, USA).

value: liver

tag: cell line

value: immune cells and non-immune cell

tag: genotype

value: Orthotopic mouse models of colorectal cancer


title: con-3-30-10


title: pre-metastatic niches,replicate 1,scRNAseq

description:
Library name: PMN1
BD Rhapsody system


title: con-YY230330-36


title: con-YY230330-35


title: control,replicate 2,scRNAseq

description:
Library name: ctrl2
BD Rhapsody system

value: ctrl


title: con-YY230330-34


title: CD45+ EPC tumor 4

city: Wuhan

first: Zhi-Zhong

last: Wu

address: No.237 Luoyu Road

institute: School & Hospital of Stomatology, Wuhan University

description: CD45+ EPC T 4

data_processing:
BGISEQ platform
Sequence reads were filtered using SOAPnuke software by BGI platform
Filtered sequence reads were mapped to NCBI/GCF_000001635.26_GRCm38.p6
Read count extraction and normalization were performed by BGI platform
Assembly: NCBI/GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: immune cells

growth_protocol: Female C3H/HeN mice were injected with SCC7 tumor cells. When the tumors grew up, EPCs in spleen and tumor were sorted by FACS.

extract_protocol:
RNA extraction using TRIZOL was performed by BGI.
RNA libraries for RNA-seq were prepared by BGI following manufacturer's protocols.

tag: disease state

value: HNSCC

value: tumor

value: EPC

tag: sorted cell type

value: CD45+ EPC

value: WT


title: control,replicate 1,scRNAseq

description:
Library name: ctrl1
BD Rhapsody system


title: con-YY230330-32

value: M


title: CD45+ EPC tumor 3

description: CD45+ EPC T 3


title: con-YY230330-28


title: CD45+ EPC tumor 2

description: CD45+ EPC T 2


title: CD45+ EPC tumor 1

description: CD45+ EPC T 1


title: splenic CD45+ EPC 3

description: CD45+ EPC 3

value: spleen


title: con-YY230330-26


title: splenic CD45+ EPC 2

description: CD45+ EPC 2


title: con-YY230330-27


title: con-YY230330-25


title: con-YY230330-24


title: splenic CD45+ EPC 1

description: CD45+ EPC 1


title: con-YY230330-23


title: con-YY230330-22


title: splenic CD45- EPC 2

description: CD45- EPC 2

value: CD45- EPC


title: SCC7 cells aCD71 10 Days 2

data_processing:
BGISEQ platform
Sequence reads were filtered using SOAPnuke software by BGI platform
Filtered sequence reads were mapped to NCBI/GCF_000001635.26_GRCm38.p6
Read count extraction and normalization were performed by BGI platform
Assembly: NCBI/GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: tumor

growth_protocol: SCC7 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 °C and 5% CO2. SCC7 cells (3 × 105/per mouse) were subcutaneously injected into the dorsal sides of C3H/HeN mice to construct ectopic HNSCC transplantation model.

treatment_protocol: SCC7 tumor-bearing mice were treated with anti-CD71 on day 6 and day 9

value: SCC7 cell

value: murine HNSCC cell

tag: time point


title: splenic CD45- EPC 1

description: CD45- EPC 1


title: con-YY230330-20


title: SCC7 cells aCD71 10 Days 1


title: SCC7 cells control 10 Days 2

value: Control


title: con-YY230328-9

value: Blood


title: con-YY230328-6

value: F


title: con-YY230330-33


title: con-YY230328-2


title: IL-1β+DAPA treatment_4

city: Xi'an

first: Xue

last: Hao

address: Shanghua Road

institute: Xi'an Honghui Hospital

data_processing:
Hisat2 (v2.2.1)
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)
Assembly: GRCh38
Supplementary files format and content: excel file includes count values for each sample

molecule: polyA RNA

source_name: cartilage

growth_protocol: The human primary chondrocytes were purchased from Procell (CP-H096), and cultured in medium specific for primary chondrocytes (CM-H096).

extract_protocol:
The chondrocytes were harvested and lysed in TRIzol reagent (Invitrogen). The mRNA was purified using Dynabeads®  mRNA Purification Kit (Invitrogen).
cDNA library was prepared using Library Preparation VAHTS mRNA Capture Beads (Vazyme) and MGIEasy RNA Directional Library Prep Set (MGI).

treatment_protocol: The chondrocytes were treated with 1ng/mL recombinant human IL-1β (200-01B, PEPROTECH) together with TRULI (HY-138489, MCE) or DAPA (short for Dapagliflozin, HY-10450, MCE) .

value: cartilage

value: primary chondrocytes

value: chondrocytes

value: IL-1Beta+DAPA treatment


title: SCC7 cells control 10 Days 1


title: con-6-45


title: con-YY230328-1


title: IL-1β+DAPA treatment_2


title: con-4-4-20


title: con-4-4-19


title: IL-1β+DAPA treatment_3


title: IL-1β+DAPA treatment_1


title: IL-1β+TRULI treatment_4

value: IL-1Beta+TRULI treatment


title: con-4-4-10


title: con-3-30-6


title: splenic CD45- EPC 3

description: CD45- EPC 3

value: HNSCC


title: IL-1β+TRULI treatment_1


title: IL-1β+TRULI treatment_3


title: IL-1β+TRULI treatment_2


title: con-YY230330-21


title: IL-1β treatment_4

value: IL-1Beta treatment


title: con-3-30-3-CZ


title: IL-1β treatment_3


title: IL-1β treatment_2


title: con-3-30-1-CZ


title: control_4

value: no treatment


title: T2065-10-02; 47 mg

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

data_processing:
Quality control and adapter trimming were performed using FastQC.
Reads were aligned to hg38 using STAR
Gene counts were quantified using featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing read counts for each sample.

source_name: Thymus

extract_protocol:
Human thymusd was obtained from anonymous patients undergoing corrective cardiac surgery where a portion of the thymus was removed in order to expose the operative field. Portions of thymi were immediately placed in RNALater, incubated at 4C overnight, and stored in liquid nitrogen until processed.
Frozen tissues were homogenized in a Precelly's soft tissue lysing tube and RNA was extracted using Rneasy Kit according to manufacturer's protocol. RNA was cleaned and concentrated using Turbo DNA-free and Rneasy MiniElute.
Libraries were prepared using a KAPA Stranded mRNA-seq kit.

value: Thymus

tag: age (years)

value: Female


title: T2065-10-04; 34 mg


title: T2064-08-02; 45 mg

value: Male


title: control_3


title: control_2


title: MTS patient, biol rep 3

first: Yihua

last: Huang

state: Guangdong Province

address: 1838 Guangzhou Avenue, Baiyun District

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China.

description: Library name: Sample6

data_processing:
The original sequencing data was quality-controlled using FASTQC, and low-quality bases and sequencing adapters were removed using trim_galore.
HISAT2 was used to align the filtered clean reads with GRCh38 reference genome.
Samtools was used to filter out unaligned or unpaired sequencing fragments and obtain the bam file.
featureCounts software was used to quantify gene expression levels.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: cells

growth_protocol: iPSCs were cultured in mTeSR plus medium, in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
Total RNA was extracted using the Trizol kit (Invitrogen, USA) according to the manufacturer’s manual.
RNA libraries for RNA-seq were prepared using VAHTSTM mRNA-seq V2 Library Prep Kit according to the manufacturer’s manual.

treatment_protocol: iPSCs were induced toward neural differentiation using a standard monolayer differentiation protocol. Briefly,when iPSCs reached 100% confluence, the culture medium was changed with N2B27 medium, containing 50% DMEM/F12, 50% neurobasal medium, 0.5×N2 , 0.5×B27, 1% Glutamax , 1% NEAA , 5 μg/mL insulin (Sigma), in addition of 5μM SB431542 and 5μM dorsomorphin for 8 days. After 8 days, the cells were passaged and cultured in N2B27 medium. After another 8 days, the neural progenitor cells (NPCs) were picked manually and transferred to a low attachment 6-well plate in N2B27 medium containing 20 ng /mL basic fibroblast growth factor (bFGF) to expand for 7 days. For random differentiation, the NPCs were dissociated using Accutase into single cells, and subsequently seeded in poly-L-lysine and laminin pre-coated plates at a density of 10,000 cells/cm2, in the N2B27 medium which contains 20 ng/mL glial cell line-derived neurotrophic factor (GDNF) and 20 ng/mL human brain-derived neurotrophic factor (BDNF). The differentiation took 30 days, then the neurons started to mature and could be collected for examination.

value: cells

value: Mohr-Tranebjaerg syndrome (MTS)

value: iPSC-derived neurons

value: TIMM8A gene (c.225-229del)

value: neuronal differentiation


title: DUPLICATE T2059-07-01; 41 mg


title: control_1


title: T2060-06-01; 44 mg


title: MTS patient, biol rep 1

description: Library name: Sample4


title: DUPLICATE T2057-07-01; 53 mg


title: Healthy control, biol rep 2

description: Library name: Sample2

value: healthy

value: WT


title: Healthy control, biol rep 3

description: Library name: Sample3


title: T2059-07-01; 41 mg


title: Healthy control, biol rep 1

description: Library name: Sample1


title: con-3-30-2-CZ

value: Blood

value: M


title: ACHN cells, siPRR11, rep2

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ACHN

growth_protocol: ACHN cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: ACHN

value: Tumor cells


title: MTS patient, biol rep 2

description: Library name: Sample5


title: T2063-09-01; 32 mg


title: T2056-09-02; 43 mg


title: T2056-09-01; 34 mg


title: IL-1β treatment_1

value: cartilage

value: primary chondrocytes

value: chondrocytes


title: ACHN cells, siPRR11, rep1


title: T2063-09-02; 35 mg

value: Thymus


title: ACHN cells, siNC, rep2


title: ACHN cells, siNC, rep1


title: T2055-12-01; 45 mg


title: T2046-07-02; 45 mg


title: T2060-06-04; 26 mg


title: T2046-07-01; 34 mg


title: T2035-12-03; 39 mg

value: Female


title: T2044-12-02; 43 mg


title: microglia_6M_APP/PS1_3_rep1

type: RNA

city: Shanghai

first: jiyun

last: shi

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

description: circRNA expression in cortical microglia isolated from 6-month-old male APP/PS1 mice

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array V2 (8x15K, Arraystar) and incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: cortical microglia, 6-month-old male APP/PS1 mouse, replicate 1

label_protocol: Enriched circRNAs were amplified and transcribed into fluorescent cDNA using an Arraystar Super RNA Labeling Kit by a random priming method according to the Arraystar Super RNA Labeling protocol (Arraystar Super RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA from isolated cortical microglia was extracted by Trizol reagent (#15596018CN; Invitrogen). RNA quantity and quality were assessed at A260/A280 nm by NanoDrop (Wilmington, DE, USA) and Agilent 2100 (Palo Alto, CA, USA). Total RNAs were digested using Rnase R (#RNR07250; Epicentre) to eliminate linear RNAs and enrich circRNAs.

treatment_protocol: After mice were deeply anesthetized, blood was extracted by ventricular puncture and mice were perfused with phosphate-buffered saline (PBS).The brain tissue of mice was collected and temporarily placed in ice-cold Hank’s Balanced Salt Solution (HBSS) buffer.Tissue was then dissociated and digested for 15 min at 37 °C by Papain in RPMI 1640 medium.The mixture passed through a 70 μm filter. Dispersed cells were harvested by centrifugation at 800 rpm for 10 min at 4 °C. The cell pellet was resuspended in a continuous 30% Percoll gradient at 700 g for 15 min. For microglia isolation, Dynabeads Biotin Binder (#11047; Invitrogen) was pre-incubated with anti-CD11b antibody (#13-0112-82; Invitrogen) for 30 min at room temperature, and then incubated with cells for 30 min at 4 °C with gentle tilting and rotation. Microglia were then collected by magnetic sorting.

value: brain, cortex, microglia

tag: gender

value: male


title: T2057-07-01; 53 mg


title: T2035-12-02; 46 mg


title: T2067-12-02; 45 mg


title: T2067-12-01; 47 mg


title: T2055-12-02; 35 mg

value: Male


title: LPS+DHEA+Nb_2

city: Beijing

first: Yuan

last: Zheng

address: Beijing

institute: Peking University

description: Library name: Sample 8

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Tab-delimited text files include count values for each Sample.

source_name: testis

extract_protocol:
The isolated testis are quickly put into RNA later (Invitrogen, Waltham, Massachusetts, USA) and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: testis


title: LPS+DHEA+Nb_1

description: Library name: Sample 7


title: microglia_6M_APP/PS1_2_rep1


title: DUPLICATE T2039-08-01; 35 mg


title: DUPLICATE T2038-15-01; 29 mg


title: LPS+DHEA_1

description: Library name: Sample 5

value: LPS+DHEA


title: T2038-15-01; 29 mg


title: microglia_6M_APP/PS1_1_rep1


title: T2036-13-04; 34 mg


title: LPS_2

description: Library name: Sample 4

value: LPS


title: T2039-08-01; 35 mg


title: CTRL_2

description: Library name: Sample 2

value: PBS control


title: microglia_6M_WT_3_rep1

description: circRNA expression in cortical microglia isolated from 6-month-old male WT mice

source_name: cortical microglia, 6-month-old WT mouse, replicate 1


title: microglia_6M_WT_2_rep1


title: CTRL_1

description: Library name: Sample 1

value: WT


title: T2033-12-03; 29 mg


title: T2033-12-02; 40 mg


title: T2027-08-03; 35 mg


title: LPS+DHEA_2

description: Library name: Sample 6


title: con-4-4-33

value: Blood


title: T2024-09-03; 38 mg


title: MC3t3-E1 cultured on nano/microstructured PEEK with supernatant, biol rep 2

first: Yuqing

last: Zhao

address: Changle West Road No. 145

institute: The Fourth Military Medical University

description: Library name: SPS3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Assembly: We aligned reads of all samples to the Mus musculus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of thereads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch whenmappingthe reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparingthe previously unmapped reads against the database of putative junctions.
Supplementary files format and content: Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: pre-osteoblasts


title: MC3t3-E1 cultured on nano/microstructured PEEK with supernatant

description: Library name: SPS1


title: MC3t3-E1 cultured on nano/microstructured PEEK with supernatant, biol rep 1

description: Library name: SPS2


title: T2036-13-01; 54 mg


title: MC3t3-E1 cultured on nano/microstructured PEEK, biol rep 2

description: Library name: SP3

value: cultured on nano/microstructured PEEK


title: T2018-08-01; 26 mg


title: T2018-08-03; 31 mg


title: microglia_6M_WT_1_rep1


title: con-4-4-14

value: M


title: T2016-07-04; 36 mg


title: LPS_1

description: Library name: Sample 3


title: T2015-06-04; 39 mg


title: MC3t3-E1 cultured on nano/microstructured PEEK

description: Library name: SP1


title: T2015-06-01; 35 mg


title: RAW264.7 cultured on nano/microstructured PEEK, biol rep 2

description: Library name: SP30-3

value: macrophages


title: RAW264.7 cultured on nano/microstructured PEEK, biol rep 3

description: Library name: SP30-4


title: RAW264.7 cultured on nano/microstructured PEEK, biol rep 1

description: Library name: SP30-2


title: T2013-12-04; 30 mg


title: RAW264.7 cultured on smooth PEEK, biol rep 3

description: Library name: PEEK4


title: T2012-12-03; 20 mg


title: T2010-12-02; 27 mg


title: RAW264.7 cultured on nano/microstructured PEEK

description: Library name: SP30-1


title: RAW264.7 cultured on smooth PEEK, biol rep 2

description: Library name: PEEK3


title: T2025-06-01; 52 mg


title: T2010-11-03; 32 mg


title: RAW264.7 cultured on smooth PEEK, biol rep 1

description: Library name: PEEK2


title: T2012-13-04; 20 mg


title: RAW264.7 cultured on smooth PEEK

description: Library name: PEEK1


title: T2012-13-01; 27 mg


title: MC3t3-E1 cultured on nano/microstructured PEEK, biol rep 1

description: Library name: SP2


title: T2048-11-03;75 mg


title: C57BL/6J MICE, OIR, p17-2

city: Changsha

first: Dan

last: Liu

state: Hunan

address: No. 932 Lushan South Road, Changsha City, Hunan Province

institute: Central South University

description: Library name: SAMPLES 5

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count for all Sample

source_name: RETINA

extract_protocol:
Total RNA was isolated using TRIzol according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: RETINA


title: T2050-12-01; 30 mg


title: C57BL/6J MICE, normal, p17-2

description: Library name: SAMPLES 2


title: T2052-10 (T.N.S)


title: C57BL/6J MICE, OIR, p17-3

description: Library name: SAMPLES 6


title: DUPLICATE T2057-8 (T.N.S)


title: C57BL/6J MICE, OIR, p17-1

description: Library name: SAMPLES 4


title: DUPLICATE T2052-10 (T.N.S)


title: DUPLICATE T2048-11-03;75 mg


title: C57BL/6J MICE, normal, p17-3

description: Library name: SAMPLES 3


title: C57BL/6J MICE, normal, p17-1

description: Library name: SAMPLES 1


title: PKM2_KD, H3K27ac_CUT&Tag

city: Nanjing

first: Qixiang

last: Li

address: 163 xianlin road, qixia district

institute: nanjing university

data_processing:
Fastq files were checked with Fastqc (v. 0.11.9) for quality control. The adapters were removed from the raw reads with Cutadapt (v. 1.18). The alignment SAM files were sorted using Samtools (v. 1.3.1). Peak-calling was performed using MACS2 (v. 2.1.1.20160309). The peak annotation and motif analysis were realized with Homer2 (v. 4.1.5). Differential expression analysis is made using DEseq2, Data whose absolute value of log2Foldchange larger than 1 and pvalue less than 0.05 is kept for subsequent analysis.
Assembly: hg38
Supplementary files format and content: BigWig, narrowPeak

extract_protocol:
Cells were mixed with NovoNGS® Concanavalin A-coated Magnetic Beads (N251).
Resuspend cells in ice-cold Antibody buffer and add 0.5-1 µL primary antibody to each sample. Mix the secondary antibody 1:100 in Dig-wash buffer while gently vortexing to allow the solution to dislodge the beads from the sides. Mix pA-Tn5 adapter complex in Dig-300 buffer to a final concentration of 1:250 for 100 µL per sample.Squirt in 100 µL of the pA-Tn5 mix while gently vortexing to allow the solution to dislodge most or all of the beads. After a quick spin, place the tubes on a magnet stand to clear and pull off the liquid. Add 300 µL Tagmentation buffer. DNA extraction. The remainder of the CUT&Tag library preparation was performed as described TruePrep DNA Library Prep Kit V2 for Illumina (TD503). The qualified libraries were sequenced on Illumina Nova Seq 6000.

value: Triple negative breast cancer cells

value: PKM2 knockdown


title: NC, H3T11ph_CUT&Tag


title: Female E13.5, GEX, replicate 2

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description: Library name: E13-F-R2-GEX

data_processing:
All libraries demulitplexed using cellranger-arc mkfastq
Demultiplexed data was processed using cellranger-arc mkfastq
Assembly: mm10
Supplementary files format and content: cellranger-arc count atac output files: E11-F-R1.atac_fragments.tsv.gz E11-F-R2.atac_fragments.tsv.gz E11-M-R1.atac_fragments.tsv.gz E11-M-R2.atac_fragments.tsv.gz E12-F-R1.atac_fragments.tsv.gz E12-F-R2.atac_fragments.tsv.gz E12-M-R1.atac_fragments.tsv.gz E12-M-R2.atac_fragments.tsv.gz E13-F-R1.atac_fragments.tsv.gz E13-F-R2.atac_fragments.tsv.gz E13-M-R1.atac_fragments.tsv.gz E13-M-R2.atac_fragments.tsv.gz
Supplementary files format and content: cellranger-arc count matrix output files: E11-F-R1.barcodes.tsv.gz E11-F-R1.features.tsv.gz E11-F-R1.matrix.mtx.gz E11-F-R2.barcodes.tsv.gz E11-F-R2.features.tsv.gz E11-F-R2.matrix.mtx.gz E11-M-R1.barcodes.tsv.gz E11-M-R1.features.tsv.gz E11-M-R1.matrix.mtx.gz E11-M-R2.barcodes.tsv.gz E11-M-R2.features.tsv.gz E11-M-R2.matrix.mtx.gz

source_name: gonad

extract_protocol:
Whole ovaries and testes were collected at E11.5, E11.5, and E12.5. The sexes of the embryos were determined using amnion staining, as previously published20, to identify the presence (XX) or absence (XY) of the Barr body and confirmed with PCR using primers that recognize the Y chromosome. Tomato fluorescence was used to facilitate the dissection of the gonad away from the mesonephros, which was done using needles. Isolated fetal mouse gonads were isolated in PBS, and pairs of gonads or groups pooled between fetuses of the same sex and age were immediately frozen in liquid nitrogen for storage. Nuclei isolation was performed using the 10X Genomics Chromium Nuclei Isolation Kit (catalog #1000494) following the manufacturer’s protocol.
The 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Library Preparation Kit (catalog #1000284) was used to generate a 10X barcoded library of mRNA and transposed DNA from individual nuclei. The 10X barcoded single-nuclei RNA and ATAC-seq libraries were obtained from 8,687 average (1,555-20,000) nuclei per sample and sequenced with Illumina NOVAseq to a minimum sequencing depth of 129,120,442 raw reads and 22,406 read pairs/nucleus

value: gonad

value: gonadal cell populations

tag: library type

value: mRNA


title: RNA_dcp2∆pab1-AID+NAA_Replicate_1

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For SMPAT-Seq: Sequencing reads from the Sequel instrument come in the form of continuous reads around a “rolling circle.” The insert is read over multiple passes in each direction. These insert passes are referred to as subreads. Multiple passes gives circular consensus sequences (CCS; also referred to as HiFi). CCS reads were demultiplexed to individual samples using the program “lima” (v2.6 or above) using the appropriate sample barcodes utilized during library construction. Samtools was used to convert demultiplexed sample CCS reads to fastq format for further processing and alignment. CCS read IDs are assigned to transcripts through the use of PacBio minimap2 to align reads to Ensembl Saccharomyces cerevisiae.R64-1-1 release 109. To determine and assign a poly(A) tail length to a CCS ID, reads are evaluated in either direction for a poly(A) stretch abutting the adapter utilized in library construction. A one base mismatch is tolerated for the adapter sequence pattern matching.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples. For CAGE-sequencing the file contains three columns providing: Chromosome (Chr), Position of detected TSS (pos), strand information (strand) and 14 columns with read counts for different samples. For SMPAT-Seq, report.txt file contains multiple columns providing: Gene name (#Gene), Counts for each gene (Counts), mean poly(A) tail lengths (MeanPolyA), Standard error (STDERR), Minimum poly(A) tail length (Min), Quartile1 (Q1), median poly(A) tail lengths (Median), Quartile 3rd (Q3), Maximun poly(A) tail lengths (Max) and ListOfValues.

extract_protocol: RNA sequencing libraries were produced in parallel from total RNA samples by the NHLBI DNA sequencing Core at NIH (Bethesda, MD) using the TruSeq Stranded mRNA Library Prep Kit (Illumina, single-end 100 bp reads).

value: Yeast whole cells

value: 1mM 1-Napthaleneacetic acid (NAA)


title: NONO_KD, NONO_CUT&Tag

value: NONO knockdown


title: PKM2_KD, H3T11ph_CUT&Tag


title: NC, H3K27ac_CUT&Tag


title: RNA_dcp2∆pab1-AID+NAA_Replicate_3


title: RNA_dcp2∆pab1-AID+NAA_Replicate_2


title: NC, NONO_CUT&Tag


title: RNA_dcp2∆+NAA_Replicate_2

source_name: W303 PMY3 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 dcp2∆::HIS3 lys2::PADH1-OsTIR1-7myc-TADH1)


title: PKM2_KD, repeat 3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach. To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/edgeR/Limma/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includs TPM values for each Sample_and content : NONO_NC_vs_KD.deseq2.annot.xls
Supplementary files format and content: tab-delimited text file includs TPM values for each Sample_and content : PKM2_NC_vs_KD.deseq2.annot.xls

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2,OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).


title: Male E13.5, GEX, replicate 2

description: Library name: E13-M-R2-GEX


title: RNA_dcp2∆+NAA_Replicate_1


title: RNA_pab1-AID+NAA_Replicate_3


title: PKM2_KD, repeat 2


title: RNA_pab1-AID+NAA_Replicate_2


title: RNA_pab1-AID_Replicate_2

growth_protocol: Yeast cells pre-cultured in liquid YPD medium at 30°C for 4h and thereafter  KOH was added to a final concentration of 1mM and growth was continued for 6h.

value: 1mM KOH


title: Male E12.5, GEX, replicate 2

description: Library name: E12-M-R2-GEX


title: RNA_pab1-AID_Replicate_3


title: RNA_pab1-AID+NAA_Replicate_1


title: RNA_pab1-AID_Replicate_1


title: NC (correspond to PKM2_KD), repeat 3


title: Male E12.5, GEX, replicate 1

description: Library name: E12-M-R1-GEX


title: RNA_WT+NAA_Replicate_3

source_name: W303 PMY1 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1)


title: Female E13.5, GEX, replicate 1

description: Library name: E13-F-R1-GEX


title: NC (correspond to PKM2_KD), repeat 1


title: RNA_WT_Replicate_3

growth_protocol: Yeast cells pre-cultured in liquid YPD medium at 30°C for 3h and thereafter KOH was added to a final concentration of 1mM and growth was continued for 6h.


title: Female E12.5, GEX, replicate 2

description: Library name: E12-F-R2-GEX


title: RNA_WT+NAA_Replicate_1


title: RNA_dcp2∆+NAA_Replicate_3


title: RNA_WT+NAA_Replicate_2


title: NONO_KD, repeat 3


title: Ribo_dcp2∆pab1-AID+NAA_Replicate_3

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For SMPAT-Seq: Sequencing reads from the Sequel instrument come in the form of continuous reads around a “rolling circle.” The insert is read over multiple passes in each direction. These insert passes are referred to as subreads. Multiple passes gives circular consensus sequences (CCS; also referred to as HiFi). CCS reads were demultiplexed to individual samples using the program “lima” (v2.6 or above) using the appropriate sample barcodes utilized during library construction. Samtools was used to convert demultiplexed sample CCS reads to fastq format for further processing and alignment. CCS read IDs are assigned to transcripts through the use of PacBio minimap2 to align reads to Ensembl Saccharomyces cerevisiae.R64-1-1 release 109. To determine and assign a poly(A) tail length to a CCS ID, reads are evaluated in either direction for a poly(A) stretch abutting the adapter utilized in library construction. A one base mismatch is tolerated for the adapter sequence pattern matching.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples. For CAGE-sequencing the file contains three columns providing: Chromosome (Chr), Position of detected TSS (pos), strand information (strand) and 14 columns with read counts for different samples. For SMPAT-Seq, report.txt file contains multiple columns providing: Gene name (#Gene), Counts for each gene (Counts), mean poly(A) tail lengths (MeanPolyA), Standard error (STDERR), Minimum poly(A) tail length (Min), Quartile1 (Q1), median poly(A) tail lengths (Median), Quartile 3rd (Q3), Maximun poly(A) tail lengths (Max) and ListOfValues.
Library strategy: Ribo-Seq

extract_protocol: Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Hcr1/eIF3j Is a 60S Ribosomal Subunit Recycling Accessory Factor In Vivo". Young and Guydosh 2019, Cell Rep, 28, 39-50 e34.


title: NONO_KD, repeat 2


title: RNA_WT_Replicate_2


title: Ribo_dcp2∆pab1-AID+NAA_Replicate_2


title: Female E12.5, GEX, replicate 1

description: Library name: E12-F-R1-GEX


title: NONO_KD, repeat 1


title: Ribo_dcp2∆pab1-AID+NAA_Replicate_1


title: Ribo_dcp2∆+NAA_Replicate_3


title: PKM2_KD, repeat 1


title: Ribo_dcp2∆+NAA_Replicate_2


title: NC (correspond to NONO_KD), repeat 3


title: NC (correspond to PKM2_KD), repeat 2


title: Male E11.5, GEX, replicate 2

description: Library name: E11-M-R2-GEX


title: Ribo_dcp2∆+NAA_Replicate_1


title: Ribo_pab1-AID+NAA_Replicate_1


title: Ribo_pab1-AID+NAA_Replicate_2


title: Ribo_pab1-AID+NAA_Replicate_3


title: NC (correspond to NONO_KD), repeat 1


title: RNA_WT_Replicate_1


title: Ribo_pab1-AID_Replicate_3


title: Ribo_WT+NAA_Replicate_2


title: 05_S_Jun, shear, CUT&RUN

city: Seattle

first: Weiming

state: WA

address: 4032 8th ave ne

department: Center for developmental biology and regenerative medicine

institute: Seattle children's research institute

description: UW

data_processing:
Single nuclei RNA sequencing data processing and analysis started with raw data from PBMCs generated via the 10x Genomic Chromium platform. ‘cellranger-arc’ (version: 2.0.2) and ‘cellranger’ (version: 7.1.0) software were used to perform read alignment, low-quality read filtration, barcode counting, and UMI tallying, consistently applying default parameters.
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files
Library strategy: CUT&RUN

source_name: THP-1 cells

extract_protocol:
The PBMCs were isolated using the Stemcell EasySep™ Direct Human PBMC Isolation Kit. The isolated PBMCs were frozen in ice-cold cryopreservation solution – 50% FBS/40% growth media/10% DMSO
10x genomic library preparing for snRNA and snATAC

value: THP-1 cells

value: Shear


title: Ribo_WT_Replicate_3


title: Male E11.5, GEX, replicate 1

description: Library name: E11-M-R1-GEX


title: 06_S_Jun, shear, CUT&RUN

description: UW


title: Ribo_WT_Replicate_2


title: Ribo_WT+NAA_Replicate_3


title: 04_S_Jun, shear, CUT&RUN

description: UW


title: Ribo_WT_Replicate_1


title: 03_C_Jun, static, CUT&RUN

description: UW

value: Static


title: MRSA USA300, SQ, 3

first: Lulu

last: Zhang

address: 16 Dongzhimen South St, Dongcheng District, Beijing

institute: Chinese Academy of Traditional Chinese Medicine

description: Library name: SQ_3

data_processing:
cufflinks v2.1.1
Assembly: ASM1708v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Staphylococcus aureus

source_name: bacterial cell

growth_protocol: MRSA USA300 was cultured using Mueller-Hinton (MH) agar broth and placed in a thermostatic shaker at 37°C, 280 r/min until logarithmic growth.

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with RNase-free DNase I (Takara, Kusatsu, Japan). A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) .

treatment_protocol: MRSA USA300 (5 × 106 ~1 × 107 CFU/mL ) cultured to logarithmic growth stage was treated for 24h using S-PN at a final concentration of 0.5 mg/ml.

tag: strain

value: bacterial cell

value: WT


title: Female E11.5, GEX, replicate 1

description: Library name: E11-F-R1-GEX


title: NC (correspond to NONO_KD), repeat 2


title: 02_C_Jun, static, CUT&RUN

description: UW


title: Ribo_pab1-AID_Replicate_1

source_name: W303 PMY2 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 lys2::PADH1-OsTIR1-7myc-TADH1 pab1-AID (71-114)-9myc::hphNT1)


title: MRSA USA300, SQ, 2

description: Library name: SQ_2


title: Female E11.5, GEX, replicate 2

description: Library name: E11-F-R2-GEX


title: Ribo_pab1-AID_Replicate_2


title: MRSA USA300, SQ, 1

description: Library name: SQ_1


title: Ribo_WT+NAA_Replicate_1


title: MRSA USA300, Control, 3

description: Library name: Control_3


title: 01_C_Jun, static, CUT&RUN

description: UW


title: MRSA USA300, Control, 2

description: Library name: Control_2


title: Week2_Gata2 rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Library name: S39

data_processing:
Low-quality reads and adapter sequences were trimmed with Trimmomatic  (v0.38), employing the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Alignment and quantification was done using STAR  (v2.5.2b)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw read count per gene for each sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from BM-derived lineage marker negative cells with the RNeasy Micro kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTer Ultra Low RNA kit (Clontech) for illumina sequencing

value: Bone marrow

value: CD45.2 BM cells


title: mPFC, shNC, saline_3

first: Yuxiang

state: Shaanxi

address: 76 Yanta West Road

department: College of Forensic Medicine

institute: Xi’an Jiaotong University

data_processing:
Raw reads of fastq format were obtained from PromethION platform at Biomarker Technology Company
Oxford Nanopore Technologies Long Read Processing: Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.The criteria for fusion candidates is that a single transcript must: (1) must map to 2 or more loci (2) minimum coverage for each loci is 5% and minimum coverage in bp is >= 1 bp (3) total coverage is >= 95% (4) distance between the loci is at least 10kb
Transcripts were validated against known reference transcript annotations with gffcompare. AS events including IR, ES, AD, AA and MEE were identified by the AStalavista tool. SSR of the transcriptome were identified using MISA. APA analysis was conducted with TAPIS. CDS were predicted by TransDecoder. Animal transcription factors were identified from animalTFDB.
Full length reads were mapped to the reference transcriptome sequence. Expression levels were estimated by reads per gene/transcript per 10,000 reads mapped. For the samples with biological replicates, differential expression analysis using the edgeR R package (3.8.6). edgeR provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a Pvalue < 0.05 and foldchange ≥ 1.5 found by edgeR were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and CPM for each Sample

source_name: brain, mPFC

extract_protocol:
The mPFC tissues were removed, flash frozen on dry ice, and total RNA was harvested using Trizol reagent.
1ug total RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-PCS109) protocol provided by Oxford Nanopore Technologies (ONT). Briefly, the template switching activity of reverse transcriptases enrich for full-length cDNAs and add defined PCR adapters directly to both ends of the first-strand cDNA. And following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and run on PromethION platform at Biomarker Technology Company (Beijing, China).

value: brain, mPFC

value: Saline


title: 08,shear, ATAC

description: Activemotif

data_processing:
Single nuclei RNA sequencing data processing and analysis started with raw data from PBMCs generated via the 10x Genomic Chromium platform. ‘cellranger-arc’ (version: 2.0.2) and ‘cellranger’ (version: 7.1.0) software were used to perform read alignment, low-quality read filtration, barcode counting, and UMI tallying, consistently applying default parameters.
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files


title: 07,shear, ATAC

description: Activemotif


title: mPFC, shNC, saline_2


title: mPFC, shNC, saline_1


title: 06,shear, ATAC

description: Activemotif


title: Week2_Gata2 rep2

description: Library name: S37


title: mPFC, shKDM7A, saline_5

value: KDM7A knockdown


title: mPFC, shKDM7A, saline_4


title: Week2_WT rep2

description: Library name: S38


title: 04,static, ATAC

description: Activemotif


title: mPFC, shKDM7A, saline_1


title: mPFC, shKDM7A, saline_2


title: Week2_WT rep1

description: Library name: S35


title: 05,shear, ATAC

description: Activemotif


title: Week2_Gata2 rep1

description: Library name: S36


title: MRSA USA300, Control, 1

description: Library name: Control_1


title: mPFC, shNC, morphine_2

value: Morphine


title: mPFC, shNC, morphine_3


title: mPFC, shNC, morphine_4


title: mPFC, shNC, morphine_1


title: 02,static, ATAC

description: Activemotif


title: Week2_WT rep3

description: Library name: S40


title: 03,static, ATAC

description: Activemotif


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-ZF1 mutant rescue, rep4

city: Miami

first: Danny

last: Reinberg

state: FL

address: 1501 NW 10th Avenue (C227)

department: John T. MacDonald Department of Human Genetics

institute: Miller School of Medicine and Sylvester Comprehensive Cancer Center

description: Library name: CTCF_CLIP_NPC_ZF1_rep4

data_processing:
Flexbar was used to demultiplex reads based on barcodes and trim adapters. The reads were then aligned to the mm10 reference genome using STAR. PCR duplicates were removed using unique molecular identifiers (UMIs) with UMI-tools. Reads start at the position where the cDNA was truncated during reverse transcription, making the position upstream of the 5’ end of the read the ‘crosslinked nucleotide’. Bedtools was used to convert BAM files to BED files, shift the BED intervals by one base pair in the 5’ direction, and extract the 5’ positions of the new intervals. These positions were then piled up into BEDGraph files, separately for each strand. BEDGraph files were converted to BigWig files using bedGraphToBigWig. For crosslink-site calling, BAM files from replicates of the same condition were merged and used as input for PureCLIP, which outputs individual crosslink sites.
Assembly: mm10
Supplementary files format and content: bigWig file of crosslinked sites from combined replicates; BED file of PureCLIP-called crosslinks with scores
Library strategy: iCLIP2

molecule: nuclear RNA

source_name: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

growth_protocol: E14Tga2 (ATCC, CRL-1821) mouse ESCs (E14) were cultured in N2B27 media [Advanced Dulbecco's modified eagle medium (DMEM)/F12:Neurobasal-A (1:1) medium (ThermoFisher Scientific 12634028 and 10888022, respectively), with 3% ESC-grade fetal bovine serum (v/v, Gemini 900-108), 1x N2 (ThermoFisher Scientific 17502-048), 1x B27 (Thermo Fisher 17504-044), 2 mM L-glutamine (Sigma G7513), 0.1 mg/mL Penicillin-Streptomycin (Sigma P0781), 0.1 mM β-mercaptoethanol (ThermoFisher Scientific 21985023)] supplemented with leukemia inhibitory factor (homemade), 3 μM CHIR99021 (Tocris 4423) and 1 μM PD0325901 (Sigma PZ0162) on 0.1% gelatin-coated (Millipore ES-006-B) plates at 37°C and 5% CO2.

extract_protocol:
A confluent 15 cm tissue culture plate was washed once with 1x PBS. 10 mL 1x PBS was added to the plate and cells were UV-crosslinked on plate with opened lid, at 400 mJ/cm2 using SpectroLinker XL-1000 (254 nm). Two 15 cm plates were scraped and combined. Cells were pelleted, snap-frozen and stored in -80°C. ±UV cell pellets were resuspended in 20 mL HMSD (20 mM HEPES pH 7.5, 5 mM MgCl2, 25 mM NaCl, 85.5 g/L sucrose, 1 mM DTT) supplemented with protease inhibitors (0.2 mM PMSF, 1 mg/mL Pepstatin A, 1 mg/mL Leupeptin, and 1 mg/mL Aprotinin), and rotated in cold room for 25 minutes. After washing with 1x PBS, nuclei were resuspended in 1 mL cold PBS-lysis buffer (1 mM MgCl2, 0.1 mM CaCl2, 0.5% sodium deoxycholate, 0.5% NP-40 in 1x PBS) supplemented with 1x EDTA-free protease inhibitor cocktail (PIC) (Sigma 11873580001), 40 U/mL Protector RNase inhibitor (Sigma 3335402001), 1 mM DTT, and rotated in cold room for 25 minutes. 20 uL of Turbo DNase (ThermoFisher Scientific AM2238) was added and lysates were incubated at 37°C for 30 minutes, shaking 1100 rpm. Partial RNA digestion was done with a pre-titrated volume of dilute RNase I (ThermoFisher Scientific AM2295), incubated for 3 minutes at 37°C and immediately transferred to ice. 2 uL of SUPERaseIN (ThermoFisher Scientific AM2696) and 0.1% final concentration of SDS was added to stop RNA digestion. Lysates were spun down and supernatant was transferred to new 1.5 mL tubes. Flag-tagged CTCF from supernatant was immunoprecipitated with 5 uL anti-Flag magnetic beads (Millipore Sigma M8823), rotating in cold room for 2 hours. After 4 washes with PBS high-salt wash buffer (1 M NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% NP-40 in 1x PBS) and then 4 washes with PBS low-salt wash buffer (150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% NP-40 in 1x PBS), beads were treated with 0.1 U/uL Turbo DNase supplemented with 1x protease inhibitor cocktail, 0.4 U/uL Roche Protector RNase inhibitor, and 0.1 U/uL SUPERaseIn RNase inhibitor in 1x DNase buffer (ThermoFisher Scientific AM 2239). Beads were incubated at 37oC for 30 minutes, shaking at 850 rpm.
For cDNA preparation, oligos used were described previously (10.1016/j.ymeth.2019.10.003). On-beads RNA was dephosphorylated at the 3’ end using T4 PNK and ligated to a DNA oligo (L3-App) adapter using T4 RNA Ligase 1 (NEB M0204L). CTCF was eluted from beads twice using 1x flag peptide (5 mg/mL stock) (Sigma F3290) diluted 1:10 in PK buffer (100 mM Tris, pH 8.0, 150 mM NaCl, 5 mM EDTA, 0.1% SDS). Elutions were pooled and proteins were denatured and digested with 4 mg/mL proteinase K incubated in 55oC for 20 minutes, shaking 1200 rpm. 7M final concentration of urea was added and incubated in 55oC for another 20 minutes. RNA-DNA hybrids were extracted using phenol:chloroform:isoamyl alcohol, separating the aqueous phase using phase lock gel tubes (VWR 10847-802). From the aqueous phase, RNA-DNA hybrids were purified by ethanol precipitation overnight at -20oC. RNA-DNA pellet was washed with ethanol and resuspended in nuclease-free water. Reverse transcription (RT) was done using Superscript III Reverse Transcriptase (Invitrogen 18080044). The primer used for RT (RToligo) was complementary to the DNA oligo (L3-App) previously ligated to RNAs. Despite extensive digestion by proteinase K of crosslinked protein-RNA complexes, a small polypeptide remains covalently linked to RNA, which prematurely terminates RT, thereby providing positional information of the crosslinked nucleotides in the resulting cDNA library. Synthesized cDNAs were extracted using Dynabeads MyONE Silane beads (ThermoFisher Scientific 37002D). A second adapter ligation, with barcodes, was done on the 3’ end of cDNA using T4 RNA Ligase 1. Adapter-ligated cDNAs were extracted using Dynabeads MyONE Silane beads. The adapter ligations are designed in such a way that sequencing reads start at the position where the cDNA was truncated during reverse transcription. Adapters contained unique molecular identifiers (UMIs) for duplicate removal during analysis. A cDNA pre-amplification was done on beads for 6 cycles using 2x KAPA HiFI Hot Start Mix (KAPA KK2601). The primers used were P5Solexa_s and P3Solexa_s. ProNex® Size-Selective Purification System (Promega NG2001) was used to size select the pre-amplified cDNA and remove primer-dimers. A second PCR amplification was done for 9 cycles using primers P5Solexa and P3Solexa. Libraries were size selected (200-500 bp) with Agencourt AMPure XP beads.

treatment_protocol:
In vitro differentiation of ESCs to NPCs as follows: plates were coated overnight at 37°C with 10 ug/mL Laminin (R&D Systems 3446-005-01) in 1x Phosphate Buffered Saline (PBS). ESCs were dissociated with TrypLE Express (Gibco 12605-028). Cells were seeded on laminin-coated plates at a pre-titrated density of ~15,000/cm2. Cells were differentiated for 2 days in N2B27 media.
For CTCF rescue experiments, E14 - CTCF-AID2 degron; Dox inducible CTCF WT or ΔZF1 rescue cells were treated with 1 uM 5-Ph-IAA (Bio Academia 30-003) and 1 ug/mL doxycycline (Sigma D5207) for 24 hours and then harvested for downstream applications.

value: neural progenitor cell

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox

tag: clip antibody

value: Anti-Flag magnetic beads (Millipore Sigma M8823)


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-ZF1 mutant rescue, rep3

description: Library name: CTCF_CLIP_NPC_ZF1_rep3

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue


title: 01,static, ATAC

description: Activemotif


title: mPFC, shKDM7A, saline_3


title: mPFC, shKDM7A, morphine_3


title: mPFC, shKDM7A, morphine_2


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-ZF1 mutant rescue, rep2

description: Library name: CTCF_CLIP_NPC_ZF1_rep2


title: mPFC, shKDM7A, morphine_4


title: mPFC, shKDM7A, morphine_1


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-ZF1 mutant rescue, rep1

description: Library name: CTCF_CLIP_NPC_ZF1_rep1


title: Male E13.5, GEX, replicate 1

description: Library name: E13-M-R1-GEX

value: gonad

value: gonadal cell populations

value: mRNA


title: D, shear, RNA

description: Novogene

value: THP-1 cells

value: Shear


title: m3C-100

city: hangzhou

first: Yunyi

last: Gao

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: Zhejiang university

description: Library name: Sample17

library_source: other

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
Illumina sequencing reads were treated with fastp (version 0.23.2)  for adaptor removal and quality trimming.
The remaining reads were mapped to  human transcriptome using BWA-MEM with default parameters.
SAMtools(version 1.9) were used to select high-quality alignments, remove PCR duplications, and extract the reads mapping of every nucleotide in the transcriptome
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include the mismatch rate for m3C for each sample. Comma-Separated Values files include the RPKM values for each each.

molecule: other

organism: synthetic construct

source_name: synthetic RNA

extract_protocol:
Total RNA was isolated from cell lines by Trizol(Invitrogen).tRNA was purified by 7M 10% denaturing polyacrylamide TBE-urea gel. polyA+ RNA was purified using Dynabeads Oligo(dT)25 (Invitrogen).
polyA+ RNA RNA fragments or tRNAs were converted to cDNA with high-processive reverse transcriptases SuperScript IV (Invitrogen) and sequenced (Input), or precipitated by m3C antibody before cDNA synthesis (IP), and the use of demethylase treatment improves the confidence of detection (Dm).

value: synthetic RNA


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-WT rescue, rep3

description: Library name: CTCF_CLIP_NPC_WT_rep3

source_name: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: C, shear, RNA

description: Novogene


title: B, shear, RNA

description: Novogene


title: GPCR2-plasmidlib

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
library strategy: CRISPR-Flow
A custom snakemake was used to process raw data files, https://github.com/khavarilab/crispr-flow
UMIs were couted using "umi_tools count --per-contig --method unique"
Further enrichment statistics were generated from the counts files using MageCK.
Assembly: Custom
Supplementary files format and content: The counts file contains estimates of UMI numbers from umi_tools, and the guides files contain the sequences of the Cas9 CRISPR guides.

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were infected with CRISPR libraries against GPCRs and controls.

extract_protocol:
Total genomic DNA was extracted using the SPRI beads (Beckman Coulter, B23317).
Genomic DNA was extracted and amplified by specific primers via PrimeStar(Takara, #R045A) to add the index sequence for further sequencing.

treatment_protocol: The differentiatiated keratinocytes were seeded at confluent density with 1.2mM Calcium, then sorted with a KRT10 antibody (Novus, NBP2-47825AF647) by FACS into low, medium and high expression. Genomic DNA was harvested for gRNA library amplification.

tag: replicate

value: Plasmid library guides input to CRISPR flow, G-protein guide library


title: m3C-40

description: Library name: Sample15


title: m3C-0

description: Library name: Sample13


title: D, static, RNA

description: Novogene

value: Static


title: m3C-20

description: Library name: Sample14


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-WT rescue, rep2

description: Library name: CTCF_CLIP_NPC_WT_rep2

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: Mutnat 48hr treated astrocytes, Ribo-seq, batch C

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

country: Israel

institute: Tel Aviv University

data_processing:
Sequenced reads were aligned to mm10 reference genome using TopHat2 , followed by generation of gene count data using FeatureCounts.
Only genes with at least 20 counts in all replicate samples of at least one condition were included in the analysis.
Changes in Translation efficiency (TE) of the coupled Ribo-seq and RNA-seq data was calculated using DTEG analysis
Assembly: mm10
Supplementary files format and content: excel file containing data with an overall coverage of 12,205 genes.  For each gene, Ensemble ID and symbol is specified.
Supplementary files format and content: The first tab of the excel file presents the log2 fold change value of each mRNA and RPF upon (24-hr-treated vs untreated), and (48-hr-treated vs untreated)
Supplementary files format and content: together with the TE value of each gene.
Supplementary files format and content: The 2nd-6th tabs of the excel file present specific subsets of genes that were diffrentially expressed between the genotypes
Supplementary files format and content: The 7th tab of the excel file presents specific examples and p-values shown in the corresponding manuscript

source_name: Primary astrocytes

growth_protocol: Freshly thawed primary astrocytes seeded at a density of 1.3x10^6 cells per 15-cm plate and grown in ‘astrocyte medium’ (#1801; ScienCell Research Labs, Carlsbad, CA, USA)

extract_protocol:
After thorough removal of PBS 230ul of lysis buffer were added to each 15 cm plate. The lysis buffer, composed of 25mM K-HEPES pH=7.2, 10mM MgCl2, 200mM KCl
and freshly added 2% DDM, 1mM DTT, 1X complete EDTA-free protease inhibitor (Roche), 100 μg/ml cycloheximide, and 25U/ml Turbo DNase-I (Thermo Scientific, AM2238),
was added directly onto the cells for 5 min incubation on ice. Cell lysates were scraped and collected, then incubated on ice for additional 10 min.
A portion of each sample was treated with RNase-I (Thermo Scientific, AM2295) to generate ribosome footprints, while an undigested portion was used to isolate total RNA.
Following RNase treatment, the footprint samples were layered on 1M sucrose cushion, following ultracentrifugation at 78,000 rpm for 2 h at 4°C in a Beckman Coulter TLA120.2 rotor.
RNA extracted from sucrose cushion pellets were subjected to size selection, by separation of the footprint samples on a 15% PolyAcrylamide TBE-urea gel
followed by purification of 26-34 nt fragments from the gel.
libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina #20020598) following manufacturer's protocols.
libraries for Ribo-seq were generated with NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, #E7300L),
then size selected by gel electrophoresis on 8% PolyAcrylamide Gel, with ~155 bp sized product purified from the gel.

treatment_protocol:
Untreated cells were incubated for 120 hr, while trated cells were incubated for 72 hr or 96 hr followed by treatment with 20ng/ml TNFα (Peprotech #315-01A)
and 0.25ng/ml IL-1β (Peprotech #211-11B) for 48 hr or 24 hr, respectively.

value: Primary astrocytes

value: Eif2b5-R132H-R132H mutant

value: TNFα+ IL-1β  for 48 hr


title: Mutnat 48hr treated astrocytes, Ribo-seq, batch A


title: C, static, RNA

description: Novogene


title: CTCF CLIP, Non-crosslinked, NPC, CTCF-WT rescue, rep4

description: Library name: CTCF_CLIP_NPC_neg_rep4


title: Mutnat 48hr treated astrocytes, Ribo-seq, batch B


title: CTCF CLIP, Non-crosslinked, NPC, CTCF-WT rescue, rep3

description: Library name: CTCF_CLIP_NPC_neg_rep3


title: Mutnat 24hr treated astrocytes, Ribo-seq, batch B

value: TNFα+ IL-1β  for 24 hr


title: Mutnat 24hr treated astrocytes, Ribo-seq, batch C


title: CTCF CLIP, Non-crosslinked, NPC, CTCF-WT rescue, rep2

description: Library name: CTCF_CLIP_NPC_neg_rep2

value: neural progenitor cell


title: Mutnat 24hr treated astrocytes, Ribo-seq, batch A


title: Mutnat untreated astrocytes, Ribo-seq, batch A

value: Untreated


title: 04, 24h, GEX

description: 10x genomics

source_name: Blood

value: Blood

value: PBMCs


title: CTCF CLIP, Non-crosslinked, NPC, CTCF-WT rescue, rep1

description: Library name: CTCF_CLIP_NPC_neg_rep1

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox

value: Anti-Flag magnetic beads (Millipore Sigma M8823)


title: Mutnat untreated astrocytes, Ribo-seq, batch B


title: 04, 8h, GEX

description: 10x genomics


title: m3C-80

description: Library name: Sample16


title: Mutnat 48hr treated astrocytes, RNA-seq, batch C


title: 04, 24h, ATAC

description: 10x genomics


title: Mutnat 48hr treated astrocytes, RNA-seq, batch A


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-ZF1 mutant rescue, rep4

description: Library name: CTCF_CLIP_ESC_ZF1_rep4

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue

value: embryonic stem cell


title: CTCF CLIP, UV-crosslinked, NPC, CTCF-WT rescue, rep1

description: Library name: CTCF_CLIP_NPC_WT_rep1


title: B, static, RNA

description: Novogene

value: THP-1 cells


title: Mutnat 48hr treated astrocytes, RNA-seq, batch B


title: Mutnat untreated astrocytes, Ribo-seq, batch C


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-ZF1 mutant rescue, rep2

description: Library name: CTCF_CLIP_ESC_ZF1_rep2


title: Mutnat untreated astrocytes, RNA-seq, batch C


title: 04, post, GEX

description: 10x genomics

value: post


title: Mutnat 24hr treated astrocytes, RNA-seq, batch A


title: Mutnat 24hr treated astrocytes, RNA-seq, batch B


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-ZF1 mutant rescue, rep3

description: Library name: CTCF_CLIP_ESC_ZF1_rep3


title: Mutnat 24hr treated astrocytes, RNA-seq, batch C


title: Mutnat untreated astrocytes, RNA-seq, batch B


title: 04, post, ATAC

description: 10x genomics


title: 04, pre, GEX

description: 10x genomics

value: pre


title: 04, 8h, ATAC

description: 10x genomics


title: Mutnat untreated astrocytes, RNA-seq, batch A


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-WT rescue, rep3

description: Library name: CTCF_CLIP_ESC_WT_rep3


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-WT rescue, rep4

description: Library name: CTCF_CLIP_ESC_WT_rep4


title: MBT2_sh1

first: Jie

middle: wen

last: Wei

address: 28 Fuxing Road, Haidian District, Beijing, China

institute: Chinese PLA general hospital

description: MBT2 cell stably transfected with shAsns#1 plasmid

data_processing:
Illumina Casava1.7 software used for basecalling.
Low-complexity or low-quality sequence of the original data were filtered to obtain high-quality clean data, which were then compared to the reference genome of mouse species to obtain comprehensive transcript information using bowtie v0.12.2.
We took RPKM (Reads per Kilobase per Million Reads) as A measure of gene expression (Mortazavi a. et al. 2008).
The differentially expressed genes were screened from the difference multiples and the significant levels. Here, we use the absolute value of logFC >1 and pvalue<0.05 as the standard to indicate that the gene is a differentially expressed gene.
Assembly: mouse NCBI genome
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

growth_protocol: MBT2 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from MBT2 cells using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina x plus protocols

treatment_protocol: MBT2 cells transfected with shAsns#1 and compaired vector

value: bladder cancer cell


title: MBT2_sh2

description: MBT2 cell stably transfected with shAsns#2 plasmid


title: MBT2_NC

description: MBT2 cell stably transfected with scramble plasmid


title: 03, 24h, GEX

description: 10x genomics


title: 04, pre, ATAC

description: 10x genomics


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-WT rescue, rep2

description: Library name: CTCF_CLIP_ESC_WT_rep2

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-WT rescue, rep1

description: Library name: CTCF_CLIP_ESC_WT_rep1


title: 03, 24h, ATAC

description: 10x genomics


title: 03, 8h, GEX

description: 10x genomics


title: CTCF CLIP, Non-crosslinked, ESC, CTCF-WT rescue, rep4

description: Library name: CTCF_CLIP_ESC_neg_rep4


title: 14-NRR-083-Pilocytic astrocytoma

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

description: Library name: 14-NRR-083

data_processing:
FASTQ files were aligned to the human reference genome (hg19) using the STAR aligner
Sample quality was assessed for contamination using Fastq Screen, and alignment metrics were generated with Picard RNASeqMetrics
Gene expression levels were quantified using featureCounts.
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: Pilocytic astrocytoma, CNS WHO 1

extract_protocol:
Approximately 10 mg of tumor tissue was allocated for transcriptomic analysis. RNA extraction was performed using the Qiagen RNeasy Lipid Tissue Mini Kit (Catalog #74804). RNA extractions were quantified using RNA Nano Chips (Cat. #5067-1511) on an Agilent 2100 BioAnalyzer.
RNA-Seq library preps were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Cat #20020595) according to the manufacturers recommendations.  Input was 500ng of total RNA with 10 cycles of PCR amplification.  Final libraries were visualized using High Sensitivity DNA ScreenTape (Agilent, Cat. #5067-5584) on the Agilent TapeStation 2200 instrument.  Quant-It (Invitrogen, Cat. P11495) was used for final concentration determination and libraries were pooled equimolar.  The pool was sequenced single-end on an Illumina HiSeq4000 100 Cycle flowcell with 2% PhiX spike-in.

value: Pilocytic astrocytoma, CNS WHO 1

value: bulk tumor

tag: developmental stage

value: Pediatric

tag: subgroup


title: 2132-Pilocytic astrocytoma

description: Library name: 2132

tag: cell type


title: 734-Pilocytic astrocytoma

description: Library name: 734

tag: tissue


title: 03, 8h, ATAC

description: 10x genomics

tag: treatment


title: 2101-Pilocytic astrocytoma

description: Library name: 2101


title: 2085-Pilocytic astrocytoma

description: Library name: 2085


title: 15-NRR-033-Pilocytic astrocytoma

description: Library name: 15-NRR-033


title: 03, post, GEX

description: 10x genomics


title: 2105-Pilocytic astrocytoma

description: Library name: 2105


title: CTCF CLIP, Non-crosslinked, ESC, CTCF-WT rescue, rep3

description: Library name: CTCF_CLIP_ESC_neg_rep3


title: 1960-Pilocytic astrocytoma

description: Library name: 1960


title: 2044-Pilocytic astrocytoma

description: Library name: 2044


title: 03, post, ATAC

description: 10x genomics


title: CTCF CLIP, Non-crosslinked, ESC, CTCF-WT rescue, rep2

description: Library name: CTCF_CLIP_ESC_neg_rep2


title: CTCF CLIP, Non-crosslinked, ESC, CTCF-WT rescue, rep1

description: Library name: CTCF_CLIP_ESC_neg_rep1


title: 847A-Pediatric HGG-H3

description: Library name: 847A

source_name: Diffuse midline glioma, H3K27-altered, CNS WHO 4


title: 1292-Pediatric Other

description: Library name: 1292

source_name: Subependymal Giant Cell Astrocytoma CNS WHO 1


title: 03, pre, ATAC

description: 10x genomics


title: 03, pre, GEX

description: 10x genomics


title: 808-Pediatric HGG-H3

description: Library name: 808

source_name: Diffuse hemispheric glioma, H3 G34-mutant


title: 848-Pediatric HGG-H3

description: Library name: 848

value: Diffuse midline glioma, H3K27-altered, CNS WHO 4


title: RNA-seq_NPC, CTCF-ZF1 mutant rescue, rep2

description:
Library name: RNAseq_NPC_ZF1_rep2
NPC_ZF1_rep2

data_processing:
RNA-seq fastq files were processed using the route “rna-star” and “rna-star-groups-dge” from the Slide-n-Seq (sns) pipeline: https://igordot.github.io/sns/
Assembly: mm10
Supplementary files format and content: tab-delimited text file that contains raw counts of mapped reads for each gene

extract_protocol:
RNA was purified using RNeasy Plus Mini Kit (Qiagen 74136).
rRNA was depleted from 1 ug starting total RNA using NEBNext rRNA Depletion Kit v2 (NEB E7405) following manufacturer’s instructions. cDNA was synthesized using NEBNext Ultra II RNA first strand synthesis module (NEB E7771) (with random hexamers) and NEBNext Ultra II Directional RNA second strand synthesis module (NEB E7550) following manufacturer’s instructions. Libraries were prepared using NEBNext Ultra II DNA Library prep kit for Illumina (E7645S) in conjunction with NEBNext Multiplex Oligos for Illumina (E7600S or E7335S) for barcoding.

value: neural progenitor cells


title: RNA-seq_NPC, CTCF-ZF1 mutant rescue, rep1

description:
Library name: RNAseq_NPC_ZF1_rep1
NPC_ZF1_rep1


title: 617-Pediatric HGG-H3

description: Library name: 617


title: 2340-Pediatric Other

description: Library name: 2340

value: Subependymal Giant Cell Astrocytoma CNS WHO 1


title: 2348-Pediatric HGG-H3

description: Library name: 2348


title: RNA-seq_NPC, CTCF-WT rescue, rep2

description:
Library name: RNAseq_NPC_WT_rep2
NPC_WT_rep2


title: 02, 24h, GEX

description: 10x genomics

value: Blood


title: 02, 8h, GEX

description: 10x genomics

value: PBMCs


title: 1991-Pediatric HGG-H3

description: Library name: 1991


title: 1494-Pediatric HGG-H3

description: Library name: 1494


title: 02, post, GEX

description: 10x genomics


title: 853-Pediatric HGG-H3

description: Library name: 853


title: 2289-Pediatric HGG-H3

description: Library name: 2289

value: Diffuse hemispheric glioma, H3 G34-mutant


title: 2284-Pediatric HGG-H3

description: Library name: 2284


title: RNA-seq_ESC, CTCF-ZF1 mutant rescue, rep2

description:
Library name: RNAseq_ESC_ZF1_rep2
ESC_ZF1_rep2

value: embryonic stem cells

value: 1 uM 5-Ph-IAA + 1 ug/mL Dox


title: 2205-Pediatric GBM-RTK

description: Library name: 2205

source_name: Glioblastoma CNS WHO 4

value: Glioblastoma CNS WHO 4


title: 1062-Pediatric HGG-H3

description: Library name: 1062


title: RNA-seq_NPC, CTCF-WT rescue, rep1

description:
Library name: RNAseq_NPC_WT_rep1
NPC_WT_rep1


title: 02, pre, GEX

description: 10x genomics


title: 2117-Pediatric GBM-RTK

description: Library name: 2117


title: RNA-seq_ESC, CTCF-ZF1 mutant rescue, rep1

description:
Library name: RNAseq_ESC_ZF1_rep1
ESC_ZF1_rep1

value: E14 CTCF-AID2 degron; Dox inducible CTCF-ZF1 mutant rescue


title: 1583-Pediatric GBM-RTK

description: Library name: 1583


title: 01, 24h, GEX

description: 10x genomics


title: 1526-Pediatric GBM-RTK

description: Library name: 1526


title: 1021-Pediatric GBM-RTK

description: Library name: 1021


title: RNA-seq_ESC, CTCF-WT rescue, rep2

description:
Library name: RNAseq_ESC_WT_rep2
ESC_WT_rep2


title: 15-NRR-110-Adult GBM

description: Library name: 15-NRR-110

value: Adult


title: RNA-seq_ESC, CTCF-WT rescue, rep1

description:
Library name: RNAseq_ESC_WT_rep1
ESC_WT_rep1


title: 15-NRR-070-Adult GBM

description: Library name: 15-NRR-070


title: 15-NRR-062-Adult GBM

description: Library name: 15-NRR-062


title: 01, 8h, ATAC

description: 10x genomics


title: NPC, CTCF-ΔZF1 rescue, rep2

description: Library name: NPC_ZF1_rep2

data_processing:
Micro-C analysis was performed according to the pipeline described by Dovetail Genomics in https://micro-c.readthedocs.io/en/latest/index.html. Briefly, multiple pairs of fastq files (2 biological replicates per condition) were aligned to the mm10 reference genome using BWA-MEM split alignment. Pairtools was used for the next steps: identifying valid ligation events (pairs), removing PCR duplicates, generating and down-sampling the final pairs files. Pairs files were down-sampled such that all samples being compared together had equal number of valid pairs. The down-sampled pairs files were used for downstream analysis. Cool and mcool files were generated using cooler. Hic contact matrices were generated using Juicer Tools. Fithic2 was used to determine the contact counts of each pair-wise 5-kb bins, and calculate the likelihood of a contact to be significantly higher than expected for its genomic distance (q-value).
Assembly: mm10
Supplementary files format and content: pairs, cool, mcool, and hic of combined replicates; txt.gz file of FitHiC2 ouput
Library strategy: MicroC

extract_protocol:
Cells in a confluent 15 cm tissue culture plate (~30 million (M) cells) were dissociated with TrypLE Express and crosslinked with freshly made 3 mM ethylene glycol bis (EGS) in PBS (5 mL per 5M cells), incubated at room temperature for 45 minutes. Crosslinking reaction was quenched by adding Tris pH 7.5 to final 0.75 M concentration and incubated at room temperature for 5 minutes. EGS-crosslinked cells were washed twice with 0.5% BSA in PBS and subjected to the second crosslinking with 1% formaldehyde in PBS (5 mL per 5M cells), incubated at room temperature for 10 minutes. Crosslinking reaction was quenched again by adding Tris pH 7.5 to final 0.75 M concentration, incubated at room temperature for 5 minutes. Cells were washed twice with 0.5% BSA in PBS and aliquoted into 5M cells per 1.5 mL tube. Cell pellets were spun down, snap-frozen, and stored in −80°C. Crosslinked cells (5M in 1.5 mL tubes) were thawed on ice and permeabilized in cold Micro-C Buffer (MB) #1 (50mM NaCl, 10mM Tris pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 minutes on ice. Chromatin from permeabilized cells was digested by adding micrococcal nuclease (MNase) (NEB M0247SVIAL) at 1:100 dilution and incubated at 37°C for 10 minutes, shaking at 850 rpm. Dilution of MNase was pre-titrated such that chromatin is digested efficiently into nucleosome-sized fragments. Enzyme activity was stopped by adding EGTA to a final concentration of 4 mM and incubated at 65°C for 10 minutes. MNase-digested chromatin was washed twice with ice-cold MB #2 (50mM NaCl, 10mM Tris pH 7.5, 10mM MgCl2). Digested chromatin fragments were then subjected to 3’-dephosphorylation and 5’-phosphorylation by 0.5 U/uL T4 Polynucleotide Kinase in 1x NEBuffer 2.1 (NEB B6002S) with 2 mM ATP and 5 mM DTT, incubated for 15 minutes at 37°C with interval mixing. 3’-end-chewing was done by adding 0.5 U/uL DNA Polymerase I Klenow Fragment and incubating another 15 minutes in 37°C. Blunt-end reaction was triggered by adding biotin-dATP, biotin-dCTP, dGTP, and dTTP to a final concentration of 66 uM and incubated at 25°C for 45 minutes. The reaction was stopped by adding 30 mM EDTA final concentration and incubating at 65°C for 20 minutes. Chromatin was washed once with cold MB #3 (50mM Tris pH 7.5, 10mM MgCl2). Chromatin fragments with biotin-dNTPs were then ligated with 20 U/uL T4 DNA ligase (NEB M0202M), incubated at room temperature for at least 2.5 hours with slow rotation. Unligated ends containing biotin-dNTPs were then removed by 5 U/uL exonuclease III in 1x NEBuffer 1 (NEB B7001S), incubated at 37°C for 15 minutes. Chromatin was subjected to reverse crosslinking with 1 mg/mL Proteinase K (Sigma 3115879001), 1% SDS, and 100 ug/mL RNase A (ThermoFisher Scientific EN0531), incubated at 65°C overnight. DNA was extracted by adding 1x volume Phenol:Chloroform:Isoamyl Alcohol (25:24:1) solution (Thermofisher Scientific 15593049) and isolating aqueous phase after centrifugation. DNA was purified from the aqueous phase using a PCR purification kit (Zymo Research DCC-5 D4013) following manufacturer’s instructions. Separation of monomers and dimers was done by running purified DNA on 3% TBE agarose gel. 200-400 bp DNA was then extracted from the gel by Zymo Gel DNA recovery kit (Zymo Research D4008). DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (ThermoFisher Scientific 65001).
Standard library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with enzymes from NEBNext Ultra II DNA Library prep kit for Illumina (E7645S). NEBNext Multiplex Oligos for Illumina® (Dual Index Primers Set 1, E7600S) were used for barcoding. Sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA KK2601).


title: 15-NRR-061-Adult GBM

description: Library name: 15-NRR-061


title: NPC, CTCF-ΔZF1 rescue, rep1

description: Library name: NPC_ZF1_rep1


title: 15-NRR-043-Adult GBM

description: Library name: 15-NRR-043


title: 01, post, GEX

description: 10x genomics

value: post


title: 15-NRR-037-Adult GBM

description: Library name: 15-NRR-037


title: 01, post, ATAC

description: 10x genomics


title: 14-NRR-130-Adult GBM

description: Library name: 14-NRR-130


title: 14-NRR-063-Adult GBM

description: Library name: 14-NRR-063


title: CTCF CLIP, UV-crosslinked, ESC, CTCF-ZF1 mutant rescue, rep1

description: Library name: CTCF_CLIP_ESC_ZF1_rep1

value: embryonic stem cell

value: Anti-Flag magnetic beads (Millipore Sigma M8823)


title: NPC, CTCF-WT rescue, rep1

description: Library name: NPC_WT_rep1

value: E14 CTCF-AID2 degron; Dox inducible CTCF-WT rescue


title: 01, pre, GEX

description: 10x genomics

value: pre


title: 01, 24h, ATAC

description: 10x genomics


title: ESC, CTCF-ΔZF1 rescue, rep2

description: Library name: ESC_ZF1_rep2


title: 01, 8h, GEX

description: 10x genomics


title: ESC, CTCF-ΔZF1 rescue, rep1

description: Library name: ESC_ZF1_rep1


title: 01, pre, ATAC

description: 10x genomics


title: AD 2

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: TS_3.0 genome annotation（http://www.treeshrewdb.org/download.html）
Supplementary files format and content: Tab-separated values files and matrix files

organism: Tupaia belangeri

source_name: hippocampus

extract_protocol:
100-200mg samples were flash frozen immediately after collection for downstream processing. Nucleus isolation was done as previously described(https://pubmed.ncbi.nlm.nih.gov/32587393/).  Briefly, tissue samples were cut into pieces <0.5 cm and homogenized using a glass Dounce tissue grinder (Sigma, cat.  no.  D8938).  The tissue was homogenized 25 times with pestle A and 25 times with pestle B in 2 ml of ice-cold nuclei EZ lysis buffer.  The sample was then incubated on ice for 5 min, with an additional 3 ml of cold EZ lysis buffer.  Nuclei were centrifuged at 500g for 5 min at 4 °C, washed with 5 ml ice-cold EZ lysis buffer and incubated on ice for 5 min. After centrifugation, the nucleus pellet was washed with 5 ml nuclei suspension buffer (NSB;  consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor (Clontech, cat.  no.  2313A)).  Isolated nuclei were resuspended in 2 ml NSB, filtered through a 35 μm cell strainer (Corning-Falcon, cat.  no.  352235) and counted.  A final concentration of 1,000 nuclei per μl was used for loading on a 10x channel.
We prepared single-nucleus RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).  The nuclei suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.   Captured nuclei were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.   Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100.   Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per nucleus and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: hippocampus


title: 14-NRR-009-Adult GBM

description: Library name: 14-NRR-009

value: bulk tumor


title: 14-NRR-006-Adult GBM

description: Library name: 14-NRR-006


title: AD 3

description: 10x Genomics


title: 13-NRR-057-Adult GBM

description: Library name: 13-NRR-057


title: ESC, CTCF-WT rescue, rep2

description: Library name: ESC_WT_rep2


title: HD_exosome - biol rep 3

city: Siegen

first: Florian

last: Centler

state: NRW

address: Am Eichenhang 50

department: School of Life Sciences

institute: University of Siegen

data_processing:
Trimmomatic & cutadapt was used for adapter trimming and quality filtering, monitored by FastQC
Salmon was used for mapping and quantifying transcripts
R package tximport was used for collapsing results on the gene level
Assembly: GRCh38.p14
Supplementary files format and content: tsv, salmon pseudocounts (TPM)

extract_protocol:
For the isolation of totalRNAfromexosomes and cytoplasmic RNA granule cores, mirVana™ miRNA227Isolation Kit (Invitrogen) was used according to the manufacturers protocol.
Illumina stranded total RNA, NovaSeq S1 2x100 bp

value: exosome

value: HD-induced


title: AD 1

description: 10x Genomics


title: HD_SG - biol rep 1

value: RNA granule


title: ESC, CTCF-WT rescue, rep1

description: Library name: ESC_WT_rep1


title: Normal 3

description: 10x Genomics


title: control_SG - biol rep 5

value: control


title: 13-NRR-054-Adult GBM

description: Library name: 13-NRR-054


title: NPC, CTCF-WT rescue, rep2

description: Library name: NPC_WT_rep2

value: neural progenitor cells


title: 14-NRR-073-Adult GBM

description: Library name: 14-NRR-073


title: HFD Male

city: Ann Arbor

first: Kanakadurga

last: Singer

state: MI

address: D1205 MPB 1500 E Medical Center Drive

institute: University of Michigan

description: Library name: HFDWTM

data_processing:
The BD Rhapsody pipeline was further used to read the barcoded RNA sequences and generate gene expression matrices of the individual cells from the HFD and ND mice.
Assembly: GCF_000001635.27
Supplementary files format and content: .csv files with cell counts

source_name: bone marrow

extract_protocol:
The BD Rhapsody single-cell analysis system was used to isolate and capture mRNA from the whole genome of young mice started either on normal chow or HFD.
Library was made using paired end fastq R1 and R2 files.  Skewed pooling. 30K reads/cell GEX. 1K reads/cell Ab-seq.

treatment_protocol: Male Mice were fed chow or a 60% HFD for 16 weeks. Their bone marrow was isolated.

value: bone marrow

value: Wild type

value: high fat diet


title: 13-NRR-047-Adult GBM

description: Library name: 13-NRR-047

value: Glioblastoma CNS WHO 4


title: HD_exosome - biol rep 2