title: Batch1_Patient11600-15149_AA05_2

description:
AA05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.


title: HV1_CTR_1: Huvec Isolate #1 - DMSO (R1)

status: Public on Nov 01 2023

type: SRA

city: San Antonio

first: Henry

last: Miller

state: TX

address: 8403 Floyd Curl Drive

department: Cell Systems and Anatomy

country: USA

institute: UT Health San Antonio

description: Cell Isolate: Huvec Isolate #1, Treatment: DMSO, Replicate: R1

library_source: transcriptomic

data_processing:
Fastq files were trimmed and filtered automatically using fastp v0.20.0  with default settings
Filtered reads were mapped to the Gencode v30 hg38 transcriptome and quantified using Salmon v0.14.1 with the following settings: -l A --validateMappings --gcBias
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix was generated using the tximport R package to summarize transcript-level counts to the gene level. Matrix contains counts for each gene (rows) by sample (column). First column contains gene symbol, and first row contains sample name.

molecule: total RNA

organism: Homo sapiens

source_name: Human umbilical vein endothelial cells

growth_protocol: Medium 199 (Earle’s Salts, GIBCOTM) supplemented with 1mM sodium pyruvate, 1.82mM glutamine, 10mM HEPES, 2% LSGS, 8% FBS and 1% PS (to keep physiologically relevant glucose and glutamine levels, 5.5mM and 2mM respectively). 16-20h before experiments, cells were washed twice with HBSS (Corning) and media changed to low serum (2% LSGS only). HUVECs were kept at 3% Oxygen and 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented using divalent cautions under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final RNA-seq library. After RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequent 50bp single read sequencing run with Illumina HiSeq 3000 platform.

treatment_protocol: Cells were treated with either 5uM KU60019, 10uM KU55933, or vehicle (DMSO) for 8 hours.

tag: tissue

value: Human umbilical vein endothelial cells

tag: cell isolate

value: Huvec Isolate #1

tag: treatment

value: DMSO

tag: replicate


title: intrahepatic injection alone - Control

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

description: Single-cell RNA

data_processing:
The Cell Ranger output of single-cell RNA sequencing data were analyzed using Seurat in R-program (https://satijalab.org/seurat/).
Genome_build: mm10
Supplementary_files_format_and_content: Archive with barcodes, features and matrix of each sample

organism: Mus musculus

source_name: Liver metastases

growth_protocol: 250 000 MC38-luciferase (luc) expressing cells (colorectal (CRC) tumor cell line, from c57Black/6 mice background, that express luciferase reporter gene for in vivo tumor growth monitoring) were injected intra-hepatic (IH) in the liver of B6 mice (by microsurgery procedure). Only IH implantation were performed in the mice (group IH alone) or they were performed concomitantly with intra-colon(IC) injection of 500 000 MC38 (parental) cells (by microsurgery procedure) (group IH+IC). At day 10, IH tumors were harvested and an immune-score (or MicroEnvironment (ME)-score; % CD8+ T cells*% dendritic cells/ % macrophages infiltrating IH tumors) was determined by flow cytometry analyses. Than IH tumor samples were segregated depending on their low, intermediate or high ME-score and 7 low ME-score tumors were pooled, 7 intermediate ME-score were pooled and 7 low ME-score were pooled for scRNA-seq analyses.

extract_protocol:
CD45+ cells were enriched by positive selection from tumor cell suspension by magnetic cell sorting.
3’ gene expression single-cell libraries were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 3′ Kit v3 and Dual Index TT Set A, according to the manufacturer’s instructions starting with 16500 cells per sample pool. Library size and quality were confirmed on Fragment analyzer. KAPA quantification kit for Illumina platforms was used to quantify libraries. Samples were pooled in equimolar fashion. The libraries were sequenced on a NextSeq 550 in pair end sequencing 28 bp (read1) x 90 bp (read2) and dual index 10 bp.

value: Liver metastases

tag: cell line

tag: time

value: day 10 of in vivo tumor development

tag: microenvironment (me)-score

value: Control


title: Batch1_Patient11600-15149_AA05_1

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
AA05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

library_source: transcriptomic single cell

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2

molecule: polyA RNA

source_name: Fallopian tube

growth_protocol: Fallopian tube WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

value: Fallopian tube


title: A549 Mix moderate 100 nM replicate 2

city: Daejeon

first: Yoosik

last: Kim

state: Daejeon

address: Daejeon

country: South Korea

institute: KAIST

data_processing:
Basecalls performed using bcl2fastq
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with HISAT2 v2.1.0 using default parameters except with the option "--rna-strandness RF".
Only uniquely and concordantly mapped reads were then used in the further analyses.
featureCounts function of the Rsubread v2.4.2 R package was used by employing transcriptome information from the GENCODE v27 to assign and summarize reads to genomic features.
DESeq2 v.1.30.1 R package analyzed the differentially expressed genes with the summarized raw read counts for each gene.
ViSEAGO v1.4.0 was used to cluster biological functions using Gene Ontology and semantic similarity analysis.
GSEA v4.1.0 was performed using gene sets from Molecular Signatures Database (MSigDB) v7.4
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: csv of DESeq2 output containing log2 fold change upon ammonium nitrate and sulfate treatment

extract_protocol:
Total RNA was extracted using the Trizol reagent
2x101 paired-end RNA-seq library was constructed using TruSeq stranded mRNA LT sample prep kit and sequenced using the Illumina NovaSeq 6000 platform.

value: Ammonium nitrate/sulfate 100 nM


title: KD_PA_3

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

country: China

institute: Haijun Tu

data_processing:
The image data measured by the high-throughput sequencer is converted into sequence data (reads) by Casava base recognition.
It mainly includes the removal of reads with adapter, the removal of reads containing n (n indicates that the base information cannot be determined), and the removal of low-quality reads (the base number with qphred < =20 accounts for more than 50% of the whole read length).
The raw gene expression matrix was imported into the R environment for further processing and analysis. Genes with low read counts (less than 50 reads in all eight libraries) were filtered out.
Reads were mapped to the worm reference genome (Wbcel235) using HISAT2. Uniquely mapped reads were summarised to Worm Base annotated genes using feature Counts.
Assembly: Wbcel235
Supplementary files format and content: CT_OP_1_1.fq and CT_OP_1_2.fq files include complete reads for each sample.
Supplementary files format and content: count and fpkm

organism: Caenorhabditis elegans

source_name: C. elegans whole body

growth_protocol: Transferring L4 stage worms, which were maintained in NGM plate at 20C, to new plate  at  25C.

extract_protocol:
RNA was harvested using TransZol  Up Plus RNA Kit(Thermo Fisher).
>=1ug total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Using pathogenic bacterial PA14 to infect worms.

value: C. elegans whole body

value: DCL569 + inx-14 RNAi

tag: cell type

tag: genotype

value: PA14 infection


title: DGY1743_RPF_rep02

city: NEW YORK

first: Pieter

last: Spealman

state: NY

address: 12 Waverly Pl.

institute: New York University

library_source: other

data_processing:
*library strategy: Ribosome profiling
adapter_sequence = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
cutadapt -a ${adapter_seq} --cores=20 --revcomp -e 0.12 -m 12
STAR align against Saccharomyces_cerevisiae.R64-1-1.ncrna_wo_ncrna_genes.fa to filter out
Remainder of reads STAR align against Ensembl S288C reference genome: S288C_reference_sequence_R64-3-1
bedtools coverage strand sensitive counts (-s -counts)
Assembly: Ensembl S288C_reference_sequence_R64-3-1
Supplementary files format and content: Tab-delimited. Unique reads counts per feature: [chromosome][source][type][start][stop][dot][sign][dot][details][counts]

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Colonies were grown overnight on YEPD then used to inoculate 500 mL of minimal glutamine growth media in chemostats. These were then grown to saturation (approximately 48 hours ~1e7 cells / mL, measured using Coulter Counter) at 30°C in aerobic conditions. After saturation was achieved chemostats were switched to continuous mode with an inflow rate of fresh minimal glutamine growth media at a rate of 0.12 hour / L (corresponding to a population doubling time of ~5.8 hours). This was maintained for 24 hours before the cells were harvested. (glutamine-limited media: 800 μM and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins as previously described [PMID: 30562346]

extract_protocol:
Cells were harvested following previously described methods (Spealman et al. 2016). Briefly, cycloheximide was added to the media to a final concentration of 100μg/L and incubated for 2 min, before being separated from the media using rapid vacuum filtration using Millipore 0.22μm filters. Cells were resuspended from filters using polysome lysis buffer with cycloheximide and then flash frozen immediately in liquid nitrogen before being transferred and stored at -80°C.
Ribosome profiling was performed by TB-SEQ, Inc. (Palo Alto, CA)

tag: strain background

tag: strain

value: glutamine-limited growth in chemostat


title: DGY1743_RPF_rep01


title: Batch1_Patient11600-15149_AA04_1

description:
AA04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KD_PA_2


title: A549 Mix moderate 10 nM replicate 1

value: Ammonium nitrate/sulfate 10 nM


title: A549 Mix moderate 10 nM replicate 2


title: intracolorectal and intrahepatic injection - Intermediate ME-score

description: Single-cell RNA

value: Intermediate ME-score


title: CT_PA_3


title: A549 Mix moderate 100 nM replicate 1


title: intracolorectal and intrahepatic injection - High ME-score

description: Single-cell RNA

value: High ME-score


title: KD_PA_1


title: DGY1741_RPF_rep02


title: Batch1_Patient11600-15149_AA03_1

description:
AA03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_AA02_2

description:
AA02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: DGY1735_RPF_rep02


title: CT_PA_2


title: DGY1741_RPF_rep01


title: Batch1_Patient11600-15149_AA03_2

description:
AA03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 Mix moderate NC replicate 1

value: Media


title: DGY1735_RPF_rep01


title: A549 Mix moderate NC replicate 2


title: Batch1_Patient11600-15149_AA02_1

description:
AA02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CT_PA_1


title: A549 Mix high 5 mM replicate 2

value: Ammonium nitrate/sulfate 5 mM


title: DGY1726_RPF_rep02


title: Batch1_Patient11600-15149_AA04_2

description:
AA04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KD_OP_3

value: OP50 normal feeding


title: Batch1_Patient11600-15149_AA01_2

description:
AA01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: A549 Mix high 5 mM replicate 1


title: KD_OP_2


title: A549 Sul high 5 mM replicate 2

value: Ammonium sulfate 5 mM


title: KD_OP_1


title: DGY1657_RPF_rep02


title: Batch1_Patient11600-15149_AA01_1

description:
AA01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: CT_OP_3


title: A549 Sul high 5 mM replicate 1


title: A549 Nit high 10 mM replicate 2

value: Ammonium nitrate 10 mM


title: DGY1743_RNA_rep01

data_processing:
adapter_sequence = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
cutadapt -a ${adapter_seq} --cores=20 --revcomp -e 0.12 -m 12
STAR align against Saccharomyces_cerevisiae.R64-1-1.ncrna_wo_ncrna_genes.fa to filter out
Remainder of reads STAR align against Ensembl S288C reference genome: S288C_reference_sequence_R64-3-1
bedtools coverage strand sensitive counts (-s -counts)
Assembly: Ensembl S288C_reference_sequence_R64-3-1
Supplementary files format and content: Tab-delimited. Unique reads counts per feature: [chromosome][source][type][start][stop][dot][sign][dot][details][counts]

extract_protocol:
Cells were harvested following previously described methods (Spealman et al. 2016). Briefly, cycloheximide was added to the media to a final concentration of 100μg/L and incubated for 2 min, before being separated from the media using rapid vacuum filtration using Millipore 0.22μm filters. Cells were resuspended from filters using polysome lysis buffer with cycloheximide and then flash frozen immediately in liquid nitrogen before being transferred and stored at -80°C.
RNA-seq was performed by TB-SEQ, Inc. (Palo Alto, CA)


title: DGY1657_RPF_rep01


title: A549 NC high replicate 2


title: Batch2_Patient11597


title: DGY1743_RNA_rep02


title: MED211, Input

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for nextseq output.
ChIRP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIRP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package.
Assembly: GRCh38.p14
Supplementary files format and content: bigwig; peaks
Library strategy: ChIRP-seq

molecule: genomic DNA

source_name: Human medulloblastoma

growth_protocol: Cell lines were authenticated using single tandem repeat profiling. D425 cells were cultured in DMEM/F12 with 10% serum and 1% glutamate/penicillin/streptomycin.  All cells were grown in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
For ChIRP-seq, cells were cross-linked with 0.3% formaldehyde for 10 min, quenched with 0.125 M glycine for 5 min, and washed with phosphate-buffered saline. Sheared chromatin was prepared by sonication using a Bioruptor 300 (Diagenode) to produce DNA between 100 and 500 bp. Chromatin was diluted three times with hybridization buffer, and probes were added (15 pmol per chromatin from 1 million cells). The mixture was incubated overnight at 37°C with rotation. Streptavidin magnetic C1 beads (Thermo Fisher Scientific) were added and mixed for another 2 hours at 37°C. After extensive washing, the beads were resuspended in a buffer containing proteinase K (Sigma-Aldrich) and incubated at 50°C for 45 min, followed by overnight incubation at 65°C for reverse cross-linking. Beads were resuspended in 3x original volume DNA elution buffer (50mM NaHCO3, 1%SDS, 200mM NaCl), and DNA was eluted with a cocktail of 100ug/ml RNase A and 0.1U/ul RNase H. DNA was then purified by using the ChIP DNA Clean and concentrator kit (Zymo Research, Irvine, CA). Purified DNA was proceeded for high-throughput sequencing library preparation.
DNA high-throughput sequencing library preparation were prepared for sequencing using standard Illumina protocols

value: Human medulloblastoma

value: Medulloblastoma cell line


title: MED211, probeset1


title: A549 Nit high 10 mM replicate 1


title: DGY1741_RNA_rep02


title: MED211, probeset2


title: CT_OP_1


title: CT_OP_2


title: DGY1726_RPF_rep01


title: znf-598ANSDisomeRep2

city: Santa Cruz

first: Joshua

last: Arribere

state: CA

address: 1156 High St

department: Department of Molecular, Cell, and Developmental Biology

institute: University of California at Santa Cruz

description:
disome-associated RNA
50-62nt disome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004); znf-598(srf2119)

data_processing:
Library strategy: Ribo-Seq
Reads were trimmed using cutadapt v2.9
PCR duplicates were collapsed using custom scripts
Reads were mapped to a custom C. elegans genome including annotated splice junctions using STAR v2.5.4b allowing for zero mismatches
All downstream analyses were restricted to uniquely mapping reads
Genome_build: Ensembl, WBCel235
Supplementary_files_format_and_content: processed jam file containing uniquely-mapping reads with additional information pertaining to gene assignment

growth_protocol: Animals were synchronized by hypochlorite treatment, propagated on NGM plates with OP50 at 16C, and harvested at the L4/young adult stage. Animals were washed off with N50, passed through a 5% sucrose cushion in N50 to remove E. coli, and snap frozen in liquid nitrogen.

extract_protocol:
Animals were lysed by grinding in a mortar and pestle cooled in liquid nitrogen in the presence of frozen PLB (20mM Tris pH8.0, 140mM KCl, 1.5mM MgCl2, 1% Triton).
Ribo-seq library construction: Polysome fractionation to isolate monosomes/disomes, 3' end capture by adaptor ligation, reverse transcription, and PCR amplification.
RNA-seq library construction: RNA extracted, rRNA depleted by C. elegans-specific hybridization oligos, library prep using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina sequencing.

tag: developmental stage

value: young adult

tag: Sex

value: hermaphrodite

value: whole body

tag: growth conditions

value: NGM + OP50


title: DGY1735_RNA_rep02


title: D425, probeset2


title: znf-598ANSMonosomeRep2

description:
monosome-associated RNA
18-30nt monosome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004); znf-598(srf2119)


title: KO2

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

institute: Emory University

description: ATAD3A knockout cells

data_processing:
CASAVA  was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that could not be determined) and  low-quality reads, then mapped to hg19 whole genome using STAR (v2.5).
The counts coincide with those produced by htseq-count with default parameters. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Differential expression analysis of two conditions was performed using the edgeR R package (v3.16.5).
Differential expression analysis between WT and KO was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene of each sample
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each Sample

source_name: Head and neck squamous cell carcinoma

growth_protocol: ATAD3A knockout and its parental HN12 cells were grown in DMEM medium containing 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Total RNA of cells was extracted with Trizol reagent. NEBNext Ultra™ II RNA Library Prep Kit (Cat#NEB-E7765) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Head and neck squamous cell carcinoma

value: ATAD3A knockout


title: D425, probeset1


title: DGY1735_RNA_rep01

value: glutamine-limited growth in chemostat


title: znf-598CHXDisomeRep2

description:
disome-associated RNA
50-62nt disome Ribo-seq performed with cycloheximide of C. elegans unc-54(srf1004); znf-598(srf2119)


title: D425, Input


title: A549 NC high replicate 1


title: WT2

description: parental knockout control cells

value: WT


title: DGY1741_RNA_rep01


title: DGY1726_RNA_rep02


title: DGY1726_RNA_rep01


title: znf-598CHXMonosomeRep2

description:
monosome-associated RNA
28-30nt monosome Ribo-seq performed with cycloheximide of C. elegans unc-54(srf1004); znf-598(srf2119)


title: TGFBneg_Celastrol_500nM

city: Saskatoon

first: Andrew

last: Leask

state: Saskatchewan

address: 105 Wiggins

department: College of Dentistry

country: Canada

institute: University of Saskatchewan

data_processing:
Partek Flow v10.0.22
fastq files were aligned to hg38 using Star 2.7.3a and annotated with Ensembl Transcripts release 100
Features were excluded if maximum reads <=11.0
Reads were normalized using SESeq2 (median ratio)
Fold changes and p-values were caluclated using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including fold change and statistical significance value for each gene

source_name: Celastrol 6h

growth_protocol: CCD-1077Sk cells (>P8) was cultured in high glucose DMEM+10%FBS+1%anti-anti until 70% confluency before treatment

extract_protocol:
The RNA was extracted using the TriZol extraction method.
Total RNA samples were processed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (PN NR603) from Vazyme Biotech Co. Ltd.

treatment_protocol: Cells were treated with either DMSO or TGFB1 with or without Celastrol for 6h

value: Skin

value: Fibroblasts

tag: condition

value: Normal Skin

value: BSA+Citric Acid+Celastrol


title: DGY1657_RNA_rep02


title: TGFBneg_Celastrolneg 2

source_name: Control 2 6h

value: BSA+Citric Acid+DMSO


title: wildtypeANSDisomeShortRep2

description:
disome-associated RNA
40-49nt disome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004)

source_name: unc-54(srf1004) C. elegans


title: WT1

description: parental knockout control cells


title: znf-598ANSDisomeShortRep2

description:
disome-associated RNA
40-49nt disome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004); znf-598(srf2119)


title: shUSP16#2

city: shanghai

first: Jianchao

last: Ge

state: shanghai

address: N0.801,Heqing Road,Minhang District

department: Shanghai Fifth People's Hospital

institute: Fudan University

data_processing:
CASAVA used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 in the human genome using HISAT2
The gene transcript expression count was performed by Hiseq RNA-seq to generate a matrix of transcripts per kilobase of exon model per million mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample

source_name: PC3 cells

extract_protocol: RNA was harvested using Trizol reagent.Illumina TruseqTM RNA sample prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: PC3 prostate cancer cells


title: wildtypeANSDisomeRep2

description:
disome-associated RNA
50-62nt disome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004)


title: shUSP16#1


title: TGFBneg_Celastrolneg

source_name: Control 6h


title: DGY1657_RNA_rep01


title: wildtypeANSMonosomeRep2

description:
monosome-associated RNA
18-30nt monosome Ribo-seq performed with anisomycin of C. elegans unc-54(srf1004)


title: shCON

description: RFP

value: control


title: TGFBplus_Celastrol_500nM 2

source_name: TGFB_Celastrol 2 6h

value: TGFB+Celastrol


title: wildtypeCHXDisomeRep2

description:
disome-associated RNA
50-62nt disome Ribo-seq performed with cycloheximide of C. elegans unc-54(srf1004)


title: KO1

description: ATAD3A knockout cells


title: TGFBplus_Celastrol_500nM

source_name: TGFB_Celastrol 6h


title: rat_F_input

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
ChromHMM was used to annotate chromatin states using the rat alignments
macs was used to calculate CTCF fold-enrichment tracks
Assembly: rn6
Supplementary files format and content: Processed data

organism: Rattus norvegicus

source_name: Liver

extract_protocol: ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.

tag: antibody

value: Common rat

value: F


title: TGFBneg_Celastrol_500nM 2

source_name: Celastrol 3 6h


title: healthy control [C.343]

type: genomic

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

hyb_protocol: refer to Product Datasheet: http://www.illumina.com/products/infinium-methylation-epic-array.html

scan_protocol: Illumina protocol

data_processing:
After filtering probes, intra-cell type normalization was done using BMIQ normalization method (Teschendorff et al., 2013) to avoid the bias introduced by the Infinium type 2 probe design.We obtained intensity data from ChAMP  version 1.11.0 software. After Beta Mixture Quantile dilation (BMIQ) normalization which have been described to be an effective method to correct for batch effects (Marabita et al., 2013), we corrected the log transformed data using the ComBat normalization method (Johnson et al., 2007), which is an empirical Bayes based method to correct for technical variation related to the slide.
After pre-processing, R/Bioconducto limma package (Limma 3.28.14) was used to compute a moderated F-statistic (for PD outcome) adjusted by the effect of confounding factors, such as sex.

label: biotin

source_name: whole blood

label_protocol: Illumina protocol

extract_protocol: 30 ml of blood were collected from each subject into ACD tubes (BD Vacutainer).  Blood sample was split into four aliquots. Monocytes (10 ml blood+250ul beads) were isolated by using magnetic cell sorting included in the Whole Blood CD14 MicroBeads (Miltenyi Biotech, Bergisch Gladbach, Germany) and a magnetic cell separator, an autoMACS Instrument (Miltenyi Biotech) B cells (10 ml+250ul beads) using Whole Blood CD19 kit, T cells (5 ml+125ul beads) using Whole Blood CD3 Microbeads kit and neutrophils (5 ml blood+125ul beads) using Whole Blood CD15 Microbeads kit  by as described by the manufacturer (Miltenyi Biotec)

tag: disease

value: healthy control

tag: age

tag: gender

value: male


title: wildtypeCHXMonosomeRep2

description:
monosome-associated RNA
28-30nt monosome Ribo-seq performed with cycloheximide of C. elegans unc-54(srf1004)

value: young adult

value: hermaphrodite

tag: tissue

value: whole body

value: NGM + OP50


title: TGFBplus_Celastrolneg 2

source_name: Positive Control 2 6h

tag: treatment

value: TGFB+DMSO


title: Parkinson's disease [MP.881]

value: Parkinson's disease


title: healthy control [C-404]


title: rat_M_CTCF

description:
merged-rat-CTCF-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw
rat-CTCF-peaks-combined-merge200bp-sorted.bed

value: CTCF

value: M


title: TGFBplus_Celastrolneg

source_name: Positive Control 6h

value: Skin

tag: cell line

value: Fibroblasts

value: Normal Skin


title: rat_F_CTCF


title: znf-598RNASeq

description:
ribo-depleted RNA
RNA-seq of C. elegans unc-54(srf1004); znf-598(srf2119)

data_processing:
Reads were trimmed using cutadapt v2.9
PCR duplicates were collapsed using custom scripts
Reads were mapped to a custom C. elegans genome including annotated splice junctions using STAR v2.5.4b allowing for zero mismatches
All downstream analyses were restricted to uniquely mapping reads
Genome_build: Ensembl, WBCel235
Supplementary_files_format_and_content: processed jam file containing uniquely-mapping reads with additional information pertaining to gene assignment


title: Parkinson's disease [MP-918]


title: A427-Floating

city: Maebashi

first: Noriaki

last: Sunaga

state: Gunma

address: 3-39-15 Showa-machi

department: Department of Respiratory Medicine

country: Japan

institute: Gunma University Graduate School of Medicine

data_processing:
Basecalls and adapter trimming were performed using GenerateFASTQWorker Version=1.37.0 for NextSeq output.
RNA-seq reads were comfirmed to have a read quality score > 30 and no residual adaptor sequence using FastQC v0.11.1.
The reads were aligned to the UCSC human reference genome 19 (hg19) for calculation of expression values (read counting and TPM (Transcripts Per Million) normalized value) using the STAR (version 2.5.3a)-RSEM (version 1.3.3) pipeline with the following options: -paired-end, -star, -strandedness reverse, and -estimate-rspd.
Assembly: hg19
Supplementary files format and content: Tab-separated matrix file of count values
Supplementary files format and content: Tab-separated matrix file of TPM values

source_name: cell line

growth_protocol: RPMI 1640 medium with 5% fetal bovine serum was used for culturing cell lines.

extract_protocol:
Qiagen RNeasy kit including DNaseI treatment. 1.0 ug of total RNA with RIN >8 was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

treatment_protocol: The A427 NSCLC cell line was used in the current study. Sphere-forming and adherent A427 cells were separately collected and total RNA was extracted from the cells. Gene expression was examined in sphere-forming and adherent A427 cells.

value: cell line

value: Human non-small cell lung carcinoma

value: WT

value: Floating cells


title: rat_M_input

value: Common rat


title: znf-598ANSDisomeShortRep1


title: znf-598ANSMonosomeRep1


title: rat_F_H3K27ac

description: merged-rat-H3K27ac-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw

value: F


title: znf-598CHXDisomeRep1

value: young adult


title: rat_M_H3K4me1

description: merged-rat-H3K4me1-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw


title: healthy control [C-354]

value: healthy control

value: male


title: HCC15-siTax

extract_protocol:
Qiagen RNeasy kit including DNaseI treatment.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit following manufacturer's protocols.

treatment_protocol: NSCLC cells were transfected with siRNAs targeting LGR6 and were collected at 48 h post-transfection, followed by total RNA extraction from the cells.

value: Tax siRNA


title: znf-598CHXMonosomeRep1

value: hermaphrodite

value: whole body

value: NGM + OP50


title: rat_F_H3K4me1


title: rat_M_H3K27me3

description: merged-rat-H3K27me3-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw

value: M


title: HCC15-siLGR6-2

value: LGR6 siRNA_no2


title: Parkinson's disease [MP-957]

value: Parkinson's disease


title: healthy control [C-373]


title: wildtypeRNASeq

description:
ribo-depleted RNA
RNA-seq of C. elegans unc-54(srf1004)


title: A427-siLGR6-4

value: LGR6 siRNA_no4


title: znf-598ANSDisomeRep1


title: rat_F_H3K27me3


title: A427-siLGR6-2

value: cell line


title: rat_M_H3K27ac


title: wildtypeANSDisomeRep1


title: rat_M_H3K4me3

description: merged-rat-H3K4me3-ChIP-bowtie2-30qual-filter_FE.sorted.bdg.bw


title: Parkinson's disease [MP-968]


title: Parkinson's disease [MP-929]


title: A427-Adherent

value: Human non-small cell lung carcinoma

value: Adherent cells


title: wildtypeANSDisomeShortRep1


title: healthy control [C-378]


title: Parkinson's disease [MP-982]


title: HCC15-siLGR6-4

value: WT


title: A427-siTax


title: wildtypeANSMonosomeRep1


title: wildtypeCHXDisomeRep1


title: CRC04-OG

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

data_processing:
The pipeline is built using Nextflow and processes data using the following steps: (1) FastQC (2) TrimGalore (3) Bowtie (4) SAMtools (5) edgeR (6) Bowtie (7) mirtop (8) miRTrace, and (9) MultiQC
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: patient derived organoid

extract_protocol:
Total RNA from spheroids, organoids, and cell lines was isolated using phenol/chloroform extraction.
Libraries were prepared using 50ng total RNA with the NEXTFLEX® Small RNA-Seq Kit v3 (PerkinElmer). The NEXTflex 3’ and NEXTflex 5’ 4N Adapter were diluted 1:2, and the amplification was performed with 18 cycles. The amplified libraries were purified with AMPure XP beads (Beckman Coulter, Krefeld, Germany) by using a 2:1 bead:sample ratio.

value: patient derived organoid

value: colon cancer


title: LT3A

city: Providence

first: Surendra

last: Sharma

state: RI

address: 200 Chestnut St

department: Pediatrics

institute: Women and Infants Hospital of Rhode Island

data_processing:
Reads were filtered based on quality and adapter content using BGI's software SOAPnuke v1.5.2.
Clean reads were mapped using Bowtie2 v2.2.5 with the following parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 and expression was quantified with RSEM v1.2.8 -p 8 --forward-prob 0 --paired-end.
DESeq2 was used to identify differentially expressed genes
Afformetioned steps were done by BGI analysis pipeline
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Placenta

extract_protocol:
IL10 -/- At gd17 mice were sacrificed, and placenta was collected, put into RNAlater, and save in -20 degree. RNA was isolated using RNeasy Plus Mini kit, RNA quality was check and Only samples with  RIN > 6.0 and 28S/18S > 2.0 go for sequence.
Library was prepared following BGIs DNBSEQ Eukaryotic Stranded Transcriptome library preparation pipeline.  mRNA was enriched with Oligo dT selection, framentation and first strand cDNA synthesis using random N6-primed reverse transcription and dUTP for second strand synethesis. Ends were repaired, 3' adenylated. and adapters ligated.  cDNA was PCR amplified, denatured by heat and cyclized by splint oligo and DNA ligase. Sequenxing of library was done on the DNBSEQ platform.

treatment_protocol: Mice were i.p. injected with vehicle or disaccharides (2g/kg) at gd9, gd11, and gd14

value: placenta

tag: agent

value: treated with human PE serum and lactotrehalose


title: healthy control [C-335]

value: healthy control

value: male


title: LT2A


title: wildtypeCHXMonosomeRep1

value: young adult

value: hermaphrodite


title: rat_F_H3K4me3

value: Common rat

value: F


title: CRC03-OG


title: healthy control [C-382]


title: LT1A


title: Parkinson's disease [MP-987]


title: healthy control [C-260]


title: CRC03-SP

source_name: patient derived spheroid

value: patient derived spheroid


title: Treh3A

value: treated with human PE serum and Trehalose


title: CRC02X-SP


title: Parkinson's disease [MP-996]

value: Parkinson's disease


title: Treh2A


title: CRC02-SP


title: healthy control [C-321]


title: CUP01-OG

value: cancer of unknown primary


title: CRC01NM-OG


title: Parkinson's disease [MP-1037]


title: Treh1A


title: PES3A

value: treated with human PE serum


title: CRC01-OG


title: healthy control [C-374]

value: female


title: WM1366DTi

value: melanoma


title: Parkinson's disease [MP-898]


title: PES1A


title: PES2A


title: WT+A1-2

type: RNA

city: Freiburg

first: Marcus

last: Ziemann

state: Baden württemberg

address: Schänzlestraße 1

institute: Albert-Ludwigs-Universität Freiburg

description: Gene expression in wild type after 1h Phage A1 infection

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: PCC7120, WT+Phage A1,replicate 2

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid culture in BG11 medium under standard illumination at 30 centigrades.

extract_protocol: RNA was prepared using a hot phenol-based protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: WT culture was split into two cultures of the same size. Cyanophage A1 was added to one of the cultures with a multitude of infection (MOI) of 2. The cultures incubated 1 hour under the same conditions.

value: WT + Phage A1


title: WM1366VCi


title: NPS3A

value: treated with normal preg serum


title: ∆SI3* biol rep1 OD0.47

city: Madison

first: Robert

last: Landick

state: Wisconsin

address: 1550 Linden drive

department: Department of Biochemistry

institute: University of Wisconsin–Madison

data_processing:
NET-seq data analysis was performed using open-sourced packages in Python and custom scripts written in R 4.1.0. Adaptor sequence in raw NET-seq reads was removed with Cutadapt and aligned to E. coli MG1655 reference genome (NCBI Reference Sequence: NC_000913.3) with Bowtie. Unwanted reads in ribosomal RNA regions and t-RNA regions were removed with SAMtools and converted to BED format with BEDTools. Full length NET-seq reads were then trimmed to 15 nt from 3' ends. The total read numbers and 3' end read numbers in genome positions were quantified with BEDTools. To scale reads among strains and replicates, 3' end read numbers (R(raw)) were normalized according to the E. coli cell genomic DNA amount in cell harvested (M(E. coli)), the B. subtilis spike-in cell number (N(spike-in)) and the reads (R(spike-in)) specifically aligned to B. subtilis genome (NCBI Reference Sequence: NC_000964.3): scaled 3' end read R(scaled) = 2.5 * 10^8 * R(raw) * N(spike-in) / ( M(E. coli) * R(spike-in)). M(E. coli) was calculated with pre-determined equation for the two NET-seq strains: for WT NET-seq strain, M(E. coli) = (7.24 * OD + 3.98) * 500; for ∆SI3* NET-seq strain, M(E. coli) = (9.83 * OD + 9.34) * 500.
For pause calling, we used a multi-round sliding window strategy: for each position in a transcription unit, if its 3' end read number is larger than the mean + 4*standard deviation of the non-zero read pool containing this position, 100 bp upstream and 99 bp downstream, then it is classified as a pause signal. The pause reads defined in the first round is removed from the pool and the remaining sites were subjected to pause calling in the next round. Four rounds of pause calling in total were conducted and common pause positions from 3 biological replicates were used as the final pause positions. Detected pause signals located in several tRNA and sRNA genes were filtered due to their high probability of contamination during NET-seq library preparation. In addition, pause signals matching mature RNA 3' ends were also removed based on the published E. coli SEnd-seq results.
Assembly: E. coli: NC_000913.3, B. sub: NC_000964.3
Supplementary files format and content: Tab-delimited text files recording normalized nascent RNA 3' end reads and total reads (read trimmed to 15 nt) covering each genomic position.
Library strategy: NET-seq

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: A single colony of E. coli NET-seq strains was inoculated into MOPS rich defined medium with 0.2% (w/v) glucose (RDM) and 50 µg/mL kanamycin for overnight growth at 37 °C. 2.5 mL of the overnight culture was inoculated into 0.5 L RDM with 50 µg/mL kanamycin (freshly prepared and sterilized with 0.22 µM filter) in Erlenmeyer flasks and culture with 200 revolution per minute orbital shaking at 37 °C until cell density reached early log-phase (OD~0.4, record OD value at harvesting). At 37 °C, quickly filter cells through a 0.22 µM cellulose filter unit and transform all cell pellets into liquid nitrogen with a spatula. Frozen cells were stored at –80 °C before homogenizing. Biological triplicate samples were collected for each NET-seq strain. As for B. subtilis spike-in cells (RL3116), a single colony was inoculated into 5 mL LB with 7.5 µg/mL kanamycin for overnight growth at 37 °C. 2.5 mL of the overnight culture was inoculated into 0.5 L LB with 7.5 µg/mL kanamycin at 37 °C until cell density reached early log-phase (OD~0.4, record OD value at harvesting). Spin down cells with centrifugation at 4,000 Xg for 10 min for the cell pellet. Resuspend cells with 10 mL ice cold sterile PBS (with 20% (v/v) glycerol and 0.5 mL 1X protease inhibitor cocktail) and flash frozen in liquid nitrogen.

extract_protocol:
Frozen cells were pulverized on a Retsch MM400 Mixer Mill (canisters pre-cooled in liquid nitrogen) 6 times at 15 Hz for 3 min in the presence of 400 µL frozen lysis buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 100 mM NH4Cl, 10 mM MnCl2, 250 Unit RNaseIn (Promega), 1X protease inhibitor cocktail, 0.4 mg/mL puromycin). Spike-in cells were thawed on ice and added proportional to the E. coli cell amount (500 µL*OD E.coli) to homogenize with E. coli cells. The lysate was resuspended on ice with extra 5 mL of lysis buffer by gentle pipetting. RQ1 DNase I (110 Unit total, Promega) was added and incubated for 15 min on ice. The reaction was quenched with EDTA (25 mM final), which releases ribosomes from the transcript. The lysate was clarified at 4 °C by centrifugation at 25,000 xg for 10 min and incubated with 0.5 mL anti-FLAG M2 affinity resin (Sigma-Aldrich) for 3 hours at 4 °C. The resin was washed with 10 mL Wash Buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 300 mM KCl, 1 mM EDTA) 4 times at 4 °C and the RNAP was eluted with 600 µL Elution Buffer (20 mM Tris-HCl, pH=8.0, 0.4% Triton-X 100, 0.1% NP-40, 2 mg/mL FLAG peptide (Sigma-Aldrich)). Nascent RNA was extracted from the eluate with miRNeasy Mini Kit (Qiagen) following manufacturer’s instructions. The nascent RNA sample was further purified by EtOH precipitation, dissolved in DEPC-treated water and store at –80 °C.
The adaptor oligo(/5Phos/CTGTAGGCACCATCAAT/3ddC/, 6 µM) was 5' adenylated by incubating with 80 µM ATP, 6 µM Mth RNA ligase (NEB), 25% (v/v) PEG 8000 in 1X NEB Buffer 1 at 65 °C for 4 hours, then 85 °C for 5 min. Nascent RNA (16.7 ng/µL, normally 1.5 µg for each sample) was ligated to the adaptor by incubating with 1X T4 RNA ligase buffer (NEB), 25% PEG 8000, 6.7 Unit/µL T4 RNA ligase 2, truncated (NEB), 2 µM adaptor, 1.3 Unit/µL RNaseIn at 37 °C for 3 hours. The ligation was stopped by adding 16 mM EDTA. The adaptor-ligated RNA was alkaline fragmented by incubating with 6 mM Na2CO3, 44 mM NaHCO3, 1 mM EDTA at 95 °C for 35 min (time may vary depending on the freshness of the alkaline solution) and the RNA was precipitated by isopropanol precipitation with NaOAc (pH=5.5) and GlycoBlue coprecipitant (Thermo Fisher). The fragmented, adaptor-ligated RNA was run on a 15% TBE urea polyacrylamide gel (Novex, Thermo Fisher) and RNA species ranging from 50 to 100 nt was excised and gel extracted. The RNA was reversely transcribed into cDNA by mixing with 1X First Strand Buffer (Thermo Fisher), 0.5 mM dNTPs, 0.3 µM RT adaptor (/5Phos/AGATCGGAAGAGCACACGTCTGAAC/iSp18/CACTCA/iSp18/CCTACACGACGCTCTTCCGATCTTCCGACGATCATTGATGGTGCCTACAG), 0.6 Unit/µL SuperaseIn, 5 mM DTT, 10 Unit/µL Superscript III (Thermo Fisher) and incubating at 50 °C for 60 min. The RNA template in the cDNA was eliminated by adding 0.1 M NaOH and incubating at 95 °C for 20 min followed by adding 0.1 M HCl. The cDNA was run on a 10% TBE urea polyacrylamide gel (Novex, Thermo Fisher) and DNA species ranging from 100 to 200 nt was excised and gel extracted. The cDNA library was circularized by incubating with 1X Reaction Buffer (Lucigen), 50 µM ATP, 2.5 µM MnCl2, 5 Unit/µL CircLigase (Lucigen) at 60 °C for 1 hour followed by 80 °C for 10 min. The cDNA libraries were amplified with Q5 DNA polymerase (NEB) PCR system using dual indexed primers for NovaSeq 6000 (Illumina) sequencing platform using 150-nt paired-end sequencing.

value: bacterial cell

tag: spike-in control

value: Bacillus subtilis RL3116

value: F- lambda- ilvG468+ rfb-50 rph+ ybhJ(L54->I) yebN(G25xxx->D) ycfK::97bp  deltaInsB-5 deltaInsA-5 deltaInsAB-5 rpoC(A941T, deltaSI3)::3XFLAG, B. subtilis 168 trpC2 rpoC::3XFLAG

value: Mixing with spike-in control cells

tag: fraction

value: Nascent RNA


title: WM1366P

tag: cell type


title: WT-1

description: Gene expression in wild type

source_name: PCC7120, WT,replicate 1

value: WT


title: WT-2

description: Gene expression in wild type

source_name: PCC7120, WT,replicate 2


title: healthy control [C-377]

value: healthy control


title: Parkinson's disease [MP-964]


title: WT+A1-1

source_name: PCC7120, WT+Phage A1,replicate 1


title: NPS2A

tag: genotype

value: placenta


title: NPS1A


title: healthy control [C-327]


title: WT biol rep1 OD0.45

tag: strain

value: F- lambda- ilvG468+ rfb-50 rph+ ybhJ(L54->I) yebN(G25xxx->D) ycfK::97bp  deltaInsB-5 deltaInsA-5 deltaInsAB-5 rpoC::3XFLAG; B. subtilis 168 trpC2 rpoC::3XFLAG


title: TER01-PT

source_name: teratoma

extract_protocol:
Total RNA from patient tumors was isolated using the miRNeasy RNA isolation mini kit (Qiagen) according to the manufacturer’s protocol. Total RNA from tumor micro-dissected FFPE tissue was isolated using the RNeasy FFPE Kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared using SMARTer® smRNA-Seq Kit for Illumina® (Takara Bio) according to the manufacturer´s instructions using the bead based size selection.

value: teratoma


title: WT biol rep2 OD0.55


title: TER01-SP

value: patient derived spheroid


title: Parkinson's disease [MP-986]

value: Parkinson's disease


title: ∆SI3* biol rep3 OD0.49


title: MNaseseq_Setdb1KO

city: Hong Kong

first: Lut Fei

last: Tam

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon

department: LIFS

country: Hong Kong

institute: HKUST

data_processing:
Adapter sequence contamination of the raw reads of each MNase-seq libraries were removed by Trim Galore v0.6.6 with parameters --paired -a AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA -a2 AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG.
Trimmed reads were mapped to mouse reference genome mm10 (GRCm38) using Bowtie2 v2.4.2 with parameters -q --phred33 --end-to-end --sensitive --no-mixed --no-discordant.
PCR duplicates were excluded in downstream analysis using Picard MarkDuplicates v2.23.8.
Mapped read pairs with less than 4 mismatches were retained using bamtools v2.5.1 with parameter filter -tag “XM:<4”.
Based on the inferred fragment size of each pair, fragments with length between 141 to 190 bp were passed to DANPOS v2.2.2 with parameter dpos -m 1 to predict the location of nucleosome.
Nucleosome occupancy was quantile normalized with WIQ function in DANPOS v2.2.3
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent the normalized RPM signal of predicted nucleosome

source_name: Embryonic stem cell

growth_protocol: ES cells were maintained in ES medium (DMEM with 15% certified FBS (Life Technologies), 20 mM HEPES, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.05 mM streptomycin, 1 U/ml Leukemia-inhibitory factor (LIF) and 2mM glutamine). Cells were passaged at 80% confluence. Setdb1 conditional KO ES cells were induced by the addition of 800 nM (Z)-4-Hydroxytamoxifen (4-OHT) (Abcam, 141943) for 4 days and harvested on day 6 post 4-OHT treatment.

extract_protocol:
Cells were lysed in cold homogenization buffer (10 mM Tris-HCl pH7.5, 4 mM MgCl2, 1 mM CaCl2, 1X PIC) and fragmented with MNase (Thermo Scientific™,  88216).
MNase-seq library were built using KAPA HyperPrep kit according to manufacturer protocol and converted to DNBSEQ-G400 compatible library using MGIEasy Universal Library Conversion Kit (App-A) (MGI tech, 1000004155) following manufacture instructions.

value: Embryonic stem cell

value: TT2 (C57BL/6/CBA F1)

value: Setdb1 KO


title: TER01-FFPE


title: blood sap 3

city: Beijing

first: Yiqiu

last: Peng

state: China

address: No.17 Qihelou Road, Dongcheng District

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

description:
SAP_blood.3
blood all_fpkm.txt

data_processing:
Clustering and sequencing:  TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
Illumina Novaseq platform
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.
Assembly: MusMusculus(GRCm38/mm10)
Supplementary files format and content: processed data  for lung: lung all_fpkm.txt
Supplementary files format and content: processed data  for spleen: spleen all_fpkm.txt
Supplementary files format and content: processed data  for blood: blood all_fpkm.txt

source_name: blood

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After total RNA extraction and DNA digestion with DNaseI, eukaryotic mRNA with poly-A tail was enriched by magnetic beads with Oligo (dT) according to the manufacturer´s instructions. The bound mRNA was eluted, interrupted by divalent cations and high temperature conditions in interruption buffer, and reverse transcribed using random primers.First strand cDNA synthesis; The cDNA complementary strand was synthesized by RNaseH digestion of the mRNA strand in the heterozygous duplex to achieve the second strand of cDNA. Two-stranded cDNA was synthesized and purified by magnetic beads, followed by end repair, addition of base "A" at the 3 'end and ligation of an adaptor, and fragment size selection.Finally PCR amplification was performed.

value: blood

value: wild type

value: intraperitoneal injections of caerulein and LPS


title: healthy control [C-342]

value: female


title: MNaseseq_WT

data_processing:
Adapter sequence contamination of the raw reads of each MNase-seq libraries were removed by Trim Galore v0.6.6 with parameters --paired -a AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA -a2 AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG.
Trimmed reads were mapped to mouse reference genome mm10 (GRCm38) using Bowtie2 v2.4.2 with parameters -q --phred33 --end-to-end --sensitive --no-mixed --no-discordant.
PCR duplicates were excluded in downstream analysis using Picard MarkDuplicates v2.23.8.
Mapped read pairs with less than 4 mismatches were retained using bamtools v2.5.1 with parameter filter -tag “XM:<4”.
Based on the inferred fragment size of each pair, fragments with length between 141 to 190 bp were passed to DANPOS v2.2.2 with parameter dpos -m 1 to predict the location of nucleosome.
Nucleosome occupancy was quantile normalized with WIQ function in DANPOS v2.2.2
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent the normalized RPM signal of predicted nucleosome


title: blood sap 2

description:
SAP_blood.2
blood all_fpkm.txt


title: ∆SI3* biol rep2 OD0.49

value: bacterial cell

value: Bacillus subtilis RL3116

value: F- lambda- ilvG468+ rfb-50 rph+ ybhJ(L54->I) yebN(G25xxx->D) ycfK::97bp  deltaInsB-5 deltaInsA-5 deltaInsAB-5 rpoC(A941T, deltaSI3)::3XFLAG, B. subtilis 168 trpC2 rpoC::3XFLAG


title: healthy control [C-366]


title: TER01-PDCM


title: blood sap 1

description:
SAP_blood.1
blood all_fpkm.txt


title: WT biol rep3 OD 0.52

value: Mixing with spike-in control cells

value: Nascent RNA


title: Parkinson's disease [MP-1014]


title: Muscle, 30-C (10000 U vit. D3/kg of feed)

city: Balice

first: Anna

middle: Dominika

last: Steg

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Quality control (fastQC)
Processing fastq files with the QuantSeq Data Analysis Pipeline on BlueBee® Genomics
Filtration of low raw reads number samples. Minimal counts of reads set to 9 mln.
Assembly: Sus Scrofa 11.1
Supplementary files format and content: counts

organism: Sus scrofa

source_name: Muscle tissue

extract_protocol:
RNA was isolated with A&A Biotechnology Total RNA Mini kit
Libraries were prepared using  QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer recommendations.

value: Muscle tissue

tag: breed

value: Polish Large White sows covered with a Landrace boars

value: 10000 U vit. D3/kg of feed


title: blood con 3

description:
Normal_blood.3
blood all_fpkm.txt

value: intraperitoneal injection of normal saline


title: Parkinson's disease [MP-1018]

value: Parkinson's disease


title: MAM01-PT

source_name: mamma carcinoma

value: mamma carcinoma


title: Muscle, 28-A (control)

value: control


title: Muscle, 29-B (5000 U vit. D3/kg of feed)

value: 5000 U vit. D3/kg of feed


title: blood con 2

description:
Normal_blood.2
blood all_fpkm.txt

value: blood


title: healthy control [C-350]

source_name: whole blood

value: healthy control


title: MAM01-PDCM


title: Muscle, 27-C (10000 U vit. D3/kg of feed)


title: blood con 1

description:
Normal_blood.1
blood all_fpkm.txt

value: wild type


title: spleen sap 3

description:
SAP_spleen.3
spleen all_fpkm.txt

source_name: slpeen

value: slpeen

value: intraperitoneal injections of caerulein and LPS


title: Parkinson's disease [PD-CELL-3 N (PD3N)]

source_name: neutrophils

value: male


title: Parkinson's disease [MP-1028]

value: female


title: MEL01-PT

source_name: melanoma

value: melanoma


title: MEL01-PDCM


title: Muscle, 26-C (10000 U vit. D3/kg of feed)


title: Muscle, 25-B (5000 U vit. D3/kg of feed)


title: Parkinson's disease [PD-CELL-3 M (PD3M)]

source_name: monocytes


title: Muscle, 24-B (5000 U vit. D3/kg of feed)


title: spleen sap 1

description:
SAP_spleen.1
spleen all_fpkm.txt


title: CRC05-PT

source_name: colon adenocarcinoma

value: colon adenocarcinoma


title: spleen sap 2

description:
SAP_spleen.2
spleen all_fpkm.txt


title: MEL01-FFPE


title: slpeen con 3

description:
Normal_spleen.3
spleen all_fpkm.txt


title: MAM01-FFPE


title: Muscle, 23-A (control)

value: Muscle tissue


title: Parkinson's disease [PD-CELL-3 LT (PD3LT)]

source_name: lymphocytes T


title: CRC05-FFPE


title: Parkinson's disease [PD-CELL-2-LT (PD2LT)]


title: slpeen con 1

description:
Normal_spleen.1
spleen all_fpkm.txt


title: CRC05-PDCM


title: Muscle, 18-B (5000 U vit. D3/kg of feed)

value: Polish Large White sows covered with a Landrace boars


title: Parkinson's disease [PD-CELL-3 LB (PD3LB)]

source_name: lymphocytes B


title: Parkinson's disease [PD-CELL-2 N (PD2N)]


title: Muscle, 21-C (10000 U vit. D3/kg of feed)

value: 10000 U vit. D3/kg of feed


title: lung sap 3

description:
SAP_lung.3
lung all_fpkm.txt

source_name: lung

value: lung


title: slpeen con 2

description:
Normal_spleen.2
spleen all_fpkm.txt

value: intraperitoneal injection of normal saline


title: Muscle, 20-C (10000 U vit. D3/kg of feed)


title: Parkinson's disease [PD-CELL-2 LB (PD2LB)]

value: Parkinson's disease


title: Muscle, 17-A (control)

value: control


title: neuroepithelial stem cells, CTRL1

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

data_processing:
Reads were mapped with Bowtie2
Assembly: hg19
Supplementary files format and content: feature_counts_rnaseq_hg19.txt

source_name: Neuroepithelial stem cells

growth_protocol: Reinhardt et al., 2013

extract_protocol:
RNA was extracted using Allprep DNA/RNA mini kit (QIAGEN #80204). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries  were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L).

value: Neuroepithelial stem cells

tag: disease state

value: Healthy

tag: Sex

value: Female


title: Muscle, 16-A (control)


title: neuroepithelial stem cells, CTRL2


title: lung sap 1

description:
SAP_lung.1
lung all_fpkm.txt

value: wild type


title: Parkinson's disease [PD-CELL-2 M (PD2M)]


title: lung sap 2

description:
SAP_lung.2
lung all_fpkm.txt


title: Muscle, 15-B (5000 U vit. D3/kg of feed)

value: 5000 U vit. D3/kg of feed


title: neuroepithelial stem cells, IPD2

value: IPD


title: neuroepithelial stem cells, IPD1


title: lung con 2

description:
Normal_lung.2
lung all_fpkm.txt


title: lung con 3

description:
Normal_lung.3
lung all_fpkm.txt


title: Muscle, 14-A (control)


title: neuroepithelial stem cells, CTRL3


title: Muscle, 13-C (10000 U vit. D3/kg of feed)


title: lung con 1

description:
Normal_lung.1
lung all_fpkm.txt


title: PDAC cell, shControl Paf1 knockdown RNA-seq-2

first: Xiangzheng

last: Liu

address: Tsinghua University, Haidian  District, Beijing

institute: Tsinghua University

data_processing:
The paired-end reads were trimmed and quality check were carried out using trim-galore (version 0.6.4)
Trimmed reads were aligned to the mouse genome (GRCm38.p6) from GENCODE using STAR(2.7.1a)
Reads in BAM files were counted using featureCounts(v.1.6.4).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts numbers of all samples generated by featureCounts

source_name: pancreatic ductal adenocarcinoma cells

growth_protocol: PDAC cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual.
500ng RNA of each sample was used to prepare libraries, total RNA-seq libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NR603).

treatment_protocol: 1μg/mL doxycycline was added into medium to induc dCas9-KRAB expression for Paf1 knockdown groups

value: pancreatic ductal adenocarcinoma cells

value: Paf1 knockdown


title: Parkinson's disease [PD-CELL- 5 N (PD5N)]

value: female


title: Muscle, 11-B (5000 U vit. D3/kg of feed)


title: PDAC cell, shControl RNA-seq-2

value: WT


title: Muscle, 10-A (control)

value: Muscle tissue


title: Parkinson's disease [PD-CELL-1 LB (PD1LB)]

value: male


title: Parkinson's disease [PD-CELL- 5 M (PD5M)]


title: Parkinson's disease [PD-CELL- 5 LT (PD5LT)]


title: Muscle, 7-C (10000 U vit. D3/kg of feed)

value: Polish Large White sows covered with a Landrace boars

value: 10000 U vit. D3/kg of feed


title: neuroepithelial stem cells, IPD3


title: Parkinson's disease [PD-CELL1-LT (PD1LT)]


title: PDAC cell, shControl Paf1 knockdown RNA-seq-1


title: Late_2cell_DRB_3

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic. Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools. Duplicates were removed using picard to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values (average signal of all three biological replicates).
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.

source_name: 2-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 10-20 blastomeres (5 to 10 2-cell embryos) were collected in 2 μL DamID buffer (10mM TRIS acetate pH 7.5, 10mM magnesium acetate, 50mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.
Low-input LaminB1 DamID

treatment_protocol: For early 2-cell DamID, zygotes (18 h post hCG) were isolated and injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 and cultured in auxin (500μM)-containing medium. Auxin was removed just after mitosis for 4–6 h and early 2-cell embryos were collected at 34–36 h post hCG. For DamID in transcription inhibited late 2-cell embryos, zygotes (18 h post hCG) were injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 coding mRNA and cultured in KSOM containing 500 μM auxin and either 0.1 mg/mL alpha-amanitin (BioChemica) or 100 μM DRB (Santa Cruz). To allow methylation of LADs in the late 2-cell stage, auxin was washed out from 42 to 48 h post hCG and embryos were cultured in KSOM containing either 0.1mg/mL  alpha-amanitin or 100 μM DRB.

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J

value: DRB


title: Parkinson's disease [PD-CELL- 5 LB (PD5LB)]

value: Parkinson's disease


title: PDAC cell, shControl RNA-seq-1


title: Parkinson's disease [PD-CELL-1 N (PD1N)]


title: PDAC cell, shMyc,Paf1 knockdown RNA-seq-2

value: MYC and Paf1 knockdown


title: Parkinson's disease [PD-CELL-1 M (PD1M)]


title: Late_2cell_DRB_2


title: Muscle, 6-B (5000 U vit. D3/kg of feed)


title: PDAC cell, shMyc RNA-seq-2

value: Myc knockdown


title: Late_2cell_DRB_1


title: Parkinson's disease [PD-CELL- 4 M (PD4M)]


title: Muscle, 5-B (5000 U vit. D3/kg of feed)


title: Muscle, 3-A (control)

value: control


title: PDAC cell, shMyc,Paf1 knockdown RNA-seq-1

value: Myc knockdown and Paf1 knockdown


title: Late_2cell_amanitin_3

value: alpha-amanitin


title: Muscle, 9-A (control)


title: Muscle, 2-C (10000 U vit. D3/kg of feed)


title: Parkinson's disease [PD-CELL- 4 LT (PD4LT)]


title: PDAC cell, shMyc RNA-seq

value: pancreatic ductal adenocarcinoma cells


title: Muscle, 1-C (10000 U vit. D3/kg of feed)


title: Late_2cell_amanitin_1


title: Late_2cell_amanitin_2


title: Parkinson's disease [PD-CELL- 4 LB (PD4LB)]


title: PDAC cells, Random9270 control, Chromatin RNA-seq

data_processing:
The paired-end reads were trimmed and quality check were carried out using trim-galore (version 0.6.4)
Trimmed reads were aligned to the mouse genome (GRCm38.p6) from GENCODE using STAR(v.2.7.7a)
Reads in BAM files were counted using featureCounts(v.2.0.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts numbers of all samples generated by featureCounts

growth_protocol: The PDAC cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual.
500ng RNA of each sample was used to prepare libraries. RNA libraries were prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, NR603).

treatment_protocol: The cells were treated with 1μg/mL doxycycline to induce dCas9-KRAB expression


title: healthy control [C-CELL- 9 M (C9M)]

value: healthy control


title: healthy control [C-CELL- 9 N (C9N)]


title: Parkinson's disease [PD-CELL- 4 N (PD4N)]

value: female


title: RNA-seq_w303_wt_2

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

description: Control wildtype on a w303 background.  The chromosomal Pcf11 gene was deleted by insertion of TRP1 gene, with Pcf11 carried on a low copy centromeric plasmid that also has the LEU2 gene

data_processing:
trimmomatic 0.38, arguments -Xms1000m -Xmx1000m, minlen=15, trailing=3, end_mode=PE, phred=33, with default adapter sequences, as obtained from the fastqc website on 30 Aug 2018
alignment with STAR v2.6.1b, aligned to yeast genome sequence sacCer3, as included with Ensembl release 93, with STAR index generated using an SJDB=100; The sSTAR command used (not including input files and genome index): STAR --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outBAMcompression 10 --outFileNamePrefix w303wtrep1samp7_R1_001.trimmed.fastq.transcriptome.star2. --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout --outSAMattributes All --outSAMmode Full --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outStd Log --quantMode TranscriptomeSAM --runMode alignReads --runThreadN 8 --sjdbOverhang 100 --sjdbScore 1
Output SAM files were converted to BAM and indexed with version 1.10
A modified GTF file for annotation of genes on sacCer3 was locally created using the Ensembl version 93 provided sample as a starting point, but extending in the 3'-direction where possible according to the polyadenylation sites mapped in Park D, et al, Nucleic Acids Research, 2014, vol 42, no. 6 doi:10.1093/nar/gkt1366
RSEM version 1.3, command rsem-calculate-expression, with command (not including local files): rsem-calculate-expression --no-bam-output --num-threads 8 --paired-end --quiet --seed 1234
Individual sample output was merged into an experiment-level matrix, and then normalized with the rlog function found in the R package DESeq2 version 1.26.0
Genome_build: sacCer3 (ensembl release 93)
Supplementary_files_format_and_content: file pcf11_rnaseq_gene_counts.txt is a tab-separated-value text table file with the gene quantifications from RSEM as described above
Supplementary_files_format_and_content: 9 bigwig-formatted files are also provided with bigwig formatted coverage of RNA-seq aligned data

source_name: cell

growth_protocol: Yeast were inoculated in 5 ml of YPAD and grown overnight at 30ºC with light shaking.  The following day, cells were diluted back to an O.D.600 of 0.2 and grown at 30ºC.  Cells were harvested or treated with caffeine between 1.0 and 1.2 O.D600 units

extract_protocol:
Cells from all cultures were spun down, washed once with water, transferred to 1.5 ml tubes and flash frozen using liquid nitrogen.  Total RNA was extracted by the hot phenol method (Rio et al. 2011) and Phase-Lock gels (5Prime) according to the manufacturer’s manual.  RNA was DNase treated using the RNase-Free DNase kit (Qiagen).  RNA quality was evaluated by formamide agarose gel analysis and by Bioanalyzer. An aliquot of sample was not immunoprecipitated, but deproteinized and used as input
RNA was prepared from three biological replicates of each strain as described above and 5 mg submitted to Genewiz for polyA selection and standard RNA sequencing using the Illumina HiSeq 3000 platform, with 2x150 bp paired end runs, and a return of 15-20 million read pairs per sample

treatment_protocol: Caffeine treated cultures were brought up to 20 mM caffeine and grown at 30ºC for two hours.

value: cell

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-V5-PCF11-MYC]

value: glucose


title: healthy control [C-CELL- 9 LT (C9LT)]

value: male


title: healthy control [C-CELL- 9 LB (C9LB)]


title: PDAC cells, sgiPaf1-1, Paf1 KD Chromatin RNA-seq

value: Paf1 knockdown


title: PDAC cells, Random4841 control, Chromatin RNA-seq

value: WT


title: P5 cortex

first: jingyu

last: wang

address: xueyuan street

institute: THU

description: 10x Genomics

data_processing:
Sequencing data were prepared for analysis by application of the Cell Ranger pipeline. First, Illumina BCL output files were de-multiplexed into FASTQ format files. Feature counts were computed for individual GEM wells. STAR aligner was applied to perform splicing aware alignment to the GRCm38 reference genome, and then reads were bucketed into exonic, intronic and intergenic categories. Reads were classified as confidently aligned if they corresponded to a single gene annotation. Only confidently aligned reads were carried forward to UMI counting. A cell calling algorithm in conjunction with the barcode rank plot was applied to filter low RNA content cells and remove empty droplets. The output is a read count matrix. The R package Seurat was used to performing the bulk of our subsequent data analysis, including filtering, normalisation, scaling and other downstream processing.
Assembly: GRCm38

source_name: Brain

extract_protocol:
The neocortex of E16.5, P1, and P5 SstCre/+;RCEfl/+ mice was dissected in an ice-cold HBSS buffer supplement with 25 mM of glucose. For E16.5, tissue from 6 animals was pooled together. For P1 and P5, tissue from 3 animals was pooled together. Tissues were cut into small pieces and digested for 15 min at 37°C with carbogen oxygenation using 10ml of pronase dissociation buffer solution, pH7.5, Osmolarity 300-315, with the following composition: 0.2 mg/ml PronaseE (Sigma), 50mM of Trehalose, 20 mM glucose, 0.8 mM kynurenic acid, 0.05 mM APV, 0.09M Na2SO4, 0.03M K2SO4 and 0.014M MgCl2. For P5 tissue, tissue was incubated for 10 mins with dissociation buffer containing pronase, after which 500ul of 2.5% trypsin and 200ul of 10mg/ml DNAseI were added and incubated at 37°C for 2 more minutes. Post enzymatic digestion, tissues were washed once in ice-cold dissociation buffer without enzyme and the tissue was mechanically triturated into single cells in 2 ml of OptiMEM (Invitrogen) supplement with 2% Trehalose, 20 mM glucose, 0.8 mM kynurenic acid and 0.05 mM APV using 3 glass fire polished pipettes with decreasing diameter. For P1 and P5 tissue, we removed myelin by overlaying single cell suspension on top of a 30% percoll and centrifuge at 700 g for 10 mins. The cell pellet was resuspended in 300-500 µl of OptiMEM with 2% Trehalose, 20mM glucose, 0.8 mM kynurenic acid and 0.05 mM APV and tissue chunks were eliminated by passing cells suspension through a 40 µm cell strainer (BD).  GFP+ and DAPI negative cells were isolated using fluorescence-activated cell sorting (FACS) with a flow cytometer (Becton Dickinson) using a 100 µm nozzle. Cells were sorted in bulk. In all experiments, we only proceed toward scRNAseq with > 80% viability. About 4000-6000 isolated single cells for each sample were added to a 10X Genomic single-cell machine for single-cell capture and cDNA library preparation. RNA-seq was performed in an Illumina high-seq 2500 platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Neurons

value: Brain

value: Sst-Cre; RCEloxP


title: RNA-seq_w303_wt_3


title: RNA-seq_w303_wt_1


title: P1 cortex

description: 10x Genomics


title: E16.5 cortex

description: 10x Genomics


title: PDAC cells, sgiPaf1-2, Paf1 KD Chromatin RNA-seq


title: RNA-seq_w303_Pcf11-DNL_3

description: Pcf11-deltaNL mutant on a w303 background.  The chromosomal Pcf11 gene was deleted by insertion of TRP1 gene, with Pcf11-deltaNL carried on a low copy centromeric plasmid that also has the LEU2 gene

value: w303 strain; MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,12; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2--V5-pcf11-deltaN-linkMYC]


title: CT2A-luc ex vivo bulk tumor, Sample 48

city: Boston

first: Catherine

middle: J.

last: Wu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequencing data were aligned to the mm10 reference transcriptome with STAR (v2.7.7a)
Expression metrics for each gene were computed using RSEM (v1.3.3)
Differential expression analysis was performed using DESeq2 (v1.30.1), including genes with normalized transcript counts >10
Gene set enrichment analysis with the fgsea R package (v1.20.0) was performed across all genes pre-ranked by log10(p-value) * -(sign of the LFC)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited output text files from RSEM include RPKM, TPM, and expected count values for each sample
Supplementary files format and content: Tab-delimited output text files from Salmon include TPM values for each sample

source_name: ex vivo tumor

extract_protocol:
RNA was harvested using RNeasy Plus Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers' protocols.

value: ex vivo tumor


title: CT2A-luc ex vivo bulk tumor, Sample 47


title: screen 3, old, day 14 reactivated [SC8_O_RA]

city: Stanford

first: Tyson

middle: Joel

last: Ruetz

address: 290 Jane Stranford Way

department: Genetics

institute: Stanford University

description: PCR ampllified DNA library

data_processing:
All of the source scripts can be found here: https://bitbucket.org/dmorgens/castle/downloads/.
fastq files were aligned to the sgRNA library sequence (“mm-Cas9-10”, or one of custom 10 gene library + control sgRNAs) to make count files using the “makeCounts” script.
The count files were then analyzed using the “analyzeCounts” CasTLE script, comparing each screen timepoint to the starting plasmid sgRNA library count file (in vitro screens) or the sequenced 24-hour SVZ count file (in vivo screens), which we sequenced in parallel with screen libraries.
P-values for all genes in each screen by running 100,000 (in vitro screens) or 10,000 (in vivo screens) permutations with the “addPermutations” CasTLE script.
For each genome-wide screen, we corrected for multiple hypotheses on the ~23,000 gene associated P-values using the Python Statsmodel module, with Benjamini/Hochberg method,
Genome_build: mm10
Supplementary_files_format_and_content: csv count files of every sgRNA

source_name: NSCs in vitro

growth_protocol:
Complete ‘aNSC media’ Neurobasal-A (Gibco, 10888-022) supplemented with 2% B27 minus vitamin A (Gibco, 12587-010), 1% penicillin–streptomycin–glutamine (Gibco, 10378-016), 20 ng/mL of EGF (Peprotech, AF-100-15), and 20 ng/mL of bFGF (Peprotech, 100-18B), placed in a humidified incubator, 37°C, 5% CO2. Complete qNSC media’ is: Neurobasal-A (Gibco, 10888-022) supplemented with 2% B27 minus vitamin A (Gibco, 12587-010), 1x penicillin–streptomycin– glutamine (Gibco, 10378-016), 50 ng/mL of BMP4 (Biolegend, 94073), and 20 ng/mL of bFGF (Peprotech, 100-18B). .To expand the aNSCs up to the 1.4x109 cells (the equivalent of 140 15cm plates) required for each biological replicate, 1x107 aNSCs were passaged and expanded into 15cm plates every 2-3 days, with feedings every 2 days (alternating between doubling the media (with 2x growth factor aNSC media) or complete media exchange). For each screen, 70 plates of 2x107 qNSCs were seeded at day 0 (see below for library coverage calculations). After 4 days in quiescence media, the cells were incubated with the genome-wide sgRNA lentivirus library
[[delete]]

extract_protocol:
genomic DNAwas extracted with Qiagen QiaAmp DNA Blood Maxi Kit (51194), adding 5x107 cells per column and according to the manufacturer’s protocol.
sgRNA was amplified from the genome in 2 successive, nested PCR reactions. For the nested PCR reactions, we used either Herculase II Fusion Polymerase (Agilent, 600679) for screen 1, or Q5 DNA polymerase (Fisher Scientific, M0491L) for screens 2 and 3, and Q5 DNA polymerase for in vivo screens, according to manufacturer’s protocol. In optimizing this PCR reaction, we found that Herculase II Polymerase was outperformed by Q5 polymerase outperformed Herculase II Polymerase, Q5 polymerase requiring fewer PCR cycles to get more amplicon product, which is why we switched to Q5 DNA polymerase. We used 5 μg genomic DNA in 50 μL reactions to run on thermocycler. For the first PCR, we used primers MCB1562 (aggcttggatttctataacttcgtatagcatacattatac) and MCB1563 (acatgcatggcggtaatacggttatc) (1 µM final concentration), with PCR cycles as follows: 98°C for 2 minutes, 19 cycles of [98°C/30s, 59.1°C/30s, 72°C/45s], followed by 72°C for 3 minutes. We pooled all the PCR#1 cycle products and then used 5 µL of the pool in a second PCR reaction (PCR#2) with the same conditions but using different primers; MCB1439 (caagcagaagacggcatacgagatgcacaaaaggaaactcaccct) and a barcoded primer (aatgatacggcgaccaccgagatctacacGATCGGAAGAGCACACGTCTGAACTCCAGTCACXXXXXXCGACTCGGTGCCACTTTTTC, where XXXXXX is the 6-digit barcode for high throughput sequencing sample identification). The second PCR reaction was run for either 30 cycles (in vitro screen 1 and in vivo screens), or 18 cycles (in vitro screens 2 and 3).

tag: tissue/cell type

value: NSCs in vitro

value: Whole genome sgRNA library

tag: age-young/old

value: Old

value: sgRNA lentivirus library was freshly thawed at room temperature and diluted 1:5 in Neurobasal media and then B27 and growth factors were added to make it qNSC media, and 18 mL of this mix was added to plates for 16-hour overnight infection. The virus dilution added was based on viral titering experiments determined to achieve ~30% culture infection of cells to ensure each cell only received a single sgRNA


title: screen 1/2, old, quiescent [SC36_O_Q]

description: PCR ampllified DNA library


title: healthy control [C-CELL- 8 N (C8N)]

data_processing:
After filtering probes, intra-cell type normalization was done using BMIQ normalization method (Teschendorff et al., 2013) to avoid the bias introduced by the Infinium type 2 probe design.We obtained intensity data from ChAMP  version 1.11.0 software. After Beta Mixture Quantile dilation (BMIQ) normalization which have been described to be an effective method to correct for batch effects (Marabita et al., 2013), we corrected the log transformed data using the ComBat normalization method (Johnson et al., 2007), which is an empirical Bayes based method to correct for technical variation related to the slide.
After pre-processing, R/Bioconducto limma package (Limma 3.28.14) was used to compute a moderated F-statistic (for PD outcome) adjusted by the effect of confounding factors, such as sex.

extract_protocol: 30 ml of blood were collected from each subject into ACD tubes (BD Vacutainer).  Blood sample was split into four aliquots. Monocytes (10 ml blood+250ul beads) were isolated by using magnetic cell sorting included in the Whole Blood CD14 MicroBeads (Miltenyi Biotech, Bergisch Gladbach, Germany) and a magnetic cell separator, an autoMACS Instrument (Miltenyi Biotech) B cells (10 ml+250ul beads) using Whole Blood CD19 kit, T cells (5 ml+125ul beads) using Whole Blood CD3 Microbeads kit and neutrophils (5 ml blood+125ul beads) using Whole Blood CD15 Microbeads kit  by as described by the manufacturer (Miltenyi Biotec)

tag: disease

value: healthy control


title: RNA-seq_w303_Pcf11-DNL_2


title: healthy control [C-CELL- 8 M (C8M)]

tag: age


title: healthy control [C-CELL- 8 LT (C8LT)]

tag: gender


title: CT2A-luc ex vivo bulk tumor, Sample 40

tag: tissue


title: RNA-seq_w303_Pcf11-13_3

description: Pcf11-13 mutant on a w303 background.  The chromosomal Pcf11 gene was deleted by insertion of TRP1 gene, with Pcf11-13 carried on a low copy centromeric plasmid that also has the LEU2 gene

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-pcf11-13]

tag: treatment


title: RNA-seq_w303_Pcf11-DNL_1

value: cell


title: screen 3, old, day 4 Ki67+ [SC8_O_Kp]

description: PCR ampllified DNA library


title: screen 3, young, day 14 reactivated [SC7_Y_RA]

description: PCR ampllified DNA library

value: Young


title: healthy control [C-CELL- 8 LB (C8LB)]


title: healthy control [C-CELL- 7 N (C7N)]

value: female


title: RNA-seq_w303_Pcf11-13_2

value: glucose


title: RNA-seq_w303_Pcf11-13_1


title: screen 3, young, day 4 Ki67+ [SC7_Y_Kp]

description: PCR ampllified DNA library


title: healthy control [C-CELL- 7 M (C7M)]


title: healthy control [C-CELL- 7 LT (C7LT)]


title: DRS_DHch08_Pcf11-DNL_caff

description: Pcf11-dNL mutant in 20mM caffeine, experiment 2

data_processing:
Library strategy: Helicos Direct RNA Sequencing (DRS)
Using custom scripts, DRS reads were processed to remove leading T bases (which are ambiguous with regard to polyA site), and truncated to 20nt, and then finally reduced to unique representatives, retaining the count of each 20-mer
Unique sequences were aligned to the yeast genome (sacCer3) using blat, with arguments -t=dna -q=dna -tileSize=10 -stepSize=3 -minScore=27 -minIdentity=85
PSL files were processed into gene count vectors and matrixes as described previously in Graber JH et al, Genome Research 2013 Oct;23(10):1690-703. doi: 10.1101/gr.144964.112
Genome_build: sacCer3
Supplementary_files_format_and_content: file pcf11_geneCounts.txt: tab-separated-value formatted file giving the measured gene counts for each transcript across all samples based on the alignment of DRS tags
Supplementary_files_format_and_content: file pcf11_av3UTRL.txt: tab-separated-value formatted file giving the estimated average 3'UTR length for each gene based on all DRS tags that map downstream of the annotated open reading frame
Supplementary_files_format_and_content: file pcf11_fracTrunc.txt: tab-separated-value formatted file giving the fraction of tags assigned to the gene that imply truncation upstream of the annotated stop codon
Supplementary_files_format_and_content: file pcf11_proPrx.txt: tab-separated-value formatted file giving the fraction of DRS tags assigned to each gene that imply truncation no more than 100 nt downstream of the annotated start codon (including 5'-UTR alignments)

extract_protocol:
Cells from all cultures were spun down, washed once with water, transferred to 1.5 ml tubes and flash frozen using liquid nitrogen.  Total RNA was extracted by the hot phenol method (Rio et al. 2011) and Phase-Lock gels (5Prime) according to the manufacturer’s manual.  RNA was DNase treated using the RNase-Free DNase kit (Qiagen).  RNA quality was evaluated by formamide agarose gel analysis and by Bioanalyzer.
Total RNA (3 µg) was submitted to Helicos for Direct RNA Sequencing (DRS) of polyadenyated 3’ ends as described previously (Ozsolak et al. 2010)

value: 20mM caffeine


title: GL261-luc2 ex vivo bulk tumor, Sample 417

tag: cell line


title: GL261-luc2 ex vivo bulk tumor, Sample 412


title: screen 2, old, day 4 Ki67+ [SC6_O_Kp]

description: PCR ampllified DNA library


title: screen 2, old, day 14 reactivated [SC6_O_RA]

description: PCR ampllified DNA library


title: DRS_DHch06_WT2_caff

description: WT control in 20mM caffeine, experiment 2

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-V5-PCF11-MYC]


title: healthy control [C-CELL- 7 LB (C7LB)]


title: DRS_DHch07_Pcf11-DNL_glu

description: Pcf11-dNL mutant , experiment 2


title: screen 2, young, quiescent [SC5_Y_Q]

description: PCR ampllified DNA library


title: screen 2, young, day 14 reactivated [SC5_Y_RA]

description: PCR ampllified DNA library


title: healthy control [C-CELL- 6 N (C6N)]


title: CT2A-luc ex vivo bulk tumor, Sample 39


title: DRS_DHch05_WT2_glu

description: WT control, experiment 2


title: healthy control [C-CELL- 6 M (C6M)]


title: screen 2, young, day 4 Ki67+ [SC5_Y_Kp]

description: PCR ampllified DNA library


title: dsDNA1

first: jieming

last: Qu

address: Ruijin 2 road

institute: ruijin hospital

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to mm10 genome using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: excel file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj

growth_protocol: Adipose tissue was harvested from the inguinal area of 8 weeks old male mice and then digested with 0.1% (vol/vol) collagenase type I. Suspension was then centrifuged at 1200 rpm for 10 minutes. ASCs were cultured in the mixed medium of Dulbecco’s modified Eagle’s medium and Nutrient Mixture F-12 supplemented with 10% (vol/vol) fetal bovine serum  and 1% (vol/vol) penicillin/streptomycin. After 24 hours, medium was replaced with fresh media and culture media was changed every 2-3 days. Cells of the fourth generation were used in our study.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ASCs were seeded in 6-well dishes grown overnight and then were transfected with dsDNA at 400 ng/ml using Lipofectamine® 3000 or LPS (100 ng/ml). 4 hours later, the cells were collected for RNA extracting.

value: 8 weeks

value: male

value: adipose tissue-derived mesenchymal stem cells (ASCs)

tag: passages

value: dsDNA (400 ng/ml) using Lipofectamine® 3000


title: dsDNA2


title: DRS_DHch04_Pcf11-13_caff

description: Pcf11-13 mutant in 20mM caffeine, experiment 1


title: DRS_DHch03_Pcf11-13_glu

description: Pcf11-13 mutant , experiment 1


title: GL261-luc2 ex vivo bulk tumor, Sample 414

value: ex vivo tumor


title: LIPO2

value: Lipofectamine® 3000 reagent


title: healthy control [C-CELL- 6 LB (C6LB)]

first: Mario

last: Ezquerra

address: Villarroel 170

institute: Fundacio Clinic/IDIBAPS


title: LIPO1


title: healthy control [C-CELL- 6 LT (C6LT)]


title: healthy control [C-CELL- 10 N (C10N)]


title: GL261-luc2 ex vivo bulk tumor, Sample 405


title: screen 1, young, quiescent [SC4_Y_Q]

description: PCR ampllified DNA library

value: NSCs in vitro

value: Whole genome sgRNA library


title: DRS_DHch02_WT1_caff

description: WT control in 20mM caffeine, experiment 1


title: healthy control [C-CELL- 10 M (C10M)]


title: LPS2

value: LPS (100 ng/ml)


title: osnrpd1-1

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

description: osnrpd1-1 (WGBS-seq)

data_processing:
sRNA-seq: Cutadapt2.9 was used to find and trim adapter sequences from sRNA-seq reads. 18–-30 nt sequences with adapters trimmed were retained. Clean reads were converted into FASTA format to meet the requirement of miRDeep-P, a software for miRNA identification in plants. The reads in FASTA format were mapped to the rice genome (RGAP7.0) with Bowtie-1.2.3, allowing no mismatches. Small RNA abundance was calculated as reads per million (RPM).  WGBS-seq: Cutadapt2.9 was used to find and trim adapter sequences from Bisulifite-seq reads. Adapters and low-quality reads were removed and clean reads were mapped to the rice genome (RGAP7.0) using BRAT-BW, allowing up to three mismatches. Only uniquely mapped reads were retained. Only uniquely mapped reads were retained. Fractional DNA methylation levels were calculated using BRAT-BW.
Assembly: Oryza sativa RGAP7.0
Supplementary files format and content: bw
Supplementary files format and content: bed

organism: Oryza sativa

source_name: 4-week-old seedling

growth_protocol: Rice plants were grown in a greenhouse at 70% humidity under long-day conditions with daily cycles of 14 h of light at 30°C and 10 h of dark at 25°C. 4-week-old seedlings that start tillering were collected and used for the experiments.

extract_protocol:
sRNA-seq: total RNA was purified from 4-week-old seedlings using TRIzol reagent (Invitrogen, 15596026). Large RNAs were selectively precipitated using 5% polyethylene glycol 8000 (PEG8000; Sigma, P5413) and 0.5 M NaCl (Sigma, S3014). sRNAs were recovered from the supernatant by ethanol precipitation and then separated by electrophoresis using a 15% denaturing PAGE gel. sRNAs that were 18–28 nt long were excised from the gel and purified.  WGBS-seq: genomic DNA was purified from the 4-week-old seedlings using the DNeasy Plant Mini Kit (Qiagen, 69104).
sRNA-seq: purified sRNAs were ligated with the 3’ adaptors and 5’ adaptors. The products were reversely transcribed using SuperScript III Reverse Transcriptase (Invitrogen, 18080093). The cDNAs obtained were amplified by PCR to generate the libraries. The libraries were sequenced on an Illumina HiSeq2500 platform to obtain 50-bp single end reads.   WGBS-seq: Paired-end bisulfite sequencing libraries were constructed using the NEXTflex Bisulfite-Seq kit (Bioo Scientific, Nova-511911). Genomic DNA was sonicated to ~300 bp, end repaired, and 3’ adenylated. The products were ligated with methylated adapters. After size selection with Ampure XP purification beads (Beckman, A63881), the products were subjected to bisulfite conversion by using the EZ DNA Methylation-Gold kit (ZYMO Research, D5005). Bisulfite-converted DNA products were amplified by PCR for 15 cycles using EX Taq DNA polymerase (Takara, RR001C). The PCR products were cleaned up using Ampure XP purification beads (Beckman, A63881). The libraries were validated using the Agilent 2100 Bioanalyzer and sequenced on an Illumina X-Ten platform to obtain 150-bp paired-end reads.

value: 4-week-old seedling


title: DRS_DHch01_WT1_glu

description: WT control, experiment 1


title: LPS1

city: shanghai


title: healthy control [C-CELL- 10 LT (C10LT)]

value: healthy control


title: N2

value: none (control)


title: screen 1, young, day 4 Ki67+ [SC4_Y_Kp]

description: PCR ampllified DNA library

value: Young

value: sgRNA lentivirus library was freshly thawed at room temperature and diluted 1:5 in Neurobasal media and then B27 and growth factors were added to make it qNSC media, and 18 mL of this mix was added to plates for 16-hour overnight infection. The virus dilution added was based on viral titering experiments determined to achieve ~30% culture infection of cells to ensure each cell only received a single sgRNA


title: screen 1, old,  day 4 Ki67+  [SC3_O_Kp]

description: PCR ampllified DNA library

value: Old


title: screen 1, old,  day 14 reactivated [SC3_O_RA]

description: PCR ampllified DNA library


title: N1


title: dcl3a-17

description: dcl3a-17 (WGBS-seq)


title: screen 1, young, day 14 reactivated [SC4_Y_RA]

description: PCR ampllified DNA library


title: screen 1 library [SC3_lib]

description: PCR ampllified DNA library

growth_protocol:
NA
[[delete]]


title: healthy control [C-CELL- 10 LB (C10LB)]


title: NIP

description: Nipponbare (WGBS-seq)

value: NIP


title: ChIP_WT_for_g_del_Rad21_rep2

status: Public on Oct 31 2023

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Assembly: Mus Musculus UCSC mm9
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

source_name: cortex

extract_protocol:
2 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. For neuron sample, additional SDS was then added to the lysis solution to adjust final SDS concentration to 0.4% to help sonication. Cells were then sonicated to break DNA fragments to about 100-10000 bp using the Bioruptor system (25% energy, with working time 15s and resting time of 45s, 20cycles). After sonication, lysis buffer not containing SDS was added to adjust final SDS concentration to 0.1% to allow binding of antibodies to proteins while cultured cell move directly to the antibody binding step. After removing the insoluble debris by centrifuging at 14000g for 10 min, the lysate was precleaned with protein-A agarose beads (16-157; Millipore) for 1hr with slow rotation to remove non-specificity binding and incubated with specific antibodies overnight with slow rotation at 4°C. The next day the antibody-protein-DNA complex was purified by adding protein A-agarose beads and incubate for 4hr with slow rotation, followed by washing with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer and finally eluted into elution buffer (0.1M NaHCO3, 1% SDS). Reverse cross-link and DNA purification was performed and the sample were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s instruction. The ChIP-seq libraries were sequenced using an Illumina Novaseq6000 platform.

value: cortex

value: cortex neuron

value: wildtype


title: ChIP_WT_for_g_del_Rad21_rep1


title: ChIP_g_del_Rad21_rep4

value: G del


title: ChIP_g_del_Rad21_rep3


title: ChIP_g_del_Rad21_rep1